Add Makefile and config file for Sphinx, nbsphinx (Add Sphinx docs - Part 3)

.gitignore

@@ -1,7 +1,8 @@
+_build
 .ipynb_checkpoints/
 download-any-bam-file/Aligned.sortedByCoord.out.bam
 download-smartseq2-matrix-scanpy/matrix.results
 download-smartseq2-matrix-scanpy/matrix.tsv
 download-smartseq2-matrix-scanpy/matrix2.results
 download-smartseq2-matrix-scanpy/matrix2.tsv
-explore-hca-dataset-scanpy-may-2019/pancreas.loom
+explore-hca-dataset-scanpy/pancreas.loom

Makefile

@@ -0,0 +1,36 @@
+include common.mk
+
+# Minimal makefile for Sphinx documentation
+#
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+.PHONY: help Makefile
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+refresh_all_requirements:
+	@echo '' >| requirements-docs.txt
+	@if [ $$(uname -s) == "Darwin" ]; then sleep 1; fi  # this is require because Darwin HFS+ only has second-resolution for timestamps.
+	@touch requirements-docs.txt.in
+	@$(MAKE) requirements-docs.txt
+
+requirements-docs.txt : %.txt : %.txt.in
+	[ ! -e .requirements-env ] || exit 1
+	virtualenv -p $(shell which python3) .$<-env
+	.$<-env/bin/pip install -r $@
+	.$<-env/bin/pip install -r $<
+	echo "# You should not edit this file directly.  Instead, you should edit $<." >| $@
+	.$<-env/bin/pip freeze >> $@
+	rm -rf .$<-env
+
+html: Makefile
+	@$(SPHINXBUILD) -M html "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(0)
+
+# to make sphinx documentation in any other format, use the command sphinx-build -b <format>

common.mk

@@ -0,0 +1,3 @@
+ifeq ($(shell which pandoc),)
+$(error Please install pandoc using "apt-get install pandoc" or "brew install pandoc")
+endif

conf.py

@@ -0,0 +1,55 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+# import os
+# import sys
+# sys.path.insert(0, os.path.abspath('.'))
+
+
+# -- Project information -----------------------------------------------------
+
+project = 'Data Consumer Vignettes'
+copyright = '2019, Human Cell Atlas'
+author = 'Human Cell Atlas'
+
+
+# -- General configuration ---------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+   'nbsphinx'
+]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = [
+    'vp', 'dcv', '_src', '_build', 'Thumbs.db', '.DS_Store', '**.ipynb_checkpoints'
+]
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = 'alabaster'
+
+# 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']

download-10x-liver/README.md

@@ -0,0 +1,6 @@
+# Download Data for All Liver Cells Sequenced with 10x
+
+In this notebook, we cover how to search the Human Cell Atlas Data Store (DSS) for bundles containing liver cells
+that were sequenced with 10x, and download all of the data that is found.
+
+See the [notebook](download-10x-liver.ipynb).