Merge pull request #463 from Remi-Gau/autodoc

[DOC] auto doc main CLI

.github/workflows/docs.yml

@@ -16,7 +16,9 @@ jobs:
       - name: Install neurodocker
         run: python -m pip install --editable .[docs]
       - name: build docs
-        run: sphinx-build docs docs-build
+        run: |
+          make -C docs cli
+          sphinx-build docs docs-build
       - name: Deploy
         uses: JamesIves/github-pages-deploy-action@v4
         with:

README.md

@@ -2,7 +2,6 @@
 
 [![build status](https://github.com/ReproNim/neurodocker/actions/workflows/pull-request.yml/badge.svg)](https://github.com/ReproNim/neurodocker/actions/workflows/pull-request.yml)
 [![docker pulls](https://img.shields.io/docker/pulls/repronim/neurodocker.svg)](https://hub.docker.com/r/repronim/neurodocker/)
-[![docker pulls](https://img.shields.io/docker/pulls/kaczmarj/neurodocker.svg)](https://hub.docker.com/r/kaczmarj/neurodocker/)
 [![python versions](https://img.shields.io/pypi/pyversions/neurodocker.svg)](https://pypi.org/project/neurodocker/)
 [![DOI](https://zenodo.org/badge/88654995.svg)](https://zenodo.org/badge/latestdoi/88654995)
 

docs/Makefile

@@ -14,7 +14,10 @@ help:
 
 .PHONY: help Makefile
 
+cli:
+	bash generate_cli_help.sh
+
 # Catch-all target: route all unknown targets to Sphinx using the new
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
-%: Makefile
+%: Makefile cli
 	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/conf.py

@@ -39,12 +39,9 @@
     "sphinx.ext.githubpages",
     "sphinx.ext.intersphinx",
     "sphinx.ext.coverage",
-    # "sphinx.ext.mathjax",
-    # "sphinx.ext.ifconfig",
     "sphinx.ext.napoleon",
     "sphinx.ext.todo",
     "sphinx.ext.viewcode",
-    # "sphinx.ext.linkcode",
     "sphinxcontrib.apidoc",
 ]
 
@@ -63,10 +60,34 @@
 #
 html_theme = "pydata_sphinx_theme"
 
+html_theme_options = {
+    "use_edit_page_button": True,
+    "icon_links": [
+        {
+            "name": "GitHub",
+            "url": "https://github.com/ReproNim/neurodocker",
+            "icon": "fa-brands fa-github",
+        },
+        {
+            "name": "Docker Hub",
+            "url": "https://hub.docker.com/r/repronim/neurodocker",
+            "icon": "fa-brands fa-docker",
+        },
+    ],
+}
+
+
+html_context = {
+    "github_user": "ReproNim",
+    "github_repo": "neurodocker",
+    "github_version": "master",
+    "doc_path": "docs",
+}
+
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ["_static"]
+# html_static_path = ["_static"]
 
 # -- Options for extensions ---------------------------------------------------
 

docs/generate_cli_help.sh

@@ -0,0 +1,11 @@
+#! /bin/bash
+
+# quick and dirty way to make sure the CLI help is up to date
+
+echo "Generating CLI help for Neurodocker and its subcommands..."
+
+neurodocker --help > user_guide/cli_help.txt
+neurodocker generate --help > user_guide/generate_cli_help.txt
+neurodocker generate docker --help > user_guide/generate_docker_cli_help.txt
+neurodocker generate singularity --help > user_guide/generate_singularity_cli_help.txt
+neurodocker minify --help > user_guide/minify_cli_help.txt

docs/index.rst

@@ -16,7 +16,6 @@ This website is in progress. Is there is something you would like to see here, p
    :caption: Contents:
 
    user_guide/index
-   build_results
    api
 
 

docs/user_guide/.gitignore

@@ -0,0 +1 @@
+*.txt