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Merge branch 'develop' into diffusionsmap_parallel
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@talagayev
talagayev authored Dec 19, 2024
2 parents 4cef414 + ac145ec commit d89a2d5
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Showing 394 changed files with 10,027 additions and 5,139 deletions.
34 changes: 17 additions & 17 deletions .github/workflows/deploy.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -38,7 +38,7 @@ jobs:
matrix:
buildplat:
- [ubuntu-22.04, manylinux_x86_64, x86_64]
- [macos-12, macosx_*, x86_64]
- [macos-13, macosx_*, x86_64]
- [windows-2019, win_amd64, AMD64]
- [macos-14, macosx_*, arm64]
python: ["cp310", "cp311", "cp312", "cp313"]
Expand All @@ -63,7 +63,7 @@ jobs:
if: |
(github.event_name == 'push' && startsWith(github.ref, 'refs/tags/package')) ||
(github.event_name == 'release' && github.event.action == 'published')
uses: actions/upload-artifact@v4
uses: actions/upload-artifact@v3
with:
path: wheelhouse/*.whl
retention-days: 7
Expand All @@ -88,7 +88,7 @@ jobs:
if: |
(github.event_name == 'push' && startsWith(github.ref, 'refs/tags/package')) ||
(github.event_name == 'release' && github.event.action == 'published')
uses: actions/upload-artifact@v4
uses: actions/upload-artifact@v3
with:
path: package/dist/*.tar.gz
retention-days: 7
Expand All @@ -113,7 +113,7 @@ jobs:
if: |
(github.event_name == 'push' && startsWith(github.ref, 'refs/tags/package')) ||
(github.event_name == 'release' && github.event.action == 'published')
uses: actions/upload-artifact@v4
uses: actions/upload-artifact@v3
with:
path: testsuite/dist/*.tar.gz
retention-days: 7
Expand All @@ -131,18 +131,18 @@ jobs:
runs-on: ubuntu-latest
needs: [build_wheels, build_sdist, build_sdist_tests]
steps:
- uses: actions/download-artifact@v4
- uses: actions/download-artifact@v3
with:
name: artifact
path: dist

- name: move_test_dist
run: |
mkdir -p testsuite/dist
mv dist/MDAnalysisTests-* testsuite/dist
mv dist/mdanalysistests-* testsuite/dist
- name: upload_source_and_wheels
uses: pypa/gh-action-pypi-publish@v1.10.2
uses: pypa/gh-action-pypi-publish@v1.11.0
with:
skip_existing: true
repository_url: https://test.pypi.org/legacy/
Expand All @@ -160,18 +160,18 @@ jobs:
runs-on: ubuntu-latest
needs: [build_wheels, build_sdist, build_sdist_tests]
steps:
- uses: actions/download-artifact@v4
- uses: actions/download-artifact@v3
with:
name: artifact
path: dist

- name: move_test_dist
run: |
mkdir -p testsuite/dist
mv dist/MDAnalysisTests-* testsuite/dist
mv dist/mdanalysistests-* testsuite/dist
- name: upload_tests
uses: pypa/gh-action-pypi-publish@v1.10.2
uses: pypa/gh-action-pypi-publish@v1.11.0
with:
packages_dir: testsuite/dist
skip_existing: true
Expand All @@ -190,18 +190,18 @@ jobs:
runs-on: ubuntu-latest
needs: [build_wheels, build_sdist, build_sdist_tests]
steps:
- uses: actions/download-artifact@v4
- uses: actions/download-artifact@v3
with:
name: artifact
path: dist

- name: move_test_dist
run: |
mkdir -p testsuite/dist
mv dist/MDAnalysisTests-* testsuite/dist
mv dist/mdanalysistests-* testsuite/dist
- name: upload_source_and_wheels
uses: pypa/gh-action-pypi-publish@v1.10.2
uses: pypa/gh-action-pypi-publish@v1.11.0

upload_pypi_mdanalysistests:
if: |
Expand All @@ -216,18 +216,18 @@ jobs:
runs-on: ubuntu-latest
needs: [build_wheels, build_sdist, build_sdist_tests]
steps:
- uses: actions/download-artifact@v4
- uses: actions/download-artifact@v3
with:
name: artifact
path: dist

- name: move_test_dist
run: |
mkdir -p testsuite/dist
mv dist/MDAnalysisTests-* testsuite/dist
mv dist/mdanalysistests-* testsuite/dist
- name: upload_tests
uses: pypa/gh-action-pypi-publish@v1.10.2
uses: pypa/gh-action-pypi-publish@v1.11.0
with:
packages_dir: testsuite/dist

Expand Down Expand Up @@ -256,7 +256,7 @@ jobs:
- uses: actions/checkout@v4

- name: setup_micromamba
uses: mamba-org/setup-micromamba@v1
uses: mamba-org/setup-micromamba@v2
with:
environment-name: mda
create-args: >-
Expand Down
8 changes: 4 additions & 4 deletions .github/workflows/gh-ci-cron.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -104,7 +104,7 @@ jobs:
os-type: "ubuntu"

- name: setup_micromamba
uses: mamba-org/setup-micromamba@v1
uses: mamba-org/setup-micromamba@v2
with:
environment-name: mda
create-args: >-
Expand Down Expand Up @@ -146,7 +146,7 @@ jobs:
strategy:
fail-fast: false
matrix:
os: [ubuntu-20.04, macos-12]
os: [ubuntu-20.04, macos-13]

steps:
- uses: actions/checkout@v4
Expand All @@ -157,7 +157,7 @@ jobs:
os-type: ${{ matrix.os }}

- name: setup_micromamba
uses: mamba-org/setup-micromamba@v1
uses: mamba-org/setup-micromamba@v2
with:
environment-name: mda
create-args: >-
Expand Down Expand Up @@ -249,7 +249,7 @@ jobs:
os-type: ${{ matrix.os }}

- name: setup_micromamba
uses: mamba-org/setup-micromamba@v1
uses: mamba-org/setup-micromamba@v2
with:
environment-name: mda
create-args: >-
Expand Down
6 changes: 3 additions & 3 deletions .github/workflows/gh-ci.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -38,7 +38,7 @@ jobs:
full-deps: false
codecov: true
- name: macOS_monterey_py311
os: macOS-12
os: macos-13
python-version: "3.12"
full-deps: true
codecov: true
Expand Down Expand Up @@ -72,7 +72,7 @@ jobs:
os-type: ${{ matrix.os }}

- name: setup_micromamba
uses: mamba-org/setup-micromamba@v1
uses: mamba-org/setup-micromamba@v2
with:
environment-name: mda
create-args: >-
Expand Down Expand Up @@ -150,7 +150,7 @@ jobs:
- uses: actions/checkout@v4

- name: setup_micromamba
uses: mamba-org/setup-micromamba@v1
uses: mamba-org/setup-micromamba@v2
with:
environment-name: mda
create-args: >-
Expand Down
2 changes: 1 addition & 1 deletion .github/workflows/linters.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -76,7 +76,7 @@ jobs:
- uses: actions/checkout@v4

- name: setup_micromamba
uses: mamba-org/setup-micromamba@v1
uses: mamba-org/setup-micromamba@v2
with:
environment-name: mda
create-args: >-
Expand Down
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