UNM-CARC/foss · docs
A self-paced course that teaches researchers core open-science skills: open science, data management, the command line, LLMs, version contro
Open source Repository Open in the app JSON README (API)
About
# Foundational Open Science Skills (FOSS) { .carc-visually-hidden }
<div class="carc-hero" markdown>
<p class="carc-hero__title">Foundational Open Science Skills</p>
<p class="carc-hero__tagline">A self-paced course in the open-science skills every researcher needs — from FAIR data and the command line to Git, containers, HPC, and the cloud.</p>
<div class="carc-actions" markdown>
[:material-rocket-launch: Start lesson 1](lessons/01-open-science.md){ .md-button .md-button--primary }
[:material-clipboard-check-outline: Before you start](course/setup.md){ .md-button }
[:material-format-list-numbered: All lessons](lessons/index.md){ .md-button }
[:material-github: Source on GitHub](https://github.com/UNM-CARC/foss){ .md-button target=_blank }
</div>
</div>
<div class="grid cards" markdown>
- :material-calendar-check:{ .lg .middle } __Course information__
---
Accounts and software to set up first, the schedule of the last live
offering, the code of conduct, and a glossary of terms
Details
- Kind
- OKF bundles
- Topic
- Version control
- Publisher
- unm-carc
- Origin
- okf_github
- Category
- dados
- Version
- 0.2
- Last push
- 2026-09-11T13:53:57Z
- Repository state
- ativo
- Language
- Python
- License
- NOASSERTION
- Added
- 2026-09-13 14:03:47
- Updated
- 2026-09-13 14:03:47
- Origin id
UNM-CARC/foss:docs/index.md
README
# Foundational Open Science Skills (FOSS)
A self-paced course that teaches researchers core open-science skills — open
science, data management, the command line, LLMs, version control, software
environments, containers, HPC, and CyVerse cloud computing — published by the
[UNM Center for Advanced Research Computing (CARC)](https://carc.unm.edu) at
**<https://unm-carc.github.io/foss/>**.
The course is adapted from [CyVerse](https://cyverse.org)'s
[Foundational Open Science Skills](https://github.com/CyVerse-learning-materials/foss)
under CC BY 4.0. It is built with [Zensical](https://zensical.org), styled
after the [CARC documentation](https://carc.unm.edu/docs/), and structured as
an [Open Knowledge Format (OKF) v0.2](https://github.com/GoogleCloudPlatform/open-knowledge-format)
knowledge bundle so the content is first-class for both humans and AI agents.
## Quick start
```bash
python3 -m venv .venv && source .venv/bin/activate
pip install -r requirements.txt # zensical + pyyaml (Python 3.11+)
zensical serve # live preview at http://localhost:8000
zensical build --clean # static site in ./site
```
## Repository layout
```
├── zensical.toml # Site configuration (theme, nav, extensions)
├── docs/ # The OKF knowledge bundle + site content
│ ├── index.md # Landing page (declares okf_version: "0.2")
│ ├── log.md # OKF update log (reserved filename)
│ ├── course/ # Setup, dated schedule, code of conduct, glossary
│ ├── lessons/ # Lessons 01–09 plus extras
│ ├── capstone/ # Capstone project guidance
│ ├── about/ # Credits, contributing, guidance for AI agents
│ ├── assets/ # Images, logos, and the Nextflow tutorial files
│ ├── stylesheets/extra.css # UNM cherry + turquoise theme
│ └── llms.txt, llms-full.txt # Generated agent indexes (do not edit)
├── scripts/
│ ├── okf_validate.py # OKF v0.2 conformance checker (CI)
│ ├── check_links.py # Links, images, and nav coverage (CI)
│ ├── gen_llms_txt.py # Builds docs/llms.txt + docs/llms-full.txt
│ ├── postbuild_agent_surface.py # Markdown mirror, OKF meta tags, robots.txt
│ └── externalize_links.py # Adds {target=_blank} to external links
├── MIGRATION.md # Old foss.cyverse.org URLs -> new URLs
├── AGENTS.md / CLAUDE.md # Rules for coding agents working in this repo
└── .github/workflows/docs.yml # Validation + GitHub Pages deployment
```
## Machine readability (OKF)
Every content page carries YAML frontmatter with:
- `type` — `Lesson`, `Guide`, `Reference`, `Policy`, or `Schedule` (required by OKF)
- `title`, `description`, `tags` — used by search, indexes, and agents
- `generated: { by, at }` — who or what produced the current content
- `sources` — provenance links to the exact upstream CyVerse file and commit,
with `last_modified` from git history
- `status` / `stale_after` — lifecycle markers (the course schedule records a
dated offering and carries a `stale_after` date)
Pages migrated by an agent are intentionally **unverified** (no `verified`
key). When CARC staff review a page, they add:
```yaml
verified: { by: "human:<netid>", at: "2026-XX-XXT00:00:00Z" }
```
The deployed site is directly consumable by AI agents:
- `/llms.txt` ([convention](https://llmstxt.org)) — linked outline;
`/llms-full.txt` — the full corpus with frontmatter in one file.
- **Markdown mirror**: any page URL + `index.md` returns that page's source
with OKF frontmatter (e.g. `/lessons/05-version-control/index.md`).
- Rendered pages carry `<link rel="alternate" type="text/markdown">` and
`okf:*` meta tags; `robots.txt` advertises all of the above.
`docs/about/ai-agents.md` is the human- and agent-readable guide.
After content changes, regenerate the indexes (CI fails on drift) and check
the bundle:
```bash
python scripts/okf_validate.py docs
python scripts/check_links.py docs
python scripts/gen_llms_txt.py
zensical build --clean && python scripts/postbuild_agent_surface.py site
```
## Credits
FOSS was created by CyVerse at the University of Arizona. Cite the original
course as:
> Michele Cosi, Jeffrey K. Gillan, Tyson L. Swetnam. (2024, May 2).
> CyVerse-learning-materials/foss: FOSS 2024 Spring. Zenodo.
> <https://doi.org/10.5281/zenodo.11105956>
CyVerse is funded by the US National Science Foundation (awards DBI-0735191,
DBI-1265383, and DBI-1743442). See
[docs/about/credits.md](docs/about/credits.md) for authors, funding, and the
list of changes made in this adaptation. Content is licensed
[CC BY 4.0](LICENSE).
## Deployment
Pushing to `main` on [UNM-CARC/foss](https://github.com/UNM-CARC/foss) runs
OKF validation and the link check, verifies the llms.txt indexes are current,
builds the site, adds the agent surface, and deploys to GitHub Pages at
<https://unm-carc.github.io/foss/> via `.github/workflows/docs.yml`. The
workflow enables Pages automatically (`configure-pages` with
`enablement: true`); if the first deploy fails on permissions, set
Settings → Pages → Source to "GitHub Actions" once.