Development guidelines¶

Coding guidelines¶

The following are some guidelines on how new code should be written. Of course, there are special cases and there will be exceptions to these rules. However, following these rules when submitting new code makes the review easier so new code can be integrated in less time.

Uniformly formatted code makes it easier to share code ownership. The pydov project tries to closely follow the official Python guidelines detailed in PEP8 which detail how code should be formatted and indented. Please read it and follow it.

In addition, we add the following guidelines:

Use underscores to separate words in non class names: n_samples rather than nsamples.
Avoid multiple statements on one line. Prefer a line return after a control flow statement (if/for).
Please don’t use import * in any case. It is considered harmful by the official Python recommendations. It makes the code harder to read as the origin of symbols is no longer explicitly referenced, but most important, it prevents using a static analysis tool like pyflakes to automatically find bugs.
Use the numpy docstring standard in all your docstrings.
The attributes for specific classes are Pandas data.frames, please use lowercase names (eventually with _) as column names.

Contributing workflow¶

The preferred workflow for contributing is to fork the main repository on GitHub, clone locally, and develop on a branch. For more information on this workflow, see the github workflow.

The workflow is provided for command line usage and using the Github for Desktop application. Feel free to use the environment you like the most.

Fork the project repository by clicking on the ‘Fork’ button near the top right of the page. This creates a copy of the code under your personal GitHub user account.
You’ve successfully forked the pydov repository, but so far, it only exists on GitHub. To be able to work on the project, you will need to clone it to your computer.

Clone your fork of the pydov repo from your GitHub account to your local disk:
```
$ git clone https://github.com/YOUR-GITHUB-USERNAME/pydov.git
$ cd pydov
```
If you’re using the GitHub for Desktop application, navigate over to the bottom on the right hand side bar and click Clone in Desktop. Once you’ve clicked this, it’ll ask you if you want to launch our desktop application to clone the repository, and where you want to save it. Pick a location on your computer that you feel comfortable with creating files and folders.
Create a my-feature branch (give it the name of the feature you want to develop) to hold your development changes:
```
$ git checkout -b my-feature
```
When using Github for Desktop, in the top left corner of the repository view, create a new branch.

Always use a my-feature branch. It’s good practice to never work on the master branch.
Make sure your development environment is setup to have all the required tooling available (code, unit tests, documentation,…).

Create a development environment, for example using conda or venv:
```
# using conda:
   $ conda create -n pydov python=3.11
   $ conda activate pydov

# or using venv (commands are OS dependent):
   # linux users
   $ python3 -m venv pydov/venv              # linux users
   $ source pydov/venv/bin/activate          # linux users

   # windows users
   $ python3 -m venv pydov\venv              # windows users
   $ pydov\venv\Scripts\activate             # windows users
```
The Python documentation on virtual environments provides more guidance on using a development environment.

From inside the “pydov” repository folder, install all development dependencies and the package in development mode:
```
$ pip install -e .[devs]
```
To build the documentation, make sure to also install pandoc as it is required by Sphinx, the tool used to generate the documentation website. See the pandoc installation instructions.

Note

If the sphinx-build (or make html) CLI command returns an error, try to reinstall sphinx separately in the environment using pip install -U sphinx.

Have a look at the development guidelines to see how we develop the pydov package and get more information on the workflow.
Note

The repository contains multiple requirements_*.txt files:
- requirements.txt required packages to use pydov
- requirements_geom.txt required packages to use geometry fields and vector files (GeometryFilter and GeopandasFilter) in pydov
- requirements_proxy.txt required packages to use proxy server autodiscovery in pydov
- requirements_dev.txt required packages to run the pydov test suite and contribute to pydov code
- requirements_doc.txt required packages to build the pydov documentation and contribute to the pydov documentation
- binder/requirements.txt requirements setup to setup a Binder environment
When adding dependencies, make sure to make the appropriate adjustments in the individual file!
Develop the feature on your feature branch. Add changed files using git add and then git commit files:
```
$ git add modified_files
$ git commit
```
which is similar in Github for Desktop, just craft your commit message in the UI.

Make sure you split your contribution in small commits with well-describing names. Write unit tests for new features and make sure these tests are successful. Have a look at the section on unit tests on how to run the unit tests. Don’t forget to update the documentation pages, see the section on sphinx documentation.
Right now, you’ve essentially told Git, “Okay, I’ve taken a snapshot of my changes!” You can continue to make more changes, and take more commit snapshots. When you’re ready to push your changes up to GitHub.com, push the changes to your GitHub account with:
```
$ git push -u origin my-feature
```
or, using the Github for Desktop, click on the Sync button, which is right above your list of changes.
Go to the GitHub web page of your fork of the pydov repo.

Click the ‘Pull request’ button to send your changes to the project’s maintainers for review. This will send an email to the committers.

If any of the above seems like magic to you, please look up the Git documentation on the web, or ask a friend or another contributor for help.

Running the unit tests¶

To run the unit tests, pytest is used. In the common line, you can run all the tests from the terminal, using the command line. Navigate to the pydov main directory and do:

pytest

When adding new functionality or adjusting code, make sure to check/update/add the unit tests. Test files are grouped by the functionality. Each file name starts with test_* (required for pytest), followed by the module name (e.g. search, types,…).

Creating the documentation¶

We are glad to accept any sort of documentation: function docstrings, reStructuredText documents, tutorials, etc. Documentation lives in the docs/ directory.

You can edit the documentation using any text editor and then generate the HTML output by typing make html from the doc/ directory. For building the documentation, you will need Sphinx and pandoc. The _build directory is not included in the repository as we rely on CI tooling for the documentation building. The documentation is checked on Travis and build by Read the docs.

For the notebooks in Tutorials, the default is to always run the code of the notebooks when the documentation is created. This is defined by the nbsphinx_execute = 'always' option in the conf.py file.

However, when appropriate, this behavior can be undone on the individual level of the notebook as explained in the nbsphinx documentation.

In short, to make sure a notebook is not rerun, but the content used as such, add the following to the notebook(!) metadata:

"nbsphinx": {
 "execute": "never"
}

Release new version¶

In order to create a new release, the following steps need to be done ( on master branch):

Update the History file with the changes compared to the previous version. You could take into account the following sections: New features, Minor improvements, Major improvements, Documentation fixes. Commit the edits (git commit).

2. Adjust the version of the code. The repo uses the bumpversion package to keep track of the package version. use the following commands to switch the version:

bumpversion patch to increase version from 1.0.0 to 1.0.1.

bumpversion minor to increase version from 1.0.0 to 1.1.0.

bumpversion major to increase version from 1.0.0 to 2.0.0.

Push the code to GitHub, git push origin master
Push the tags to GitHub, git push --tags to create the release in Github

The new release can be installed using pip, pip install --upgrade pydov.