Merge branch 'scverse-bot-template-update-v2-carmonalab-pyucell-v0.7.0'

Author: mass-a

.cruft.json

@@ -1,7 +1,7 @@
 {
   "template": "https://github.com/scverse/cookiecutter-scverse",
-  "commit": "9d275b8a25284cfe0b0a592374e5a75426128081",
-  "checkout": null,
+  "commit": "6ff5b92b5d44ea6d8a88e47538475718d467db95",
+  "checkout": "v0.7.0",
   "context": {
     "cookiecutter": {
       "project_name": "pyUCell",
@@ -36,7 +36,8 @@
         "trim_blocks": true
       },
       "_template": "https://github.com/scverse/cookiecutter-scverse",
-      "_commit": "9d275b8a25284cfe0b0a592374e5a75426128081"
+      "_commit": "6ff5b92b5d44ea6d8a88e47538475718d467db95"
+
     }
   },
   "directory": null

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -1,6 +1,6 @@
 name: Bug report
 description: Report something that is broken or incorrect
-labels: bug
+type: Bug
 body:
   - type: markdown
     attributes:
@@ -9,8 +9,7 @@ body:
         detailing how to provide the necessary information for us to reproduce your bug. In brief:
           * Please provide exact steps how to reproduce the bug in a clean Python environment.
           * In case it's not clear what's causing this bug, please provide the data or the data generation procedure.
-          * Sometimes it is not possible to share the data, but usually it is possible to replicate problems on publicly
-            available datasets or to share a subset of your data.
+          * Replicate problems on public datasets or share data subsets when full sharing isn't possible.
 
   - type: textarea
     id: report

.github/ISSUE_TEMPLATE/feature_request.yml

@@ -1,6 +1,6 @@
 name: Feature request
 description: Propose a new feature for pyUCell
-labels: enhancement
+type: Enhancement
 body:
   - type: textarea
     id: description

.github/workflows/build.yaml

@@ -10,23 +10,16 @@ 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
+      - uses: actions/checkout@v5
         with:
           filter: blob:none
           fetch-depth: 0
       - name: Install uv
-        uses: astral-sh/setup-uv@v5
-        with:
-          cache-dependency-glob: pyproject.toml
+        uses: astral-sh/setup-uv@v7
       - name: Build package
         run: uv build
       - name: Check package

.github/workflows/release.yaml

@@ -4,11 +4,6 @@ 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:
@@ -20,14 +15,12 @@ jobs:
     permissions:
       id-token: write # IMPORTANT: this permission is mandatory for trusted publishing
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           filter: blob:none
           fetch-depth: 0
       - name: Install uv
-        uses: astral-sh/setup-uv@v5
-        with:
-          cache-dependency-glob: pyproject.toml
+        uses: astral-sh/setup-uv@v7
       - name: Build package
         run: uv build
       - name: Publish package distributions to PyPI

.github/workflows/test.yaml

@@ -12,11 +12,6 @@ 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:
   # Get the test environment from hatch as defined in pyproject.toml.
   # This ensures that the pyproject.toml is the single point of truth for test definitions and the same tests are
@@ -28,12 +23,12 @@ jobs:
     outputs:
       envs: ${{ steps.get-envs.outputs.envs }}
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           filter: blob:none
           fetch-depth: 0
       - name: Install uv
-        uses: astral-sh/setup-uv@v5
+        uses: astral-sh/setup-uv@v7
       - name: Get test environments
         id: get-envs
         run: |
@@ -51,6 +46,8 @@ jobs:
   # Run tests through hatch. Spawns a separate runner for each environment defined in the hatch matrix obtained above.
   test:
     needs: get-environments
+    permissions:
+       id-token: write  # for codecov OIDC
 
     strategy:
       fail-fast: false
@@ -60,35 +57,38 @@ jobs:
 
     name: ${{ matrix.env.label }}
     runs-on: ${{ matrix.os }}
+    continue-on-error: ${{ contains(matrix.env.name, 'pre') }}  # make "all-green" pass even if pre-release job fails
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           filter: blob:none
           fetch-depth: 0
       - name: Install uv
-        uses: astral-sh/setup-uv@v5
+        uses: astral-sh/setup-uv@v7
         with:
           python-version: ${{ matrix.env.python }}
-          cache-dependency-glob: pyproject.toml
       - name: create hatch environment
         run: uvx hatch env create ${{ matrix.env.name }}
       - name: run tests using hatch
         env:
           MPLBACKEND: agg
           PLATFORM: ${{ matrix.os }}
           DISPLAY: :42
-        run: uvx hatch run ${{ matrix.env.name }}:run-cov
+        run: uvx hatch run ${{ matrix.env.name }}:run-cov -v --color=yes -n auto
       - name: generate coverage report
         run: |
-          # See https://coverage.readthedocs.io/en/latest/config.html#config-run-parallel
+          # See https://coverage.readthedocs.io/en/latest/config.html#run-patch
           test -f .coverage || uvx hatch run ${{ matrix.env.name }}:cov-combine
           uvx hatch run ${{ matrix.env.name }}:cov-report   # report visibly
           uvx hatch run ${{ matrix.env.name }}:coverage xml # create report for upload
       - name: Upload coverage
         uses: codecov/codecov-action@v5
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
+          fail_ci_if_error: true
+          use_oidc: true
+
 
   # Check that all tests defined above pass. This makes it easy to set a single "required" test in branch
   # protection instead of having to update it frequently. See https://github.com/re-actors/alls-green#why.

.gitignore

@@ -14,6 +14,7 @@ __pycache__/
 # Tests and coverage
 /data/
 /node_modules/
+/.coverage*
 
 # docs
 /docs/generated/

.pre-commit-config.yaml

@@ -9,16 +9,16 @@ ci:
   autofix_prs: true
 repos:
   - repo: https://github.com/biomejs/pre-commit
-    rev: v2.2.4
+    rev: v2.3.10
     hooks:
       - 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: v2.6.0
+    rev: v2.11.1
     hooks:
       - id: pyproject-fmt
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.13.0
+    rev: v0.14.10
     hooks:
       - id: ruff-check
         types_or: [python, pyi, jupyter]

.readthedocs.yaml

@@ -3,7 +3,8 @@ version: 2
 build:
   os: ubuntu-24.04
   tools:
-    python: "3.12"
+    python: "3.13"
+    nodejs: latest
   jobs:
     create_environment:
       - asdf plugin add uv

docs/conf.py

@@ -6,21 +6,26 @@
 
 # -- Path setup --------------------------------------------------------------
 
+import shutil
 import sys
 from datetime import datetime
 from importlib.metadata import metadata
 from pathlib import Path
 
+from sphinxcontrib import katex
+
 HERE = Path(__file__).parent
 SRC = HERE.parent / "src"
-sys.path.insert(0, str(SRC)) 
+sys.path.insert(0, str(SRC))
 sys.path.insert(0, str(HERE / "extensions"))
 
 # -- Project information -----------------------------------------------------
 
 # NOTE: If you installed your project in editable mode, this might be stale.
 #       If this is the case, reinstall it to refresh the metadata
-info = metadata("pyucell")
+
+info = metadata("pyUCell")
+project = "pyucell"
 project_name = "pyucell"
 author = "Massimo Andreatta"
 copyright = f"{datetime.now():%Y}, {author}."
@@ -56,9 +61,9 @@
     "sphinx.ext.autosummary",
     "sphinx.ext.napoleon",
     "sphinxcontrib.bibtex",
+    "sphinxcontrib.katex",
     "sphinx_autodoc_typehints",
     "sphinx_tabs.tabs",
-    "sphinx.ext.mathjax",
     "IPython.sphinxext.ipython_console_highlighting",
     "sphinxext.opengraph",
     *[p.stem for p in (HERE / "extensions").glob("*.py")],
@@ -94,7 +99,8 @@
 }
 
 intersphinx_mapping = {
-    "python": ("https://docs.python.org/3", None),
+    # TODO: replace `3.13` with `3` once ReadTheDocs supports building with Python 3.14
+    "python": ("https://docs.python.org/3.13", None),
     "anndata": ("https://anndata.readthedocs.io/en/stable/", None),
     "scanpy": ("https://scanpy.readthedocs.io/en/stable/", None),
     "numpy": ("https://numpy.org/doc/stable/", None),
@@ -115,7 +121,7 @@
 html_static_path = ["_static"]
 html_css_files = ["css/custom.css"]
 
-html_title = project_name
+html_title = project
 
 html_theme_options = {
     "repository_url": repository_url,
@@ -125,6 +131,7 @@
 }
 
 pygments_style = "default"
+katex_prerender = shutil.which(katex.NODEJS_BINARY) is not None
 
 nitpick_ignore = [
     # If building the documentation fails because of a missing link that is outside your control,