Merge pull request #102 from MobleyLab/gha

Migrate from Travis CI to GitHub Actions

.github/workflows/ci.yaml

@@ -0,0 +1,65 @@
+name: CI
+
+on:
+  push:
+    branches:
+      - "main"
+      - "master"
+  pull_request:
+    branches:
+      - "main"
+      - "master"
+
+defaults:
+  run:
+    shell: bash -l {0}
+
+jobs:
+  test:
+    name: ${{ matrix.os }}, 🐍=${{ matrix.python-version }}, OpenEye=${{ matrix.openeye }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [macOS-latest, ubuntu-latest]
+        openeye: ["false"]
+        python-version: ["3.8", "3.9", "3.10"]
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - uses: conda-incubator/setup-miniconda@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+        activate-environment: test
+        mamba-version: "*"
+        channels: conda-forge,defaults
+        channel-priority: true
+        environment-file: devtools/conda-envs/test_env_rdk.yaml
+        auto-activate-base: false
+
+    - name: Additional info about the build
+      shell: bash
+      run: |
+        uname -a
+        df -h
+        ulimit -a
+
+    - name: Environment Information
+      run: |
+        conda info
+        conda list
+
+    - name: Install package
+      run: |
+        python setup.py develop --no-deps
+
+    - name: Run tests
+      run: |
+        py.test -vv -s --nbval-lax --cov=chemper/ --cov-report=xml chemper/tests/ 
+
+    - name: Codecov
+      uses: codecov/codecov-action@v3
+      with:
+        file: ./coverage.xml
+        fail_ci_if_error: false

README.md

@@ -1,9 +1,5 @@
 # <img src="https://github.com/mobleylab/chemper/blob/master/chemper_logo.svg" height=150>
 
-[![Travis build](https://img.shields.io/travis/MobleyLab/chemper/master.svg?logo=linux&logoColor=white)](https://travis-ci.org/MobleyLab/chemper)
-[![Travis build](https://img.shields.io/travis/MobleyLab/chemper/master.svg?logo=apple&logoColor=white)](https://travis-ci.org/MobleyLab/chemper)
-[![AppVeyor build](https://img.shields.io/travis/MobleyLab/chemper/master.svg?logo=windows&logoColor=white)](https://ci.appveyor.com/project/bannanc/chemper)
-
 [![Documentation Status](https://readthedocs.org/projects/chemper/badge/?version=latest)](http://chemper.readthedocs.io/en/latest/?badge=latest)
 [![Language grade: Python](https://img.shields.io/lgtm/grade/python/g/MobleyLab/chemper.svg?logo=lgtm&logoWidth=18)](https://lgtm.com/projects/g/MobleyLab/chemper/context:python)
 [![codecov](https://codecov.io/gh/MobleyLab/chemper/branch/master/graph/badge.svg)](https://codecov.io/gh/MobleyLab/chemper)
@@ -25,45 +21,41 @@ practical use in force field parameterization [2].
 
 For a more extensive history and explanation, see our [preprint](http://doi.org/10.26434/chemrxiv.8304578.v1) [3].
 
-## Prerequisites
-
-We test with Python 3.6 and 3.7 and expect any version above 3.5 to behave well.
+## Installation
 
-This is a python tool kit with a few dependencies. We recommend installing
-[miniconda](http://conda.pydata.org/miniconda.html). Then you can create an
-environment with the following commands:
+Chemper is available via `conda-forge`:
 
-```bash
-conda create -n [my env name] python=3.6 numpy networkx pytest
-source activate [my env name]
+```shell
+conda install -c conda-forge chemper
 ```
 
 This command will install all dependencies besides a toolkit for cheminformatics or storing of molecule
-information. We seek to keep this tool independent of cheminformatics toolkit, but currently only support
-[RDKit](http://www.rdkit.org/docs/index.html) and [OpenEye Toolkits](https://www.eyesopen.com/).
-If you wish to add support please feel free to submit a pull request.
-Make sure one of these tool kits is installed in your environment before installing chemper.
+information. Also install [RDKit](http://www.rdkit.org/docs/Install.html) and/or
+[OpenEye toolkits](https://docs.eyesopen.com/toolkits/python/quickstart-python/linuxosx.html) by
+running:
 
-#### RDKit environment
-
-Conda installation according to [RDKit documentation](http://www.rdkit.org/docs/Install.html):
 ```bash
-conda install -c rdkit rdkit
+conda install -c conda-forge rdkit
 ```
 
-#### OpenEye environment
-Conda installation according to [OpenEye documentation](https://docs.eyesopen.com/toolkits/python/quickstart-python/linuxosx.html)
+and/or
+
 ```bash
 conda install -c openeye openeye-toolkits
 ```
 
-## Installation
 
-Hopefully chemper will be conda installable in the near future, but for now the best option
-is to download or clone this repository and then install `chemper` from inside the `chemper` directory with:
-```bash
-pip install -e .
-```
+## Supported Python versions
+
+We test with whatever Python versions are found in `.github/workflows/ci.yaml`. Chemper may function
+on some older and/or newer versions as well.
+
+## Supported chemiformatics toolkits
+
+We seek to keep this tool independent of cheminformatics toolkit, but currently only support
+[RDKit](http://www.rdkit.org/docs/index.html) and [OpenEye Toolkits](https://www.eyesopen.com/).
+If you wish to add support please feel free to submit a pull request.
+Make sure one of these toolkits is installed in your environment before installing chemper.
 
 # Documentation
 
@@ -155,6 +147,8 @@ for automated chemical perception. However, the API is still in flux and nothing
 This release matches the work published in our [preprint](http://doi.org/10.26434/chemrxiv.8304578.v1).
 While the code is stable and there are tests showing how it should work the science it represents is still in the early stages and big changes to the algorithms and API should be expected in future releases.
 
+### Version 1.0.1
+This release includes non-behavior-breaking changes to support distribution on Python 3.10.
 
 ## Contributors
 

chemper/chemper_utils.py

@@ -6,7 +6,7 @@
 """
 
 import os
-import collections
+from collections.abc import MutableMapping
 
 def get_data_path(relative_path, package='chemper'):
     """
@@ -120,7 +120,7 @@ def is_valid_smirks(smirks):
 """
 
 
-class TransformedDict(collections.MutableMapping):
+class TransformedDict(MutableMapping):
     """A dictionary that applies an arbitrary key-altering
        function before accessing the keys"""
 

devtools/README.md

@@ -6,28 +6,13 @@ conda installation, and other development tools not directly related to the codi
 
 ## Manifest
 
-### Continuous Integration
-
-You should test your code, but do not feel compelled to use these specific programs. You also may not need Unix and 
-Windows testing if you only plan to deploy on specific platforms. These are just to help you get started
-
-* `travis-ci`: Linux and OSX based testing through [Travis-CI](https://about.travis-ci.com/) 
-  * `before_install.sh`: Pip/Miniconda pre-package installation script for Travis 
-* `appveyor`: Windows based testing through [AppVeyor](https://www.appveyor.com/) (there are no files directly related to this)
-
 ### Conda Environment:
 
 This directory contains the files to setup the Conda environment for testing purposes
 
 * `conda-envs`: directory containing the YAML file(s) which fully describe Conda Environments, their dependencies, and those dependency provenance's
   * `test_env.yaml`: Simple test environment file with base dependencies. Channels are not specified here and therefore respect global Conda configuration
 
-### Additional Scripts:
-
-This directory contains OS agnostic helper scripts which don't fall in any of the previous categories
-* `scripts`
-  * `create_conda_env.py`: Helper program for spinning up new conda environments based on a starter file with Python Version and Env. Name command-line options
-
 
 ## How to contribute changes
 - Clone the repository if you have write access to the main repo, fork the repository if you are a collaborator.

devtools/conda-envs/test_env_rdk.yaml

@@ -10,6 +10,7 @@ dependencies:
 
   - rdkit
   - numpy
+  - networkx
 
     # Testing
   - pytest