Addition of molSimplify structure overhaul

setup.cfg → .flake8

@@ -1,6 +1,3 @@
-[aliases]
-test=pytest
-
 [flake8]
 max-complexity = 15
 max-line-length = 127

.github/workflows/build.yaml

@@ -0,0 +1,73 @@
+name: Publish Python 🐍 distribution 📦 to PyPI and TestPyPI
+# This follows https://packaging.python.org/en/latest/guides/publishing-package-distribution-releases-using-github-actions-ci-cd-workflows/
+
+on:
+  push:
+    tags:
+      - v*
+
+jobs:
+  build:
+    name: Build distribution 📦
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: "3.x"
+    - name: Install pypa/build
+      run: >-
+        python3 -m
+        pip install
+        build
+        --user
+    - name: Build a binary wheel and a source tarball
+      run: python3 -m build
+    - name: Store the distribution packages
+      uses: actions/upload-artifact@v3
+      with:
+        name: python-package-distributions
+        path: dist/
+
+  publish-to-pypi:
+    name: Publish Python 🐍 distribution 📦 to PyPI
+    if: startsWith(github.ref, 'refs/tags/')  # only publish to PyPI on tag pushes
+    needs:
+    - build
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/molSimplify
+    permissions:
+      id-token: write  # IMPORTANT: mandatory for trusted publishing
+    steps:
+    - name: Download all the dists
+      uses: actions/download-artifact@v4.1.7
+      with:
+        name: python-package-distributions
+        path: dist/
+    - name: Publish distribution 📦 to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+
+  publish-to-testpypi:
+    name: Publish Python 🐍 distribution 📦 to TestPyPI
+    needs:
+    - build
+    runs-on: ubuntu-latest
+    environment:
+      name: testpypi
+      url: https://test.pypi.org/p/molSimplify
+    permissions:
+      id-token: write  # IMPORTANT: mandatory for trusted publishing
+    steps:
+    - name: Download all the dists
+      uses: actions/download-artifact@v4.1.7
+      with:
+        name: python-package-distributions
+        path: dist/
+    - name: Publish distribution 📦 to TestPyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        repository-url: https://test.pypi.org/legacy/

.github/workflows/codeql.yml

@@ -2,9 +2,9 @@ name: "CodeQL"
 
 on:
   push:
-    branches: [ "master" ]
+    branches: [ "master", "main" ]
   pull_request:
-    branches: [ "master" ]
+    branches: [ "master", "main" ]
   schedule:
     - cron: "59 11 * * 6"
 

.github/workflows/CI.yaml → .github/workflows/pytest.yaml

@@ -1,36 +1,26 @@
-name: CI
+name: Pytest
 
 on:
-  # GitHub has started calling new repo's first branch "main" https://github.com/github/renaming
-  # Existing codes likely still have "master" as the primary branch
-  # Both are tracked here to keep legacy and new codes working
   push:
     branches:
-      - "master"
       - "main"
   pull_request:
     branches:
-      - "master"
       - "main"
-#   schedule:
-#     # Nightly tests run on master by default:
-#     #   Scheduled workflows run on the latest commit on the default or base branch.
-#     #   (from https://help.github.com/en/actions/reference/events-that-trigger-workflows#scheduled-events-schedule)
-#     - cron: "0 0 * * *"
 
 jobs:
-  CI:
-    name: Test on ${{ matrix.os }}, Python ${{ matrix.python-version }}
+  pytest_conda:
+    name: Pytest (conda) on ${{ matrix.os }}, Python ${{ matrix.python-version }}
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
         os: ["ubuntu-latest"]
-        python-version: ["3.7", "3.8"]
+        python-version: ["3.8", "3.10"]
     defaults:
       run:
         shell: bash -l {0}
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Additional info about the build
       run: |
@@ -42,7 +32,7 @@ jobs:
       uses: josStorer/get-current-time@v2.0.2
       id: current-time
     - name: Cache conda env
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       id: cache
       env:
         # Increase this value to reset cache if mols.yml has not changed
@@ -57,10 +47,10 @@ jobs:
 
     # More info on the whole conda setup: https://github.com/conda-incubator/setup-miniconda
     - name: Setup Conda
-      uses: conda-incubator/setup-miniconda@v2
+      uses: conda-incubator/setup-miniconda@v3
       id: conda-setup
       with:
-        # mamba-version: "*" # uncomment to activate mamba 
+        # mamba-version: "*" # uncomment to activate mamba
         python-version: ${{ matrix.python-version }}
         miniforge-variant: Mambaforge
         channels: conda-forge,defaults
@@ -74,13 +64,18 @@ jobs:
         pip install -e . --no-deps
         pip install pytest-cov
         conda list
-    
+
     - name: Run tests
       run: |
         pytest -v --cov=molSimplify --cov-report=xml
-
+
+    - name: Run doctest
+      # For now still excluding several subfolders and files
+      run: |
+        pytest --doctest-modules --ignore=molSimplify/Informatics/MOF --ignore=molSimplify/Informatics/protein --ignore=molSimplify/Scripts/in_b3lyp_usetc.py --ignore=molSimplify/Informatics/jupyter_vis.py --ignore=molSimplify/Informatics/macrocycle_synthesis.py --ignore=molSimplify/Informatics/organic_fingerprints.py molSimplify
+
     - name: Upload coverage report to codecov
-      uses: codecov/codecov-action@v3
+      uses: codecov/codecov-action@v4
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
         directory: ./coverage/reports/
@@ -89,16 +84,39 @@ jobs:
         flags: unittests
         name: codecov-umbrella
         verbose: true
-    
+
     - name: Report Status
       # Slack notifications only on the main repo
-      if: ${{ github.event_name != 'pull_request' && github.repository == 'hjkgrp/molSimplify' }}
+      if: ${{job.status == 'failure' && github.event_name != 'pull_request' && github.repository == 'hjkgrp/molSimplify' }}
       #uses: ravsamhq/notify-slack-action@v1
       uses: 8398a7/action-slack@v3
       with:
-        job_name: Test on ${{ matrix.os }}, Python ${{ matrix.python-version }}
+        job_name: Pytest (conda) on ${{ matrix.os }}, Python ${{ matrix.python-version }}
         fields: message,commit,author,workflow,job,took
         status: ${{ job.status }}
       env:
         SLACK_WEBHOOK_URL: ${{secrets.SLACK_WEBHOOK}}
         #MATRIX_CONTEXT: ${{ toJson(matrix) }} # required
+
+  pytest_pip:
+    name: Pytest (pip) on ${{ matrix.os }}, Python ${{ matrix.python-version }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: ["ubuntu-latest"]
+        python-version: ["3.8"]
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install package
+      run: |
+        pip install -e .[dev]
+
+    - name: Run pytest
+      run: |
+        pytest -v

.github/workflows/python-linter.yaml

@@ -1,18 +1,21 @@
 name: Linter
 
-on: [push, pull_request]
+on:
+  pull_request:
+  push:
+    branches: ["master", "main"]
 
 jobs:
   flake8:
 
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v3
-    - name: Set up Python 3.7
-      uses: actions/setup-python@v2
+    - uses: actions/checkout@v4
+    - name: Set up Python 3.8
+      uses: actions/setup-python@v5
       with:
-        python-version: 3.7
+        python-version: 3.8
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
@@ -48,19 +51,18 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v3
-    - name: Set up Python 3.7
-      uses: actions/setup-python@v2
+    - uses: actions/checkout@v4
+    - name: Set up Python 3.8
+      uses: actions/setup-python@v5
       with:
-        python-version: 3.7
+        python-version: 3.8
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install mypy types-setuptools types-PyYAML types-requests
+        pip install mypy types-setuptools types-PyYAML types-requests types-tensorflow types-beautifulsoup4 pandas-stubs PyQt5-stubs
     - name: Typecheck with mypy
       run: |
-        # Exclude parts of Informatics for now
-        mypy --ignore-missing-imports --exclude '(frag_functionalizer.py|bridge_functionalizer.py|macrocycle_synthesis.py)' molSimplify
+        mypy --ignore-missing-imports molSimplify
 
     - name: Report Status
       # Slack notifications only on the main repo

.pre-commit-config.yaml

@@ -1,12 +1,18 @@
+ci:
+    autofix_commit_msg: '[pre-commit.ci] auto fixes from pre-commit hooks'
+    autofix_prs: true
+    autoupdate_commit_msg: '[pre-commit.ci] pre-commit autoupdate'
+    autoupdate_schedule: monthly
+
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v2.3.0
+    rev: v4.6.0
     hooks:
     -   id: check-yaml
     -   id: end-of-file-fixer
     -   id: trailing-whitespace
 -   repo: https://github.com/pycqa/flake8
-    rev: '3.8.4'
+    rev: '7.1.1'
     hooks:
     -   id: flake8
         args: ['--select=E9,F63,F7,F82', '--exclude=fragment_classes.py,frag_functionalizer.py,bridge_functionalizer.py']

.readthedocs.yml

@@ -1,15 +1,16 @@
 version: 2
 
-conda:
-  environment: docs/environment.yaml
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.8"
 
 python:
-  version: 3.7
   install:
     - method: pip
       path: .
       extra_requirements:
-          - rtd
+          - docs
 
 sphinx:
   builder: html