Merge remote-tracking branch 'origin/master' into get_geometry_edits

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@v3
+      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@v3
+      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/CI.yaml → .github/workflows/pytest.yaml

@@ -1,9 +1,6 @@
-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"
@@ -12,15 +9,10 @@ on:
     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:
@@ -82,7 +74,7 @@ jobs:
     - name: Run doctest
       # For now still excluding several subfolders and files
       run: |
-        pytest --doctest-modules --ignore=molSimplify/job_manager --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
+        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
@@ -101,9 +93,32 @@ jobs:
       #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@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install package
+      run: |
+        pip install -e .[dev]
+
+    - name: Run pytest
+      run: |
+        pytest -v

.pre-commit-config.yaml

@@ -6,13 +6,13 @@ ci:
 
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v4.5.0
     hooks:
     -   id: check-yaml
     -   id: end-of-file-fixer
     -   id: trailing-whitespace
 -   repo: https://github.com/pycqa/flake8
-    rev: '6.1.0'
+    rev: '7.0.0'
     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: "3.7"
 
 python:
-  version: 3.7
   install:
     - method: pip
       path: .
       extra_requirements:
-          - rtd
+          - docs
 
 sphinx:
   builder: html

README.md

@@ -1,14 +1,42 @@
 ![](./molSimplify/icons/logo.png)
-[![CI](https://github.com/hjkgrp/molSimplify/actions/workflows/CI.yaml/badge.svg)](https://github.com/hjkgrp/molSimplify/actions/workflows/CI.yaml)
+[![Pytest](https://github.com/hjkgrp/molSimplify/actions/workflows/pytest.yaml/badge.svg)](https://github.com/hjkgrp/molSimplify/actions/workflows/pytest.yaml)
 [![Documentation Status](https://readthedocs.org/projects/molsimplify/badge/?version=latest)](http://molsimplify.readthedocs.io/?badge=latest)
 [![Linter](https://github.com/hjkgrp/molSimplify/actions/workflows/python-linter.yaml/badge.svg)](https://github.com/hjkgrp/molSimplify/actions/workflows/python-linter.yaml)
 
 molSimplify is an open source toolkit for the automated, first-principles screening and discovery of new inorganic molecules and intermolecular complexes. molSimplify is developed by the [Kulik Group](http://hjkgrp.mit.edu) in the [Department of Chemical Engineering](http://web.mit.edu/cheme/) at [MIT](http://web.mit.edu). The software can generate a variety of coordination complexes of metals coordinated by ligands in a mono- or multi-dentate fashion. The code can build a coordination complex directly from a central atom or functionalize a more complex structure (e.g. a porphyrin or other metal-ligand complex) by including additional ligands or replacing existing ones. molSimplify also generates inter-molecular complexes for evaluating binding interactions and generating candidate reactants and intermediates for catalyst reaction mechanism screening. molSimplify also ships neural network models that can predict the [metal-ligand bond lengths](https://pubs.rsc.org/en/content/articlehtml/2017/sc/c7sc01247k), [spin-splitting energy](https://pubs.acs.org/doi/abs/10.1021/acs.jpca.7b08750), [frontier orbital energies](https://pubs.acs.org/doi/abs/10.1021/acs.iecr.8b04015), [spin-state dependent reaction energies](https://pubs.acs.org/doi/abs/10.1021/acscatal.9b02165), and [simulation outcomes](https://pubs.acs.org/doi/abs/10.1021/acs.jctc.9b00057) for octahedral transition metal complexes. See the Tutorials at the [Kulik group webpage](http://hjkgrp.mit.edu/molSimplify-tutorials) for a more complete list of jobs molSimplify can do.
 
 ## Installation
 
+### via pip, from PyPI
+
+Starting with version `1.7.4` molSimplify is available on [PyPI](https://pypi.org) enabled by the [openbabel-wheel](https://pypi.org/project/openbabel-wheel/) project.
+
+```bash
+pip install molSimplify
+```
+
+### via pip, from GitHub
+
+To obtain the latest development version or if you plan to modify the code we recommend installation from GitHub.
+
+1. Clone molSimplify source from github and change into the directory.
+
+   ```bash
+   git clone https://github.com/hjkgrp/molSimplify.git
+   cd molSimplify
+   ```
+2. Locally install the molSimplify package using pip.
+   ```bash
+   pip install -e .[dev]
+   ```
+3. To test your installation, you can run the command below at the root directory of molSimplify. You are good to go if all the tests are passed! Note, some test will be skipped because none of the optional dependencies are installed this way.
+   ```bash
+   pytest
+   ```
+
 ### via conda, from GitHub
-We currently recommend installation via the [Conda](https://conda.io/docs/) package management system.
+
+The easiest way of installing molSimplify including optional dependencies such as [xtb](https://github.com/grimme-lab/xtb) is via the [Conda](https://conda.io/docs/) package management system.
 1. Prerequisite: have [Anaconda or miniconda](https://www.anaconda.com/distribution/) installed on your system. **For M1 Macs, please use [Miniforge](https://github.com/conda-forge/miniforge) for Mac OSX arm64.** (We do not recommend simultaneously installing Anaconda and Miniforge - only install Miniforge.)
 
 2. Clone molSimplify source from github and change into the directory.

devtools/conda-envs/mols.yml

@@ -8,9 +8,11 @@ dependencies:
   - pandas
   - scipy
   - libffi
+  - importlib_resources
   - pip
   - pip:
     - pytest
+    - pytest-resource-path
 
   # Optional
   # GUI / plotting