Merge branch 'master' into type-hinting

setup.cfg → .flake8

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

.github/workflows/build.yaml

@@ -0,0 +1,55 @@
+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:
+    branches:
+      - "master"
+
+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-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: '6.0.0'
+    rev: '6.1.0'
     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

@@ -1,13 +1,13 @@
 ![](./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 conda
+### via conda, from GitHub
 We currently recommend installation 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.)
 
@@ -37,14 +37,33 @@ We currently recommend installation via the [Conda](https://conda.io/docs/) pack
    pytest
    ```
 
+### via conda, from Anaconda
+Releases of molSimplify are also available on Anaconda on the [conda-forge channel](https://anaconda.org/conda-forge/molsimplify) and the [hjkgroup channel](https://anaconda.org/hjkgroup/molsimplify).
+
+### via pip, 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 docker
 We also maintain an active [docker image on dockerhub](https://hub.docker.com/repository/docker/hjkgroup/molsimplify) for plug-and-play use.
 
 For line by line instructions on an installation via docker, please visit [molSimplify installation webpage of Kulik group](http://hjkgrp.mit.edu/content/installing-molsimplify).
 
 ## Tutorials
 
-A set of tutorials covering common use cases is available at the [Kulik group webpage](http://hjkgrp.mit.edu/molSimplify-tutorials).
+A set of tutorials covering common use cases is available at the [Kulik group webpage](http://hjkgrp.mit.edu/molSimplify-tutorials). Note that the GUI is no longer supported, so users are encouraged to generate structures through the command line or using the Python command [startgen_pythonic](molSimplify/Scripts/generator.py).
 
 ## Documentation
 
@@ -82,6 +101,6 @@ year = {2018},
 }
 ```
 
-If you use any machine learning (ML) models in molSimplify that results in a publication, please cite the corresponding reference in [this MLmodel reference page](https://github.com/hjkgrp/molSimplify/blob/master/MLmodel-reference.md).
+If you use any machine learning (ML) models in molSimplify that results in a publication, please cite the corresponding reference in [this ML model reference page](https://github.com/hjkgrp/molSimplify/blob/master/MLmodel-reference.md).
 
 **Note that we have disabled developers' supports for Python 2.7 and will only release conda builds on Python 3.**

devtools/conda-envs/mols.yml

@@ -8,14 +8,16 @@ dependencies:
   - pandas
   - scipy
   - libffi
+  - importlib_resources
   - pip
   - pip:
     - pytest
+    - pytest-resource-path
 
   # Optional
   # GUI / plotting
-  - pyqt
-  - qt
+  # - pyqt
+  # - qt
   - matplotlib
   # Database
   - pymongo