-
Notifications
You must be signed in to change notification settings - Fork 2
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Merge branch 'reconcile-dev-branches' into 1.x
- Loading branch information
Showing
57 changed files
with
1,185 additions
and
1,341 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,29 @@ | ||
| # Contributing | ||
| As a product of the Genomic Knowledge Standards Workstream of GA4GH, the development of the projects and contributions of this repository are expected to hew relatively close to the standards utilized in [the VRS development process]((https://vrs.ga4gh.org/en/stable/appendices/development_process.html)). The additional information presented here are guidelines for issues, branches, commits, and pull requests. Before adding documentation, please also review the [docs style guide](docs/source/appendices/style.rst). | ||
|
|
||
| ## Discussions | ||
| [Discussions](https://github.com/ga4gh/cat-vrs/discussions) are for discussion, design decisions, bug | ||
| reports, and feature requests. When creating an issue, use sentence case | ||
| for the issue title and avoid the use of periods at the end of titles. | ||
|
|
||
| ## Issues | ||
| [Issues](https://github.com/ga4gh/cat-vrs/issues) are for used to track additions, bugs fixes, or other issues that are intended to be implmented, often as the outcome of a [discussion](https://github.com/ga4gh/cat-vrs/discussions). When creating an issue, use sentence case for the issue title and avoid the use of periods at the end of titles. | ||
|
|
||
| ## Branches | ||
| [Branches](https://github.com/ga4gh/cat-vrs/branches) are used for | ||
| versioning and feature additions. Version branches are to be created by | ||
| repo administrators only. Feature branches must be associated with an | ||
| open issue describing the desired feature, and named after the issue | ||
| as <issue number>-<short-description>. For example, the associated | ||
| branch for [issue 15](https://github.com/ga4gh/cat-vrs/tree/Issue-15) could | ||
| be `15-bug fix`. | ||
|
|
||
| ## Pull Requests | ||
| [Pull Requests](https://github.com/ga4gh/cat-vrs/pulls) (PRs) for new | ||
| features should target the `main` branch. For version | ||
| patches, the PR should target the appropriate minor version branch. | ||
| PRs must be approved by at least one project maintainer before they may | ||
| be merged. PR titles must reflect the issue associated with the PR. For | ||
| example, the associated PR title for | ||
| [issue 15](https://github.com/ga4gh/cat-vrs/tree/Issue-15) would be | ||
| `#15: fix Bug`. |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,60 @@ | ||
| # Contributors | ||
|
|
||
| |Name | Affiliations | | ||
| |-----------------| ------------ | | ||
| |Daniel Puthawala | [[1](#1)] | | ||
| |Alex H Wagner | [[1](#1)][[2](#2)] | | ||
| |Lawrence Babb | [[3](#3)] | | ||
| |Wesley A Goar | [[1](#1)] | | ||
| |Kori Kuzma | [[1](#1)] | | ||
| |James S Stevenson | [[1](#1)] | | ||
| |Catherine Procknow | [[4](#4)] | | ||
| |Mrinal Thomas | [[4](#4)] | | ||
| |Robert H Dolin | [[5](#5)] | | ||
| |Brendan Reardon | [[6](#6)] | | ||
| |Robert R Freimuth | [[7](#7)] | | ||
| |Salem Bajjali | [[7](#7)] | | ||
| |Malachi Griffith | [[8](#8)] | | ||
| |Tristan Nelson | [[9](#9)] | | ||
| |Andrew D Yates | [[10](#10)] | | ||
| |Beth A Pitel | [[11](#11)] | | ||
| |Parijat Kundu | [[12](#1)] | | ||
| <!-- Add yourself below | ||
| | | | | ||
| | | | | ||
| | | | | ||
| | | | --> | ||
|
|
||
|
|
||
|
|
||
|
|
||
| See also | ||
| [Cat-VRS contributors](https://github.com/ga4gh/cat-vrs/graphs/contributors) | ||
|
|
||
|
|
||
| # Affiliations | ||
|
|
||
| ## 1 | ||
| The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH 43215, USA | ||
| ## 2 | ||
| Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH 43210, USA | ||
| ## 3 | ||
| Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA | ||
| ## 4 | ||
| Epic Systems, Madison, WI, USA | ||
| ## 5 | ||
| Elimu Informatics | ||
| ## 6 | ||
| Dana-Farber Cancer Institute, Boston, MA | ||
| ## 7 | ||
| Center for Individualized Medicine, Division of Digital Health Sciences, Mayo Clinic, Rochester, MN 55905, USA | ||
| ## 8 | ||
| Washington University School of Medicine, St. Louis, MO 63108, USA | ||
| ## 9 | ||
| Gesinger Health, Danville, PA 17822, USA | ||
| ## 10 | ||
| European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom | ||
| ## 11 | ||
| Mayo Clinic, Department of Laboratory Medicine and Pathology | ||
| # 12 | ||
| Velsera |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,55 +1,31 @@ | ||
| # Cat-VRS | ||
| # Categorical Variation Representation Specification (Cat-VRS) | ||
|
|
||
| [A terminology and data model for describing categorical variation concepts](https://vrsatile.readthedocs.io/en/latest/catvars/index.html), built on top of the | ||
| [GA4GH Variation Representation Specification (VRS)](https://vrs.ga4gh.org). | ||
| [](https://cat-vrs.readthedocs.io/en/latest/) | ||
|
|
||
|  | ||
|
|
||
| ## Using the schema | ||
|
|
||
| The schema is available in the [schema/](./schema/) directory, in both yaml and json versions. | ||
| It conforms to JSON Schema Draft 2020-12. For a list of | ||
| libraries that support JSON schema, see | ||
| [JSONSchema>Tools](https://json-schema.org/tools). | ||
|
|
||
| ## Installing for development | ||
|
|
||
| Fork the repo at <https://github.com/ga4gh/cat-vrs>. | ||
|
|
||
| git clone --recurse-submodules git@github.com:YOUR_GITHUB_ID/cat-vrs.git | ||
| cd cat-vrs | ||
| make devready | ||
| source venv/3.12/bin/activate | ||
| The [GA4GH](https://www.ga4gh.org/) [Categorical Variation Representation Specification](https://www.ga4gh.org/product/categorical-variation-catvar/) provides a [A terminology and data model for describing categorical variation concepts](https://vrsatile.readthedocs.io/en/latest/catvars/index.html), built on top of the [GA4GH Variation Representation Specification (VRS)](https://vrs.ga4gh.org). Cat-VRS is the result of a collaboration among [contributors](CONTRIBUTORS.md) representing national information resource providers, major international public initiatives, and bioinformatics laboratories. | ||
|
|
||
| If you already cloned the repo, but forgot to include `--recurse-submodules` you can run: | ||
| Cat-VRS is licensed under the [Apache License 2.0](LICENSE). | ||
|
|
||
| git submodule update --init --recursive | ||
|
|
||
| ## Contributing to the schema | ||
| # Test Set | ||
|
|
||
| Cat-VRS uses [cat-vrs-source.yaml](./schema/cat-vrs/cat-vrs-source.yaml) as the source | ||
| document for JSON Schema. | ||
| Categorical variant classes intended to be covered by this specification can be [appended to this CatVar test set document](https://docs.google.com/document/d/1aV-SqxdmuRN_EKvafzTSe0GoGC9yOzPsjrdWE0LXqYc/edit) to direct future specification development efforts. | ||
|
|
||
| To create the corresponding def and json files after making changes to the source | ||
| document, from the root directory: | ||
|
|
||
| cd schema | ||
| make all | ||
|
|
||
| ## Contributing to the docs | ||
|
|
||
| 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#>. | ||
|
|
||
| To build documentation locally, you must install [entr](https://eradman.com/entrproject/): | ||
|
|
||
| brew install entr | ||
|
|
||
| Then from the root directory: | ||
|  | ||
|
|
||
| cd docs | ||
| make clean watch & | ||
|
|
||
| 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.) | ||
| # How to set up a venv and update the schemata from the source.yaml files: (Guide for VSCode) | ||
|
|
||
| 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` |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,80 @@ | ||
|
|
||
| This page shows style conventions used in these docs. It will be | ||
| built with other pages and you can view it (at | ||
| docs/build/html/style.html). Unfortunately, because it's intentionally | ||
| not included in the published docs, it generates the annoying warning | ||
| "WARNING: document isn't included in any toctree". | ||
|
|
||
|
|
||
| Headings | ||
| !!!!!!!! | ||
|
|
||
| ReST heading levels are determined by the character used beneath text. | ||
| Within a file, each new character creates a new heading level. | ||
|
|
||
| This documentation uses the characters ``!``, ``@``, ``#``, and ``$``. | ||
| That is, the first four shifted digit characters across a US keyboard. | ||
|
|
||
| For example:: | ||
|
|
||
| A Heading | ||
| !!!!!!!!! | ||
|
|
||
| The first subheading | ||
| @@@@@@@@@@@@@@@@@@@@ | ||
|
|
||
| The first subsubeheading | ||
| ######################## | ||
|
|
||
| The second subheading | ||
| @@@@@@@@@@@@@@@@@@@@@ | ||
|
|
||
| Another Heading | ||
| !!!!!!!!!!!!!!! | ||
|
|
||
|
|
||
| To aid comprehension, the Text Styles section source looks like this:: | ||
|
|
||
| .. _text-styles-target: | ||
| Text Styles | ||
| !!!!!!!!!!! | ||
|
|
||
|
|
||
| .. _text-styles-target: | ||
|
|
||
| Text Styles | ||
| !!!!!!!!!!! | ||
|
|
||
| A cheat sheet for making references, links, and literals in sphinx. | ||
|
|
||
| * For external links, use ``target_``. | ||
|
|
||
| * See ``epilog.rst`` for pre-defined links. | ||
| * e.g, ``Base64_`` renders as Base64_ and ```Compact URI (CURIE)`_`` | ||
| renders as `Compact URI (CURIE)`_. | ||
|
|
||
| * *Within* VRS documentation, use ``.. _refname:`` to create link | ||
| target, and use ``:ref:`refname``` to reference it. | ||
|
|
||
| * Create explicit link targets for all headings. | ||
| * Do not rely on the implicit targets created by sphinx because | ||
| changing the heading will break the link. | ||
| * e.g., ``:ref:`text-styles-target``` renders as | ||
| :ref:`text-styles-target` and uses the heading text as | ||
| the link name. | ||
| * e.g., ``:ref:`Alleles <Allele>``` renders as :ref:`Alleles | ||
| <Allele>`, with custom link text. | ||
| * Use class names verbatim when making link targets (e.g., | ||
| ``.. _SequenceLocation:``). Use (lowercase) kebab-case for other | ||
| sections (e.g., ``.. computed-identifiers:``). | ||
|
|
||
| * Use \* for attributes. | ||
|
|
||
| * ``*attribute*`` renders as *attribute*. | ||
| * e.g., The :ref:`Allele` *location* attribute must be set. | ||
|
|
||
| * Use double backticks for literals. | ||
|
|
||
| * ````literal```` renders as ``literal`` | ||
| * e.g., The :ref:`Allele` *type* attribute must be set to ``"Allele"``. |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Oops, something went wrong.