4.5.5: dendropy backwards compatibility #5
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name: SEPP_github_tests | |
on: | |
push: | |
branches: [ master ] | |
pull_request: | |
branches: [ master ] | |
jobs: | |
python_tests: | |
strategy: | |
matrix: | |
python-version: ["3.9", "3.10"] | |
runs-on: ubuntu-latest | |
steps: | |
- name: Checkout Repo | |
uses: actions/checkout@v3 | |
- name: setup conda | |
uses: conda-incubator/setup-miniconda@v3 | |
with: | |
# This uses *miniforge*, rather than *minicond*. The primary difference | |
# is that the defaults channel is not enabled at all | |
miniforge-version: latest | |
# These properties enable the use of mamba, which is much faster and far | |
# less error prone than conda while being completely compatible with the | |
# conda CLI | |
use-mamba: true | |
mamba-version: "*" | |
python-version: ${{ matrix.python-version }} | |
environment-file: ci/environment.yml | |
auto-activate-base: true | |
activate-environment: sepp_ci | |
- name: install sepp | |
shell: bash -el {0} | |
run: | | |
python setup.py config -c | |
python setup.py install | |
- name: run tests | |
shell: bash -el {0} | |
run: | | |
conda list | |
nosetests -w test/unittest --with-doctest --with-coverage | |
- name: convert coverage | |
shell: bash -el {0} | |
run: | | |
coverage lcov | |
- name: send coverage report. | |
uses: coverallsapp/github-action@master | |
with: | |
github-token: ${{ secrets.GITHUB_TOKEN }} | |
path-to-lcov: "coverage.lcov" | |
linting: | |
strategy: | |
matrix: | |
python-version: ["3.9", "3.10"] | |
runs-on: ubuntu-latest | |
steps: | |
- name: Checkout Repo | |
uses: actions/checkout@v3 | |
- name: setup conda | |
uses: conda-incubator/setup-miniconda@v3 | |
with: | |
# This uses *miniforge*, rather than *minicond*. The primary difference | |
# is that the defaults channel is not enabled at all | |
miniforge-version: latest | |
# These properties enable the use of mamba, which is much faster and far | |
# less error prone than conda while being completely compatible with the | |
# conda CLI | |
use-mamba: true | |
mamba-version: "*" | |
python-version: ${{ matrix.python-version }} | |
environment-file: ci/env_lint.yml | |
auto-activate-base: true | |
activate-environment: sepp_lint | |
- name: linting | |
shell: bash -el {0} | |
run: | | |
flake8 setup.py split_sequences.py distribute_setup.py run_ensemble.py run_sepp.py run_upp.py merge_script.py test/unittest/ sepp/ |