[!NOTE]
This repository is in early development. We are currently in the process of reviewing, pruning, and consolidating our documentation.
This repository contains the content that we compile into our documentation website.
This repository has the following sections:
./content
: Current, high-level content about NMDC./legacy
: Legacy content we include in the website to support legacy references/publications./src
: Code we use to compile local and remote content into a website./
: Repository-level configuration files and documentation[!NOTE]
TODO
Most of the files in the legacy/nmdc-documentation
directory are files that we copied from
commit 8786ff5a
in the NMDC_documentation repository.
That was the latest commit on the main
branch as of August 28, 2024.
This documentation is implemented within the Sphinx documentation framework.
In addition to the files we copied, the directory also contains some files that are exclusive to this repository;
e.g., Dockerfile
and .gitignore
.
When copying the aforementioned files from the NMDC_documentation
repository, we omitted the following files:
docs/reference/metadata
docs/_static/images/reference/metadata
docs/_static/jsonschema
Instead of maintaining a local copy of that documentation here, we redirect visitors to the standalone schema documentation.
Example: When someone visits
/reference/metadata/xylene.html
on this documentation website, they'll be automatically redirected to https://microbiomedata.github.io/nmdc-schema/xylene/. This redirection is configured inlegacy/nmdc-documentation/src/conf.py
.
You can compare the legacy/nmdc-documentation/src
directory with the corresponding directory in the
upstream repository, by following these steps:
# Clone the upstream repository onto your computer.
git clone https://github.com/microbiomedata/NMDC_documentation.git /tmp/NMDC_documentation
# Use Git to compare the corresponding directories.
git diff --stat /tmp/NMDC_documentation/docs ./legacy/nmdc-documentation/src
Most of the files in the legacy/workflow-documentation
directory are files that we copied from
commit 40b5a313
in the workflow_documentation repository.
That was the latest commit on the main
branch as of August 28, 2024.
This documentation is implemented within the Sphinx documentation framework.
In addition to the files we copied, the directory also contains some files that are exclusive to this repository;
e.g., Dockerfile
and .gitignore
.
When copying the aforementioned files from the workflow_documentation
repository, we omitted files that were used
to fetch content from even higher upstream; i.e. from individual workflow repositories.
You can compare the legacy/workflow-documentation/src
directory with the corresponding directory in the
upstream repository, by following these steps:
# Clone the upstream repository onto your computer.
git clone https://github.com/microbiomedata/workflow_documentation.git /tmp/workflow_documentation
# Use Git to compare the corresponding directories.
git diff --stat /tmp/workflow_documentation/docs ./legacy/workflow-documentation/src
[!NOTE]
TODO
.github/workflows
: GitHub Actions workflowsdocker-compose.yml
: Specification for a set of container images you can use when editing any section of our documentation websiteREADME.md
: This documentThe .github/workflows
directory contains YAML files that we use to configure GitHub Actions.
We use GitHub Actions to (a) compile local and remote content into a website,
and to (b) publish that website to the Internet.
Assuming you have Docker installed, you can spin up the development environment by running:
docker compose up
That will run a web server, serving the legacy section of the website at the following URL:
In addition, whenever you make changes to content, the associated sections of the website will automatically be rebuilt (at which point, you can refresh your web browser to see the newly-rebuilt sections).
requirements.txt
files to indicate specific versions.rst
files into Markdown (.md
)