Applied formatters

.github/ISSUE_TEMPLATE/add-a-new-reference.md

@@ -9,7 +9,7 @@ assignees: chaplin89
 
 Hi.
 I'd like WGSE-NG to support a new reference:
-- [URL](https://url to FASTA here): 
+- [URL](https://url to FASTA here):
 - Build (e.g., 37, 38)
 
 Thank you,

.github/workflows/python-pyinstaller.yml

@@ -24,5 +24,5 @@ jobs:
     - uses: actions/upload-artifact@v2
       with:
         name: WGSE
-        path: ./dist/windows/WGSE-NG.exe 
+        path: ./dist/windows/WGSE-NG.exe
         retention-days: 1

.gitignore

@@ -13,4 +13,5 @@ dist
 configuration/main.ini
 _build
 _static
-_templates
+_templates
+wgse/VERSION.py

.pre-commit-config.yaml

@@ -17,11 +17,3 @@ repos:
     hooks:
       - id: isort
         name: isort (python)
-
-  - repo: local
-    hooks:
-      - id: run-tests
-        name: Run Tests
-        entry: pytest test
-        language: system
-        types: [python]

.vscode/launch.json

@@ -12,4 +12,4 @@
             "preLaunchTask": "Compile UI"
         }
     ]
-}
+}

.vscode/settings.json

@@ -84,4 +84,4 @@
     ],
     "cmake.configureOnOpen": false,
     "git.ignoreLimitWarning": true
-}
+}

.vscode/tasks.json

@@ -12,4 +12,4 @@
             }
         }
     ]
-}
+}

docs/basic-usage.md

@@ -17,7 +17,7 @@ python -m venv .venv
 python -m pip install -r requirements.txt
 python -m pip install -e .
 python main.py
-# If this is run from the terminal of an IDE, 
+# If this is run from the terminal of an IDE,
 # at this point you should restart the IDE as
 # there are some executables that are installed
 # by pip that otherwise won't be found by the IDE.
@@ -73,4 +73,4 @@ temporary = repository\temp
 [alignment_stats]
 skip = 40000
 samples = 20000
-```
+```

docs/conf.py

@@ -31,7 +31,7 @@
     "sphinx.ext.autodoc",
     "sphinx.ext.autosummary",
     "sphinx.ext.intersphinx",
-    "myst_parser"
+    "myst_parser",
 ]
 
 intersphinx_mapping = {
@@ -61,4 +61,4 @@
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ["_static"]
+html_static_path = ["_static"]

docs/index.rst

@@ -17,4 +17,3 @@ Indices and tables
 * :ref:`genindex`
 * :ref:`modindex`
 * :ref:`search`
-

docs/reference-genome.md

@@ -35,4 +35,4 @@ manager.genomes.append(
 GenomeMetadataLoader().save(manager.genomes)
 ```
 
-A GUI/CLI way will be added in the future.
+A GUI/CLI way will be added in the future.

docs/requirements.in

@@ -1,3 +1,3 @@
 Sphinx>=5,<6
 sphinx_rtd_theme
-myst_parser
+myst_parser

docs/wgse-library.md

@@ -1 +1 @@
-# WGSE Library
+# WGSE Library

pyproject.toml

@@ -36,6 +36,7 @@ dependencies = [
     "jinja2",
     "vcf_parser",
     "WGSE-NG-3rd-party",
+    "sentry-sdk"
 ]
 
 [project.urls]
@@ -67,3 +68,14 @@ wgse = "wgse.main:main"
 
 [tool.setuptools_scm]
 version_file = "wgse/VERSION.py"
+
+[tool.isort]
+profile = "black"
+line_length = 88
+
+[tool.pytest.ini_options]
+minversion = "6.0"
+addopts = "--strict-markers"
+testpaths = [
+    "test"
+]

test/test_buckets.py

@@ -16,13 +16,14 @@ def test_single_bucket():
     assert 0 in sut
     assert len(sut) == 1
     assert sut[0] == 99
-
+
+
 def test_more_run_in_single_bucket():
     # Arrange
     sequence = LetterRunCollection("Foo", 1000)
     sequence.open_run(0)
     sequence.close_run(50)
-    
+
     sequence.open_run(51)
     sequence.close_run(60)
     # Act
@@ -32,7 +33,8 @@ def test_more_run_in_single_bucket():
     assert 0 in sut
     assert len(sut) == 1
     assert sut[0] == 59
-
+
+
 def test_run_in_multiple_buckets():
     # Arrange
     sequence = LetterRunCollection("Foo", 1000)
@@ -45,9 +47,10 @@ def test_run_in_multiple_buckets():
     assert 0 in sut
     assert 1 in sut
     assert len(sut) == 2
-    assert sut[0] == 99 # 0 -> 99
-    assert sut[1] == 50 # 99 -> 151
-
+    assert sut[0] == 99  # 0 -> 99
+    assert sut[1] == 50  # 99 -> 151
+
+
 def test_too_many_buckets():
     sequence = LetterRunCollection("Foo", 1000)
 
@@ -59,7 +62,8 @@ def test_too_many_buckets():
 
     sut = LetterRunBuckets(sequence, 1001, 0).buckets
     assert len(sut) == 0
-
+
+
 def test_run_end_to_end_divisible():
     sequence = LetterRunCollection("Foo", 1000)
 
@@ -79,11 +83,11 @@ def test_run_end_to_end_non_divisible():
     sut = LetterRunBuckets(sequence, 3, 0).buckets
     assert 0 in sut
     assert 1 in sut
-    assert 2 in sut    
+    assert 2 in sut
     assert 3 in sut
-    
+
     assert len(sut) == 4
     assert sut[0] == 332
     assert sut[1] == 332
     assert sut[2] == 332
-    assert sut[3] == 1
+    assert sut[3] == 1

test/test_fasta.py

@@ -26,12 +26,13 @@ def test_no_dictionary():
         "@HD\tVN:1.0\tSO:unsorted",
         "@SQ\tSN:1\tLN:10\tM5:dummy\tUR:file://c:/foo.fa.gz",
     ]
-   
+
     with pytest.raises(RuntimeError) as e:
-        genome = MockGenome(MockPath(fa_lines), MockPath(None,False))
+        genome = MockGenome(MockPath(fa_lines), MockPath(None, False))
         sut = FASTALetterCounter(genome)
     assert "Unable to find dictionary" in str(e.value)
 
+
 def test_sequence_not_in_dictionary():
     fa_lines = [
         ">1 irrelevant\n",
@@ -44,12 +45,13 @@ def test_sequence_not_in_dictionary():
         "@SQ\tSN:1\tLN:10\tM5:dummy\tUR:file://c:/foo.fa.gz",
     ]
     pytest.MonkeyPatch().setattr("gzip.open", gzip_open)
-   
+
     with pytest.raises(ValueError) as e:
         genome = MockGenome(MockPath(fa_lines), MockPath(dict_lines))
         FASTALetterCounter(genome).count_letters()
     assert "not present in dictionary" in str(e.value)
-
+
+
 def test_fastq():
     fa_lines = [
         ">1 irrelevant\n",
@@ -62,12 +64,13 @@ def test_fastq():
         "@SQ\tSN:1\tLN:10\tM5:dummy\tUR:file://c:/foo.fa.gz",
     ]
     pytest.MonkeyPatch().setattr("gzip.open", gzip_open)
-   
+
     with pytest.raises(RuntimeError) as e:
         genome = MockGenome(MockPath(fa_lines), MockPath(dict_lines))
         FASTALetterCounter(genome).count_letters()
     assert "Expected a FASTA" in str(e.value)
-
+
+
 def test_duplicate_sequence():
     fa_lines = [
         ">1 irrelevant\n",
@@ -80,25 +83,22 @@ def test_duplicate_sequence():
         "@SQ\tSN:1\tLN:10\tM5:dummy\tUR:file://c:/foo.fa.gz",
     ]
     pytest.MonkeyPatch().setattr("gzip.open", gzip_open)
-   
+
     with pytest.raises(RuntimeError) as e:
         genome = MockGenome(MockPath(fa_lines), MockPath(dict_lines))
         FASTALetterCounter(genome).count_letters()
     assert "duplicated sequence" in str(e.value)
-    
-    
+
+
 def test_only_comments():
-    fa_lines = [
-        "#Hello\n",
-        f"#Foo\n"
-    ]
+    fa_lines = ["#Hello\n", f"#Foo\n"]
     dict_lines = [
         "@HD\tVN:1.0\tSO:unsorted",
         "@SQ\tSN:1\tLN:10\tM5:dummy\tUR:file://c:/foo.fa.gz",
     ]
     pytest.MonkeyPatch().setattr("gzip.open", gzip_open)
-   
+
     with pytest.raises(RuntimeError) as e:
         genome = MockGenome(MockPath(fa_lines), MockPath(dict_lines))
         FASTALetterCounter(genome).count_letters()
-    assert "no sequences" in str(e.value)
+    assert "no sequences" in str(e.value)

test/test_fasta_dictionary.py

@@ -11,6 +11,7 @@ def test_header_parsed_correctly():
     assert sut.metadata.sorted == Sorting.Coordinate
     assert sut.metadata.version == "1.0"
 
+
 def test_unsorted_parsed_correctly():
     lines = [
         "@HD\tVN:1.0\tSO:unsorted",
@@ -19,7 +20,8 @@ def test_unsorted_parsed_correctly():
     assert len(sut.sequences) == 0
     assert sut.metadata.sorted == Sorting.Unsorted
     assert sut.metadata.version == "1.0"
-
+
+
 def test_unsorted_parsed_correctly():
     lines = [
         "@HD\tVN:1.0\tSO:unknown",
@@ -29,10 +31,9 @@ def test_unsorted_parsed_correctly():
     assert sut.metadata.sorted == Sorting.Unknown
     assert sut.metadata.version == "1.0"
 
+
 def test_sequences_parsed_correctly():
-    lines = [
-        "@SQ\tSN:Seq1\tLN:123\tM5:abcdefabcdef123123\tUR:/directory/genome.fasta"
-    ]
+    lines = ["@SQ\tSN:Seq1\tLN:123\tM5:abcdefabcdef123123\tUR:/directory/genome.fasta"]
     sut = AlignmentMapHeader(lines)
     assert sut.metadata is None
     assert len(sut.sequences) == 1

test/test_microarray_converter.py

@@ -1,4 +1,3 @@
-
 from pathlib import Path
 from test.test_fasta import MockPath
 from test.utility import MockFile
@@ -11,35 +10,43 @@
 from wgse.microarray.microarray_converter import MicroarrayConverter
 from wgse.microarray.microarray_line_formatter import TARGET_FORMATTER_MAP
 
-
 # def test_every_target_has_formatter():
 #     assert all(x in TARGET_FORMATTER_MAP for x in MicroarrayConverterTarget)
-
+
+
 def test_inexistent_head_folder_raise():
     config = RepositoryConfig()
     config.metadata = MockPath(exists=False)
     microarray_templates = MockPath(exists=False, name="microarray_templates")
-    microarray_templates.joinpath = lambda x: MockPath([], False if x=="body" else True, x)
+    microarray_templates.joinpath = lambda x: MockPath(
+        [], False if x == "body" else True, x
+    )
     config.metadata.joinpath = lambda _: microarray_templates
     with pytest.raises(FileNotFoundError) as e:
         MicroarrayConverter(config)
     assert "template body"
-
+
+
 def test_inexistent_head_folder_raise():
     config = RepositoryConfig()
     config.metadata = MockPath(exists=False)
     microarray_templates = MockPath(exists=False, name="microarray_templates")
-    microarray_templates.joinpath = lambda x: MockPath([], False if x=="head" else True, x)
+    microarray_templates.joinpath = lambda x: MockPath(
+        [], False if x == "head" else True, x
+    )
     config.metadata.joinpath = lambda _: microarray_templates
     with pytest.raises(FileNotFoundError) as e:
         MicroarrayConverter(config)
     assert "template head"
 
+
 def test_inexistent_head_folder_raise():
     config = RepositoryConfig()
     config.metadata = MockPath(exists=False)
     microarray_templates = MockPath(exists=False, name="microarray_templates")
-    microarray_templates.joinpath = lambda x: MockPath([], False if x=="body" else True, x)
+    microarray_templates.joinpath = lambda x: MockPath(
+        [], False if x == "body" else True, x
+    )
     config.metadata.joinpath = lambda _: microarray_templates
     with pytest.raises(FileNotFoundError) as e:
         MicroarrayConverter(config)
@@ -56,7 +63,7 @@ def test_inexistent_head_folder_raise():
 #     input_file = MockFile(["rs1\t1\t1\tAA"])
 #     output_file = MockFile([])
 #     output_file.write = lambda x: output_lines.append(x)
-    
+
 #     mock_open.side_effect = [input_file, output_file]
 #     mock_exists.side_effect = [True, True, True, True]
 #     mock_gzip_open.side_effect = [template_body]
@@ -65,4 +72,4 @@ def test_inexistent_head_folder_raise():
 #     config.metadata = Path("blah")
 #     sut = MicroarrayConverter(config)
 #     sut.convert(Path("foo"), MicroarrayConverterTarget.Ancestry_v1)
-#     pass
+#     pass