Merge branch 'f-doc' into 'dev'

WIP ENH: Documentation

See merge request caosdb/caosdb-advanced-user-tools!67

.docker/Dockerfile

 FROM debian:latest
 RUN apt-get update && \
-	 apt-get install \
-	 curl \
-	 python3 \
-	 python3-pip \
-	 python3-requests \
-	 python3-pandas \
-	 python3-html2text \
-	 tox \
-	 git \
-	 openjdk-11-jdk-headless \
-	 python-autopep8 \
-     python3-pytest \
-     libxml2 \
-	 -y
+    apt-get install \
+    curl \
+    python3 \
+    python3-pip \
+    python3-requests \
+    python3-pandas \
+    python3-html2text \
+    python3-sphinx python3-recommonmark \
+    tox \
+    git \
+    openjdk-11-jdk-headless \
+    python-autopep8 \
+    python3-pytest \
+    libxml2 \
+    -y
 COPY .docker/wait-for-it.sh /wait-for-it.sh
 ADD https://gitlab.com/api/v4/projects/13656973/repository/branches/dev \
    pylib_version.json

.gitignore

-__pycache__
-.tox
+# -*- mode:conf; -*-
+
+# compiled python and dist stuff
+*.egg
 .eggs
-.coverage
+*.egg-info/
+__pycache__/
+/.cache
 *cache.db
-*.egg-info
+*.pyc
+build/
+.tox
+.coverage
 .docker/cert
-src/caosadvancedtools/version.py
-version.py
+
+# documentation
+_apidoc

.gitlab-ci.yml

@@ -3,7 +3,9 @@
 #
 # Copyright (C) 2018 Research Group Biomedical Physics,
 # Max-Planck-Institute for Dynamics and Self-Organization Göttingen
-# Copyright (C) 2019 Henrik tom Wörden 
+# Copyright (C) 2019 Henrik tom Wörden
+# Copyright (C) 2020 Indiscale GmbH <info@indiscale.com>
+# Copyright (C) 2020 Daniel Hornung <d.hornung@indiscale.com>
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU Affero General Public License as
@@ -33,9 +35,10 @@ stages:
   - style
   - unittest
   - integrationtest
+  - deploy
 
 test:
-  tags: [docker]
+  tags: [cached-dind]
   stage: integrationtest
   image: $CI_REGISTRY_IMAGE_BASE
   script:
@@ -73,8 +76,8 @@ build-testenv:
   tags: [cached-dind]
   image: docker:18.09
   stage: setup
-  #only:
-  #- schedules
+  only:
+      - schedules
   script: 
       - df -h
       - docker login -u gitlab-ci-token -p $CI_JOB_TOKEN $CI_REGISTRY
@@ -116,3 +119,22 @@ unittest:
   image: $CI_REGISTRY_IMAGE
   script:
       - tox
+
+# Build the sphinx documentation and make it ready for deployment by Gitlab Pages
+# documentation:
+#   stage: deploy
+
+# Special job for serving a static website. See https://docs.gitlab.com/ee/ci/yaml/README.html#pages
+pages:
+  stage: deploy
+  image: $CI_REGISTRY_IMAGE
+  tags: [docker]
+  only:
+    - dev
+  script:
+    - echo "Deploying"
+    - make doc
+    - cp -r build/doc/html public
+  artifacts:
+    paths:
+      - public

CHANGELOG.md

@@ -21,6 +21,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - new assure_name_is function
 - two utility functions when working with files: NameCollector and 
   get_file_via_download
+- Automated documentation builds: `make doc`
 
 ### Changed ###
 

Makefile

+# ** header v3.0
+# This file is a part of the CaosDB Project.
+#
+# Copyright (C) 2020 IndiScale GmbH <info@indiscale.com>
+# Copyright (C) 2020 Daniel Hornung <d.hornung@indiscale.com>
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero General Public License as
+# published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU Affero General Public License for more details.
+#
+# You should have received a copy of the GNU Affero General Public License
+# along with this program. If not, see <https://www.gnu.org/licenses/>.
+#
+# ** end header
+
+# This Makefile is a wrapper for several other scripts.
+
+.PHONY: help doc install
+
+help:
+	@echo 'Type `make doc` for documentation, or `make install` for (local) installation.'
+
+doc:
+	$(MAKE) -C src/doc html
+
+install:
+	@echo "Not implemented yet, use pip for installation."

README_SETUP.md

@@ -29,3 +29,13 @@ autopep8 -i -r ./
 
 test:
 - scifolder package from https://gitlab.com/henrik_indiscale/scifolder
+
+# Documentation #
+
+Build documentation in `build/` with `make doc`.
+
+## Requirements ##
+
+- sphinx
+- sphinx-autoapi
+- recommonmark

src/doc/Makefile

+# ** header v3.0
+# This file is a part of the CaosDB Project.
+#
+# Copyright (C) 2020 IndiScale GmbH <info@indiscale.com>
+# Copyright (C) 2020 Daniel Hornung <d.hornung@indiscale.com>
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero General Public License as
+# published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU Affero General Public License for more details.
+#
+# You should have received a copy of the GNU Affero General Public License
+# along with this program. If not, see <https://www.gnu.org/licenses/>.
+#
+# ** end header
+
+# This Makefile is a wrapper for sphinx scripts.
+#
+# It is based upon the autocreated makefile for Sphinx documentation.
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?= -a
+SPHINXBUILD   ?= sphinx-build
+SPHINXAPIDOC   ?= sphinx-apidoc
+PY_BASEDIR    = ../caosadvancedtools
+SOURCEDIR     = .
+BUILDDIR      = ../../build/doc
+
+
+.PHONY: doc-help Makefile
+
+# Put it first so that "make" without argument is like "make help".
+doc-help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile apidoc
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+apidoc:
+	@$(SPHINXAPIDOC) -o _apidoc $(PY_BASEDIR)

src/doc/concepts.rst

+========================
+The concepts of pycaosdb
+========================
+
+Some text...
+

src/doc/conf.py

+# -*- coding: utf-8 -*-
+#
+# 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('../caosdb'))
+
+
+# -- Project information -----------------------------------------------------
+
+project = 'caosadvancedtools'
+copyright = '2020, IndiScale GmbH'
+author = 'Daniel Hornung'
+
+# The short X.Y version
+version = '0.X.Y'
+# The full version, including alpha/beta/rc tags
+release = '0.x.y-beta-rc2'
+
+
+# -- 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.ext.autodoc',
+    'sphinx.ext.intersphinx',
+    'sphinx.ext.napoleon',     # For Google style docstrings
+    "recommonmark",            # For markdown files.
+]
+
+# 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'
+
+# 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 pattern also affects html_static_path and html_extra_path.
+exclude_patterns = []
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = None
+
+
+# -- 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'
+
+# 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']
+
+# Custom sidebar templates, must be a dictionary that maps document names
+# to template names.
+#
+# The default sidebars (for documents that don't match any pattern) are
+# defined by theme itself.  Builtin themes are using these templates by
+# default: ``['localtoc.html', 'relations.html', 'sourcelink.html',
+# 'searchbox.html']``.
+#
+# html_sidebars = {}
+
+
+# -- Options for HTMLHelp output ---------------------------------------------
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'caosadvancedtoolsdoc'
+
+
+# -- 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, 'caosadvancedtools.tex', 'caosadvancedtools Documentation',
+     'IndiScale GmbH', '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, 'caosadvancedtools', 'caosadvancedtools 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, 'caosadvancedtools', 'caosadvancedtools Documentation',
+     author, 'caosadvancedtools ', 'One line description of project.',
+     'Miscellaneous'),
+]
+
+
+# -- Options for Epub output -------------------------------------------------
+
+# Bibliographic Dublin Core info.
+epub_title = project
+
+# The unique identifier of the text. This can be a ISBN number
+# or the project homepage.
+#
+# epub_identifier = ''
+
+# A unique identification for the text.
+#
+# epub_uid = ''
+
+# A list of files that should not be packed into the epub file.
+epub_exclude_files = ['search.html']
+
+
+# -- Extension configuration -------------------------------------------------
+
+# -- Options for intersphinx extension ---------------------------------------
+
+# Example configuration for intersphinx: refer to the Python standard library.
+intersphinx_mapping = {'https://docs.python.org/': None}
+
+# TODO Which options do we want?
+autodoc_default_options = {
+    'members': None,
+    'undoc-members': None,
+}

src/doc/getting_started.md

+# Getting started with pycaosdb #
+
+1. Install
+2. import
+3. enjoy

src/doc/index.rst

+
+Welcome to caosdb-pylib's documentation!
+========================================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+   :hidden:
+
+   Getting started <getting_started>
+   Concepts <concepts>
+   tutorials
+   _apidoc/modules
+
+Welcome to the advanced Python tools for CaosDB!
+
+This documentation helps you to :doc:`get started<getting_started>`, explains the most important
+:doc:`concepts<concepts>` and offers a range of :doc:`tutorials<tutorials>`.
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`