diff --git a/.gitignore b/.gitignore index 341bfea4f1381b6eb59e548f395859bad35520d7..b522b1da9176e59756bffe89cd4eafe0d751a23c 100644 --- a/.gitignore +++ b/.gitignore @@ -1,3 +1,5 @@ +# -*- mode:conf; -*- + # dot files .* !/.gitignore @@ -11,3 +13,6 @@ __pycache__/ dist/ build/ src/caosdb/version.py + +# documentation +_apidoc \ No newline at end of file diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 1db4c0394de48cbd82d5abbe4d7c581abcb9b277..b45dde5de1e4cafdbc02a15c4b775b763d5447bd 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -4,6 +4,8 @@ # Copyright (C) 2018 Research Group Biomedical Physics, # Max-Planck-Institute for Dynamics and Self-Organization Göttingen # 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 @@ -88,3 +90,21 @@ build-testenv: --cache-from $CI_REGISTRY_IMAGE -t $CI_REGISTRY_IMAGE . - docker push $CI_REGISTRY_IMAGE + +# 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 + only: + # TODO this should be for master only, once releases are more regularly + - dev + script: + - echo "Deploying" + - make doc + - cp -r build/doc/html public + artifacts: + paths: + - public diff --git a/CHANGELOG.md b/CHANGELOG.md index 7ba0d8c13f4375ccd27d81b8c8733eab0edba42f..fd2bbfd27503488cbb7b2e7aef30ff959f3f323d 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -12,6 +12,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 * Versioning support (experimental). The version db.Version class can represents particular entity versions and also the complete history of an entity. +* Automated documentation builds: `make doc` ### Changed ### diff --git a/Makefile b/Makefile new file mode 100644 index 0000000000000000000000000000000000000000..4bc3459d209936c17a445c64e77180d9559e4653 --- /dev/null +++ b/Makefile @@ -0,0 +1,33 @@ +# ** 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 + +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." diff --git a/README_SETUP.md b/README_SETUP.md index 290350105740a206ac47cb5bd761a3c6655b2c15..896ee67ed03a493379c182ef617f0654a18f3ae4 100644 --- a/README_SETUP.md +++ b/README_SETUP.md @@ -9,3 +9,13 @@ tox # Code Formatting autopep8 -i -r ./ + +# Documentation # + +Build documentation in `build/` with `make doc`. + +## Requirements ## + +- sphinx +- sphinx-autoapi +- recommonmark diff --git a/src/caosdb/__init__.py b/src/caosdb/__init__.py index 75847bb15b8a64345119e0f0aefc00bd9f116081..1989080f4bcf6eb043a8ec8424418eb4c20d652d 100644 --- a/src/caosdb/__init__.py +++ b/src/caosdb/__init__.py @@ -22,6 +22,9 @@ # ** end header # +"""CaosDB Python bindings +""" + from os import environ, getcwd # Import of the connection function (which is used to connect to the DB): from os.path import expanduser, join diff --git a/src/caosdb/common/__init__.py b/src/caosdb/common/__init__.py index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..436281df8077b2cbf357537d36b21567b86ea5a2 100644 --- a/src/caosdb/common/__init__.py +++ b/src/caosdb/common/__init__.py @@ -0,0 +1 @@ +"""Commonly used classes for CaosDB.""" diff --git a/src/doc/Makefile b/src/doc/Makefile new file mode 100644 index 0000000000000000000000000000000000000000..5458c5300efc82e55686bc1cd6934182c5c8e39a --- /dev/null +++ b/src/doc/Makefile @@ -0,0 +1,47 @@ +# ** 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 = ../caosdb +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) diff --git a/src/doc/concepts.rst b/src/doc/concepts.rst new file mode 100644 index 0000000000000000000000000000000000000000..23e5fc4f6ddb666757fb9c79e192e07ffed8fb44 --- /dev/null +++ b/src/doc/concepts.rst @@ -0,0 +1,6 @@ +======================== +The concepts of pycaosdb +======================== + +Some text... + diff --git a/src/doc/conf.py b/src/doc/conf.py new file mode 100644 index 0000000000000000000000000000000000000000..eecfa112cfa20121b2c901389f1bcbe2ac7a3c8c --- /dev/null +++ b/src/doc/conf.py @@ -0,0 +1,191 @@ +# -*- 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 = 'caosdb-pylib' +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 = 'caosdb-pylibdoc' + + +# -- 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, 'caosdb-pylib.tex', 'caosdb-pylib 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, 'caosdb-pylib', 'caosdb-pylib 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, 'caosdb-pylib', 'caosdb-pylib Documentation', + author, 'caosdb-pylib', '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, +} diff --git a/src/doc/getting_started.md b/src/doc/getting_started.md new file mode 100644 index 0000000000000000000000000000000000000000..6805181e73a7f338fbacb74bdd9f734360404372 --- /dev/null +++ b/src/doc/getting_started.md @@ -0,0 +1,5 @@ +# Getting started with pycaosdb # + +1. Install +2. import +3. enjoy diff --git a/src/doc/index.rst b/src/doc/index.rst new file mode 100644 index 0000000000000000000000000000000000000000..c95559d92b344a08bf33f9398789174fb00742b2 --- /dev/null +++ b/src/doc/index.rst @@ -0,0 +1,26 @@ + +Welcome to caosdb-pylib's documentation! +======================================== + +.. toctree:: + :maxdepth: 2 + :caption: Contents: + :hidden: + + Getting started <getting_started> + Concepts <concepts> + tutorials + API documentation<_apidoc/modules> + +Welcome to the Python client library for CaosDB, ``pycaosdb``! + +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` diff --git a/unittests/docker/Dockerfile b/unittests/docker/Dockerfile index da45618fa6f60fdcc20042dcaf3df30f4e2d166c..8b3190845b3f288872d159e32a89e7216639cc94 100644 --- a/unittests/docker/Dockerfile +++ b/unittests/docker/Dockerfile @@ -1,7 +1,9 @@ FROM debian:latest RUN apt-get update && \ - apt-get install pylint3 python3-pip tox git \ - curl pycodestyle -y + apt-get install -y \ + pylint3 python3-pip tox git \ + curl pycodestyle \ + python3-sphinx python3-recommonmark ARG COMMIT="dev" RUN git clone -b dev https://gitlab.com/caosdb/caosdb-pylib.git && \ cd caosdb-pylib && git checkout $COMMIT && pip3 install .