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|
name: GH Actions Cron CI
on:
schedule:
# 3 am Tuesdays and Fridays
- cron: "0 3 * * 2,5"
concurrency:
# Probably overly cautious group naming.
# Commits to develop/master will cancel each other, but PRs will only cancel
# commits within the same PR
group: "${{ github.ref }}-${{ github.head_ref }}-${{ github.workflow }}"
cancel-in-progress: true
defaults:
run:
shell: bash -l {0}
env:
CYTHON_TRACE_NOGIL: 1
MPLBACKEND: agg
jobs:
numpy_and_scipy_dev:
if: "github.repository == 'MDAnalysis/mdanalysis'"
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
- name: setup_os
uses: ./.github/actions/setup-os
with:
os-type: "ubuntu"
- name: setup_miniconda
uses: conda-incubator/setup-miniconda@v2
with:
python-version: "3.10"
miniforge-variant: Mambaforge
miniforge-version: latest
channel-priority: strict
channels: conda-forge, bioconda
add-pip-as-python-dependency: true
architecture: x64
- name: install_deps
uses: ./.github/actions/setup-deps
with:
mamba: true
full-deps: true
# overwrite installs by picking up nightly wheels
- name: nightly_wheels
run: |
pip install --pre -U -i https://pypi.anaconda.org/scipy-wheels-nightly/simple scipy numpy h5py matplotlib
- name: list_deps
run: |
mamba list
pip list
# Intentionally going with setup.py builds so we can build with latest
- name: build_srcs
uses: ./.github/actions/build-src
with:
build-hole: true
build-tests: true
build-docs: false
- name: run_tests
run: |
pytest -n $numprocs testsuite/MDAnalysisTests --durations=50 -W error::FutureWarning
# Issue #3442
native_march:
if: "github.repository == 'MDAnalysis/mdanalysis'"
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
- name: setup_os
uses: ./.github/actions/setup-os
with:
os-type: "ubuntu"
- name: setup_miniconda
uses: conda-incubator/setup-miniconda@v2
with:
python-version: 3.9
auto-update-conda: true
channel-priority: flexible
channels: conda-forge, bioconda
mamba-version: "*"
add-pip-as-python-dependency: true
architecture: x64
- name: install_deps
uses: ./.github/actions/setup-deps
- name: set_extra_flags
run: |
sed -i "s/#extra_cflags =/extra_cflags = -march=native -mtune=native/g" package/setup.cfg
cat package/setup.cfg
- name: build_srcs
uses: ./.github/actions/build-src
with:
build-hole: true
build-tests: true
build-docs: false
- name: run_tests
run: |
pytest -n $numprocs testsuite/MDAnalysisTests --disable-pytest-warnings --durations=50
# Issue 1727
pip-only:
if: "github.repository == 'MDAnalysis/mdanalysis'"
runs-on: ubuntu-latest
strategy:
fail-fast: false
matrix:
python-version: ["3.10", "3.11"]
steps:
- uses: actions/checkout@v3
- name: setup_os
uses: ./.github/actions/setup-os
with:
os-type: "ubuntu"
- uses: actions/setup-python@v4
with:
python-version: ${{ matrix.python-version }}
- name: pip install mdanalysis
run: |
cd package && pip install .
- name: pip install mdanalysistests
run: |
cd testsuite && pip install .
- name: install_pip_extras
run: |
pip install pytest-xdist
- name: run_tests
run: |
pytest -n $numprocs testsuite/MDAnalysisTests --disable-pytest-warnings --durations=50
|
