[med-svn] [Git][med-team/nipype][upstream] repair upstream branch
Alexandre Detiste (@detiste-guest)
gitlab at salsa.debian.org
Sat Feb 8 22:04:54 GMT 2025
Alexandre Detiste pushed to branch upstream at Debian Med / nipype
Commits:
210fff47 by Alexandre Detiste at 2025-02-08T23:04:37+01:00
repair upstream branch
- - - - -
2 changed files:
- .github/workflows/tests.yml
- .zenodo.json
Changes:
=====================================
.github/workflows/tests.yml
=====================================
@@ -1,22 +1,11 @@
-name: Stable tests
-
-# This file tests the claimed support range of nipype including
-#
-# * Operating systems: Linux, OSX
-# * Dependencies: minimum requirements, optional requirements
-# * Installation methods: setup.py, sdist, wheel, archive
+name: Tox
on:
push:
- branches:
- - master
- - maint/*
- tags:
- - "*"
+ branches: [ master, main, 'maint/*' ]
+ tags: [ '*' ]
pull_request:
- branches:
- - master
- - maint/*
+ branches: [ master, main, 'maint/*' ]
schedule:
# 8am EST / 9am EDT Mondays
- cron: "0 13 * * 1"
@@ -26,27 +15,28 @@ defaults:
shell: bash
concurrency:
- group: tests-${{ github.ref }}
+ group: ${{ github.workflow }}-${{ github.ref }}
cancel-in-progress: true
-permissions: {}
+permissions:
+ contents: read
+
+env:
+ # Force tox and pytest to use color
+ FORCE_COLOR: true
+
+
jobs:
build:
- permissions:
- contents: read # to fetch code (actions/checkout)
-
runs-on: ubuntu-latest
steps:
- uses: actions/checkout at v4
with:
fetch-depth: 0
- - uses: actions/setup-python at v5
- with:
- python-version: 3
- - run: pip install --upgrade build twine
- - name: Build sdist and wheel
- run: python -m build
- - run: twine check dist/*
+ - name: Install the latest version of uv
+ uses: astral-sh/setup-uv at v4
+ - run: uv build
+ - run: uvx twine check dist/*
- uses: actions/upload-artifact at v4
with:
name: dist
@@ -82,72 +72,52 @@ jobs:
- name: Run tests
run: pytest --doctest-modules -v --pyargs nipype
- stable:
+ test:
# Check each OS, all supported Python, minimum versions and latest releases
- permissions:
- contents: read # to fetch code (actions/checkout)
-
runs-on: ${{ matrix.os }}
strategy:
matrix:
- os: ["ubuntu-22.04"]
- python-version: ["3.9", "3.10", "3.11", "3.12"]
- check: ["test"]
- pip-flags: [""]
- depends: ["REQUIREMENTS"]
- deb-depends: [false]
- nipype-extras: ["doc,tests,profiler"]
+ os: ["ubuntu-latest"]
+ python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
+ dependencies: [none, full, pre]
include:
- - os: ubuntu-22.04
+ - os: ubuntu-latest
python-version: "3.9"
- check: test
- pip-flags: ""
- depends: REQUIREMENTS
- deb-depends: true
- nipype-extras: doc,tests,profiler,duecredit,ssh
- - os: ubuntu-20.04
- python-version: "3.9"
- check: test
- pip-flags: ""
- depends: REQUIREMENTS
- deb-depends: true
- nipype-extras: doc,tests,nipy,profiler,duecredit,ssh
+ dependencies: min
+ exclude:
+ # Skip some intermediate versions for full tests
+ - python-version: "3.10"
+ dependencies: full
+ - python-version: "3.11"
+ dependencies: full
+ # Do not test pre-releases for versions out of SPEC0
+ - python-version: "3.9"
+ dependencies: pre
+ - python-version: "3.10"
+ dependencies: pre
+
env:
- DEPENDS: ${{ matrix.depends }}
- CHECK_TYPE: ${{ matrix.check }}
- EXTRA_PIP_FLAGS: ${{ matrix.pip-flags }}
- INSTALL_DEB_DEPENDENCIES: ${{ matrix.deb-depends }}
- NIPYPE_EXTRAS: ${{ matrix.nipype-extras }}
- INSTALL_TYPE: pip
- CI_SKIP_TEST: 1
+ DEPENDS: ${{ matrix.dependencies }}
steps:
- uses: actions/checkout at v4
+ - name: Install the latest version of uv
+ uses: astral-sh/setup-uv at v4
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python at v5
with:
python-version: ${{ matrix.python-version }}
- name: Display Python version
run: python -c "import sys; print(sys.version)"
- - name: Create virtual environment
- run: tools/ci/create_venv.sh
- - name: Build archive
+ - name: Install tox
run: |
- source tools/ci/build_archive.sh
- echo "ARCHIVE=$ARCHIVE" >> $GITHUB_ENV
- - name: Install Debian dependencies
- run: tools/ci/install_deb_dependencies.sh
- if: ${{ matrix.os == 'ubuntu-latest' }}
- - name: Install dependencies
- run: tools/ci/install_dependencies.sh
- - name: Install Nipype
- run: tools/ci/install.sh
- - name: Run tests
- run: tools/ci/check.sh
- if: ${{ matrix.check != 'skiptests' }}
- - uses: codecov/codecov-action at v4
+ uv tool install tox --with=tox-uv --with=tox-gh-actions
+ - name: Show tox config
+ run: tox c
+ - name: Run tox
+ run: tox -v --exit-and-dump-after 1200
+ - uses: codecov/codecov-action at v5
with:
- file: coverage.xml
token: ${{ secrets.CODECOV_TOKEN }}
if: ${{ always() }}
- name: Upload pytest test results
@@ -160,7 +130,7 @@ jobs:
publish:
runs-on: ubuntu-latest
environment: "Package deployment"
- needs: [stable, test-package]
+ needs: [test, test-package]
if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/')
steps:
- uses: actions/download-artifact at v4
@@ -171,3 +141,21 @@ jobs:
with:
user: __token__
password: ${{ secrets.PYPI_API_TOKEN }}
+
+ checks:
+ runs-on: 'ubuntu-latest'
+ continue-on-error: true
+ strategy:
+ matrix:
+ check: ['specs', 'style']
+
+ steps:
+ - uses: actions/checkout at v4
+ - name: Install the latest version of uv
+ uses: astral-sh/setup-uv at v4
+ - name: Show tox config
+ run: uvx tox c
+ - name: Show tox config (this call)
+ run: uvx tox c -e ${{ matrix.check }}
+ - name: Run check
+ run: uvx tox -e ${{ matrix.check }}
=====================================
.zenodo.json
=====================================
@@ -285,6 +285,11 @@
{
"name": "Mordom, David"
},
+ {
+ "affiliation": "Child Mind Institute",
+ "name": "Cluce, Jon",
+ "orcid": "0000-0001-7590-5806"
+ },
{
"affiliation": "ARAMIS LAB, Brain and Spine Institute (ICM), Paris, France.",
"name": "Guillon, Jérémy",
View it on GitLab: https://salsa.debian.org/med-team/nipype/-/commit/210fff474acb2845857010c224fd2fc3ec9f379d
--
View it on GitLab: https://salsa.debian.org/med-team/nipype/-/commit/210fff474acb2845857010c224fd2fc3ec9f379d
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