CSOgroup · scverse-bot · Apr 2, 2025 · Jun 24, 2025 · Jun 24, 2025
diff --git a/.cruft.json b/.cruft.json
@@ -1,7 +1,7 @@
 {
   "template": "https://github.com/scverse/cookiecutter-scverse",
-  "commit": "384fc74318d2afc7ad1d5bda7d0fb3dfbe2fea28",
-  "checkout": null,
+  "commit": "94ef9fb6f9ad8cfe65a3d9575679c03c80c49cd1",
+  "checkout": "v0.5.0",
   "context": {
     "cookiecutter": {
       "project_name": "torchgmm",
@@ -10,19 +10,33 @@
       "author_full_name": "Marco Varrone",
       "author_email": "[email protected]",
       "github_user": "marcovarrone",
-      "project_repo": "https://github.com/CSOgroup/torchgmm",
+      "github_repo": "torchgmm",
       "license": "MIT License",
+      "ide_integration": true,
       "_copy_without_render": [
         ".github/workflows/build.yaml",
         ".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

diff --git a/.editorconfig b/.editorconfig
@@ -8,10 +8,7 @@ charset = utf-8
 trim_trailing_whitespace = true
 insert_final_newline = true
 
-[*.{yml,yaml}]
-indent_size = 2
-
-[.cruft.json]
+[{*.{yml,yaml,toml},.cruft.json}]
 indent_size = 2
 
 [Makefile]

diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.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
diff --git a/.github/workflows/build.yaml b/.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@v3
-      - name: Set up Python 3.10
-        uses: actions/setup-python@v4
+      - uses: actions/checkout@v4
+        with:
+          filter: blob:none
+          fetch-depth: 0
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
         with:
-          python-version: "3.10"
-          cache: "pip"
-          cache-dependency-path: "**/pyproject.toml"
-      - name: Install build dependencies
-        run: python -m pip install --upgrade pip wheel twine build
+          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
diff --git a/.github/workflows/release.yaml b/.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@v4
+      - 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
diff --git a/.github/workflows/test.yaml b/.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
@@ -41,29 +43,19 @@ jobs:
       PYTHON: ${{ matrix.python }}
 
     steps:
-      - uses: actions/checkout@v3
-      - name: Set up Python ${{ matrix.python }}
-        uses: actions/setup-python@v4
+      - uses: actions/checkout@v4
         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: |
-          coverage run -m pytest -v --color=yes
-      - name: Report coverage
-        run: |
-          coverage report
+        run: uvx hatch test --cover --python ${{ matrix.python }}
       - name: Upload coverage
-        uses: codecov/codecov-action@v3
+        uses: codecov/codecov-action@v4
diff --git a/.gitignore b/.gitignore
@@ -6,24 +6,15 @@ buck-out/
 # Compiled files
 .venv/
 __pycache__/
-.mypy_cache/
-.ruff_cache/
+.*cache/
 
 # Distribution / packaging
-/build/
 /dist/
-/*.egg-info/
 
 # Tests and coverage
-/.pytest_cache/
-/.cache/
 /data/
 /node_modules/
 
 # docs
 /docs/generated/
 /docs/_build/
-
-# IDEs
-/.idea/
-/.vscode/
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -6,12 +6,17 @@ 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
+    hooks:
+      - id: pyproject-fmt
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.12.0
+    rev: v0.11.2
     hooks:
       - id: ruff
         types_or: [python, pyi, jupyter]

diff --git a/.vscode/extensions.json b/.vscode/extensions.json
@@ -0,0 +1,18 @@
+{
+    "recommendations": [
+        // GitHub integration
+        "github.vscode-github-actions",
+        "github.vscode-pull-request-github",
+        // Language support
+        "ms-python.python",
+        "ms-python.vscode-pylance",
+        "ms-toolsai.jupyter",
+        "tamasfe.even-better-toml",
+        // Dependency management
+        "ninoseki.vscode-mogami",
+        // Linting and formatting
+        "editorconfig.editorconfig",
+        "charliermarsh.ruff",
+        "biomejs.biome",
+    ],
+}