Fix table 115 #28
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name: integration tests & code style | |
on: | |
push: | |
branches: [ master ] | |
pull_request: | |
branches: [ master ] | |
jobs: | |
build-linux: | |
runs-on: ubuntu-latest | |
steps: | |
- name: Checkout Repo | |
uses: actions/checkout@v3 | |
- name: Set up Python | |
uses: actions/setup-python@v3 | |
- name: setup conda | |
uses: conda-incubator/setup-miniconda@v2 | |
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: "*" | |
environment-file: environment.yml | |
python-version: "3.10" | |
- name: Lint with flake8 | |
# Bash shells do not use ~/.profile or ~/.bashrc so these shells need to | |
# be explicitely declared as shell: bash -el {0} on steps that need to be | |
# properly activated (or use a default shell). This is because bash shells | |
# are executed with bash --noprofile --norc -eo pipefail {0} thus ignoring | |
# updated on bash profile files made by conda init bash. See Github | |
# Actions Documentation and thread. | |
shell: bash -el {0} | |
run: | | |
flake8 phylofiller/ | |
- name: run python tests | |
shell: bash -el {0} | |
run: | | |
nosetests phylofiller --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" |