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Contributing to autodE

Contributing to autodE#

Contributions in any form are very much welcome. To make managing these easier, we kindly ask that you follow the guidelines below.

Reporting a bug or suggesting changes/improvements#

If you think you’ve found a bug in autode, please let us know by opening an issue on the main autodE GitHub repository. This will give the autodE developers a chance to confirm the bug, investigate it and… fix it!

When reporting an issue, we suggest you follow the following template:

  • Operating System: (e.g. Ubuntu Linux 20.04)

  • Python version: (e.g 3.9.4)

  • autodE version: (e.g. 1.1.2)

Description: A one-line description of the bug.

To Reproduce: The exact steps to reproduce the bug.

Expected behaviour: A description of what you expected instead of the observed behaviour.

When it comes to reporting bugs, the more details the better. Do not hesitate to include command line output or screenshots as part of your bug report.

An idea for a fix?, feel free to describe it in your bug report.

Contributing to the code#

Anybody is free to modify their own copy of autodE. We would also love for you to contribute your changes back to the main repository, so that other autodE users can benefit from them.

The high-level view of the contributing workflow is:

  1. Fork the main repository (duartegroup/autode).

  2. Implement changes and tests on your own fork on a given branch (<gh-username>/autode:<branch-name>).

  3. Create a new pull request on the main autodE repository from your development branch onto autode:v1.X, where X is the latest version.

To learn more about GitHub forks and pull requests, read Fork a repo and Creating a pull request on the GitHub docs.

Guidelines for pull requests#

First, install from source in a new environment and setup pre-commit with:

$ git clone https://github.com/duartegroup/autodE.git && cd autodE
$ conda create -n ade python=3.9 --file requirements.txt --channel conda-forge
$ conda activate ade
$ pip install '.[dev]'
$ pre-commit install

Forks instead of branches#

By default, contributors do not have permission to push branches to the main autodE remote repository (duartegroup/autode). In most cases, you should contribute to autodE through a pull request from a fork.

Several, smaller pull requests instead of one big PR#

Smaller pull requests (PRs) are reviewed faster, and more accurately. We therefore encourage contributors to keep the set of changes within a single pull request as small as possible. If your pull request modifies more than 5 files, and/or several hundred lines of code, please break it down into two or more pull requests.

Pull requests are more than code#

A pull request is difficult to review without a description of context and motivation for the attached set of changes. Whenever you open a new pull request, please include the following information:

  • A title that explicits the main change addressed by the pull request. If you struggle to come out with a short and descriptive title, this is an indication that your PR could (should?) be broken down into smaller PRs.

  • A description of the context and motivation for the attached set of changes. What is the current state of things?, Why should it be changed?.

  • A summary of changes outlining the main points addressed by your pull request, and how they relate to each other. Be sure to mention any assumption(s) and/or choices that your made and alternative design/implementaions that you considered. What did you change or add? How?. Anything you could have done differently? Why not?.

  • Some advice for reviewers. Indicate the parts of your changes on which you would expect reviewers to focus their attention. These are often parts that you are unsure about or code that may be difficult to read.

Draft pull requests#

Draft pull requests are a way to signal to other developers that you are currently working on something and open for discussion about it. It’s also providing the development team a glimpse of future code reviews.

Look out for the “Convert to draft” button on the right hand side pane when creating a pull request.

Style guidelines#

Enforcing code style in contributions is key to maintain a consistent code base.

Formatting#

autodE’s code loosely follows the PEP8 guidelines for code formatting. At the very least, we expect all contributors to use formatters like Black, autopep8 or YAPF.

Naming#

  1. Variables

    • Variable names should be snake_case.

  2. Functions

    • Like variables, function names should be snake_case.

    • Functions should always exit with an explicit return statement, even if means return None.

    • Functions should raise ValueError for invalid input.

    • Functions should return None rather than raising exceptions upon failure. If something is irrevocably wrong they should raise a RuntimeError.

    • Docstrings are in Google format. See Comments and Docstrings in the Google Python Style Guide.

    • Functions should be type annotated:

      def _plot_reaction_profile_with_complexes(self,
                      units:       'autode.units.Unit',
                      free_energy: bool,
                      enthalpy:    bool) -> None:
    """Plot a reaction profile with the association complexes of R, P"""

    # ...

      To learn more about type annotations, read Type Checking in Python (realpython.com).

  3. Classes

    • Classes names should be ‘CamelCase’.

Custom types instead of primitive types#

For numbers and arrays that have associated units autode makes use of custom floats (autode.values.Value) and numpy arrays (autode.values.ValueArray). These have unit conversion with a to() method and enable comparison of quantities independent of units.

>>> from autode.values import Distance
>>> r = Distance(1.0)
>>> r                                  # Values have default units
Distance(1.0 Å)
>>> r.to('nm')                         # and to() methods
Distance(0.1 nm)
>>> r.to('nanometer')                  # that allow for unit name alises
Distance(0.1 nm)
>>> r > Distance(9.0, units='pm')      # also allow for comparisons
True
>>> r.to('eV')              # and raise exceptions for impossible conversion
...
TypeError: No viable unit conversion from Unit(Å) -> eV

New quantities with units should be autode values.

Versioning#

Versioning is semantic in the X.Y.Z style. X is unlikely to exceed 1 baring a complete rewrite; Y should be updated whenever there are backwards incompatible changes; Z should be incremented for bugfixes and tweaks that maintain all components of the public facing API.

Tests#

As much as possible, contributions should be tested.

Tests live in tests/, with roughly one test_<module> per module or class. Unless your contribution adds a new module, your tests should be added to an existing test file.

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