pre-commit, setup and args setup

.github/workflows/release.yml

@@ -0,0 +1,29 @@
+
+name: Create Release
+
+on:
+  push:
+    tags:
+      - 'v*' # Push events to matching v*, i.e. v1.0, v20.15.10
+
+jobs:
+  build:
+    name: Create Release
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          fetch-depth: 0
+      - uses: notlmn/release-with-changelog@v3
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          exclude: '^Meta'
+          commit-template: '- {title} ← {hash}'
+          template: |
+            ### Changelog
+
+            {commits}
+
+            {range}
+
+            ❤

.github/workflows/pythonapp.yml → .github/workflows/test.yml

@@ -1,4 +1,4 @@
-name: Conda/Python pytest
+name: Test
 
 on: [push]
 
@@ -24,23 +24,18 @@ jobs:
         # Pip install requirments
         python -m pip install --upgrade pip
         pip install -r requirements.txt
-    - name: Lint with flake8
+        pip install -r requirements.dev.txt
+    - name: Test format
       run: |
         # Activate
         source $(conda info --root)/etc/profile.d/conda.sh
         conda activate ./env
         # Make sure it is installed
-        pip install flake8
-        # stop the build if there are Python syntax errors or undefined names
-        flake8 *.py --count --select=E9,F63,F7,F82 --show-source --statistics
-        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-        flake8 *.py --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
-    - name: Test with pytest
+        pre-commit run --all-files
+    - name: Unittest
       run: |
         # Activate
         source $(conda info --root)/etc/profile.d/conda.sh
         conda activate ./env
-        # Make sure pytest is avaliabel
-        pip install pytest
         # Test files
-        pytest -v test.py
+        pytest -vv test.py

.gitignore

@@ -1,5 +1,11 @@
+# test left-overs
+nul
+run.out
+
+# dev
 *.cprof
 .pytest_cache
+.vim
 
 # Byte-compiled / optimized / DLL files
 __pycache__/

.pre-commit-config.yaml

@@ -0,0 +1,95 @@
+repos:
+
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v3.4.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml
+        args: ["--unsafe"]
+      - id: check-added-large-files
+
+  - repo: https://github.com/myint/autoflake
+    rev: v1.4
+    hooks:
+      - id: autoflake
+        name: Removes unused variables
+        args:
+          - --in-place
+          - --remove-all-unused-imports
+          - --remove-unused-variables
+          - --expand-star-imports
+          - --ignore-init-module-imports
+
+  - repo: https://github.com/pre-commit/mirrors-isort
+    rev: v5.7.0
+    hooks:
+      - id: isort
+        name: Sorts imports
+        args: [
+          # Align isort with black formatting
+          "--multi-line=3",
+          "--trailing-comma",
+          "--force-grid-wrap=0",
+          "--use-parentheses",
+          "--line-width=99",
+        ]
+
+  - repo: https://github.com/psf/black
+    rev: 20.8b1
+    hooks:
+      - id: black
+        name: Fixes formatting
+        language_version: python3
+        args: ["--line-length=99"]
+
+
+  - repo: https://gitlab.com/pycqa/flake8
+    rev: 3.8.4
+    hooks:
+      - id: flake8
+        name: Checks pep8 style
+        args: [
+          "--max-line-length=99",
+          # Ignore imports in init files
+          "--per-file-ignores=*/__init__.py:F401,setup.py:E121",
+          # ignore long comments (E501), as long lines are formatted by black
+          # ignore Whitespace before ':' (E203)
+          # ignore Line break occurred before a binary operator (W503)
+          "--ignore=E501,E203,W503",
+        ]
+
+  # - repo: https://github.com/pre-commit/mirrors-mypy
+  #   rev: v0.790
+  #   hooks:
+  #     - id: mypy
+  #       name: Checks code types
+  #       args: ["--strict"]
+
+  # - repo: https://github.com/pycqa/pylint
+  #   rev: pylint-2.6.0
+  #   hooks:
+  #     - id: pylint
+  #       name: Checks code quality
+  #       args:
+  #         - --max-line-length=80
+  #         - --ignore-imports=yes
+  #         - -d duplicate-code
+
+  # - repo: local
+  #   hooks:
+  #     - id: jupyisort
+  #       name: Sorts ipynb imports
+  #       entry: jupytext --pipe-fmt ".py" --pipe "isort - --multi-line=3 --trailing-comma --force-grid-wrap=0 --use-parentheses --line-width=99"
+  #       files: .ipynb
+  #       language: python
+  #     - id: jupyblack
+  #       name: Fixes ipynb format
+  #       entry: jupytext --pipe-fmt ".py" --pipe "black - --line-length=99"
+  #       files: .ipynb
+  #       language: python
+  #     - id: nbconvert
+  #       name: Removes ipynb content
+  #       entry: jupyter nbconvert --ClearOutputPreprocessor.enabled=True --ClearMetadataPreprocessor.enabled=True RegexRemovePreprocessor.enabled=True --to=notebook --log-level=ERROR --inplace
+  #       files: .ipynb
+  #       language: python

Makefile

@@ -3,6 +3,8 @@ PYTHON=python
 CONDA=conda
 FLAKE=flake8
 
+.PHONY: build
+
 all: env
 
 setup: env pip
@@ -22,3 +24,6 @@ test-lint:
 	@# exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
 	${FLAKE} *.py --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
 
+
+build:
+	${PYTHON} setup.py sdist bdist_wheel

README.md

@@ -46,3 +46,36 @@ Read in xyz file with a charge and print out the SMILES
     rdkit # (version 2019.9.1 or later needed for huckel option)
     networkx
 
+## Development
+
+Setup development enviroment with
+
+    conda create env xyz2mol_dev -f requirements.yml
+    conda activate xyz2mol_dev
+    python -m pip install -r requriments.txt
+    python -m pip install -r requriments.dev.txt
+
+### Testing
+
+Run all tests with pytest
+
+    python -m pytest -vv test.py
+
+
+### Code standard and commit
+
+To keep code standard and ensure quality code, we use `pre-commit`.
+Please install `pre-commit` in your local repository
+
+    pre-commit install
+
+which will install a hook into your git, and run a format and code-quality check with each commit.
+
+### Releases
+
+To do a release we use GitHub actions on Git Tags.
+Increment the release by
+
+    git commit . -m "We did some changes" # Do some commits
+    git tag v1.1.5 # Add this tag to the newest commit
+    git push origin v1.1.5 # This will trigger the release build

requirements.dev.txt

@@ -0,0 +1,2 @@
+pytest
+pre-commit

requirements.txt

@@ -1,6 +1,3 @@
 numpy
 scipy
 networkx
-rmsd
-pytest
-flake8

setup.py

@@ -0,0 +1,10 @@
+from setuptools import setup
+
+setup(
+    name="xyz2mol",
+    version="1.0",
+    description="Convert Cartesian coordinates to one or more molecular graphs",
+    url="https://github.com/jensengroup/xyz2mol",
+    py_modules=["xyz2mol"],
+    entry_points={"console_scripts": ["xyz2mol=xyz2mol:main"]},
+)