From 0bc9691d6900eab37fa18a94648d4def8f79d3d8 Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Sun, 14 Apr 2024 08:58:56 -0400
Subject: [PATCH 01/17] update parser

---
 trackhub/parse.py | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/trackhub/parse.py b/trackhub/parse.py
index 4accdde5..c1200a6f 100644
--- a/trackhub/parse.py
+++ b/trackhub/parse.py
@@ -161,6 +161,12 @@ def keep(tag):
     for i in d:
 
         div = i.parent
+
+        # 2024-04-13: maxWindowCoverage appears to be wrapped in an
+        # additional <code>, so we need to get *it's* parent.
+        if div.name == 'code':  # not 'div'...
+            div = div.parent
+
         _id = div.attrs['class']
         assert len(_id) == 1
         _id = _id[0]

From 5a4e73ffb3eb8d585662c481e13a00371e9d1cbc Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Sun, 14 Apr 2024 08:59:10 -0400
Subject: [PATCH 02/17] add new parsed params

---
 trackhub/parsed_params.py | 173 ++++++++++++++++++++++++++++++++++++--
 1 file changed, 167 insertions(+), 6 deletions(-)

diff --git a/trackhub/parsed_params.py b/trackhub/parsed_params.py
index 3b383009..5a36cfc5 100644
--- a/trackhub/parsed_params.py
+++ b/trackhub/parsed_params.py
@@ -132,7 +132,21 @@
         fmt=['bamSkipPrintQualScore .'],
         types=['bam'],
         required=False,
-        validator=set(['.'])),
+        validator=str),
+
+    Param(
+        name="barChartBarMinPadding",
+        fmt=['barChartBarMinPadding <num>'],
+        types=['bigBarChart'],
+        required=False,
+        validator=str),
+
+    Param(
+        name="barChartBarMinWidth",
+        fmt=['barChartBarMinWidth <num>'],
+        types=['bigBarChart'],
+        required=False,
+        validator=str),
 
     Param(
         name="barChartBars",
@@ -155,6 +169,13 @@
         required=False,
         validator=str),
 
+    Param(
+        name="barChartFacets",
+        fmt=['barChartFacets <column1,column2,...columnN>'],
+        types=['bigBarChart'],
+        required=False,
+        validator=str),
+
     Param(
         name="barChartLabel",
         fmt=['barChartLabel <label>'],
@@ -174,7 +195,14 @@
         fmt=['barChartMaxSize <small/medium/large>'],
         types=['bigBarChart'],
         required=False,
-        validator=['small', 'medium', 'large']),
+        validator=str),
+
+    Param(
+        name="barChartMerge",
+        fmt=['barChartMerge on'],
+        types=['bigBarChart'],
+        required=False,
+        validator=str),
 
     Param(
         name="barChartMetric",
@@ -197,6 +225,20 @@
         required=False,
         validator=str),
 
+    Param(
+        name="barChartStatsUrl",
+        fmt=['barChartStatsUrl <url>'],
+        types=['bigBarChart'],
+        required=False,
+        validator=str),
+
+    Param(
+        name="barChartStretchToItem",
+        fmt=['barChartStretchToItem on'],
+        types=['bigBarChart'],
+        required=False,
+        validator=str),
+
     Param(
         name="barChartUnit",
         fmt=['barChartUnit <unit>'],
@@ -333,6 +375,13 @@
         required=False,
         validator=str),
 
+    Param(
+        name="decorator",
+        fmt=['decorator.default.*'],
+        types=['bigBed', 'bigGenePred', 'bigPsl'],
+        required=False,
+        validator=str),
+
     Param(
         name="defaultLabelFields",
         fmt=['defaultLabelFields <fieldName[,fieldName]>'],
@@ -345,7 +394,21 @@
         fmt=['denseCoverage <maxVal>'],
         types=['bigBed'],
         required=False,
-        validator=float),
+        validator=str),
+
+    Param(
+        name="detailsDynamicTable",
+        fmt=['detailsDynamicTable <fieldName1|table title,fieldName2|table title,...>'],
+        types=['bigBed'],
+        required=False,
+        validator=str),
+
+    Param(
+        name="detailsStaticTable",
+        fmt=['detailsStaticTable <url/relativePath>'],
+        types=['bigBed'],
+        required=False,
+        validator=str),
 
     Param(
         name="dimensionAchecked",
@@ -380,7 +443,14 @@
         fmt=['doWiggle on'],
         types=['bam'],
         required=False,
-        validator=set(['on'])),
+        validator=str),
+
+    Param(
+        name="downloadUrl",
+        fmt=['downloadUrl <label> <URL>'],
+        types=['all'],
+        required=False,
+        validator=str),
 
     Param(
         name="dragAndDrop",
@@ -403,6 +473,20 @@
         required=False,
         validator=str),
 
+    Param(
+        name="extraDetailsTable",
+        fmt=['extraDetailsTable <url/relativePath>'],
+        types=['bigBed'],
+        required=False,
+        validator=str),
+
+    Param(
+        name="extraTableFields",
+        fmt=['extraTableFields <fieldName1|table title,fieldName2|table title,...>'],
+        types=['bigBed'],
+        required=False,
+        validator=str),
+
     Param(
         name="filter",
         fmt=['filter.<fieldName> <default integer>', 'filterByRange.<fieldName> <off/on>', 'filterLimits.<fieldName> <low>[:<high>]'],
@@ -523,6 +607,20 @@
         required=False,
         validator=str),
 
+    Param(
+        name="hicDistanceMax",
+        fmt=['hicDistanceMax <integer>'],
+        types=['hic'],
+        required=False,
+        validator=str),
+
+    Param(
+        name="hicDistanceMin",
+        fmt=['hicDistanceMin <integer>'],
+        types=['hic'],
+        required=False,
+        validator=str),
+
     Param(
         name="hideEmptySubtracks",
         fmt=['hideEmptySubtracks <on/off>'],
@@ -665,6 +763,13 @@
         required=False,
         validator=str),
 
+    Param(
+        name="logo",
+        fmt=['logo on'],
+        types=['bigWig'],
+        required=False,
+        validator=str),
+
     Param(
         name="lollyField",
         fmt=['lollyField <integer>'],
@@ -713,7 +818,14 @@
         fmt=['maxLimit<#>'],
         types=['bigBarChart'],
         required=False,
-        validator=int),
+        validator=str),
+
+    Param(
+        name="maxWindowCoverage",
+        fmt=['maxWindowCoverage <integer>'],
+        types=['bam', 'bigWig'],
+        required=False,
+        validator=str),
 
     Param(
         name="maxWindowToDraw",
@@ -771,6 +883,20 @@
         required=False,
         validator=str),
 
+    Param(
+        name="mouseOverFunction",
+        fmt=['mouseOverFunction <noAverage>'],
+        types=['bigWig'],
+        required=False,
+        validator=str),
+
+    Param(
+        name="multiRegionsBedUrl",
+        fmt=['multiRegionsBedUrl <url/relativePath>'],
+        types=['all'],
+        required=False,
+        validator=str),
+
     Param(
         name="negateValues",
         fmt=['negateValues <on>'],
@@ -821,6 +947,13 @@
         required=False,
         validator=str),
 
+    Param(
+        name="otherTwoBitUrl",
+        fmt=['otherTwoBitUrl <url/relativePath>'],
+        types=['bigChain', 'bigPsl'],
+        required=False,
+        validator=str),
+
     Param(
         name="pairEndsByName",
         fmt=['pairEndsByName .'],
@@ -968,7 +1101,14 @@
         fmt=['showDiffBasesAllScales on'],
         types=['all'],
         required=False,
-        validator=set(['on'])),
+        validator=str),
+
+    Param(
+        name="showDiffBasesMaxZoom",
+        fmt=['showDiffBasesMaxZoom <basesPerPixel>'],
+        types=['all'],
+        required=False,
+        validator=str),
 
     Param(
         name="showNames",
@@ -1112,6 +1252,27 @@
         required=False,
         validator=str),
 
+    Param(
+        name="vcfDoFilter",
+        fmt=['vcfDoFilter <on/off>'],
+        types=['vcfPhasedTrio', 'vcfTabix'],
+        required=False,
+        validator=str),
+
+    Param(
+        name="vcfDoMaf",
+        fmt=['vcfDoMaf <on/off>'],
+        types=['vcfPhasedTrio', 'vcfTabix'],
+        required=False,
+        validator=str),
+
+    Param(
+        name="vcfDoQual",
+        fmt=['vcfDoQual <on/off>'],
+        types=['vcfPhasedTrio', 'vcfTabix'],
+        required=False,
+        validator=str),
+
     Param(
         name="vcfParentSamples",
         fmt=['vcfParentSamples <sampleName|altName,sampleName|altName>'],

From 79a348bd4ca90465914082f266d166d3961b81a6 Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Sun, 14 Apr 2024 10:05:31 -0400
Subject: [PATCH 03/17] refactor tests to pytest fixtures

---
 trackhub/test/deprecated_upload_test.py |  89 ++++++++------
 trackhub/test/test_components.py        | 153 +++++++++++++-----------
 trackhub/test/upload_test.py            |  74 +++++++-----
 3 files changed, 174 insertions(+), 142 deletions(-)

diff --git a/trackhub/test/deprecated_upload_test.py b/trackhub/test/deprecated_upload_test.py
index 820856ba..0a13ee61 100644
--- a/trackhub/test/deprecated_upload_test.py
+++ b/trackhub/test/deprecated_upload_test.py
@@ -10,8 +10,9 @@
 
 d = data_dir()
 
-class TestUpload(object):
-    def setup(self):
+
+class Upload(object):
+    def __init__(self):
         with pytest.warns(DeprecationWarning):
             self.hub = Hub(
                 hub='example_hub',
@@ -41,40 +42,50 @@ def setup(self):
             self.genome.add_trackdb(self.trackdb)
             self.trackdb.add_tracks(self.tracks)
 
-    def test_staging(self):
-        staging_dir, linknames = upload.stage_hub(self.hub)
-
-        assert open(os.path.join(staging_dir, 'example_hub.genomes.txt')).read() == dedent(
-            """\
-            genome dm3
-            trackDb dm3/trackDb.txt
-
-            """)
-
-        assert open(os.path.join(staging_dir, 'example_hub.hub.txt')).read() == dedent(
-            """\
-            hub hub
-            shortLabel example hub
-            longLabel an example hub for testing
-            genomesFile example_hub.genomes.txt
-            email none@example.com""")
-
-        print(staging_dir)
-
-    #@unittest.skipUnless(os.path.exists('data/track1.bam'), 'No test data')
-    def test_upload(self):
-        d = tempfile.mkdtemp()
-        upload.upload_hub(
-            hub=self.hub,
-            remote_dir=d,
-            user=None,
-            host=None,
-        )
-
-    def test_render(self):
-        trackdb = str(self.trackdb)
-        print(self.trackdb)
-        # make sure some of the trackdb rendered correctly
-        assert 'track track1' in trackdb
-        assert 'bigDataUrl ../1.bigbed' in trackdb
-        assert 'bigDataUrl ../2.bw' in trackdb
+
+@pytest.fixture
+def upload_obj():
+    return Upload()
+
+
+def test_staging(upload_obj):
+    staging_dir, linknames = upload.stage_hub(upload_obj.hub)
+
+    assert open(os.path.join(staging_dir, "example_hub.genomes.txt")).read() == dedent(
+        """\
+        genome dm3
+        trackDb dm3/trackDb.txt
+
+        """
+    )
+
+    assert open(os.path.join(staging_dir, "example_hub.hub.txt")).read() == dedent(
+        """\
+        hub hub
+        shortLabel example hub
+        longLabel an example hub for testing
+        genomesFile example_hub.genomes.txt
+        email none@example.com"""
+    )
+
+    print(staging_dir)
+
+
+# @unittest.skipUnless(os.path.exists('data/track1.bam'), 'No test data')
+def test_upload(upload_obj):
+    d = tempfile.mkdtemp()
+    upload.upload_hub(
+        hub=upload_obj.hub,
+        remote_dir=d,
+        user=None,
+        host=None,
+    )
+
+
+def test_render(upload_obj):
+    trackdb = str(upload_obj.trackdb)
+    print(upload_obj.trackdb)
+    # make sure some of the trackdb rendered correctly
+    assert "track track1" in trackdb
+    assert "bigDataUrl ../1.bigbed" in trackdb
+    assert "bigDataUrl ../2.bw" in trackdb
diff --git a/trackhub/test/test_components.py b/trackhub/test/test_components.py
index 5b7b3c6b..2a7a1bde 100644
--- a/trackhub/test/test_components.py
+++ b/trackhub/test/test_components.py
@@ -4,8 +4,8 @@
 import os
 
 
-class TestComponents(object):
-    def setup(self):
+class Components(object):
+    def __init__(self):
         self.hub = Hub(
             hub='example_hub',
             short_label='example hub',
@@ -35,98 +35,109 @@ def DISCONNECT(self):
         Re-run the setup, which results in unconnected components. Run
         CONNECT() to connect them up.
         """
-        self.setup()
+        self.__init__()
+
+
+@pytest.fixture
+def components():
+    return Components()
+
+
+def test_components_connection(components):
+    """
+    meta test: make sure the test class's connect/disconnect is working
+    """
+    assert components.hub.genomes_file is None
+
+    components.CONNECT()
+    assert components.hub.genomes_file is components.genomes_file
+
+    components.DISCONNECT()
+    assert components.hub.genomes_file is None
+
+
+# Filenames ---------------------------------------------------------------
 
-    def test_self_connection(self):
-        """
-        meta test: make sure the test class's connect/disconnect is working
-        """
-        assert self.hub.genomes_file is None
 
-        self.CONNECT()
-        assert self.hub.genomes_file is self.genomes_file
+def test_hub_fns(components):
+    # Default unconnected
+    assert components.hub.filename == "example_hub.hub.txt"
 
-        self.DISCONNECT()
-        assert self.hub.genomes_file is None
+    # Connecting components should not change hub
+    components.CONNECT()
+    assert components.hub.filename == "example_hub.hub.txt"
+    components.DISCONNECT()
 
-    # Filenames ---------------------------------------------------------------
 
-    def test_hub_fns(self):
-        # Default unconnected
-        assert self.hub.filename == 'example_hub.hub.txt'
+def test_genome_file_fns(components):
+    with pytest.raises(AttributeError):
+        getattr(components.genomes_file, "url")
 
-        # Connecting components should not change hub
-        self.CONNECT()
-        assert self.hub.filename == 'example_hub.hub.txt'
-        self.DISCONNECT()
+    # When unconnected, filenames should be None
+    assert components.genomes_file.filename is None
 
-    def test_genome_file_fns(self):
-        with pytest.raises(AttributeError):
-            getattr(self.genomes_file, 'url')
+    # ...though you can set them manually
+    components.genomes_file.filename = "local.genomes"
+    assert components.genomes_file.filename == "local.genomes"
+    components.genomes_file.filename = None
 
-        # When unconnected, filenames should be None
-        assert self.genomes_file.filename is None
+    components.CONNECT()
+    assert components.genomes_file.filename == "example_hub.genomes.txt"
 
-        #...though you can set them manually
-        self.genomes_file.filename = 'local.genomes'
-        assert self.genomes_file.filename == 'local.genomes'
-        self.genomes_file.filename = None
+    # when connected, overriding works
+    components.genomes_file.filename = "local.genomes"
+    assert components.genomes_file.filename == "local.genomes"
+    components.genomes_file.filename = None
 
-        self.CONNECT()
-        assert self.genomes_file.filename == 'example_hub.genomes.txt'
+    # disconnecting brings it back to None
+    components.DISCONNECT()
+    assert components.genomes_file.filename is None
 
-        # when connected, overriding works
-        self.genomes_file.filename = 'local.genomes'
-        assert self.genomes_file.filename == 'local.genomes'
-        self.genomes_file.filename = None
+    # set the hub's local_dir; genomes_file should follow.
+    components.CONNECT()
 
-        # disconnecting brings it back to None
-        self.DISCONNECT()
-        assert self.genomes_file.filename is None
+    # what happens if the hub's local FN is changed?
+    components.hub.filename = "localhub/hub.txt"
+    assert components.genomes_file.filename == "localhub/example_hub.genomes.txt"
 
-        # set the hub's local_dir; genomes_file should follow.
-        self.CONNECT()
 
-        # what happens if the hub's local FN is changed?
-        self.hub.filename = 'localhub/hub.txt'
-        assert self.genomes_file.filename == 'localhub/example_hub.genomes.txt'
+def test_trackdb_fns(components):
 
-    def test_trackdb_fns(self):
+    # when unconnected, no defaults
+    assert components.trackdb.filename is None
 
-        # when unconnected, no defaults
-        assert self.trackdb.filename is None
+    components.CONNECT()
+    assert components.trackdb.filename == "dm3/trackDb.txt"
 
-        self.CONNECT()
-        assert self.trackdb.filename == 'dm3/trackDb.txt'
+    # setting filename overrides
+    components.trackdb.filename = "mytrackdb.txt"
+    assert components.trackdb.filename == "mytrackdb.txt", components.trackdb.filename
 
-        # setting filename overrides
-        self.trackdb.filename = 'mytrackdb.txt'
-        assert self.trackdb.filename == 'mytrackdb.txt', self.trackdb.filename
+    # genomes_file fn overrides
+    components.trackdb.filename = None
+    components.genomes_file.filename = "anotherdir/genomes.txt"
+    assert components.trackdb.filename == "anotherdir/dm3/trackDb.txt"
 
-        # genomes_file fn overrides
-        self.trackdb.filename = None
-        self.genomes_file.filename = 'anotherdir/genomes.txt'
-        assert self.trackdb.filename == 'anotherdir/dm3/trackDb.txt'
+    # reset parent hub and genomes file to get back to the default
+    components.genomes_file.filename = None
+    assert components.trackdb.filename == "dm3/trackDb.txt"
 
-        # reset parent hub and genomes file to get back to the default
-        self.genomes_file.filename = None
-        assert self.trackdb.filename == 'dm3/trackDb.txt'
 
-    def test_track_fns(self):
+def test_track_fns(components):
 
-        self.CONNECT()
-        # local fns should still be None
-        for track in self.tracks:
-            assert track.source is None
+    components.CONNECT()
+    # local fns should still be None
+    for track in components.tracks:
+        assert track.source is None
 
-        # filename is relative to the hub's filename
-        assert self.tracks[0].filename == 'dm3/track1.bam'
-        assert self.tracks[1].filename == 'dm3/track2.bigWig'
+    # filename is relative to the hub's filename
+    assert components.tracks[0].filename == "dm3/track1.bam"
+    assert components.tracks[1].filename == "dm3/track2.bigWig"
 
-        # URL is relative to the trackDb
-        assert self.tracks[0].url == 'track1.bam'
+    # URL is relative to the trackDb
+    assert components.tracks[0].url == "track1.bam"
 
 
-    def test_track_creation(self):
-        track = Track(name='track0', tracktype='bam', source='t0.bam')
-        assert track.source == 't0.bam'
+def test_track_creation(components):
+    track = Track(name="track0", tracktype="bam", source="t0.bam")
+    assert track.source == "t0.bam"
diff --git a/trackhub/test/upload_test.py b/trackhub/test/upload_test.py
index 408c2595..a6f34804 100644
--- a/trackhub/test/upload_test.py
+++ b/trackhub/test/upload_test.py
@@ -9,8 +9,9 @@
 
 d = data_dir()
 
-class TestUpload(object):
-    def setup(self):
+
+class Upload(object):
+    def __init__(self):
         self.hub = Hub(
             hub='example_hub',
             short_label='example hub',
@@ -43,38 +44,47 @@ def setup(self):
         self.genome.add_trackdb(self.trackdb)
         self.trackdb.add_tracks(self.tracks)
 
-    def test_staging(self):
-        staging_dir, linknames = upload.stage_hub(self.hub)
 
-        assert open(os.path.join(staging_dir, 'example_hub.genomes.txt')).read() == dedent(
-            """\
-            genome dm3
-            trackDb dm3/trackDb.txt
+@pytest.fixture
+def upload_obj():
+    return Upload()
+
+
+def test_staging(upload_obj):
+    staging_dir, linknames = upload.stage_hub(upload_obj.hub)
+
+    assert open(os.path.join(staging_dir, "example_hub.genomes.txt")).read() == dedent(
+        """\
+        genome dm3
+        trackDb dm3/trackDb.txt
+
+        """
+    )
+
+    assert open(os.path.join(staging_dir, "example_hub.hub.txt")).read() == dedent(
+        """\
+        hub hub
+        shortLabel example hub
+        longLabel an example hub for testing
+        genomesFile example_hub.genomes.txt
+        email none@example.com"""
+    )
 
-            """)
 
-        assert open(os.path.join(staging_dir, 'example_hub.hub.txt')).read() == dedent(
-            """\
-            hub hub
-            shortLabel example hub
-            longLabel an example hub for testing
-            genomesFile example_hub.genomes.txt
-            email none@example.com""")
+def test_upload(upload_obj):
+    d = tempfile.mkdtemp()
+    print(d)
+    upload.upload_hub(
+        hub=upload_obj.hub,
+        remote_dir=d,
+        user=None,
+        host=None,
+    )
 
-    #@unittest.skipUnless(os.path.exists('data/track1.bam'), 'No test data')
-    def test_upload(self):
-        d = tempfile.mkdtemp()
-        print(d)
-        upload.upload_hub(
-            hub=self.hub,
-            remote_dir=d,
-            user=None,
-            host=None,
-        )
 
-    def test_render(self):
-        trackdb = str(self.trackdb)
-        # make sure some of the trackdb rendered correctly
-        assert 'track track1' in trackdb
-        assert 'bigDataUrl track1.bigBed' in trackdb
-        assert 'bigDataUrl ../3.bw' in trackdb
+def test_render(upload_obj):
+    trackdb = str(upload_obj.trackdb)
+    # make sure some of the trackdb rendered correctly
+    assert "track track1" in trackdb
+    assert "bigDataUrl track1.bigBed" in trackdb
+    assert "bigDataUrl ../3.bw" in trackdb

From 3c423051f26482498447bf10fe5ccc5a62d81167 Mon Sep 17 00:00:00 2001
From: daler <dalerr@niddk.nih.gov>
Date: Sat, 20 Apr 2024 13:09:19 -0400
Subject: [PATCH 04/17] pep8

---
 trackhub/__init__.py                          |   23 +-
 trackhub/assembly.py                          |   54 +-
 trackhub/base.py                              |   36 +-
 trackhub/compatibility.py                     |   11 +-
 trackhub/constants.py                         |    4 +-
 trackhub/genome.py                            |   19 +-
 trackhub/genomes_file.py                      |   16 +-
 trackhub/groups.py                            |   29 +-
 trackhub/helpers.py                           |   53 +-
 trackhub/hub.py                               |   40 +-
 trackhub/parse.py                             |  132 +-
 trackhub/parsed_params.py                     | 1721 +++++++++--------
 trackhub/test/construct_example_data.py       |   83 +-
 trackhub/test/construct_example_genome.py     |   62 +-
 trackhub/test/deprecated_upload_test.py       |   40 +-
 trackhub/test/test_add_tracks.py              |  157 +-
 trackhub/test/test_assembly.py                |   11 +-
 trackhub/test/test_components.py              |   32 +-
 trackhub/test/test_example_data.py            |   15 +-
 .../test/test_parentonoff/test_parentonoff.py |   47 +-
 trackhub/test/test_supertrack.py              |   73 +-
 trackhub/test/upload_test.py                  |   46 +-
 trackhub/track.py                             |  192 +-
 trackhub/trackdb.py                           |   19 +-
 trackhub/trackhub_from_excel                  |   21 +-
 trackhub/upload.py                            |   57 +-
 trackhub/validate.py                          |  129 +-
 trackhub/version.py                           |    2 +-
 28 files changed, 1673 insertions(+), 1451 deletions(-)

diff --git a/trackhub/__init__.py b/trackhub/__init__.py
index a8f29a4e..533a177a 100644
--- a/trackhub/__init__.py
+++ b/trackhub/__init__.py
@@ -11,12 +11,21 @@
 from .assembly import Assembly
 from .groups import GroupsFile, GroupDefinition
 from .trackdb import TrackDb
-from .track import BaseTrack, Track, SubGroupDefinition, CompositeTrack, \
-    ViewTrack, SuperTrack, AggregateTrack
+from .track import (
+    BaseTrack,
+    Track,
+    SubGroupDefinition,
+    CompositeTrack,
+    ViewTrack,
+    SuperTrack,
+    AggregateTrack,
+)
 from .version import version as __version__
 
 
-def default_hub(hub_name, genome, email, short_label=None, long_label=None, defaultPos=None):
+def default_hub(
+    hub_name, genome, email, short_label=None, long_label=None, defaultPos=None
+):
     """
     Returns a fully-connected set of hub components using default filenames.
 
@@ -46,15 +55,11 @@ def default_hub(hub_name, genome, email, short_label=None, long_label=None, defa
     if long_label is None:
         long_label = short_label
 
-    hub = Hub(
-        hub=hub_name,
-        short_label=short_label,
-        long_label=long_label,
-        email=email)
+    hub = Hub(hub=hub_name, short_label=short_label, long_label=long_label, email=email)
 
     genome_kwargs = {}
     if defaultPos:
-        genome_kwargs['defaultPos'] = defaultPos
+        genome_kwargs["defaultPos"] = defaultPos
     genome = Genome(genome, **genome_kwargs)
     genomes_file = GenomesFile()
     trackdb = TrackDb()
diff --git a/trackhub/assembly.py b/trackhub/assembly.py
index a3c04274..94789d61 100644
--- a/trackhub/assembly.py
+++ b/trackhub/assembly.py
@@ -53,7 +53,8 @@ def filename(self):
         return os.path.join(
             os.path.dirname(self.assembly.genomes_file.filename),
             self.assembly.genome,
-            self.assembly.genome + '.2bit')
+            self.assembly.genome + ".2bit",
+        )
 
     def validate(self):
         if not os.path.exists(self.source):
@@ -63,20 +64,22 @@ def validate(self):
     def filename(self, fn):
         self._filename = fn
 
-    def _render(self, staging='staging'):
+    def _render(self, staging="staging"):
         pass
 
 
 class Assembly(Genome):
-    def __init__(self,
-                 genome,
-                 twobit_file=None,
-                 groups=None,
-                 trackdb=None,
-                 genome_file_obj=None,
-                 html_string=None,
-                 html_string_format='rst',
-                 **kwargs):
+    def __init__(
+        self,
+        genome,
+        twobit_file=None,
+        groups=None,
+        trackdb=None,
+        genome_file_obj=None,
+        html_string=None,
+        html_string_format="rst",
+        **kwargs
+    ):
         """
         Represents a genome stanza within a "genomes.txt" file for a non-UCSC genome.
 
@@ -106,8 +109,8 @@ def __init__(self,
         self._orig_kwargs = kwargs
 
         self.track_field_order = []
-        self.track_field_order.extend(constants.track_fields['assembly'])
-        self.track_field_order.extend(constants.track_fields['all'])
+        self.track_field_order.extend(constants.track_fields["assembly"])
+        self.track_field_order.extend(constants.track_fields["all"])
 
         self.add_params(**kwargs)
 
@@ -145,8 +148,9 @@ def add_params(self, **kw):
         for k, v in kw.items():
             if k not in self.track_field_order:
                 raise ParameterError(
-                    '"{0}" is not a valid parameter for {1}'
-                    .format(k, self.__class__.__name__)
+                    '"{0}" is not a valid parameter for {1}'.format(
+                        k, self.__class__.__name__
+                    )
                 )
             constants.param_dict[k].validate(v)
 
@@ -181,11 +185,11 @@ def __str__(self):
 
         s = []
 
-        s.append('genome %s' % self.genome)
-        s.append('trackDb %s' % self.trackdb.filename)
-        s.append('twoBitPath %s' % self.twobit.filename)
+        s.append("genome %s" % self.genome)
+        s.append("trackDb %s" % self.trackdb.filename)
+        s.append("twoBitPath %s" % self.twobit.filename)
         if self.groups is not None:
-            s.append('groups %s' % self.groups.filename)
+            s.append("groups %s" % self.groups.filename)
 
         for name in self.track_field_order:
             value = self.kwargs.pop(name, None)
@@ -194,10 +198,10 @@ def __str__(self):
                     s.append("%s %s" % (name, value))
 
         if self._html is not None:
-            s.append('htmlDocumentation %s' % self._html.filename)
+            s.append("htmlDocumentation %s" % self._html.filename)
 
         self.kwargs = self._orig_kwargs.copy()
-        return '\n'.join(s) + '\n'
+        return "\n".join(s) + "\n"
 
     def validate(self):
         Genome.validate(self)
@@ -213,7 +217,8 @@ def filename(self):
         return os.path.join(
             os.path.dirname(self.genomes_file.filename),
             self.genome.genome,
-            '%s_info.html' % self.genome.genome)
+            "%s_info.html" % self.genome.genome,
+        )
 
     @property
     def genomes_file(self):
@@ -235,6 +240,7 @@ def genome(self):
 
     def validate(self):
         if not self.genome:
-            raise ValueError("HTMLDoc object must be connected to an"
-                             "Assembly subclass instance")
+            raise ValueError(
+                "HTMLDoc object must be connected to an" "Assembly subclass instance"
+            )
         return True
diff --git a/trackhub/base.py b/trackhub/base.py
index db7ef8e5..540399ca 100644
--- a/trackhub/base.py
+++ b/trackhub/base.py
@@ -6,25 +6,28 @@
 
 
 def deprecation_handler(source, filename, kwargs):
-    if 'local_fn' in kwargs:
+    if "local_fn" in kwargs:
         warnings.warn(
-            'Please use the argument "source" instead of "local_fn"',
-            DeprecationWarning)
+            'Please use the argument "source" instead of "local_fn"', DeprecationWarning
+        )
         if source is not None:
             raise ValueError(
                 'Both "source" and "local_fn" are specified. Please use '
-                'just "source"')
-        source = kwargs.pop('local_fn')
+                'just "source"'
+            )
+        source = kwargs.pop("local_fn")
 
-    if 'remote_fn' in kwargs:
+    if "remote_fn" in kwargs:
         warnings.warn(
             'Please use the argument "source" instead of "remote_fn"',
-            DeprecationWarning)
+            DeprecationWarning,
+        )
         if filename is not None:
             raise ValueError(
                 'Both "filename" and "remote_fn" are specified. Please use '
-                'just "filename"')
-        filename = kwargs.pop('remote_fn')
+                'just "filename"'
+            )
+        filename = kwargs.pop("remote_fn")
     return source, filename
 
 
@@ -33,11 +36,12 @@ class HubComponent(object):
     Base class for various track hub components.  Several methods must be
     overridden by subclasses.
     """
+
     def __init__(self):
         self.children = []
         self.parent = None
 
-    def _render(self, staging='staging'):
+    def _render(self, staging="staging"):
         """
         Renders the object to file.  Must be overridden by subclass.
 
@@ -45,7 +49,8 @@ def _render(self, staging='staging'):
         """
         raise NotImplementedError(
             "%s: subclasses must define their own _render() method"
-            % self.__class__.__name__)
+            % self.__class__.__name__
+        )
 
     def validate(self):
         """
@@ -54,7 +59,8 @@ def validate(self):
         """
         raise NotImplementedError(
             "%s: subclasses must define their own validate() method"
-            % self.__class__.__name__)
+            % self.__class__.__name__
+        )
 
     def add_child(self, child):
         """
@@ -112,10 +118,8 @@ def leaves(self, cls, level=0, intermediate=False):
                 raise StopIteration
 
         for child in self.children:
-            for leaf, _level in child.leaves(
-                cls, level + 1, intermediate=intermediate
-            ):
-                    yield leaf, _level
+            for leaf, _level in child.leaves(cls, level + 1, intermediate=intermediate):
+                yield leaf, _level
 
     def render(self, staging=None):
         """
diff --git a/trackhub/compatibility.py b/trackhub/compatibility.py
index 2afcebca..5a96fe11 100644
--- a/trackhub/compatibility.py
+++ b/trackhub/compatibility.py
@@ -10,17 +10,16 @@
 PY2 = PY == 2
 
 if PY3:
-    string_types = str,
+    string_types = (str,)
 
 if PY2:
-    string_types = basestring,
+    string_types = (basestring,)
 
 
 def py2_unicode(cls):
     if PY2:
-        if '__str__' not in cls.__dict__:
-            raise ValueError(
-                'no __str__method defined for {}'.format(cls.__name__))
+        if "__str__" not in cls.__dict__:
+            raise ValueError("no __str__method defined for {}".format(cls.__name__))
         cls.__unicode__ = cls.__str__
-        cls.__str__ = lambda self: self.__unicode__().encode('utf-8')
+        cls.__str__ = lambda self: self.__unicode__().encode("utf-8")
     return cls
diff --git a/trackhub/constants.py b/trackhub/constants.py
index 4ae6894f..274a1d93 100644
--- a/trackhub/constants.py
+++ b/trackhub/constants.py
@@ -8,7 +8,7 @@
 param_dict = {i.name: i for i in param_defs}
 
 # These should at least be first...
-initial_params = ['track', 'bigDataUrl', 'shortLabel', 'longLabel', 'type']
+initial_params = ["track", "bigDataUrl", "shortLabel", "longLabel", "type"]
 trackhub_specific = ["source", "tracktype", "name"]
 
 
@@ -24,4 +24,4 @@
         if tracktype in param.types:
             lst.append(param.name)
 
-INDENT = '    '
+INDENT = "    "
diff --git a/trackhub/genome.py b/trackhub/genome.py
index a6e6b613..89d68663 100644
--- a/trackhub/genome.py
+++ b/trackhub/genome.py
@@ -35,7 +35,7 @@ def __init__(self, genome, trackdb=None, genome_file_obj=None, **kwargs):
         self._orig_kwargs = kwargs
 
         self.track_field_order = []
-        self.track_field_order.extend(constants.track_fields['genome'])
+        self.track_field_order.extend(constants.track_fields["genome"])
 
         self.add_params(**kwargs)
 
@@ -62,8 +62,7 @@ def add_params(self, **kw):
             if k not in self.track_field_order:
                 raise ParameterError(
                     '"{0}" is not a valid parameter for {1} with '
-                    'tracktype {2}'
-                    .format(k, self.__class__.__name__, self.tracktype)
+                    "tracktype {2}".format(k, self.__class__.__name__, self.tracktype)
                 )
             constants.param_dict[k].validate(v)
 
@@ -88,12 +87,11 @@ def __str__(self):
         except ValidationError:
             return "Unconfigured <Genome> object"
         s = []
-        s.append('genome %s' % self.genome)
+        s.append("genome %s" % self.genome)
         s.append(
-            'trackDb %s'
+            "trackDb %s"
             % os.path.relpath(
-                self.trackdb.filename,
-                os.path.dirname(self.genome_file_obj.filename)
+                self.trackdb.filename, os.path.dirname(self.genome_file_obj.filename)
             )
         )
 
@@ -105,16 +103,15 @@ def __str__(self):
 
         self.kwargs = self._orig_kwargs.copy()
 
-        return '\n'.join(s) + '\n'
+        return "\n".join(s) + "\n"
 
     def validate(self):
         if len(self.children) == 0:
-            raise ValidationError(
-                "No TrackDb objects provided")
+            raise ValidationError("No TrackDb objects provided")
         if self.trackdb is None:
             raise ValidationError("No TrackDb objects provided")
 
-    def _render(self, staging='staging'):
+    def _render(self, staging="staging"):
         """
         No file is created from a Genome object -- only from its parent
         GenomesFile object.
diff --git a/trackhub/genomes_file.py b/trackhub/genomes_file.py
index 0dc03811..eaf2f93e 100644
--- a/trackhub/genomes_file.py
+++ b/trackhub/genomes_file.py
@@ -38,8 +38,8 @@ def filename(self):
         if self.hub is None:
             return None
         return os.path.join(
-            os.path.dirname(self.hub.filename),
-            self.hub.hub + '.genomes.txt')
+            os.path.dirname(self.hub.filename), self.hub.hub + ".genomes.txt"
+        )
 
     @filename.setter
     def filename(self, fn):
@@ -51,8 +51,7 @@ def hub(self):
         if level is None:
             return None
         if level != -1:
-            raise ValueError(
-                "Found a hub at %s levels away -- needs to be -1" % level)
+            raise ValueError("Found a hub at %s levels away -- needs to be -1" % level)
         return hub
 
     def add_genome(self, genome):
@@ -63,17 +62,16 @@ def __str__(self):
         s = []
         for genome in self.genomes:
             s.append(str(genome))
-        return '\n'.join(s) + '\n'
+        return "\n".join(s) + "\n"
 
-    def _render(self, staging='staging'):
+    def _render(self, staging="staging"):
         rendered_filename = os.path.join(staging, self.filename)
         self.makedirs(rendered_filename)
-        fout = open(rendered_filename, 'w')
+        fout = open(rendered_filename, "w")
         fout.write(str(self))
         fout.close()
         return fout.name
 
     def validate(self):
         if len(self.children) == 0:
-            raise ValueError(
-                "No defined Genome objects to use")
+            raise ValueError("No defined Genome objects to use")
diff --git a/trackhub/groups.py b/trackhub/groups.py
index 5b821620..9b252b4c 100644
--- a/trackhub/groups.py
+++ b/trackhub/groups.py
@@ -8,7 +8,6 @@
 
 
 class GroupDefinition(object):
-
     def __init__(self, name, label=None, priority=1, default_is_closed=0):
         """
         Represents a group of tracks in a trackhub.
@@ -43,12 +42,12 @@ def __init__(self, name, label=None, priority=1, default_is_closed=0):
 
     def __str__(self):
         s = [
-            'name %s' % self.name,
-            'label %s' % self.label,
-            'priority %s' % self.priority,
-            'defaultIsClosed %d' % self.default_is_closed
+            "name %s" % self.name,
+            "label %s" % self.label,
+            "priority %s" % self.priority,
+            "defaultIsClosed %d" % self.default_is_closed,
         ]
-        return '\n'.join(s) + '\n'
+        return "\n".join(s) + "\n"
 
 
 class GroupsFile(HubComponent):
@@ -85,7 +84,7 @@ def __str__(self):
         """
         Render groups.txt file.
         """
-        return '\n'.join(g.__str__() for g in self.groups)
+        return "\n".join(g.__str__() for g in self.groups)
 
     @property
     def genomes_file(self):
@@ -102,7 +101,7 @@ def genome(self):
         if level is None:
             return None
         if level != -1:
-            raise ValueError('Genome is level %s, not -1' % level)
+            raise ValueError("Genome is level %s, not -1" % level)
         return genome
 
     @property
@@ -117,8 +116,11 @@ def filename(self):
             return None
 
         else:
-            return os.path.join(os.path.dirname(self.genomes_file.filename),
-                                self.genome.genome, 'groups.txt')
+            return os.path.join(
+                os.path.dirname(self.genomes_file.filename),
+                self.genome.genome,
+                "groups.txt",
+            )
 
     @filename.setter
     def filename(self, fn):
@@ -128,16 +130,17 @@ def validate(self):
         if self.genome is None:
             raise ValidationError(
                 "GroupsFile object must be attached to an Genome instance "
-                "or subclass")
+                "or subclass"
+            )
         pass
 
-    def _render(self, staging='staging'):
+    def _render(self, staging="staging"):
         """
         Renders the children GroupDefinition objects to file
         """
         rendered_filename = os.path.join(staging, self.filename)
         self.makedirs(rendered_filename)
-        fout = open(rendered_filename, 'w')
+        fout = open(rendered_filename, "w")
         fout.write(str(self))
         fout.close()
         return fout.name
diff --git a/trackhub/helpers.py b/trackhub/helpers.py
index 7c520053..888a835e 100644
--- a/trackhub/helpers.py
+++ b/trackhub/helpers.py
@@ -18,9 +18,8 @@ def dimensions_from_subgroups(s):
     ----------
     s : list of SubGroup objects (or anything with a `name` attribute)
     """
-    letters = 'XYABCDEFGHIJKLMNOPQRSTUVWZ'
-    return ' '.join(['dim{0}={1}'.format(dim, sg.name)
-                     for dim, sg in zip(letters, s)])
+    letters = "XYABCDEFGHIJKLMNOPQRSTUVWZ"
+    return " ".join(["dim{0}={1}".format(dim, sg.name) for dim, sg in zip(letters, s)])
 
 
 def filter_composite_from_subgroups(s):
@@ -40,10 +39,10 @@ def filter_composite_from_subgroups(s):
         used, just the number of items.
     """
     dims = []
-    for letter, sg in zip('ABCDEFGHIJKLMNOPQRSTUVWZ', s[2:]):
-        dims.append('dim{0}'.format(letter))
+    for letter, sg in zip("ABCDEFGHIJKLMNOPQRSTUVWZ", s[2:]):
+        dims.append("dim{0}".format(letter))
     if dims:
-        return ' '.join(dims)
+        return " ".join(dims)
 
 
 def hex2rgb(h):
@@ -58,13 +57,18 @@ def hex2rgb(h):
     >>> hex2rgb("#ff0033")
     '255,0,51'
     """
-    if not h.startswith('#') or len(h) != 7:
+    if not h.startswith("#") or len(h) != 7:
         raise ValueError("Does not look like a hex color: '{0}'".format(h))
-    return ','.join(map(str, (
-        int(h[1:3], 16),
-        int(h[3:5], 16),
-        int(h[5:7], 16),
-    )))
+    return ",".join(
+        map(
+            str,
+            (
+                int(h[1:3], 16),
+                int(h[3:5], 16),
+                int(h[5:7], 16),
+            ),
+        )
+    )
 
 
 def sanitize(s, strict=True):
@@ -82,20 +86,20 @@ def sanitize(s, strict=True):
         If True, only alphanumeric characters are allowed. If False, a limited
         set of additional characters (-._) will be allowed.
     """
-    allowed = ''.join(
+    allowed = "".join(
         [
-            'ABCDEFGHIJKLMNOPQRSTUVWXYZ',
-            'abcdefghijklmnopqrstuvwxyz',
-            '0123456789',
+            "ABCDEFGHIJKLMNOPQRSTUVWXYZ",
+            "abcdefghijklmnopqrstuvwxyz",
+            "0123456789",
         ]
     )
 
     if not strict:
-        allowed += '-_.'
+        allowed += "-_."
 
-    s = str(s).replace(' ', '_')
+    s = str(s).replace(" ", "_")
 
-    return ''.join([i for i in s if i in allowed])
+    return "".join([i for i in s if i in allowed])
 
 
 def auto_track_url(track):
@@ -112,7 +116,8 @@ def auto_track_url(track):
 
     if hub is None:
         raise ValueError(
-            "track is not fully connected because the root is %s" % repr(hub))
+            "track is not fully connected because the root is %s" % repr(hub)
+        )
     if hub.url is None:
         raise ValueError("hub.url is not set")
     if track.source is None:
@@ -139,11 +144,13 @@ def print_rendered_results(results_dict):
     Rendered results can be multiply-nested dictionaries; this uses JSON
     serialization to print a nice representation.
     """
+
     class _HubComponentEncoder(json.JSONEncoder):
         def default(self, o):
             if isinstance(o, base.HubComponent):
                 return repr(o)
             return json.JSONEncoder.default(self, o)
+
     formatted = json.dumps(results_dict, indent=4, cls=_HubComponentEncoder)
     # the returned string contains lines with trailing spaces, which causes
     # doctests to fail.  So fix that here.
@@ -156,7 +163,7 @@ def data_dir():
     Returns the data directory that contains example files for tests and
     documentation.
     """
-    return os.path.join(os.path.dirname(_here), 'test', 'data')
+    return os.path.join(os.path.dirname(_here), "test", "data")
 
 
 def example_bigbeds():
@@ -167,7 +174,7 @@ def example_bigbeds():
     d = data_dir()
     for fn in os.listdir(d):
         fn = os.path.join(d, fn)
-        if os.path.splitext(fn)[-1] == '.bigBed':
+        if os.path.splitext(fn)[-1] == ".bigBed":
             hits.append(os.path.abspath(fn))
     return hits
 
@@ -180,6 +187,6 @@ def example_bigwigs():
     d = data_dir()
     for fn in os.listdir(d):
         fn = os.path.join(d, fn)
-        if os.path.splitext(fn)[-1] == '.bw':
+        if os.path.splitext(fn)[-1] == ".bw":
             hits.append(os.path.abspath(fn))
     return hits
diff --git a/trackhub/hub.py b/trackhub/hub.py
index 2220b1bd..46b072b6 100644
--- a/trackhub/hub.py
+++ b/trackhub/hub.py
@@ -10,9 +10,17 @@ class Hub(HubComponent):
     # map proper track hub stanza field names to pythonic attribute names in
     # this class.
 
-    def __init__(self, hub, short_label=None, long_label=None,
-                 genomes_file=None, genomes_filename=None, email="",
-                 url=None, filename=None):
+    def __init__(
+        self,
+        hub,
+        short_label=None,
+        long_label=None,
+        genomes_file=None,
+        genomes_filename=None,
+        email="",
+        url=None,
+        filename=None,
+    ):
         """
         Represents a top-level track hub container.
 
@@ -44,8 +52,7 @@ def __init__(self, hub, short_label=None, long_label=None,
         HubComponent.__init__(self)
         if url is not None:
             self.url = url
-            warnings.DeprecationWarning(
-                'url is no longer used for Hub objects')
+            warnings.DeprecationWarning("url is no longer used for Hub objects")
         self.hub = hub
         if not short_label:
             short_label = hub
@@ -60,13 +67,14 @@ def __init__(self, hub, short_label=None, long_label=None,
             self.add_genomes_file(genomes_file)
 
         if filename is None:
-            filename = hub + '.hub.txt'
+            filename = hub + ".hub.txt"
         self.filename = filename
 
     def validate(self):
         if self.genomes_file is None:
             raise ValidationError(
-                'No GenomesFile attached to Hub (use add_genomes_file())')
+                "No GenomesFile attached to Hub (use add_genomes_file())"
+            )
         self.genomes_file.validate()
         return True
 
@@ -83,23 +91,23 @@ def __str__(self):
         if self.genomes_file:
             genomes_file = self.genomes_file.filename
         for label, value in [
-            ('hub', 'hub'),
-            ('shortLabel', self.short_label),
-            ('longLabel', self.long_label),
-            ('genomesFile', genomes_file),
-            ('email', self.email),
+            ("hub", "hub"),
+            ("shortLabel", self.short_label),
+            ("longLabel", self.long_label),
+            ("genomesFile", genomes_file),
+            ("email", self.email),
         ]:
-            s.append('{0} {1}'.format(label, value))
-        return '\n'.join(s)
+            s.append("{0} {1}".format(label, value))
+        return "\n".join(s)
 
-    def _render(self, staging='staging'):
+    def _render(self, staging="staging"):
         """
         Render just this object, and not all the underlying GenomeFiles and
         their TrackDb.
         """
         rendered_filename = os.path.join(staging, self.filename)
         self.makedirs(rendered_filename)
-        fout = open(rendered_filename, 'w')
+        fout = open(rendered_filename, "w")
         fout.write(str(self))
         fout.close()
         return fout.name
diff --git a/trackhub/parse.py b/trackhub/parse.py
index c1200a6f..1422820e 100644
--- a/trackhub/parse.py
+++ b/trackhub/parse.py
@@ -12,8 +12,9 @@ def make_soup():
     # Initial workarounds chopped up the file and parsed individually, but the
     # most lenient html5lib parse seems to do the trick.
     response = requests.get(
-        'https://genome.ucsc.edu/goldenPath/help/trackDb/trackDbHub.html')
-    soup = bs4.BeautifulSoup(response.text, 'html5lib')
+        "https://genome.ucsc.edu/goldenPath/help/trackDb/trackDbHub.html"
+    )
+    soup = bs4.BeautifulSoup(response.text, "html5lib")
     return soup
 
 
@@ -38,44 +39,44 @@ def get_supported_types(soup):
             </ul>
             <li> (don't care about this one since not in a ul)
     """
-    abam = soup.find('a', href=re.compile('#bam'))
+    abam = soup.find("a", href=re.compile("#bam"))
     ol = abam.parent.parent.parent.parent
     supported_types = []
-    for ul in ol.find_all('ul'):
-        for a in ul.find_all('a'):
-            ref = a['href'].replace('#', '')
+    for ul in ol.find_all("ul"):
+        for a in ul.find_all("a"):
+            ref = a["href"].replace("#", "")
 
             # some have text like "#bigMaf_-_Multiple_Alignments", so split on
             # the '_'
-            ref = ref.split('_')[0]
+            ref = ref.split("_")[0]
             supported_types.append(ref)
 
     # multiWig is not included in this table, but it's considered a type in the
     # divs.
-    supported_types.append('multiWig')
+    supported_types.append("multiWig")
 
     # If a setting pertains to all types, they are not all listed, rather, the
     # "all" type is specified.
-    supported_types.append('all')
+    supported_types.append("all")
 
     return supported_types
 
 
 def support_level(soup):
     # Another set of tables stores the support level
-    settings_tables = soup.find_all('table', class_='settingsTable')
+    settings_tables = soup.find_all("table", class_="settingsTable")
     support_levels = {}
     for t in settings_tables:
-        for td in t.find_all('td'):
-            if not td.has_attr('class'):
+        for td in t.find_all("td"):
+            if not td.has_attr("class"):
                 continue
-            key = td['class']
+            key = td["class"]
             assert len(key) == 1
             key = key[0]
-            code = td.find('code')
-            if not code or not code.has_attr('class'):
+            code = td.find("code")
+            if not code or not code.has_attr("class"):
                 continue
-            support = code['class']
+            support = code["class"]
             support_levels[key] = support
     return support_levels
 
@@ -141,16 +142,16 @@ def keep(tag):
         they're from. However some are examples that luckily are tagged as such
         (e.g., bed_example).
         """
-        if tag.name != 'span':
+        if tag.name != "span":
             return
-        if tag.parent.has_attr('class'):
-            for c in tag.parent['class']:
-                if 'example' in c:
+        if tag.parent.has_attr("class"):
+            for c in tag.parent["class"]:
+                if "example" in c:
                     return
 
-        if tag.has_attr('class'):
-            if 'types' in tag['class']:
-                if 'customTracks' not in tag['class']:
+        if tag.has_attr("class"):
+            if "types" in tag["class"]:
+                if "customTracks" not in tag["class"]:
                     return True
 
     d = soup.find_all(keep)
@@ -164,10 +165,10 @@ def keep(tag):
 
         # 2024-04-13: maxWindowCoverage appears to be wrapped in an
         # additional <code>, so we need to get *it's* parent.
-        if div.name == 'code':  # not 'div'...
+        if div.name == "code":  # not 'div'...
             div = div.parent
 
-        _id = div.attrs['class']
+        _id = div.attrs["class"]
         assert len(_id) == 1
         _id = _id[0]
 
@@ -176,26 +177,26 @@ def keep(tag):
         # though.
         debug[_id] = div
 
-        types = set(i.attrs['class']).intersection(supported_types)
+        types = set(i.attrs["class"]).intersection(supported_types)
 
         if len(types.intersection(supported_types)) == 0:
             continue
 
         types = list(types)
-        fmt = div.find_all(name='div', attrs='format')
+        fmt = div.find_all(name="div", attrs="format")
         assert len(fmt) == 1
         fmt = fmt[0]
 
-        required_p = div.find_all(name='p', attrs='isRequired')
+        required_p = div.find_all(name="p", attrs="isRequired")
         required = False
         if required_p:
             for i in required_p:
-                if 'yes' in i.text.lower() or 'for hubs' in i.text.lower():
+                if "yes" in i.text.lower() or "for hubs" in i.text.lower():
                     required = True
 
         # Some, like bamGrayMode, have several "sub names" like bamGrayMode,
         # aliQualRnage, baseQualRange. Handle those here.
-        formats = fmt.find_all('code')
+        formats = fmt.find_all("code")
         if formats is None:
             continue
         else:
@@ -204,37 +205,36 @@ def keep(tag):
         # Most non-hub-relevant settings are filtered out py the supported
         # types filter, but some sneak through (e.g. several only used by
         # ENCODE).
-        no_hub = div.find_all('p', string=re.compile('NOT FOR HUBS'))
+        no_hub = div.find_all("p", string=re.compile("NOT FOR HUBS"))
         if no_hub:
             continue
 
-        example = div.find('pre')
+        example = div.find("pre")
         if example is not None:
             example = str(example.string)
 
-        desc = div.find_all('p')
+        desc = div.find_all("p")
         if desc is not None:
-            desc = ' '.join([' '.join(''.join(i.strings).split()) for i in
-                             desc])
+            desc = " ".join([" ".join("".join(i.strings).split()) for i in desc])
         if _id in specs:
             raise ValueError("duplicate value for {}".format(_id))
 
         # We are only concerned with settings, not types. Types (bigBed, bam,
         # etc) have "type" in their format.
-        if any([i.split()[0] == 'type' for i in formats]):
+        if any([i.split()[0] == "type" for i in formats]):
             continue
 
         # Special cases
         #
-        if _id in ['view', 'subGroupN', 'parent_view']:
+        if _id in ["view", "subGroupN", "parent_view"]:
             continue
 
         spec = {
-            'format': formats,
-            'types': sorted(types),
-            'required': required,
-            'example': example,
-            'desc': desc,
+            "format": formats,
+            "types": sorted(types),
+            "required": required,
+            "example": example,
+            "desc": desc,
         }
         specs[_id] = spec
 
@@ -260,38 +260,50 @@ def print_parsed(specs):
     specs : dict
         Returned dictionary from parse_divs()
     """
+
     observed_types = set()
     for i in specs.values():
-        observed_types.update(i['types'])
+        observed_types.update(i["types"])
     observed_types = sorted(observed_types)
 
-    s = ['# Observed types from the parsed document']
-    s.append('TRACKTYPES = [')
+    s = ["# Observed types from the parsed document"]
+    s.append("TRACKTYPES = [")
     for i in observed_types:
-        s.append("    '{}',".format(i))
-    s.append(']')
-    print('\n'.join(s) + '\n')
+        s.append('    "{}",'.format(i))
+    s.append("]")
+    print("\n".join(s) + "\n")
 
-    data_types = specs['bigDataUrl']['types']
+    data_types = specs["bigDataUrl"]["types"]
 
-    s = ['# Tracks for which the definition specifies bigDataUrl']
-    s.append('DATA_TRACKTYPES = [')
+    s = ["# Tracks for which the definition specifies bigDataUrl"]
+    s.append("DATA_TRACKTYPES = [")
     for i in data_types:
-        s.append("    '{}',".format(i))
-    s.append(']')
-    print('\n'.join(s) + '\n')
-    print('param_defs = [')
+        s.append('    "{}",'.format(i))
+    s.append("]")
+    print("\n".join(s) + "\n")
+    print("param_defs = [")
     print()
+
+    def _quote(x):
+        """
+        Python __repr__ uses single quotes, but we're aiming for a pep8
+        format with double quotes. Fix that here.
+        """
+        s = str(x)
+        if '"' in s:
+            return s
+        return s.replace("'", '"')
+
     for k, v in sorted(specs.items()):
         print(
             (
-    '''
+                f"""
     Param(
         name="{k}",
-        fmt={v[format]},
-        types={v[types]},
-        required={v[required]},
-        validator=str),'''.format(**locals())
+        fmt={_quote(v['format'])},
+        types={_quote(v['types'])},
+        required={_quote(v['required'])},
+        validator=str),"""
             )
         )
 
diff --git a/trackhub/parsed_params.py b/trackhub/parsed_params.py
index 5a36cfc5..4b12cc12 100644
--- a/trackhub/parsed_params.py
+++ b/trackhub/parsed_params.py
@@ -14,960 +14,1015 @@
 
 # Observed types from the parsed document
 TRACKTYPES = [
-    'all',
-    'bam',
-    'bigBarChart',
-    'bigBed',
-    'bigChain',
-    'bigGenePred',
-    'bigInteract',
-    'bigLolly',
-    'bigMaf',
-    'bigNarrowPeak',
-    'bigPsl',
-    'bigWig',
-    'compositeTrack',
-    'halSnake',
-    'hic',
-    'multiWig',
-    'subGroups',
-    'superTrack',
-    'vcfPhasedTrio',
-    'vcfTabix',
-    'view',
-
+    "all",
+    "bam",
+    "bigBarChart",
+    "bigBed",
+    "bigChain",
+    "bigGenePred",
+    "bigInteract",
+    "bigLolly",
+    "bigMaf",
+    "bigNarrowPeak",
+    "bigPsl",
+    "bigWig",
+    "compositeTrack",
+    "halSnake",
+    "hic",
+    "multiWig",
+    "subGroups",
+    "superTrack",
+    "vcfPhasedTrio",
+    "vcfTabix",
+    "view",
     # assembly tracks are not defined in the document; we need to add
     # separately.
-    'assembly',
-
+    "assembly",
     # neither are genome objects, but we want to support arguments like
     # defaultPos so it needs to be added here.
-    'genome',
+    "genome",
 ]
 
 # Tracks for which the definition specifies bigDataUrl
 DATA_TRACKTYPES = [
-    'bam',
-    'bigBarChart',
-    'bigBed',
-    'bigChain',
-    'bigInteract',
-    'bigLolly',
-    'bigMaf',
-    'bigPsl',
-    'bigWig',
-    'hic',
-    'vcfPhasedTrio',
-    'vcfTabix',
+    "bam",
+    "bigBarChart",
+    "bigBed",
+    "bigChain",
+    "bigInteract",
+    "bigLolly",
+    "bigMaf",
+    "bigPsl",
+    "bigWig",
+    "hic",
+    "vcfPhasedTrio",
+    "vcfTabix",
 ]
 
 
 param_defs = [
-
     Param(
         name="aggregate",
-        fmt=['aggregate <transparentOverlay/stacked/solidOverlay/none>'],
-        types=['multiWig'],
+        fmt=["aggregate <transparentOverlay/stacked/solidOverlay/none>"],
+        types=["multiWig"],
         required=False,
-        validator=set(['transparentOverlay', 'stacked', 'solidOverlay', 'none'])),
-
+        validator=set(["transparentOverlay", "stacked", "solidOverlay", "none"]),
+    ),
     Param(
         name="aliQualRange",
-        fmt=['bamGrayMode <aliQual/baseQual/unpaired>', 'aliQualRange <min:max>', 'baseQualRange <min:max>'],
-        types=['bam'],
-        required=False,
-        validator=validate.ColSV2),
-
+        fmt=[
+            "bamGrayMode <aliQual/baseQual/unpaired>",
+            "aliQualRange <min:max>",
+            "baseQualRange <min:max>",
+        ],
+        types=["bam"],
+        required=False,
+        validator=validate.ColSV2,
+    ),
     Param(
         name="allButtonPair",
-        fmt=['allButtonPair on'],
-        types=['compositeTrack'],
+        fmt=["allButtonPair on"],
+        types=["compositeTrack"],
         required=False,
-        validator=set(['on'])),
-
+        validator=set(["on"]),
+    ),
     Param(
         name="altColor",
-        fmt=['altColor <red,green,blue>'],
-        types=['all'],
+        fmt=["altColor <red,green,blue>"],
+        types=["all"],
         required=False,
-        validator=validate.RGB),
-
+        validator=validate.RGB,
+    ),
     Param(
         name="alwaysZero",
-        fmt=['alwaysZero  <off/on>'],
-        types=['bigWig'],
+        fmt=["alwaysZero  <off/on>"],
+        types=["bigWig"],
         required=False,
-        validator=set(['on', 'off'])),
-
+        validator=set(["on", "off"]),
+    ),
     Param(
         name="autoScale",
-        fmt=['autoScale <off/on/group>'],
-        types=['bigWig', 'hic', 'compositeTrack'],
+        fmt=["autoScale <off/on/group>"],
+        types=["bigWig", "hic", "compositeTrack"],
         required=False,
-        validator=set(['on', 'off', 'group'])),
-
+        validator=set(["on", "off", "group"]),
+    ),
     Param(
         name="bamColorMode",
-        fmt=['bamColorMode <strand/gray/tag/off>'],
-        types=['bam'],
+        fmt=["bamColorMode <strand/gray/tag/off>"],
+        types=["bam"],
         required=False,
-        validator=set(['strand', 'gray', 'tag', 'off'])),
-
+        validator=set(["strand", "gray", "tag", "off"]),
+    ),
     Param(
         name="bamColorTag",
-        fmt=['bamColorTag <XX>'],
-        types=['bam'],
+        fmt=["bamColorTag <XX>"],
+        types=["bam"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="bamGrayMode",
-        fmt=['bamGrayMode <aliQual/baseQual/unpaired>', 'aliQualRange <min:max>', 'baseQualRange <min:max>'],
-        types=['bam'],
-        required=False,
-        validator=set(['aliQual', 'baseQual', 'unpaired'])),
-
+        fmt=[
+            "bamGrayMode <aliQual/baseQual/unpaired>",
+            "aliQualRange <min:max>",
+            "baseQualRange <min:max>",
+        ],
+        types=["bam"],
+        required=False,
+        validator=set(["aliQual", "baseQual", "unpaired"]),
+    ),
     Param(
         name="bamSkipPrintQualScore",
-        fmt=['bamSkipPrintQualScore .'],
-        types=['bam'],
+        fmt=["bamSkipPrintQualScore ."],
+        types=["bam"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="barChartBarMinPadding",
-        fmt=['barChartBarMinPadding <num>'],
-        types=['bigBarChart'],
+        fmt=["barChartBarMinPadding <num>"],
+        types=["bigBarChart"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="barChartBarMinWidth",
-        fmt=['barChartBarMinWidth <num>'],
-        types=['bigBarChart'],
+        fmt=["barChartBarMinWidth <num>"],
+        types=["bigBarChart"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="barChartBars",
-        fmt=['barChartBars <label1 label2...>'],
-        types=['bigBarChart'],
+        fmt=["barChartBars <label1 label2...>"],
+        types=["bigBarChart"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="barChartCategoryUrl",
-        fmt=['barChartCategoryUrl <url>'],
-        types=['bigBarChart'],
+        fmt=["barChartCategoryUrl <url>"],
+        types=["bigBarChart"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="barChartColors",
-        fmt=['barChartColors <color1 color2...>'],
-        types=['bigBarChart'],
+        fmt=["barChartColors <color1 color2...>"],
+        types=["bigBarChart"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="barChartFacets",
-        fmt=['barChartFacets <column1,column2,...columnN>'],
-        types=['bigBarChart'],
+        fmt=["barChartFacets <column1,column2,...columnN>"],
+        types=["bigBarChart"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="barChartLabel",
-        fmt=['barChartLabel <label>'],
-        types=['bigBarChart'],
+        fmt=["barChartLabel <label>"],
+        types=["bigBarChart"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="barChartMatrixUrl",
-        fmt=['barChartMatrixUrl <url>'],
-        types=['bigBarChart'],
+        fmt=["barChartMatrixUrl <url>"],
+        types=["bigBarChart"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="barChartMaxSize",
-        fmt=['barChartMaxSize <small/medium/large>'],
-        types=['bigBarChart'],
+        fmt=["barChartMaxSize <small/medium/large>"],
+        types=["bigBarChart"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="barChartMerge",
-        fmt=['barChartMerge on'],
-        types=['bigBarChart'],
+        fmt=["barChartMerge on"],
+        types=["bigBarChart"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="barChartMetric",
-        fmt=['barChartMetric <metric>'],
-        types=['bigBarChart'],
+        fmt=["barChartMetric <metric>"],
+        types=["bigBarChart"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="barChartSampleUrl",
-        fmt=['barChartSampleUrl <url>'],
-        types=['bigBarChart'],
+        fmt=["barChartSampleUrl <url>"],
+        types=["bigBarChart"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="barChartSizeWindows",
-        fmt=['barChartSizeWindows <largeMax> <smallMin>'],
-        types=['bigBarChart'],
+        fmt=["barChartSizeWindows <largeMax> <smallMin>"],
+        types=["bigBarChart"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="barChartStatsUrl",
-        fmt=['barChartStatsUrl <url>'],
-        types=['bigBarChart'],
+        fmt=["barChartStatsUrl <url>"],
+        types=["bigBarChart"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="barChartStretchToItem",
-        fmt=['barChartStretchToItem on'],
-        types=['bigBarChart'],
+        fmt=["barChartStretchToItem on"],
+        types=["bigBarChart"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="barChartUnit",
-        fmt=['barChartUnit <unit>'],
-        types=['bigBarChart'],
+        fmt=["barChartUnit <unit>"],
+        types=["bigBarChart"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="baseColorDefault",
-        fmt=['baseColorDefault\n                    <diffBases/diffCodons/itemBases/itemCodons/genomicCodons>'],
-        types=['all'],
-        required=False,
-        validator=set(['diffBases', 'diffCodons', 'itemBases', 'itemCodons', 'genomicCodons'])),
-
+        fmt=[
+            "baseColorDefault\n                    <diffBases/diffCodons/itemBases/itemCodons/genomicCodons>"
+        ],
+        types=["all"],
+        required=False,
+        validator=set(
+            ["diffBases", "diffCodons", "itemBases", "itemCodons", "genomicCodons"]
+        ),
+    ),
     Param(
         name="baseColorUseCds",
-        fmt=['baseColorUseCds <given/table <table>>'],
-        types=['bigPsl'],
+        fmt=["baseColorUseCds <given>"],
+        types=["bigPsl"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="baseColorUseSequence",
-        fmt=['baseColorUseSequence < <extFile {seqTable} <extFile> /\n                        hgPcrResult / lfExtra / nameIsSequence / seq1Seq2 / ss >'],
-        types=['all'],
+        fmt=[
+            "baseColorUseSequence  <extFile {seqTable} /\n                  hgPcrResult / lfExtra / nameIsSequence / seq1Seq2 / ss / 2bit >"
+        ],
+        types=["all"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="baseQualRange",
-        fmt=['bamGrayMode <aliQual/baseQual/unpaired>', 'aliQualRange <min:max>', 'baseQualRange <min:max>'],
-        types=['bam'],
-        required=False,
-        validator=validate.ColSV2),
-
+        fmt=[
+            "bamGrayMode <aliQual/baseQual/unpaired>",
+            "aliQualRange <min:max>",
+            "baseQualRange <min:max>",
+        ],
+        types=["bam"],
+        required=False,
+        validator=validate.ColSV2,
+    ),
     Param(
         name="bedNameLabel",
-        fmt=['bedNameLabel <label>'],
-        types=['bigBed'],
+        fmt=["bedNameLabel <label>"],
+        types=["bigBed"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="bigDataIndex",
-        fmt=['bigDataIndex <url/relativePath>'],
-        types=['bam', 'vcfPhasedTrio', 'vcfTabix'],
+        fmt=["bigDataIndex <url/relativePath>"],
+        types=["bam", "vcfPhasedTrio", "vcfTabix"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="bigDataUrl",
-        fmt=['bigDataUrl <url/relativePath>'],
-        types=['bam', 'bigBarChart', 'bigBed', 'bigChain', 'bigInteract',
-               'bigLolly', 'bigMaf', 'bigPsl', 'bigWig', 'hic',
-               'vcfPhasedTrio', 'vcfTabix'],
+        fmt=["bigDataUrl <url/relativePath>"],
+        types=[
+            "bam",
+            "bigBarChart",
+            "bigBed",
+            "bigChain",
+            "bigInteract",
+            "bigLolly",
+            "bigMaf",
+            "bigPsl",
+            "bigWig",
+            "hic",
+            "vcfPhasedTrio",
+            "vcfTabix",
+        ],
         required=True,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="bigDataUrl2",
-        fmt=['bigDataUrl <url/relativePath>'],
-        types=['bam', 'bigBed', 'bigWig', 'vcfTabix'],
+        fmt=["bigDataUrl2 <url/relativePath>"],
+        types=["bam", "bigBed", "bigWig", "vcfTabix"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="boxedCfg",
-        fmt=['boxedCfg <on/off>'],
-        types=['all'],
+        fmt=["boxedCfg <on/off>"],
+        types=["all"],
         required=False,
-        validator=set(['on', 'off'])),
-
+        validator=set(["on", "off"]),
+    ),
     Param(
         name="centerLabelsDense",
-        fmt=['centerLabelsDense <off/on>'],
-        types=['compositeTrack'],
+        fmt=["centerLabelsDense <off/on>"],
+        types=["compositeTrack"],
         required=False,
-        validator=set(['on', 'off'])),
-
+        validator=set(["on", "off"]),
+    ),
     Param(
         name="chromosomes",
-        fmt=['chromosomes <chr1,chr2,...>'],
-        types=['all'],
+        fmt=["chromosomes <chr1,chr2,...>"],
+        types=["all"],
         required=False,
-        validator=validate.CSV),
-
+        validator=validate.CSV,
+    ),
     Param(
         name="color",
-        fmt=['color <red,green,blue>'],
-        types=['all'],
+        fmt=["color <red,green,blue>"],
+        types=["all"],
         required=False,
-        validator=validate.RGB),
-
+        validator=validate.RGB,
+    ),
     Param(
         name="colorByStrand",
-        fmt=['colorByStrand <red,green,blue> <red,green,blue>'],
-        types=['bigBed'],
+        fmt=["colorByStrand <red,green,blue> <red,green,blue>"],
+        types=["bigBed"],
         required=False,
         validator=validate.RGBList,
-        min_bed_fields=6),
-
+        min_bed_fields=6,
+    ),
     Param(
         name="compositeTrack",
-        fmt=['compositeTrack on'],
-        types=['compositeTrack'],
+        fmt=["compositeTrack on"],
+        types=["compositeTrack"],
         required=False,
-        validator=set(['on'])),
-
+        validator=set(["on"]),
+    ),
     Param(
         name="configurable",
-        fmt=['configurable <off/on>'],
-        types=['view'],
+        fmt=["configurable <off/on>"],
+        types=["view"],
         required=False,
-        validator=set(['on', 'off'])),
-
+        validator=set(["on", "off"]),
+    ),
     Param(
         name="container",
-        fmt=['container multiWig'],
-        types=['multiWig'],
+        fmt=["container multiWig"],
+        types=["multiWig"],
         required=False,
-        validator=set(['multiWig'])),
-
+        validator=set(["multiWig"]),
+    ),
     Param(
         name="darkerLabels",
-        fmt=['darkerLabels on'],
-        types=['all'],
+        fmt=["darkerLabels on"],
+        types=["all"],
         required=False,
-        validator=set(['on'])),
-
+        validator=set(["on"]),
+    ),
     Param(
         name="dataVersion",
-        fmt=['dataVersion <str>'],
-        types=['all'],
+        fmt=["dataVersion <str>"],
+        types=["all"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="decorator",
-        fmt=['decorator.default.*'],
-        types=['bigBed', 'bigGenePred', 'bigPsl'],
+        fmt=["decorator.default.*"],
+        types=["bigBed", "bigGenePred", "bigPsl"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="defaultLabelFields",
-        fmt=['defaultLabelFields <fieldName[,fieldName]>'],
-        types=['bigBarChart', 'bigBed', 'bigGenePred', 'bigNarrowPeak', 'bigPsl'],
+        fmt=["defaultLabelFields <fieldName[,fieldName]>"],
+        types=["bigBarChart", "bigBed", "bigGenePred", "bigNarrowPeak", "bigPsl"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="denseCoverage",
-        fmt=['denseCoverage <maxVal>'],
-        types=['bigBed'],
+        fmt=["denseCoverage <maxVal>"],
+        types=["bigBed"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="detailsDynamicTable",
-        fmt=['detailsDynamicTable <fieldName1|table title,fieldName2|table title,...>'],
-        types=['bigBed'],
+        fmt=["detailsDynamicTable <fieldName1|table title,fieldName2|table title,...>"],
+        types=["bigBed"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="detailsStaticTable",
-        fmt=['detailsStaticTable <url/relativePath>'],
-        types=['bigBed'],
+        fmt=["detailsStaticTable <url/relativePath>"],
+        types=["bigBed"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="dimensionAchecked",
-        fmt=['dimension<?>checked <mTag1a> [mTag1b ...]'],
-        types=['subGroups'],
+        fmt=[
+            "dimension<?>checked <mTag1a>\n                                [mTag1b …]"
+        ],
+        types=["subGroups"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="dimensions",
-        fmt=['dimensions <dimX=gTag#> [dimY=gTag#] [dimA=gTag# ...]'],
-        types=['subGroups'],
+        fmt=["dimensions <dimX=gTag#> [dimY=gTag#] [dimA=gTag# ...]"],
+        types=["subGroups"],
         required=False,
-        validator=validate.key_val),
-
+        validator=validate.key_val,
+    ),
     Param(
         name="directUrl",
-        fmt=['directUrl <url>'],
-        types=['all'],
+        fmt=["directUrl <url>"],
+        types=["all"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="directUrl_for_hubs",
-        fmt=['directUrl <url>'],
-        types=['all'],
+        fmt=["directUrl <url>"],
+        types=["all"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="doWiggle",
-        fmt=['doWiggle on'],
-        types=['bam'],
+        fmt=["doWiggle on"],
+        types=["bam"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="downloadUrl",
-        fmt=['downloadUrl <label> <URL>'],
-        types=['all'],
+        fmt=["downloadUrl <label> <URL>"],
+        types=["all"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="dragAndDrop",
-        fmt=['dragAndDrop subTracks'],
-        types=['compositeTrack'],
+        fmt=["dragAndDrop subTracks"],
+        types=["compositeTrack"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="drawMode",
-        fmt=['drawMode <triangle|square|arc>'],
-        types=['hic'],
+        fmt=["drawMode <triangle|square|arc>"],
+        types=["hic"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="exonNumbers",
-        fmt=['exonNumbers <on/off>'],
-        types=['bigBed', 'bigGenePred'],
+        fmt=["exonNumbers <on/off>"],
+        types=["bigBed", "bigGenePred"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="extraDetailsTable",
-        fmt=['extraDetailsTable <url/relativePath>'],
-        types=['bigBed'],
+        fmt=["extraDetailsTable <url/relativePath>"],
+        types=["bigBed"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="extraTableFields",
-        fmt=['extraTableFields <fieldName1|table title,fieldName2|table title,...>'],
-        types=['bigBed'],
+        fmt=["extraTableFields <fieldName1|table title,fieldName2|table title,...>"],
+        types=["bigBed"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="filter",
-        fmt=['filter.<fieldName> <default integer>', 'filterByRange.<fieldName> <off/on>', 'filterLimits.<fieldName> <low>[:<high>]'],
-        types=['bigBed'],
+        fmt=[
+            "filter.<fieldName> <default integer>",
+            "filterByRange.<fieldName> <off/on>",
+            "filterLimits.<fieldName> <low>[:<high>]",
+        ],
+        types=["bigBed"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="filter.<fieldName>",
-        fmt=['filter.<fieldName> <default integer>', 'filterByRange.<fieldName> <off/on>', 'filterLimits.<fieldName> <low>[:<high>]'],
-        types=['bigBed'],
+        fmt=[
+            "filter.<fieldName> <default integer>",
+            "filterByRange.<fieldName> <off/on>",
+            "filterLimits.<fieldName> <low>[:<high>]",
+        ],
+        types=["bigBed"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="filterByRange.<fieldName>",
-        fmt=['filter.<fieldName> <default integer>', 'filterByRange.<fieldName> <off/on>', 'filterLimits.<fieldName> <low>[:<high>]'],
-        types=['bigBed'],
+        fmt=[
+            "filter.<fieldName> <default integer>",
+            "filterByRange.<fieldName> <off/on>",
+            "filterLimits.<fieldName> <low>[:<high>]",
+        ],
+        types=["bigBed"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="filterComposite",
-        fmt=['filterComposite <dim[A/B/C][=one]> [dimB dimC ...]'],
-        types=['subGroups'],
+        fmt=["filterComposite <dim[A/B/C][=one]> [dimB dimC ...]"],
+        types=["subGroups"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="filterLabel",
-        fmt=['filterLabel.<fieldName> <label>'],
-        types=['bigBed'],
+        fmt=["filterLabel.<fieldName> <label>"],
+        types=["bigBed"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="filterLimits.<fieldName>",
-        fmt=['filter.<fieldName> <default integer>', 'filterByRange.<fieldName> <off/on>', 'filterLimits.<fieldName> <low>[:<high>]'],
-        types=['bigBed'],
+        fmt=[
+            "filter.<fieldName> <default integer>",
+            "filterByRange.<fieldName> <off/on>",
+            "filterLimits.<fieldName> <low>[:<high>]",
+        ],
+        types=["bigBed"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="filterText",
-        fmt=['filterText.<fieldName> <default search string>', 'filterType.<fieldName> <wildcard/regexp>'],
-        types=['bigBed'],
+        fmt=[
+            "filterText.<fieldName> <default search string>",
+            "filterType.<fieldName> <wildcard/regexp>",
+        ],
+        types=["bigBed"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="filterText.<fieldName>",
-        fmt=['filterText.<fieldName> <default search string>', 'filterType.<fieldName> <wildcard/regexp>'],
-        types=['bigBed'],
+        fmt=[
+            "filterText.<fieldName> <default search string>",
+            "filterType.<fieldName> <wildcard/regexp>",
+        ],
+        types=["bigBed"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="filterType.<fieldName>",
-        fmt=['filterValues.<fieldName> <value1,value2,value3...>',
-             'filterValuesDefault.<fieldName> <value1,value2,value3...>',
-             'filterType.<fieldName> <singleList/multipleListOr/multipleListAnd/multipleListOnlyOr/multipleListOnlyAnd>'],
-        types=['bigBed'],
+        fmt=[
+            "filterValues.<fieldName> <value1,value2,value3...>",
+            "filterValuesDefault.<fieldName> <value1,value2,value3...>",
+            "filterType.<fieldName> <single/singleList/multiple/multipleListOr/multipleListAnd/multipleListOnlyOr/multipleListOnlyAnd>",
+        ],
+        types=["bigBed"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="filterValues",
-        fmt=['filterValues.<fieldName> <value1,value2,value3...>',
-             'filterValuesDefault.<fieldName> <value1,value2,value3...>',
-             'filterType.<fieldName> <singleList/multipleListOr/multipleListAnd/multipleListOnlyOr/multipleListOnlyAnd>'],
-        types=['bigBed'],
+        fmt=[
+            "filterValues.<fieldName> <value1,value2,value3...>",
+            "filterValuesDefault.<fieldName> <value1,value2,value3...>",
+            "filterType.<fieldName> <single/singleList/multiple/multipleListOr/multipleListAnd/multipleListOnlyOr/multipleListOnlyAnd>",
+        ],
+        types=["bigBed"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="filterValues.<fieldName>",
-        fmt=['filterValues.<fieldName> <value1,value2,value3...>',
-             'filterValuesDefault.<fieldName> <value1,value2,value3...>',
-             'filterType.<fieldName> <singleList/multipleListOr/multipleListAnd/multipleListOnlyOr/multipleListOnlyAnd>'],
-        types=['bigBed'],
+        fmt=[
+            "filterValues.<fieldName> <value1,value2,value3...>",
+            "filterValuesDefault.<fieldName> <value1,value2,value3...>",
+            "filterType.<fieldName> <single/singleList/multiple/multipleListOr/multipleListAnd/multipleListOnlyOr/multipleListOnlyAnd>",
+        ],
+        types=["bigBed"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="filterValuesDefault.<fieldName>",
-        fmt=['filterValues.<fieldName> <value1,value2,value3...>',
-             'filterValuesDefault.<fieldName> <value1,value2,value3...>',
-             'filterType.<fieldName> <singleList/multipleListOr/multipleListAnd/multipleListOnlyOr/multipleListOnlyAnd>'],
-        types=['bigBed'],
+        fmt=[
+            "filterValues.<fieldName> <value1,value2,value3...>",
+            "filterValuesDefault.<fieldName> <value1,value2,value3...>",
+            "filterType.<fieldName> <single/singleList/multiple/multipleListOr/multipleListAnd/multipleListOnlyOr/multipleListOnlyAnd>",
+        ],
+        types=["bigBed"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="frames",
-        fmt=['frames <table/url>'],
-        types=['bigMaf'],
+        fmt=["frames <table/url>"],
+        types=["bigMaf"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="geneTrack",
-        fmt=['geneTrack <track>'],
-        types=['vcfPhasedTrio'],
+        fmt=["geneTrack <track>"],
+        types=["vcfPhasedTrio"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="graphTypeDefault",
-        fmt=['graphTypeDefault points'],
-        types=['bigWig'],
+        fmt=["graphTypeDefault points"],
+        types=["bigWig"],
         required=False,
-        validator=set(['points', 'bar'])),
-
+        validator=set(["points", "bar"]),
+    ),
     Param(
         name="gridDefault",
-        fmt=['yLineMark <#>', 'yLineOnOff <off/on>', 'gridDefault   on'],
-        types=['bigWig'],
+        fmt=["yLineMark <#>", "yLineOnOff <off/on>", "gridDefault   on"],
+        types=["bigWig"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="hicDistanceMax",
-        fmt=['hicDistanceMax <integer>'],
-        types=['hic'],
+        fmt=["hicDistanceMax <integer>"],
+        types=["hic"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="hicDistanceMin",
-        fmt=['hicDistanceMin <integer>'],
-        types=['hic'],
+        fmt=["hicDistanceMin <integer>"],
+        types=["hic"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="hideEmptySubtracks",
-        fmt=['hideEmptySubtracks <on/off>'],
-        types=['compositeTrack'],
+        fmt=["hideEmptySubtracks <on/off>"],
+        types=["compositeTrack"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="hideEmptySubtracksLabel",
-        fmt=['hideEmptySubtracksLabel <label>'],
-        types=['compositeTrack'],
+        fmt=["hideEmptySubtracksLabel <label>"],
+        types=["compositeTrack"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="hideEmptySubtracksMultiBedUrl",
-        fmt=['hideEmptySubtracksMultiBedUrl file.bb'],
-        types=['compositeTrack'],
+        fmt=["hideEmptySubtracksMultiBedUrl file.bb"],
+        types=["compositeTrack"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="hideEmptySubtracksSourcesUrl",
-        fmt=['hideEmptySubtracksSourcesUrl file.tab'],
-        types=['compositeTrack'],
-        required=False,
-        validator=str),
-
-    Param(
-        name="html",
-        fmt=['html'],
-        types=['all'],
+        fmt=["hideEmptySubtracksSourcesUrl file.tab"],
+        types=["compositeTrack"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
+    Param(name="html", fmt=["html"], types=["all"], required=False, validator=str),
     Param(
         name="idInUrlSql",
-        fmt=['url <url>', 'urlLabel <label>', 'idInUrlSql <sql for id>'],
-        types=['all'],
+        fmt=["url <url>", "urlLabel <label>", "idInUrlSql <sql for id>"],
+        types=["all"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="iframeOptions",
-        fmt=['iframeOptions <string>'],
-        types=['all'],
+        fmt=["iframeOptions <string>"],
+        types=["all"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="iframeUrl",
-        fmt=['iframeUrl <url>'],
-        types=['all'],
+        fmt=["iframeUrl <url>"],
+        types=["all"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="indelDoubleInsert",
-        fmt=['indelDoubleInsert <off/on>', 'indelQueryInsert <off/on>', 'indelPolyA <off/on>'],
-        types=['bam'],
-        required=False,
-        validator=set(['on', 'off'])),
-
+        fmt=[
+            "indelDoubleInsert <off/on>",
+            "indelQueryInsert <off/on>",
+            "indelPolyA <off/on>",
+        ],
+        types=["bam"],
+        required=False,
+        validator=set(["on", "off"]),
+    ),
     Param(
         name="indelPolyA",
-        fmt=['indelDoubleInsert <off/on>', 'indelQueryInsert <off/on>', 'indelPolyA <off/on>'],
-        types=['bam'],
-        required=False,
-        validator=set(['on', 'off'])),
-
+        fmt=[
+            "indelDoubleInsert <off/on>",
+            "indelQueryInsert <off/on>",
+            "indelPolyA <off/on>",
+        ],
+        types=["bam"],
+        required=False,
+        validator=set(["on", "off"]),
+    ),
     Param(
         name="indelQueryInsert",
-        fmt=['indelDoubleInsert <off/on>', 'indelQueryInsert <off/on>', 'indelPolyA <off/on>'],
-        types=['bam'],
-        required=False,
-        validator=set(['on', 'off'])),
-
+        fmt=[
+            "indelDoubleInsert <off/on>",
+            "indelQueryInsert <off/on>",
+            "indelPolyA <off/on>",
+        ],
+        types=["bam"],
+        required=False,
+        validator=set(["on", "off"]),
+    ),
     Param(
         name="interactDirectional",
-        fmt=['interactDirectional <true|offsetSource|offsetTarget|clusterSource|clusterTarget>'],
-        types=['bigInteract'],
+        fmt=[
+            "interactDirectional <true|offsetSource|offsetTarget|clusterSource|clusterTarget>"
+        ],
+        types=["bigInteract"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="interactMultiRegion",
-        fmt=['interactMultiRegion <true|padding>'],
-        types=['bigInteract'],
+        fmt=["interactMultiRegion <true|padding>"],
+        types=["bigInteract"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="interactUp",
-        fmt=['interactUp <true|false>'],
-        types=['bigInteract'],
+        fmt=["interactUp <true|false>"],
+        types=["bigInteract"],
         required=False,
-        validator=set(['true', 'false'])),
-
+        validator=set(["true", "false"]),
+    ),
     Param(
         name="itemRgb",
-        fmt=['itemRgb on'],
-        types=['bigBed'],
+        fmt=["itemRgb on"],
+        types=["bigBed"],
         required=False,
-        validator=set(['on']),
+        validator=set(["on"]),
         min_bed_fields=9,
     ),
-
     Param(
         name="labelFields",
-        fmt=['labelFields <fieldName[,fieldName]>'],
-        types=['bigBarChart', 'bigBed', 'bigGenePred', 'bigNarrowPeak', 'bigPsl'],
+        fmt=["labelFields <fieldName[,fieldName]>"],
+        types=["bigBarChart", "bigBed", "bigGenePred", "bigNarrowPeak", "bigPsl"],
         required=False,
-        validator=validate.CSV),
-
+        validator=validate.CSV,
+    ),
     Param(
         name="labelOnFeature",
-        fmt=['labelOnFeature <on/off>'],
-        types=['bigBed'],
+        fmt=["labelOnFeature <on/off>"],
+        types=["bigBed"],
         required=False,
-        validator=set(['on', 'off'])),
-
+        validator=set(["on", "off"]),
+    ),
     Param(
         name="labelSeparator",
-        fmt=['labelSeparator <text>'],
-        types=['bigBed', 'bigGenePred', 'bigNarrowPeak', 'bigPsl'],
+        fmt=["labelSeparator <text>"],
+        types=["bigBed", "bigGenePred", "bigNarrowPeak", "bigPsl"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="linkDataUrl",
-        fmt=['linkDataUrl <url/relativePath>'],
-        types=['bigChain'],
-        required=['bigChain'],
-        validator=str),
-
+        fmt=["linkDataUrl <url/relativePath>"],
+        types=["bigChain"],
+        required=["bigChain"],
+        validator=str,
+    ),
     Param(
         name="linkIdInName",
-        fmt=['linkIdInName on'],
-        types=['bigBed'],
+        fmt=["linkIdInName on"],
+        types=["bigBed"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
-        name="logo",
-        fmt=['logo on'],
-        types=['bigWig'],
-        required=False,
-        validator=str),
-
+        name="logo", fmt=["logo on"], types=["bigWig"], required=False, validator=str
+    ),
     Param(
         name="lollyField",
-        fmt=['lollyField <integer>'],
-        types=['bigLolly'],
+        fmt=["lollyField <integer>"],
+        types=["bigLolly"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="lollyMaxSize",
-        fmt=['lollyMaxSize <integer>'],
-        types=['bigLolly'],
+        fmt=["lollyMaxSize <integer>"],
+        types=["bigLolly"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="lollySizeField",
-        fmt=['lollySizeField <integer>'],
-        types=['bigLolly'],
+        fmt=["lollySizeField <integer>"],
+        types=["bigLolly"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="longLabel",
-        fmt=['longLabel'],
-        types=['all'],
+        fmt=["longLabel"],
+        types=["all"],
         required=True,
-        validator=validate.long_label),
-
+        validator=validate.long_label,
+    ),
     Param(
         name="maxHeightPixels",
-        fmt=['maxHeightPixels <max:default:min>'],
-        types=['bigInteract', 'bigWig'],
+        fmt=["maxHeightPixels <max:default:min>"],
+        types=["bigInteract", "bigWig"],
         required=False,
-        validator=validate.ColSV3),
-
+        validator=validate.ColSV3,
+    ),
     # TODO: Improve verification to check that values is less than 100,000
     Param(
         name="maxItems",
-        fmt=['maxItems <integer>'],
-        types=['bigBed'],
+        fmt=["maxItems <integer>"],
+        types=["bigBed"],
         required=False,
-        validator=int),
-
+        validator=int,
+    ),
     Param(
         name="maxLimit",
-        fmt=['maxLimit<#>'],
-        types=['bigBarChart'],
+        fmt=["maxLimit <#>"],
+        types=["bigBarChart"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="maxWindowCoverage",
-        fmt=['maxWindowCoverage <integer>'],
-        types=['bam', 'bigWig'],
+        fmt=["maxWindowCoverage <integer>"],
+        types=["bam", "bigWig"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="maxWindowToDraw",
-        fmt=['maxWindowToDraw <integer>'],
-        types=['bam', 'bigWig','vcfTabix'],
+        fmt=["maxWindowToDraw <integer>"],
+        types=["bam", "bigWig"],
         required=False,
-        validator=int),
-
+        validator=int,
+    ),
     Param(
         name="maxWindowToQuery",
-        fmt=['maxWindowToQuery <integer>'],
-        types=['bigWig'],
+        fmt=["maxWindowToQuery <integer>"],
+        types=["bigWig"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="mergeSpannedItems",
-        fmt=['mergeSpannedItems <on/off>'],
-        types=['bigBed'],
-        required=False,
-        validator=str),
-
-    Param(
-        name="meta",
-        fmt=['meta'],
-        types=['all'],
+        fmt=["mergeSpannedItems <on/off>"],
+        types=["bigBed"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
+    Param(name="meta", fmt=["meta"], types=["all"], required=False, validator=str),
     Param(
         name="minAliQual",
-        fmt=['minAliQual <#>'],
-        types=['bam'],
+        fmt=["minAliQual <#>"],
+        types=["bam"],
         required=False,
-        validator=int),
-
+        validator=int,
+    ),
     Param(
         name="minGrayLevel",
-        fmt=['minGrayLevel  <1-9>'],
-        types=['bigBed'],
+        fmt=["minGrayLevel  <1-9>"],
+        types=["bigBed"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="mouseOver",
-        fmt=['mouseOver <pattern>'],
-        types=['bigBed'],
+        fmt=["mouseOver <pattern>"],
+        types=["bigBed"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="mouseOverField",
-        fmt=['mouseOverField <fieldName1>'],
-        types=['bigBed'],
+        fmt=["mouseOverField <fieldName1>"],
+        types=["bigBed"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="mouseOverFunction",
-        fmt=['mouseOverFunction <noAverage>'],
-        types=['bigWig'],
+        fmt=["mouseOverFunction <noAverage>"],
+        types=["bigWig"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="multiRegionsBedUrl",
-        fmt=['multiRegionsBedUrl <url/relativePath>'],
-        types=['all'],
+        fmt=["multiRegionsBedUrl <url/relativePath>"],
+        types=["all"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="negateValues",
-        fmt=['negateValues <on>'],
-        types=['bigWig'],
+        fmt=["negateValues <on>"],
+        types=["bigWig"],
         required=False,
-        validator=set(['on'])),
-
+        validator=set(["on"]),
+    ),
     Param(
         name="nextExonText",
-        fmt=['nextExonText <str>', 'prevExonText <str>'],
-        types=['all'],
+        fmt=["nextExonText <str>", "prevExonText <str>"],
+        types=["all"],
         required=False,
         validator=str,
-        min_bed_fields=10),
-
+        min_bed_fields=10,
+    ),
     Param(
         name="noColorTag",
-        fmt=['noColorTag .'],
-        types=['bam'],
+        fmt=["noColorTag ."],
+        types=["bam"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="noStems",
-        fmt=['noStems <on/off>'],
-        types=['bigLolly'],
+        fmt=["noStems <on/off>"],
+        types=["bigLolly"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="normalization",
-        fmt=['normalization <NONE|VC|VC_SQRT|KR>'],
-        types=['hic'],
+        fmt=["normalization <NONE|VC|VC_SQRT|KR>"],
+        types=["hic"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="otherDb",
-        fmt=['otherDb <otherDb>'],
-        types=['all'],
+        fmt=["otherDb <otherDb>"],
+        types=["all"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="otherSpecies",
-        fmt=['otherSpecies <otherSpecies>'],
-        types=['all'],
+        fmt=["otherSpecies <otherSpecies>"],
+        types=["all"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="otherTwoBitUrl",
-        fmt=['otherTwoBitUrl <url/relativePath>'],
-        types=['bigChain', 'bigPsl'],
+        fmt=["otherTwoBitUrl <url/relativePath>"],
+        types=["bigChain", "bigPsl"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="pairEndsByName",
-        fmt=['pairEndsByName .'],
-        types=['bam'],
+        fmt=["pairEndsByName ."],
+        types=["bam"],
         required=False,
-        validator=set(['.'])),
-
+        validator=set(["."]),
+    ),
     Param(
         name="pairSearchRange",
-        fmt=['pairSearchRange <#>'],
-        types=['bam'],
+        fmt=["pairSearchRange <#>"],
+        types=["bam"],
         required=False,
-        validator=int),
-
+        validator=int,
+    ),
     # NOTE in the spec there is "parent_container", "parent_supertrack", and
     # "parent". The reason appears to be so that there are unique div
     # names in the HTML, but they all refer to the parameter "parent".
@@ -979,441 +1034,427 @@
     #   - remove the Params for "parent_container" and "parent_supertrack"
     #   - include the Param for "parent"
     #   - set types to "all" and just validate on str
-
     Param(
         name="parent",
-        fmt=['parent <composite> [off/on]', 'parent <containerTrack>'],
-        types=['all'],
+        fmt=["parent <composite> [off/on]", "parent <containerTrack>"],
+        types=["all"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="pennantIcon",
-        fmt=['pennantIcon <iconFile>/<text color> [html [tip]] \n[; <iconFile>/<text color> [html [tip]]]'],
-        types=['all'],
+        fmt=[
+            "pennantIcon <iconFile>/<text color> [html [tip]] \n[; <iconFile>/<text color> [html [tip]]]"
+        ],
+        types=["all"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="prevExonText",
-        fmt=['nextExonText <str>', 'prevExonText <str>'],
-        types=['all'],
+        fmt=["nextExonText <str>", "prevExonText <str>"],
+        types=["all"],
         required=False,
         validator=str,
-        min_bed_fields=10),
-
+        min_bed_fields=10,
+    ),
     Param(
         name="priority",
-        fmt=['priority <float>'],
-        types=['all'],
+        fmt=["priority <float>"],
+        types=["all"],
         required=False,
-        validator=float),
-
+        validator=float,
+    ),
     Param(
         name="refUrl",
-        fmt=['refUrl <url>'],
-        types=['bam'],
+        fmt=["refUrl <url>/%s"],
+        types=["bam"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="resolution",
-        fmt=['resolution <Auto|integer>'],
-        types=['hic'],
+        fmt=["resolution <Auto|integer>"],
+        types=["hic"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="saturationScore",
-        fmt=['saturationScore <float>'],
-        types=['hic'],
+        fmt=["saturationScore <float>"],
+        types=["hic"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="scoreFilter",
-        fmt=['scoreFilter <low>[:<high>]', 'scoreFilterLimits <low>[:<high>]'],
-        types=['bigBed'],
+        fmt=["scoreFilter <low>[:<high>]", "scoreFilterLimits <low>[:<high>]"],
+        types=["bigBed"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     # TODO: worth a custom validator?
     Param(
         name="scoreFilterLimits",
-        fmt=['scoreFilter <low>[:<high>]', 'scoreFilterLimits <low>[:<high>]'],
-        types=['bigBed'],
+        fmt=["scoreFilter <low>[:<high>]", "scoreFilterLimits <low>[:<high>]"],
+        types=["bigBed"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="scoreLabel",
-        fmt=['scoreLabel <label>'],
-        types=['bigBed', 'bigGenePred', 'bigNarrowPeak', 'bigPsl'],
+        fmt=["scoreLabel <label>"],
+        types=["bigBed", "bigGenePred", "bigNarrowPeak", "bigPsl"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="scoreMax",
-        fmt=['spectrum on', 'scoreMax <integer>', 'scoreMin <integer>'],
-        types=['all'],
+        fmt=["spectrum on", "scoreMax <integer>", "scoreMin <integer>"],
+        types=["all"],
         required=False,
         validator=int,
-        min_bed_fields=5),
-
+        min_bed_fields=5,
+    ),
     Param(
         name="scoreMin",
-        fmt=['spectrum on', 'scoreMax <integer>', 'scoreMin <integer>'],
-        types=['all'],
+        fmt=["spectrum on", "scoreMax <integer>", "scoreMin <integer>"],
+        types=["all"],
         required=False,
         validator=int,
-        min_bed_fields=5),
-
+        min_bed_fields=5,
+    ),
     Param(
         name="searchIndex",
-        fmt=['searchIndex <str>'],
-        types=['bigBed'],
+        fmt=["searchIndex <str>"],
+        types=["bigBed"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="searchTrix",
-        fmt=['searchTrix <url/relativePath>'],
-        types=['bigBed'],
+        fmt=["searchTrix <url/relativePath>"],
+        types=["bigBed"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="sepFields",
-        fmt=['sepFields <fieldName1>="<url1>" <fieldName2>="<url2>" ...'],
-        types=['bigBed', 'bigChain', 'bigGenePred', 'bigMaf', 'bigNarrowPeak', 'bigPsl'],
-        required=False,
-        validator=validate.key_val),
-
+        fmt=["sepFields fieldName1,fieldName2 ..."],
+        types=[
+            "bigBed",
+            "bigChain",
+            "bigGenePred",
+            "bigMaf",
+            "bigNarrowPeak",
+            "bigPsl",
+        ],
+        required=False,
+        validator=validate.key_val,
+    ),
     Param(
         name="shortLabel",
-        fmt=['shortLabel'],
-        types=['all'],
+        fmt=["shortLabel"],
+        types=["all"],
         required=True,
-        validator=validate.short_label),
-
+        validator=validate.short_label,
+    ),
     Param(
         name="showDiffBasesAllScales",
-        fmt=['showDiffBasesAllScales on'],
-        types=['all'],
+        fmt=["showDiffBasesAllScales on"],
+        types=["all"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="showDiffBasesMaxZoom",
-        fmt=['showDiffBasesMaxZoom <basesPerPixel>'],
-        types=['all'],
+        fmt=["showDiffBasesMaxZoom <basesPerPixel>"],
+        types=["all"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="showNames",
-        fmt=['showNames <on/off>'],
-        types=['bam'],
+        fmt=["showNames <on/off>"],
+        types=["bam"],
         required=False,
-        validator=set(['on', 'off'])),
-
+        validator=set(["on", "off"]),
+    ),
     Param(
         name="showSnpWidth",
-        fmt=['showSnpWidth <integer>'],
-        types=['halSnake'],
+        fmt=["showSnpWidth <integer>"],
+        types=["halSnake"],
         required=False,
-        validator=int),
-
+        validator=int,
+    ),
     Param(
         name="showSubtrackColorOnUi",
-        fmt=['showSubtrackColorOnUi on'],
-        types=['multiWig'],
+        fmt=["showSubtrackColorOnUi on"],
+        types=["multiWig"],
         required=False,
-        validator=set(['on'])),
-
+        validator=set(["on"]),
+    ),
     Param(
         name="skipEmptyFields",
-        fmt=['skipEmptyFields on'],
-        types=['bigBed', 'bigChain', 'bigGenePred', 'bigMaf', 'bigNarrowPeak', 'bigPsl'],
-        required=False,
-        validator=set(['on'])),
-
+        fmt=["skipEmptyFields on"],
+        types=[
+            "bigBed",
+            "bigChain",
+            "bigGenePred",
+            "bigMaf",
+            "bigNarrowPeak",
+            "bigPsl",
+        ],
+        required=False,
+        validator=set(["on"]),
+    ),
     Param(
         name="skipFields",
         fmt=['skipFields <fieldName1>="<url1>" <fieldName2>="<url2>" ...'],
-        types=['bigBed', 'bigChain', 'bigGenePred', 'bigMaf', 'bigNarrowPeak', 'bigPsl'],
-        required=False,
-        validator=validate.key_val),
-
+        types=[
+            "bigBed",
+            "bigChain",
+            "bigGenePred",
+            "bigMaf",
+            "bigNarrowPeak",
+            "bigPsl",
+        ],
+        required=False,
+        validator=validate.key_val,
+    ),
     Param(
         name="smoothingWindow",
-        fmt=['smoothingWindow <off/1-16>'],
-        types=['bigWig'],
+        fmt=["smoothingWindow <off/1-16>"],
+        types=["bigWig"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="sortOrder",
-        fmt=['sortOrder <gTag#=+/-> [gTag#=- ...]'],
-        types=['subGroups'],
+        fmt=["sortOrder <gTag#=+/-> [gTag#=- …]"],
+        types=["subGroups"],
         required=False,
-        validator=validate.key_val),
-
+        validator=validate.key_val,
+    ),
     Param(
         name="spectrum",
-        fmt=['spectrum on', 'scoreMax <integer>', 'scoreMin <integer>'],
-        types=['all'],
+        fmt=["spectrum on", "scoreMax <integer>", "scoreMin <integer>"],
+        types=["all"],
         required=False,
-        validator=set(['on']),
-        min_bed_fields=5),
-
+        validator=set(["on"]),
+        min_bed_fields=5,
+    ),
     Param(
         name="subGroups",
-        fmt=['subGroups <gTag1=mTag1?> [gTag2= mTag2?]'],
-        types=['subGroups'],
+        fmt=["subGroups <gTag1=mTag1?> [gTag2= mTag2?]"],
+        types=["subGroups"],
         required=False,
-        validator=validate.key_val),
-
+        validator=validate.key_val,
+    ),
     Param(
         name="summary",
-        fmt=['summary <tableName/url>'],
-        types=['bigMaf'],
+        fmt=["summary <tableName/url>"],
+        types=["bigMaf"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="superTrack",
-        fmt=['superTrack on'],
-        types=['superTrack'],
+        fmt=["superTrack on show"],
+        types=["superTrack"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="tableBrowser",
-        fmt=['tableBrowser <off/on/noGenome> [table1 ...]'],
-        types=['all'],
+        fmt=["tableBrowser <off/on/noGenome/tbNoGenome> [table1 ...]"],
+        types=["all"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="thickDrawItem",
-        fmt=['thickDrawItem <off/on>'],
-        types=['bigBed'],
+        fmt=["thickDrawItem <off/on>"],
+        types=["bigBed"],
         required=False,
-        validator=set(['on', 'off']),
-        min_bed_fields=8),
-
-    Param(
-        name="track",
-        fmt=['track'],
-        types=['all'],
-        required=True,
-        validator=str),
-
+        validator=set(["on", "off"]),
+        min_bed_fields=8,
+    ),
+    Param(name="track", fmt=["track"], types=["all"], required=True, validator=str),
     Param(
         name="transformFunc",
-        fmt=['transformFunc <NONE/LOG>'],
-        types=['bigWig'],
+        fmt=["transformFunc <NONE/LOG>"],
+        types=["bigWig"],
         required=False,
-        validator=set(['NONE', 'LOG'])),
-
+        validator=set(["NONE", "LOG"]),
+    ),
     Param(
         name="url",
-        fmt=['url <url>', 'urlLabel <label>'],
-        types=['all'],
+        fmt=["url <url>", "urlLabel <label>"],
+        types=["all"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
-        name="url_for_hubs",
-        fmt=['url <url>', 'urlLabel <label>'],
-        types=['all'],
+        name="urlLabel",
+        fmt=["url <url>", "urlLabel <label>"],
+        types=["all"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
-        name="urlLabel",
-        fmt=['url <url>', 'urlLabel <label>'],
-        types=['all'],
+        name="url_for_hubs",
+        fmt=["url <url>", "urlLabel <label>"],
+        types=["all"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="urls",
         fmt=['urls <fieldName1>="<url1>" <fieldName2>="<url2>" ...'],
-        types=['bigBarChart', 'bigBed'],
+        types=["bigBarChart", "bigBed"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="vcfChildSample",
-        fmt=['vcfChildSample <sampleName|altName>'],
-        types=['vcfPhasedTrio'],
+        fmt=["vcfChildSample <sampleName|altName>"],
+        types=["vcfPhasedTrio"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="vcfDoFilter",
-        fmt=['vcfDoFilter <on/off>'],
-        types=['vcfPhasedTrio', 'vcfTabix'],
+        fmt=["vcfDoFilter <on/off>"],
+        types=["vcfPhasedTrio", "vcfTabix"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="vcfDoMaf",
-        fmt=['vcfDoMaf <on/off>'],
-        types=['vcfPhasedTrio', 'vcfTabix'],
+        fmt=["vcfDoMaf <on/off>"],
+        types=["vcfPhasedTrio", "vcfTabix"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="vcfDoQual",
-        fmt=['vcfDoQual <on/off>'],
-        types=['vcfPhasedTrio', 'vcfTabix'],
+        fmt=["vcfDoQual <on/off>"],
+        types=["vcfPhasedTrio", "vcfTabix"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="vcfParentSamples",
-        fmt=['vcfParentSamples <sampleName|altName,sampleName|altName>'],
-        types=['vcfPhasedTrio'],
+        fmt=["vcfParentSamples <sampleName|altName,sampleName|altName>"],
+        types=["vcfPhasedTrio"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="vcfUseAltSampleNames",
-        fmt=['vcfUseAltSampleNames <on/off>'],
-        types=['vcfPhasedTrio'],
+        fmt=["vcfUseAltSampleNames <on/off>"],
+        types=["vcfPhasedTrio"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
-        name='view',
-        fmt='view <viewName>',
-        types=['view'],
+        name="view",
+        fmt="view <viewName>",
+        types=["view"],
         required=False,
-        validator=str),
-
-
+        validator=str,
+    ),
     Param(
         name="viewLimits",
-        fmt=['viewLimits <lower:upper>', 'viewLimitsMax <lower:upper>'],
-        types=['bigWig'],
+        fmt=["viewLimits <lower:upper>", "viewLimitsMax <lower:upper>"],
+        types=["bigWig"],
         required=False,
-        validator=validate.ColSV2),
-
+        validator=validate.ColSV2,
+    ),
     Param(
         name="viewLimitsMax",
-        fmt=['viewLimits <lower:upper>', 'viewLimitsMax <lower:upper>'],
-        types=['bigWig'],
+        fmt=["viewLimits <lower:upper>", "viewLimitsMax <lower:upper>"],
+        types=["bigWig"],
         required=False,
-        validator=validate.ColSV2),
-
+        validator=validate.ColSV2,
+    ),
     Param(
         name="viewUi",
-        fmt=['viewUi on'],
-        types=['view'],
+        fmt=["viewUi on"],
+        types=["view"],
         required=False,
-        validator=set(['on'])),
-
+        validator=set(["on"]),
+    ),
     Param(
         name="visibility",
-        fmt=['visibility'],
-        types=['all'],
+        fmt=["visibility"],
+        types=["all"],
         required=False,
-        validator=set(['hide', 'dense', 'squish', 'pack', 'full'])),
-
+        validator=set(["hide", "dense", "squish", "pack", "full"]),
+    ),
     Param(
         name="windowingFunction",
-        fmt=['windowingFunction  <mean/mean+whiskers/maximum/minimum>'],
-        types=['bigWig'],
+        fmt=["windowingFunction  <mean/mean+whiskers/maximum/minimum>"],
+        types=["bigWig"],
         required=False,
-        validator=set(['mean', 'mean+whiskers', 'maximum', 'minimum'])),
-
+        validator=set(["mean", "mean+whiskers", "maximum", "minimum"]),
+    ),
     Param(
         name="yAxisLabel",
-        fmt=['yAxisLabel.<integer> <integer> <on/off> <R,G,B> <string> '],
-        types=['bigLolly'],
+        fmt=["yAxisLabel.<integer> <integer> <on/off> <R,G,B> <string> "],
+        types=["bigLolly"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="yAxisNumLabels",
-        fmt=['yAxisNumLabels.<on/off> <integer>'],
-        types=['bigLolly'],
+        fmt=["yAxisNumLabels.<on/off> <integer>"],
+        types=["bigLolly"],
         required=False,
-        validator=str),
-
+        validator=str,
+    ),
     Param(
         name="yLineMark",
-        fmt=['yLineMark <#>', 'yLineOnOff <off/on>', 'gridDefault   on'],
-        types=['bigWig'],
+        fmt=["yLineMark <#>", "yLineOnOff <off/on>", "gridDefault   on"],
+        types=["bigWig"],
         required=False,
-        validator=float),
-
+        validator=float,
+    ),
     Param(
         name="yLineOnOff",
-        fmt=['yLineMark <#>', 'yLineOnOff <off/on>', 'gridDefault   on'],
-        types=['bigWig'],
+        fmt=["yLineMark <#>", "yLineOnOff <off/on>", "gridDefault   on"],
+        types=["bigWig"],
         required=False,
-        validator=set(['on', 'off'])),
-
+        validator=set(["on", "off"]),
+    ),
     # NOTE: Assembly parameters are not defined in the database, so they need
     # to be added separately here.
+    Param(name="description", fmt="", types=["all"], required=False, validator=str),
+    Param(name="organism", fmt="", types=["assembly"], required=False, validator=str),
     Param(
-        name='description',
-        fmt='',
-        types=['all'],
-        required=False,
-        validator=str),
-
-    Param(
-        name='organism',
-        fmt='',
-        types=['assembly'],
-        required=False,
-        validator=str),
-
-    Param(
-        name='scientificName',
-        fmt='',
-        types=['assembly'],
-        required=False,
-        validator=str),
-
-    Param(
-        'orderKey',
-        fmt='',
-        types=['assembly'],
-        required=False,
-        validator=str),
-
+        name="scientificName", fmt="", types=["assembly"], required=False, validator=str
+    ),
+    Param("orderKey", fmt="", types=["assembly"], required=False, validator=str),
     Param(
-        'defaultPos',
-        fmt='',
-        types=['all','assembly', 'genome'],
+        "defaultPos",
+        fmt="",
+        types=["all", "assembly", "genome"],
         required=False,
-        validator=validate.ucsc_position),
-
-
+        validator=validate.ucsc_position,
+    ),
     # Add a param for types
     Param(
-        name='type',
-        fmt='',
+        name="type",
+        fmt="",
         types=TRACKTYPES,
         required=True,
-        validator=validate.tracktypes),
-
+        validator=validate.tracktypes,
+    ),
     # Add a param for group, which is used in assembly hubs (but not documented
     # in the Track Hub Database Definition document)
-    Param(
-        name='group',
-        fmt='',
-        types=TRACKTYPES,
-        required=False,
-        validator=str),
-
-    ]
+    Param(name="group", fmt="", types=TRACKTYPES, required=False, validator=str),
+]
 
 
 # TODO: Some params are not specified for bigBed, only BED.
diff --git a/trackhub/test/construct_example_data.py b/trackhub/test/construct_example_data.py
index 65713282..aaa9a087 100644
--- a/trackhub/test/construct_example_data.py
+++ b/trackhub/test/construct_example_data.py
@@ -4,77 +4,76 @@
 import numpy as np
 from trackhub import helpers
 
+
 def make_files():
     np.random.seed(0)
 
     data_dir = helpers.data_dir()
 
-    with open('chromsizes', 'w') as fout:
-        fout.write('chr1\t10000\n')
+    with open("chromsizes", "w") as fout:
+        fout.write("chr1\t10000\n")
 
     # First, make some example BED files to convert to bigBed
 
-
-    for i, x in enumerate([
-        pybedtools.BedTool(
-            """
+    for i, x in enumerate(
+        [
+            pybedtools.BedTool(
+                """
             chr1 10 50
             chr1 100 125
             chr1 300 400
-            """, from_string=True),
-        pybedtools.BedTool(
-            """
+            """,
+                from_string=True,
+            ),
+            pybedtools.BedTool(
+                """
             chr1 500 600
-            """, from_string=True),
-        pybedtools.BedTool(
-            """
+            """,
+                from_string=True,
+            ),
+            pybedtools.BedTool(
+                """
             chr1 20 60
             chr1 40 100
             chr1 80 90
             chr1 250 300
-            """, from_string=True)
-    ]):
-        out = os.path.join(data_dir, 'random-hg38-%s.bigBed' % i)
-        cmds = [
-            'bedToBigBed',
-            x.fn,
-            'chromsizes',
-            out]
+            """,
+                from_string=True,
+            ),
+        ]
+    ):
+        out = os.path.join(data_dir, "random-hg38-%s.bigBed" % i)
+        cmds = ["bedToBigBed", x.fn, "chromsizes", out]
         subprocess.check_call(cmds)
 
     # make some sine waves for bigWigs
 
-
-
     def sine(resolution=10, power=2):
         resolution = 10
         x = np.arange(0, 10000, resolution)
         y = np.sin(x / resolution ** power) + np.random.random(x.shape[0])
         for xi, yi in zip(x, y):
-            yield pybedtools.create_interval_from_list([
-                'chr1',
-                str(xi),
-                str(xi + resolution),
-                '{0:.3f}'.format(yi)
-            ])
-
+            yield pybedtools.create_interval_from_list(
+                ["chr1", str(xi), str(xi + resolution), "{0:.3f}".format(yi)]
+            )
 
-    for i, x in enumerate([
-        sine(resolution=10, power=2.0),
-        sine(resolution=10, power=2.5),
-        sine(resolution=10, power=3.0),
-    ]):
-        x = pybedtools.BedTool(x).saveas(os.path.join(data_dir, 'sine-hg38-%d.bedgraph' % i))
-        out = x.fn + '.bw'
-        cmds = [
-            'bedGraphToBigWig',
-            x.fn,
-            'chromsizes',
-            out]
+    for i, x in enumerate(
+        [
+            sine(resolution=10, power=2.0),
+            sine(resolution=10, power=2.5),
+            sine(resolution=10, power=3.0),
+        ]
+    ):
+        x = pybedtools.BedTool(x).saveas(
+            os.path.join(data_dir, "sine-hg38-%d.bedgraph" % i)
+        )
+        out = x.fn + ".bw"
+        cmds = ["bedGraphToBigWig", x.fn, "chromsizes", out]
         subprocess.check_call(cmds)
         os.unlink(x.fn)
 
-    os.unlink('chromsizes')
+    os.unlink("chromsizes")
+
 
 if __name__ == "__main__":
     make_files()
diff --git a/trackhub/test/construct_example_genome.py b/trackhub/test/construct_example_genome.py
index 95dfe76c..876dd9fb 100644
--- a/trackhub/test/construct_example_genome.py
+++ b/trackhub/test/construct_example_genome.py
@@ -6,21 +6,19 @@
 import numpy as np
 from trackhub import helpers
 
+
 def make_files():
     random.seed(0)
     np.random.seed(0)
 
     data_dir = helpers.data_dir()
 
-    chromsizes = OrderedDict([
-        ("chr1", (0, 100000)),
-        ("chr2", (0, 75000)),
-        ("chr3", (0, 50000))
-    ])
-
+    chromsizes = OrderedDict(
+        [("chr1", (0, 100000)), ("chr2", (0, 75000)), ("chr3", (0, 50000))]
+    )
 
     def random_dna(length, chars="ATGC"):
-        return ''.join(random.choice(chars) for _ in range(length)) + "\n"
+        return "".join(random.choice(chars) for _ in range(length)) + "\n"
 
     fasta = open(os.path.join(data_dir, "newOrg1.fa"), "w")
 
@@ -31,11 +29,7 @@ def random_dna(length, chars="ATGC"):
             fasta.write(random_dna(80))
         fasta.write(random_dna(r))
 
-    cmds = [
-        "faToTwoBit",
-        fasta.name,
-        fasta.name[0:-2] + "2bit"
-    ]
+    cmds = ["faToTwoBit", fasta.name, fasta.name[0:-2] + "2bit"]
 
     p = subprocess.check_call(cmds)
 
@@ -46,22 +40,18 @@ def random_dna(length, chars="ATGC"):
 
     # Make some randomized bigBed files
     for i in range(3):
-        x = pybedtools.BedTool(
-            "chr1 0 100000", from_string=True)\
-            .window_maker(g=g, w=100 * (i + 1))\
-            .shuffle(g=g, seed=i)\
+        x = (
+            pybedtools.BedTool("chr1 0 100000", from_string=True)
+            .window_maker(g=g, w=100 * (i + 1))
+            .shuffle(g=g, seed=i)
             .sort()
+        )
 
-        out = os.path.join(data_dir, 'random-no1-%s.bigBed' % i)
+        out = os.path.join(data_dir, "random-no1-%s.bigBed" % i)
 
-        cmds = [
-            'bedToBigBed',
-            x.fn,
-            g,
-            out]
+        cmds = ["bedToBigBed", x.fn, g, out]
         p = subprocess.check_call(cmds)
 
-
     # make some sine waves for bigWigs
     def sine(factor):
 
@@ -70,20 +60,20 @@ def sine(factor):
             x = np.arange(0, size, 10000)
             y = np.sin(x / factor / np.pi) + np.random.random(len(x)) / 3
             for xi, yi in zip(x, y):
-                yield pybedtools.create_interval_from_list(list(map(str, [
-                    chrom, xi, xi + 1000, yi])))
-
-    for f in [100., 1000.]:
-        x = pybedtools.BedTool(sine(f)).saveas(os.path.join(data_dir, 'sine-no1-%d.bedgraph' % f))
-        out = x.fn + '.bw'
-
-        cmds = [
-            'bedGraphToBigWig',
-            x.fn,
-            g,
-            out]
+                yield pybedtools.create_interval_from_list(
+                    list(map(str, [chrom, xi, xi + 1000, yi]))
+                )
+
+    for f in [100.0, 1000.0]:
+        x = pybedtools.BedTool(sine(f)).saveas(
+            os.path.join(data_dir, "sine-no1-%d.bedgraph" % f)
+        )
+        out = x.fn + ".bw"
+
+        cmds = ["bedGraphToBigWig", x.fn, g, out]
         p = subprocess.check_call(cmds)
         os.unlink(x.fn)
 
-if __name__ == '__main__':
+
+if __name__ == "__main__":
     make_files()
diff --git a/trackhub/test/deprecated_upload_test.py b/trackhub/test/deprecated_upload_test.py
index 0a13ee61..2acabc18 100644
--- a/trackhub/test/deprecated_upload_test.py
+++ b/trackhub/test/deprecated_upload_test.py
@@ -5,8 +5,17 @@
 import tempfile
 from trackhub import upload
 from trackhub.helpers import data_dir
-from trackhub import Hub, GenomesFile, Genome, Track, CompositeTrack, \
-    TrackDb, ViewTrack, SuperTrack, AggregateTrack
+from trackhub import (
+    Hub,
+    GenomesFile,
+    Genome,
+    Track,
+    CompositeTrack,
+    TrackDb,
+    ViewTrack,
+    SuperTrack,
+    AggregateTrack,
+)
 
 d = data_dir()
 
@@ -15,26 +24,27 @@ class Upload(object):
     def __init__(self):
         with pytest.warns(DeprecationWarning):
             self.hub = Hub(
-                hub='example_hub',
-                short_label='example hub',
-                long_label='an example hub for testing',
-                email='none@example.com')
+                hub="example_hub",
+                short_label="example hub",
+                long_label="an example hub for testing",
+                email="none@example.com",
+            )
             self.genomes_file = GenomesFile()
-            self.genome = Genome('dm3')
+            self.genome = Genome("dm3")
             self.trackdb = TrackDb()
 
             self.tracks = [
                 Track(
-                    name='track1',
-                    tracktype='bigBed',
-                    local_fn=os.path.join(d, 'random-hg38-0.bigBed'),
-                    remote_fn='1.bigbed',
+                    name="track1",
+                    tracktype="bigBed",
+                    local_fn=os.path.join(d, "random-hg38-0.bigBed"),
+                    remote_fn="1.bigbed",
                 ),
                 Track(
-                    name='track2',
-                    tracktype='bigWig',
-                    local_fn=os.path.join(d, 'sine-hg38-0.bedgraph.bw'),
-                    remote_fn='2.bw',
+                    name="track2",
+                    tracktype="bigWig",
+                    local_fn=os.path.join(d, "sine-hg38-0.bedgraph.bw"),
+                    remote_fn="2.bw",
                 ),
             ]
             self.hub.add_genomes_file(self.genomes_file)
diff --git a/trackhub/test/test_add_tracks.py b/trackhub/test/test_add_tracks.py
index cde3e12f..526b04da 100644
--- a/trackhub/test/test_add_tracks.py
+++ b/trackhub/test/test_add_tracks.py
@@ -1,99 +1,117 @@
 import trackhub
 
+
 def test_composite_args():
     """Tests to see if different types can be handled by 'add_tracks' in the class CompositeTrack"""
 
-    c1 = trackhub.track.CompositeTrack(name='testcomposite', tracktype='bigWig')
-    t1 = trackhub.track.Track(name='testtrack', tracktype='bigWig')
-    t2 = trackhub.track.Track(name='testtrack2', tracktype='bigWig')
-    v1 = trackhub.track.ViewTrack(name='a', view='v', tracktype='bigWig')
+    c1 = trackhub.track.CompositeTrack(name="testcomposite", tracktype="bigWig")
+    t1 = trackhub.track.Track(name="testtrack", tracktype="bigWig")
+    t2 = trackhub.track.Track(name="testtrack2", tracktype="bigWig")
+    v1 = trackhub.track.ViewTrack(name="a", view="v", tracktype="bigWig")
 
-    d = {'track1': t1, 'track2': t2}
+    d = {"track1": t1, "track2": t2}
 
-    c1 = trackhub.track.CompositeTrack(name='testcomposite', tracktype='bigWig')
+    c1 = trackhub.track.CompositeTrack(name="testcomposite", tracktype="bigWig")
     c1.add_tracks(v1, [t1, t2])
     res1 = str(c1)
 
-    c2 = trackhub.track.CompositeTrack(name='testcomposite', tracktype='bigWig')
+    c2 = trackhub.track.CompositeTrack(name="testcomposite", tracktype="bigWig")
     c2.add_tracks(v1, t1, t2)
     res2 = str(c2)
 
-    c3 = trackhub.track.CompositeTrack(name='testcomposite', tracktype='bigWig')
+    c3 = trackhub.track.CompositeTrack(name="testcomposite", tracktype="bigWig")
     c3.add_tracks(v1, d.values())
     res3 = str(c3)
 
-    c4 = trackhub.track.CompositeTrack(name='testcomposite', tracktype='bigWig')
+    c4 = trackhub.track.CompositeTrack(name="testcomposite", tracktype="bigWig")
     c4.add_tracks(t1, [v1, t2])
     res4 = str(c4)
 
     assert res1 == res2 == res3 == res4
 
+
 def test_agg_args():
-    """ Tests for backward compatibility. Compares the output of the
+    """Tests for backward compatibility. Compares the output of the
     old method 'add_subtracks' with the new one 'add_tracks' in the class AggregateTrack."""
 
-    a1 = trackhub.track.AggregateTrack(name='testagg',tracktype='bigWig',aggregate='transparentOverlay')
-    t1 = trackhub.track.Track(name='test',tracktype='bigWig')
+    a1 = trackhub.track.AggregateTrack(
+        name="testagg", tracktype="bigWig", aggregate="transparentOverlay"
+    )
+    t1 = trackhub.track.Track(name="test", tracktype="bigWig")
     a1.add_tracks(t1)
     agg1 = str(a1)
 
-    a2 = trackhub.track.AggregateTrack(name='testagg',tracktype='bigWig',aggregate='transparentOverlay')
-    t2 = trackhub.track.Track(name='test',tracktype='bigWig')
+    a2 = trackhub.track.AggregateTrack(
+        name="testagg", tracktype="bigWig", aggregate="transparentOverlay"
+    )
+    t2 = trackhub.track.Track(name="test", tracktype="bigWig")
     a2.add_subtrack(t2)
     agg2 = str(a2)
 
     assert agg1 == agg2
 
+
 def test_add_multiple_agg_args():
-    """ Tests to see if different object types can be handled by 'add_tracks' in the class AggregateTrack."""
+    """Tests to see if different object types can be handled by 'add_tracks' in the class AggregateTrack."""
 
-    t1 = trackhub.track.Track(name='test',tracktype='bigWig')
-    t2 = trackhub.track.Track(name='test',tracktype='bigWig')
-    t3 = trackhub.track.Track(name='test',tracktype='bigWig')
+    t1 = trackhub.track.Track(name="test", tracktype="bigWig")
+    t2 = trackhub.track.Track(name="test", tracktype="bigWig")
+    t3 = trackhub.track.Track(name="test", tracktype="bigWig")
 
-    a1 = trackhub.track.AggregateTrack(name='testagg',tracktype='bigWig',aggregate='transparentOverlay')
-    a1.add_tracks(t1,t2,t3)
+    a1 = trackhub.track.AggregateTrack(
+        name="testagg", tracktype="bigWig", aggregate="transparentOverlay"
+    )
+    a1.add_tracks(t1, t2, t3)
     agg1 = str(a1)
 
-    a2 = trackhub.track.AggregateTrack(name='testagg',tracktype='bigWig',aggregate='transparentOverlay')
-    a2.add_tracks([t1,t2,t3])
+    a2 = trackhub.track.AggregateTrack(
+        name="testagg", tracktype="bigWig", aggregate="transparentOverlay"
+    )
+    a2.add_tracks([t1, t2, t3])
     agg2 = str(a2)
 
-    a3 = trackhub.track.AggregateTrack(name='testagg',tracktype='bigWig',aggregate='transparentOverlay')
-    a3.add_tracks(t1,[t2,t3])
+    a3 = trackhub.track.AggregateTrack(
+        name="testagg", tracktype="bigWig", aggregate="transparentOverlay"
+    )
+    a3.add_tracks(t1, [t2, t3])
     agg3 = str(a3)
 
-    a4 = trackhub.track.AggregateTrack(name='testagg',tracktype='bigWig',aggregate='transparentOverlay')
-    dagg = {'t1':t1,'t2':t2,'t3':t3}
+    a4 = trackhub.track.AggregateTrack(
+        name="testagg", tracktype="bigWig", aggregate="transparentOverlay"
+    )
+    dagg = {"t1": t1, "t2": t2, "t3": t3}
     a4.add_tracks(dagg.values())
     agg4 = str(a4)
 
     assert agg1 == agg2 == agg3 == agg4
 
+
 def test_composite_tracks():
-    """ Tests for backwards compatibility. Compares the old methods 'add_view' and 'add_subtrack'
+    """Tests for backwards compatibility. Compares the old methods 'add_view' and 'add_subtrack'
     with the new one 'add_tracks' in the class CompositeTrack."""
 
-    c1 = trackhub.track.CompositeTrack(name='testcomposite', tracktype='bigWig')
-    t1 = trackhub.track.Track(name='testtrack', tracktype='bigWig')
-    v1 = trackhub.track.ViewTrack(name='a', view='v', tracktype='bigWig')
+    c1 = trackhub.track.CompositeTrack(name="testcomposite", tracktype="bigWig")
+    t1 = trackhub.track.Track(name="testtrack", tracktype="bigWig")
+    v1 = trackhub.track.ViewTrack(name="a", view="v", tracktype="bigWig")
     c1.add_tracks(t1)
     c1.add_tracks(v1)
 
     assert isinstance(v1, trackhub.track.ViewTrack)
     assert c1.views == [v1]
 
-    c2 = trackhub.track.CompositeTrack(name='testcomposite', tracktype='bigWig')
-    t2 = trackhub.track.Track(name='testtrack', tracktype='bigWig')
-    v2 = trackhub.track.ViewTrack(name='a', view='v', tracktype='bigWig')
+    c2 = trackhub.track.CompositeTrack(name="testcomposite", tracktype="bigWig")
+    t2 = trackhub.track.Track(name="testtrack", tracktype="bigWig")
+    v2 = trackhub.track.ViewTrack(name="a", view="v", tracktype="bigWig")
     c2.add_subtrack(t2)
     c2.add_view(v2)
 
     results1 = str(c1)
     results2 = str(c2)
 
-    assert results1 == results2 == \
-"""track testcomposite
+    assert (
+        results1
+        == results2
+        == """track testcomposite
 shortLabel testcomposite
 longLabel testcomposite
 type bigWig
@@ -112,35 +130,40 @@ def test_composite_tracks():
     longLabel testtrack
     type bigWig
     parent testcomposite"""
+    )
 
 
 def test_super_track():
-    """ Tests to see if different object types can be handled by 'add_tracks' in the class SuperTrack
-     and that it produces the same result as before it was updated"""
+    """Tests to see if different object types can be handled by 'add_tracks' in the class SuperTrack
+    and that it produces the same result as before it was updated"""
 
-    t1 = trackhub.track.Track(name='test1',tracktype='bigWig')
-    t2 = trackhub.track.Track(name='test2',tracktype='bigWig')
-    t3 = trackhub.track.Track(name='test3',tracktype='bigWig')
+    t1 = trackhub.track.Track(name="test1", tracktype="bigWig")
+    t2 = trackhub.track.Track(name="test2", tracktype="bigWig")
+    t3 = trackhub.track.Track(name="test3", tracktype="bigWig")
 
     s1 = trackhub.track.SuperTrack(name="super")
-    s1.add_tracks(t1,t2,[t3])
+    s1.add_tracks(t1, t2, [t3])
     sup1 = str(s1)
 
     s2 = trackhub.track.SuperTrack(name="super")
-    s2.add_tracks([t1,t2,t3]) 
+    s2.add_tracks([t1, t2, t3])
     sup2 = str(s2)
 
     s3 = trackhub.track.SuperTrack(name="super")
-    s3.add_tracks(t1,t2,t3)
+    s3.add_tracks(t1, t2, t3)
     sup3 = str(s3)
 
     s4 = trackhub.track.SuperTrack(name="super")
-    dsup = {'t1':t1,'t2':t2,'t3':t3}
+    dsup = {"t1": t1, "t2": t2, "t3": t3}
     s4.add_tracks(dsup.values())
     sup4 = str(s4)
 
-    assert sup1 == sup2 == sup3 == sup4 == \
-"""track super
+    assert (
+        sup1
+        == sup2
+        == sup3
+        == sup4
+        == """track super
 shortLabel super
 longLabel super
 type superTrack
@@ -163,35 +186,40 @@ def test_super_track():
     longLabel test3
     type bigWig
     parent super"""
+    )
 
-def test_add_tracks_view():
-    """ Tests to see if different object types can be handled by 'add_tracks' in the class ViewTrack
-     and that it produces the same result as before it was updated"""
-
-    t1 = trackhub.track.Track(name='testtrack', tracktype='bigWig')
-    t2 = trackhub.track.Track(name='testtrack', tracktype='bigWig')
-    t3 = trackhub.track.Track(name='testtrack', tracktype='bigWig')
-    v1 = trackhub.track.ViewTrack(name='a', view='v', tracktype='bigWig')
-    v2 = trackhub.track.ViewTrack(name='a', view='v', tracktype='bigWig')
-    v3 = trackhub.track.ViewTrack(name='a', view='v', tracktype='bigWig')
-    v4 = trackhub.track.ViewTrack(name='a', view='v', tracktype='bigWig')
 
-
-    v1.add_tracks([t1,t2,t3])
+def test_add_tracks_view():
+    """Tests to see if different object types can be handled by 'add_tracks' in the class ViewTrack
+    and that it produces the same result as before it was updated"""
+
+    t1 = trackhub.track.Track(name="testtrack", tracktype="bigWig")
+    t2 = trackhub.track.Track(name="testtrack", tracktype="bigWig")
+    t3 = trackhub.track.Track(name="testtrack", tracktype="bigWig")
+    v1 = trackhub.track.ViewTrack(name="a", view="v", tracktype="bigWig")
+    v2 = trackhub.track.ViewTrack(name="a", view="v", tracktype="bigWig")
+    v3 = trackhub.track.ViewTrack(name="a", view="v", tracktype="bigWig")
+    v4 = trackhub.track.ViewTrack(name="a", view="v", tracktype="bigWig")
+
+    v1.add_tracks([t1, t2, t3])
     view1 = str(v1)
 
-    v2.add_tracks(t1,[t2,t3])
+    v2.add_tracks(t1, [t2, t3])
     view2 = str(v2)
 
-    v3.add_tracks(t1,t2,t3)
+    v3.add_tracks(t1, t2, t3)
     view3 = str(v3)
 
-    dview = {'t1': t1, 't2': t2, 't3': t3}
+    dview = {"t1": t1, "t2": t2, "t3": t3}
     v4.add_tracks(dview.values())
     view4 = str(v4)
 
-    assert view1 == view2 == view3 == view4 == \
-"""track a
+    assert (
+        view1
+        == view2
+        == view3
+        == view4
+        == """track a
 shortLabel a
 longLabel a
 type bigWig
@@ -217,3 +245,4 @@ def test_add_tracks_view():
     type bigWig
     parent a
     subGroups view=v"""
+    )
diff --git a/trackhub/test/test_assembly.py b/trackhub/test/test_assembly.py
index 93a362c2..b67be68a 100644
--- a/trackhub/test/test_assembly.py
+++ b/trackhub/test/test_assembly.py
@@ -8,7 +8,8 @@
     "assembly_hub",
     short_label="assembly_hub",
     long_label="an example of an assembly hub",
-    email="none@example.com")
+    email="none@example.com",
+)
 
 genome = trackhub.Assembly(
     genome="newOrg1",
@@ -18,7 +19,7 @@
     scientificName="Biggus Footus",
     description="BigFoot V4",
     html_string="BIGFOOT V4 INFO\n",
-    orderKey=4800
+    orderKey=4800,
 )
 
 genomes_file = trackhub.GenomesFile()
@@ -34,9 +35,9 @@
     track = trackhub.Track(
         name=trackhub.helpers.sanitize(name),
         source=bw,
-        tracktype='bigWig',
-        autoScale="on")
+        tracktype="bigWig",
+        autoScale="on",
+    )
     trackdb.add_tracks(track)
 
 trackhub.upload.stage_hub(hub)
-
diff --git a/trackhub/test/test_components.py b/trackhub/test/test_components.py
index 2a7a1bde..80a87282 100644
--- a/trackhub/test/test_components.py
+++ b/trackhub/test/test_components.py
@@ -1,23 +1,33 @@
 import pytest
-from trackhub import Hub, GenomesFile, Genome, Track, CompositeTrack, \
-    TrackDb, ViewTrack, SuperTrack, AggregateTrack
+from trackhub import (
+    Hub,
+    GenomesFile,
+    Genome,
+    Track,
+    CompositeTrack,
+    TrackDb,
+    ViewTrack,
+    SuperTrack,
+    AggregateTrack,
+)
 import os
 
 
 class Components(object):
     def __init__(self):
         self.hub = Hub(
-            hub='example_hub',
-            short_label='example hub',
-            long_label='an example hub for testing',
-            email='none@example.com')
+            hub="example_hub",
+            short_label="example hub",
+            long_label="an example hub for testing",
+            email="none@example.com",
+        )
         self.genomes_file = GenomesFile()
-        self.genome = Genome('dm3')
+        self.genome = Genome("dm3")
         self.trackdb = TrackDb()
 
         self.tracks = [
-            Track(name='track1', tracktype='bam'),
-            Track(name='track2', tracktype='bigWig'),
+            Track(name="track1", tracktype="bam"),
+            Track(name="track2", tracktype="bigWig"),
         ]
 
     def CONNECT(self):
@@ -32,8 +42,8 @@ def CONNECT(self):
 
     def DISCONNECT(self):
         """
-        Re-run the setup, which results in unconnected components. Run
-        CONNECT() to connect them up.
+        Re-run __init__ which results in unconnected components. Run CONNECT()
+        to connect them up.
         """
         self.__init__()
 
diff --git a/trackhub/test/test_example_data.py b/trackhub/test/test_example_data.py
index 7e9d30bb..1ce447b2 100644
--- a/trackhub/test/test_example_data.py
+++ b/trackhub/test/test_example_data.py
@@ -3,10 +3,13 @@
 import hashlib
 from trackhub import helpers
 
+
 def test_example_data_md5s():
     data_dir = helpers.data_dir()
 
-    data = [i.strip().split() for i in '''
+    data = [
+        i.strip().split()
+        for i in """
     3735b696b3a416a59f8755eaf5664e5a  sine-hg38-0.bedgraph.bw
     73ad8ba3590d0895810d069599b0e443  sine-hg38-1.bedgraph.bw
     85478d1ecc5906405ccb43d1ca426d29  sine-hg38-2.bedgraph.bw
@@ -18,16 +21,20 @@ def test_example_data_md5s():
     72934b760f1f5ee8f99d596536ef8b4c  random-no1-0.bigBed
     19116a3295e5679cb79ffc8904fa5abe  random-no1-1.bigBed
     d628cd0d3b91d8426bb9d0f99b39be52  random-no1-2.bigBed
-    '''.splitlines(False) if not i.strip().startswith('#') and len(i.strip()) > 0]
+    """.splitlines(
+            False
+        )
+        if not i.strip().startswith("#") and len(i.strip()) > 0
+    ]
 
     # for some reason, only faToTwoBit under py27 results in a different md5 than under py3.
     if sys.version_info[0] == 3:
-        data.append(('ba2fd8b22bcad65bb6583da937ff5222', 'newOrg1.2bit'))
+        data.append(("ba2fd8b22bcad65bb6583da937ff5222", "newOrg1.2bit"))
 
     success = True
     for md5, fn in data:
         fn = os.path.join(data_dir, fn)
-        obs = hashlib.md5(open(fn, 'rb').read()).hexdigest()
+        obs = hashlib.md5(open(fn, "rb").read()).hexdigest()
         success = success and (obs == md5)
         print(obs, md5, fn)
     assert success
diff --git a/trackhub/test/test_parentonoff/test_parentonoff.py b/trackhub/test/test_parentonoff/test_parentonoff.py
index b13a69dd..9bae0619 100644
--- a/trackhub/test/test_parentonoff/test_parentonoff.py
+++ b/trackhub/test/test_parentonoff/test_parentonoff.py
@@ -3,6 +3,7 @@
 
 HERE = os.path.abspath(os.path.dirname(__file__))
 
+
 def test_parentonoff():
 
     hub, genomes_file, genome, trackdb = trackhub.default_hub(
@@ -10,7 +11,7 @@ def test_parentonoff():
         short_label="TestHub",
         long_label="TestHub",
         email="karen.kapur@novartis.com",
-        genome="hg19"
+        genome="hg19",
     )
 
     testcomposite = trackhub.track.CompositeTrack(
@@ -18,7 +19,7 @@ def test_parentonoff():
         short_label="testlabelshort",
         long_label="testlabellong",
         tracktype="bigWig",
-        visibility="full"
+        visibility="full",
     )
 
     viewtrack = trackhub.track.ViewTrack(
@@ -31,36 +32,42 @@ def test_parentonoff():
 
     trackoff = trackhub.track.Track(
         name="E003DNase",
-        url=("http://egg2.wustl.edu/roadmap/data/byFileType/signal/"
-             "consolidated/macs2signal/pval/E003-DNase.pval.signal."
-             "bigwig"),
+        url=(
+            "http://egg2.wustl.edu/roadmap/data/byFileType/signal/"
+            "consolidated/macs2signal/pval/E003-DNase.pval.signal."
+            "bigwig"
+        ),
         tracktype="bigWig",
         short_label="E003DNase",
         long_label="E003DNase",
         visibility="full",
-        parent="off"
-        )
+        parent="off",
+    )
     trackon = trackhub.track.Track(
         name="E004DNase",
-        url=("http://egg2.wustl.edu/roadmap/data/byFileType/signal/"
-             "consolidated/macs2signal/pval/E004-DNase.pval.signal"
-             ".bigwig"),
+        url=(
+            "http://egg2.wustl.edu/roadmap/data/byFileType/signal/"
+            "consolidated/macs2signal/pval/E004-DNase.pval.signal"
+            ".bigwig"
+        ),
         tracktype="bigWig",
         short_label="E004DNase",
         long_label="E004DNase",
         visibility="full",
-        parent="on"
-        )
+        parent="on",
+    )
     trackdefault = trackhub.track.Track(
         name="E005DNase",
-        url=("http://egg2.wustl.edu/roadmap/data/byFileType/signal/"
-             "consolidated/macs2signal/pval/E005-DNase.pval.signal"
-             ".bigwig"),
+        url=(
+            "http://egg2.wustl.edu/roadmap/data/byFileType/signal/"
+            "consolidated/macs2signal/pval/E005-DNase.pval.signal"
+            ".bigwig"
+        ),
         tracktype="bigWig",
         short_label="E005DNase",
         long_label="E005DNase",
-        visibility="full"
-        )
+        visibility="full",
+    )
 
     viewtrack.add_tracks(trackoff)
     viewtrack.add_tracks(trackon)
@@ -71,7 +78,7 @@ def test_parentonoff():
 
     tmpdir, linknames = trackhub.upload.stage_hub(hub)
 
-    assert(
-        open(os.path.join(tmpdir, 'hg19/trackDb.txt')).read() ==
-        open(os.path.join(HERE, 'expected/hg19/trackDb.txt')).read()
+    assert (
+        open(os.path.join(tmpdir, "hg19/trackDb.txt")).read()
+        == open(os.path.join(HERE, "expected/hg19/trackDb.txt")).read()
     )
diff --git a/trackhub/test/test_supertrack.py b/trackhub/test/test_supertrack.py
index afe3b1f8..ac702dcc 100644
--- a/trackhub/test/test_supertrack.py
+++ b/trackhub/test/test_supertrack.py
@@ -6,79 +6,75 @@
 
 import trackhub
 
+
 def test_supertrack():
     hub, genomes_file, genome, trackdb = trackhub.default_hub(
         hub_name="supertrack",
-        short_label='example supertrack hub',
-        long_label='example supertrack hub',
+        short_label="example supertrack hub",
+        long_label="example supertrack hub",
         genome="hg38",
-        email="dalerr@nih.gov")
+        email="dalerr@nih.gov",
+    )
 
     trackdb.add_tracks(
         trackhub.Track(
-            url='https://google.com',
-            tracktype='bigWig',
-            name='top_level_track')
+            url="https://google.com", tracktype="bigWig", name="top_level_track"
+        )
     )
 
-    supertrack = trackhub.SuperTrack(
-        name='super',
-        short_label='Super track'
-    )
+    supertrack = trackhub.SuperTrack(name="super", short_label="Super track")
     trackdb.add_tracks(supertrack)
 
     supertrack.add_tracks(
         trackhub.Track(
-            url='https://google.com',
-            tracktype='bigWig',
-            name='under_supertrack')
+            url="https://google.com", tracktype="bigWig", name="under_supertrack"
+        )
     )
 
     overlay = trackhub.AggregateTrack(
-        aggregate='transparentOverlay',
-        visibility='full',
-        tracktype='bigWig',
-        viewLimits='-2:2',
-        maxHeightPixels='8:80:128',
-        showSubtrackColorOnUi='on',
-        name='agg_under_supertrack')
+        aggregate="transparentOverlay",
+        visibility="full",
+        tracktype="bigWig",
+        viewLimits="-2:2",
+        maxHeightPixels="8:80:128",
+        showSubtrackColorOnUi="on",
+        name="agg_under_supertrack",
+    )
     supertrack.add_tracks(overlay)
 
     overlay.add_subtrack(
         trackhub.Track(
-            url='https://google.com',
-            tracktype='bigWig',
-            name='track_under_agg_under_supertrack')
+            url="https://google.com",
+            tracktype="bigWig",
+            name="track_under_agg_under_supertrack",
+        )
     )
 
-    composite = trackhub.CompositeTrack(name='composite_under_supertrack', tracktype='bigWig')
-    view = trackhub.ViewTrack(name='view', view='viewtrack', tracktype='bigWig')
+    composite = trackhub.CompositeTrack(
+        name="composite_under_supertrack", tracktype="bigWig"
+    )
+    view = trackhub.ViewTrack(name="view", view="viewtrack", tracktype="bigWig")
 
     view.add_tracks(
         trackhub.Track(
-            url='https://google.com',
-            tracktype='bigWig',
-            name='track_under_view')
+            url="https://google.com", tracktype="bigWig", name="track_under_view"
+        )
     )
     composite.add_view(view)
 
-
     composite.add_subtrack(
         trackhub.Track(
-            url='https://google.com',
-            tracktype='bigWig',
-            name='track_under_composite')
+            url="https://google.com", tracktype="bigWig", name="track_under_composite"
+        )
     )
     supertrack.add_tracks(composite)
 
-
     orig_indent = trackhub.constants.INDENT
-    trackhub.constants.INDENT = '  '
+    trackhub.constants.INDENT = "  "
     results = str(trackdb)
     trackhub.constants.INDENT = orig_indent
 
-    expected = \
-"""track top_level_track
+    expected = """track top_level_track
 bigDataUrl https://google.com
 shortLabel top_level_track
 longLabel top_level_track
@@ -146,11 +142,10 @@ def test_supertrack():
     type bigWig
     parent composite_under_supertrack
 """
-    with open('super.test.observed', 'w') as fout:
+    with open("super.test.observed", "w") as fout:
         fout.write(results)
 
-    with open('super.test.expected', 'w') as fout:
+    with open("super.test.expected", "w") as fout:
         fout.write(expected)
 
     assert results == expected
-
diff --git a/trackhub/test/upload_test.py b/trackhub/test/upload_test.py
index a6f34804..b3d5a322 100644
--- a/trackhub/test/upload_test.py
+++ b/trackhub/test/upload_test.py
@@ -4,8 +4,17 @@
 import tempfile
 from trackhub import upload
 from trackhub.helpers import data_dir
-from trackhub import Hub, GenomesFile, Genome, Track, CompositeTrack, \
-    TrackDb, ViewTrack, SuperTrack, AggregateTrack
+from trackhub import (
+    Hub,
+    GenomesFile,
+    Genome,
+    Track,
+    CompositeTrack,
+    TrackDb,
+    ViewTrack,
+    SuperTrack,
+    AggregateTrack,
+)
 
 d = data_dir()
 
@@ -13,31 +22,32 @@
 class Upload(object):
     def __init__(self):
         self.hub = Hub(
-            hub='example_hub',
-            short_label='example hub',
-            long_label='an example hub for testing',
-            email='none@example.com')
+            hub="example_hub",
+            short_label="example hub",
+            long_label="an example hub for testing",
+            email="none@example.com",
+        )
         self.genomes_file = GenomesFile()
-        self.genome = Genome('dm3')
+        self.genome = Genome("dm3")
         self.trackdb = TrackDb()
 
         self.tracks = [
             Track(
-                name='track1',
-                tracktype='bigBed',
-                source=os.path.join(d, 'random-hg38-0.bigBed')
+                name="track1",
+                tracktype="bigBed",
+                source=os.path.join(d, "random-hg38-0.bigBed"),
             ),
             Track(
-                name='track2',
-                tracktype='bigWig',
-                source=os.path.join(d, 'sine-hg38-0.bedgraph.bw'),
+                name="track2",
+                tracktype="bigWig",
+                source=os.path.join(d, "sine-hg38-0.bedgraph.bw"),
             ),
             Track(
-                name='track3',
-                tracktype='bigWig',
-                source=os.path.join(d, 'sine-hg38-1.bedgraph.bw'),
-                filename='3.bw',
-            )
+                name="track3",
+                tracktype="bigWig",
+                source=os.path.join(d, "sine-hg38-1.bedgraph.bw"),
+                filename="3.bw",
+            ),
         ]
         self.hub.add_genomes_file(self.genomes_file)
         self.genomes_file.add_genome(self.genome)
diff --git a/trackhub/track.py b/trackhub/track.py
index e9b612e3..b347865a 100644
--- a/trackhub/track.py
+++ b/trackhub/track.py
@@ -10,15 +10,29 @@
 from trackhub import settings
 
 
-TRACKTYPES = ['bigWig', 'bam', 'bigBed', 'vcfTabix', 'bigNarrowPeak', None,
-              'bigBarChart', 'bigChain', 'bigGenePred', 'bigNarrowPeak',
-              'bigMaf', 'bigPsl', 'halSnake']
+TRACKTYPES = [
+    "bigWig",
+    "bam",
+    "bigBed",
+    "vcfTabix",
+    "bigNarrowPeak",
+    None,
+    "bigBarChart",
+    "bigChain",
+    "bigGenePred",
+    "bigNarrowPeak",
+    "bigMaf",
+    "bigPsl",
+    "halSnake",
+]
+
 
 def _check_name(name):
-    regex = re.compile('[^a-zA-Z0-9-_]')
+    regex = re.compile("[^a-zA-Z0-9-_]")
     if regex.search(name):
         raise ValueError('Non-alphanumeric character in name "%s"' % name)
 
+
 class ParameterError(Exception):
     pass
 
@@ -101,14 +115,24 @@ def __str__(self):
         s = []
         s.append(self.name)
         s.append(self.label)
-        s.extend('%s=%s' % (k, v) for k, v in self.mapping.items())
-        return ' '.join(s)
+        s.extend("%s=%s" % (k, v) for k, v in self.mapping.items())
+        return " ".join(s)
 
 
 class BaseTrack(HubComponent):
-    def __init__(self, name, tracktype=None, short_label=None,
-                 long_label=None, subgroups=None, source=None, filename=None,
-                 html_string=None, html_string_format="rst", **kwargs):
+    def __init__(
+        self,
+        name,
+        tracktype=None,
+        short_label=None,
+        long_label=None,
+        subgroups=None,
+        source=None,
+        filename=None,
+        html_string=None,
+        html_string_format="rst",
+        **kwargs
+    ):
         """
         Represents a single track stanza, base class for other track types.
 
@@ -180,8 +204,9 @@ def __init__(self, name, tracktype=None, short_label=None,
         # set. Other subclasses (Composite and View) will add their own special
         # params in the class definition.
         self.track_field_order = []
-        self.track_field_order = update_list(self.track_field_order,
-                                             constants.track_fields['all'])
+        self.track_field_order = update_list(
+            self.track_field_order, constants.track_fields["all"]
+        )
 
         # NOTE: when setting track type, it will update the track field order
         # according to the known params for that track...so
@@ -202,16 +227,15 @@ def __init__(self, name, tracktype=None, short_label=None,
         self.add_subgroups(subgroups)
 
         # Convert pythonic strings to UCSC versions
-        kwargs['track'] = name
-        kwargs['type'] = tracktype
-        kwargs['longLabel'] = kwargs.get('longLabel', long_label)
-        kwargs['shortLabel'] = kwargs.get('shortLabel', short_label)
+        kwargs["track"] = name
+        kwargs["type"] = tracktype
+        kwargs["longLabel"] = kwargs.get("longLabel", long_label)
+        kwargs["shortLabel"] = kwargs.get("shortLabel", short_label)
 
         self.kwargs = kwargs
 
         self._orig_kwargs = kwargs.copy()
 
-
     @property
     def _html(self):
         if not self.html_string:
@@ -223,6 +247,7 @@ def _html(self):
     @property
     def trackdb(self):
         from trackhub import TrackDb
+
         return self.root(TrackDb)[0]
 
     @property
@@ -256,7 +281,8 @@ def filename(self):
                 return None
             return os.path.join(
                 os.path.dirname(self.trackdb.filename),
-                self.name + '.' + self.tracktype.split(' ')[0])
+                self.name + "." + self.tracktype.split(" ")[0],
+            )
         return None
 
     @filename.setter
@@ -304,13 +330,12 @@ def add_params(self, **kw):
             if k not in self.track_field_order and constants.VALIDATE:
                 raise ParameterError(
                     '"{0}" is not a valid parameter for {1} with '
-                    'tracktype {2}'
-                    .format(k, self.__class__.__name__, self.tracktype)
+                    "tracktype {2}".format(k, self.__class__.__name__, self.tracktype)
                 )
             if not constants.param_dict[k].validate(v) and constants.VALIDATE:
                 raise ParameterError(
-                    'value "{0}" did not validate for parameter "{1}"'
-                    .format(k, v))
+                    'value "{0}" did not validate for parameter "{1}"'.format(k, v)
+                )
 
         self._orig_kwargs.update(kw)
         self.kwargs = self._orig_kwargs.copy()
@@ -355,17 +380,17 @@ def __str__(self):
         kwargs = self.kwargs.copy()
         for name in self.track_field_order:
             value = kwargs.pop(name, None)
-            if name == 'parent':
+            if name == "parent":
                 if isinstance(self.parent, BaseTrack):
                     if value is not None:
-                        s.append('parent {0} {1}'.format(self.parent.name, value))
+                        s.append("parent {0} {1}".format(self.parent.name, value))
                     else:
-                        s.append('parent {0}'.format(self.parent.name))
+                        s.append("parent {0}".format(self.parent.name))
                 continue
 
-            if name == 'bigDataUrl' and value is None:
+            if name == "bigDataUrl" and value is None:
                 # fall back to `url` if set
-                value = getattr(self, 'url', None)
+                value = getattr(self, "url", None)
 
             if value is not None:
                 if constants.param_dict[name].validate(value) or not settings.VALIDATE:
@@ -373,8 +398,10 @@ def __str__(self):
 
                 else:
                     raise ParameterError(
-                        "The value '{0}' did not validate for parameter '{1}'"
-                        .format(value, name))
+                        "The value '{0}' did not validate for parameter '{1}'".format(
+                            value, name
+                        )
+                    )
         # Handle subgroups differently depending on if this is a composite
         # track or not.
         s.extend(self._str_subgroups())
@@ -383,16 +410,17 @@ def __str__(self):
             if len(kwargs) > 0:
                 raise ParameterError(
                     "The following parameters are unknown for track type {0}: "
-                    "{1}".format(self.tracktype, kwargs))
+                    "{1}".format(self.tracktype, kwargs)
+                )
         else:
             for k, v in kwargs.items():
                 s.append("%s %s" % (k, v))
 
         self.kwargs = self._orig_kwargs.copy()
 
-        return '\n'.join(s)
+        return "\n".join(s)
 
-    def _render(self, staging='staging'):
+    def _render(self, staging="staging"):
         if self._html:
             self._html.render(staging)
 
@@ -402,9 +430,11 @@ def _str_subgroups(self):
         """
         if not self.subgroups:
             return ""
-        return ['subGroups %s'
-                % ' '.join(['%s=%s' % (k, v) for (k, v) in
-                           self.subgroups.items()])]
+        return [
+            "subGroups %s"
+            % " ".join(["%s=%s" % (k, v) for (k, v) in self.subgroups.items()])
+        ]
+
     def validate(self):
         pass
 
@@ -412,8 +442,8 @@ def validate(self):
     def html_fn(self):
         if self.filename and self.trackdb:
             return os.path.join(
-                os.path.dirname(self.trackdb.filename),
-                self.name + '.html')
+                os.path.dirname(self.trackdb.filename), self.name + ".html"
+            )
         else:
             raise ValueError(self.filename)
 
@@ -439,12 +469,12 @@ def __init__(self, url=None, *args, **kwargs):
         See :class:`BaseTrack` for details on other arguments.
         """
 
-        if 'bigDataUrl' in kwargs and url is not None:
-            raise ValueError('Only one of bigDataUrl or url should be specified')
+        if "bigDataUrl" in kwargs and url is not None:
+            raise ValueError("Only one of bigDataUrl or url should be specified")
 
-        kwargs['bigDataUrl'] = kwargs.get('bigDataUrl', url)
+        kwargs["bigDataUrl"] = kwargs.get("bigDataUrl", url)
         super(Track, self).__init__(*args, **kwargs)
-        self._url = kwargs['bigDataUrl']
+        self._url = kwargs["bigDataUrl"]
 
     @property
     def url(self):
@@ -453,8 +483,7 @@ def url(self):
         if self.filename is None:
             return None
         return os.path.relpath(
-            self.filename,
-            start=os.path.dirname(self.trackdb.filename)
+            self.filename, start=os.path.dirname(self.trackdb.filename)
         )
 
     @url.setter
@@ -463,7 +492,6 @@ def url(self, fn):
 
 
 class CompositeTrack(BaseTrack):
-
     def __init__(self, *args, **kwargs):
         """
         Represents a composite track.  Subclasses :class:`BaseTrack`, and adds
@@ -482,9 +510,11 @@ def __init__(self, *args, **kwargs):
         super(CompositeTrack, self).__init__(*args, **kwargs)
 
         self.track_field_order = update_list(
-            self.track_field_order, constants.track_fields['compositeTrack'])
+            self.track_field_order, constants.track_fields["compositeTrack"]
+        )
         self.track_field_order = update_list(
-            self.track_field_order, constants.track_fields['subGroups'])
+            self.track_field_order, constants.track_fields["subGroups"]
+        )
 
         # TODO: are subtracks and views mutually exclusive, or can a composite
         # have both "view-ed" and "non-view-ed" subtracks?
@@ -570,15 +600,14 @@ def _str_subgroups(self):
         if len(self.views) > 0:
             mapping = dict((i.view, i.view) for i in self.views)
             view_subgroup = SubGroupDefinition(
-                name='view',
-                label='Views',
-                mapping=mapping)
+                name="view", label="Views", mapping=mapping
+            )
             i += 1
-            s.append('subGroup%s %s' % (i, view_subgroup))
+            s.append("subGroup%s %s" % (i, view_subgroup))
 
         for subgroup in self.subgroups.values():
             i += 1
-            s.append('subGroup%s %s' % (i, subgroup))
+            s.append("subGroup%s %s" % (i, subgroup))
         return s
 
     def __str__(self):
@@ -586,7 +615,7 @@ def __str__(self):
         s = []
 
         s.append(super(CompositeTrack, self).__str__())
-        s.append('compositeTrack on')
+        s.append("compositeTrack on")
 
         for view in self.views:
             s.append("")
@@ -625,10 +654,11 @@ def __init__(self, view, *args, **kwargs):
 
         """
         self.view = view
-        kwargs['view'] = view
+        kwargs["view"] = view
         super(ViewTrack, self).__init__(*args, **kwargs)
         self.track_field_order = update_list(
-            self.track_field_order, constants.track_fields['view'])
+            self.track_field_order, constants.track_fields["view"]
+        )
         self.subtracks = []
 
     def add_tracks(self, *args):
@@ -645,7 +675,7 @@ def add_tracks(self, *args):
             if isinstance(arg, BaseTrack):
                 arg = [arg]
             for track in arg:
-                track.subgroups['view'] = self.view
+                track.subgroups["view"] = self.view
                 self.add_child(track)
                 self.subtracks.append(track)
 
@@ -657,7 +687,7 @@ def __str__(self):
             s.append("")
             for line in str(subtrack).splitlines(False):
                 s.append(constants.INDENT + line)
-        return '\n'.join(s)
+        return "\n".join(s)
 
 
 class SuperTrack(BaseTrack):
@@ -675,9 +705,10 @@ def __init__(self, *args, **kwargs):
 
         See :class:`BaseTrack` for details on arguments.
         """
-        super(SuperTrack, self).__init__(tracktype='superTrack', *args, **kwargs)
+        super(SuperTrack, self).__init__(tracktype="superTrack", *args, **kwargs)
         self.track_field_order = update_list(
-            self.track_field_order, constants.track_fields['superTrack'])
+            self.track_field_order, constants.track_fields["superTrack"]
+        )
 
         self.subtracks = []
 
@@ -703,13 +734,13 @@ def __str__(self):
         s = []
 
         s.append(super(SuperTrack, self).__str__())
-        s.append('superTrack on')
+        s.append("superTrack on")
 
         for subtrack in self.subtracks:
             s.append("")
             for line in str(subtrack).splitlines(False):
                 s.append(constants.INDENT + line)
-        return '\n'.join(s)
+        return "\n".join(s)
 
 
 class AggregateTrack(BaseTrack):
@@ -739,10 +770,11 @@ def __init__(self, aggregate, *args, **kwargs):
         """
 
         self.aggregate = aggregate
-        kwargs['aggregate'] = aggregate
+        kwargs["aggregate"] = aggregate
         super(AggregateTrack, self).__init__(*args, **kwargs)
         self.track_field_order = update_list(
-            self.track_field_order, constants.track_fields['multiWig'])
+            self.track_field_order, constants.track_fields["multiWig"]
+        )
         self.subtracks = []
 
     def add_subtrack(self, subtrack):
@@ -751,7 +783,7 @@ def add_subtrack(self, subtrack):
         """
         self.add_tracks(subtrack)
 
-    def add_tracks(self,*args):
+    def add_tracks(self, *args):
         """
         Add one or more tracks.
 
@@ -774,7 +806,7 @@ def __str__(self):
         s = []
 
         s.append(super(AggregateTrack, self).__str__())
-        s.append('container multiWig')
+        s.append("container multiWig")
 
         for subtrack in self.subtracks:
             s.append("")
@@ -782,6 +814,7 @@ def __str__(self):
                 s.append(constants.INDENT + line)
         return "\n".join(s)
 
+
 class HTMLDoc(HubComponent):
     def __init__(self, contents, html_string_format, filename=None):
         """
@@ -819,8 +852,8 @@ def filename(self):
         if self.trackdb is None or self.track is None:
             return None
         return os.path.join(
-            os.path.dirname(self.trackdb.filename),
-            self.track.name + '.html')
+            os.path.dirname(self.trackdb.filename), self.track.name + ".html"
+        )
 
     @filename.setter
     def filename(self, fn):
@@ -829,6 +862,7 @@ def filename(self, fn):
     @property
     def trackdb(self):
         from trackhub import TrackDb
+
         obj, level = self.root(cls=TrackDb)
         return obj
 
@@ -836,39 +870,41 @@ def trackdb(self):
     def track(self):
         return self.parent
 
-    def _render(self, staging='staging'):
+    def _render(self, staging="staging"):
         self.validate()
         dirname = os.path.dirname(self.filename)
         if not os.path.exists(dirname):
             os.makedirs(dirname)
-        fout = open(os.path.join(staging, self.filename), 'w')
+        fout = open(os.path.join(staging, self.filename), "w")
         fout.write(str(self))
         fout.close()
         return fout.name
 
     def validate(self):
         if not self.trackdb:
-            raise ValueError("HTMLDoc object must be connected to a "
-                             "BaseTrack subclass instance and a TrackDb "
-                             "instance")
+            raise ValueError(
+                "HTMLDoc object must be connected to a "
+                "BaseTrack subclass instance and a TrackDb "
+                "instance"
+            )
         return True
 
     def __str__(self):
-        if self.html_string_format == 'html':
+        if self.html_string_format == "html":
             return self.contents
-        elif self.html_string_format == 'rst':
+        elif self.html_string_format == "rst":
 
             # docutils still internally uses a "U" mode for opening files.
             with warnings.catch_warnings():
-                warnings.simplefilter('ignore')
+                warnings.simplefilter("ignore")
                 parts = publish_parts(
-                    self.contents, writer_name='html',
-                    settings_overrides={'output_encoding': 'unicode'}
+                    self.contents,
+                    writer_name="html",
+                    settings_overrides={"output_encoding": "unicode"},
                 )
-            return parts['html_body']
+            return parts["html_body"]
         else:
             raise ValueError(
-                "html_string_format '{}' not supported".format(
-                    self.html_string_format)
+                "html_string_format '{}' not supported".format(self.html_string_format)
             )
         return self.contents
diff --git a/trackhub/trackdb.py b/trackhub/trackdb.py
index 63d920ea..1a2a60f8 100644
--- a/trackhub/trackdb.py
+++ b/trackhub/trackdb.py
@@ -50,7 +50,7 @@ def genome(self):
         if level is None:
             return None
         if level != -1:
-            raise ValueError('Genome is level %s, not -1' % level)
+            raise ValueError("Genome is level %s, not -1" % level)
         return genome
 
     @property
@@ -65,8 +65,11 @@ def filename(self):
             return None
 
         else:
-            return os.path.join(os.path.dirname(self.genomes_file.filename),
-                                self.genome.genome, 'trackDb.txt')
+            return os.path.join(
+                os.path.dirname(self.genomes_file.filename),
+                self.genome.genome,
+                "trackDb.txt",
+            )
 
     @filename.setter
     def filename(self, fn):
@@ -84,6 +87,7 @@ def add_tracks(self, track):
             object.
         """
         from trackhub import BaseTrack
+
         if isinstance(track, BaseTrack):
             self.add_child(track)
             self._tracks.append(track)
@@ -95,6 +99,7 @@ def add_tracks(self, track):
     @property
     def tracks(self):
         from trackhub import Track
+
         return [i for i, level in self.leaves(Track)]
 
     def add_genome(self, genome):
@@ -107,18 +112,18 @@ def __str__(self):
             for line in str(track).splitlines(False):
                 line = line.rstrip()
                 s.append(line)
-            s.append('')
+            s.append("")
 
-        return '\n'.join(s)
+        return "\n".join(s)
 
     def validate(self):
         if len(self.children) == 0:
             raise ValueError("No Track objects specified")
 
-    def _render(self, staging='staging'):
+    def _render(self, staging="staging"):
         rendered_filename = os.path.join(staging, self.filename)
         self.makedirs(rendered_filename)
-        fout = open(rendered_filename, 'w')
+        fout = open(rendered_filename, "w")
         fout.write(str(self))
         fout.close()
         return fout.name
diff --git a/trackhub/trackhub_from_excel b/trackhub/trackhub_from_excel
index 1ec58e6b..0527cbe6 100755
--- a/trackhub/trackhub_from_excel
+++ b/trackhub/trackhub_from_excel
@@ -2,15 +2,14 @@
 
 import importlib.resources
 import trackhub
-#from trackhub import settings
 from collections import defaultdict
 from openpyxl import load_workbook, Workbook
 
 
 def sheet_to_dict(workbook, sheet_name):
     """
-    Read a two column sheet and make it into a dictionary with the first
-    column as keys and the second as the values of a dictionary
+    Convert a two-column spreadsheet into a dictionary. First column keys,
+    second column values.
 
     Parameters
     ----------
@@ -93,9 +92,15 @@ def prepare_track_dict(track_dictionary, validation):
     if validation:
         track_dict_new = {k: v for k, v in new_dict.items() if k in parameters}
     else:
-        track_dict_new = {k: v for k, v in new_dict.items() if k not in ["super", "container_type", "container", "composite", "subgroups"]}
+        track_dict_new = {
+            k: v
+            for k, v in new_dict.items()
+            if k
+            not in ["super", "container_type", "container", "composite", "subgroups"]
+        }
     return track_dict_new
 
+
 def make_assembly(wb, d):
     """
     Makes an assembly hub. Requires sheets labeled "hub" and "genome".
@@ -658,7 +663,7 @@ def main(filename, staging, validation):
     # Get the sheet names from the Excel Workbook
     sheets = load_workbook(filename).sheetnames
 
-    # The dictionary `d` holds all of the containter tracks and hub and
+    # The dictionary `d` holds all of the container tracks and hub and
     # trackdb. It is keyed by the name of the type of container and the value
     # is a dictionary of the container objects keyed by name with values as the
     # container objects. Note that individual Tracks are not included in this
@@ -680,7 +685,7 @@ def main(filename, staging, validation):
     #       },
     #       ...
     #   }
-    if validation =="off":
+    if validation == "off":
         trackhub.settings.VALIDATE = False
     else:
         trackhub.settings.VALIDATE = True
@@ -706,7 +711,9 @@ def main(filename, staging, validation):
 
     # Now that all the container tracks are made, the tracks can be added
     # We also keep track of which subgroups belong to which composite tracks
-    d, comp2subgroup = add_tracks_and_make_subgroups(wb, d, sheets, trackhub.settings.VALIDATE)
+    d, comp2subgroup = add_tracks_and_make_subgroups(
+        wb, d, sheets, trackhub.settings.VALIDATE
+    )
 
     # Add the subgroups to the respective composite tracks
     d = add_subgroups_to_composite(comp2subgroup, d)
diff --git a/trackhub/upload.py b/trackhub/upload.py
index 29edea48..f2628556 100644
--- a/trackhub/upload.py
+++ b/trackhub/upload.py
@@ -13,7 +13,7 @@
 logging.basicConfig(level=logging.INFO)
 logger = logging.getLogger(__name__)
 
-RSYNC_OPTIONS = '--progress -rvL'
+RSYNC_OPTIONS = "--progress -rvL"
 
 
 def run(cmds, **kwargs):
@@ -22,8 +22,13 @@ def run(cmds, **kwargs):
 
     Additional kwargs are passed to subprocess.run.
     """
-    proc = sp.Popen(cmds, bufsize=-1, stdout=sp.PIPE, stderr=sp.STDOUT,
-                    close_fds=sys.platform != 'win32')
+    proc = sp.Popen(
+        cmds,
+        bufsize=-1,
+        stdout=sp.PIPE,
+        stderr=sp.STDOUT,
+        close_fds=sys.platform != "win32",
+    )
     for line in proc.stdout:
         print(line[:-1].decode())
     retcode = proc.wait()
@@ -93,19 +98,19 @@ def upload(host, user, local_dir, remote_dir, rsync_options=RSYNC_OPTIONS):
         user = ""
     else:
         user = user + "@"
-    if host is None or host == 'localhost':
+    if host is None or host == "localhost":
         host = ""
     else:
         host = host + ":"
 
-    if not local_dir.endswith('/'):
-        local_dir = local_dir + '/'
+    if not local_dir.endswith("/"):
+        local_dir = local_dir + "/"
 
-    if not remote_dir.endswith('/'):
-        remote_dir = remote_dir + '/'
+    if not remote_dir.endswith("/"):
+        remote_dir = remote_dir + "/"
 
-    remote_string = '{user}{host}{remote_dir}'.format(**locals())
-    cmds = ['rsync']
+    remote_string = "{user}{host}{remote_dir}".format(**locals())
+    cmds = ["rsync"]
     cmds += shlex.split(rsync_options)
     cmds += [local_dir, remote_string]
     run(cmds)
@@ -167,28 +172,27 @@ def stage(x, staging):
     # Track objects don't represent files, but their documentation does
     linknames.append(x.render(staging))
 
-    if hasattr(x, 'source') and hasattr(x, 'filename'):
-        def _stg(x, ext=''):
+    if hasattr(x, "source") and hasattr(x, "filename"):
+
+        def _stg(x, ext=""):
             # A remote track hosted elsewhere does not need staging. This is
             # defined by a track with a url, but no source or filename.
             if (
                 x.source is None
                 and x.filename is None
-                and getattr(x, 'url', None) is not None
+                and getattr(x, "url", None) is not None
             ):
                 return
 
-            linknames.append(
-                local_link(x.source + ext, x.filename + ext, staging)
-            )
+            linknames.append(local_link(x.source + ext, x.filename + ext, staging))
 
         _stg(x)
 
         if isinstance(x, track.Track):
-            if x.tracktype == 'bam':
-                _stg(x, ext='.bai')
-            if x.tracktype == 'vcfTabix':
-                _stg(x, ext='.tbi')
+            if x.tracktype == "bam":
+                _stg(x, ext=".bai")
+            if x.tracktype == "vcfTabix":
+                _stg(x, ext=".tbi")
 
         if isinstance(x, track.CompositeTrack):
             if x._html:
@@ -197,7 +201,6 @@ def _stg(x, ext=''):
     return linknames
 
 
-
 def stage_hub(hub, staging=None):
     """
     Stage a hub by symlinking all its connected files to a local directory.
@@ -211,7 +214,9 @@ def stage_hub(hub, staging=None):
     return staging, linknames
 
 
-def upload_hub(hub, host, remote_dir, user=None, port=22, rsync_options=RSYNC_OPTIONS, staging=None):
+def upload_hub(
+    hub, host, remote_dir, user=None, port=22, rsync_options=RSYNC_OPTIONS, staging=None
+):
     """
     Renders, stages, and uploads a hub.
     """
@@ -220,5 +225,11 @@ def upload_hub(hub, host, remote_dir, user=None, port=22, rsync_options=RSYNC_OP
         staging = tempfile.mkdtemp()
     staging, linknames = stage_hub(hub, staging=staging)
     local_dir = os.path.join(staging)
-    upload(host, user, local_dir=local_dir, remote_dir=remote_dir, rsync_options=rsync_options)
+    upload(
+        host,
+        user,
+        local_dir=local_dir,
+        remote_dir=remote_dir,
+        rsync_options=rsync_options,
+    )
     return linknames
diff --git a/trackhub/validate.py b/trackhub/validate.py
index 515fb17e..f03c6eec 100644
--- a/trackhub/validate.py
+++ b/trackhub/validate.py
@@ -23,6 +23,7 @@ def validator(*example):
     """
     Decorator that runs a self-test on the validator it decorates
     """
+
     def wrapper(func):
 
         # Try running validation on the function's own example . . . it better
@@ -32,19 +33,22 @@ def wrapper(func):
             for ex in example:
                 func(ex)
                 example_string.append(ex)
-            example_string = 'Example value(s): %s' \
-                % (" or ".join('%r' % i for i in example_string))
+            example_string = "Example value(s): %s" % (
+                " or ".join("%r" % i for i in example_string)
+            )
 
         except Exception as e:
             raise ValueError(
-                'Error validating example (func=%s, example=%r)! '
-                '\nOriginal error:\n\t%s: %s'
-                % (func.__name__, example, e.__class__.__name__, e.message))
+                "Error validating example (func=%s, example=%r)! "
+                "\nOriginal error:\n\t%s: %s"
+                % (func.__name__, example, e.__class__.__name__, e.message)
+            )
 
         class Validator(object):
             """
             Class to wrap a function and display an example value.
             """
+
             _func = func
 
             def __call__(self, v):
@@ -54,21 +58,26 @@ def __call__(self, v):
                     result = False
                 if not result and settings.VALIDATE:
                     raise ValidationError(
-                        'Value {0} failed {1} validation; {2}'
-                        .format(v, func.__name__, example_string))
+                        "Value {0} failed {1} validation; {2}".format(
+                            v, func.__name__, example_string
+                        )
+                    )
                 return result
 
             def __str__(self):
-                return "<Validator [%s] at %s> sample: %s" \
-                    % (func.__name__, id(func), example)
+                return "<Validator [%s] at %s> sample: %s" % (
+                    func.__name__,
+                    id(func),
+                    example,
+                )
 
         return Validator()
+
     return wrapper
 
 
 class Param(object):
-    def __init__(self, name, fmt, types, required, validator,
-                 min_bed_fields=None):
+    def __init__(self, name, fmt, types, required, validator, min_bed_fields=None):
         """
         Parameters
         ----------
@@ -115,8 +124,7 @@ def __init__(self, name, fmt, types, required, validator,
         self.validator = validator
 
     def __str__(self):
-        return '<%s "%s" at %s>' \
-            % (self.__class__.__name__, self.name, id(self))
+        return '<%s "%s" at %s>' % (self.__class__.__name__, self.name, id(self))
 
     def validate(self, value):
 
@@ -132,7 +140,7 @@ def validate(self, value):
                 self.validator(value)
                 return True
 
-        if hasattr(self.validator, '__call__'):
+        if hasattr(self.validator, "__call__"):
             return self.validator(value)
 
         elif value == self.validator:
@@ -143,9 +151,9 @@ def validate(self, value):
 @validator("tag=value", "tag1=val1 tag2=val2")
 def key_val(v):
     try:
-        assert '=' in v
+        assert "=" in v
         items = v.split()
-        assert len(items) == v.count('=')
+        assert len(items) == v.count("=")
         return True
 
     except AssertionError:
@@ -164,8 +172,8 @@ def CSV(v):
 def ColSV3(v):
     nvalues = 3
     if not isinstance(v, string_types):
-        raise ValueError('not a string')
-    vs = v.split(':')
+        raise ValueError("not a string")
+    vs = v.split(":")
     assert len(vs) == nvalues
     return True
 
@@ -174,8 +182,8 @@ def ColSV3(v):
 def ColSV2(v):
     nvalues = 2
     if not isinstance(v, string_types):
-        raise ValueError('not a string')
-    vs = v.split(':')
+        raise ValueError("not a string")
+    vs = v.split(":")
     assert len(vs) == nvalues
     return True
 
@@ -183,42 +191,41 @@ def ColSV2(v):
 @validator("1:5", 3, "3")
 def ColSV2_numbers_or_single_number(v):
     v = str(v)
-    vs = v.split(':')
+    vs = v.split(":")
     assert len(vs) in [1, 2]
     for i in vs:
         try:
             float(i)
         except ValueError:
             raise ValueError(
-                "{0} in parameter {1} cannot be converted "
-                "into a number".format(i, v)
+                "{0} in parameter {1} cannot be converted " "into a number".format(i, v)
             )
     return True
 
 
 @validator("128,0,255")
 def RGB(v):
-    if ' ' in v:
-        raise ValueError('Space in RGB tuple')
+    if " " in v:
+        raise ValueError("Space in RGB tuple")
     if "." in v:
         raise ValueError('"." in RGB tuple')
     assert isinstance(v, string_types), "RGB tuple is not a string"
-    if ',' not in v:
+    if "," not in v:
         raise ValueError("no commas in RGB tuple")
-    rgb = v.split(',')
+    rgb = v.split(",")
     assert len(rgb) == 3, "RGB tuple does not have 3 values"
     try:
         rgb = map(int, rgb)
     except ValueError:
-        raise ValueError('RGB tuple does not contain ints')
+        raise ValueError("RGB tuple does not contain ints")
     for i in rgb:
-        assert (0 <= i <= 255)
+        assert 0 <= i <= 255
     return True
 
 
 @validator("128,0,0 90,90,5")
 def RGBList(v):
-    rgbs = v.split(' ')
+    rgbs = v.split(" ")
     assert len(rgbs) == 2, "RGBList not a space-separated list of RGB tuples"
     for i in rgbs:
         RGB(i)
@@ -231,7 +238,7 @@ def off_or_int(v):
         int(v)
         return True
     except ValueError:
-        if v == 'off':
+        if v == "off":
             return True
         raise
 
@@ -251,12 +258,12 @@ def ucsc_position(v):
     return True
 
 
-@validator('asdf1234_33', 'AZ90')
+@validator("asdf1234_33", "AZ90")
 def alphanumeric_(v):
-    valid = 'abcdefghijklmnopqrstuvwxyz'
-    valid += 'ABCDEFGHIJKLMNOPQRSTUVWXYZ'
-    valid += '01234556789'
-    valid += '_'
+    valid = "abcdefghijklmnopqrstuvwxyz"
+    valid += "ABCDEFGHIJKLMNOPQRSTUVWXYZ"
+    valid += "01234556789"
+    valid += "_"
     assert isinstance(v, string_types)
     for i in v:
         if i not in valid:
@@ -264,37 +271,39 @@ def alphanumeric_(v):
     return True
 
 
-@validator('one two three', 'aaaaaaaaaaaaaaaaa')
+@validator("one two three", "aaaaaaaaaaaaaaaaa")
 def short_label(v):
     assert isinstance(v, string_types)
     if len(v) > 17:
         warnings.warn(
             "shortLabel is limited to 17 characters "
-            "in the browser, some characters will be truncated")
+            "in the browser, some characters will be truncated"
+        )
     return True
 
 
-@validator('a' * 76, 'four five six')
+@validator("a" * 76, "four five six")
 def long_label(v):
     assert isinstance(v, string_types)
     if len(v) > 76:
         warnings.warn(
             "longLabel is limited to 76 characters "
-            "in the browser, some characters will be truncated")
+            "in the browser, some characters will be truncated"
+        )
     return True
 
 
-@validator('https://example.com', 'path/to/a.html')
+@validator("https://example.com", "path/to/a.html")
 def full_or_local_url(v):
     return isinstance(v, string_types)
 
 
-@validator('https://example.com', 'path/to/a.html')
+@validator("https://example.com", "path/to/a.html")
 def full_url(v):
     return isinstance(v, string_types)
 
 
-@validator(1, '1', '500')
+@validator(1, "1", "500")
 def int_like(v):
     try:
         int(v)
@@ -303,7 +312,7 @@ def int_like(v):
         return False
 
 
-@validator(1.0, '5.556')
+@validator(1.0, "5.556")
 def float_like(v):
     try:
         float(v)
@@ -312,24 +321,40 @@ def float_like(v):
         return False
 
 
-@validator('#ff0000', 'maroon')
+@validator("#ff0000", "maroon")
 def hex_or_named(v):
-    valid = '0123456789ABCDEF'
+    valid = "0123456789ABCDEF"
     try:
-        if v.startswith('#'):
+        if v.startswith("#"):
             assert len(v.upper()[1:]) == 6
             for i in v[1:]:
                 assert i in valid
         else:
-            assert v in set([
-                'black', 'silver', 'gray', 'white', 'maroon', 'red', 'purple',
-                'fuchsia', 'green', 'lime', 'olive', 'yellow', 'navy', 'blue',
-                'teal', 'aqua'])
+            assert v in set(
+                [
+                    "black",
+                    "silver",
+                    "gray",
+                    "white",
+                    "maroon",
+                    "red",
+                    "purple",
+                    "fuchsia",
+                    "green",
+                    "lime",
+                    "olive",
+                    "yellow",
+                    "navy",
+                    "blue",
+                    "teal",
+                    "aqua",
+                ]
+            )
     except AssertionError:
         return False
     return True
 
 
-@validator('bigBed', 'bigBed 6+3')
+@validator("bigBed", "bigBed 6+3")
 def tracktypes(v):
     return True
diff --git a/trackhub/version.py b/trackhub/version.py
index 6c879bdd..b4de043b 100644
--- a/trackhub/version.py
+++ b/trackhub/version.py
@@ -1 +1 @@
-version="0.2.4"
+version = "0.2.4"

From 3d821ae383054744db06fbbf691295f7fd72a4a2 Mon Sep 17 00:00:00 2001
From: daler <dalerr@niddk.nih.gov>
Date: Sat, 20 Apr 2024 13:09:36 -0400
Subject: [PATCH 05/17] use pathlib to get example file

---
 trackhub/trackhub_from_excel | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/trackhub/trackhub_from_excel b/trackhub/trackhub_from_excel
index 0527cbe6..759720fb 100755
--- a/trackhub/trackhub_from_excel
+++ b/trackhub/trackhub_from_excel
@@ -1,5 +1,7 @@
 #!/usr/bin/env python
 
+import sys
+import os
 import importlib.resources
 import trackhub
 from collections import defaultdict
@@ -585,8 +587,9 @@ def create_example(filename):
     This uses the example file that is shipped with the trackhub package, and
     adds two new sheets to include absolute paths to the example data.
     """
-    # Find the package's data directory
-    data = importlib.resources.files("trackhub") / "test" / "data"
+    # In Python >=3.9, importlib.resources.files would work, but the method
+    # used here is agnostic to Python versions.
+    data = Path(sys.modules["trackhub"].__file__).parent / "test" / "data"
 
     wb = load_workbook(data / "example.xlsx", data_only=True)
 

From d19717902f9ca92c4a14fd802b007bc336ba7134 Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Fri, 19 Apr 2024 19:25:43 -0400
Subject: [PATCH 06/17] docs cleanup

---
 doc/source/excelinstructions.rst | 2 +-
 doc/source/index.rst             | 1 -
 test-requirements.txt            | 1 +
 3 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/doc/source/excelinstructions.rst b/doc/source/excelinstructions.rst
index 4c9425e7..70c8f12f 100644
--- a/doc/source/excelinstructions.rst
+++ b/doc/source/excelinstructions.rst
@@ -107,7 +107,7 @@ Super tracks are within the track hub and therefore do not need special fields.
 
 
 Example ``view_config`` sheet
-````````````````````````````
+`````````````````````````````
 
 .. list-table::
     :header-rows: 1
diff --git a/doc/source/index.rst b/doc/source/index.rst
index cfc8b6e3..f08401fb 100644
--- a/doc/source/index.rst
+++ b/doc/source/index.rst
@@ -14,5 +14,4 @@ Contents:
     groupAutoScale
     tracktypes
     autodocs
-    tests
     changelog
diff --git a/test-requirements.txt b/test-requirements.txt
index e03fc99c..209de255 100644
--- a/test-requirements.txt
+++ b/test-requirements.txt
@@ -5,6 +5,7 @@ pybedtools
 pytest
 sphinx>4
 pygments
+sphinx_rtd_theme
 ucsc-bedgraphtobigwig
 ucsc-fatotwobit
 ucsc-bedtobigbed

From ba737f26f449656bb0d585454279ab571e6b39ff Mon Sep 17 00:00:00 2001
From: daler <dalerr@niddk.nih.gov>
Date: Fri, 19 Apr 2024 20:51:38 -0400
Subject: [PATCH 07/17] include test data in package

---
 MANIFEST.in | 1 +
 1 file changed, 1 insertion(+)

diff --git a/MANIFEST.in b/MANIFEST.in
index 3f09cd92..f15ede46 100644
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -1,3 +1,4 @@
 include ez_setup.py
 include *.rst
 include *.txt
+recursive-include trackhub/test/data *

From a993c8a0428757206969660fda0ea1f56a0071a2 Mon Sep 17 00:00:00 2001
From: daler <dalerr@niddk.nih.gov>
Date: Sat, 20 Apr 2024 11:18:01 -0400
Subject: [PATCH 08/17] updates to GHA tests

---
 .github/workflows/main.yml | 103 +++++++++++++------------------------
 setup.py                   |   9 ++--
 2 files changed, 43 insertions(+), 69 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index cbf40f40..fe543c3a 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -2,16 +2,15 @@ name: main
 on: [push]
 
 jobs:
-  conda-env:
+  test:
+    strategy:
+      matrix:
+        python-version: ["3.8", "3.9", "3.10"]
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
-
-
+    - uses: actions/checkout@v4
     - name: git setup
       # Set up git and export env vars to be used in later steps.
-      #   Note the unconventional mechanism for exporting envs by appending to
-      #   $GITHUB_ENV.
       id: git-setup
       run: |
         git config --global user.email "action@github.com"
@@ -19,54 +18,41 @@ jobs:
         echo "BRANCH=${GITHUB_REF##*/}" >> $GITHUB_ENV
         echo "WORKDIR=$(pwd)" >> $GITHUB_ENV
 
-
-    - name: load cached conda env
-      # Load cached env.
-      #   This looks for a cache based on the hash of requirements.txt and
-      #   test-requirements.txt; if it's found the cached directory is
-      #   restored. There's an extra "v1" on the end so it can be forced to be
-      #   regenerated when needed.
-      id: cache-env
-      uses: actions/cache@v2
-      with:
-        path: /tmp/test-env
-        key: ${{ hashFiles('requirements.txt') }}-${{ hashFiles('test-requirements.txt') }}-v1
-
-
     - name: build new conda env
-      # Build cache if needed.
-      #   Only runs if there was a cache miss. If this is created. there's
-      #   a "Post load cached env" job (which is automatically created, it's
-      #   not defined here) that  will load this into the cache for use next
-      #   time.
-      if: steps.cache-env.outputs.cache-hit != 'true'
       run: |
         eval "$(conda shell.bash hook)"
-        conda create -p /tmp/test-env -y --file requirements.txt --file test-requirements.txt --channel conda-forge --channel bioconda
-
+        conda install -n base mamba -y --channel conda-forge
+        mamba create -p ./env -y python=${{ matrix.python-version }} --file test-requirements.txt --channel conda-forge --channel bioconda
+        conda activate ./env
+        pip install -e .
 
-    - name: run pytests and build docs
+    - name: run pytests
       # pytests and doctests happen here
       run: |
         eval "$(conda shell.bash hook)"
-        source activate /tmp/test-env
-        python setup.py install
+        conda activate ./env
         pytest -vv --doctest-modules trackhub
 
+    - name: build docs
+      run: |
         # To make sure that the links in the built docs refer to the correct
         # branch on the trackhub-demo repo, we replace the branch names in the
         # .rst files. Note if we're on master branch then this is a no-op.
-        cd doc
-        find . -name "*.rst" | xargs sed -i "s|trackhub-demo/master|trackhub-demo/$BRANCH|g"
-        make doctest html
-        conda deactivate
+        eval "$(conda shell.bash hook)"
+        conda activate ./env
+        conda env export
+        (
+          cd doc
+          find . -name "*.rst" | xargs sed -i "s|trackhub-demo/master|trackhub-demo/$BRANCH|g"
+          make doctest html
+        )
 
     - name: test command-line script
       # Ensure that the installed command-line script can be run and creates
       # the correct files
       run: |
         eval "$(conda shell.bash hook)"
-        source activate /tmp/test-env
+        conda activate ./env
         trackhub_from_excel --template
         trackhub_from_excel --create-example a.xlsx
         trackhub_from_excel --excel-file a.xlsx
@@ -77,32 +63,27 @@ jobs:
             err=1
           fi
         done
-        if [ err == 1 ]; then
+        if [ $err == 1 ]; then
           exit 1
         fi
 
 
     - name: upload the just-built docs as an artifact
-      # The built docs will be uploaded as a zip file (called docs.zip).
-      #   This file will be available on the Actions page and can be used to
-      #   inspect the final rendered docs. This is useful when building on
-      #   a branch and for contributors to make corrections to the docs without
-      #   needing to set everything up locally.
-      uses: actions/upload-artifact@v2
+      if: ${{ matrix.python-version == '3.10' }} && github.event-name == 'pull_request'
+      uses: actions/upload-artifact@v4
       with:
-        name: docs
+        name: docs-${{ github.run_id }}
         path: doc/build/html
+        overwrite: true  # v4 requires unique names; this will delete existing before uploading
 
 
-    - name: commit built docs to gh-pages branch
-      # Commit to the gh-pages branch.
-      #   Note that this step is not restricted to the master branch, which
-      #   lets us better test the process. The changes aren't actually pushed
-      #   though unless we're on the master branch (see next step).
+    - name: commit built docs to gh-pages
+      # The changes aren't actually pushed unless we're on the master branch
+      # (see next step).
       #
-      #   Note that cloning just the gh-pages branch to a new directory ended
-      #   up being easier than staying in this directory and copying stuff
-      #   around within it.
+      # Note that cloning just the gh-pages branch to a new directory ended
+      # up being easier than staying in this directory and copying stuff
+      # around within it.
       run: |
         git clone \
           --single-branch \
@@ -145,7 +126,7 @@ jobs:
         git branch
         git checkout $BRANCH
         eval "$(conda shell.bash hook)"
-        source activate /tmp/test-env
+        conda activate ./env
         ci/build_examples.py
 
 
@@ -192,7 +173,7 @@ jobs:
 
         # It's possible that the $BRANCH here in the trackhub repo does not yet
         # exist over in the trackhub-demo repo. In that case, we should be good
-        # to push.
+        # to push immediately.
         if [[ -z $(git ls-remote --heads origin $BRANCH) ]]; then
           echo "remote branch $BRANCH does not exist"
           git commit -m 'update hub'
@@ -200,7 +181,7 @@ jobs:
           exit 0
         fi
 
-        # Otherwise, only push if there are changes.
+        # Otherwise, only push to existing branch if there are changes.
         if git diff origin/$BRANCH --quiet; then
             echo "no changes to push to branch $BRANCH!";
         else
@@ -219,7 +200,7 @@ jobs:
       run: |
         git checkout $BRANCH
         eval "$(conda shell.bash hook)"
-        source activate /tmp/test-env
+        conda activate ./env
         ci/check_hubs.py
 
 
@@ -231,13 +212,3 @@ jobs:
       run: |
         ssh-add -D
         rm -Rf  *
-
-
-  pip-install:
-    # Separate, parallel job for testing pip installation
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v2
-      - run: python setup.py sdist
-      - run: pip install dist/*.tar.gz
-      - run: python -c 'import trackhub'
diff --git a/setup.py b/setup.py
index 2c21b692..fe7902b8 100644
--- a/setup.py
+++ b/setup.py
@@ -26,14 +26,17 @@
     package_dir = {"trackhub": "trackhub"},
     scripts=["trackhub/trackhub_from_excel"],
     license = 'MIT',
-    author_email="dalerr@niddk.nih.gov",
+    author_email="ryan.dale@nih.gov",
     classifiers=[
         'Intended Audience :: Science/Research',
         'License :: OSI Approved :: GNU General Public License (GPL)',
         'Topic :: Scientific/Engineering :: Bio-Informatics',
         'Programming Language :: Python',
-        'Programming Language :: Python :: 2',
-        'Programming Language :: Python :: 2.7',
+        'Programming Language :: Python :: 3.8',
+        'Programming Language :: Python :: 3.9',
+        'Programming Language :: Python :: 3.10',
+        'Programming Language :: Python :: 3.11',
+        'Programming Language :: Python :: 3.12',
         'Programming Language :: Python :: 3',
         'Topic :: Software Development :: Libraries :: Python Modules',
     ],

From 1a799da6dfe7794a7c86192c105f76dcb9e3a087 Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Fri, 19 Apr 2024 19:46:14 -0400
Subject: [PATCH 09/17] pin theme

---
 test-requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test-requirements.txt b/test-requirements.txt
index 209de255..e8e1d904 100644
--- a/test-requirements.txt
+++ b/test-requirements.txt
@@ -5,7 +5,7 @@ pybedtools
 pytest
 sphinx>4
 pygments
-sphinx_rtd_theme
+sphinx_rtd_theme>=1.2.2
 ucsc-bedgraphtobigwig
 ucsc-fatotwobit
 ucsc-bedtobigbed

From e64f46aab2b3cb96b2f22b5da8fa0df7e7cdaf1c Mon Sep 17 00:00:00 2001
From: daler <dalerr@niddk.nih.gov>
Date: Sat, 20 Apr 2024 09:42:20 -0400
Subject: [PATCH 10/17] add tests.rst

---
 doc/source/index.rst |  1 +
 doc/source/tests.rst | 19 +++++++++++++++++++
 2 files changed, 20 insertions(+)
 create mode 100644 doc/source/tests.rst

diff --git a/doc/source/index.rst b/doc/source/index.rst
index f08401fb..faf9e293 100644
--- a/doc/source/index.rst
+++ b/doc/source/index.rst
@@ -13,5 +13,6 @@ Contents:
     assembly_example
     groupAutoScale
     tracktypes
+    tests
     autodocs
     changelog
diff --git a/doc/source/tests.rst b/doc/source/tests.rst
new file mode 100644
index 00000000..f0a86349
--- /dev/null
+++ b/doc/source/tests.rst
@@ -0,0 +1,19 @@
+
+.. _tests:
+
+Testing infrastructure
+======================
+Tests are run on GitHub Actions, configured in ``.github/workflows/main.yml``.
+
+In addition to unit tests, now any code in the documentation that shows how to
+build example track hubs is handled like this:
+
+- extract code from documentation (see ``ci/example_hubs.tsv`` for the list of
+  files from which code is extracted)
+- execute code to build track hub (see ``ci//build_examples.py``)
+- upload code and built track hub (and data, if relevant) to the `trackhub-demo
+  <https://github.com/daler/trackhub-demo>`_ repository
+- run ``hubCheck`` on the just-uploaded hubs (see ``ci/check_hubs.py``)
+
+The just-built track hubs are then live, and linked to from within the
+documentation.

From eed60e85d5b29749945943b23705f58a5f4c3d5b Mon Sep 17 00:00:00 2001
From: daler <dalerr@niddk.nih.gov>
Date: Sat, 20 Apr 2024 10:06:16 -0400
Subject: [PATCH 11/17] use pathlib

---
 trackhub/trackhub_from_excel | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/trackhub/trackhub_from_excel b/trackhub/trackhub_from_excel
index 759720fb..4a807dbb 100755
--- a/trackhub/trackhub_from_excel
+++ b/trackhub/trackhub_from_excel
@@ -2,7 +2,7 @@
 
 import sys
 import os
-import importlib.resources
+from pathlib import Path
 import trackhub
 from collections import defaultdict
 from openpyxl import load_workbook, Workbook

From b2ea467e6e53cb882251f5896df1d75f9e5bef30 Mon Sep 17 00:00:00 2001
From: daler <dalerr@niddk.nih.gov>
Date: Sat, 20 Apr 2024 10:15:28 -0400
Subject: [PATCH 12/17] add minimal pyproject.toml

---
 pyproject.toml | 3 +++
 1 file changed, 3 insertions(+)
 create mode 100644 pyproject.toml

diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 00000000..68847bb5
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,3 @@
+[build-system]
+requires = ["setuptools >= 61.0"]
+build-backend = "setuptools.build_meta"

From 065bef60ebb6ed8cf2d969842c2220746485199d Mon Sep 17 00:00:00 2001
From: daler <dalerr@niddk.nih.gov>
Date: Sat, 20 Apr 2024 11:10:52 -0400
Subject: [PATCH 13/17] allow hic hubCheck "error" to pass

---
 ci/check_hubs.py | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

diff --git a/ci/check_hubs.py b/ci/check_hubs.py
index 7b0435c5..7534361f 100755
--- a/ci/check_hubs.py
+++ b/ci/check_hubs.py
@@ -35,7 +35,7 @@
 
 for line in open(args.tsv):
     line = line.strip()
-    if line.startswith('#') or not line:
+    if line.startswith("#") or not line:
         continue
 
     # Dest in trackhub demo is the second column of TSV, without the initial directory
@@ -59,7 +59,15 @@
             # with "can't find database hg19 in hg.conf, should have a default
             # named "db"". When checking the hub in the Genome Browser it seems
             # fine. So allowing this as a "pass".
-            if line.startswith("can't find database") and "hic_hub" in str(dest):
+            #
+            # Some time later...
+            # hubCheck for those same tracks is now showing "can't find profile
+            # central in hg.conf" error. Aain the tracks look fine the browser,
+            # so we'll consider that OK as well.
+            if "hic_hub" in str(dest) and (
+                line.startswith("can't find database")
+                or line.startswith("can't find profile central in hg.conf")
+            ):
                 warnings = True
             elif not (line.startswith("Found") or line.startswith("warning:")):
                 error = True

From d070d53bb3cc098cc66b2f5524fa2846cf9d6622 Mon Sep 17 00:00:00 2001
From: daler <dalerr@niddk.nih.gov>
Date: Sat, 20 Apr 2024 12:08:48 -0400
Subject: [PATCH 14/17] update changelog

---
 doc/source/changelog.rst | 49 +++++++++++++++++++++++++++++-----------
 1 file changed, 36 insertions(+), 13 deletions(-)

diff --git a/doc/source/changelog.rst b/doc/source/changelog.rst
index fc34c5c5..e5c56789 100644
--- a/doc/source/changelog.rst
+++ b/doc/source/changelog.rst
@@ -1,28 +1,51 @@
 Changelog
 =========
 
-Version 0.3
------------
+Version 1.0 (April 2024)
+------------------------
+
+This major release is backwards-compatible but adds many new features and tests.
 
 Testing infrastructure overhaul
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-See :ref:`tests` for details.
+Extensive example hubs that demonstrate the various track types and
+configuration options. These use data provided by UCSC and are built as part of
+the testing framework. Thanks to Eva Jason (@evajason).
 
-Documentation updates
-~~~~~~~~~~~~~~~~~~~~~
+See :ref:`tests` and :ref:`tracktypes` for details.
 
-- Examples have been added for all of the available track types. See
-  :ref:`tracktypes` for details.
-- New section that details how validation works (see :ref:`validation`).
+Build a trackhub configured in Excel
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Build a trackhub using only a command-line tool and configuration in Excel.
+This new tool, ``trackhub_from_excel``, can write out a template you can use to
+fill in details on what tracks should be included, how to organize them, and
+configuration options like color, visibility, etc.
+
+Running the tool on your filled-out Excel file will build a trackhub ready to
+be uploaded.
+
+Thanks Eva Jason (@evajason) for this new feature.
+
+Semi-automated updating of validated parameters
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+Dramatically improved semi-automatic updating mechanism for making sure
+parameters are up-to-date with the main UCSC instance (see
+``trackhub/parse.py`` and ``trackhub/parsed_params.py``). These scrape the UCSC
+database document HTML to identify parameters, and writes this out to Python
+module that can be diffed against the existing ``parsed_params.py`` module. In
+addition to supporting validation, this highlights what has changed in the UCSC
+Genome Browser since the last trackhub Python package update.
 
 Other changes
 ~~~~~~~~~~~~~
+- New section that details how validation works (see :ref:`validation`).
+
 - `defaultPos` can now be set when using the `default_hub` helper function
 
 - Support for all track types supported in track hubs (see :ref:`tracktypes`)
 
-
 - There is now one naming convention, `add_tracks`, rather than multiple
   methods names that perform this for different track types. `add_view` and
   `add_subtracks` can now simply be replaced with `add_tracks`. These methods
@@ -30,15 +53,15 @@ Other changes
   two. The older method names are retained for backwards compatibility, but all
   documentation has been updated to reflect this change.
 
-- dramatically improved semi-automatic updating mechanism for making sure
-  parameters are up-to-date with the main UCSC instance (see
-  ``trackhub/parse.py`` and ``trackhub/parsed_params.py``).
-
 - fixed indentation when super tracks, composite tracks, and view tracks are
   nested.
 
 - improved handling of rsync and handling symlink modification times
 
+- Dropped support for Python 2.7
+
+- Migrated tests from Travis CI to GitHub Actions and to use pytest fixtures.
+
 Version 0.2.4 (Dec 2017)
 ------------------------
 

From 8873cfa45f2a0e65ce083392dd8fd7c507fe87e9 Mon Sep 17 00:00:00 2001
From: daler <dalerr@niddk.nih.gov>
Date: Sat, 20 Apr 2024 12:08:56 -0400
Subject: [PATCH 15/17] version bump

---
 trackhub/version.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/trackhub/version.py b/trackhub/version.py
index b4de043b..346c93fc 100644
--- a/trackhub/version.py
+++ b/trackhub/version.py
@@ -1 +1 @@
-version = "0.2.4"
+version = "1.0"

From c92c7632542578caee8cfddd3516be10ae8752c4 Mon Sep 17 00:00:00 2001
From: daler <dalerr@niddk.nih.gov>
Date: Sat, 20 Apr 2024 13:19:34 -0400
Subject: [PATCH 16/17] build docs on each python version

---
 .github/workflows/main.yml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index fe543c3a..c75b28ca 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -69,10 +69,9 @@ jobs:
 
 
     - name: upload the just-built docs as an artifact
-      if: ${{ matrix.python-version == '3.10' }} && github.event-name == 'pull_request'
       uses: actions/upload-artifact@v4
       with:
-        name: docs-${{ github.run_id }}
+        name: docs-${{matrix.python-version}}-${{ github.run_id }}
         path: doc/build/html
         overwrite: true  # v4 requires unique names; this will delete existing before uploading
 

From 96878b0968db8f28928031e691d8ec98bf4288ed Mon Sep 17 00:00:00 2001
From: daler <dalerr@niddk.nih.gov>
Date: Sat, 20 Apr 2024 13:23:31 -0400
Subject: [PATCH 17/17] try adding release workflow

---
 .github/workflows/release.yml | 15 +++++++++++++++
 1 file changed, 15 insertions(+)
 create mode 100644 .github/workflows/release.yml

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
new file mode 100644
index 00000000..97cc8bba
--- /dev/null
+++ b/.github/workflows/release.yml
@@ -0,0 +1,15 @@
+on: workflow_dispatch
+jobs:
+  publish-testpypi:
+    name: Upload release to Test PyPI
+    runs-on: ubuntu-latest
+    environment:
+      name: testpypi
+      url: https://pypi.org/p/trackhub
+    permissions:
+      id-token: write
+    steps:
+    - name: Publish to Test PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        repository-url: https://test.pypi.org/legacy