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Merge pull request #220 from Becksteinlab/update-ci-codecov-python
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CI updates
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orbeckst authored Nov 17, 2022
2 parents 39fd002 + 06eb469 commit 2973cf6
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37 changes: 20 additions & 17 deletions .github/workflows/ci.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -16,6 +16,10 @@ concurrency:
group: "${{ github.ref }}-${{ github.head_ref }}"
cancel-in-progress: true

defaults:
run:
shell: bash -l {0}

jobs:
test:
runs-on: ${{ matrix.os }}
Expand All @@ -27,28 +31,31 @@ jobs:
# macos runners (latest GROMACS, oldest and latest Python)

os: [ubuntu-latest]
python-version: ["3.9"]
python-version: ["3.10"]
gromacs-version: ["4.6.5", "2018.6", "2020.6", "2021.1"]
include:
- os: ubuntu-latest
python-version: "3.6"
gromacs-version: "2021.1"
- os: ubuntu-latest
python-version: "3.7"
gromacs-version: "2021.1"
- os: ubuntu-latest
python-version: "3.8"
gromacs-version: "2021.1"
- os: ubuntu-latest
python-version: "3.9"
gromacs-version: "2021.1"
- os: macos-latest
python-version: "3.9"
gromacs-version: "2021.1"
- os: macos-latest
python-version: "3.10"
gromacs-version: "2021.1"

env:
MPLBACKEND: agg


steps:
- uses: actions/checkout@v2
- uses: actions/checkout@v3

- uses: conda-incubator/setup-miniconda@v2
with:
Expand All @@ -60,45 +67,41 @@ jobs:
show-channel-urls: true

- name: Conda info
shell: bash -l {0}
run: |
conda info
conda list
conda config --show-sources
conda config --show
- name: Python version
shell: bash -l {0}
run: |
python -c "import sys; print(sys.version)"
- name: Install non-versioned package dependencies
shell: bash -l {0}
- name: Install package dependencies
run: |
mamba install six numpy scipy matplotlib-base pandas scikit-learn pyyaml mdanalysis numexpr numkit gromacswrapper
mamba install six numpy scipy matplotlib-base pandas scikit-learn pyyaml "mdanalysis>=2" numkit gromacswrapper "alchemlyb<2"
- name: Install pytest+plugins and pybol
shell: bash -l {0}
run: |
mamba install pytest pytest-pep8 pytest-cov codecov
python -m pip install pybol
- name: Install GROMACS (${{ matrix.gromacs-version }})
shell: bash -l {0}
run: |
mamba install 'gromacs==${{ matrix.gromacs-version }}' pocl
- name: Install package (and alchemlyb with dependencies)
shell: bash -l {0}
- name: Install package (with no dependencies)
run: |
python -m pip install .
python -m pip install . --no-deps
- name: Run tests
shell: bash -l {0}
run: |
pytest -v --durations=20 --cov=mdpow --cov-report=xml --color=yes ./mdpow/tests
- name: Codecov
uses: codecov/codecov-action@v1
uses: codecov/codecov-action@v3
with:
token: ${{ secrets.CODECOV_TOKEN }}
name: codecov-${{ matrix.os }}-py${{ matrix.python-version }}
file: ./coverage.xml
fail_ci_if_error: true
11 changes: 9 additions & 2 deletions CHANGES
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Expand Up @@ -2,11 +2,18 @@
CHANGES for MDPOW
=================

Add summary of changes for each release. Use ISO dates. Reference
Add summary of changes for each release. Use ISO 8061 dates. Reference
GitHub issues numbers and PR numbers.



2022-??-?? 0.8.1
cadeduckworth
cadeduckworth, orbeckst

Changes

* added support for Python 3.10
* dropped testing on Python 3.6

Fixes

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5 changes: 3 additions & 2 deletions setup.py
Original file line number Diff line number Diff line change
Expand Up @@ -29,6 +29,7 @@
"Programming Language :: Python :: 3.7",
"Programming Language :: Python :: 3.8",
"Programming Language :: Python :: 3.9",
"Programming Language :: Python :: 3.10",
"Topic :: Scientific/Engineering :: Chemistry",
"Topic :: Scientific/Engineering :: Physics",
],
Expand All @@ -54,8 +55,8 @@
'GromacsWrapper>=0.5.1',
'numkit',
'six',
'mdanalysis',
'alchemlyb',
'mdanalysis>=2',
'alchemlyb<2',
'pandas',
'pymbar',
],
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