diff --git a/README.rst b/README.rst index 63c5f2f5e6..0295b5a0d0 100644 --- a/README.rst +++ b/README.rst @@ -14,13 +14,12 @@ :target: https://cgap-portal.readthedocs.io/en/latest/ :alt: Documentation Status -.. image:: https://codebuild.us-east-1.amazonaws.com/badges?uuid=eyJlbmNyeXB0ZWREYXRhIjoiMWtFYjJTeXkzcXZVYkpmbkd3VUlOQ0pSTnlLRGloVENJcitGS1g1RTV1THgxQkc3M2tDY0NFUFUxOXRBeS92dUNtbXdRZU5YWEkzbUhaMm1lUlNDZ2NZPSIsIml2UGFyYW1ldGVyU3BlYyI6Ijl6OUZkY3JvaWlyZDduUnEiLCJtYXRlcmlhbFNldFNlcmlhbCI6MX0%3D&branch=master - :alt: CodeBuild Status - Welcome to CGAP! ================ +CGAP is the Computational Genome Analysis Platform. + We are a team of scientists, clinicians, and developers who aim to streamline the clinical genetics workflow. @@ -37,7 +36,7 @@ who aim to streamline the clinical genetics workflow. * CGAP is an open source system under continuous development. For documentation, see `the CGAP Portal page at ReadTheDocs - `_. + `_. * For information about governance and other policies, see `the CGAP Governance repository @@ -49,19 +48,19 @@ Repository Structure These are some important files and directories you might want to be aware of: - * ``.github/workflows/`` contains Github Action Workflows - * ``bin/`` contains a few legacy scripts, though most are in ``scripts/`` - * ``deploy/docker`` contains containerization related scripts/configuration - * ``docs/ contains`` documentation - * ``scripts/`` contains misc scripts - * ``src/encoded/`` where the code is - * ``.dockerignore`` specifies paths ignored by the Dockerfile - * ``Dockerfile`` contains the Docker build instructions for the cgap-portal - see ``docker-production.rst`` - * ``Makefile`` contains macros for common build operations - see ``make info`` - * ``docker-compose.yml`` builds the new local deployment - see ``docker-local.rst`` - * ``package.json`` and ``package-lock.json`` specify the front-end dependencies - * ``pyproject.toml`` and ``poetry.lock`` specify the back-end dependencies - * ``setup_eb.py`` performs final installation setup +* ``.dockerignore`` specifies paths ignored by the Dockerfile +* ``.github/workflows/`` contains Github Action Workflows +* ``bin/`` contains a few legacy scripts, though most are in ``scripts/`` +* ``deploy/docker`` contains containerization related scripts/configuration +* ``docker-compose.yml`` builds the new local deployment (see ``docker-local.rst``) +* ``Dockerfile`` contains the Docker build instructions for the cgap-portal (see ``docker-production.rst``) +* ``docs/ contains`` documentation +* ``Makefile`` contains macros for common build operations (see ``make info``) +* ``package.json`` and ``package-lock.json`` specify the front-end dependencies +* ``pyproject.toml`` and ``poetry.lock`` specify the back-end dependencies +* ``scripts/`` contains misc scripts +* ``setup_eb.py`` performs final installation setup +* ``src/encoded/`` where the code is Navigating core functionality (src/encoded/) @@ -70,16 +69,16 @@ Navigating core functionality (src/encoded/) Top level files are modules that make up the core functionality of the back-end. Some modules differ greatly from or do not even exist in fourfront. Directories are outlined below. - * ``annotations/`` contains mapping table and ingestion related metadata - * ``commands/`` contains Python commands that can be run on the system from the command line - * ``docs/`` contains ReadTheDocs documentation - * ``ingestion/`` contains ingestion related code, such as mapping table intake and VCF processing - * ``schemas/`` contains the metadata schemas - * ``search/`` contains the search/filter_set APIs - * ``static/`` contains front-end code - * ``tests/`` contains back-end unit tests and insert data - * ``types/`` contains metadata type definitions - * ``upgrade/`` contains collection schema version upgraders +* ``annotations/`` contains mapping table and ingestion related metadata +* ``commands/`` contains Python commands that can be run on the system from the command line +* ``docs/`` contains ReadTheDocs documentation +* ``ingestion/`` contains ingestion related code, such as mapping table intake and VCF processing +* ``schemas/`` contains the metadata schemas +* ``search/`` contains the search/filter_set APIs +* ``static/`` contains front-end code +* ``tests/`` contains back-end unit tests and insert data +* ``types/`` contains metadata type definitions +* ``upgrade/`` contains collection schema version upgraders Related Repositories @@ -88,10 +87,10 @@ Related Repositories Note that ``cgap-portal`` is bound on supporting functionality in numerous libaries, but importantly: - * **dcicsnovault** - [`pypi library `_] - [`source repo `_] +* **dcicsnovault** + [`pypi library `_] + [`source repo `_] - * **dcicutils** - [`pypi library `_] - [`source repo `_] +* **dcicutils** + [`pypi library `_] + [`source repo `_]