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* added initial monorepo set-up * added database-ci.yaml * updated database > databases in __init__ and tool.pytest.ini_options * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * updated databases-ci.yaml for database > databases name change * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * absolute instead of relative path for databases tests * black formatted databases sub-package * flake8 in databases and added path to CI * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * black * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * udpated test path * udpated test path CI * more database > databases and specified file in tests directory * black * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * changed --cov argument to missense_kinase_toolkit/databases directory * changed relative to absolute reference * --cov=databases * specify file * specify test Python file and remove test sub-directory * fixed typo * --cov=./ * removed src directory and pyproject.toml/poetry.lock from outer directory * removed CI file * --cov=missense_kinase_toolkit/databases * moving test to sub-directory and --cov=./ * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * install package in right directory * flake8 for test_databases.py * using ASAP trick for codecov * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * reverting back to shell: bash -l {0} * removed -n auto --durations=10 * added line break to tests * added strip to Abl sequence * added strip to both Abl sequences * reverted to one line Abl sequence * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * noqa E501 for Abl sequence * removed boilerplate cookiecutter info * moved setup.cfg to database * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * .codecov.yml updates * changing coverage report location * black, pyproject.toml to outer directory * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fixing .coverage.xml location and removign direct test reference * reverting .codecov.yml and duplicate column widths in setup.cfg * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * added __init__.py file in intermediate missense_kinase_toolkit and tests directories * created TestDatabases class in test file * clarified that others are for databases sub-package * commented out tool.pytest.ini_options and tool.coverage.run options for now * added python3 -m to pip install instructions: * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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Original file line number | Diff line number | Diff line change |
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@@ -1,14 +1,18 @@ | ||
name: CI | ||
name: databases-ci | ||
|
||
on: | ||
# GitHub has started calling new repo's first branch "main" https://github.com/github/renaming | ||
# The cookiecutter uses the "--initial-branch" flag when it runs git-init | ||
push: | ||
branches: | ||
- "main" | ||
paths: | ||
- "missense_kinase_toolkit/databases/**" | ||
pull_request: | ||
branches: | ||
- "main" | ||
paths: | ||
- "missense_kinase_toolkit/databases/**" | ||
schedule: | ||
# Weekly tests run on main by default: | ||
# Scheduled workflows run on the latest commit on the default or base branch. | ||
|
@@ -27,9 +31,6 @@ jobs: | |
steps: | ||
- uses: actions/checkout@v3 | ||
|
||
# - name: Install poetry | ||
# run: pipx install poetry | ||
|
||
- name: Additional info about the build | ||
shell: bash | ||
run: | | ||
|
@@ -45,37 +46,35 @@ jobs: | |
environment-name: test | ||
# conda-forge is the default channel now and does not need to be specified | ||
channels: conda-forge,defaults | ||
# cache: 'poetry' | ||
extra-specs: | | ||
python=${{ matrix.python-version }} | ||
- name: Install package | ||
# conda setup requires this special shell | ||
shell: bash -l {0} | ||
run: | | ||
python -m pip install . --no-deps | ||
# python -m pip install poetry | ||
# python -m venv .venv --copies | ||
# poetry config virtualenvs.create false | ||
# poetry install | ||
python -m pip install ./missense_kinase_toolkit/databases --no-deps | ||
micromamba list | ||
- name: Run tests | ||
# conda setup requires this special shell | ||
shell: bash -l {0} | ||
run: | | ||
pytest -v --cov=missense_kinase_toolkit --cov-report=xml --color=yes tests/ | ||
# poetry run pytest -v --cov=missense_kinase_toolkit --cov-report=xml --color=yes tests/ | ||
# run each package test suite; append to coverage file | ||
# exit immediately if a command exits with a non-zero status | ||
set -e | ||
# pytest -n auto --durations=10 -v --cov-report=xml --cov-report=term --color=yes \ | ||
pytest -v --cov-report=xml --color=yes \ | ||
--cov=missense_kinase_toolkit/databases \ | ||
missense_kinase_toolkit/databases/missense_kinase_toolkit/databases/tests/ | ||
- name: Upload coverage reports to Codecov | ||
uses: codecov/[email protected] | ||
with: | ||
fail_ci_if_error: false # optional (default = false) | ||
file: ./coverage.xml | ||
flags: unittests # optional | ||
flags: databases # optional | ||
name: codecov-${{ matrix.os }}-py${{ matrix.python-version }} | ||
# https://github.com/codecov/codecov-action | ||
token: ${{ secrets.CODECOV_TOKEN }} # required | ||
verbose: true # optional (default = false) | ||
# env: | ||
# slug: choderalab/missense-kinase-toolkit |
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# databases |
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