Merge pull request #260 from JacksonBurns/aimsim-v2.1.0

`AIMSim` v2.1.0 updates

.github/workflows/ci.yml

@@ -0,0 +1,98 @@
+name: Run Tests
+on:
+  schedule:
+    - cron:  '0 8 * * 1-5'
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+  workflow_dispatch:
+
+jobs:
+  code-format:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - name: Setup python
+        uses: actions/setup-python@v1
+        with:
+          python-version: '3.9'
+          architecture: x64
+      - name: Install Dependencies
+        run: |
+          python -m pip install rdkit-pypi
+          python -m pip install networkx==2.1
+          python -m pip install pycodestyle autopep8
+          python -m pip install -r requirements.txt
+          python -m pip install -e .
+          python -m pip install sphinx sphinx-rtd-theme m2r mistune==0.8.4
+      
+      - name: Check Errors
+        run: |
+          pycodestyle --statistics --count --max-line-length=150 --show-source --exclude=interfaces/UI/libraries .
+  
+  build:
+    strategy:      
+      fail-fast: false
+      matrix:
+        python-version: ['3.8', '3.9', '3.10', '3.11']
+        os: [ubuntu-latest, windows-latest, macos-latest]
+
+    runs-on: ${{ matrix.os }}
+    defaults:
+      run:
+        shell: bash -el {0}
+    name: ${{ matrix.os }} Python ${{ matrix.python-version }} Subtest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: conda-incubator/setup-miniconda@v2
+        with:
+          auto-update-conda: true
+          python-version: ${{ matrix.python-version }}
+      - name: Install Dependencies
+        run: |
+          python -m pip install openpyxl
+          python -m pip install -r requirements.txt
+          python -m pip install -e .
+          python -m pip install coverage
+      - name: Run Tests
+        run: |
+          coverage run --source=. --omit=interfaces/*,aimsim/__main__.py,aimsim/tasks/__init__.py,aimsim/ops/__init__.py,aimsim/chemical_datastructures/__init__.py,aimsim/utils/__init__.py,setup.py,tests/*,aimsim/__init__.py,aimsim/utils/plotting_scripts.py -m unittest discover
+      - name: Show Coverage
+        run: |
+          coverage report -m
+
+  pypi:
+    name: Build and publish Python 🐍 distributions 📦 to PyPI
+    runs-on: ubuntu-latest
+    # only run if the tests pass
+    needs: build
+    # run only on pushes to master on AIMSim
+    if:  ${{ github.event_name == 'push' && github.ref == 'refs/heads/master' && github.repository == 'VlachosGroup/AIMSim'}}
+    steps:
+      - uses: actions/checkout@master
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v3
+        with:
+          python-version: "3.10"
+      - name: Install pypa/build
+        run: >-
+          python -m
+          pip install
+          build
+          --user
+      - name: Build a binary wheel and a source tarball
+        run: >-
+          python -m
+          build
+          --sdist
+          --wheel
+          --outdir dist/
+          .
+      - name: Publish distribution 📦 to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          password: ${{ secrets.PYPI_API_TOKEN }}
+          skip-existing: true
+          verbose: true

.gitignore

@@ -1,5 +1,5 @@
 # vscode configuration files
-*.json
+.vscode
 
 # intellij configuration files
 .idea/*

AIMSim-demo.ipynb

@@ -8,16 +8,21 @@
     "This notebook demonstrates the key uses of _AIMSim_ as a graphical user interface, command line tool, and scripting utility. For detailed explanations and to view the source code for _AIMSim_, visit our [documentation page](https://vlachosgroup.github.io/AIMSim/)."
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": []
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
     "## Installing _AIMSim_\n",
     "For users with Python already in use on their devices, it is _highly_ recommended to first create a virtual environment before installing _AIMSim_. This package has a large number of dependencies with only a handful of versions supported, so conflicts are likely unless a virtual environment is used.\n",
     "\n",
-    "For new Python users, the authors recommended installing anaconda navigator to manage dependencies for _AIMSim_ and make installation easier overall. Once anaconda navigator is ready, create a new environment with Python 3.7, open a terminal or command prompt in this environment, and follow the instructions below. \n",
+    "For new Python users, the authors recommended installing anaconda navigator to manage dependencies for _AIMSim_ and make installation easier overall. Once anaconda navigator is ready, create a new environment with Python 3.8 or newer, open a terminal or command prompt in this environment, and follow the instructions below. \n",
     "\n",
-    "We reccomend installing _AIMSim_ using the commands shown below (omit exclamation points and the %%capture, unless you are running in a Jupyter notebook):"
+    "We recommend installing _AIMSim_ using the commands shown below (omit exclamation points and the %%capture, unless you are running in a Jupyter notebook):"
    ]
   },
   {
@@ -195,6 +200,9 @@
     "global_random_seed (int / str):  # int or 'random'\n",
     "    \n",
     "tasks:\n",
+    "  get_extended_similarity_indices:\n",
+    "    # Extended Similarity Indices has no options\n",
+    "\n",
     "  compare_target_molecule:\n",
     "    target_molecule_smiles (str):\n",
     "    draw_molecule (bool):  # If true, strucures of target, most and least similar molecules are displayed\n",

README.md

@@ -47,16 +47,17 @@ When proposing a novel reaction it is essential for the practicing chemist to ev
 Many of the substrates appear similar to one another and thereby redundant, but in reality the core sulfone moiety and the use of the same coupling partner when evaluating functional group tolerance accounts for this apparent shortcoming. Also of note is the region of high similarity along the diagonal where the substrates often differ by a single halide heteratom or substitution pattern.
 
 ## Installing AIMSim
-`AIMSim` can be installed with a single command:
+`AIMSim` can be installed with a single command using Python's package manager `pip`:
 `pip install aimsim`
-This command also installs the required dependencies. It is recommended to install `AIMSim` in a separate virtual environment.
+This command also installs the required dependencies.
+It is recommended to install `AIMSim` in a virtual environment with [`conda`](https://docs.conda.io/en/latest/) or Python's [`venv`](https://docs.python.org/3/library/venv.html).
 
-_Optional:_ Previous versions of AIMSim provided direct support for the descriptors provided in the `mordred` package. Unforunately, `mordred` is no longer recieving updates and causes significant depdendency conflicts. Because of this, it is an _optional_ add-on to `AIMSim` that is only compatible with Python 3.8. To install with `mordred` support, use `pip install 'aimsim[mordred]'` (note the single quotes, necessary in `zsh`).
-
-Unit tests from previous versions of `AIMSim` have been kept but are not actively maintained due to the limitations above. Use `mordred` at your own risk.
+### Note for mordred-descriptor
+AIMSim v1 provided direct support for the descriptors provided in the `mordred` package but unfortunately the original `mordred` is now abandonware.
+The **unofficial** [`mordredcommunity`](https://github.com/JacksonBurns/mordred-community) is now used in version 2.1 and newer to deliver the same features but with support for modern Python.
 
 ## Running AIMSim
-`AIMSim` is compatible with Python 3.7 to 3.9.
+`AIMSim` is compatible with Python 3.8 to 3.11.
 Start `AIMSim` with a graphical user interface:
 
 `aimsim`
@@ -117,6 +118,10 @@ Developer: Himaghna Bhattacharjee, Vlachos Research Lab. ([LinkedIn](www.linkedi
 
 Developer: Jackson Burns, Don Watson Lab. ([Personal Site](https://www.jacksonwarnerburns.com/))
 
+## `AIMSim` in the Literature
+ - [Applications of Artificial Intelligence and Machine Learning Algorithms to Crystallization](https://doi.org/10.1021/acs.chemrev.2c00141)
+ - [Recent Advances in Machine-Learning-Based Chemoinformatics: A Comprehensive Review](https://doi.org/10.3390/ijms241411488)
+
 ## Developer Notes
 Issues and Pull Requests are welcomed! To propose an addition to `AIMSim` open an issue and the developers will tag it as an _enhancement_ and start discussion.
 
@@ -141,12 +146,12 @@ Be sure to bump the version in `__init__.py`.
 ## Citation
 If you use this code for scientific publications, please cite the following paper.
 
-Bhattacharjee, H.҂; Burns, J.҂; Vlachos, D.G. (2021): AIMSim: An Accessible Cheminformatics Platform for Similarity Operations on Chemicals Datasets. ChemRxiv. Preprint. https://doi.org/10.26434/chemrxiv-2022-nw6f5
+Himaghna Bhattacharjee, Jackson Burns, Dionisios G. Vlachos, AIMSim: An accessible cheminformatics platform for similarity operations on chemicals datasets, Computer Physics Communications, Volume 283, 2023, 108579, ISSN 0010-4655, https://doi.org/10.1016/j.cpc.2022.108579.
 
 ## License
 This code is made available under the terms of the _MIT Open License_:
 
-Copyright (c) 2020 Himaghna Bhattacharjee & Jackson Burns
+Copyright (c) 2020-2027 Himaghna Bhattacharjee & Jackson Burns
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal