Merge pull request #246 from scverse/pr-240

Update to template 0.6.0

Author: PauBadiaM

.cruft.json

@@ -1,7 +1,7 @@
 {
   "template": "https://github.com/scverse/cookiecutter-scverse",
-  "commit": "5842d5cb8510e1d4a037a8f772630d51ec86de96",
-  "checkout": null,
+  "commit": "d383d94fadff9e4e6fdb59d77c68cb900d7cedec",
+  "checkout": "v0.6.0",
   "context": {
     "cookiecutter": {
       "project_name": "decoupler",
@@ -36,7 +36,7 @@
         "trim_blocks": true
       },
       "_template": "https://github.com/scverse/cookiecutter-scverse",
-      "_commit": "5842d5cb8510e1d4a037a8f772630d51ec86de96"
+      "_commit": "d383d94fadff9e4e6fdb59d77c68cb900d7cedec"
     }
   },
   "directory": null

.github/workflows/test.yaml

@@ -43,7 +43,7 @@ jobs:
                 | {
                     name: .key,
                     label: (if (.key | contains("pre")) then .key + " (PRE-RELEASE DEPENDENCIES)" else .key end),
-                    python: .value.python | sub("3[.]13"; "3.13.3"),  # https://github.com/numba/numba/issues/10101
+                    python: .value.python
                   }
               )')
           echo "envs=${ENVS_JSON}" | tee $GITHUB_OUTPUT
@@ -78,14 +78,15 @@ jobs:
           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: uvx hatch run ${{ matrix.env.name }}:coverage xml
+        run: |
+          # 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@v4
-        with:
-          token: ${{ secrets.CODECOV_TOKEN }}
-
+        uses: codecov/codecov-action@v5
 
   # 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

@@ -14,10 +14,8 @@ __pycache__/
 # Tests and coverage
 /data/
 /node_modules/
+/.coverage*
 
 # docs
 /docs/generated/
 /docs/_build/
-
-# jupyter
-.ipynb_checkpoints/

.pre-commit-config.yaml

@@ -7,18 +7,18 @@ default_stages:
 minimum_pre_commit_version: 2.16.0
 repos:
   - repo: https://github.com/biomejs/pre-commit
-    rev: v2.3.2
+    rev: v2.2.4
     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: v2.11.0
+    rev: v2.6.0
     hooks:
       - id: pyproject-fmt
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.14.3
+    rev: v0.13.2
     hooks:
-      - id: ruff
+      - id: ruff-check
         types_or: [python, pyi, jupyter]
         args: [--fix, --exit-non-zero-on-fix]
       - id: ruff-format
@@ -36,19 +36,3 @@ repos:
       # Check that there are no merge conflicts (could be generated by template sync)
       - id: check-merge-conflict
         args: [--assume-in-merge]
-  - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.18.2
-    hooks:
-      - id: mypy
-        args: [--no-strict-optional, --ignore-missing-imports]
-        additional_dependencies:
-          ["types-setuptools", "types-requests", "types-attrs"]
-  - repo: local
-    hooks:
-      - id: forbid-to-commit
-        name: Don't commit rej files
-        entry: |
-          Cannot commit .rej files. These indicate merge conflicts that arise during automated template updates.
-          Fix the merge conflicts manually and remove the .rej files.
-        language: fail
-        files: '.*\.rej$'

.readthedocs.yaml

@@ -1,18 +1,18 @@
+# https://docs.readthedocs.io/en/stable/config-file/v2.html
 version: 2
 build:
   os: ubuntu-24.04
   tools:
-    python: "3.13"
+    python: "3.12"
   jobs:
     create_environment:
       - asdf plugin add uv
       - asdf install uv latest
       - asdf global uv latest
-      - uv venv
-      - uv pip install .[doc,full]
     build:
       html:
-        - UV_LINK_MODE=copy uv run sphinx-build -T -W -b html docs $READTHEDOCS_OUTPUT/html
+        - uvx hatch run docs:build
+        - mv docs/_build $READTHEDOCS_OUTPUT
 
 submodules:
-    include: all
+  include: all

README.md

@@ -1,6 +1,5 @@
 # decoupler - Ensemble of methods to infer enrichment scores
-<img src="https://raw.githubusercontent.com/scverse/decoupler/refs/heads/2.0.8/docs/_static/images/logo.svg" align="right" width="120" class="no-scaled-link" />
-
+<img src="https://raw.githubusercontent.com/scverse/decoupler/refs/heads/main/docs/_static/images/logo.svg" align="right" width="120" class="no-scaled-link" />
 
 [![Tests][badge-tests]][tests]
 [![Documentation][badge-docs]][documentation]

biome.jsonc

@@ -1,9 +1,10 @@
 {
-    "$schema": "https://biomejs.dev/schemas/1.9.4/schema.json",
+    "$schema": "https://biomejs.dev/schemas/2.2.0/schema.json",
+    "vcs": { "enabled": true, "clientKind": "git", "useIgnoreFile": true },
     "formatter": { "useEditorconfig": true },
     "overrides": [
         {
-            "include": ["./.vscode/*.json", "**/*.jsonc"],
+            "includes": ["./.vscode/*.json", "**/*.jsonc"],
             "json": {
                 "formatter": { "trailingCommas": "all" },
                 "parser": {

docs/conf.py

@@ -21,7 +21,7 @@
 info = metadata("decoupler")
 project_name = info["Name"]
 author = info["Author"]
-copyright = f"{datetime.now():%Y}, scverse"
+copyright = f"{datetime.now():%Y}, scverse."
 version = info["Version"]
 urls = dict(pu.split(", ") for pu in info.get_all("Project-URL"))
 repository_url = urls["Source"]
@@ -114,6 +114,7 @@
 html_theme = "sphinx_book_theme"
 html_static_path = ["_static"]
 html_css_files = ["css/custom.css"]
+
 html_title = project_name
 html_logo = "_static/images/logo.png"
 html_favicon = "_static/images/logo.png"
@@ -127,7 +128,7 @@
 
 pygments_style = "default"
 
-nitpick_ignore: list = [
+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"),

pyproject.toml

@@ -21,7 +21,6 @@ classifiers = [
   "Programming Language :: Python :: 3.11",
   "Programming Language :: Python :: 3.12",
   "Programming Language :: Python :: 3.13",
-  "Programming Language :: Python :: 3.14",
 ]
 dependencies = [
   "adjusttext",
@@ -47,7 +46,7 @@ optional-dependencies.doc = [
   "pandas",
   # Until pybtex >0.24.0 releases: https://bitbucket.org/pybtex-devs/pybtex/issues/169/
   "setuptools",
-  "sphinx>=4",
+  "sphinx>=8.1",
   "sphinx-autodoc-typehints",
   "sphinx-book-theme>=1",
   "sphinx-copybutton",
@@ -59,17 +58,20 @@ optional-dependencies.full = [
   "dcor",
   "igraph",
   "ipywidgets",
+  "pydeseq2",
+  "scanpy",
   "xgboost",
 ]
 optional-dependencies.test = [
-  "coverage",
+  "coverage>=7.10",
   "dcor",
   "gseapy",
   "igraph",
   "ipywidgets",
   "memory-profiler",
   "pydeseq2",
   "pytest",
+  "pytest-cov",      # For VS Code’s coverage functionality
   "scanpy",
   "statsmodels",
   "xgboost",
@@ -85,14 +87,29 @@ features = [ "dev" ]
 
 [tool.hatch.envs.docs]
 features = [ "doc" ]
-scripts.build = "sphinx-build -M html docs docs/_build {args}"
+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" ]
+
+# Test the newest supported Python version also with pre-release deps
+[[tool.hatch.envs.hatch-test.matrix]]
+deps = [ "pre" ]
+python = [ "3.13" ]
+
 [tool.hatch.envs.hatch-test]
-features = [ "test" ]
+features = [ "dev", "test" ]
+
+[tool.hatch.envs.hatch-test.overrides]
+# If the matrix variable `deps` is set to "pre",
+# set the environment variable `UV_PRERELEASE` to "allow".
+matrix.deps.env-vars = [
+  { key = "UV_PRERELEASE", value = "allow", if = [ "pre" ] },
+]
 
 [tool.ruff]
 line-length = 120
@@ -143,6 +160,7 @@ addopts = [
 
 [tool.coverage.run]
 source = [ "decoupler" ]
+patch = [ "subprocess" ]
 omit = [
   "**/test_*.py",
 ]