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GHA: update actions to use Node.js 20 (#2278)
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* GHA: update actions to use Node.js 20

Fixes this warnings:
> Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/setup-python@v4, actions/checkout@v3, actions/upload-artifact@v3

Closes #2277

* unique artifact names

* [email protected]
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dweindl authored Jan 25, 2024
1 parent 35cd14e commit 854eac5
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Showing 15 changed files with 57 additions and 57 deletions.
6 changes: 3 additions & 3 deletions .github/workflows/deploy_branch.yml
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Expand Up @@ -13,11 +13,11 @@ jobs:

steps:
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v4
uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}

- uses: actions/checkout@v3
- uses: actions/checkout@v4
with:
fetch-depth: 20

Expand All @@ -31,7 +31,7 @@ jobs:
scripts/buildSdist.sh
- name: "Upload artifact: sdist"
uses: actions/upload-artifact@v3
uses: actions/upload-artifact@v4
with:
name: sdist
path: python/sdist/dist/amici-*.gz
4 changes: 2 additions & 2 deletions .github/workflows/deploy_protected.yml
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Expand Up @@ -25,10 +25,10 @@ jobs:

steps:
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v4
uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}
- uses: actions/checkout@v3
- uses: actions/checkout@v4
- run: git archive -o container/amici.tar.gz --format=tar.gz HEAD
- name: Set up QEMU
uses: docker/setup-qemu-action@v2
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4 changes: 2 additions & 2 deletions .github/workflows/deploy_release.yml
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Expand Up @@ -23,11 +23,11 @@ jobs:

steps:
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v4
uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}

- uses: actions/checkout@v3
- uses: actions/checkout@v4
with:
fetch-depth: 20

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8 changes: 4 additions & 4 deletions .github/workflows/test_benchmark_collection_models.yml
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Expand Up @@ -29,11 +29,11 @@ jobs:

steps:
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v4
uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}

- uses: actions/checkout@v3
- uses: actions/checkout@v4
with:
fetch-depth: 20

Expand Down Expand Up @@ -66,9 +66,9 @@ jobs:
&& cd tests/benchmark-models && pytest ./test_petab_benchmark.py
# upload results
- uses: actions/upload-artifact@v3
- uses: actions/upload-artifact@v4
with:
name: computation times
name: computation-times-${{ matrix.python-version }}-${{ matrix.extract_subexpressions }}
path: |
tests/benchmark-models/computation_times.csv
tests/benchmark-models/computation_times.png
8 changes: 4 additions & 4 deletions .github/workflows/test_doc.yml
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Expand Up @@ -24,11 +24,11 @@ jobs:

steps:
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v4
uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}

- uses: actions/checkout@v3
- uses: actions/checkout@v4
- run: git fetch --prune --unshallow

- name: Set up doxygen
Expand All @@ -47,11 +47,11 @@ jobs:

steps:
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v4
uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}

- uses: actions/checkout@v3
- uses: actions/checkout@v4
- run: git fetch --prune --unshallow

- run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
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12 changes: 6 additions & 6 deletions .github/workflows/test_install.yml
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Expand Up @@ -13,11 +13,11 @@ jobs:

steps:
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v4
uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}

- uses: actions/checkout@v3
- uses: actions/checkout@v4
- run: git fetch --prune --unshallow

- run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
Expand Down Expand Up @@ -54,11 +54,11 @@ jobs:

steps:
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v4
uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}

- uses: actions/checkout@v3
- uses: actions/checkout@v4
- run: git fetch --prune --unshallow

- run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
Expand Down Expand Up @@ -87,11 +87,11 @@ jobs:

steps:
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v4
uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}

- uses: actions/checkout@v3
- uses: actions/checkout@v4
- run: git fetch --prune --unshallow

- run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
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2 changes: 1 addition & 1 deletion .github/workflows/test_matlab.yml
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Expand Up @@ -15,7 +15,7 @@ jobs:
runs-on: ubuntu-20.04

steps:
- uses: actions/checkout@v3
- uses: actions/checkout@v4
- run: git fetch --prune --unshallow

- run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
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6 changes: 3 additions & 3 deletions .github/workflows/test_performance.yml
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Expand Up @@ -27,11 +27,11 @@ jobs:

steps:
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v4
uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}

- uses: actions/checkout@v3
- uses: actions/checkout@v4
with:
fetch-depth: 20

Expand Down Expand Up @@ -64,7 +64,7 @@ jobs:
AMICI_IMPORT_NPROCS=2 check_time.sh petab_import python tests/performance/test.py import
- name: "Upload artifact: CS_Signalling_ERBB_RAS_AKT_petab"
uses: actions/upload-artifact@v3
uses: actions/upload-artifact@v4
with:
name: model_performance_test
path: model_performance_test
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6 changes: 3 additions & 3 deletions .github/workflows/test_petab_test_suite.yml
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Expand Up @@ -26,11 +26,11 @@ jobs:

steps:
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v4
uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}

- uses: actions/checkout@v3
- uses: actions/checkout@v4
with:
fetch-depth: 20

Expand Down Expand Up @@ -86,7 +86,7 @@ jobs:
- name: Codecov
if: github.event_name == 'pull_request' || github.repository_owner == 'AMICI-dev'
uses: codecov/[email protected].0
uses: codecov/[email protected].4
with:
token: ${{ secrets.CODECOV_TOKEN }}
file: coverage.xml
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2 changes: 1 addition & 1 deletion .github/workflows/test_pypi.yml
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Expand Up @@ -36,7 +36,7 @@ jobs:
fi
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v4
uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}

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28 changes: 14 additions & 14 deletions .github/workflows/test_python_cplusplus.yml
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Expand Up @@ -19,11 +19,11 @@ jobs:

steps:
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v4
uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}

- uses: actions/checkout@v3
- uses: actions/checkout@v4
- run: git fetch --prune --unshallow

- run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
Expand Down Expand Up @@ -67,7 +67,7 @@ jobs:
- name: Codecov Python
if: github.event_name == 'pull_request' || github.repository_owner == 'AMICI-dev'
uses: codecov/[email protected].0
uses: codecov/[email protected].4
with:
token: ${{ secrets.CODECOV_TOKEN }}
file: build/coverage_py.xml
Expand All @@ -87,7 +87,7 @@ jobs:
- name: Codecov CPP
if: github.event_name == 'pull_request' || github.repository_owner == 'AMICI-dev'
uses: codecov/[email protected].0
uses: codecov/[email protected].4
with:
token: ${{ secrets.CODECOV_TOKEN }}
file: coverage.info
Expand All @@ -114,11 +114,11 @@ jobs:

steps:
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v4
uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}

- uses: actions/checkout@v3
- uses: actions/checkout@v4
- run: git fetch --prune --unshallow

- run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
Expand All @@ -142,7 +142,7 @@ jobs:
- name: Codecov Python
if: github.event_name == 'pull_request' || github.repository_owner == 'AMICI-dev'
uses: codecov/[email protected].0
uses: codecov/[email protected].4
with:
token: ${{ secrets.CODECOV_TOKEN }}
file: build/coverage_py.xml
Expand All @@ -162,7 +162,7 @@ jobs:
- name: Codecov CPP
if: github.event_name == 'pull_request' || github.repository_owner == 'AMICI-dev'
uses: codecov/[email protected].0
uses: codecov/[email protected].4
with:
token: ${{ secrets.CODECOV_TOKEN }}
file: coverage.info
Expand Down Expand Up @@ -190,11 +190,11 @@ jobs:

steps:
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v4
uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}

- uses: actions/checkout@v3
- uses: actions/checkout@v4
- run: git fetch --prune --unshallow

- run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
Expand Down Expand Up @@ -224,11 +224,11 @@ jobs:

steps:
- name: Set up Python
uses: actions/setup-python@v4
uses: actions/setup-python@v5
with:
python-version: 3.9

- uses: actions/checkout@v3
- uses: actions/checkout@v4
- run: git fetch --prune --unshallow

- name: Install dependencies
Expand Down Expand Up @@ -266,11 +266,11 @@ jobs:

steps:
- name: Set up Python
uses: actions/setup-python@v4
uses: actions/setup-python@v5
with:
python-version: 3.9

- uses: actions/checkout@v3
- uses: actions/checkout@v4
- run: git fetch --prune --unshallow

- name: Install dependencies
Expand Down
4 changes: 2 additions & 2 deletions .github/workflows/test_python_ver_matrix.yml
Original file line number Diff line number Diff line change
Expand Up @@ -33,11 +33,11 @@ jobs:
- run: echo "BNGPATH=${AMICI_DIR}/ThirdParty/BioNetGen-2.7.0" >> $GITHUB_ENV

- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v4
uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}

- uses: actions/checkout@v3
- uses: actions/checkout@v4
with:
fetch-depth: 20

Expand Down
10 changes: 5 additions & 5 deletions .github/workflows/test_sbml_semantic_test_suite.yml
Original file line number Diff line number Diff line change
Expand Up @@ -33,11 +33,11 @@ jobs:

steps:
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v4
uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}

- uses: actions/checkout@v3
- uses: actions/checkout@v4
with:
fetch-depth: 1

Expand All @@ -48,14 +48,14 @@ jobs:
- run: AMICI_PARALLEL_COMPILE="" ./scripts/run-SBMLTestsuite.sh ${{ matrix.cases }}

- name: "Upload artifact: SBML semantic test suite results"
uses: actions/upload-artifact@v3
uses: actions/upload-artifact@v4
with:
name: amici-semantic-results
name: amici-semantic-results-${{ matrix.cases }}
path: tests/amici-semantic-results

- name: Codecov SBMLSuite
if: github.event_name == 'pull_request' || github.repository_owner == 'AMICI-dev'
uses: codecov/[email protected].0
uses: codecov/[email protected].4
with:
token: ${{ secrets.CODECOV_TOKEN }}
file: coverage_SBMLSuite.xml
Expand Down
8 changes: 4 additions & 4 deletions .github/workflows/test_valgrind.yml
Original file line number Diff line number Diff line change
Expand Up @@ -25,11 +25,11 @@ jobs:

steps:
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v4
uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}

- uses: actions/checkout@v3
- uses: actions/checkout@v4
- run: git fetch --prune --unshallow

- name: Install apt dependencies
Expand Down Expand Up @@ -64,11 +64,11 @@ jobs:

steps:
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v4
uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}

- uses: actions/checkout@v3
- uses: actions/checkout@v4
- run: git fetch --prune --unshallow

- name: Install apt dependencies
Expand Down
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