diff --git a/.docker/Dockerfile b/.docker/Dockerfile index dac12f9161bbc6b8060082c190dd27a82ab5ccc1..1990f031d0c9bf13e3de94b4f92ac8e2b8b27cc7 100644 --- a/.docker/Dockerfile +++ b/.docker/Dockerfile @@ -1,19 +1,20 @@ 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 diff --git a/.gitignore b/.gitignore index b1d651a7852d96ddb67170e80c1522f24573112b..bea8a04f8e93b7659fdc4d7b8d5246a19b8759ad 100644 --- a/.gitignore +++ b/.gitignore @@ -1,9 +1,17 @@ -__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 diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index dfd6a0bf8d5b2985528ef7f69a8608ae6824dd48..9f746e473a799c027e40b84e3f3a6b36e7539c62 100644 --- a/.gitlab-ci.yml +++ b/.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 diff --git a/CHANGELOG.md b/CHANGELOG.md index 3618c3fec9e9cab7c48e9d2182b364d14fb97b38..ad0105443e981e661337e4b7827abd987c06e782 100644 --- a/CHANGELOG.md +++ b/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 ### diff --git a/Makefile b/Makefile new file mode 100644 index 0000000000000000000000000000000000000000..cbac0ea0a77e5523529ef181d83ffb9738d72faf --- /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 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." diff --git a/README_SETUP.md b/README_SETUP.md index 1400ac5e7428db0143b5180228b097dfbd661f78..4f3a6998b676e04bc5729b54aa2a27103a1850cf 100644 --- a/README_SETUP.md +++ b/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 diff --git a/src/doc/Makefile b/src/doc/Makefile new file mode 100644 index 0000000000000000000000000000000000000000..d28503eb0e883e6c879898c12dac07f91bd2df68 --- /dev/null +++ b/src/doc/Makefile @@ -0,0 +1,48 @@ +# ** 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) 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..62a8cbb9c9d5ca80a35e3aa686d1b6c4d29b8bb6 --- /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 = '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, +} 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..84580c215806385b09fd7140ce1d4de22f30f021 --- /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 + _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`