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samcunliffe authored Nov 4, 2024
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4 changes: 3 additions & 1 deletion .markdownlint.yaml
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@@ -1,2 +1,4 @@
---
MD013: false
# Markdown linting rules to ignore.
MD013: false # line-length
MD033: false # no-inline-html
46 changes: 45 additions & 1 deletion CONTRIBUTING.md
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Expand Up @@ -26,7 +26,7 @@ To contribute a change, please:

1. Create a new branch (or fork if you're not in [@UCL-ARC/collaborations]).
2. Modify an existing page, create a new one, or tweak the template. a. Run
[pre-commit](https://pre-commit.com) which will lint your changes. b. Check
[pre-commit] which will lint your changes. b. Check
the tests pass if you modified the template (`pytest -s`).
3. Open a _pull request_ (PR) with changes.
4. Ask someone who did not contribute to the PR from [@UCL-ARC/collaborations]
Expand All @@ -35,6 +35,46 @@ To contribute a change, please:
6. If changes are requested, the PR author should address the comments, and then
ask for review again.

### Developing the cookiecutter template

We quite like installing cookiecutter as a [uv tool], so it's available globally:

```sh
uv tool install cookiecutter
```

To run cookiecutter using a specific branch of the template:

```sh
cookiecutter gh:UCL-ARC/python-tooling --checkout <branch-name>
```

If you have this repo locally (presumably the case if you're developing), you
can instead run the following:

```sh
cookiecutter /path/to/your/checkout/of/python-tooling --checkout <branch-name>
```

You can omit the `--checkout` option if you're already on the
branch you want to test.

### Developing the recommended tooling pages

Pages all live in the `docs/pages` sub-directory, and are written in markdown.

To build the webpage locally (for testing)

1. [Install jekyll]
2. Run `bundle install` from the `docs/` directory of this repository to
install dependencies.
3. Run `bundle exec jekyll serve` from the root directory of this repository.
This should fire up a local web server and tell you its address. By default
the server will automatically refresh the HTML pages if any changes are made
to the markdown sources.

See the [jekyll docs] for more info.

<!-- links here -->

<!-- prettier-ignore-start -->
Expand All @@ -43,5 +83,9 @@ To contribute a change, please:
[open an issue]: https://github.com/UCL-ARC/python-tooling/issues/new/choose
[Discussions tab]: https://github.com/UCL-ARC/python-tooling/discussions
[Research software engineers]: https://society-rse.org/about/history
[pre-commit]: https://pre-commit.com
[@UCL-ARC/collaborations]: https://github.com/orgs/UCL-ARC/teams/collaborations
[uv tool]: https://docs.astral.sh/uv/guides/tools
[Install jekyll]: https://jekyllrb.com/docs/installation
[jekyll docs]: https://jekyllrb.com/docs
<!-- prettier-ignore-end -->
184 changes: 51 additions & 133 deletions README.md
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<!-- markdownlint-disable MD033 MD041 -->
<!-- markdownlint-disable MD041 -->
<div style="text-align: center;" align="center">
<img src="https://raw.githubusercontent.com/UCL-ARC/python-tooling/main/images/logo.svg" alt="UCL ARC Python tooling logo" width="120"/>
<h1> UCL ARC Python Recommendations</h1>
Expand All @@ -19,12 +19,61 @@ Python packages with our recommended tooling set up and ready to go.
> package template (e.g., [`scikit-hep`](https://github.com/scikit-hep/cookie)),
> we recommend using their template instead of this one.
## Tutorial

Some quick instructions for using our template are below.
We also have a [tutorial](./tutorial.md) that has been presented in a couple of workshops aimed at researchers at UCL.

## Using our template

If you have [uv] installed, you can use our template with the following one-liner:

```sh
uvx cookiecutter gh:ucl-arc/python-tooling --checkout latest
```

Alternatively you can [install cookiecutter] (following the recommended instructions).
Do this if you don't use [uv], or if you're likely to want to use cookiecutter again.

Then you'll need to run cookiecutter with our template:

```sh
cookiecutter gh:ucl-arc/python-tooling --checkout latest
```

When [cookiecutter] runs, it will ask you a series of questions to configure your project.
Type the answer or hit return without typing anything to use the default option (shown in parenthesis).
At the end, it will print some more follow-up information in the terminal for things like creating a remote repository and making a website for your package.

It will have created a directory for your project.
You can see the structure with the `tree` command.
In our example we've called our project `example-research-software-project`:

```sh
ls -ltr | tail -n1 # Shows the last directory that was created
tree example-research-software-project
```

To work on your project, initialise a `git` repository and _install_ your new package editable mode.
You probably want to do this in a [virtual environment](./docs/pages/virtual.md).
The comments show how to do this in [uv] with `uv venv`:

```sh
cd example-research-software-project
git init
# uv venv
# source .venv/bin/activate
uv pip install -e ".[dev]"
```

<!-- links here -->

<!-- prettier-ignore-start -->
[website]: https://github-pages.arc.ucl.ac.uk/python-tooling
[UCL ARC]: https://ucl.ac.uk/arc
[cookiecutter]: https://libraries.io/pypi/cookiecutter
[cookiecutter]: https://cookiecutter.readthedocs.io/en/stable
[install cookiecutter]: https://cookiecutter.readthedocs.io/en/stable/README.html#installation
[uv]: https://docs.astral.sh/uv
<!-- prettier-ignore-end -->

## Contributors
Expand Down Expand Up @@ -68,134 +117,3 @@ Python packages with our recommended tooling set up and ready to go.
<!-- prettier-ignore-end -->

<!-- ALL-CONTRIBUTORS-LIST:END -->

## Using this template

Some quick instructions for using our template are below.
We also have a detailed [tutorial](tutorial.md) that has been given in a couple of workshops geared towards researchers at UCL.
The tutorial goes into much more pedagogical detail, it both describes using the template to create a package
and how to use the newly created package with some of the tools included.

1. Install [cookiecutter] in a `uv venv` or `conda` environment (commented lines for
`uv venv` example).

```sh
# uv venv # creates a .venv directory wherever you are
# source ./.venv/bin/activate
uv pip install cookiecutter
```

2. Run cookiecutter in the desired directory

```sh
cookiecutter gh:ucl-arc/python-tooling --checkout latest
```

If you have this repo locally (this may be the case if you are developing),
you can run the following:

```sh
cookiecutter /path/to/your/checkout/of/python-tooling --checkout latest
```

3. A series of questions will pop up to configure the project. Type the answer
or hit return to use the default option (shown in parenthesis).

Note that these project variables are defined in the `cookiecutter.json`
file.

4. This will create a specific directory structure.

For example, for a project with the following variables:

```yaml
project_name [Python Template]: PROJECT_NAME
project_slug [python-template]: PROJECT_SLUG
package_name [python_template]: PACKAGE_NAME
```

5. To work on your project, initialise a Git repository and _install_ it in
editable mode.

```sh
cd PROJECT_SLUG
git init
uv pip install -e ".[dev]"
```

6. Build your package

```sh
python -m build
```

## Notes for developers

<details><summary>Click to expand...</summary> <!-- markdownlint-disable-line MD033 -->

First, clone repository

- (Optional) Generate your SSH keys as suggested
[here](https://docs.github.com/en/github/authenticating-to-github/generating-a-new-ssh-key-and-adding-it-to-the-ssh-agent)
- (Optional) GitHub CLI as suggested
[here](https://docs.github.com/en/authentication/connecting-to-github-with-ssh/adding-a-new-ssh-key-to-your-github-account?tool=cli)
- Clone the repository by typing (or copying) the following line in a terminal
at your selected path in your machine:

```sh
git clone [email protected]:UCL-ARC/python-tooling.git
cd python-tooling
```

### Developing the cookiecutter template

- To create and remove your virtual environment

```sh
uv venv
source .venv/bin/activate
# do your work
deactivate
```

- To run template in the same path of this repo. We do a test cookiecut of a
dummy package and install it to ensure the template setup works.

```sh
cookiecutter .
cd python-template
git init
uv pip install -e ".[dev]"
```

- To run cookiecutter using a specific branch of the template:

```sh
cookiecutter https://github.com/UCL-ARC/python-tooling --checkout <branch-name>
```

- To run the tests locally:

```sh
pytest -s
```

### Developing the recommended tooling pages

Pages all live in the
[docs/pages](https://github.com/UCL-ARC/python-tooling/tree/main/docs/pages)
sub-directory, and are written in markdown.

To build the webpage locally (for testing)

1. [Install jekyll](https://jekyllrb.com/docs/installation)
2. Run `bundle install` from the `docs/` directory of this repository to
install dependencies.
3. Run `bundle exec jekyll serve` from the root directory of this repository.
This should fire up a local web server and tell you its address. By default
the server will automatically refresh the HTML pages if any changes are made
to the markdown sources.

See the [jekyll docs](https://jekyllrb.com/docs) for more info.

</details>

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