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Improve READMEs & fix header in deploy-docs action
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README.md

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# LinkML Project Copier Template
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# A Copier Template for LinkML Projects
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> This is a new LinkML project template that uses copier instead of cruft/cookiecutter and
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> replaces make by [just](https://github.com/casey/just) as command runner.
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>
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> The starting point was https://github.com/linkml/linkml-project-cookiecutter/ (commit [1094cf2](https://github.com/linkml/linkml-project-cookiecutter/commit/1094cf2ce542028ab0017eaa059dd49cdde81fb5), date 2025-01-10).
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> The code from the [just command runner PR](https://github.com/linkml/linkml-project-cookiecutter/pull/127) was included (up to commit [3eb2522](https://github.com/linkml/linkml-project-cookiecutter/tree/3eb2522f5baa9e8f27ffb4ae28c0134a42d72c9d)).
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This template uses the code-scaffolding tool [copier](https://copier.readthedocs.io/) to create a [LinkML](https://github.com/linkml/linkml) project.
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Copier supports code lifecycle management, allowing you to seamlessly incorporate updates into your project when the template is enhanced.
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A [copier](https://copier.readthedocs.io/) template for projects using [LinkML](https://github.com/linkml/linkml).
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* Early releases (0.1.x) maintain backwards compatibility with [linkml-project-cookiecutter](https://github.com/linkml/linkml-project-cookiecutter/). This facilitates to experiment with the migration of existing cruft/cookiecutter-based projects.
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* Later releases starting with 0.2.0 will gradually give up compatibility.
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The generated project uses [just](https://github.com/casey/just) as preferred command runner, even in the 0.1.x releases.
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> The starting point of this template was [linkml-project-cookiecutter](https://github.com/linkml/linkml-project-cookiecutter/) (commit [1094cf2](https://github.com/linkml/linkml-project-cookiecutter/commit/1094cf2ce542028ab0017eaa059dd49cdde81fb5), date 2025-01-10).
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> The code from the [just command runner PR](https://github.com/linkml/linkml-project-cookiecutter/pull/127) was also included (up to commit [3eb2522](https://github.com/linkml/linkml-project-cookiecutter/tree/3eb2522f5baa9e8f27ffb4ae28c0134a42d72c9d)).
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## Prerequisites
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The following are required and recommended tools for using this copier template and the LinkML project that it generates. This is all one-time setup, so if you have already done it skip to the [next section](#creating-a-new-project)! We assume that you have full internet access. If not please read our section on `working in isolated environments` (tbw).
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The following are required and recommended tools for using this copier template and the LinkML project that it generates. This is all one-time setup, so if you have already done it skip to the [next section](#creating-a-new-project)! We assume that you have full internet access.
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* **git / GitHub account**
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1. Go to https://github.com/new and follow the instructions, being sure to NOT add a `README` or `.gitignore` file (this copier template will add those files for you)
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2. Add the remote to your local git repository
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2. Add the remote to your local git repository:
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```bash
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git remote add origin https://github.com/{github-user-or-organization}/{project-name}.git
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Feedback and suggestions for improvement based on your experiences are very welcome.
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The commands are written to be run at the root of your project.
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- Start with a clean state of the existing project (check with `git status`)
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- Create a new branch and activate it
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* Start with a clean state of the existing project (check with `git status`).
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* Create a new branch and activate it:
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`git switch -c migrate-to-copier`
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- Adapt your project and create a copier answers file (`.copier-answers`) by running
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* Adapt your project and create a copier answers file (`.copier-answers`) by running:
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`copier copy --trust --skip-tasks --vcs-ref=HEAD gh:dalito/linkml-project-copier .`
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If you start from a linkml-project-cookiecutter based project,
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look into the `.cruft.json` file to find out which values you chose when you configured your project.
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Be sure to enter the same values when answering the copier questions.
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- Carefully review the changes that copier made to your project.
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- If you used a cruft/cookiecutter template before, you may delete the cruft file `.cruft.json`.
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- If you are happy, commit all changes to the `migrate-to-copier` branch.
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- To finalise the migration, merge the `migrate-to-copier` branch to your main branch.
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* Carefully review the changes that copier made to your project.
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* If you used a cruft/cookiecutter template before, you may delete the cruft file `.cruft.json`.
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* If you are happy, commit all changes to the `migrate-to-copier` branch.
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* To finalise the migration, merge the `migrate-to-copier` branch to your main branch.
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## Keeping your project up to date or changing its configuration
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template/.github/workflows/deploy-docs.yaml.jinja

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name: Auto-deployment of {{project_slug}} Documentation
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name: Auto-deployment of {{project_name}} documentation
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on:
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push:
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branches: [main]

template/README.md.jinja

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To run commands you may use good old make or the command runner [just](https://github.com/casey/just/),
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which is a better choice on Windows.
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Use the `make` command or `duty` commands to generate project artefacts:
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Use the `make` command or `just` commands to generate project artefacts:
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* `make help` or `just --list`: list all pre-defined tasks
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* `make all` or `just all`: make everything
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* `make deploy` or `just deploy`: deploys site

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