update package infrastructure

desihub · Sep 18, 2024 · b5b47a6 · b5b47a6
1 parent 094511c
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diff --git a/.coveragerc b/.coveragerc
diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
@@ -18,23 +18,23 @@ jobs:
             matrix:
                 os: [ubuntu-latest]
                 python-version: ['3.9', '3.10']  #, '3.11'] possible conflicts between numpy & astropy on 3.11.
-                astropy-version: ['<5.1', '<5.3', '<6.0']
-                desiutil-version: ['3.3.1', 'main']
+                astropy-version: ['<6.0', '<6.1', '<7.0']
+                desiutil-version: ['3.4.3', 'main']
 
         steps:
             - name: Checkout code
-              uses: actions/checkout@v3
+              uses: actions/checkout@v4
               with:
                 fetch-depth: 0
             - name: Set up Python ${{ matrix.python-version }}
-              uses: actions/setup-python@v4
+              uses: actions/setup-python@v5
               with:
                 python-version: ${{ matrix.python-version }}
             - name: Install Python dependencies
               run: |
                 python -m pip install --upgrade pip setuptools wheel
                 python -m pip install pytest jinja2
-                python -m pip install numpy\<1.23
+                python -m pip install numpy\<2.0
                 python -m pip install "git+https://github.com/desihub/desiutil.git@${{ matrix.desiutil-version }}#egg=desiutil"
                 python -m pip install "astropy${{ matrix.astropy-version }}"
             - name: Run the test
@@ -52,19 +52,19 @@ jobs:
 
         steps:
             - name: Checkout code
-              uses: actions/checkout@v3
+              uses: actions/checkout@v4
               with:
                 fetch-depth: 0
             - name: Set up Python ${{ matrix.python-version }}
-              uses: actions/setup-python@v4
+              uses: actions/setup-python@v5
               with:
                 python-version: ${{ matrix.python-version }}
             - name: Install Python dependencies
               run: |
                 python -m pip install --upgrade pip setuptools wheel
                 python -m pip install pytest pytest-cov coveralls
+                python -m pip install numpy\<2.0
                 python -m pip install -r requirements.txt
-                python -m pip install --upgrade numpy\<1.23
             - name: Run the test with coverage
               run: |
                 pytest --cov
@@ -86,11 +86,11 @@ jobs:
 
         steps:
             - name: Checkout code
-              uses: actions/checkout@v3
+              uses: actions/checkout@v4
               with:
                 fetch-depth: 0
             - name: Set up Python ${{ matrix.python-version }}
-              uses: actions/setup-python@v4
+              uses: actions/setup-python@v5
               with:
                 python-version: ${{ matrix.python-version }}
             - name: Install Python dependencies
@@ -112,15 +112,15 @@ jobs:
             matrix:
                 os: [ubuntu-latest]
                 python-version: ['3.10']
-                desiutil-version: ['3.3.0']
+                desiutil-version: ['3.4.3']
 
         steps:
             - name: Checkout code
-              uses: actions/checkout@v3
+              uses: actions/checkout@v4
               with:
                 fetch-depth: 0
             - name: Set up Python ${{ matrix.python-version }}
-              uses: actions/setup-python@v4
+              uses: actions/setup-python@v5
               with:
                 python-version: ${{ matrix.python-version }}
             - name: Install Python dependencies
@@ -144,11 +144,11 @@ jobs:
 
         steps:
             - name: Checkout code
-              uses: actions/checkout@v3
+              uses: actions/checkout@v4
               with:
                 fetch-depth: 0
             - name: Set up Python ${{ matrix.python-version }}
-              uses: actions/setup-python@v4
+              uses: actions/setup-python@v5
               with:
                 python-version: ${{ matrix.python-version }}
             - name: Install Python dependencies

diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -22,7 +22,5 @@ sphinx:
 
 # Optionally set the version of Python and requirements required to build your docs
 python:
-    # version: 3
-    # system_packages: true
     install:
         - requirements: doc/rtd-requirements.txt
diff --git a/LICENSE.rst b/LICENSE.rst
@@ -1,4 +1,4 @@
-Copyright (c) 2014-2022, DESI Collaboration <[email protected]>
+Copyright (c) 2014-2024, DESI Collaboration <[email protected]>
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without modification,

diff --git a/MANIFEST.in b/MANIFEST.in
@@ -1,12 +1,2 @@
-include LICENSE.rst
-include README.rst
-include requirements.txt
-
-graft bin
-graft doc
-graft etc
-
-prune build
-prune dist
-prune htmlcov
-prune doc/_build
+prune .github
+global-exclude .gitignore .readthedocs.yml
diff --git a/doc/changes.rst b/doc/changes.rst
@@ -5,7 +5,9 @@ desidatamodel Change Log
 24.10 (unreleased)
 ------------------
 
-* No changes yet.
+* Update package infrastructure, ... (PR `#200`_).
+
+.. _`#200`: https://github.com/desihub/desidatamodel/pull/200
 
 24.9 (2024-09-12)
 -----------------

diff --git a/py/desidatamodel/__init__.py b/py/desidatamodel/__init__.py
@@ -7,7 +7,7 @@
 
 This package provides support for the DESI_ Data Model.
 
-.. _DESI: http://desi.lbl.gov
+.. _DESI: https://www.desi.lbl.gov
 """
 #
 # Set version string.

diff --git a/py/desidatamodel/check.py b/py/desidatamodel/check.py
@@ -328,16 +328,16 @@ def extract_metadata(self, error=False):
                 spanend = int(g[1])
                 log.debug('Detected range specification from HDU %d to HDU %d',
                           spanstart, spanend)
-                spanref = [l for l in section if l.startswith('Data:')][0]
+                spanref = [ln for ln in section if ln.startswith('Data:')][0]
                 spanext = spanref[spanref.lower().index('see') + 4:].replace('.', '')
                 try:
                     spanmeta = self.hdumeta[spanext]
                 except KeyError:
                     m = "Cannot find EXTNAME = '%s' which is supposed to define HDU %d to HDU %d!"
                     log.critical(m, spanext, spanstart, spanend)
                     raise DataModelError(m % (spanext, spanstart, spanend))
-                spanname = [l.split('=')[1].strip() for l in section
-                            if l.startswith('EXTNAME = ')][0]
+                spanname = [ln.split('=')[1].strip() for ln in section
+                            if ln.startswith('EXTNAME = ')][0]
                 extnames = [p.strip() for p in spanname.split(',')]
                 if len(range(spanstart, spanend+1)) == len(extnames):
                     for i, l in enumerate(range(spanstart, spanend+1)):
@@ -357,7 +357,7 @@ def extract_metadata(self, error=False):
             meta = dict()
             meta['number'] = k
             meta['title'] = section[0]
-            hdu_cross_ref = [l for l in section if l.startswith('See `')]
+            hdu_cross_ref = [ln for ln in section if ln.startswith('See `')]
             if hdu_cross_ref:
                 log.debug("Found HDU cross-reference: %s", hdu_cross_ref[0])
                 hcr = self._cross_reference(hdu_cross_ref[0]).split('#')
@@ -372,7 +372,7 @@ def extract_metadata(self, error=False):
             if 'Empty HDU.' in section:
                 meta['extension'] = 'IMAGE'
                 meta['format'] = 'Empty HDU.'
-            image_data = [l for l in section if l.startswith('Data:')]
+            image_data = [ln for ln in section if ln.startswith('Data:')]
             if image_data:
                 meta['extension'] = 'IMAGE'
                 meta['format'] = image_data[0]
@@ -439,8 +439,8 @@ def extract_metadata(self, error=False):
             # the detailed policy on EXTNAME.
             #
             try:
-                meta['extname'] = [l.split()[2] for l in section
-                                   if l.startswith('EXTNAME = ')][0]
+                meta['extname'] = [ln.split()[2] for ln in section
+                                   if ln.startswith('EXTNAME = ')][0]
             except IndexError:
                 meta['extname'] = 'HDU{0:02d}'.format(k)
                 if (k > 0 or (k == 0 and meta['format'] != 'Empty HDU.')):

diff --git a/py/desidatamodel/test/datamodeltestcase.py b/py/desidatamodel/test/datamodeltestcase.py
@@ -95,9 +95,12 @@ def assertInLog(self, logger, message=''):
     def badUnitMessage(self, unit):
         """Returns a string that can be used to match errors related to bad units.
         """
-        m = "'{0}' did not parse as fits unit: At col {1:d}, Unit 'ergs' not supported by the FITS standard. Did you mean erg?".format(unit, unit.index('ergs'))
+        m = ("'{0}' did not parse as fits unit: At col {1:d}, Unit 'ergs' not " +
+             "supported by the FITS standard. Did you mean erg?").format(unit, unit.index('ergs'))
         if self.astropyVersion >= version.parse('4.0'):
-            m += " If this is meant to be a custom unit, define it with 'u.def_unit'. To have it recognized inside a file reader or other code, enable it with 'u.add_enabled_units'. For details, see http://docs.astropy.org/en/latest/units/combining_and_defining.html"
+            m += (" If this is meant to be a custom unit, define it with 'u.def_unit'. " +
+                  "To have it recognized inside a file reader or other code, enable it with " +
+                  "'u.add_enabled_units'. For details, see http://docs.astropy.org/en/latest/units/combining_and_defining.html")
         if self.astropyVersion >= version.parse('4.0.2'):
             m = m.replace('http', 'https')
         return m
diff --git a/py/desidatamodel/test/test_check.py b/py/desidatamodel/test/test_check.py
@@ -471,7 +471,9 @@ def test_validate_prototype_hdu_mismatch(self):
         foo = f.extract_metadata()
         f.hdumeta['foobar'] = 'baz'
         f.validate_prototype(error=True)
-        self.assertLog(log, -2, "{0} has the wrong number of sections (HDUs) according to {1}, skipping to next candidate.".format(str(modelfile).replace('.rst', '.fits'), modelfile))
+        self.assertLog(log, -2, ("{0} has the wrong number of sections (HDUs) " +
+                                 "according to {1}, skipping to next " +
+                                 "candidate.").format(str(modelfile).replace('.rst', '.fits'), modelfile))
         self.assertLog(log, -1, "No useful prototype files found for {0}!".format(modelfile))
 
     def test_validate_prototype_hdu_keyword_mismatch(self):
@@ -484,7 +486,8 @@ def test_validate_prototype_hdu_keyword_mismatch(self):
         f.validate_prototype()
         f._stub_meta[0]['keywords'].append(('BUNIT', 'erg', 'str', 'This is a test.'))
         f.validate_prototype(error=True)
-        self.assertLog(log, -1, "Prototype file {0} has these keywords in HDU0 missing from model: {{'BUNIT'}}".format(str(modelfile).replace('.rst', '.fits')))
+        self.assertLog(log, -1, ("Prototype file {0} has these keywords " +
+                                 "in HDU0 missing from model: {{'BUNIT'}}").format(str(modelfile).replace('.rst', '.fits')))
 
     def test_validate_prototype_hdu_keyword_type_mismatch(self):
         """Test the data model validation method with a keyword type mismatch.
@@ -496,7 +499,9 @@ def test_validate_prototype_hdu_keyword_type_mismatch(self):
         f.extract_metadata()
         f.hdumeta['PRIMARY']['keywords'][2] = ('BSCALE', '1.2', 'float', '')
         f.validate_prototype()
-        self.assertLog(log, -1, "File %s HDU%d keyword %s has different keyword type according to %s (%s != %s)." % (f.prototype, 0, 'BSCALE', modelfile, 'int', 'float'))
+        self.assertLog(log, -1, ("File %s HDU%d keyword %s has different keyword " +
+                                 "type according to %s (%s != %s).") %
+                                (f.prototype, 0, 'BSCALE', modelfile, 'int', 'float'))
 
     def test_validate_prototype_hdu_wrong_keyword(self):
         """Test the data model validation method with wrong HDU keyword names.
@@ -521,7 +526,9 @@ def test_validate_prototype_hdu_extension_type(self):
         f.validate_prototype()
         f._stub_meta[1]['extension'] = 'IMAGE'
         f.validate_prototype(error=True)
-        self.assertLog(log, -1, "Prototype file {0} has an extension type mismatch in HDU1 (IMAGE != BINTABLE) according to {1}.".format(str(modelfile).replace('.rst', '.fits'), modelfile))
+        self.assertLog(log, -1, ("Prototype file {0} has an extension type " +
+                                 "mismatch in HDU1 (IMAGE != BINTABLE) according " +
+                                 "to {1}.").format(str(modelfile).replace('.rst', '.fits'), modelfile))
         # f._stub_meta[1]['extname'] = ''
         # f.validate_prototype(error=True)
         # self.assertLog(log, -1, "Prototype file {0} has no EXTNAME in HDU1.".format(str(modelfile).replace('.rst', '.fits')))
@@ -536,7 +543,9 @@ def test_validate_prototype_hdu_extension_name(self):
         f.validate_prototype()
         f._stub_meta[1]['extname'] = 'GALAXY'
         f.validate_prototype(error=True)
-        self.assertLog(log, -1, "Prototype file {0} has an EXTNAME mismatch in HDU1 (GALAXY != Galaxies) according to {1}.".format(str(modelfile).replace('.rst', '.fits'), modelfile))
+        self.assertLog(log, -1, ("Prototype file {0} has an EXTNAME mismatch in " +
+                                 "HDU1 (GALAXY != Galaxies) according to " +
+                                 "{1}.").format(str(modelfile).replace('.rst', '.fits'), modelfile))
         f._stub_meta[1]['extname'] = ''
         f.validate_prototype(error=True)
         self.assertLog(log, -2, "Prototype file {0} has no EXTNAME in HDU1.".format(str(modelfile).replace('.rst', '.fits')))

diff --git a/py/desidatamodel/test/test_scan.py b/py/desidatamodel/test/test_scan.py
@@ -129,13 +129,30 @@ def test_union_metadata(self, mock_update, mock_mark):
         foo = model.get_regexp('/desi/spectro/data')
         union_metadata(model, stubs)
         mock_mark.assert_called_once()
-        mock_update.assert_has_calls([call(0, [('NAXIS1', '100', 'int', ''), ('NAXIS2', '100', 'int', ''), ('BSCALE', '1', 'int', ''), ('BZERO', '32768', 'int', 'Data are really unsigned 16-bit int.')]),
-                                      call(1, [('NAXIS1', '32', 'int', 'length of dimension 1'), ('NAXIS2', '3', 'int', 'length of dimension 2')]),
-                                      call(1, [('Name', 'Type', 'Units', 'Description'), ('target', 'char[20]', '', ''), ('V_mag', 'float32', 'mag', ''), ('vdisp', 'float64', 'km/s', '')], columns=True),
-                                      call(0, [('NAXIS1', '100', 'int', ''), ('NAXIS2', '100', 'int', ''), ('BSCALE', '1', 'int', ''), ('BZERO', '32768', 'int', 'Data are really unsigned 16-bit int.')]),
-                                      call(1, [('NAXIS1', '32', 'int', 'length of dimension 1'), ('NAXIS2', '3', 'int', 'length of dimension 2')]),
-                                      call(1, [('Name', 'Type', 'Units', 'Description'), ('target', 'char[20]', '', ''), ('V_mag', 'float32', 'mag', ''), ('vdisp', 'float64', 'km/s', '')], columns=True),
-                                      call(0, [('NAXIS1', '100', 'int', ''), ('NAXIS2', '100', 'int', ''), ('BSCALE', '1', 'int', ''), ('BZERO', '32768', 'int', 'Data are really unsigned 16-bit int.')])])
+        mock_update.assert_has_calls([call(0, [('NAXIS1', '100', 'int', ''),
+                                               ('NAXIS2', '100', 'int', ''),
+                                               ('BSCALE', '1', 'int', ''),
+                                               ('BZERO', '32768', 'int', 'Data are really unsigned 16-bit int.')]),
+                                      call(1, [('NAXIS1', '32', 'int', 'length of dimension 1'),
+                                               ('NAXIS2', '3', 'int', 'length of dimension 2')]),
+                                      call(1, [('Name', 'Type', 'Units', 'Description'),
+                                               ('target', 'char[20]', '', ''),
+                                               ('V_mag', 'float32', 'mag', ''),
+                                               ('vdisp', 'float64', 'km/s', '')], columns=True),
+                                      call(0, [('NAXIS1', '100', 'int', ''),
+                                               ('NAXIS2', '100', 'int', ''),
+                                               ('BSCALE', '1', 'int', ''),
+                                               ('BZERO', '32768', 'int', 'Data are really unsigned 16-bit int.')]),
+                                      call(1, [('NAXIS1', '32', 'int', 'length of dimension 1'),
+                                               ('NAXIS2', '3', 'int', 'length of dimension 2')]),
+                                      call(1, [('Name', 'Type', 'Units', 'Description'),
+                                               ('target', 'char[20]', '', ''),
+                                               ('V_mag', 'float32', 'mag', ''),
+                                               ('vdisp', 'float64', 'km/s', '')], columns=True),
+                                      call(0, [('NAXIS1', '100', 'int', ''),
+                                               ('NAXIS2', '100', 'int', ''),
+                                               ('BSCALE', '1', 'int', ''),
+                                               ('BZERO', '32768', 'int', 'Data are really unsigned 16-bit int.')])])
 
     @patch('sys.argv', ['deep_scan_metadata', '--verbose', '--number', '1000', 'DESI_SPECTRO_DATA/NIGHT/EXPID/desi-EXPID.rst', '/desi/spectro/data'])
     def test_options(self):

diff --git a/pyproject.toml b/pyproject.toml
@@ -0,0 +1,4 @@
+[build-system]
+requires = ["setuptools",
+            "wheel"]
+build-backend = 'setuptools.build_meta'
diff --git a/requirements.txt b/requirements.txt
@@ -1,4 +1,4 @@
 astropy
 sphinx-toolbox
 jinja2
-git+https://github.com/desihub/desiutil.git@3.3.1#egg=desiutil
+git+https://github.com/desihub/desiutil.git@3.4.3#egg=desiutil