Contributing

Welcome to laue-dials developer’s guide.

This document focuses on outlining development processes, but other kinds of contributions are also appreciated.

Please note that all users and contributors are expected to be open, considerate, reasonable, honest, and respectful when contributing ideas, issues, documentation, or code.

Issue Reports

If you experience bugs or general issues with laue-dials, please have a look on the issue tracker. If you don’t see anything useful there, please feel free to fire an issue report.

New issue reports should include information about your programming environment (e.g., operating system, Python version) and steps to reproduce the problem. Please try also to simplify the reproduction steps to a very minimal example that still illustrates the problem you are facing. By removing other factors, you help us to identify the root cause of the issue.

Documentation Improvements

You can help improve laue-dials docs by making them more readable and coherent, or by adding missing information and correcting mistakes.

laue-dials documentation uses Sphinx as its main documentation compiler. This means that the docs are kept in the same repository as the project code, and that any documentation update is done in the same way as a code contribution. When working on documentation changes in your local machine, make sure you have installed the “docs” extension of the package:

pip install laue-dials[docs]

or if, more likely, you’ve cloned the repo and are installing from your local copy:

pip install -e ".[docs]"

This makes sure that in addition to laue-dials, you’ve also installed Sphinx and all of the necessary Sphinx extensions to build the docs. In particular, pandoc is a required dependency for building the docs. pandoc is available and can be installed with:

conda install -c conda-forge pandoc

To build a copy of the docs locally using your current environment, you can navigate into the docs/ subdirectory and call:

make clean
make html

Alternatively, to perform a clean build from the ground-up, you can run:

tox -e docs

The docs/_build/html/ directory should now contain .html files which can be opened in your web browser.

Adding docs for new command-line functions

In order for a command-line function to be added to the documention, you must do two things:

Create a file in the docs/cli/ directory called {function-name}.rst. The contents of this file should match the contents of the other .rst files in this directory, using the new function’s name as appropriate. The easiest thing is to just copy one of the existing files and update it. Note that if the ==== underlining the header laue_dials.{function-name} isn’t at least as long as the text, Sphinx will print the following: WARNING: Title underline too short.
Add the new function to the table of contents in docs/cli/functions.md. Otherwise, your new page will exist, but there will be no link to it anywhere!

In order for a new command-line function to be maximally compatible with this documentation format, three things should be true:

The function’s help_message should exist and contain a useful introduction to the function and it’s usage.
The function’s most commonly used parameters should have expert level 0.
Any parameters of the function that ever need to be available to the user should have expert level no higher than 2.

Adding other pages to the docs

New pages can be added to the docs by creating new files in the docs/ directory. Files can be either .rst (reStructuredText) or .md (Markdown) formats. Additionally, .md files can contain chunks of reStructuredText wrapped inside of {eval-rst} triple backticks:

## Markdown heading
Lots of *markdown* code.

```{eval-rst}
.. rstcommand::

```

Additionally, you must add any new pages to the table of contents listed in docs/index.rst. List your new page as Display Name <filename>, and place it where you’d like it to appear in order in the Table of Contents.

If you wish to make html directly, be sure to install pandoc via

conda install pandoc

first.

Code Contributions

To the extent possible, this software is to be written such that it functions as an extension of DIALS for the user. Software should be written in a modular form with a command-line interface for common crystallographic tasks needed during data analysis. The scope of this package is limited to Laue (i.e. wide spectral-bandwidth) crystallographic experiments, although multiple types of experiments under this umbrella can be supported.

Submit an issue

Before you work on any non-trivial code contribution it’s best to first create a report in the issue tracker to start a discussion on the subject. This often provides additional considerations and avoids unnecessary work. Please add an issue even when working on new features that don’t involve changes to existing code, to prevent overlaps in work with others.

Create an environment

Before you start coding, we recommend creating an isolated virtual environment to avoid any problems with your installed Python packages. This can easily be done via Miniconda:

conda create -n laue-dials python=3 six virtualenv pytest pytest-cov
conda activate laue-dials

Clone the repository

Create an user account on GitHub if you do not already have one.
Fork the project repository: click on the Fork button near the top of the page. This creates a copy of the code under your account on GitHub.

Clone this copy to your local disk:

git clone git@github.com:YourLogin/laue-dials.git
cd laue-dials

You should run:
```
pip install -U pip setuptools -e .
```
to be able to import the package under development in the Python REPL.
Install pre-commit:
```
pip install pre-commit
pre-commit install
```
laue-dials comes with a lot of hooks configured to automatically help the developer to check the code being written. Compliance with all hooks is necessary to contribute code to maintain code quality.

Implement your changes

Create a branch to hold your changes:
```
git checkout -b my-feature
```
and start making changes. Never work on the main branch!
Start your work on this branch. Don’t forget to add docstrings to new functions, modules and classes. Sphinx will automatically build documentation for your work.
Add yourself to the list of contributors in AUTHORS.rst if you are not already listed.
When you’re done editing, do:
```
git add <MODIFIED FILES>
git commit
```
to record your changes in git.

Please make sure to see the validation messages from pre-commit and fix any eventual issues. This should automatically use flake8/black to check/fix the code style in a way that is compatible with the project. Any unfixed issues will result in a rejected contribution.

Don’t forget to add unit tests and documentation in case your contribution adds an additional feature and is not just a bugfix.

Moreover, writing a descriptive commit message is mandatory. In case of doubt, you can check the commit history with:
```
git log --graph --decorate --pretty=oneline --abbrev-commit --all
```
to look for recurring communication patterns.
Please check that your changes don’t break any unit tests with:
```
tox
```
(after having installed tox-conda with pip install tox-conda or pipx).

You can also use tox-conda to run several other pre-configured tasks in the repository. Try tox -av to see a list of the available checks.

Submit your contribution

If everything works fine, push your local branch to GitHub with:
```
git push -u origin my-feature
```
Go to the web page of your fork and click “Create pull request” to send your changes for review. Find more detailed information in creating a PR.

Troubleshooting

The following tips can be used when facing problems to build or test the package:

Make sure to fetch all the tags from the upstream repository. The command git describe --abbrev=0 --tags should return the version you are expecting. If you are trying to run CI scripts in a fork repository, make sure to push all the tags. You can also try to remove all the egg files or the complete egg folder, i.e., .eggs, as well as the *.egg-info folders in the src folder or potentially in the root of your project.
Sometimes tox-conda misses out when new dependencies are added, especially to setup.cfg and docs/requirements.txt. If you find any problems with missing dependencies when running a command with tox-conda, try to recreate the tox environment using the -r flag. For example, instead of:
```
tox -e docs
```
Try running:
```
tox -r -e docs
```
Make sure to have a reliable tox-conda installation that uses the correct Python version (e.g., 3.7+). When in doubt you can run:
```
tox --version
# OR
which tox
```
Pytest can drop you in an interactive session in the case an error occurs. In order to do that you need to pass a --pdb option (for example by running tox -- -k <NAME OF THE FAILING TEST> --pdb). You can also setup breakpoints manually instead of using the --pdb option.

Maintainer tasks

Releases

If you are part of the group of maintainers and have correct user permissions on PyPI, the following steps can be used to release a new version for laue-dials:

Make sure all unit tests are successful.
Update CHANGELOG.rst with new features and changes for the new release.
Run git pull, resolve any merge conflicts, and then git push the source code.
Tag the current commit on the main branch with a release tag, e.g., git tag -a v0.1 -m 'Version message'.
Push the new tag to the upstream repository, e.g., git push origin v0.1
Navigate to https://github.com/rs-station/laue-dials/releases/new.
Select the appropriate tag and write a description for the release.
Set as a pre-release if necessary, and then publish the release on Github.
After Github Actions workflows have executed, check PyPI to ensure they worked correctly.

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