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Cookiecutter for Computational Molecular Sciences (CMS) Python Packages

A cookiecutter template for those interested in developing computational molecular packages in Python. Skeletal starting repositories can be created from this template to create the file structure semi-autonomously, so you can focus on what's important: the science!

The skeletal structure is designed to help you get started, but do not feel limited by the skeleton's features included here. Just to name a few things you can alter to suit your needs: change continuous integration options, remove deployment platforms, or test with a different suite.

Features

• Python-centric skeletal structure with initial module files
• Pre-configured pyproject.toml and setup.cfg for installation and packaging
• Pre-configured Windows, Linux, and OSX continuous integration on GitHub Actions.
• Choice of dependency locations through conda-forge, default conda, or pip
• Basic testing structure with PyTest
• Automatic git initialization + tag
• GitHub Hooks
• Automatic package version control with Versioningit
• Sample data inclusion with packaging instructions
• Basic documentation structure powered by Sphinx
• Automatic license file inclusion from several common Open Source licenses (optional)

Requirements

• Python 3.8, 3.9, or 3.10
• Cookiecutter
• Git

Usage

With cookiecutter installed, execute the following command inside the folder you want to create the skeletal repository.

cookiecutter gh:molssi/cookiecutter-cms

Which fetches this repository from github automatically and prompts the user for some simple information such as package name, author(s), and licences.

Supported Python Versions

The MolSSI Cookiecutter will strive to support the current version of Python, two minor versions before. This philosophy is in align with Conda-Forge's guidelines and gives projects ample time to implement new features.

When to drop support for older Python versions?

Project developers can freely choose when to drop support for older versions of Python, or if they don't want to support as many. The general rules we recommend are:

• Support at least two Python versions: The most recent and the preceding minor version. E.g. 3.9 and 3.8
• Dropping Python versions should require a minor Project Version increment.
• New Python versions have been supported for at least one minor revision. E.g Project X.Y supports Python 3.8 and 3.9; Project X.Y+1 supports Python 3.8, 3.9 and 3.10; Project X.Y+2 supports Python 3.9 and 3.10.
• Add deprecation warnings if features will be removed.

Where is setup.py?

For a long time, many Python projects relied on one of the libraries distutils or setuptools and a corresponding meta-data defining file often called setup.py. These dependencies required python to run, and by its nature limited how much configuration could be done. setup.py has since been superseded by a new file called pyproject.toml, which is a build-system agnostic file which serves much of the same purpose, but can be extended to any number of tools, many of which can be retrieved from the internet simply by defining it in the pyproject.toml file. Many of the features which were in setup.py can be replaced by equivalent keys in the pyproject.toml. By default, the cookiecutter uses the setuptools backend anyways, just with the modernized install specification.

Next steps and web integrations

The repository contains a number of "hooks" that integrate with a variety of web services. To fully integrate the project with these web services and to get started developing your project please proceed through the following directions.

Local installation

For development work it is often recommended to do a "local" python install via pip install -e .. This command will insert your new project into your Python site-packages folder so that it can be found in any directory on your computer.

Setting up with GitHub

Upon creation, this project will initialize the output as a git repository. However, this does not automatically register the repository with GitHub. To do this, follow the instructions for Adding an existing project to GitHub using the command line . Follow the first step to create the repository on GitHub, but ignore the warnings about the README, license, and .gitignore files as this repo creates them. From there, you can skip to after the "first commit" instructions and proceed from there.

Testing

The Python testing framework was chosen to be pytest for this project. Other testing frameworks are available; however, the authors believe the combination of easy parametrization of tests, fixtures, and test marking make pytest particularly well suited for molecular software packages.

To get started additional tests can be added to the project/tests/ folder. Any function starting with test_* will automatically be included in the testing framework. While these can be added in anywhere in your directory structure, it is highly recommended to keep them contained within the project/tests/ folder.

Tests can be run with the pytest -v command. There are a number of additional command line arguments to explore.

Continuous Integration (GitHub Actions)

As of version 1.3, we provide preconfigured workflows for GitHub Actions, with support for Linux, MacOS and Windows. Conda support is possible thanks to the excellent @mamba-org's provision-with-micromamba action. We encourage you read its documentation for further details on GitHub Actions themselves.

The Cookiecutter's GitHub Actions does a number of things differently than the output Actions. We detail those differences below, but none of this is needed to understand the output GitHub Action Workflows, which are much simpler.

The Cookiecutter ability to test GitHub Actions it generates has some limitations, but are still properly tested. This repository has a multi-job GitHub Action Workflow to do a few things:

• Run the Cookiecutter and generate outputs.
• Compare the output CI's to references.
• Run an approximate implementation of the generated CI files.

If the reference files need re-generated, there is a script to help with this.

Ideally, the Cookiecutter would run the generated output files in real time. However, that is currently impossible with GitHub Actions (as of October 14 2020). We Cookiecutter-CMS maintainers have also looked at reactive PR’s which implement on different branches and make new PR’s and setting up dummy repositories and pushing to those and then monitoring the test/return from that. This was all determined to be overly complicated, although we welcome suggestions and ideas for improvements.

Discontinued CI Strategies: Travis & AppVeyor

We no longer recommend projects to use Travis-CI or AppVeyor for CI services. We found the AppVeyor service to be notorious slow in practice, and Travis updated their billing model to charge for OSX testing and further limit their Linux concurrency, even for fully open source software. Given the rise of GitHub Actions, we feel it was appropriate to transition off these platforms as of the CMS Cookiecutter's 1.5 release.

The final version of the CMS-Cookiecutter with Travis and AppVeyor support can be found here: https://github.com/MolSSI/cookiecutter-cms/releases/tag/1.4 for legacy purposes.

Pre-caching common build data

Some continuous integration platforms allow for caching of build data, which you may, or may not, find advantageous. The general purpose of the caches are to store and fetch files and folders which may take a long time to either generate or download every time you want to run a CI build; often because build (and developer) time is limited. However, if the cached data changes any time during a build, then the whole targeted cache is updated and uploaded. So, you should only cache things you do not expect to change.

You may be tempted to cache the Conda installer or Python dependencies fetched from conda or pip, however, this is an ill advised idea for two main reasons:

1. Your package's dependencies are constantly updating, so you want catch things which break due to dependencies before your user does. Having CI automatically trigger when you make changes and at scheduled intervals helps catch these things as soon as possible.
   • Because you should expect dependencies updating, you will have to upload a new cache each build anyways, somewhat invalidating one of the advantages of a cache.
2. It is a good idea to make sure your testing emulates the most basic user of your code if possible. If your target users include people who will try to download your package and have it "just work" for their project, then your CI testing should try to do this as well. This would include getting newest, updated installer and dependencies. One example of this may be industry, non-developer users, who do not know all the nuances and inner workings of package dependencies or versions. It is not reasonable to expect them to know these nuances either, its why you are the developer.

There may be some times where the caching feature is helpful for you. One example: including test data which is too large to store on GitHub, but also has a slow mirror hosting it. A cache will help speed up the test since you will not have to download from the slower mirror. If you this sounds like a helpful feature, you can check out the links below. We do not implement them for this Cookiecutter, but they can be added to your package as needed.

• GitHub Actions Caching

There are caching capabilities for the mamba-org/provision-with-micromamba action, if you are using it as well.

• Setup Micromamba GHA Caching

Documentation

Make a ReadTheDocs account and turn on the git hook. Although you can manually make the documentation yourself through Sphinx, you can also configure ReadTheDocs to automatically build and publish the documentation for you. The initial skeleton of the documentation can be found in the docs folder of your output.

Static Code Analysis

Make a LGTM account and add your project. If desired you can add code review integration by clicking the large green button!

Static code analysis dramatically enhances the quality of your code by finding a large number of common mistakes that both novice and advanced programmers make. There are many static analysis codes on the market, but we have seen that LGTM is a delicate balance between verbosity and catching true errors.

Additional Python Settings in setup.cfg

This Cookiecutter generates the package, but there are a several package-specific Python settings you can tune to your package's installation needs. These are settings in the setup.cfg file, which contains instructions for Python on how to install your package. Each of the options in the file are commented with what it does and when it should be used.

Versioningit

Versioningit automatically provides a version string based on the git tag and commit hash, which is then exposed through a project.__version__ attribute in your project/__init__.py. For example, if you mint a tag (a release) for a project through git tag -a 0.1 -m "Release 0.1." (push to GitHub through git push origin 0.1), this tag will then reflect in your project: project.__version__ == 0.1. Otherwise, a per-commit version is available which looks like 0.3.0+81.g332bfc1. This string shows the current git (the "g") hash 332bfc1 is 81 commits beyond the version 0.3 tag.

Conda and PyPI (pip)

Should you deploy and/or develop on Conda (with the conda-build tool) or PyPI (with the pip tool)? Good question, both have their own advantages and weaknesses as they both are designed to do very different things. Fortunately, many of the features you will need for this Cookiecutter overlap. We will not advocate here for one or the other, nor will we cover all the differences. We can however recommend some additional resources where you can read and find out more at the end of this section.

We will cover the major differences that you the developer will see between the two as they relate to this Cookiecutter.

For testing purpose, the PyPi tool, pip, is much faster about building your packages than the Conda tool, conda-build, will be. Depending on the number of dependencies, you may have conditions where conda-build takes 10-20 min to resolve, download, configure, and install all dependencies before your tests start, whereas pip would do the same in about 5 min. It is also important to note that both pip and conda-build are not testing tools in and of themselves; they are deployment and dependency resolution tools. For pure testing, we include other packages like pytest.

From a deployment perspective, it is possible to deploy your package on both platforms, although doing so is beyond the scope of this Cookiecutter.

Lastly, these are optional features! You could choose to not rely on either Conda or PyPI, assuming your package does not need dependencies. We do highly recommend you pick one of them for dependency resolution so you (and your potential users) are not having to manually find and install all the dependencies you may have. To put some historical perspective on this, NumPy and SciPy used to ask the users to install the BLAS and LAPACK libraries on their own, and then also make sure they were linked correctly to use in Python. These hurdles are no longer required through the package managers, Huzzah!

Additional reading for Conda and PyPI

• Author of the Python Data Science Handbook from O'Rilley's Blog on Conda Myths and Misconceptions
• Conda's Package Management docs
• pip User Guide

Conda Build vs. Conda Environments

We recommend creating Conda environments rather than relying on conda build for testing purposes, assuming you have opted for Conda as a dependency manager. Earlier versions of this Cookiecutter would conduct testing by first bundling the package for distribution through Conda Build, and then installing the package locally to execute tests on. This had the advantage of ensuring your package could be bundled for distribution and that all of its dependencies resolved correctly. However, it had the disadvantage of being painfully slow and rather confusing to debug should things go wrong on the build, even before the testing.

The replacement option to this is to pre-create the conda environment and then install your package into it with no dependency resolution for testing. This helps separate out the concepts of testing and deployment which are separate actions, even though deployment should only come after testing, and you should be ready to do both. This should simplify and accelerate the testing process, but does mean maintaining two, albeit similar, files since a Conda Environment file has a different YAML syntax than a Conda Build meta.yaml file. We feel these benefits outweigh the costs and have adopted this model.

Deploying your code

Simply testing your code is insufficient for good coding practices; you should be ready to deploy your code as well. Do not be afraid of deployment though; Python deployment over the last several years has been getting easier, especially when there are others to manage your deployment for you. There are several ways to handle this. We will cover a couple here, depending on the conditions which best suit your needs. The list below is neither exhaustive nor exclusive. There are times when you may want to build your packages yourself and upload them for developmental purposes, but we recommend letting others handle (and help you) with deployment. These are meant to serve as guides to help you get started.

Deployment should not get in the way of testing. You could configure the GitHub Action scripts to handle the build stage after the test stage, but this should only be done by advanced users or those looking to deploy themselves.

Deployment Method 1: Conda Forge

The Conda Forge community is great, and it is the recommended location to deploy your packages. The community is highly active and many scientific developers have been moving here to access not only Conda Forge's deployment tools, but also for easy access to all the other Python packages which have been deployed on the platform. Even though they provide the deployment architecture, you need to still test your program's ability to be packaged through conda-build. If you choose either Conda dependency option, additional tests will be added to GitHub Actions which only package through conda-build.

This method relies on the conda meta.yaml file.

Deployment Method 2: Conda through someone else's manager

This option is identical to the Conda Forge method, but relies on a different group's deployment platform such as Bioconda or Omnia. Each platform has their own rules, which may include packaging your program yourself and uploading. Check each platform's instructions and who else deploys to them before choosing this option to ensure its right for you.

This method relies on the conda meta.yaml file.

Deployment Method 3: Upload package to PyPi

The Python Package Index (PyPi) is another place to manage your package and have dependencies resolve. This option typically relies on pip to create your packages and dependencies must be specified in your pyproject.toml file to resolve correctly.

Deployment Method 4: Manually upload your package to some source

Sometimes, your package is niche enough, developmental enough, or proprietary enough to warrant manually packaging and uploading your program. This may also apply if you want regular developmental builds which you upload manually to test. In this case, you will want to change your CI scripts to include a build, and optional upload step on completion of tests.

Output Skeleton

This will be the skeleton made by this cookiecutter, the items marked in {{ }} will be replaced by your choices upon setup.

.
├── CODE_OF_CONDUCT.md              <- Code of Conduct for developers and users
├── LICENSE                         <- License file
├── MANIFEST.in                     <- Packaging information for pip
├── README.md                       <- Description of project which GitHub will render
├── {{repo_name}}                   <- Basic Python Package import file
│   ├── {{first_module_name}}.py    <- Starting packge module
│   ├── __init__.py                 <- Basic Python Package import file
│   ├── _version.py                 <- Generated file from VersionInGit. Created on package install, not initilization.
│   ├── data                        <- Sample additional data (non-code) which can be packaged. Just an example, delete in production
│   │   ├── README.md
│   │   └── look_and_say.dat
│   ├── py.typed                    <- Marker file indicating PEP 561 type hinting.
│   └── tests                       <- Unit test directory with sample tests
│       ├── __init__.py
│       └── test_{{repo_name}}.py
├── devtools                        <- Deployment, packaging, and CI helpers directory
│   ├── README.md
│   ├── conda-envs                  <- Conda environments for testing
│   │   └── test_env.yaml
│   └── scripts
│       └── create_conda_env.py     <- OS agnostic Helper script to make conda environments based on simple flags
├── docs                            <- Documentation template folder with many settings already filled in
│   ├── Makefile
│   ├── README.md                   <- Instructions on how to build the docs
│   ├── _static
│   │   └── README.md
│   ├── _templates
│   │   └── README.md
│   ├── api.rst
│   ├── conf.py
│   ├── getting_started.rst
│   ├── index.rst
│   ├── make.bat
│   └── requirements.yaml           <- Documenation building specific requirements. Usually a smaller set than the main program
├── pyproject.toml                  <- Generic Python build system configuration (PEP-517).
├── readthedocs.yml
├── setup.cfg                       <- Near-master config file to make house INI-like settings for Coverage, Flake8, YAPF, etc.
├── .codecov.yml                    <- Codecov config to help reduce its verbosity to more reasonable levels
├── .github                         <- GitHub hooks for user contribution, pull request guides and GitHub Actions CI
│   ├── CONTRIBUTING.md
│   ├── PULL_REQUEST_TEMPLATE.md
│   └── workflows
│       └── CI.yaml
├── .gitignore                      <- Stock helper file telling git what file name patterns to ignore when adding files
├── .gitattributes                  <- Stock helper file telling GitHub how to bundle files in the tarball, should not need to be touched most times
└── .lgtm.yml

Acknowledgments

This cookiecutter is developed by Levi N. Naden and Jessica A. Nash from the Molecular Sciences Software Institute (MolSSI); and Daniel G. A. Smith of ENTOS. Additional major development has been provided by M. Eric Irrgang. Copyright (c) 2022.

Directory structure template based on recommendation from the Chodera Lab's Software Development Guidelines .

Original hosting of repository owned by the Chodera Lab

Elements of this repository drawn from the cookiecutter-data-science by Driven Data and the MolSSI Python Template