Merge pull request #289 from scverse/template-v0.7.0

Update scverse template to v0.7.0

Author: PauBadiaM

.cruft.json

@@ -1,7 +1,7 @@
 {
   "template": "https://github.com/scverse/cookiecutter-scverse",
-  "commit": "d383d94fadff9e4e6fdb59d77c68cb900d7cedec",
-  "checkout": "v0.6.0",
+  "commit": "6ff5b92b5d44ea6d8a88e47538475718d467db95",
+  "checkout": "v0.7.0",
   "context": {
     "cookiecutter": {
       "project_name": "decoupler",

.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:

.github/ISSUE_TEMPLATE/feature_request.yml

@@ -1,6 +1,6 @@
 name: Feature request
 description: Propose a new feature for decoupler
-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/notebooks.yaml

@@ -37,7 +37,7 @@ jobs:
                     ]
 
         steps:
-            - uses: actions/checkout@v4
+            - uses: actions/checkout@v5
               with:
                 filter: blob:none
                 fetch-depth: 0
@@ -47,13 +47,11 @@ jobs:
               with:
                   python-version: "3.13"
             - name: Install uv
-              uses: astral-sh/setup-uv@v6
-              with:
-                enable-cache: true
-                cache-dependency-glob: pyproject.toml
+              uses: astral-sh/setup-uv@v7
             - name: Install dependencies
               run: |
-                  uv pip install --system ${{ matrix.pip-flags }} ".[dev,test]"
+                  uv pip install --system .
+                  uv pip install --system --group dev --group test
                   uv pip install --system nbconvert ipykernel
             - name: Run ${{ matrix.notebook }} Notebook
               run: jupyter nbconvert --to notebook --execute ${{ env.NOTEBOOK_PATH }}/${{ matrix.notebook }}

.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

@@ -12,10 +12,8 @@ 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}
+permissions:
+  id-token: write
 
 jobs:
   # Get the test environment from hatch as defined in pyproject.toml.
@@ -27,13 +25,14 @@ jobs:
     runs-on: ubuntu-latest
     outputs:
       envs: ${{ steps.get-envs.outputs.envs }}
+      allowed-failures: ${{ steps.get-envs.outputs.allowed-failures }}
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           filter: blob:none
           fetch-depth: 0
       - name: Install uv
-        uses: astral-sh/setup-uv@v5
+        uses: astral-sh/setup-uv@v7
       - name: Get test environments
         id: get-envs
         run: |
@@ -47,6 +46,8 @@ jobs:
                   }
               )')
           echo "envs=${ENVS_JSON}" | tee $GITHUB_OUTPUT
+          ALLOWED=$(echo "${ENVS_JSON}" | jq -c 'map(select(.name | contains("pre")) | .name)')
+          echo "allowed-failures=${ALLOWED}" | tee -a $GITHUB_OUTPUT
 
   # Run tests through hatch. Spawns a separate runner for each environment defined in the hatch matrix obtained above.
   test:
@@ -60,17 +61,17 @@ jobs:
 
     name: ${{ matrix.env.label }}
     runs-on: ${{ matrix.os }}
+    continue-on-error: ${{ contains(matrix.env.name, 'pre') }}
 
     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
@@ -87,6 +88,9 @@ jobs:
           uvx hatch run ${{ matrix.env.name }}:coverage xml # create report for upload
       - name: Upload coverage
         uses: codecov/codecov-action@v5
+        with:
+          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.
@@ -100,4 +104,5 @@ jobs:
     steps:
         - uses: re-actors/alls-green@release/v1
           with:
+            allowed-failures: ${{ needs.get-environments.outputs.allowed-failures }}
             jobs: ${{ toJSON(needs) }}

.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

@@ -5,11 +5,14 @@
 # https://www.sphinx-doc.org/en/master/usage/configuration.html
 
 # -- 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
 sys.path.insert(0, str(HERE / "extensions"))
 
@@ -19,7 +22,7 @@
 # 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("decoupler")
-project_name = info["Name"]
+project = info["Name"]
 author = info["Author"]
 copyright = f"{datetime.now():%Y}, scverse."
 version = info["Version"]
@@ -37,7 +40,7 @@
 html_context = {
     "display_github": True,  # Integrate GitHub
     "github_user": "scverse",
-    "github_repo": project_name,
+    "github_repo": project,
     "github_version": "main",
     "conf_py_path": "/docs/",
 }
@@ -56,7 +59,7 @@
     "sphinxcontrib.bibtex",
     "sphinx_autodoc_typehints",
     "sphinx_tabs.tabs",
-    "sphinx.ext.mathjax",
+    "sphinxcontrib.katex",
     "IPython.sphinxext.ipython_console_highlighting",
     "sphinxext.opengraph",
     *[p.stem for p in (HERE / "extensions").glob("*.py")],
@@ -92,7 +95,8 @@
 }
 
 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 +119,7 @@
 html_static_path = ["_static"]
 html_css_files = ["css/custom.css"]
 
-html_title = project_name
+html_title = project
 html_logo = "_static/images/logo.png"
 html_favicon = "_static/images/logo.png"
 
@@ -127,9 +131,11 @@
 }
 
 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,
     # you can add an exception to this list.
     #     ("py:class", "igraph.Graph"),
+    ("py:class", "pandas.core.frame.DataFrame"),
 ]

pyproject.toml

@@ -14,10 +14,9 @@ maintainers = [
 authors = [
   { name = "Pau Badia i Mompel" },
 ]
-requires-python = ">=3.10"
+requires-python = ">=3.11"
 classifiers = [
   "Programming Language :: Python :: 3 :: Only",
-  "Programming Language :: Python :: 3.10",
   "Programming Language :: Python :: 3.11",
   "Programming Language :: Python :: 3.12",
   "Programming Language :: Python :: 3.13",
@@ -35,75 +34,75 @@ dependencies = [
   "session-info2",
   "tqdm",
 ]
-optional-dependencies.dev = [
+# https://docs.pypi.org/project_metadata/#project-urls
+urls.Documentation = "https://decoupler.readthedocs.io/"
+urls.Homepage = "https://github.com/scverse/decoupler"
+urls.Source = "https://github.com/scverse/decoupler"
+
+[dependency-groups]
+dev = [
   "pre-commit",
   "twine>=4.0.2",
 ]
-optional-dependencies.doc = [
-  "docutils>=0.8,!=0.18.*,!=0.19.*",
+test = [
+  "coverage>=7.10",
+  "dcor",
+  "gseapy",
+  "igraph",
+  "ipywidgets",
+  "memory-profiler",
+  "pydeseq2",
+  "pytest",
+  "pytest-cov",      # For VS Code’s coverage functionality
+  "scanpy",
+  "statsmodels",
+  "xgboost",
+]
+doc = [
   "ipykernel",
   "ipython",
   "myst-nb>=1.1",
   "pandas",
-  # Until pybtex >0.24.0 releases: https://bitbucket.org/pybtex-devs/pybtex/issues/169/
-  "setuptools",
   "sphinx>=8.1",
   "sphinx-autodoc-typehints",
   "sphinx-book-theme>=1",
   "sphinx-copybutton",
   "sphinx-tabs",
   "sphinxcontrib-bibtex>=1",
+  "sphinxcontrib-katex",
   "sphinxext-opengraph",
 ]
-optional-dependencies.full = [
+full = [
   "dcor",
   "igraph",
   "ipywidgets",
   "pydeseq2",
   "scanpy",
   "xgboost",
 ]
-optional-dependencies.test = [
-  "coverage>=7.10",
-  "dcor",
-  "gseapy",
-  "igraph",
-  "ipywidgets",
-  "memory-profiler",
-  "pydeseq2",
-  "pytest",
-  "pytest-cov",      # For VS Code’s coverage functionality
-  "scanpy",
-  "statsmodels",
-  "xgboost",
-]
-# https://docs.pypi.org/project_metadata/#project-urls
-urls.Documentation = "https://decoupler.readthedocs.io/"
-urls.Homepage = "https://github.com/scverse/decoupler"
-urls.Source = "https://github.com/scverse/decoupler"
 
 [tool.hatch.envs.default]
 installer = "uv"
-features = [ "dev" ]
+dependency-groups = [ "dev" ]
 
 [tool.hatch.envs.docs]
-features = [ "doc" ]
+dependency-groups = [ "doc" ]
 scripts.build = "sphinx-build -M html docs docs/_build -W {args}"
 scripts.open = "python -m webbrowser -t docs/_build/html/index.html"
 scripts.clean = "git clean -fdX -- {args:docs}"
 
 # Test the lowest and highest supported Python versions with normal deps
 [[tool.hatch.envs.hatch-test.matrix]]
 deps = [ "stable" ]
-python = [ "3.10", "3.13" ]
+python = [ "3.11", "3.14" ]
 
 # Test the newest supported Python version also with pre-release deps
 [[tool.hatch.envs.hatch-test.matrix]]
 deps = [ "pre" ]
-python = [ "3.13" ]
+python = [ "3.14" ]
 
 [tool.hatch.envs.hatch-test]
-features = [ "dev", "test" ]
+dependency-groups = [ "dev", "test" ]
 
 [tool.hatch.envs.hatch-test.overrides]
 # If the matrix variable `deps` is set to "pre",
@@ -152,9 +151,9 @@ lint.per-file-ignores."docs/*" = [ "I" ]
 lint.per-file-ignores."tests/*" = [ "D" ]
 lint.pydocstyle.convention = "numpy"
 
-[tool.pytest.ini_options]
+[tool.pytest]
+strict = true
 testpaths = [ "tests" ]
-xfail_strict = true
 addopts = [
   "--import-mode=importlib", # allow using test files with same name
 ]