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Fix CI (#19)
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* CI to exclude python 3.12 + the latest release of MDAnalysis
* go py3.10+
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IAlibay authored Apr 29, 2024
1 parent 5699b0b commit dac4cd6
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42 changes: 14 additions & 28 deletions .github/workflows/gh-ci.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -23,31 +23,21 @@ defaults:
shell: bash -l {0}

jobs:
environment-config:
runs-on: ubuntu-latest
outputs:
stable-python-version: ${{ steps.get-compatible-python.outputs.stable-python }}
python-matrix: ${{ steps.get-compatible-python.outputs.python-versions }}
steps:
- uses: actions/setup-python@v4
with:
python-version: "3.11"

- id: get-compatible-python
uses: MDAnalysis/mdanalysis-compatible-python@main
with:
release: "latest"

main-tests:
if: "github.repository == 'MDAnalysis/pathsimanalysis'"
needs: environment-config
runs-on: ${{ matrix.os }}
strategy:
fail-fast: false
matrix:
os: [macOS-latest, ubuntu-latest, windows-latest]
python-version: ${{ fromJSON(needs.environment-config.outputs.python-matrix) }}
python-version: ["3.10", "3.11", "3.12"]
mdanalysis-version: ["latest", "develop"]
# Manually exclude any combinations of the test matrix that can't be run
exclude:
# The latest release of MDAnalysis only supports up to Python 3.11
# so we exclude 3.12 from the test matrix (issue #20)
- python-version: "3.12"
mdanalysis-version: "latest"

steps:
- uses: actions/checkout@v4
Expand All @@ -58,10 +48,9 @@ jobs:
df -h
ulimit -a
# More info on options: https://github.com/conda-incubator/setup-miniconda
- name: Install conda dependencies
uses: conda-incubator/setup-miniconda@v2
uses: conda-incubator/setup-miniconda@v3
with:
python-version: ${{ matrix.python-version }}
environment-file: devtools/conda-envs/test_env.yaml
Expand All @@ -77,7 +66,6 @@ jobs:
auto-activate-base: false
show-channel-urls: true


- name: Install MDAnalysis version
uses: MDAnalysis/install-mdanalysis@main
with:
Expand All @@ -100,23 +88,22 @@ jobs:
conda info
conda list
- name: Run tests
run: |
pytest -n 2 -v --cov=pathsimanalysis --cov-report=xml --color=yes pathsimanalysis/tests/
pytest -n auto -v --cov=pathsimanalysis --cov-report=xml --color=yes pathsimanalysis/tests/
- name: codecov
if: github.repository == 'MDAnalysis/pathsimanalysis' && github.event_name != 'schedule'
uses: codecov/codecov-action@v3
uses: codecov/codecov-action@v4
with:
file: coverage.xml
name: codecov-${{ matrix.os }}-py${{ matrix.python-version }}
token: ${{ secrets.CODECOV_TOKEN }}
verbose: True


pylint_check:
if: "github.repository == 'MDAnalysis/pathsimanalysis'"
needs: environment-config
runs-on: ubuntu-latest

steps:
Expand All @@ -125,7 +112,7 @@ jobs:
- name: Set up Python
uses: actions/setup-python@v4
with:
python-version: ${{ needs.environment-config.outputs.stable-python-version }}
python-version: "3.11"

- name: Install Pylint
run: |
Expand All @@ -142,16 +129,15 @@ jobs:
pypi_check:
if: "github.repository == 'MDAnalysis/pathsimanalysis'"
needs: environment-config
runs-on: ubuntu-latest

steps:
- uses: actions/checkout@v4

- name: Set up Python ${{ needs.environment-config.outputs.stable-python-version }}
- name: Set up Python
uses: actions/setup-python@v4
with:
python-version: ${{ needs.environment-config.outputs.stable-python-version }}
python-version: "3.11"

- name: Install dependencies
run: |
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11 changes: 11 additions & 0 deletions CHANGELOG.md
Original file line number Diff line number Diff line change
Expand Up @@ -16,6 +16,17 @@ The rules for this file:
* accompany each entry with github issue/PR number (Issue #xyz)
-->

## Unreleased

### Authors
- IAlibay

### Changed
- In accordance with SPEC0 the minimum Python version has been
raised to v3.10 (PR #36)
- Minimum supported MDAnalysis version has been raised to
v2.1.0 (PR #36)

## [1.1.0] -- 2024-01-06

### Authors
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5 changes: 2 additions & 3 deletions pyproject.toml
Original file line number Diff line number Diff line change
Expand Up @@ -22,17 +22,16 @@ classifiers = [
"License :: OSI Approved :: GNU General Public License v2 or later (GPLv2+)",
"Programming Language :: C",
"Programming Language :: Python",
"Programming Language :: Python :: 3.9",
"Programming Language :: Python :: 3.10",
"Programming Language :: Python :: 3.11",
"Programming Language :: Python :: 3.12",
"Topic :: Scientific/Engineering",
"Topic :: Software Development :: Libraries :: Python Modules",
]
readme = "README.md"
requires-python = ">=3.9"
requires-python = ">=3.10"
dependencies = [
"MDAnalysis>=2.0.0",
"MDAnalysis>=2.1.0",
"scipy>=1.5.0",
"matplotlib>=1.5.1",
"numpy>=1.22.3",
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