From 86cd3888b4c2f436270abb832f4b31b1f1d50a5e Mon Sep 17 00:00:00 2001 From: Sara Ogaz Date: Wed, 4 Apr 2018 11:04:54 -0400 Subject: [PATCH 1/4] first pass at getting sphinx and automodapi running, not storing automodapi generated docs for now. #51 --- .gitignore | 4 +- docs/Makefile | 20 +++++ docs/source/api_docs.rst | 7 ++ docs/source/conf.py | 170 +++++++++++++++++++++++++++++++++++++++ docs/source/index.rst | 30 +++++++ 5 files changed, 230 insertions(+), 1 deletion(-) create mode 100644 docs/Makefile create mode 100644 docs/source/api_docs.rst create mode 100644 docs/source/conf.py create mode 100644 docs/source/index.rst diff --git a/.gitignore b/.gitignore index dfaaafd6a..1c8d2c110 100644 --- a/.gitignore +++ b/.gitignore @@ -4,4 +4,6 @@ utils/config.json build/ dist/ -jwql.egg-info/ \ No newline at end of file +jwql.egg-info/ +docs/build/ +docs/source/api/ \ No newline at end of file diff --git a/docs/Makefile b/docs/Makefile new file mode 100644 index 000000000..f88da7e2b --- /dev/null +++ b/docs/Makefile @@ -0,0 +1,20 @@ +# Minimal makefile for Sphinx documentation +# + +# You can set these variables from the command line. +SPHINXOPTS = +SPHINXBUILD = sphinx-build +SPHINXPROJ = jwql +SOURCEDIR = source +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) \ No newline at end of file diff --git a/docs/source/api_docs.rst b/docs/source/api_docs.rst new file mode 100644 index 000000000..73d9da6dc --- /dev/null +++ b/docs/source/api_docs.rst @@ -0,0 +1,7 @@ +Preview Image Test +================== +.. automodapi:: jwql.preview_image.preview_image + +Utils Test +========== +.. automodapi:: jwql.utils.utils diff --git a/docs/source/conf.py b/docs/source/conf.py new file mode 100644 index 000000000..6427bd81c --- /dev/null +++ b/docs/source/conf.py @@ -0,0 +1,170 @@ +#!/usr/bin/env python3 +# -*- coding: utf-8 -*- +# +# jwql documentation build configuration file, created by +# sphinx-quickstart on Wed Apr 4 10:30:20 2018. +# +# This file is execfile()d with the current directory set to its +# containing dir. +# +# Note that not all possible configuration values are present in this +# autogenerated file. +# +# All configuration values have a default; values that are commented out +# serve to show the default. + +# 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('.')) +import stsci_rtd_theme + +# -- General configuration ------------------------------------------------ + +# If your documentation needs a minimal Sphinx version, state it here. +# +# needs_sphinx = '1.0' + +# Add any Sphinx extension module names here, as strings. They can be +# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom +# ones. +extensions = ['sphinx_automodapi.automodapi', + 'sphinx_automodapi.automodsumm', + 'numpydoc', + 'sphinx.ext.autodoc', + 'sphinx.ext.mathjax', + 'sphinx.ext.viewcode'] + +# Add any paths that contain templates here, relative to this directory. +templates_path = ['_templates'] + +# The suffix(es) of source filenames. +# You can specify multiple suffix as a list of string: +# +# source_suffix = ['.rst', '.md'] +source_suffix = '.rst' + +# The master toctree document. +master_doc = 'index' + +# General information about the project. +project = 'jwql' +copyright = '2018, STScI' +author = 'STScI' + +# The version info for the project you're documenting, acts as replacement for +# |version| and |release|, also used in various other places throughout the +# built documents. +# +# The short X.Y version. +version = '0.4.1' +# The full version, including alpha/beta/rc tags. +release = '0.4.1' + +# The language for content autogenerated by Sphinx. Refer to documentation +# for a list of supported languages. +# +# This is also used if you do content translation via gettext catalogs. +# Usually you set "language" from the command line for these cases. +language = None + +# List of patterns, relative to source directory, that match files and +# directories to ignore when looking for source files. +# This patterns also effect to html_static_path and html_extra_path +exclude_patterns = [] + +# The name of the Pygments (syntax highlighting) style to use. +pygments_style = 'sphinx' + +# If true, `todo` and `todoList` produce output, else they produce nothing. +todo_include_todos = False + + +# -- 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 = 'stsci_rtd_theme' + +# Theme options are theme-specific and customize the look and feel of a theme +# further. For a list of options available for each theme, see the +# documentation. +# +# html_theme_options = {} + +# 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_theme_path = [stsci_rtd_theme.get_html_theme_path()] + +# Custom sidebar templates, must be a dictionary that maps document names +# to template names. +# +# This is required for the alabaster theme +# refs: http://alabaster.readthedocs.io/en/latest/installation.html#sidebars +#html_sidebars = {} + + +# -- Options for HTMLHelp output ------------------------------------------ + +# Output file base name for HTML help builder. +htmlhelp_basename = 'jwqldoc' + + +# -- Options for LaTeX output --------------------------------------------- + +latex_elements = { + # The paper size ('letterpaper' or 'a4paper'). + # + # 'papersize': 'letterpaper', + + # The font size ('10pt', '11pt' or '12pt'). + # + # 'pointsize': '10pt', + + # Additional stuff for the LaTeX preamble. + # + # 'preamble': '', + + # Latex figure (float) alignment + # + # 'figure_align': 'htbp', +} + +# Grouping the document tree into LaTeX files. List of tuples +# (source start file, target name, title, +# author, documentclass [howto, manual, or own class]). +latex_documents = [ + (master_doc, 'jwql.tex', 'jwql Documentation', + 'STScI', 'manual'), +] + + +# -- Options for manual page output --------------------------------------- + +# One entry per manual page. List of tuples +# (source start file, name, description, authors, manual section). +man_pages = [ + (master_doc, 'jwql', 'jwql Documentation', + [author], 1) +] + + +# -- Options for Texinfo output ------------------------------------------- + +# Grouping the document tree into Texinfo files. List of tuples +# (source start file, target name, title, author, +# dir menu entry, description, category) +texinfo_documents = [ + (master_doc, 'jwql', 'jwql Documentation', + author, 'jwql', 'One line description of project.', + 'Miscellaneous'), +] + + + diff --git a/docs/source/index.rst b/docs/source/index.rst new file mode 100644 index 000000000..4c3820628 --- /dev/null +++ b/docs/source/index.rst @@ -0,0 +1,30 @@ +.. jwql documentation master file, created by + sphinx-quickstart on Wed Apr 4 10:30:20 2018. + You can adapt this file completely to your liking, but it should at least + contain the root `toctree` directive. + +Welcome to jwql's documentation! +================================ + +General JWQL description here. + +.. toctree:: + :maxdepth: 2 + :caption: Contents: + +API documentation +================= + +.. toctree:: + :maxdepth: 1 + :caption: Contents: + + api_docs.rst + + +Indices and tables +================== + +* :ref:`genindex` +* :ref:`modindex` +* :ref:`search` From b700d07858f346075c469ffc7185cd66cef3de1f Mon Sep 17 00:00:00 2001 From: Sara Ogaz Date: Wed, 4 Apr 2018 11:14:06 -0400 Subject: [PATCH 2/4] Adding readthedocs files, issue #51 --- docs/environment.yml | 14 ++++++++++++++ readthedocs.yml | 5 +++++ 2 files changed, 19 insertions(+) create mode 100644 docs/environment.yml create mode 100644 readthedocs.yml diff --git a/docs/environment.yml b/docs/environment.yml new file mode 100644 index 000000000..a72b38e5d --- /dev/null +++ b/docs/environment.yml @@ -0,0 +1,14 @@ +name: stak-notebooks +channels: + - http://ssb.stsci.edu/astroconda + - conda-forge +dependencies: + - numpy + - scipy + - astropy + - numpydoc + - sphinx>=1.5 + - sphinx_rtd_theme + - stsci_rtd_theme + - pip: + - sphinx-automodapi diff --git a/readthedocs.yml b/readthedocs.yml new file mode 100644 index 000000000..ddcd2ca67 --- /dev/null +++ b/readthedocs.yml @@ -0,0 +1,5 @@ +type: sphinx +python: + version: 3 +conda: + file: docs/environment.yml \ No newline at end of file From cf5c37a58cff30d6f934d77695abac089bf1494e Mon Sep 17 00:00:00 2001 From: Sara Ogaz Date: Wed, 4 Apr 2018 11:31:30 -0400 Subject: [PATCH 3/4] deleting these rtd files for now, rtd will not run on a private repo --- docs/environment.yml | 14 -------------- readthedocs.yml | 5 ----- 2 files changed, 19 deletions(-) delete mode 100644 docs/environment.yml delete mode 100644 readthedocs.yml diff --git a/docs/environment.yml b/docs/environment.yml deleted file mode 100644 index a72b38e5d..000000000 --- a/docs/environment.yml +++ /dev/null @@ -1,14 +0,0 @@ -name: stak-notebooks -channels: - - http://ssb.stsci.edu/astroconda - - conda-forge -dependencies: - - numpy - - scipy - - astropy - - numpydoc - - sphinx>=1.5 - - sphinx_rtd_theme - - stsci_rtd_theme - - pip: - - sphinx-automodapi diff --git a/readthedocs.yml b/readthedocs.yml deleted file mode 100644 index ddcd2ca67..000000000 --- a/readthedocs.yml +++ /dev/null @@ -1,5 +0,0 @@ -type: sphinx -python: - version: 3 -conda: - file: docs/environment.yml \ No newline at end of file From aa88a2321f30422d4b92ec156f94d37d1d13f03c Mon Sep 17 00:00:00 2001 From: Sara Ogaz Date: Wed, 4 Apr 2018 11:51:58 -0400 Subject: [PATCH 4/4] Updated environment file and a small conf tweak. --- docs/source/conf.py | 3 +++ environment.yml | 3 +++ 2 files changed, 6 insertions(+) diff --git a/docs/source/conf.py b/docs/source/conf.py index 6427bd81c..c4c75e108 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -50,6 +50,9 @@ # The master toctree document. master_doc = 'index' +# Numpy doc setting, right now this supresses some warnings, not exactly sure why? +numpydoc_show_class_members = False + # General information about the project. project = 'jwql' copyright = '2018, STScI' diff --git a/environment.yml b/environment.yml index 1985e77b5..ff3c2a99a 100644 --- a/environment.yml +++ b/environment.yml @@ -8,10 +8,13 @@ dependencies: - jwst=0.7.8rc9 - matplotlib=2.1.1 - numpy=1.14.0 +- numpydoc=0.8.0 - postgresql=9.6.6 - python=3.6.4 - python-dateutil=2.6.1 - sphinx=1.6.6 +- sphinx_rtd_theme=0.1.9 - sqlalchemy=1.2.0 +- stsci_rtd_theme=0.0.1 - pip: - sphinx-automodapi==0.7 \ No newline at end of file