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* Avoid simple pass in Exceptions * Restrict coverage folders in GH action * Removed ipython from poetry * Refactored copy_log in cli.py * How to setup for dev * Improved exception handling * Added a janitor fixture for pytest * Fixed ver_today with pcregrep (linux/macos) * Remove ipython dev dependency * Test verboless * Fixed bug for sorted atomPairs * Test ILDN with -z exception * Test ILDN with -z exception improved * Corrected logger().exception use * Install poetry via curl * Pytest in random order * Test for corrupt glycam * Added sphinx and docs * Adding docs, just starting * Fixed some badges * Added info about documenting * Improved doc example * Trying to refine actions * Use dynamic year for copyright * Tests for mol and mdl formats * Test sqm fails due to wrong charge input * Typings and docs * Test for ekFlag * Try/exception around setResNameCheckCoords() * Remove try/exception around os.chdir(mol.rootDir) * Tests about resname * tests for empty amber files * Test mol geometry * Check resname * convertSmilesToMol2: redundant obabel check * Increasing coverage about charges * Fixed regex in ver_today.sh * Poetry added pyupgrade, pre-commit and sphinx * Make check_acpype.py to work, still need more * Pyupgraded * Added printErrorQuoted * pre-commit end-of-file-fixer * pid and docstrings errors cleared
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,114 +1,120 @@ | ||
| # This workflow will install Python dependencies, run tests and lint with a single version of Python | ||
| # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions | ||
| name: check_acpype | ||
|
|
||
| on: | ||
| push: | ||
| branches: | ||
| - master | ||
| pull_request: | ||
| branches: | ||
| - master | ||
| push: | ||
| branches: | ||
| - master | ||
| pull_request: | ||
| branches: | ||
| - master | ||
| paths: | ||
| - "acpype/**" | ||
| - "tests/**" | ||
|
|
||
| jobs: | ||
| check-test: | ||
| runs-on: ubuntu-latest | ||
| strategy: | ||
| matrix: | ||
| python-version: ["3.6", "3.7", "3.8", "3.9", "3.10"] | ||
|
|
||
| steps: | ||
| - uses: actions/checkout@v2 | ||
|
|
||
| - name: Set up Python ${{ matrix.python-version }} | ||
| uses: actions/setup-python@v2 | ||
| with: | ||
| python-version: ${{ matrix.python-version }} | ||
|
|
||
| # - name: Python Poetry Action | ||
| # uses: abatilo/[email protected] | ||
|
|
||
| - name: Cache pip | ||
| uses: actions/cache@v2 | ||
| with: | ||
| # This path is specific to Ubuntu | ||
| path: ~/.cache/pip | ||
| # Look to see if there is a cache hit for the corresponding requirements file | ||
| key: ${{ runner.os }}-pip-${{ hashFiles('requirements.txt') }} | ||
| restore-keys: | | ||
| ${{ runner.os }}-pip- | ||
| ${{ runner.os }}- | ||
| - name: Set Env | ||
| run: | | ||
| echo "DEBIAN_FRONTEND=noninteractive" >> $GITHUB_ENV | ||
| echo "AMBERHOME=$PWD/acpype/amber21-11_linux" >> $GITHUB_ENV | ||
| echo "$PWD/acpype/amber21-11_linux/bin" >> $GITHUB_PATH | ||
| - name: Install dependencies | ||
| run: | | ||
| sudo apt-get update | ||
| sudo apt-get install -y --no-install-recommends tzdata libarpack++2-dev | ||
| - name: Install OpenBabel | ||
| run: | | ||
| sudo apt-get install --no-install-recommends -y openbabel | ||
| - name: Poetry install dependencies | ||
| run: | | ||
| pip3 install poetry | ||
| poetry add openbabel-wheel | ||
| poetry install | ||
| - name: Lint with flake8 | ||
| run: poetry run flake8 -v --count | ||
|
|
||
| - name: Check format with black | ||
| run: poetry run black --diff --check . | ||
|
|
||
| - name: Run isort | ||
| run: poetry run isort . --check-only --profile black | ||
|
|
||
| - name: Test with PyTest | ||
| run: | | ||
| poetry run pytest --color=yes --cov=./ --cov-report=xml | ||
| - name: Upload coverage to Codecov | ||
| if: matrix.python-version == 3.6 | ||
| uses: codecov/codecov-action@v2 | ||
| with: | ||
| fail_ci_if_error: true | ||
|
|
||
| release: | ||
| needs: check-test | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - name: Get current date | ||
| id: date | ||
| run: echo "::set-output name=date::$(date +'%Y.%-m.%-d')" | ||
|
|
||
| - name: Create tag | ||
| # will only create a new release if the commit message is 'new_release' to master branch | ||
| if: github.ref == 'refs/heads/master' && contains(github.event.head_commit.message, 'new_tag') | ||
| uses: actions/github-script@v3 | ||
| with: | ||
| # github-token: ${{ github.token }} # optional | ||
| script: | | ||
| github.git.createRef({ | ||
| owner: context.repo.owner, | ||
| repo: context.repo.repo, | ||
| ref: "refs/tags/${{ steps.date.outputs.date }}", | ||
| sha: context.sha | ||
| }) | ||
| - name: Create Release | ||
| # will only create a new release if the commit message is 'new_release' to master branch | ||
| if: github.ref == 'refs/heads/master' && contains(github.event.head_commit.message, 'new_release') | ||
| id: create_release | ||
| uses: actions/create-release@v1 | ||
| env: | ||
| # This token is provided by Actions, you do not need to create your own token | ||
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | ||
| with: | ||
| tag_name: ${{ steps.date.outputs.date }} | ||
| release_name: Release ${{ steps.date.outputs.date }} | ||
| draft: false | ||
| prerelease: false | ||
| check-test: | ||
| runs-on: ubuntu-latest | ||
| strategy: | ||
| matrix: | ||
| python-version: ["3.6", "3.7", "3.8", "3.9", "3.10"] | ||
|
|
||
| steps: | ||
| - uses: actions/checkout@v2 | ||
|
|
||
| - name: Set up Python ${{ matrix.python-version }} | ||
| uses: actions/setup-python@v2 | ||
| with: | ||
| python-version: ${{ matrix.python-version }} | ||
|
|
||
| # - name: Python Poetry Action | ||
| # uses: abatilo/[email protected] | ||
|
|
||
| - name: Cache pip | ||
| uses: actions/cache@v2 | ||
| with: | ||
| # This path is specific to Ubuntu | ||
| path: ~/.cache/pip | ||
| # Look to see if there is a cache hit for the corresponding requirements file | ||
| key: ${{ runner.os }}-pip-${{ hashFiles('requirements.txt') }} | ||
| restore-keys: | | ||
| ${{ runner.os }}-pip- | ||
| ${{ runner.os }}- | ||
| - name: Set Env | ||
| run: | | ||
| echo "PYTEST_ADDOPTS=--random-order" >> $GITHUB_ENV | ||
| echo "DEBIAN_FRONTEND=noninteractive" >> $GITHUB_ENV | ||
| echo "AMBERHOME=$PWD/acpype/amber21-11_linux" >> $GITHUB_ENV | ||
| echo "$PWD/acpype/amber21-11_linux/bin" >> $GITHUB_PATH | ||
| - name: Install dependencies | ||
| run: | | ||
| sudo apt-get update | ||
| sudo apt-get install -y --no-install-recommends tzdata libarpack++2-dev | ||
| - name: Install OpenBabel | ||
| run: | | ||
| sudo apt-get install --no-install-recommends -y openbabel | ||
| - name: Poetry install dependencies | ||
| run: | | ||
| pip3 install poetry | ||
| poetry add openbabel-wheel | ||
| poetry install | ||
| - name: Lint with flake8 | ||
| run: poetry run flake8 -v --count | ||
|
|
||
| - name: Check format with black | ||
| run: poetry run black --diff --check . | ||
|
|
||
| - name: Run isort | ||
| run: poetry run isort . --check-only --profile black | ||
|
|
||
| - name: Test with PyTest | ||
| run: | | ||
| poetry run pytest --color=yes --cov=acpype --cov=tests --cov-report=xml | ||
| - name: Upload coverage to Codecov | ||
| if: matrix.python-version == 3.6 | ||
| uses: codecov/codecov-action@v2 | ||
| with: | ||
| fail_ci_if_error: true | ||
|
|
||
| release: | ||
| needs: check-test | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - name: Get current date | ||
| id: date | ||
| run: echo "::set-output name=date::$(date +'%Y.%-m.%-d')" | ||
|
|
||
| - name: Create tag | ||
| # will only create a new release if the commit message is 'new_release' to master branch | ||
| if: github.ref == 'refs/heads/master' && contains(github.event.head_commit.message, 'new_tag') | ||
| uses: actions/github-script@v3 | ||
| with: | ||
| # github-token: ${{ github.token }} # optional | ||
| script: | | ||
| github.git.createRef({ | ||
| owner: context.repo.owner, | ||
| repo: context.repo.repo, | ||
| ref: "refs/tags/${{ steps.date.outputs.date }}", | ||
| sha: context.sha | ||
| }) | ||
| - name: Create Release | ||
| # will only create a new release if the commit message is 'new_release' to master branch | ||
| if: github.ref == 'refs/heads/master' && contains(github.event.head_commit.message, 'new_release') | ||
| id: create_release | ||
| uses: actions/create-release@v1 | ||
| env: | ||
| # This token is provided by Actions, you do not need to create your own token | ||
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | ||
| with: | ||
| tag_name: ${{ steps.date.outputs.date }} | ||
| release_name: Release ${{ steps.date.outputs.date }} | ||
| draft: false | ||
| prerelease: false |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -55,6 +55,7 @@ coverage.xml | |
|
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| # Sphinx documentation | ||
| docs/_build/ | ||
| docs/_autosummary | ||
|
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| pip-selfcheck.json | ||
| *.acpype | ||
|
|
||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,71 @@ | ||
| # Instructions for setting up a development environment | ||
|
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| ## For Coding | ||
|
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| For `Linux` (Ubuntu 20 recommended) and `macOS`. Anyway, `CONDA` is strongly recommended. | ||
| Also recommended is GPG key, so do accordingly in [GitHub](https://docs.github.com/articles/generating-a-gpg-key/). | ||
|
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| ```bash | ||
| curl -sSL https://install.python-poetry.org | python3 - | ||
|
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| conda create -n acpype python=3.9 ambertools openbabel ocl-icd-system ipython gromacs=2019.1 -y | ||
| # ocl-icd-system: case you have GPU | ||
|
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| conda activate acpype | ||
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| git clone https://github.com/alanwilter/acpype.git | ||
|
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| cd acpype | ||
|
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| poetry install | ||
|
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| pre-commit install | ||
|
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| pre-commit run -a | ||
|
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| sys=$(perl -e '`uname` eq "Darwin\n" ? print "os" : print "linux"') | ||
|
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| cp ./acpype/amber21-11_${sys}/bin/charmmgen $(dirname $(which antechamber)) | ||
|
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| git config user.email _email_ # as seen in 'gpg --list-secret-keys --keyid-format=long' | ||
|
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| git config user.signingkey _singing_key_ # as seen in 'gpg --list-secret-keys --keyid-format=long' | ||
|
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| git config commit.gpgsign true | ||
|
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| pytest --cov=tests --cov=acpype --cov-report=term-missing:skip-covered --cov-report=xml | ||
| ``` | ||
|
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| If using `VSCode`: | ||
|
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| - Enable `enableCommitSigning` in `settings.json` (***Workspace*** recommended): | ||
|
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| ```yml | ||
| "git.enableCommitSigning": true, | ||
| ``` | ||
| - Another `VSCode` nuisance, if using its graphic buttons for commit etc.: its environment won't necessarily recognise the dependencies installed via `poetry` under `conda` environment named `acpype` (unless you have started `VSCode` from folder repository with command `code .`). To avoid troubles do: | ||
|
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| ```bash | ||
| conda deactivate | ||
| poetry install # it will create its own virtualenv | ||
| ``` | ||
|
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||
| You could use this `poetry virtualenv` as the `Python Interpreter` for `VSCode`, however `ambertools`, `gromacs` and `openbabel` won't be available (unless you've had installed them system wide by other means rather than `conda`). | ||
| To avoid further troubles, go back to `conda activate acpype` and remember to do the instructions above if you add new dependencies to the project via `poetry`. | ||
|
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| ## For Documenting | ||
|
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| Using [Sphinx](https://www.sphinx-doc.org) with theme from `pip install sphinx-rtd-theme`. | ||
|
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| Online documentation provided by [Read the Docs](http://acpype.readthedocs.io). | ||
|
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| To test it locally: | ||
|
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| ```bash | ||
| cd docs/ | ||
| make clean | ||
| make html | ||
| ``` | ||
|
|
||
| Then open `_build/html/index.html` in a browser. |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,2 +1,2 @@ | ||
| github: [alanwilter] | ||
| custom: ["https://www.paypal.me/alanwilter"] | ||
| custom: ["https://www.paypal.me/alanwilter"] |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1 +1 @@ | ||
| theme: jekyll-theme-time-machine | ||
| theme: jekyll-theme-time-machine |
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