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Make it consistent with VRS
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![image](docs/source/images/cat-vrs-transparent-bg.png) | ||
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## Using the schema | ||
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# How to set up a venv and update the schemata from the source.yaml files: (Guide for VSCode) | ||
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1. Use the following code to install the venv in the root directory that contains the requirements.txt file. Note that requirements.txt may be hidden and not show up with `ls`, but it should show up if you ise `ls -a` to list hidden files. | ||
> `python3 -m venv venv` | ||
> | ||
> `source venv/bin/activate` | ||
> | ||
> `pip install -U setuptools pip` | ||
> | ||
> `pip install -r .requirements.txt` | ||
2. Then run the following code to pull in all of the submodule content: | ||
> `git submodule update --init --recursive` | ||
3. The venv should be all set up to update the `.rst` files as they are updated. `.rst` files inside the `docs/source` directory are static and can be edited directly. (you will need to install aan `.rst`-compatible extension to view the outputs inside the editor, however. I currently have both reStructuredText and RST Preview installed.) The `.rst` and `.json` files for the schemata are generated by making edits to the `-source.yaml` files, and thenrunning the `Makefile`. To run the `Makefile`, `cd` into the `cat-vrs/schema` directory which contains it and run the following line of code to update everything: | ||
> `make all` | ||
The schema is available in the [schema/](./schema/) directory, in both reStructuredTex | ||
(RST) and JSON versions. It conforms to JSON Schema Draft 2020-12. For a list of | ||
libraries that support JSON schema, see | ||
[JSONSchema>Implementations](https://json-schema.org/tools). | ||
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## Installing for development | ||
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Fork the repo at <https://github.com/ga4gh/cat-vrs>. | ||
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git clone --recurse-submodules [email protected]:YOUR_GITHUB_ID/cat-vrs.git | ||
cd cat-vrs | ||
make devready | ||
source venv/3.12/bin/activate | ||
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If you already cloned the repo, but forgot to include `--recurse-submodules` you can run: | ||
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git submodule update --init --recursive | ||
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## Contributing to the schema | ||
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Cat-VRS uses [cat-vrs-source.yaml](./schema/cat-vrs/cat-vrs-source.yaml) as the source | ||
document for JSON Schema. | ||
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To create the corresponding def and json files after making changes to the source | ||
document, from the root directory: | ||
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cd schema | ||
make all | ||
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## Contributing to the docs | ||
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The Cat-VRS specification documentation is written in reStructuredText and located in | ||
[docs/source](docs/source/). Commits to this repo are built automatically at | ||
<https://vrsatile.readthedocs.io/en/latest/catvars/index.html#>. | ||
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To build documentation locally, you must install [entr](https://eradman.com/entrproject/): | ||
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brew install entr | ||
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Then from the root directory: | ||
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cd docs | ||
make clean watch & | ||
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Then, open [docs/build/html/index.html](./docs/build/html/index.html). The above make | ||
command should build docs when source changes. (Some types of changes require recleaning and building.) |