add a conda package (#132)

This PR adds `astartes` to `conda` on [this
channel](https://anaconda.org/JacksonBurns/astartes) with a new GitHub
action for automatically building and uploading the package. I have also
manually gone back and added the current and previous releases to 1.0.0
to the channel.

.github/workflows/publish_packages.yml

@@ -0,0 +1,91 @@
+name: Publish Packages
+
+on:
+  push:
+    branches: [ "main" ]
+  workflow_dispatch:
+
+jobs:
+  check-for-new-release:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Check PyPI version
+        uses: maybe-hello-world/pyproject-check-version@v3
+        id: versioncheck
+        with:
+          pyproject-path: "./pyproject.toml"
+
+      - name: Report Results
+        run: |
+            echo "New Release found? ${{ steps.versioncheck.outputs.local_version_is_higher }}"
+            echo "Local version: ${{ steps.versioncheck.outputs.local_version }}"
+            echo "Public version: ${{ steps.versioncheck.outputs.public_version }}"
+    outputs:
+      do_publish: ${{ steps.versioncheck.outputs.local_version_is_higher }}
+
+  pypi:
+    name: Build and publish Python 🐍 distributions 📦 to PyPI
+    runs-on: ubuntu-latest
+    needs: check-for-new-release
+    if: needs.check-for-new-release.outputs.do_publish
+    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
+  conda:
+    name: Build and publish Conda distrbutions
+    needs: pypi  # wait for pypi build to finish
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -el {0}  # login bash for conda calls
+    steps:
+      - uses: actions/checkout@master
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v3
+        with:
+          python-version: "3.10"
+      - name: Setup miniconda
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          auto-activate-base: true
+          activate-environment: ""
+      - name: Install build dependencies
+        run: |
+          conda install conda-build anaconda-client
+          conda install -c conda-forge grayskull
+          conda config --set anaconda_upload yes
+      - name: Build and Push astartes
+        env:
+          ANACONDA_API_TOKEN: ${{ secrets.ANACONDA_API_TOKEN }}
+        run: |
+          cd ..
+          sleep 60s  # wait for the PyPI package to be visible
+          grayskull pypi astartes
+          cd astartes
+          conda build .
+      

README.md

@@ -22,7 +22,13 @@ We recommend installing `astartes` within a virtual environment, using either `v
  - To include the featurization options for chemical data, use `pip install astartes[molecules]`.
  - To install only the sampling algorithms, use `pip install astartes` (this install will have fewer dependencies and may be more readily compatible in environments with existing workflows).
 
-__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 "astartes[molecules]"`)
+The base `astartes` package is also available on `conda` with this command: `conda install -c jacksonburns astartes`.
+Note that this package _does not_ include built-in support for featurizing molecules, which is currently only available from the PyPI package or a source install.
+
+> **Note**
+> Windows Powershell and MacOS Catalina or newer may complain about square brackets, so you will need to double quote the `molecules` command (i.e. `pip install "astartes[molecules]"`)
+
+To install `astartes` from source, see the [Contributing & Developer Notes](#contributing--developer-notes) section.
 
 ## Using `astartes`
 `astartes` is designed as a drop-in replacement for `sklearn`'s `train_test_split` function. To switch to `astartes`, change `from sklearn.model_selection import train_test_split` to `from astartes import train_test_split`.
@@ -57,6 +63,8 @@ Click the badges in the table below to be taken to a live, interactive demo of `
 | Cheminformatics sample set partitioning with `astartes` | [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/JacksonBurns/astartes/main?labpath=examples%2Fbarrier_prediction_with_RDB7%2FRDB7_barrier_prediction_example.ipynb) |
 | Comparing partitioning approaches for alkanes | [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/JacksonBurns/astartes/main?labpath=examples%2Fmlpds_2023_astartes_demo%2Fmlpds_2023_demo.ipynb) |
 
+To execute these notebooks locally, clone this repository (i.e. `git clone https://github.com/JacksonBurns/astartes.git`), navigate to the `astartes` directory, run `pip install .[demos]`, then open and run the notebooks in your preferred editor.
+
 ### Rational Splitting Algorithms
 While much machine learning is done with a random choice between training/validation/test data, an alternative is the use of so-called "rational" splitting algorithms. These approaches use some similarity-based algorithm to divide data into sets. Some of these algorithms include Kennard-Stone, minimal test set dissimilarity, and sphere exclusion algorithms [as discussed by Tropsha et. al](https://pubs.acs.org/doi/pdf/10.1021/ci300338w) as well as the OptiSim as discussed in [Applied Chemoinformatics: Achievements and Future Opportunities](https://www.wiley.com/en-us/Applied+Chemoinformatics%3A+Achievements+and+Future+Opportunities-p-9783527806546). Some clustering-based splitting techniques have also been incorporated, such as [DBSCAN](http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.1016.890&rep=rep1&type=pdf).
 
@@ -148,7 +156,8 @@ When submitting a PR, please mark your PR with the "PR Ready for Review" label w
 
 To contribute to the `astartes` source code, start by cloning the repository (i.e. `git clone [email protected]:JacksonBurns/astartes.git`) and then inside the repository run `pip install -e .[molecules,dev]`. This will set you up with all the required dependencies to run `astartes` 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.).
 
-__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 ".[molecules,dev]"`)
+> **Note**
+> Windows Powershell and MacOS Catalina or newer may complain about square brackets, so you will need to double quote the `molecules` command (i.e. `pip install "astartes[molecules,dev]"`)
 
 ### Unit Testing
 All of the tests in `astartes` are written using the built-in python `unittest` module (to allow running without `pytest`) but we _highly_ recommend using `pytest`. To execute the tests from the `astartes` repository, simply type `pytest` after running the developer install (or alternately, `pytest -v` for a more helpful output).