Merge pull request #694 from katiestahl/692-readme-updates

updates to documentation

CITATION.cff

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+cff-version: 1.2.0
+message: "If you use this software, please cite it as below."
+authors:
+- family-names: "Wang"
+  given-names: "Meng"
+- family-names: "Callenberg"
+  given-names: "Keith M"
+- family-names: "Dalgleish"
+  given-names: "Raymond"
+- family-names: "Fedtsov"
+  given-names: "Alexandre"
+- family-names: "Fox"
+  given-names: "Naomi K"
+- family-names: "Freeman"
+  given-names: "Peter J"
+- family-names: "Jacobs,"
+  given-names: "Kevin B"
+- family-names: "Kaleta"
+  given-names: "Piotr"
+- family-names: "McMurry"
+  given-names: "Andrew J"
+- family-names: "Prlić"
+  given-names: "Andreas"
+- family-names: "Rajaraman"
+  given-names: "Veena"
+- family-names: "Hart"
+  given-names: "Reece K"
+title: "hgvs: A Python package for manipulating sequence variants using HGVS nomenclature: 2018 Update"
+doi: 10.1002/humu.23615
+date-released: 2018-10-20
+url: "https://github.com/biocommons/hgvs"

README.md

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+# *hgvs* - manipulate biological sequence variants according to Human Genome Variation Society recommendations
+
+**Important:** biocommons packages require Python 3.8+.
+[More](https://groups.google.com/forum/#!topic/hgvs-discuss/iLUzjzoD-28)
+
+The *hgvs* package provides a Python library to parse, format, validate,
+normalize, and map sequence variants according to [Variation
+Nomenclature](http://varnomen.hgvs.org/) (aka Human Genome Variation
+Society) recommendations.
+
+Specifically, the hgvs package focuses on the subset of the HGVS
+recommendations that precisely describe sequence-level variation
+relevant to the application of high-throughput sequencing to clinical
+diagnostics. The package does not attempt to cover the full scope of
+HGVS recommendations. Please refer to
+[issues](https://github.com/biocommons/hgvs/issues) for limitations.
+
+## Information
+
+[![rtd](https://img.shields.io/badge/docs-readthedocs-green.svg)](http://hgvs.readthedocs.io/) [![changelog](https://img.shields.io/badge/docs-changelog-green.svg)](https://hgvs.readthedocs.io/en/stable/changelog/)  [![getting_help](https://img.shields.io/badge/!-help%20me-red.svg)](https://hgvs.readthedocs.io/en/stable/getting_help.html)  [![GitHub license](https://img.shields.io/github/license/biocommons/hgvs.svg)](https://github.com/biocommons/hgvs/blob/main/LICENSE)  [![binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/biocommons/hgvs/main?filepath=examples)
+
+## Latest Release
+
+[![GitHub tag](https://img.shields.io/github/tag/biocommons/hgvs.svg)](https://github.com/biocommons/hgvs) [![pypi_rel](https://img.shields.io/pypi/v/hgvs.svg)](https://pypi.org/project/hgvs/)
+
+## Development
+
+[![coveralls](https://img.shields.io/coveralls/github/biocommons/hgvs.svg)](https://coveralls.io/github/biocommons/hgvs) [![issues](https://img.shields.io/github/issues-raw/biocommons/hgvs.svg)](https://github.com/biocommons/hgvs/issues)
+[![GitHub Open Pull Requests](https://img.shields.io/github/issues-pr/biocommons/hgvs.svg)](https://github.com/biocommons/hgvs/pull/) [![GitHub license](https://img.shields.io/github/contributors/biocommons/hgvs.svg)](https://github.com/biocommons/hgvs/graphs/contributors/) [![GitHub stars](https://img.shields.io/github/stars/biocommons/hgvs.svg?style=social&label=Stars)](https://github.com/biocommons/hgvs/stargazers) [![GitHub forks](https://img.shields.io/github/forks/biocommons/hgvs.svg?style=social&label=Forks)](https://github.com/biocommons/hgvs/network)
+
+## Features
+
+-   Parsing is based on formal grammar.
+-   An easy-to-use object model that represents most variant types
+    (SNVs, indels, dups, inversions, etc) and concepts (intronic
+    offsets, uncertain positions, intervals)
+-   A variant normalizer that rewrites variants in canonical forms and
+    substitutes reference sequences (if reference and transcript
+    sequences differ)
+-   Formatters that generate HGVS strings from internal representations
+-   Tools to map variants between genome, transcript, and protein
+    sequences
+-   Reliable handling of regions genome-transcript discrepancies
+-   Pluggable data providers support alternative sources of transcript
+    mapping data
+-   Extensive automated tests, including those for all variant types and
+    \"problematic\" transcripts
+-   Easily installed using remote data sources. Installation with local
+    data sources is straightforward and completely obviates network
+    access
+
+## Important Notes
+
+-   **You are encouraged to** [browse
+    issues](https://github.com/biocommons/hgvs/issues). All known issues
+    are listed there. Please report any issues you find.
+-   **Use a pip package specification to stay within minor releases.**
+    For example, `hgvs>=1.5,<1.6`. hgvs uses [Semantic
+    Versioning](http://semver.org/).
+
+## Installing HGVS Locally
+
+**Important:** For more detailed installation and configuration
+instructions, see the [HGVS readthedocs](https://hgvs.readthedocs.io/)
+
+### Prerequisites
+
+    libpq
+    python3
+    postgresql
+
+Examples for installation:
+
+MacOS :
+
+    brew install libpq
+    brew install python3
+    brew install postgresql@14
+
+Ubuntu :
+
+    sudo apt install gcc libpq-dev python3-dev
+
+### Installation Steps
+
+By default, hgvs uses remote data sources, which makes
+installation easy. If you would like to use local instances of the data sources, see the [readthedocs](https://hgvs.readthedocs.io/).
+
+1. Create a virtual environment using your preferred method.
+
+    **Example:**
+
+        python3 -m venv venv
+
+2. Run the following commands in your virtual environment:
+
+
+        source venv/bin/activate
+        pip install --upgrade setuptools
+        pip install hgvs
+
+
+See [Installation
+instructions](http://hgvs.readthedocs.org/en/stable/installation.html)
+for details, including instructions for installing [Universal Transcript
+Archive (UTA)](https://github.com/biocommons/uta/) and
+[SeqRepo](https://github.com/biocommons/biocommons.seqrepo/) locally.
+
+## Examples and Usage
+
+See [examples](https://github.com/biocommons/hgvs/tree/main/examples) and [readthedocs](https://hgvs.readthedocs.io/) for usage.
+
+## Contributing
+
+The hgvs package is intended to be a community project. Please see
+[Contributing](http://hgvs.readthedocs.org/en/stable/contributing.html)
+to get started in submitting source code, tests, or documentation.
+Thanks for getting involved!
+
+## See Also
+
+Other packages that manipulate HGVS variants:
+
+-   [pyhgvs](https://github.com/counsyl/hgvs)
+-   [Mutalyzer](https://mutalyzer.nl/)