Merge pull request #45 from scverse-bot/template-update-v2-quadbio-cell-annotator

Update template to v0.5.0

Author: Marius1311

.cruft.json

@@ -1,7 +1,7 @@
 {
   "template": "https://github.com/scverse/cookiecutter-scverse",
-  "commit": "5d44c58df427f884585ae9772cae81f1b6638f80",
-  "checkout": null,
+  "commit": "94ef9fb6f9ad8cfe65a3d9575679c03c80c49cd1",
+  "checkout": "v0.5.0",
   "context": {
     "cookiecutter": {
       "project_name": "cell-annotator",
@@ -18,12 +18,25 @@
         ".github/workflows/test.yaml",
         "docs/_templates/autosummary/**.rst"
       ],
+      "_exclude_on_template_update": [
+        "CHANGELOG.md",
+        "LICENSE",
+        "README.md",
+        "docs/api.md",
+        "docs/index.md",
+        "docs/notebooks/example.ipynb",
+        "docs/references.bib",
+        "docs/references.md",
+        "src/**",
+        "tests/**"
+      ],
       "_render_devdocs": false,
       "_jinja2_env_vars": {
         "lstrip_blocks": true,
         "trim_blocks": true
       },
-      "_template": "https://github.com/scverse/cookiecutter-scverse"
+      "_template": "https://github.com/scverse/cookiecutter-scverse",
+      "_commit": "94ef9fb6f9ad8cfe65a3d9575679c03c80c49cd1"
     }
   },
   "directory": null

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -23,67 +23,72 @@ body:
   - type: textarea
     id: versions
     attributes:
-      label: Version information
+      label: Versions
       description: |
-        Please paste below the output of
+        Which version of packages.
+
+        Please install `session-info2`, run the following command in a notebook,
+        click the “Copy as Markdown” button, then paste the results into the text box below.
+
+        ```python
+        In[1]: import session_info2; session_info2.session_info(dependencies=True)
+        ```
+
+        Alternatively, run this in a console:
 
         ```python
-        import session_info
-        session_info.show(html=False, dependencies=True)
+        >>> import session_info2; print(session_info2.session_info(dependencies=True)._repr_mimebundle_()["text/markdown"])
         ```
+      render: python
       placeholder: |
-        -----
-        anndata             0.8.0rc2.dev27+ge524389
-        session_info        1.0.0
-        -----
-        asttokens           NA
-        awkward             1.8.0
-        backcall            0.2.0
-        cython_runtime      NA
-        dateutil            2.8.2
-        debugpy             1.6.0
-        decorator           5.1.1
-        entrypoints         0.4
-        executing           0.8.3
-        h5py                3.7.0
-        ipykernel           6.15.0
-        jedi                0.18.1
-        mpl_toolkits        NA
-        natsort             8.1.0
-        numpy               1.22.4
-        packaging           21.3
-        pandas              1.4.2
-        parso               0.8.3
-        pexpect             4.8.0
-        pickleshare         0.7.5
-        pkg_resources       NA
-        prompt_toolkit      3.0.29
-        psutil              5.9.1
-        ptyprocess          0.7.0
-        pure_eval           0.2.2
-        pydev_ipython       NA
-        pydevconsole        NA
-        pydevd              2.8.0
-        pydevd_file_utils   NA
-        pydevd_plugins      NA
-        pydevd_tracing      NA
-        pygments            2.12.0
-        pytz                2022.1
-        scipy               1.8.1
-        setuptools          62.5.0
-        setuptools_scm      NA
-        six                 1.16.0
-        stack_data          0.3.0
-        tornado             6.1
-        traitlets           5.3.0
-        wcwidth             0.2.5
-        zmq                 23.1.0
-        -----
-        IPython             8.4.0
-        jupyter_client      7.3.4
-        jupyter_core        4.10.0
-        -----
-        Python 3.9.13 | packaged by conda-forge | (main, May 27 2022, 16:58:50) [GCC 10.3.0]
-        Linux-5.18.6-arch1-1-x86_64-with-glibc2.35
-        -----
-        Session information updated at 2022-07-07 17:55
+        anndata	0.11.3
+        ----	----
+        charset-normalizer	3.4.1
+        coverage	7.7.0
+        psutil	7.0.0
+        dask	2024.7.1
+        jaraco.context	5.3.0
+        numcodecs	0.15.1
+        jaraco.functools	4.0.1
+        Jinja2	3.1.6
+        sphinxcontrib-jsmath	1.0.1
+        sphinxcontrib-htmlhelp	2.1.0
+        toolz	1.0.0
+        session-info2	0.1.2
+        PyYAML	6.0.2
+        llvmlite	0.44.0
+        scipy	1.15.2
+        pandas	2.2.3
+        sphinxcontrib-devhelp	2.0.0
+        h5py	3.13.0
+        tblib	3.0.0
+        setuptools-scm	8.2.0
+        more-itertools	10.3.0
+        msgpack	1.1.0
+        sparse	0.15.5
+        wrapt	1.17.2
+        jaraco.collections	5.1.0
+        numba	0.61.0
+        pyarrow	19.0.1
+        pytz	2025.1
+        MarkupSafe	3.0.2
+        crc32c	2.7.1
+        sphinxcontrib-qthelp	2.0.0
+        sphinxcontrib-serializinghtml	2.0.0
+        zarr	2.18.4
+        asciitree	0.3.3
+        six	1.17.0
+        sphinxcontrib-applehelp	2.0.0
+        numpy	2.1.3
+        cloudpickle	3.1.1
+        sphinxcontrib-bibtex	2.6.3
+        natsort	8.4.0
+        jaraco.text	3.12.1
+        setuptools	76.1.0
+        Deprecated	1.2.18
+        packaging	24.2
+        python-dateutil	2.9.0.post0
+        ----	----
+        Python	3.13.2 | packaged by conda-forge | (main, Feb 17 2025, 14:10:22) [GCC 13.3.0]
+        OS	Linux-6.11.0-109019-tuxedo-x86_64-with-glibc2.39
+        Updated	2025-03-18 15:47

.github/workflows/build.yaml

@@ -10,20 +10,24 @@ concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
 
+defaults:
+  run:
+    # to fail on error in multiline statements (-e), in pipes (-o pipefail), and on unset variables (-u).
+    shell: bash -euo pipefail {0}
+
 jobs:
   package:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-      - name: Set up Python 3.12
-        uses: actions/setup-python@v5
         with:
-          python-version: "3.12"
-          cache: "pip"
-          cache-dependency-path: "**/pyproject.toml"
-      - name: Install build dependencies
-        run: python -m pip install --upgrade pip wheel twine build
+          filter: blob:none
+          fetch-depth: 0
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+        with:
+          cache-dependency-glob: pyproject.toml
       - name: Build package
-        run: python -m build
+        run: uv build
       - name: Check package
-        run: twine check --strict dist/*.whl
+        run: uvx twine check --strict dist/*.whl

.github/workflows/release.yaml

@@ -4,6 +4,11 @@ on:
   release:
     types: [published]
 
+defaults:
+  run:
+    # to fail on error in multiline statements (-e), in pipes (-o pipefail), and on unset variables (-u).
+    shell: bash -euo pipefail {0}
+
 # Use "trusted publishing", see https://docs.pypi.org/trusted-publishers/
 jobs:
   release:
@@ -19,11 +24,11 @@ jobs:
         with:
           filter: blob:none
           fetch-depth: 0
-      - uses: actions/setup-python@v5
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
         with:
-          python-version: "3.x"
-          cache: "pip"
-      - run: pip install build
-      - run: python -m build
+          cache-dependency-glob: pyproject.toml
+      - name: Build package
+        run: uv build
       - name: Publish package distributions to PyPI
         uses: pypa/gh-action-pypi-publish@release/v1

.github/workflows/test.yaml

@@ -12,12 +12,14 @@ concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
 
+defaults:
+  run:
+    # to fail on error in multiline statements (-e), in pipes (-o pipefail), and on unset variables (-u).
+    shell: bash -euo pipefail {0}
+
 jobs:
   test:
     runs-on: ${{ matrix.os }}
-    defaults:
-      run:
-        shell: bash -e {0} # -e to fail on error
 
     strategy:
       fail-fast: false
@@ -41,33 +43,24 @@ jobs:
 
     steps:
       - uses: actions/checkout@v4
-      - name: Set up Python ${{ matrix.python }}
-        uses: actions/setup-python@v5
         with:
-          python-version: ${{ matrix.python }}
-          cache: "pip"
-          cache-dependency-path: "**/pyproject.toml"
-
-      - name: Install test dependencies
-        run: |
-          python -m pip install --upgrade pip wheel
-      - name: Install dependencies
-        run: |
-          pip install ${{ matrix.pip-flags }} ".[dev,test]"
-      - name: Test
+          filter: blob:none
+          fetch-depth: 0
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+        with:
+          cache-dependency-glob: pyproject.toml
+      - name: run tests using hatch
         env:
           MPLBACKEND: agg
           PLATFORM: ${{ matrix.os }}
           DISPLAY: :42
         run: |
           if [ "${{ matrix.python }}" == "3.12" ] && [ -z "${{ matrix.pip-flags }}" ]; then
-            coverage run -m pytest -v --color=yes
+            uvx hatch test --cover --python ${{ matrix.python }}
           else
-            coverage run -m pytest -v --color=yes -m "not openai"
+            uvx hatch test --cover --python ${{ matrix.python }} -m "not openai"
           fi
-      - name: Report coverage
-        run: |
-          coverage report
       - name: Upload coverage reports to Codecov
         uses: codecov/codecov-action@v5
         with:

.pre-commit-config.yaml

@@ -6,16 +6,18 @@ default_stages:
   - pre-push
 minimum_pre_commit_version: 2.16.0
 repos:
-  - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: v4.0.0-alpha.8
+  - repo: https://github.com/biomejs/pre-commit
+    rev: v1.9.4
     hooks:
-      - id: prettier
+      - id: biome-format
+        exclude: ^\.cruft\.json$ # inconsistent indentation with cruft - file never to be modified manually.
   - repo: https://github.com/tox-dev/pyproject-fmt
+    rev: v2.5.1
     rev: v2.5.1
     hooks:
       - id: pyproject-fmt
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.11.4
+    rev: v0.11.2
     hooks:
       - id: ruff
         types_or: [python, pyi, jupyter]

.prettierrc.yaml

@@ -13,6 +13,6 @@
         // Linting and formatting
         "editorconfig.editorconfig",
         "charliermarsh.ruff",
-        "esbenp.prettier-vscode",
+        "biomejs.biome",
     ],
 }

.vscode/extensions.json

@@ -1,5 +1,5 @@
 {
-    "[python][jsonc][yaml]": {
+    "[python][json][jsonc]": {
         "editor.formatOnSave": true,
     },
     "[python]": {
@@ -9,8 +9,8 @@
             "source.organizeImports": "always",
         },
     },
-    "[jsonc][yaml]": {
-        "editor.defaultFormatter": "esbenp.prettier-vscode",
+    "[json][jsonc]": {
+        "editor.defaultFormatter": "biomejs.biome",
     },
     "python.analysis.typeCheckingMode": "basic",
     "python.testing.pytestEnabled": true,

.vscode/settings.json

@@ -0,0 +1,16 @@
+{
+    "$schema": "https://biomejs.dev/schemas/1.9.4/schema.json",
+    "formatter": { "useEditorconfig": true },
+    "overrides": [
+        {
+            "include": ["./.vscode/*.json", "**/*.jsonc"],
+            "json": {
+                "formatter": { "trailingCommas": "all" },
+                "parser": {
+                    "allowComments": true,
+                    "allowTrailingCommas": true,
+                },
+            },
+        },
+    ],
+}