This section provides details on how to configure and/or develop this codebase.

# Continuos Integration/Continuous Deployment (CI/CD) Workflow

This project uses *GitHub Workflows* to automate or ease a number of development tasks.  These
workflows can be found within the `./.github/workflows/` directory and include:
1. **pull_request.yml**

    This workflow is run whenever a pull request is opened, updated or reopened.  The following things are enforced by this workflow:

    - linting and code formatting standards
    - proper maintainance of the Poetry project
    - successful building of the project
    - successful building of the documentation
    - successful running of tests

2. **bump.yml**

    This workflow runs whenever code is pushed to the `main` branch.  It leverages the colocated `bump.sh` bash script to automatically increment the project version, and then publishes the new release.  Specifically, it:

    - Bumps the version (controlled by adding `[version:minor]` or `[version:major]` to a commit message; defaults to patch),
    - Creates a GitHub release with auto-generated notes,
    - Publishes the new version to the *Python Package Index* (*PyPI*), and
    - Triggers a documentation rebuild on *Read the Docs*.

3. **publish.yml** *(deprecated — manual fallback only)*

    This workflow can be triggered manually via `workflow_dispatch` from the GitHub Actions UI if you need to re-publish a release.  Regular publishing is handled automatically by `bump.yml`.

# Setting-up the Code

A local development copy of the code base can be obtained and configured as follows:

* Navigate to the *GitHub* page hosting the project
* If you want to fork the code so that you work on your own version of the repository (not generally needed or
  recommended):
    - Click on the `fork` button at the top of the page;
    - Edit the details you want to have for the new repoitory; and
    - Press `Create fork`.
* Obtain the URL for the repository you're going to use (denoted `<url>`) by clicking on the green `Code` button on the repository *GitHub* page
* On your local machine, navigate with your terminal to the location where you want to place the code
* Generate a local copy using `git clone <url>`;

::: {note}
Although not strictly necessary, it is recommended that you configure the branch permissions of any forked repositories as detailed in the *GitHub* configuration section below.
:::

(dev-python-env)=
# Python environments for development

Python development should always be managed using a Python environment. Both Conda and Poetry 2.x ([see here for an introduction](https://python-poetry.org)) are used to manage this project. The conda environment files install Poetry 2.x automatically. It simplifies & helps with managing the following:

1. **Creation and activation of a Python environment for the project**

    Once the code is locally installed, move to the project's root directory, and use Conda to create and activate a Python environment:

    ``` console
    $ conda env create -f env/conda_env.yml 
    $ conda activate supernnova
    ```
    or 

    ``` console
    $ conda env create -f env/conda_gpu_env.yml
    $ conda activate supernnova-cuda
    ```
    if you use `PyTorch` with CUDA support.

    
2. **Dependency management**

    As shown above, we establish a Python environment using either `env/conda_env.yml` or `conda_gpu_env.yml`. These configurations manage the Python version and directly handle our core dependency, `PyTorch`, as well as the installation of the `poetry` package, which is used to manage all other Python dependencies listed in `pyproject.toml`. This setup makes it easiler to manage different versions of `PyTorch` and CUDA support, streamlining the upgrade process for future versions as part of our CI/CD best practices. 
    
    Poetry maintains a "lock file" (which should be committed and maintained within the code repository) ensuring repeatable installs for all versions.

    After setting up the environment as described, proceed with installing all other development dependencies by executing:

    ``` console
    $ poetry install --all-extras
    ```
    In what follows, it will be assumed that this has been done.

    ::: {note}
    You can also use your preferred method of environment management, and install dependencies manually. But if you choose to use Conda + Poetry to manage the Python development environment as described above, please ensure you use `poetry` as installed by Conda. You can verify the installation path of `poetry` by running:

    ``` console
    $ which poetry
    ```
    ::: -->

3. **Publication of the project to the Python Package Index (*PyPI*) so that people can easily install it for themselves**

    Once properly configured, publishing to *PyPI* with Poetry is extremely easy.  This is generally managed by the CI/CD workflow for the project though, and developers should never have to manually do this.

# Guidelines

In the following, we lay-out some important guidelines for developing on this codebase.

## Branches

***Development should never be conducted on the `main` branch***.  If *GitHub* has been properly configured (see below), then merges to this branch are limited to Pull Requests (PRs) only.  Once a PR is opened for the `main` branch, the project tests are run.  When it is closed and code is committed to the main branch, the project version is automatically incremented (see below).

## Versioning

Semantic versioning (i.e. a scheme that follows a `vMAJOR.MINOR.PATCH` format; see <https://semver.org> for details) is used for this project.  ***The single point of truth for the current production version is the last git tag on the main branch with a `v[0-9]*` format***.  When developing locally, the reported version will often appear as `v0.0.0-dev`.

Changes are handled by a *GitHub Workflow* which increments the version and creates a new tag whenever a push occurs to the `main` branch.  This ensures that every commit on the `main` branch is assigned a unique version.  The logic by which it modifies the version is as follows:

1. if the PR message (or one of its commits' messages) contains the text `[version:major]`, then `MAJOR` is incremented;
2. else if the PR message (or one of its commits' messages) contains the text `[version:minor]`, then `MINOR` is incremented;
3. else `PATCH` is incremented.

A `MAJOR` version change should be indicated if the PR introduces a breaking change.  A `MINOR` version change should be indicated if the PR introduces new functionality.

::: {note}
Make sure you think carefully about what type of changes you are committing.  If you are adding functionality, make sure you bump the **MINOR** version; if you are making breaking changes, make sure you bump the **MAJOR** version.  ***Users will be very thankful that you did!***
:::

## Tests

*PyTest* is used to run tests for this codebase.  Make sure you run them before submitting any code to a PR by
executing the following from the project root directory:

``` console
$ pytest
```

Some further comments about how testing has been configured for this project:

### Coverage

*PyTest* has been configured for this project to create a coverage report after running.  This report will inform the developer of what fraction of the code base is exercised by the tests and give a list of lines of code in each Python filename which has not been exercised by the tests run.

While not strictly enforced, we encourage developers to make sure that anything they do to the codebase does not reduce this metric.  This report can be used to inform what parts of the codebase need further testing.

## Git Hooks

This project has been set-up with pre-configured git hooks. They should be used as a means for developers to quickly check that (at least some) of the code standards of the project are being met by commited code.  Ultimately, all standards are actually enforced by the continuous integration pipeline (see below).  Running quick checks (like linting) at the point of commiting code can save time that might otherwise be lost later (for example) at the PR or release stage when testing needs to be rigorous and policy enforcement generally fails slower.  Developers can choose to either:

1. use the git hooks defined by this project (recommended, for the reasons given above; see below for instructions),
2. not to use them, and rely purely on the CI workflow to enforce all project policies, or
3. configure their IDE of choice to manage things, in which case it is up to them to make sure that this aligns with the policies being enforced by the CI.

If developers would like to utilise the git hooks provided by this project they just need to run the following command from within the project:
``` console
$ pre-commit install
```

Some of these hooks require internet access to work.  If you are trying to commit to the
repository locally and are being prevented from doing so because you are working online, the
hooks can be ignored by using the `--no-verify` flag when running `git commit`, like so:
``` console
$ git commit --no-verify
```

Alternatively, you can disable them by running:
``` console
$ pre-commit uninstall
```

They can subsequently be re-enabled by reinstalling them.

### Maintaining Git Hooks

The git hooks are defined in the `.pre-commit-config.yaml` file.  Specific revisions for many of the tools listed should be managed with Poetry, with syncing managed with the [sync_with_poetry](https://github.com/floatingpurr/sync_with_poetry) hook.  Developers should take care not to use git hooks to *enforce* any project policies.  That should all be done within the continuous integration workflows.  Instead: these should just be quality-of-life checks that fix minor issues or prevent the propagation of quick-and-easy-to-detect problems which would otherwise be caught by the CI later with considerably more latency.  Furthermore, ensure that the checks performed here are consistant between the hooks and the CI.  For example: make sure that any linting/code quality checks are executed with the same tools and options.

## Releases

Releases are generated **automatically** whenever code is pushed to the `main` branch (typically by merging a PR).  The `bump.yml` workflow handles the full release pipeline:

1. Bumps the version (patch by default; use `[version:minor]` or `[version:major]` in a commit message to control this),
2. Creates a git tag and pushes it,
3. Creates a GitHub release with auto-generated notes,
4. Builds and publishes the package to [*PyPI*](https://pypi.org/), and
5. Triggers a documentation rebuild on *Read the Docs*.

No manual steps are needed.  If a release needs to be re-published manually, use the deprecated `publish.yml` workflow via the GitHub Actions UI (`workflow_dispatch`).

## Documentation

Documentation for this project is generated using [Sphinx](https://www.sphinx-doc.org/en/master/) and is hosted on *Read the Docs* for the latest release version.  Sphinx is configured here using [*MyST-Parser*](https://myst-parser.readthedocs.io/en/latest/)so that content can be managed with Markdown (`.md`) rather than Restructured Text (`.rst`).  *MyST-Parser* also offers [several optional Markdown extensions](https://myst-parser.readthedocs.io/en/latest/syntax/syntax.html) enabling the rendering of richer content (e.g. Latex equations).  Several of these extensions have been enabled by default, but not all.  This can be managed by overriding the behavior of the `conf.py` template (see below for directions on overriding templates) and editing the `myst_enable_extensions` list therein.

### Generating the Documentation

Documentation can be generated locally by running the following from the `docs` directory of the project:
``` console
$ make html
```

This will generate an html version of the documentation in `docs/_build/html` which can be opened in your browser.  On a Mac (for example), this can be done by running the following:
``` console
$ open docs/_build/html/index.html
```

# Configuring Services

Develpers and project owners/maintainers will require accounts with one or all of the following services to work with this codebase.  This section details how these services need to be configured.  Following these steps should only be necessarry - or partially necessary - if a developer chooses to fork the project.

1. [***GitHub***](https:/github.com)

    To work with this codebase, you will require a *GitHub* account ([go here to get one](https://github.com)).
    
    Branch permissions for the project repository should be configured as follows:
    
    - Protect the main branch to only permit merges from pull requests.  This can be done by clicking on the 'branches' tab and clicking on the 'Protect this branch' button for the 'main' branch.
    - Select 'Require status checks to pass before merging' when you set-up this branch protection rule.  This will ensure that all CI/CD tests pass before a merge to the main branch can be made.
    
    Several secrets need to be configured by navigating to `Settings->Secrets->Actions` and adding the following:
    
    - To host the project documentation on *Read the Docs** (see below), the following secrets need to be set (see below for where to find these values):
    
        - **RTD_WEBHOOK_TOKEN**, and
        - **RTD_WEBHOOK_URL**
    
    - To make code releases available on the **Python Package Index** (see below), then the following secret needs to be set (see below for where to find this value):

        - **PYPI_TOKEN**

2. [__Read the Docs__](https://readthedocs.org)

    **Read the Docs** (*RTD*) is used to build and host the project documentation.  An account is needed if you are an owner/maintainer of the project and will be publishing and managing the project's documentation online, but not needed if you are simply a contributing developer.  *RTD* can be configured in either of the following ways:

    1. **By connecting *RTD* to your *GitHub* account**
        - Ensure that your *GitHub* account has been connected.  This is done automatically if you log into *RTD* with your *GitHub* credentials.  If you logged in with your email, navigate to `<login_id>->Settings->Connected Services` by clicking on "Connect Your Accounts" and click "Connect to GitHub".  You know your account is linked if it is listed below under "Active Services".

        - Return to your *RTD* landing page by clicking on your account name at the top.  Click "Import a Project".  Your *GitHub* repository should be listed here (you may need to refresh the list if it has been created recently).  Import it.

        - To obtain **RTD_WEBHOOK_TOKEN**, navigate to `<Account>->Settings->API Tokens` on *Read the Docs*.  If a token has been created already, you can use it.  Otherwise (or if you want a token specifically for this project), create a new one.

        - To obtain **RTD_WEBHOOK_URL**, migrate to the `Admin->Integrations` tab on the *RTD* project page.  Click on your incomming webhook and get the URL there.

    2. **By creating a Generic Webhook**
        - Navigate to the `Admin->Integrations` tab on the *RTD* project page and click `Add integration`.  Then select `Generic API incoming webhook` from the dropdown and click `Add integration`.

        - To obtain **RTD_WEBHOOK_URL** and **RTD_WEBHOOK_TOKEN**, migrate to the `Admin->Integrations` tab on the *RTD* project page and click on your incomming webhook.

    Once properly configured, the documentation for this project should build automatically on *RTD* every time you generate a new release (see below for instructions).

    ::: {note}
    Make sure **RTD_WEBHOOK_URL** starts with `https://`.  Prepend it if not.
    :::

3. The [__Python Package Index (*PyPI*)__](https://pypi.org)

    This service is used to publish project releases.  An account is needed if you are the owner of the project, but not generally needed if you are simply a contributing developer.  An API token will need to be created and added to your *GitHub* project as **PYPI_TOKEN** (as detailed above).  This can be generated from the *PyPI* UI by navigating to `Account Settings->Add API Token`.

    ::: {note}
    Although `poetry` can be used to directly publish this project to *PyPI*, developers should not do this manually.  Publishing happens automatically when code is merged to the `main` branch, via the `bump.yml` workflow.
    :::