new_release New_add_doc (#71)

* 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

.github/workflows/check_acpype.yml

@@ -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

.github/workflows/codeql-analysis.yml

@@ -1,7 +1,7 @@
 # For most projects, this workflow file will not need changing; you simply need
 # to commit it to your repository.
 #
-# You may wish to alter this file to override the set of languages analyzed,
+# You may wish to alter this file to override the set of languages analysed,
 # or to provide custom queries or build logic.
 #
 # ******** NOTE ********
@@ -13,10 +13,14 @@ name: "CodeQL"
 
 on:
  push:
- branches: [master]
+ branches:
+ - master
  pull_request:
- # The branches below must be a subset of the branches above
- branches: [master]
+ branches:
+ - master
+ paths:
+ - "acpype/**"
+ - "tests/**"
  schedule:
  - cron: "15 0 * * *"
 

.gitignore

@@ -55,6 +55,7 @@ coverage.xml
 
 # Sphinx documentation
 docs/_build/
+docs/_autosummary
 
 pip-selfcheck.json
 *.acpype

.pre-commit-config.yaml

@@ -1,4 +1,12 @@
 repos:
+ - repo: https://github.com/pre-commit/pre-commit-hooks
+ rev: v4.1.0
+ hooks:
+ # - id: trailing-whitespace
+ - id: end-of-file-fixer
+ - id: check-added-large-files
+ - id: debug-statements
+
  - repo: local
  hooks:
  - id: flake8
@@ -19,6 +27,12 @@ repos:
  language: system
  types: [python]
  require_serial: true
+ - id: pyupgrade
+ name: pyupgrade
+ entry: poetry run pyupgrade --py36-plus
+ language: system
+ types: [python]
+ require_serial: true
  - id: ver_today
  name: ver_today
  entry: ./scripts/ver_today.sh

CONTRIBUTING.md

@@ -0,0 +1,71 @@
+# Instructions for setting up a development environment
+
+## For Coding
+
+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/).
+
+```bash
+curl -sSL https://install.python-poetry.org | python3 -
+
+conda create -n acpype python=3.9 ambertools openbabel ocl-icd-system ipython gromacs=2019.1 -y
+# ocl-icd-system: case you have GPU
+
+conda activate acpype
+
+git clone https://github.com/alanwilter/acpype.git
+
+cd acpype
+
+poetry install
+
+pre-commit install
+
+pre-commit run -a
+
+sys=$(perl -e '`uname` eq "Darwin\n" ? print "os" : print "linux"')
+
+cp ./acpype/amber21-11_${sys}/bin/charmmgen $(dirname $(which antechamber))
+
+git config user.email _email_ # as seen in 'gpg --list-secret-keys --keyid-format=long'
+
+git config user.signingkey _singing_key_ # as seen in 'gpg --list-secret-keys --keyid-format=long'
+
+git config commit.gpgsign true
+
+pytest --cov=tests --cov=acpype --cov-report=term-missing:skip-covered --cov-report=xml
+```
+
+If using `VSCode`:
+
+- Enable `enableCommitSigning` in `settings.json` (***Workspace*** recommended):
+
+ ```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:
+
+ ```bash
+ conda deactivate
+ poetry install # it will create its own virtualenv
+ ```
+
+ 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`.
+
+## For Documenting
+
+Using [Sphinx](https://www.sphinx-doc.org) with theme from `pip install sphinx-rtd-theme`.
+
+Online documentation provided by [Read the Docs](http://acpype.readthedocs.io).
+
+To test it locally:
+
+```bash
+cd docs/
+make clean
+make html
+```
+
+Then open `_build/html/index.html` in a browser.

FUNDING.yml

@@ -1,2 +1,2 @@
 github: [alanwilter]
-custom: ["https://www.paypal.me/alanwilter"]
+custom: ["https://www.paypal.me/alanwilter"]

README.md

@@ -15,7 +15,10 @@
 [![pre-commit](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit&logoColor=white&style=plastic)](https://github.com/pre-commit/pre-commit)
 [![Commits since release](https://img.shields.io/github/commits-since/alanwilter/acpype/2021.12.24/master?style=plastic)](https://github.com/alanwilter/acpype/commits/master)
 [![Codecov](https://img.shields.io/codecov/c/github/alanwilter/acpype?style=plastic)](https://app.codecov.io/gh/alanwilter/acpype)
-
+[![Documentation Status](https://readthedocs.org/projects/acpype/badge/?version=latest&style=plastic)](https://acpype.readthedocs.io/en/latest/?badge=latest)
+[![Citations](https://img.shields.io/static/v1?label=Citations&message=1040&color=orange&style=plastic)](https://scholar.google.com/scholar?hl=en&as_sdt=2005&sciodt=0%2C5&cites=15065215520855508960&scipsc=&q=ACPYPE-Antechamber+python+parser+interface&btnG=)
+<!-- [![DOI:doi.org/10.1186/1756-0500-5-367](https://img.shields.io/badge/DOI-10.1186%2F1756--0500--5--367-blue?style=plastic)](https://doi.org/10.1186/1756-0500-5-367) -->
+<!-- [![Google Scholar Citations](https://openbabel.org/citations.svg?maxAge=86400)](https://scholar.google.com/scholar?cites=15065215520855508960&as_sdt=2005&sciodt=0,5&hl=en) -->
 <!-- [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5601736.svg)](https://doi.org/10.1186/1756-0500-5-367)
 ![DOI](https://doi.org/10.1186/1756-0500-5-367) -->
 <!-- ![Scrutinizer code quality (GitHub/Bitbucket)](https://img.shields.io/scrutinizer/quality/g/alanwilter/acpype) -->
@@ -38,6 +41,8 @@ Several flavours of AMBER FF are ported already for GROMACS (see [ffamber](http:
 
 This code is released under **[GNU General Public License V3](https://www.gnu.org/licenses/gpl-3.0.en.html)**.
 
+See online [documentation](https://acpype.readthedocs.io/) for more.
+
 ### **NO WARRANTY AT ALL**
 
 It was inspired by:

_config.yml

@@ -1 +1 @@
-theme: jekyll-theme-time-machine
+theme: jekyll-theme-time-machine