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fix: do not use Mambaforge
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clintval committed Sep 20, 2024
1 parent 9ca141c commit 12a490a
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37 changes: 7 additions & 30 deletions .github/workflows/tests.yml
Original file line number Diff line number Diff line change
Expand Up @@ -44,7 +44,6 @@ jobs:
- name: Set up miniconda
uses: conda-incubator/setup-miniconda@v3
with:
miniforge-variant: Miniforge
miniforge-version: latest
channels: conda-forge,bioconda
activate-environment: prymer
Expand All @@ -54,38 +53,16 @@ jobs:
auto-activate-base: false
python-version: ${{ matrix.PYTHON_VERSION }}

- name: Unit tests (with doctest and coverage)
shell: bash -l {0}
run: |
conda activate prymer
poetry run pytest --cov=prymer --cov-report=xml --cov-branch --doctest-plus --doctest-modules prymer tests
- name: Install the project's dependencies
run: poetry install

- name: Test the codebase
run: poetry run pytest

- name: Upload coverage reports to Codecov
uses: codecov/[email protected]
with:
token: ${{ secrets.CODECOV_TOKEN }}

- name: Style checking
shell: bash -l {0}
run: |
conda activate prymer
poetry run ruff format --check
- name: Run lint
shell: bash -l {0}
run: |
conda activate prymer
poetry run ruff check
- name: Run mypy
shell: bash -l {0}
run: |
conda activate prymer
poetry run mypy

- name: Run docs
shell: bash -l {0}
run: |
conda activate prymer
set -euo pipefail
poetry run mkdocs build --strict
- name: Test building the documentation
run: set -euo pipefail && poetry run mkdocs build --strict
5 changes: 5 additions & 0 deletions pyproject.toml
Original file line number Diff line number Diff line change
Expand Up @@ -125,6 +125,11 @@ minversion = "7.4"
addopts = [
"--ignore=docs/scripts",
"--color=yes",
"--cov",
"--cov-report=xml",
"--cov-branch",
"--doctest-plus",
"--doctest-modules",
"--mypy",
"--ruff",
"--doctest-plus",
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