Update docs, tox, and package metadata (#105)

- use `tox-uv` - Update mypy overloads to use `...` where value doesn't need to be set - Fix note about correct compression - add py312 testing (fix flake8 config)
biopragmatics · Mar 12, 2024 · a364fdc · a364fdc
1 parent 85abe79
commit a364fdc
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Showing 4 changed files with 44 additions and 32 deletions.
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -12,15 +12,15 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [ "3.8", "3.11" ]
+        python-version: [ "3.8", "3.12" ]
     steps:
       - uses: actions/checkout@v2
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v2
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install dependencies
-        run: pip install tox
+        run: pip install tox tox-uv
       - name: Check manifest
         run: tox run -e manifest
       - name: Check code quality with flake8
@@ -34,7 +34,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [ "3.8", "3.11" ]
+        python-version: [ "3.8", "3.12" ]
     steps:
       - uses: actions/checkout@v2
       - name: Set up Python ${{ matrix.python-version }}
@@ -43,7 +43,7 @@ jobs:
           python-version: ${{ matrix.python-version }}
       - name: Install dependencies
         run: |
-          pip install tox
+          pip install tox tox-uv
           sudo apt-get install graphviz
       - name: Check RST conformity with doc8
         run: tox run -e doc8
@@ -57,7 +57,7 @@ jobs:
     strategy:
       matrix:
         os: [ ubuntu-latest ]
-        python-version: [ "3.8", "3.11" ]
+        python-version: [ "3.8", "3.12" ]
         pydantic: [ "1", "2" ]
     steps:
       - uses: actions/checkout@v2
@@ -66,7 +66,7 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install dependencies
-        run: pip install tox
+        run: pip install tox tox-uv
       - name: Test with pytest and generate coverage file
         run:
           tox run -e py-pydantic${{ matrix.pydantic }}

diff --git a/setup.cfg b/setup.cfg
@@ -28,7 +28,7 @@ license_files =
 
 # Search tags
 classifiers =
-    Development Status :: 1 - Planning
+    Development Status :: 5 - Production/Stable
     Environment :: Console
     Intended Audience :: Developers
     License :: OSI Approved :: MIT License
@@ -41,6 +41,7 @@ classifiers =
     Programming Language :: Python :: 3.9
     Programming Language :: Python :: 3.10
     Programming Language :: Python :: 3.11
+    Programming Language :: Python :: 3.12
     Programming Language :: Python :: 3 :: Only
 keywords =
     snekpack
@@ -49,6 +50,7 @@ keywords =
     compact uniform resource identifiers
     uniform resource identifiers
     curies
+    IRIs
 
 [options]
 install_requires =
@@ -138,14 +140,20 @@ strictness = short
 #########################
 [flake8]
 ignore =
-    S301 # pickle
-    S403 # pickle
+    # pickle
+    S301
+    # pickle
+    S403
     S404
     S603
-    W503  # Line break before binary operator (conflicts with black)
-    E704  # Multiple statements on one line (conflicts with black)
-    E203  # whitespace before ':'  (conflicts with black)
-    S113  # Requests call without timeout
+    # Line break before binary operator (conflicts with black)
+    W503
+    # Multiple statements on one line (conflicts with black)
+    E704
+    # whitespace before ':'  (conflicts with black)
+    E203
+    # Requests call without timeout
+    S113
 exclude =
     .tox,
     .git,

diff --git a/src/curies/api.py b/src/curies/api.py
@@ -1035,7 +1035,7 @@ def is_uri(self, s: str) -> bool:
     # docstr-coverage:excused `overload`
     @overload
     def compress_or_standardize(
-        self, uri_or_curie: str, *, strict: Literal[True] = True, passthrough: bool = False
+        self, uri_or_curie: str, *, strict: Literal[True] = True, passthrough: bool = ...
     ) -> str: ...
 
     # docstr-coverage:excused `overload`
@@ -1114,7 +1114,7 @@ def compress_strict(self, uri: str) -> str:
     # docstr-coverage:excused `overload`
     @overload
     def compress(
-        self, uri: str, *, strict: Literal[True] = True, passthrough: bool = False
+        self, uri: str, *, strict: Literal[True] = True, passthrough: bool = ...
     ) -> str: ...
 
     # docstr-coverage:excused `overload`
@@ -1144,16 +1144,27 @@ def compress(
         :raises CompressionError:
             If strict is set to true and the URI can't be compressed
 
-
         >>> from curies import Converter
         >>> converter = Converter.from_prefix_map({
         ...    "CHEBI": "http://purl.obolibrary.org/obo/CHEBI_",
         ...    "MONDO": "http://purl.obolibrary.org/obo/MONDO_",
         ...    "GO": "http://purl.obolibrary.org/obo/GO_",
+        ...    "OBO": "http://purl.obolibrary.org/obo/",
         ... })
-        >>> converter.compress("http://purl.obolibrary.org/obo/CHEBI_138488")
-        'CHEBI:138488'
+        >>> converter.compress("http://purl.obolibrary.org/obo/GO_0032571")
+        'GO:0032571'
+        >>> converter.compress("http://purl.obolibrary.org/obo/go.owl")
+        'OBO:go.owl'
         >>> converter.compress("http://example.org/missing:0000000")
+
+        .. note::
+
+            If there are partially overlapping *URI prefixes* in this converter
+            (e.g., ``http://purl.obolibrary.org/obo/GO_`` for the prefix ``GO`` and
+            ``http://purl.obolibrary.org/obo/`` for the prefix ``OBO``), the longest
+            URI prefix will always be matched. For example, parsing
+            ``http://purl.obolibrary.org/obo/GO_0032571`` will return ``GO:0032571``
+            instead of ``OBO:GO_0032571``.
         """
         prefix, identifier = self.parse_uri(uri)
         if prefix and identifier:
@@ -1221,7 +1232,7 @@ def is_curie(self, s: str) -> bool:
     # docstr-coverage:excused `overload`
     @overload
     def expand_or_standardize(
-        self, curie_or_uri: str, *, strict: Literal[True] = True, passthrough: bool = False
+        self, curie_or_uri: str, *, strict: Literal[True] = True, passthrough: bool = ...
     ) -> str: ...
 
     # docstr-coverage:excused `overload`
@@ -1300,7 +1311,7 @@ def expand_strict(self, curie: str) -> str:
     # docstr-coverage:excused `overload`
     @overload
     def expand(
-        self, curie: str, *, strict: Literal[True] = True, passthrough: bool = False
+        self, curie: str, *, strict: Literal[True] = True, passthrough: bool = ...
     ) -> str: ...
 
     # docstr-coverage:excused `overload`
@@ -1325,7 +1336,7 @@ def expand(
         :param strict: If true and the CURIE can't be expanded, returns an error. Defaults to false.
         :param passthrough: If true, strict is false, and the CURIE can't be expanded, return the input.
             Defaults to false. If your strings can either be a CURIE _or_ a URI, consider using
-            :meth:`Converter.expand_ambiguous` instead.
+            :meth:`Converter.expand_or_standardize` instead.
         :returns:
             A URI if this converter contains a URI prefix for the prefix in this CURIE
         :raises ExpansionError:
@@ -1340,15 +1351,6 @@ def expand(
         >>> converter.expand("CHEBI:138488")
         'http://purl.obolibrary.org/obo/CHEBI_138488'
         >>> converter.expand("missing:0000000")
-
-        .. note::
-
-            If there are partially overlapping *URI prefixes* in this converter
-            (e.g., ``http://purl.obolibrary.org/obo/GO_`` for the prefix ``GO`` and
-            ``http://purl.obolibrary.org/obo/`` for the prefix ``OBO``), the longest
-            URI prefix will always be matched. For example, parsing
-            ``http://purl.obolibrary.org/obo/GO_0032571`` will return ``GO:0032571``
-            instead of ``OBO:GO_0032571``.
         """
         prefix, identifier = self.parse_curie(curie)
         rv = self.expand_pair(prefix, identifier)

diff --git a/tox.ini b/tox.ini
@@ -87,7 +87,7 @@ description = Check that the MANIFEST.in is written properly and give feedback o
 skip_install = true
 deps =
     darglint
-    flake8<5.0.0
+    flake8
     flake8-black
     flake8-bandit
     flake8-bugbear
@@ -110,7 +110,9 @@ commands = pyroma --min=10 .
 description = Run the pyroma tool to check the package friendliness of the project.
 
 [testenv:mypy]
-deps = mypy
+deps =
+    mypy
+    types-requests
 skip_install = true
 commands = mypy --install-types --non-interactive --ignore-missing-imports --strict src/
 description = Run the mypy tool to check static typing on the project.