nipreps · oesteban · Oct 11, 2019 · Mar 25, 2019 · Mar 25, 2019 · Mar 26, 2019
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -429,6 +429,45 @@ jobs:
       - store_artifacts:
           path: /tmp/ds054
 
+  build_docs:
+    docker:
+      - image: python:latest
+    steps:
+      - checkout
+      - run:
+          name: Install deps
+          command: pip install -r requirements.txt && pip install -r docs_requirements.txt
+      - run:
+          name: Generate Docs
+          command: sphinx-versioning -vv build -r ci_doc_deploy ./docs ./docs/_build/html/
+      - persist_to_workspace:
+          root: docs/_build
+          paths: html
+      - store_artifacts:
+          path: ./docs/_build/html
+
+  deploy_docs:
+    docker:
+      - image: node:8.10.0
+    steps:
+      - checkout
+      - attach_workspace:
+          at: docs/_build
+      - run:
+          name: Disable jekyll builds
+          command: touch docs/_build/html/.nojekyll
+      - run:
+          name: Install and configure dependencies
+          command: |
+            npm install -g --silent gh-pages@2.0.1
+            git config user.email "rosswilsonblair+smriprep-circleci@gmail.com"
+            git config user.name "ci-build"
+      - add_ssh_keys:
+          fingerprints:
+            - "45:a6:cb:50:27:5a:c7:39:4c:1f:aa:2c:0f:87:8a:a6"
+      - run:
+          name: Deploy docs to gh-pages branch
+          command: gh-pages --dotfiles --message "[skip ci] Updates" --dist docs/_build/html
 
 workflows:
   version: 2
@@ -448,17 +487,32 @@ workflows:
             tags:
               only: /.*/
 
-      # - build_docs:
-      #     requires:
-      #       - build
-      #     filters:
-      #       branches:
-      #         ignore:
-      #           - /tests?\/.*/
-      #           - /ds005\/.*/
-      #           - /ds054\/.*/
-      #       tags:
-      #         only: /.*/
+      - build_docs:
+          #requires:
+          #  - deploy_docker
+          #  - deploy_pypi
+          filters:
+            branches:
+              ignore:
+                - /tests?\/.*/
+                - /ds005\/.*/
+                - /ds054\/.*/
+            tags:
+              only: /.*/
+
+      - deploy_docs:
+          requires:
+            - build_docs
+            - deploy_docker
+            - deploy_pypi
+          filters:
+            branches:
+              ignore:
+                - /tests?\/.*/
+                - /ds005\/.*/
+                - /ds054\/.*/
+            tags:
+              only: /^v.*/
 
       - update_cache:
           requires:

diff --git a/CHANGES.rst b/CHANGES.rst
@@ -87,4 +87,4 @@ in `poldracklab/fmriprep#1588 <https://github.com/poldracklab/fmriprep/issues/15
 0.0.2 (January 8, 2019)
 ========================
 
-First functional version after forking from fMRIPrep
+* First functional version after forking from fMRIPrep
diff --git a/README.rst b/README.rst
@@ -0,0 +1,11 @@
+.. include:: links.rst
+
+smriprep: A Robust Preprocessing Pipeline for Structural MRI Data
+=================================================================
+
+This pipeline is developed by the `Poldrack lab at Stanford University
+<https://poldracklab.stanford.edu/>`_ for use at the `Center for Reproducible
+Neuroscience (CRN) <http://reproducibility.stanford.edu/>`_, as well as for
+open-source software distribution.
+
+This package is called directly from fMRIPrep_.
diff --git a/docs/.nojekyll b/docs/.nojekyll
diff --git a/docs/Makefile b/docs/Makefile
@@ -0,0 +1,19 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
diff --git a/docs/_sources/for_git b/docs/_sources/for_git
diff --git a/docs/_sources/modules.rst b/docs/_sources/modules.rst
@@ -0,0 +1,7 @@
+smriprep
+========
+
+.. toctree::
+   :maxdepth: 4
+
+   smriprep
diff --git a/docs/_sources/smriprep.cli.rst b/docs/_sources/smriprep.cli.rst
@@ -0,0 +1,30 @@
+smriprep.cli package
+====================
+
+Submodules
+----------
+
+smriprep.cli.run module
+-----------------------
+
+.. automodule:: smriprep.cli.run
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+smriprep.cli.utils module
+-------------------------
+
+.. automodule:: smriprep.cli.utils
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: smriprep.cli
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/_sources/smriprep.interfaces.rst b/docs/_sources/smriprep.interfaces.rst
@@ -0,0 +1,22 @@
+smriprep.interfaces package
+===========================
+
+Submodules
+----------
+
+smriprep.interfaces.reports module
+----------------------------------
+
+.. automodule:: smriprep.interfaces.reports
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: smriprep.interfaces
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/_sources/smriprep.rst b/docs/_sources/smriprep.rst
@@ -0,0 +1,20 @@
+smriprep package
+================
+
+Subpackages
+-----------
+
+.. toctree::
+
+   smriprep.cli
+   smriprep.interfaces
+   smriprep.utils
+   smriprep.workflows
+
+Module contents
+---------------
+
+.. automodule:: smriprep
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/_sources/smriprep.utils.rst b/docs/_sources/smriprep.utils.rst
@@ -0,0 +1,22 @@
+smriprep.utils package
+======================
+
+Submodules
+----------
+
+smriprep.utils.bids module
+--------------------------
+
+.. automodule:: smriprep.utils.bids
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: smriprep.utils
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/_sources/smriprep.workflows.rst b/docs/_sources/smriprep.workflows.rst
@@ -0,0 +1,54 @@
+smriprep.workflows package
+==========================
+
+Submodules
+----------
+
+smriprep.workflows.anatomical module
+------------------------------------
+
+.. automodule:: smriprep.workflows.anatomical
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+smriprep.workflows.base module
+------------------------------
+
+.. automodule:: smriprep.workflows.base
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+smriprep.workflows.norm module
+------------------------------
+
+.. automodule:: smriprep.workflows.norm
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+smriprep.workflows.outputs module
+---------------------------------
+
+.. automodule:: smriprep.workflows.outputs
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+smriprep.workflows.surfaces module
+----------------------------------
+
+.. automodule:: smriprep.workflows.surfaces
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: smriprep.workflows
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/_static/ajax-loader.gif b/docs/_static/ajax-loader.gif