chore: remove Python 3.8 support (#19)

BiocPy · Dec 28, 2024 · b1cd477 · b1cd477
1 parent dcd74a5
commit b1cd477
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diff --git a/.github/workflows/pypi-publish.yml → .github/workflows/publish-pypi.yml b/.github/workflows/pypi-publish.yml → .github/workflows/publish-pypi.yml
@@ -12,12 +12,12 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
-      - name: Set up Python 3.9
-        uses: actions/setup-python@v2
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v5
         with:
-          python-version: 3.9
+          python-version: 3.11
 
       # build SQLite from source, because I need 3.35<=
       - name: Download SQLite3
@@ -61,7 +61,7 @@ jobs:
       - run: touch ./docs/_build/html/.nojekyll
 
       - name: GH Pages Deployment
-        uses: JamesIves/github-pages-deploy-action@4.1.3
+        uses: JamesIves/github-pages-deploy-action@v4
         with:
           branch: gh-pages # The branch the action should deploy to.
           folder: ./docs/_build/html
@@ -74,7 +74,7 @@ jobs:
           LD_LIBRARY_PATH: /usr/local/lib
 
       - name: Publish package
-        uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
+        uses: pypa/gh-action-pypi-publish@v1.12.2
         with:
           user: __token__
           password: ${{ secrets.PYPI_PASSWORD }}
diff --git a/.github/workflows/pypi-test.yml → .github/workflows/run-tests.yml b/.github/workflows/pypi-test.yml → .github/workflows/run-tests.yml
@@ -11,13 +11,13 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+        python-version: [ "3.9", "3.10", "3.11", "3.12", "3.13" ]
 
     name: Python ${{ matrix.python-version }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: Setup Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
           cache: "pip"

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -17,26 +17,27 @@ repos:
   - id: mixed-line-ending
     args: ['--fix=auto']  # replace 'auto' with 'lf' to enforce Linux/Mac line endings or 'crlf' for Windows
 
-- repo: https://github.com/PyCQA/docformatter
-  rev: v1.7.5
-  hooks:
-    - id: docformatter
-      additional_dependencies: [tomli]
-      args: [--in-place, --wrap-descriptions=120, --wrap-summaries=120]
-      # --config, ./pyproject.toml
+# - repo: https://github.com/PyCQA/docformatter
+#   rev: master
+#   hooks:
+#     - id: docformatter
+#       additional_dependencies: [tomli]
+#       args: [--in-place, --wrap-descriptions=120, --wrap-summaries=120]
+#       # --config, ./pyproject.toml
 
-- repo: https://github.com/psf/black
-  rev: 24.8.0
-  hooks:
-  - id: black
-    language_version: python3
+# - repo: https://github.com/psf/black
+#   rev: 24.8.0
+#   hooks:
+#   - id: black
+#     language_version: python3
 
 - repo: https://github.com/astral-sh/ruff-pre-commit
   # Ruff version.
   rev: v0.6.8
   hooks:
     - id: ruff
       args: [--fix, --exit-non-zero-on-fix]
+    - id: ruff-format
 
 ## If like to embrace black styles even in the docs:
 # - repo: https://github.com/asottile/blacken-docs

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,5 +1,10 @@
 # Changelog
 
+## Version 0.3.0
+
+- chore: Remove Python 3.8 (EOL).
+- precommit: Replace docformatter with ruff's formatter.
+
 ## Version 0.2.0
 
 - Changes to support NumPy's 2.0 release.

diff --git a/README.md b/README.md
@@ -10,7 +10,6 @@
 [![Twitter](https://img.shields.io/twitter/url/http/shields.io.svg?style=social&label=Twitter)](https://twitter.com/scrnaseq)
 -->
 
-[![Project generated with PyScaffold](https://img.shields.io/badge/-PyScaffold-005CA0?logo=pyscaffold)](https://pyscaffold.org/)
 [![PyPI-Server](https://img.shields.io/pypi/v/scrnaseq.svg)](https://pypi.org/project/scrnaseq/)
 
 # scrnaseq

diff --git a/docs/conf.py b/docs/conf.py
@@ -72,6 +72,7 @@
     "sphinx.ext.ifconfig",
     "sphinx.ext.mathjax",
     "sphinx.ext.napoleon",
+    "sphinx_autodoc_typehints",
 ]
 
 # Add any paths that contain templates here, relative to this directory.

diff --git a/pyproject.toml b/pyproject.toml
@@ -17,6 +17,10 @@ extend-ignore = ["F821"]
 [tool.ruff.pydocstyle]
 convention = "google"
 
+[tool.ruff.format]
+docstring-code-format = true
+docstring-code-line-length = 20
+
 [tool.ruff.per-file-ignores]
 "__init__.py" = ["E402", "F401"]
 

diff --git a/setup.cfg b/setup.cfg
@@ -41,17 +41,17 @@ package_dir =
     =src
 
 # Require a min/specific Python version (comma-separated conditions)
-python_requires = >=3.8
+python_requires = >=3.9
 
 # Add here dependencies of your project (line-separated), e.g. requests>=2.2,<3.0.
 # Version specifiers like >=2.2,<3.0 avoid problems due to API changes in
 # new major versions. This works if the required packages follow Semantic Versioning.
 # For more information, check out https://semver.org/.
 install_requires =
     importlib-metadata; python_version<"3.8"
-    dolomite_base
+    dolomite_base>=0.4.2
     dolomite_matrix
-    dolomite_sce>=0.1.2
+    dolomite_sce
     gypsum_client>=0.1.3
     delayedarray>=0.5.1
     summarizedexperiment

diff --git a/src/scrnaseq/fetch_dataset.py b/src/scrnaseq/fetch_dataset.py
@@ -41,7 +41,10 @@ def fetch_dataset(
 
         .. code-block:: python
 
-            sce = fetch_dataset("zeisel-brain-2015", "2023-12-14")
+            sce = fetch_dataset(
+                "zeisel-brain-2015",
+                "2023-12-14",
+            )
 
     Args:
         name:
@@ -83,12 +86,8 @@ def fetch_dataset(
         or one of its subclasses.
     """
 
-    version_path = save_version(
-        package, name, version, cache_dir=cache_dir, overwrite=overwrite
-    )
-    obj_path = (
-        version_path if path is None else os.path.join(version_path, path.rstrip("/"))
-    )
+    version_path = save_version(package, name, version, cache_dir=cache_dir, overwrite=overwrite)
+    obj_path = version_path if path is None else os.path.join(version_path, path.rstrip("/"))
 
     old = alt_read_object_function(single_cell_load_object)
 
@@ -122,7 +121,10 @@ def fetch_metadata(
 
     .. code-block:: python
 
-        meta = fetch_metadata("zeisel-brain-2015", "2023-12-14")
+        meta = fetch_metadata(
+            "zeisel-brain-2015",
+            "2023-12-14",
+        )
 
     Args:
         name:
@@ -150,9 +152,7 @@ def fetch_metadata(
         Dictionary containing metadata for the specified dataset.
     """
     remote_path = "_bioconductor.json" if path is None else f"{path}/_bioconductor.json"
-    local_path = save_file(
-        package, name, version, remote_path, cache_dir=cache_dir, overwrite=overwrite
-    )
+    local_path = save_file(package, name, version, remote_path, cache_dir=cache_dir, overwrite=overwrite)
 
     with open(local_path, "r") as f:
         metadata = json.load(f)

diff --git a/src/scrnaseq/list_datasets.py b/src/scrnaseq/list_datasets.py
@@ -14,16 +14,16 @@
 
 
 @lru_cache
-def list_datasets(
-    cache_dir: str = cache_directory(), overwrite: bool = False, latest: bool = True
-) -> pd.DataFrame:
+def list_datasets(cache_dir: str = cache_directory(), overwrite: bool = False, latest: bool = True) -> pd.DataFrame:
     """List all available datasets.
 
     Example:
 
         .. code-block:: python
 
-            datasets = list_datasets()
+            datasets = (
+                list_datasets()
+            )
 
     Args:
         cache_dir:
@@ -83,9 +83,7 @@ def _format_query_results(results: list, key_names: list):
 
 
 def _sanitize_query_to_output(results: list, latest: bool, meta_name: str = "meta"):
-    _all_paths = [
-        None if "/" not in p else p.rsplit("/", 1)[0] for p in results["path"]
-    ]
+    _all_paths = [None if "/" not in p else p.rsplit("/", 1)[0] for p in results["path"]]
 
     df = pd.DataFrame(
         {
@@ -105,33 +103,22 @@ def _sanitize_query_to_output(results: list, latest: bool, meta_name: str = "met
     )
     df["title"] = _extract_atomic_from_json(_all_metas, lambda x: x.get("title"))
     df["description"] = _extract_atomic_from_json(_all_metas, lambda x: x.get("title"))
-    df["taxonomy_id"] = _extract_charlist_from_json(
-        _all_metas, lambda x: x.get("taxonomy_id")
-    )
+    df["taxonomy_id"] = _extract_charlist_from_json(_all_metas, lambda x: x.get("taxonomy_id"))
     df["genome"] = _extract_charlist_from_json(_all_metas, lambda x: x.get("genome"))
 
     df["rows"] = _extract_atomic_from_json(
         _all_metas,
-        lambda x: x.get("applications", {})
-        .get("takane", {})
-        .get("summarized_experiment", {})
-        .get("rows"),
+        lambda x: x.get("applications", {}).get("takane", {}).get("summarized_experiment", {}).get("rows"),
     )
 
     df["columns"] = _extract_atomic_from_json(
         _all_metas,
-        lambda x: x.get("applications", {})
-        .get("takane", {})
-        .get("summarized_experiment", {})
-        .get("columns"),
+        lambda x: x.get("applications", {}).get("takane", {}).get("summarized_experiment", {}).get("columns"),
     )
 
     df["assays"] = _extract_charlist_from_json(
         _all_metas,
-        lambda x: x.get("applications", {})
-        .get("takane", {})
-        .get("summarized_experiment", {})
-        .get("assays"),
+        lambda x: x.get("applications", {}).get("takane", {}).get("summarized_experiment", {}).get("assays"),
     )
     df["column_annotations"] = _extract_charlist_from_json(
         _all_metas,
@@ -155,15 +142,9 @@ def _sanitize_query_to_output(results: list, latest: bool, meta_name: str = "met
         .get("alternative_experiments"),
     )
 
-    df["bioconductor_version"] = _extract_atomic_from_json(
-        _all_metas, lambda x: x.get("bioconductor_version")
-    )
-    df["maintainer_name"] = _extract_atomic_from_json(
-        _all_metas, lambda x: x.get("maintainer_name")
-    )
-    df["maintainer_email"] = _extract_atomic_from_json(
-        _all_metas, lambda x: x.get("maintainer_email")
-    )
+    df["bioconductor_version"] = _extract_atomic_from_json(_all_metas, lambda x: x.get("bioconductor_version"))
+    df["maintainer_name"] = _extract_atomic_from_json(_all_metas, lambda x: x.get("maintainer_name"))
+    df["maintainer_email"] = _extract_atomic_from_json(_all_metas, lambda x: x.get("maintainer_email"))
 
     sources = []
     for meta in _all_metas:
@@ -186,9 +167,7 @@ def _sanitize_query_to_output(results: list, latest: bool, meta_name: str = "met
 
 
 def _extract_atomic_from_json(metadata, extract):
-    return [
-        extract(_meta) if extract(_meta) is not None else None for _meta in metadata
-    ]
+    return [extract(_meta) if extract(_meta) is not None else None for _meta in metadata]
 
 
 def _extract_charlist_from_json(metadata, extract):

diff --git a/src/scrnaseq/list_versions.py b/src/scrnaseq/list_versions.py
@@ -14,7 +14,9 @@ def list_versions(name: str) -> List[str]:
 
         .. code-block:: python
 
-            versions = list_versions("romanov-brain-2017")
+            versions = list_versions(
+                "romanov-brain-2017"
+            )
 
     Args:
         name:
@@ -33,7 +35,9 @@ def fetch_latest_version(name: str) -> str:
 
         .. code-block:: python
 
-            version = fetch_latest_version("romanov-brain-2017")
+            version = fetch_latest_version(
+                "romanov-brain-2017"
+            )
 
     Args:
         name:

diff --git a/src/scrnaseq/save_dataset.py b/src/scrnaseq/save_dataset.py
@@ -54,15 +54,27 @@ def save_dataset(x: Any, path, metadata):
             # Fetch an existing dataset
             # or create your own ``SingleCellExperiment``
             # or ``AnnData`` object.
-            sce = scrnaseq.fetch_dataset("zeisel-brain-2015", "2023-12-14")
+            sce = scrnaseq.fetch_dataset(
+                "zeisel-brain-2015",
+                "2023-12-14",
+            )
 
             # Provide dataset level metadata for search and findability
             meta = {
                 "title": "My dataset made from ziesel brain",
                 "description": "This is a copy of the ziesel",
-                "taxonomy_id": ["10090"], # NCBI ID
-                "genome": ["GRCh38"], # genome build
-                "sources": [{"provider": "GEO", "id": "GSE12345"}],
+                "taxonomy_id": [
+                    "10090"
+                ],  # NCBI ID
+                "genome": [
+                    "GRCh38"
+                ],  # genome build
+                "sources": [
+                    {
+                        "provider": "GEO",
+                        "id": "GSE12345",
+                    }
+                ],
                 "maintainer_name": "Shizuka Mogami",
                 "maintainer_email": "[email protected]",
             }
@@ -73,14 +85,18 @@ def save_dataset(x: Any, path, metadata):
             cache_dir = tempfile.mkdtemp()
 
             # Make sure the directory is clean
-            shutil.rmtree(cache_dir)
+            shutil.rmtree(
+                cache_dir
+            )
 
             # Save the dataset
-            scrnaseq.save_dataset(sce, cache_dir, meta)
+            scrnaseq.save_dataset(
+                sce,
+                cache_dir,
+                meta,
+            )
     """
-    raise NotImplementedError(
-        f"'save_dataset' is not supported for objects of class: {type(x)}"
-    )
+    raise NotImplementedError(f"'save_dataset' is not supported for objects of class: {type(x)}")
 
 
 def _save_se(x, path, metadata):