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dbef970
updated pages
tyson-swetnam Mar 28, 2023
878149f
updated docs_dir
tyson-swetnam Mar 28, 2023
37a63a3
fixing action
tyson-swetnam Mar 28, 2023
a3ddbf6
updated docs_dir
tyson-swetnam Mar 28, 2023
337e9ce
updated docs_dir
tyson-swetnam Mar 28, 2023
58a476e
Update README.md
tyson-swetnam Mar 29, 2023
2d879b3
updated pages
tyson-swetnam Mar 30, 2023
d1a76f1
Update README.md
tyson-swetnam Mar 30, 2023
a1693f2
did more work
tyson-swetnam Mar 30, 2023
78a52f2
fixed typos
tyson-swetnam Mar 30, 2023
8ddbff5
added api
tyson-swetnam Mar 31, 2023
06edcc3
updated docs
tyson-swetnam Mar 31, 2023
69af421
updated docs
tyson-swetnam Mar 31, 2023
b58f99d
updated api docs some more
tyson-swetnam Mar 31, 2023
c89a789
made mermaid diagram
tyson-swetnam Mar 31, 2023
23fae86
updated format yml
tyson-swetnam Mar 31, 2023
4a9980e
its friday
tyson-swetnam Apr 1, 2023
68f139a
its friday
tyson-swetnam Apr 1, 2023
621dce3
updates
tyson-swetnam Apr 1, 2023
19cbf50
updates
tyson-swetnam Apr 1, 2023
4f69df9
updates
tyson-swetnam Apr 1, 2023
182a91a
Data related changes to the system overview
Apr 14, 2023
c5f4199
added SFTP to system overview
Apr 14, 2023
872e0d2
Update note about terrain API docs and default section
psarando Apr 21, 2023
68e94a2
Remove docs/services/api/schema.md
psarando Apr 21, 2023
fd31346
Update link to the DE's database schema
psarando Apr 21, 2023
22345ae
Finished the DS services page
Apr 21, 2023
93d5755
Merge pull request #1 from psarando/main
tyson-swetnam Apr 22, 2023
8b9cda9
Remove obsolete api/endpoints/tools.md docs
psarando Apr 25, 2023
e58fb26
Remove obsolete api/endpoints/app-execution.md docs
psarando Apr 25, 2023
9808757
Remove obsolete api/endpoints/collaborators.md docs
psarando Apr 25, 2023
dedbda9
Remove obsolete api/endpoints/reference-genomes.md docs
psarando Apr 25, 2023
1d91c3e
Remove obsolete api/endpoints/sharing.md docs
psarando Apr 25, 2023
7536e2d
Remove obsolete api/endpoints/tags.md docs
psarando Apr 25, 2023
7262e81
Cleanup obsolete api/endpoints/app-metadata.md docs
psarando Apr 25, 2023
c9e7e26
Cleanup obsolete api/endpoints/app-ontologies.md docs
psarando Apr 26, 2023
c5ed082
Cleanup obsolete api/endpoints/misc.md docs
psarando Apr 26, 2023
29c71c0
Remove obsolete api/endpoints/admin.md docs
psarando Apr 26, 2023
7108f3c
Remove obsolete api/endpoints/collaborator-lists.md docs
psarando Apr 26, 2023
b35a476
Remove obsolete api/endpoints/filetypes.md docs
psarando Apr 26, 2023
a3ece76
Remove obsolete api/endpoints/subjects.md docs
psarando Apr 26, 2023
e3d9742
Remove obsolete api/endpoints/teams.md docs
psarando Apr 26, 2023
ec0023d
Update DE API Authentication overview docs
psarando Apr 26, 2023
a8fd689
Update de.md
CosiMichele May 2, 2023
d8ef975
fixed typo
CosiMichele May 2, 2023
cb3eda3
Merge pull request #2 from CosiMichele/doi-patch
tyson-swetnam Jan 31, 2024
a4642d7
Create CNAME
tyson-swetnam Feb 12, 2024
58e499e
Fix typo in `ElasticSearch query DSL` link
psarando Jun 14, 2024
b6ff420
CORE-1889 Add Tapis v2 to v3 app migration guide
psarando Jun 14, 2024
302c937
CORE-1889 Update Tapis v2 to v3 app migration guide
psarando Jun 15, 2024
6ca533c
CORE-1889 Update Tapis v2 to v3 app migration guide
psarando Jun 18, 2024
93f27dc
Merge pull request #3 from psarando/tapis-v3
psarando Jun 28, 2024
8fcf392
CORE-1889 Update Tapis v2 to v3 app migration guide
psarando Jul 17, 2024
1257aae
CORE-1889 Update Tapis v2 to v3 app migration guide
psarando Aug 20, 2024
c77aa74
CORE-1889 Update Tapis v2 to v3 app migration guide
psarando Dec 20, 2024
f5e66a7
CORE-1889 Update Tapis v2 to v3 app migration guide
psarando Dec 20, 2024
c3dadd0
CORE-1889 Update Tapis v2 to v3 app migration guide
psarando Dec 20, 2024
4eaaed2
CORE-1889 Update Tapis v2 to v3 app migration guide
psarando Apr 5, 2025
67a5622
Update permanent-id-requests.md
tyson-swetnam Apr 16, 2025
ddf8312
Implement comprehensive documentation reorganization with Zensical
tyson-swetnam Jan 20, 2026
c515602
Update README.md to reflect Zensical migration
tyson-swetnam Jan 20, 2026
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36 changes: 17 additions & 19 deletions .github/workflows/gh-actions.yml
Original file line number Diff line number Diff line change
@@ -1,27 +1,25 @@
name: mkdocs

name: Publish docs via GitHub
on:
push:
branches: [ main ]
branches:
- main

jobs:
build:
name: Deploy docs
runs-on: ubuntu-latest
strategy:
matrix:
python-version: [ 3.8 ]

steps:
- uses: actions/checkout@v2

- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v2
- uses: actions/checkout@v3
- uses: actions/setup-python@v4
with:
python-version: ${{ matrix.python-version }}
architecture: x64

- name: Install requirements
run: python3 -m pip install -r requirements.txt

- name: Deploy 🚀
run: python3 -m mkdocs gh-deploy --force
python-version: 3.11
- name: Install dependencies
run: pip install -r requirements.txt
- name: Build documentation
run: zensical build
- name: Deploy to GitHub Pages
uses: peaceiris/actions-gh-pages@v3
with:
github_token: ${{ secrets.GITHUB_TOKEN }}
publish_dir: ./site
force_orphan: true
133 changes: 133 additions & 0 deletions .gitignore
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@@ -0,0 +1,133 @@
# Byte-compiled / optimized / DLL files
__pycache__/
*.py[cod]
*$py.class

# C extensions
*.so

# Distribution / packaging
.Python
build/
develop-eggs/
dist/
downloads/
eggs/
.eggs/
lib/
lib64/
parts/
sdist/
var/
wheels/
pip-wheel-metadata/
share/python-wheels/
*.egg-info/
.installed.cfg
*.egg
MANIFEST

# PyInstaller
# Usually these files are written by a python script from a template
# before PyInstaller builds the exe, so as to inject date/other infos into it.
*.manifest
*.spec

# Installer logs
pip-log.txt
pip-delete-this-directory.txt

# Unit test / coverage reports
htmlcov/
.tox/
.nox/
.coverage
.coverage.*
.cache
nosetests.xml
coverage.xml
*.cover
*.py,cover
.hypothesis/
.pytest_cache/

# Translations
*.mo
*.pot

# Django stuff:
*.log
local_settings.py
db.sqlite3
db.sqlite3-journal

# Flask stuff:
instance/
.webassets-cache

# Scrapy stuff:
.scrapy

# Sphinx documentation
docs/_build/

# PyBuilder
target/

# Jupyter Notebook
.ipynb_checkpoints

# IPython
profile_default/
ipython_config.py

# pyenv
.python-version

# pipenv
# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
# However, in case of collaboration, if having platform-specific dependencies or dependencies
# having no cross-platform support, pipenv may install dependencies that don't work, or not
# install all needed dependencies.
#Pipfile.lock

# PEP 582; used by e.g. github.com/David-OConnor/pyflow
__pypackages__/

# Celery stuff
celerybeat-schedule
celerybeat.pid

# SageMath parsed files
*.sage.py

# Environments
.env
.venv
env/
venv/
ENV/
env.bak/
venv.bak/

# Spyder project settings
.spyderproject
.spyproject

# Rope project settings
.ropeproject

# mkdocs documentation
/site

# mypy
.mypy_cache/
.dmypy.json
dmypy.json

# Pyre type checker
.pyre/

# Claude Code
CLAUDE.md
.claude/
22 changes: 22 additions & 0 deletions LICENSE
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@@ -0,0 +1,22 @@
# License for CyVerse Documentation

Documentation contained in this repo is made available under at CC BY 4.0 License:
https://creativecommons.org/licenses/by/4.0/legalcode

You may:

- Share—copy and redistribute the material in any medium or format
- Adapt—remix, transform, and build upon the material

for any purpose, even commercially. The licensor cannot revoke these freedoms as long as you follow these license terms:

**Attribution—** You must give appropriate credit (mentioning that your work is derived from work that is Copyright (c) CyVerse and, where practical, linking to http://www.cyverse.org/), provide a link to the license, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use.

No additional restrictions—You may not apply legal terms or technological measures that legally restrict others from doing anything the license permits. With the understanding that:

- You do not have to comply with the license for elements of the material in the public domain or where your use is permitted by an applicable exception or limitation.
- No warranties are given. The license may not give you all of the permissions necessary for your intended use. For example, other rights such as publicity, privacy, or moral rights may limit how you use the material.

This license is superseded by and subject to any and all other polices of CyVerse as described at: http://www.cyverse.org/policies; CyVerse is based upon work supported by the National Science Foundation under Grant No. DBI-0735191 and DBI-1265383.

Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.
47 changes: 47 additions & 0 deletions README.md
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@@ -0,0 +1,47 @@
A special thanks to [Mojib Wali](https://github.com/mb-wali) of [CyVerse-Austria](https://www.tugraz.at/sites/cyverse/home), Graz University of Technology, Austria, for creating the initial Material MkDocs pages for the global CyVerse developer and maintainer community!

CyVerse Core Software Documentation
===================================

These documents are for the deployment and maintenance of [CyVerse](https://cyverse.org)

## Zensical Static Site Generator

This documentation is built using [Zensical](https://zensical.com), a modern static site generator from the team behind Material for MkDocs. The site uses Zensical's "classic" theme which provides the familiar Material for MkDocs appearance with enhanced features.

## GitHub Actions Deployment

The `main` branch uses GitHub Actions to automatically build and deploy the documentation.

Do not commit changes directly to the `main` branch unless necessary. Please commit your updates to the `mkdocs` branch, test on CodeSpaces or locally, and then commit those merges back to `main`.

Commits to `main` will trigger the Action which re-builds and deploys the website to https://docs.cyverse.org -- which is publicly available.

## Configuration

The documentation is configured using `zensical.toml` (TOML format) instead of the traditional `mkdocs.yml`. This provides better configuration management and access to Zensical-specific features.

## Local Development

```bash
git clone https://github.com/cyverse/docs
cd docs
pip install -r requirements.txt
zensical serve
```

After starting the development server, the site will open at `http://localhost:8000`

Open in browser and view

Recommended: two monitors for easier display while working on docs.

## Building

To build the static site:

```bash
zensical build
```

Output will be in the `./site` directory.
21 changes: 0 additions & 21 deletions README.rst

This file was deleted.

1 change: 1 addition & 0 deletions docs/CNAME
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@@ -0,0 +1 @@
docs.cyverse.org
1 change: 1 addition & 0 deletions docs/assets/HTCondor_red_blk.svg
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