Merge branch 'master' of https://github.molgen.mpg.de/EditionOpenAcce…

…ss/eoa-utilities

.gitignore

@@ -0,0 +1 @@
+docs/_build/

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+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)

docs/_templates/layout.html

@@ -0,0 +1,11 @@
+{% extends '!layout.html' %}
+
+{%- block header %}
+  {%- if theme_showheader|tobool %}
+    <header id="pageheader"><h1><a href="{{ pathto(master_doc) }} ">
+        {{ docstitle }}
+      </a></h1>
+      <h3><a href="../">Main Documentation Page</a></h3>
+    </header>
+  {%- endif %}
+{%- endblock %}

docs/conf.py

@@ -0,0 +1,71 @@
+# 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('.'))
+from better import better_theme_path
+html_theme_path = [better_theme_path]
+
+
+# -- Project information -----------------------------------------------------
+
+project = 'EOA Utilities'
+copyright = '2020, Max Planck Institute for the History of Science'
+author = 'Klaus Thoden'
+
+
+# -- General configuration ---------------------------------------------------
+
+# 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.intersphinx',
+    'sphinx.ext.autosectionlabel',
+]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# 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.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+
+# -- 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 = 'better'
+
+# 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']
+
+
+# -- Extension configuration -------------------------------------------------
+
+# -- Options for intersphinx extension ---------------------------------------
+
+# Example configuration for intersphinx: refer to the Python standard library.
+intersphinx_mapping = {'https://docs.python.org/3/': None}

docs/index.rst

@@ -0,0 +1,20 @@
+.. EOA Utilities documentation master file, created by
+   sphinx-quickstart on Thu Apr  2 08:55:11 2020.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to EOA Utilities's documentation!
+=========================================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

docs/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=.
+set BUILDDIR=_build
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.http://sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

eoa.rc

@@ -11,14 +11,23 @@ di=$rootpath/EOASkripts/runtime/input
 do=$rootpath/EOASkripts/runtime/output
 e15=$rootpath/eoa-1.5
 
-# build sphinx documentation
+# build sphinx documentation and open in browser
 function msx(){
     cd $1;
+    make clean;
     make html;
     open $1/_build/html/index.html;
     cd -
 }
 
+# build sphinx documentation silently
+function msxs(){
+    cd $1;
+    make clean;
+    make html;
+    cd -
+}
+
 # get latest hashes of some django apps for inclusion in requirements.txt of eoa-1.5
 function get_head_hash(){
     current_dir=$(pwd);
@@ -46,15 +55,19 @@ function cpdi(){
 # function to import new publication
 function pimp(){
     current_dir=$(pwd);
-    pnumber=$(grep Number $do/$1/django/publication.cfg| cut -f 2 -d ":"| tr -d '[:space:]');
-    pseries=$(grep Serie $do/$1/django/publication.cfg| cut -f 2 -d ":"| tr -d '[:space:]'| tr '[:upper:]' '[:lower:]');
+    pnumber=$(grep '^Number:' $do/$1/django/publication.cfg| cut -f 2 -d ":"| tr -d '[:space:]');
+    pseries=$(grep '^Serie:' $do/$1/django/publication.cfg| cut -f 2 -d ":"| tr -d '[:space:]'| tr '[:upper:]' '[:lower:]');
 
     import_dir="import_${pseries}${pnumber}";
     mediafiles="$e15/runtime_data/res.rt/all_media_files/$pseries/$pnumber";
 
     cd $e15;
-    rm -vfr $mediafiles;
-    rm -vfr $e15/src/$import_dir;
+    if [ -d $mediafiles ]; then
+        rm -vfr $mediafiles;
+    fi
+    if [ -d $e15/src/$import_dir ]; then
+        rm -vfr $e15/src/$import_dir;
+    fi
     cp -rv $do/$1/django src/$import_dir;
     docker-compose exec webserver bash -c "python manage.py publicationimport ${import_dir}";
     cd $current_dir;