Merge pull request #17 from JacksonBurns/py2opsin106

bump to latest OPSIN release, update readme with opsin citation, etc

.github/workflows/ci.yml

@@ -0,0 +1,109 @@
+name: Continuous Integration
+on:
+  schedule:
+    - cron: "0 8 * * 1"
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+  workflow_dispatch:
+
+concurrency:
+  group: actions-id-${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  check-formatting:
+    name: Check Formatting Errors
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: Install Dependencies
+        run: |
+          python -m pip install pycodestyle autopep8
+          python -m pip install .
+      
+      - name: Run pycodestyle
+        run: |
+          pycodestyle --statistics --count --max-line-length=150 --show-source --ignore=E731 .
+
+  build-and-test:
+    needs: check-formatting
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11", "3.12"]
+        os: [ubuntu-latest, windows-latest, macos-latest]
+
+    runs-on: ${{ matrix.os }}
+    defaults:
+      run:
+        shell: bash -el {0}
+    name: ${{ matrix.os }} Python ${{ matrix.python-version }} Subtest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: mamba-org/setup-micromamba@main
+        with:
+          environment-name: temp
+          condarc: |
+            channels:
+              - defaults
+              - conda-forge
+            channel_priority: flexible
+          create-args: |
+            python=${{ matrix.python-version }}
+      - name: Install Dependencies
+        run: |
+          python -m pip install .[dev]
+          python -m pip install coverage
+      - name: Run Tests
+        run: |
+          coverage run --source=. --omit=py2opsin/__init__.py,setup.py,test/* -m unittest discover
+      - name: Show Coverage
+        run: |
+          coverage report -m
+  
+  ci-report-status:
+    name: report CI status
+    needs: build-and-test
+    runs-on: ubuntu-latest
+    steps:
+      - run: |
+          result="${{ needs.build-and-test.result }}"
+          if [[ $result == "success" ]] ; then
+            exit 0
+          else
+            exit 1
+          fi
+  
+  pypi-package:
+    name: Build and publish Python 🐍 distributions 📦 to PyPI
+    runs-on: ubuntu-latest
+    needs: ci-report-status
+    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
+

README.md

@@ -14,7 +14,7 @@
 </p> 
 
 ## Installation
-`py2opsin` can be installed with `pip install py2opsin`. It has _zero_ Python dependencies (`OPSIN v2.7.0` is included in the PyPI package) and should work inside any environment running modern Python. Java 8+ is required to run OPSIN.
+`py2opsin` can be installed with `pip install py2opsin`. It has _zero_ Python dependencies (`OPSIN v2.8.0` is included in the PyPI package) and should work inside any environment running modern Python. Java 8+ is required to run OPSIN.
 
 Try a demo of `py2opsin` live on your browser (no installation required!): [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/JacksonBurns/py2opsin/blob/main/examples/py2opsin_example.ipynb)
 
@@ -81,6 +81,17 @@ smiles_strings = py2opsin(compound_list)
 ## Online Documentation
 [Click here to read the documentation](https://JacksonBurns.github.io/py2opsin/)
 
+## Citation
+Please check [the OPSIN repository](https://github.com/dan2097/opsin#about-opsin) for the latest citation information, which as of October 2023 suggests citing this paper:
+```
+Chemical Name to Structure: OPSIN, an Open Source Solution
+Daniel M. Lowe, Peter T. Corbett, Peter Murray-Rust, Robert C. Glen
+Journal of Chemical Information and Modeling 2011 51 (3), 739-753
+```
+
+You may also see fit to mention that you used `py2opsin` to run `OPSIN`, but `py2opsin` itself isn't a significant scholarly effort and thus does not have a DOI.
+Providing a link to this GitHub repository along with the version of `py2opsin` used is sufficient.
+
 ## Contributing & Developer Notes
 Pull Requests, Bug Reports, and all Contributions are welcome! Please use the appropriate issue or pull request template when making a contribution.
 
@@ -90,9 +101,9 @@ When submitting a PR, please mark your PR with the "PR Ready for Review" label w
 
 To contribute to the `py2opsin` source code, start by cloning the repository (i.e. `git clone [email protected]:JacksonBurns/py2opsin.git`) and then inside the repository run `pip install -e .[dev]`. This will set you up with all the required dependencies to run `py2opsin` and conform to our formatting standards (`black` and `isort`), which you can configure to run automatically in vscode [like this](https://marcobelo.medium.com/setting-up-python-black-on-visual-studio-code-5318eba4cd00#:~:text=Go%20to%20settings%20in%20your,%E2%80%9D%20and%20select%20%E2%80%9Cblack%E2%80%9D.).
 
-Unit tests and performance tests can be executed with `pytest`, but note that performance tests are skipped on Windows due to speed issues with OPSIN on the platform.
+Unit and performance tests can then be executed with `pytest`.
 
-__Note for Windows Powershell or MacOS Catalina or newer__: On these systems the command line will complain about square brackets, so you will need to double quote the `molecules` command (i.e. `pip install -e ".
+__Note for Windows Powershell or MacOS Catalina or newer__: On these systems the command line will complain about square brackets, so you will need to double quote the install command (i.e. `pip install -e ".[dev]"`).
 
 ## License
 `OPSIN` and `py2opsin` are both distributed under the MIT license.

py2opsin/__init__.py

@@ -1,3 +1,3 @@
 from .py2opsin import py2opsin
 
-__version__ = "1.0.5"
+__version__ = "1.0.6"

py2opsin/py2opsin.py

@@ -71,7 +71,7 @@ def py2opsin(
     """
     # path to OPSIN jar
     if jar_fpath == "default":
-        jar_fpath = pkg_fopen("opsin-cli-2.7.0-jar-with-dependencies.jar")
+        jar_fpath = pkg_fopen("opsin-cli-2.8.0-jar-with-dependencies.jar")
 
     # default arguments to start
     arg_list = ["java", "-jar", jar_fpath]