diff --git a/.gitignore b/.gitignore index 5f5efa9..a99a635 100644 --- a/.gitignore +++ b/.gitignore @@ -1,3 +1,6 @@ __pycache__ *.pyc +examples/*/*/ + +docs/build/ diff --git a/docs/Makefile b/docs/Makefile new file mode 100644 index 0000000..e4bd14c --- /dev/null +++ b/docs/Makefile @@ -0,0 +1,193 @@ +# Makefile for Sphinx documentation +# + +# You can set these variables from the command line. +SPHINXOPTS = -W +SPHINXBUILD = python3 -m sphinx +PAPER = +BUILDDIR = build + +# User-friendly check for sphinx-build +#ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 1) +#$(error The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don't have Sphinx installed, grab it from http://sphinx-doc.org/) +#endif + +# Internal variables. +PAPEROPT_a4 = -D latex_paper_size=a4 +PAPEROPT_letter = -D latex_paper_size=letter +ALLSPHINXOPTS = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source +# the i18n builder cannot share the environment and doctrees with the others +I18NSPHINXOPTS = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source + +.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest coverage gettext + +help: + @echo "Please use \`make ' where is one of" + @echo " html to make standalone HTML files" + @echo " dirhtml to make HTML files named index.html in directories" + @echo " singlehtml to make a single large HTML file" + @echo " pickle to make pickle files" + @echo " json to make JSON files" + @echo " htmlhelp to make HTML files and a HTML help project" + @echo " qthelp to make HTML files and a qthelp project" + @echo " applehelp to make an Apple Help Book" + @echo " devhelp to make HTML files and a Devhelp project" + @echo " epub to make an epub" + @echo " latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter" + @echo " latexpdf to make LaTeX files and run them through pdflatex" + @echo " latexpdfja to make LaTeX files and run them through platex/dvipdfmx" + @echo " text to make text files" + @echo " man to make manual pages" + @echo " texinfo to make Texinfo files" + @echo " info to make Texinfo files and run them through makeinfo" + @echo " gettext to make PO message catalogs" + @echo " changes to make an overview of all changed/added/deprecated items" + @echo " xml to make Docutils-native XML files" + @echo " pseudoxml to make pseudoxml-XML files for display purposes" + @echo " linkcheck to check all external links for integrity" + @echo " doctest to run all doctests embedded in the documentation (if enabled)" + @echo " coverage to run coverage check of the documentation (if enabled)" + +clean: + rm -rf $(BUILDDIR)/* source/generated source/_extras/schema.json + +html: + $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html + @echo + @echo "Build finished. The HTML pages are in $(BUILDDIR)/html." + +dirhtml: + $(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml + @echo + @echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml." + +singlehtml: + $(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml + @echo + @echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml." + +pickle: + $(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle + @echo + @echo "Build finished; now you can process the pickle files." + +json: + $(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json + @echo + @echo "Build finished; now you can process the JSON files." + +htmlhelp: + $(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp + @echo + @echo "Build finished; now you can run HTML Help Workshop with the" \ + ".hhp project file in $(BUILDDIR)/htmlhelp." + +qthelp: + $(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp + @echo + @echo "Build finished; now you can run "qcollectiongenerator" with the" \ + ".qhcp project file in $(BUILDDIR)/qthelp, like this:" + @echo "# qcollectiongenerator $(BUILDDIR)/qthelp/datalad_gooey.qhcp" + @echo "To view the help file:" + @echo "# assistant -collectionFile $(BUILDDIR)/qthelp/datalad_gooey.qhc" + +applehelp: + $(SPHINXBUILD) -b applehelp $(ALLSPHINXOPTS) $(BUILDDIR)/applehelp + @echo + @echo "Build finished. The help book is in $(BUILDDIR)/applehelp." + @echo "N.B. You won't be able to view it unless you put it in" \ + "~/Library/Documentation/Help or install it in your application" \ + "bundle." + +devhelp: + $(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp + @echo + @echo "Build finished." + @echo "To view the help file:" + @echo "# mkdir -p $$HOME/.local/share/devhelp/datalad_gooey" + @echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/datalad_gooey" + @echo "# devhelp" + +epub: + $(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub + @echo + @echo "Build finished. The epub file is in $(BUILDDIR)/epub." + +latex: + $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex + @echo + @echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex." + @echo "Run \`make' in that directory to run these through (pdf)latex" \ + "(use \`make latexpdf' here to do that automatically)." + +latexpdf: + $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex + @echo "Running LaTeX files through pdflatex..." + $(MAKE) -C $(BUILDDIR)/latex all-pdf + @echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex." + +latexpdfja: + $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex + @echo "Running LaTeX files through platex and dvipdfmx..." + $(MAKE) -C $(BUILDDIR)/latex all-pdf-ja + @echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex." + +text: + $(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text + @echo + @echo "Build finished. The text files are in $(BUILDDIR)/text." + +man: + @echo start man + $(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man + @echo + @echo "Build finished. The manual pages are in $(BUILDDIR)/man." + +texinfo: + $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo + @echo + @echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo." + @echo "Run \`make' in that directory to run these through makeinfo" \ + "(use \`make info' here to do that automatically)." + +info: + $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo + @echo "Running Texinfo files through makeinfo..." + make -C $(BUILDDIR)/texinfo info + @echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo." + +gettext: + $(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale + @echo + @echo "Build finished. The message catalogs are in $(BUILDDIR)/locale." + +changes: + $(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes + @echo + @echo "The overview file is in $(BUILDDIR)/changes." + +linkcheck: + $(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck + @echo + @echo "Link check complete; look for any errors in the above output " \ + "or in $(BUILDDIR)/linkcheck/output.txt." + +doctest: + $(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest + @echo "Testing of doctests in the sources finished, look at the " \ + "results in $(BUILDDIR)/doctest/output.txt." + +coverage: + $(SPHINXBUILD) -b coverage $(ALLSPHINXOPTS) $(BUILDDIR)/coverage + @echo "Testing of coverage in the sources finished, look at the " \ + "results in $(BUILDDIR)/coverage/python.txt." + +xml: + $(SPHINXBUILD) -b xml $(ALLSPHINXOPTS) $(BUILDDIR)/xml + @echo + @echo "Build finished. The XML files are in $(BUILDDIR)/xml." + +pseudoxml: + $(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml + @echo + @echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml." diff --git a/docs/README.md b/docs/README.md new file mode 100644 index 0000000..ddbc7a1 --- /dev/null +++ b/docs/README.md @@ -0,0 +1,22 @@ +## Editing, building, and publishing extension documentation + + +[Sphinx](https://www.sphinx-doc.org/en/master/index.html#) is used for document generation. + +### Local testing + +``` +pip install sphinx sphinx_rtd_theme +``` + +Then build the documentation locally: + +``` +make -C docs html +``` + +Navigate to `docs/build/` and open `index.html`. + +### Remote building and testing + +The documentation can be automatically build by the GitHub Action can be published within that action. diff --git a/docs/source/PASTA/OpenSemanticLab.png b/docs/source/PASTA/OpenSemanticLab.png new file mode 100644 index 0000000..4fe5e76 Binary files /dev/null and b/docs/source/PASTA/OpenSemanticLab.png differ diff --git a/docs/source/PASTA/PASTA.png b/docs/source/PASTA/PASTA.png new file mode 100644 index 0000000..958869f Binary files /dev/null and b/docs/source/PASTA/PASTA.png differ diff --git a/docs/source/PASTA/PASTA.rst b/docs/source/PASTA/PASTA.rst new file mode 100644 index 0000000..1fb6a69 --- /dev/null +++ b/docs/source/PASTA/PASTA.rst @@ -0,0 +1,25 @@ +.. _PASTA: + +Screenshots after importing .eln files into PASTA-ELN +***************************************************** + +.. image:: kadi4mat_1.png + :width: 600 + :alt: Screenshot after importing kadi4mat's collections example + +.. image:: kadi4mat_2.png + :width: 600 + :alt: Screenshot after importing kadi4mat's records example + +.. image:: OpenSemanticLab.png + :width: 600 + :alt: Screenshot after importing OpenSemanticLab's example + +.. image:: PASTA.png + :width: 600 + :alt: Screenshot after importing PASTA's example + +.. image:: SampleDB.png + :width: 600 + :alt: Screenshot after importing SampleDB's example + diff --git a/docs/source/PASTA/SampleDB.png b/docs/source/PASTA/SampleDB.png new file mode 100644 index 0000000..79c486f Binary files /dev/null and b/docs/source/PASTA/SampleDB.png differ diff --git a/docs/source/PASTA/kadi4mat_1.png b/docs/source/PASTA/kadi4mat_1.png new file mode 100644 index 0000000..8b083f5 Binary files /dev/null and b/docs/source/PASTA/kadi4mat_1.png differ diff --git a/docs/source/PASTA/kadi4mat_2.png b/docs/source/PASTA/kadi4mat_2.png new file mode 100644 index 0000000..cbc33bf Binary files /dev/null and b/docs/source/PASTA/kadi4mat_2.png differ diff --git a/docs/source/_static/Consortium.png b/docs/source/_static/Consortium.png new file mode 100644 index 0000000..5bd19d8 Binary files /dev/null and b/docs/source/_static/Consortium.png differ diff --git a/docs/source/conf.py b/docs/source/conf.py new file mode 100644 index 0000000..b6cb895 --- /dev/null +++ b/docs/source/conf.py @@ -0,0 +1,128 @@ +# -*- coding: utf-8 -*- +# +# Documentation build configuration file, created by +# sphinx-quickstart on Tue Oct 13 08:41:19 2015. +# +# 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. + +import datetime +import sys +from os import pardir +from os.path import ( + abspath, + dirname, + exists, + join as opj, +) + +# 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. +#sys.path.insert(0, os.path.abspath('.')) + +# generate missing pieces +for setup_py_path in (opj(pardir, 'setup.py'), # travis + opj(pardir, pardir, 'setup.py')): # RTD + if exists(setup_py_path): + sys.path.insert(0, abspath(dirname(setup_py_path))) + +# -- 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.autosummary', + 'sphinx.ext.autosectionlabel', + 'sphinx.ext.doctest', + 'sphinx.ext.intersphinx', + 'sphinx.ext.todo', + 'sphinx.ext.coverage', + 'sphinx.ext.mathjax', + 'sphinx.ext.ifconfig', + 'sphinx.ext.inheritance_diagram', + 'sphinx.ext.viewcode', + 'sphinx.ext.napoleon', +] + +# for the module reference +autosummary_generate = True + +# 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 = u'The ELN Consortium / The ELN file format' +copyright = u'2022-{}, The ELN Consortium'.format(datetime.datetime.now().year) +author = u'The ELN Consortium' + +# 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. +version = "1.1" +release = version + +# 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 = 'en' + +# List of patterns, relative to source directory, that match files and +# directories to ignore when looking for source files. +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 = True + +# Example configuration for intersphinx: refer to the Python standard library. +intersphinx_mapping = {'': ('https://docs.python.org/', 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 = 'sphinx_rtd_theme' + +# The name of an image file (relative to this directory) to place at the top +# of the sidebar. +html_logo = '_static/Consortium.png' + +# 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'] + +# If true, the index is split into individual pages for each letter. +html_split_index = True + +# If true, links to the reST sources are added to the pages. +html_show_sourcelink = False + +# smart quotes are incompatible with the RST flavor of the generated manpages +# but see `smartquotes_action` for more fine-grained control, in case +# some of this functionality is needed +smartquotes = False diff --git a/docs/source/index.rst b/docs/source/index.rst new file mode 100644 index 0000000..abfe2ef --- /dev/null +++ b/docs/source/index.rst @@ -0,0 +1,15 @@ +The ELN File Format .eln +************************ + + +Overview +======== + +.. toctree:: + :maxdepth: 1 + + PASTA/PASTA + + +.. |---| unicode:: U+02014 .. em dash +