chore: remove Python 3.8 support (#11)

TileOme · Dec 20, 2024 · 0e16c4c · 0e16c4c
1 parent d12588e
commit 0e16c4c
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Showing 11 changed files with 113 additions and 118 deletions.
diff --git a/.github/workflows/pypi-publish.yml b/.github/workflows/pypi-publish.yml
@@ -9,43 +9,44 @@ on:
 
 jobs:
   build:
-
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v4
-    - name: Set up Python 3.9
-      uses: actions/setup-python@v5
-      with:
-        python-version: 3.9
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install flake8 pytest tox
-    # - name: Lint with flake8
-    #   run: |
-    #     # stop the build if there are Python syntax errors or undefined names
-    #     flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-    #     # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-    #     # flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
-    - name: Test with tox
-      run: |
-        tox
-    - name: Build docs
-      run: |
-        tox -e docs
-    - run: touch ./docs/_build/html/.nojekyll
-    - name: GH Pages Deployment
-      uses: JamesIves/[email protected]
-      with:
-        branch: gh-pages # The branch the action should deploy to.
-        folder: ./docs/_build/html
-        clean: true # Automatically remove deleted files from the deploy branch
-    - name: Build Project and Publish
-      run: |
-        python -m tox -e clean,build
-    - name: Publish package
-      uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
-      with:
-        user: __token__
-        password: ${{ secrets.PYPI_PASSWORD }}
+      - uses: actions/checkout@v4
+
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.11
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install tox
+
+      - name: Test with tox
+        run: |
+          tox
+
+      - name: Build docs
+        run: |
+          tox -e docs
+
+      - run: touch ./docs/_build/html/.nojekyll
+
+      - name: GH Pages Deployment
+        uses: JamesIves/github-pages-deploy-action@v4
+        with:
+          branch: gh-pages # The branch the action should deploy to.
+          folder: ./docs/_build/html
+          clean: true # Automatically remove deleted files from the deploy branch
+
+      - name: Build Project and Publish
+        run: |
+          python -m tox -e clean,build
+
+      - name: Publish package
+        uses: pypa/[email protected]
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_PASSWORD }}
diff --git a/.github/workflows/pypi-test.yml b/.github/workflows/pypi-test.yml
@@ -1,40 +1,33 @@
-# This workflow will install Python dependencies, run tests and lint with a single version of Python
-# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
-
-name: Test the library
+name: Run tests
 
 on:
   push:
-    branches: [ master ]
+    branches: [master]
   pull_request:
-    branches: [ master ]
+    branches: [master]
 
 jobs:
   build:
-
     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@v4
-    - name: Setup Python
-      uses: actions/setup-python@v5
-      with:
-        python-version: ${{ matrix.python-version }}
-        cache: 'pip'
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install flake8 pytest tox
-    # - name: Lint with flake8
-    #   run: |
-    #     # stop the build if there are Python syntax errors or undefined names
-    #     flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-    #     # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-    #     # flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
-    - name: Test with tox
-      run: |
-        tox
+      - uses: actions/checkout@v4
+
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: "pip"
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install tox
+
+      - name: Test with tox
+        run: |
+          tox
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -17,13 +17,13 @@ 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: eb1df347edd128b30cd3368dddc3aa65edcfac38
-  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
@@ -37,6 +37,7 @@ repos:
   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
@@ -1,7 +1,10 @@
 # Changelog
 
-## Version 0.1 (development)
+## Version 0.2.0
 
-- Feature A added
-- FIX: nasty bug #1729 fixed
-- add your changes here!
+- chore: Remove Python 3.8 (EOL)
+- precommit: Replace docformatter with ruff's formatter
+
+## Version 0.1.0
+
+- Initial version of the package
diff --git a/docs/conf.py b/docs/conf.py
@@ -179,9 +179,6 @@
 autosummary_generate = True
 autosummary_imported_members = True
 
-
-
-
 # -- Options for HTML output -------------------------------------------------
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for

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
@@ -41,7 +41,7 @@ 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

diff --git a/src/genomicarrays/GenomicArrayDataset.py b/src/genomicarrays/GenomicArrayDataset.py
@@ -8,10 +8,16 @@
 
     .. code-block:: python
 
-        from genomicarray import GenomicArrayDataset
+        from genomicarray import (
+            GenomicArrayDataset,
+        )
 
-        garr = GenomicArrayDataset(dataset_path="/path/to/genomicarray/dir")
-        result1 = garr[0:10, 0]
+        garr = GenomicArrayDataset(
+            dataset_path="/path/to/genomicarray/dir"
+        )
+        result1 = garr[
+            0:10, 0
+        ]
 
         print(result1)
 """

diff --git a/src/genomicarrays/GenomicArrayDatasetSlice.py b/src/genomicarrays/GenomicArrayDatasetSlice.py
@@ -8,11 +8,20 @@
 
     .. code-block:: python
 
-        from genomicarray import GenomicArrayDataset
+        from genomicarray import (
+            GenomicArrayDataset,
+        )
 
-        garr = GenomicArrayDataset(dataset_path="/path/to/genomicarray/dir")
-        feature_indices = slice(0, 10)
-        result1 = garr[feature_indices, 0]
+        garr = GenomicArrayDataset(
+            dataset_path="/path/to/genomicarray/dir"
+        )
+        feature_indices = (
+            slice(0, 10)
+        )
+        result1 = garr[
+            feature_indices,
+            0,
+        ]
 
         print(result1)
 """

diff --git a/src/genomicarrays/build_genomicarray.py b/src/genomicarrays/build_genomicarray.py
@@ -174,9 +174,7 @@ def build_genomicarray(
             missing = required_cols - set(input_intervals.columns)
             raise ValueError(f"Missing required columns: {missing}")
     else:
-        raise TypeError(
-            "'input_intervals' is not an expected type (either 'str' or 'Dataframe')."
-        )
+        raise TypeError("'input_intervals' is not an expected type (either 'str' or 'Dataframe').")
 
     # append start index for each interval
     input_intervals["widths"] = input_intervals["ends"] - input_intervals["starts"]
@@ -190,16 +188,13 @@ def build_genomicarray(
         counter = [1] * len(input_intervals)
         total_length = len(input_intervals)
         counter[0] = 0
-        input_intervals["genarr_feature_start_index"] = (
-            pd.Series(counter).cumsum().astype(int)
-        )
+        input_intervals["genarr_feature_start_index"] = pd.Series(counter).cumsum().astype(int)
 
     ends = input_intervals["genarr_feature_start_index"].shift(-1)
     ends.iloc[-1] = total_length
     input_intervals["genarr_feature_end_index"] = ends.astype(int)
 
     if not feature_annotation_options.skip:
-
         if "sequence" not in input_intervals.columns:
             gen_fa = Fasta(genome_fasta, as_raw=True)
             sequences = []
@@ -209,19 +204,13 @@ def build_genomicarray(
 
             input_intervals["sequences"] = sequences
 
-        _col_types = utf.infer_column_types(
-            input_intervals, feature_annotation_options.column_types
-        )
+        _col_types = utf.infer_column_types(input_intervals, feature_annotation_options.column_types)
 
         if "genarr_feature_index" not in input_intervals.columns:
             input_intervals["genarr_feature_index"] = range(0, len(input_intervals))
 
-        _feature_output_uri = (
-            f"{output_path}/{feature_annotation_options.tiledb_store_name}"
-        )
-        utf.create_tiledb_frame_from_dataframe(
-            _feature_output_uri, input_intervals, column_types=_col_types
-        )
+        _feature_output_uri = f"{output_path}/{feature_annotation_options.tiledb_store_name}"
+        utf.create_tiledb_frame_from_dataframe(_feature_output_uri, input_intervals, column_types=_col_types)
 
         if optimize_tiledb:
             uta.optimize_tiledb_array(_feature_output_uri)
@@ -251,16 +240,10 @@ def build_genomicarray(
         raise TypeError("'sample_metadata' is not an expected type.")
 
     if not sample_metadata_options.skip:
-        _col_types = utf.infer_column_types(
-            sample_metadata, sample_metadata_options.column_types
-        )
+        _col_types = utf.infer_column_types(sample_metadata, sample_metadata_options.column_types)
 
-        _sample_output_uri = (
-            f"{output_path}/{sample_metadata_options.tiledb_store_name}"
-        )
-        utf.create_tiledb_frame_from_dataframe(
-            _sample_output_uri, sample_metadata, column_types=_col_types
-        )
+        _sample_output_uri = f"{output_path}/{sample_metadata_options.tiledb_store_name}"
+        utf.create_tiledb_frame_from_dataframe(_sample_output_uri, sample_metadata, column_types=_col_types)
 
         if optimize_tiledb:
             uta.optimize_tiledb_array(_sample_output_uri)
@@ -311,9 +294,7 @@ def build_genomicarray(
     )
 
 
-def _write_intervals_to_tiledb(
-    outpath, intervals, bwpath, bwidx, agg_func, total_length
-):
+def _write_intervals_to_tiledb(outpath, intervals, bwpath, bwidx, agg_func, total_length):
     """Wrapper to extract the data for the given intervals from the bigwig file and write the output to the tiledb
     file."""
     data = ubw.wrapper_extract_bw_values(
@@ -330,6 +311,4 @@ def _write_intervals_to_tiledb(
 def _wrapper_extract_bwinfo(args):
     """Wrapper for multiprocessing multiple files and intervals."""
     counts_uri, input_intervals, bwpath, idx, agg_func, total_length = args
-    return _write_intervals_to_tiledb(
-        counts_uri, input_intervals, bwpath, idx, agg_func, total_length
-    )
+    return _write_intervals_to_tiledb(counts_uri, input_intervals, bwpath, idx, agg_func, total_length)
diff --git a/src/genomicarrays/dataloader.py b/src/genomicarrays/dataloader.py
@@ -7,7 +7,9 @@
 
     .. code-block:: python
 
-        from genomicarrays.dataloader import TorchDataset
+        from genomicarrays.dataloader import (
+            TorchDataset,
+        )
 
         ds = TorchDataset(
             dataset_path="/path/to/genarr/dir"