diff --git a/cal_tools/cal_tools/cal_tools.py b/cal_tools/cal_tools/cal_tools.py
index 1bf060c3a64ff8978a65624fa6a6e1c3760c22ff..0e106db06f2fa579769f192af90d3cc782e5a273 100644
--- a/cal_tools/cal_tools/cal_tools.py
+++ b/cal_tools/cal_tools/cal_tools.py
@@ -29,27 +29,33 @@ def combine_report(run_path, calibration):
comps = name.split("_")
if len(comps) >= 2:
comps = "_".join(comps[:-1]), comps[-1]
- group, module = comps
- if module == "None":
- module = "All Modules"
+ group, conc_param = comps
else:
- group, module = comps[0], "All Modules"
+ group, conc_param = comps[0], "None"
with open("{}/{}.rst".format(sphinx_path, group), "a") as gfile:
- title = "{} - {}".format(calibration, module)
- gfile.write(title + "\n")
- gfile.write( "=" *len (title) + "\n")
- gfile.write("\n")
+ if conc_param != "None":
+ title = "{} - Parameter {}".format(calibration, conc_param)
+ gfile.write(title + "\n")
+ gfile.write( "=" *len (title) + "\n")
+ gfile.write("\n")
with open("{}/{}".format(run_path, entry), "r") as ifile:
for line in ifile.readlines():
- gfile.write(line)
+ if conc_param == "None":
+ gfile.write(line)
+ elif " ".join(calibration.split()) != " ".join(line.split()):
+ gfile.write(line)
gfile.write("\n\n")
if isdir("{}/{}".format(run_path, entry)):
shutil.copytree("{}/{}".format(run_path, entry), "{}/{}".format(sphinx_path, entry))
return sphinx_path
-def make_report(run_path, tmp_path, out_path, project, author, version):
+def make_report(run_path, tmp_path, out_path, project, author, version, report_to):
run_path = os.path.abspath(run_path)
+ report_path, report_name = os.path.split(report_to)
+ if report_path != '':
+ out_path = report_path
+
try:
import subprocess
subprocess.check_call(["sphinx-quickstart",
@@ -63,11 +69,23 @@ def make_report(run_path, tmp_path, out_path, project, author, version):
"--ext-mathjax",
"--makefile",
"--no-batchfile", run_path])
+ # now conf.py exists in temp folder, so add latex options to remove empty pages
+ patch_path = "{}".format(os.path.abspath(os.path.dirname(__file__)))
+ patch_file = ("{}/conf_latex.patch".format(patch_path))
+ subprocess.check_call(["patch",
+ "{}/sphinx_rep/conf.py".format(tmp_path),
+ patch_file])
+
+ subprocess.check_call(["sed",
+ "-i",
+ "-e",
+ "s/{}.tex/{}.tex/g".format(project.replace(" ",""), report_name),
+ "{}/sphinx_rep/conf.py".format(tmp_path)], shell=False)
except subprocess.CalledProcessError:
raise Exception("Failed to run sphinx-quickbuild. Is sphinx installed?"
"Generated simple index.rst instead")
-
+
# quickbuild went well we need to edit the index file
from shutil import move
@@ -119,7 +137,7 @@ def make_report(run_path, tmp_path, out_path, project, author, version):
# shutil.rmtree(tmp_path)
-def finalize(joblist, run_path, out_path, project, calibration, author, version):
+def finalize(joblist, run_path, out_path, project, calibration, author, version, report_to):
print("Waiting on jobs to finish: {}".format(joblist))
@@ -134,7 +152,7 @@ def finalize(joblist, run_path, out_path, project, calibration, author, version)
break
sleep(10)
sphinx_path = combine_report(run_path, calibration)
- make_report(sphinx_path, run_path, out_path, project, author, version)
+ make_report(sphinx_path, run_path, out_path, project, author, version, report_to)
diff --git a/cal_tools/cal_tools/conf_latex.patch b/cal_tools/cal_tools/conf_latex.patch
new file mode 100644
index 0000000000000000000000000000000000000000..e2259c2d82693c70ffb14ec31547805d72dd4c77
--- /dev/null
+++ b/cal_tools/cal_tools/conf_latex.patch
@@ -0,0 +1,10 @@
+--- conf_orig.py 2018-08-27 11:53:53.069138000 +0200
++++ conf_latex.py 2018-08-27 11:53:18.472939000 +0200
+@@ -257,6 +257,7 @@
+ # Latex figure (float) alignment
+ #
+ # 'figure_align': 'htbp',
++ 'extraclassoptions': ',openany, oneside',
+ }
+
+ # Grouping the document tree into LaTeX files. List of tuples
diff --git a/cal_tools/cal_tools/conf_latex.py b/cal_tools/cal_tools/conf_latex.py
new file mode 100644
index 0000000000000000000000000000000000000000..8b0ce452a6345c0766cec73cc35d7cbe465ff14f
--- /dev/null
+++ b/cal_tools/cal_tools/conf_latex.py
@@ -0,0 +1,347 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+#
+# 'Tutorial Calculation ' documentation build configuration file, created by
+# sphinx-quickstart on Thu Aug 23 12:23:00 2018.
+#
+# 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.
+
+# 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('.'))
+
+# -- 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.intersphinx',
+ 'sphinx.ext.mathjax',
+]
+
+# 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 encoding of source files.
+#
+# source_encoding = 'utf-8-sig'
+
+# The master toctree document.
+master_doc = 'index'
+
+# General information about the project.
+project = '\'Tutorial Calculation \''
+copyright = '2018, \'Astrid Muennich\''
+author = '\'Astrid Muennich\''
+
+# 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.
+#
+# The short X.Y version.
+version = ''
+# The full version, including alpha/beta/rc tags.
+release = ''
+
+# 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
+
+# There are two options for replacing |today|: either, you set today to some
+# non-false value, then it is used:
+#
+# today = ''
+#
+# Else, today_fmt is used as the format for a strftime call.
+#
+# today_fmt = '%B %d, %Y'
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This patterns also effect to html_static_path and html_extra_path
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+# The reST default role (used for this markup: `text`) to use for all
+# documents.
+#
+# default_role = None
+
+# If true, '()' will be appended to :func: etc. cross-reference text.
+#
+# add_function_parentheses = True
+
+# If true, the current module name will be prepended to all description
+# unit titles (such as .. function::).
+#
+# add_module_names = True
+
+# If true, sectionauthor and moduleauthor directives will be shown in the
+# output. They are ignored by default.
+#
+# show_authors = False
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
+# A list of ignored prefixes for module index sorting.
+# modindex_common_prefix = []
+
+# If true, keep warnings as "system message" paragraphs in the built documents.
+# keep_warnings = False
+
+# If true, `todo` and `todoList` produce output, else they produce nothing.
+todo_include_todos = False
+
+
+# -- 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 themes here, relative to this directory.
+# html_theme_path = []
+
+# The name for this set of Sphinx documents.
+# "<project> v<release> documentation" by default.
+#
+# html_title = '\'Tutorial Calculation \' v'
+
+# A shorter title for the navigation bar. Default is the same as html_title.
+#
+# html_short_title = None
+
+# The name of an image file (relative to this directory) to place at the top
+# of the sidebar.
+#
+# html_logo = None
+
+# The name of an image file (relative to this directory) to use as a favicon of
+# the docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32
+# pixels large.
+#
+# html_favicon = None
+
+# 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']
+
+# Add any extra paths that contain custom files (such as robots.txt or
+# .htaccess) here, relative to this directory. These files are copied
+# directly to the root of the documentation.
+#
+# html_extra_path = []
+
+# If not None, a 'Last updated on:' timestamp is inserted at every page
+# bottom, using the given strftime format.
+# The empty string is equivalent to '%b %d, %Y'.
+#
+# html_last_updated_fmt = None
+
+# If true, SmartyPants will be used to convert quotes and dashes to
+# typographically correct entities.
+#
+# html_use_smartypants = True
+
+# Custom sidebar templates, maps document names to template names.
+#
+# html_sidebars = {}
+
+# Additional templates that should be rendered to pages, maps page names to
+# template names.
+#
+# html_additional_pages = {}
+
+# If false, no module index is generated.
+#
+# html_domain_indices = True
+
+# If false, no index is generated.
+#
+# html_use_index = True
+
+# If true, the index is split into individual pages for each letter.
+#
+# html_split_index = False
+
+# If true, links to the reST sources are added to the pages.
+#
+# html_show_sourcelink = True
+
+# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
+#
+# html_show_sphinx = True
+
+# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
+#
+# html_show_copyright = True
+
+# If true, an OpenSearch description file will be output, and all pages will
+# contain a <link> tag referring to it. The value of this option must be the
+# base URL from which the finished HTML is served.
+#
+# html_use_opensearch = ''
+
+# This is the file name suffix for HTML files (e.g. ".xhtml").
+# html_file_suffix = None
+
+# Language to be used for generating the HTML full-text search index.
+# Sphinx supports the following languages:
+# 'da', 'de', 'en', 'es', 'fi', 'fr', 'h', 'it', 'ja'
+# 'nl', 'no', 'pt', 'ro', 'r', 'sv', 'tr', 'zh'
+#
+# html_search_language = 'en'
+
+# A dictionary with options for the search language support, empty by default.
+# 'ja' uses this config value.
+# 'zh' user can custom change `jieba` dictionary path.
+#
+# html_search_options = {'type': 'default'}
+
+# The name of a javascript file (relative to the configuration directory) that
+# implements a search results scorer. If empty, the default will be used.
+#
+# html_search_scorer = 'scorer.js'
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'TutorialCalculationdoc'
+
+# -- 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',
+ 'extraclassoptions': ',openany, oneside',
+}
+
+# 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, 'TutorialCalculation.tex', '\'Tutorial Calculation \' Documentation',
+ '\'Astrid Muennich\'', 'manual'),
+]
+
+# The name of an image file (relative to this directory) to place at the top of
+# the title page.
+#
+# latex_logo = None
+
+# For "manual" documents, if this is true, then toplevel headings are parts,
+# not chapters.
+#
+# latex_use_parts = False
+
+# If true, show page references after internal links.
+#
+# latex_show_pagerefs = False
+
+# If true, show URL addresses after external links.
+#
+# latex_show_urls = False
+
+# Documents to append as an appendix to all manuals.
+#
+# latex_appendices = []
+
+# It false, will not define \strong, \code, itleref, \crossref ... but only
+# \sphinxstrong, ..., \sphinxtitleref, ... To help avoid clash with user added
+# packages.
+#
+# latex_keep_old_macro_names = True
+
+# If false, no module index is generated.
+#
+# latex_domain_indices = True
+
+
+# -- 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, 'tutorialcalculation', '\'Tutorial Calculation \' Documentation',
+ [author], 1)
+]
+
+# If true, show URL addresses after external links.
+#
+# man_show_urls = False
+
+
+# -- 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, 'TutorialCalculation', '\'Tutorial Calculation \' Documentation',
+ author, 'TutorialCalculation', 'One line description of project.',
+ 'Miscellaneous'),
+]
+
+# Documents to append as an appendix to all manuals.
+#
+# texinfo_appendices = []
+
+# If false, no module index is generated.
+#
+# texinfo_domain_indices = True
+
+# How to display URL addresses: 'footnote', 'no', or 'inline'.
+#
+# texinfo_show_urls = 'footnote'
+
+# If true, do not generate a @detailmenu in the "Top" node's menu.
+#
+# texinfo_no_detailmenu = False
+
+
+# Example configuration for intersphinx: refer to the Python standard library.
+intersphinx_mapping = {'https://docs.python.org/': None}
diff --git a/cal_tools/cal_tools/conf_orig.py b/cal_tools/cal_tools/conf_orig.py
new file mode 100644
index 0000000000000000000000000000000000000000..5074430ad326f5b22dff8cb009190d9033bcdbfd
--- /dev/null
+++ b/cal_tools/cal_tools/conf_orig.py
@@ -0,0 +1,346 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+#
+# 'Tutorial Calculation ' documentation build configuration file, created by
+# sphinx-quickstart on Thu Aug 23 12:23:00 2018.
+#
+# 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.
+
+# 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('.'))
+
+# -- 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.intersphinx',
+ 'sphinx.ext.mathjax',
+]
+
+# 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 encoding of source files.
+#
+# source_encoding = 'utf-8-sig'
+
+# The master toctree document.
+master_doc = 'index'
+
+# General information about the project.
+project = '\'Tutorial Calculation \''
+copyright = '2018, \'Astrid Muennich\''
+author = '\'Astrid Muennich\''
+
+# 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.
+#
+# The short X.Y version.
+version = ''
+# The full version, including alpha/beta/rc tags.
+release = ''
+
+# 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
+
+# There are two options for replacing |today|: either, you set today to some
+# non-false value, then it is used:
+#
+# today = ''
+#
+# Else, today_fmt is used as the format for a strftime call.
+#
+# today_fmt = '%B %d, %Y'
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This patterns also effect to html_static_path and html_extra_path
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+# The reST default role (used for this markup: `text`) to use for all
+# documents.
+#
+# default_role = None
+
+# If true, '()' will be appended to :func: etc. cross-reference text.
+#
+# add_function_parentheses = True
+
+# If true, the current module name will be prepended to all description
+# unit titles (such as .. function::).
+#
+# add_module_names = True
+
+# If true, sectionauthor and moduleauthor directives will be shown in the
+# output. They are ignored by default.
+#
+# show_authors = False
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
+# A list of ignored prefixes for module index sorting.
+# modindex_common_prefix = []
+
+# If true, keep warnings as "system message" paragraphs in the built documents.
+# keep_warnings = False
+
+# If true, `todo` and `todoList` produce output, else they produce nothing.
+todo_include_todos = False
+
+
+# -- 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 themes here, relative to this directory.
+# html_theme_path = []
+
+# The name for this set of Sphinx documents.
+# "<project> v<release> documentation" by default.
+#
+# html_title = '\'Tutorial Calculation \' v'
+
+# A shorter title for the navigation bar. Default is the same as html_title.
+#
+# html_short_title = None
+
+# The name of an image file (relative to this directory) to place at the top
+# of the sidebar.
+#
+# html_logo = None
+
+# The name of an image file (relative to this directory) to use as a favicon of
+# the docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32
+# pixels large.
+#
+# html_favicon = None
+
+# 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']
+
+# Add any extra paths that contain custom files (such as robots.txt or
+# .htaccess) here, relative to this directory. These files are copied
+# directly to the root of the documentation.
+#
+# html_extra_path = []
+
+# If not None, a 'Last updated on:' timestamp is inserted at every page
+# bottom, using the given strftime format.
+# The empty string is equivalent to '%b %d, %Y'.
+#
+# html_last_updated_fmt = None
+
+# If true, SmartyPants will be used to convert quotes and dashes to
+# typographically correct entities.
+#
+# html_use_smartypants = True
+
+# Custom sidebar templates, maps document names to template names.
+#
+# html_sidebars = {}
+
+# Additional templates that should be rendered to pages, maps page names to
+# template names.
+#
+# html_additional_pages = {}
+
+# If false, no module index is generated.
+#
+# html_domain_indices = True
+
+# If false, no index is generated.
+#
+# html_use_index = True
+
+# If true, the index is split into individual pages for each letter.
+#
+# html_split_index = False
+
+# If true, links to the reST sources are added to the pages.
+#
+# html_show_sourcelink = True
+
+# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
+#
+# html_show_sphinx = True
+
+# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
+#
+# html_show_copyright = True
+
+# If true, an OpenSearch description file will be output, and all pages will
+# contain a <link> tag referring to it. The value of this option must be the
+# base URL from which the finished HTML is served.
+#
+# html_use_opensearch = ''
+
+# This is the file name suffix for HTML files (e.g. ".xhtml").
+# html_file_suffix = None
+
+# Language to be used for generating the HTML full-text search index.
+# Sphinx supports the following languages:
+# 'da', 'de', 'en', 'es', 'fi', 'fr', 'h', 'it', 'ja'
+# 'nl', 'no', 'pt', 'ro', 'r', 'sv', 'tr', 'zh'
+#
+# html_search_language = 'en'
+
+# A dictionary with options for the search language support, empty by default.
+# 'ja' uses this config value.
+# 'zh' user can custom change `jieba` dictionary path.
+#
+# html_search_options = {'type': 'default'}
+
+# The name of a javascript file (relative to the configuration directory) that
+# implements a search results scorer. If empty, the default will be used.
+#
+# html_search_scorer = 'scorer.js'
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'TutorialCalculationdoc'
+
+# -- 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, 'TutorialCalculation.tex', '\'Tutorial Calculation \' Documentation',
+ '\'Astrid Muennich\'', 'manual'),
+]
+
+# The name of an image file (relative to this directory) to place at the top of
+# the title page.
+#
+# latex_logo = None
+
+# For "manual" documents, if this is true, then toplevel headings are parts,
+# not chapters.
+#
+# latex_use_parts = False
+
+# If true, show page references after internal links.
+#
+# latex_show_pagerefs = False
+
+# If true, show URL addresses after external links.
+#
+# latex_show_urls = False
+
+# Documents to append as an appendix to all manuals.
+#
+# latex_appendices = []
+
+# It false, will not define \strong, \code, itleref, \crossref ... but only
+# \sphinxstrong, ..., \sphinxtitleref, ... To help avoid clash with user added
+# packages.
+#
+# latex_keep_old_macro_names = True
+
+# If false, no module index is generated.
+#
+# latex_domain_indices = True
+
+
+# -- 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, 'tutorialcalculation', '\'Tutorial Calculation \' Documentation',
+ [author], 1)
+]
+
+# If true, show URL addresses after external links.
+#
+# man_show_urls = False
+
+
+# -- 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, 'TutorialCalculation', '\'Tutorial Calculation \' Documentation',
+ author, 'TutorialCalculation', 'One line description of project.',
+ 'Miscellaneous'),
+]
+
+# Documents to append as an appendix to all manuals.
+#
+# texinfo_appendices = []
+
+# If false, no module index is generated.
+#
+# texinfo_domain_indices = True
+
+# How to display URL addresses: 'footnote', 'no', or 'inline'.
+#
+# texinfo_show_urls = 'footnote'
+
+# If true, do not generate a @detailmenu in the "Top" node's menu.
+#
+# texinfo_no_detailmenu = False
+
+
+# Example configuration for intersphinx: refer to the Python standard library.
+intersphinx_mapping = {'https://docs.python.org/': None}
diff --git a/docs/source/conf.py b/docs/source/conf.py
index 2d12d2d83092f961e8ded13adc53f89a069b3996..3dedb841bc822aaa2274c81dc8d463ce8d785da5 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -31,12 +31,22 @@
# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
# ones.
extensions = [
+ 'sphinx.ext.autodoc',
'sphinx.ext.intersphinx',
'sphinx.ext.todo',
'sphinx.ext.mathjax',
'sphinx.ext.ifconfig',
+ 'sphinx.ext.viewcode',
]
+import sys
+import os
+from subprocess import Popen
+
+sys.path.append(os.path.abspath("../pycalibration/"))
+p = Popen(["./makeAllDocs.sh"])
+p.communicate()
+
# Add any paths that contain templates here, relative to this directory.
templates_path = ['_templates']
@@ -259,6 +269,7 @@ latex_elements = {
# Latex figure (float) alignment
#
# 'figure_align': 'htbp',
+ 'extraclassoptions': 'openany, oneside',
}
# Grouping the document tree into LaTeX files. List of tuples
@@ -266,7 +277,7 @@ latex_elements = {
# author, documentclass [howto, manual, or own class]).
latex_documents = [
(master_doc, 'EuropeanXFELOfflineCalibration.tex', 'European XFEL Offline Calibration Documentation',
- 'The European XFEL Detector Group', 'manual'),
+ 'The European XFEL Detector Group', 'manual', True),
]
# The name of an image file (relative to this directory) to place at the top of
diff --git a/docs/source/index.rst b/docs/source/index.rst
index a55b1f41d11a73757b1b68786f0a410d99e28860..561aa4a85f1308d921af058aa6bba98131d6ccf8 100644
--- a/docs/source/index.rst
+++ b/docs/source/index.rst
@@ -18,6 +18,7 @@ Contents:
available_notebooks
advanced
tutorial
+ _notebooks/index
Indices and tables
diff --git a/docs/source/makeAllDocs.sh b/docs/source/makeAllDocs.sh
new file mode 100755
index 0000000000000000000000000000000000000000..f1c2d96b063a72af2b033bb0c3d7a60120b97964
--- /dev/null
+++ b/docs/source/makeAllDocs.sh
@@ -0,0 +1,37 @@
+#!/bin/bash
+
+# first convert notebooks to rst files
+# the list of notebooks to convert:
+
+notebooks=(calversion)
+
+cd _notebooks
+
+echo "Tutorial Example"> index.rst
+echo "================">> index.rst
+echo "" >> index.rst
+echo "Tutorial Notebook:" >> index.rst
+echo "" >> index.rst
+echo ".. toctree::" >> index.rst
+echo " :maxdepth: 5" >> index.rst
+echo " :titlesonly:" >> index.rst
+echo "" >> index.rst
+
+for nb in ${notebooks[*]}
+do
+ jupyter nbconvert --to rst ../../../notebooks/Tutorial/${nb}.ipynb --output-dir=./
+ ##fix code blocks
+ sed -i.bak 's/code::/code-block::/g' ${nb}.rst
+ sed -i.bak 's/ipython3/python/g' ${nb}.rst
+ sed -i.bak 's/raw:: latex/math::/g' ${nb}.rst
+ sed -i.bak 's/``/`/g' ${nb}.rst
+ mv ${nb}.rst ${nb}.rst.end
+ echo ".. _${nb}:" > ${nb}.rst
+ cat ${nb}.rst.end >> ${nb}.rst
+ rm ${nb}.rst.end
+ echo " ${nb}" >> index.rst
+done
+rm *.bak
+
+#cd .. rm api/* sphinx-apidoc -o ./api/ -E ../../iCalibrationDB/
+
diff --git a/notebooks/Tutorial/calversion.ipynb b/notebooks/Tutorial/calversion.ipynb
index 14933bab4ff9399154c657de68c43ae2f98dac2e..7f81d1b26540b4cf1f9c3ecbff0d362556c57d5c 100644
--- a/notebooks/Tutorial/calversion.ipynb
+++ b/notebooks/Tutorial/calversion.ipynb
@@ -6,7 +6,9 @@
"source": [
"# Tutorial Calculation #\n",
"\n",
- "Author: Astrid Muennich, Version 0.1\n",
+ "Author: Astrid Muennich\n",
+ "\n",
+ "Version: 0.1\n",
"\n",
"A small example how to adapt a notebook to run with the offline calibration package \"pycalibation\".\n",
"\n",
diff --git a/xfel_calibrate/calibrate.py b/xfel_calibrate/calibrate.py
index 96860b64069c1e7fe9cd868a602635b9564e7457..fd3321668913b1b6b617f9462f692c44f3ddc059 100755
--- a/xfel_calibrate/calibrate.py
+++ b/xfel_calibrate/calibrate.py
@@ -44,6 +44,10 @@ def make_initial_parser():
action="store_true",
default=False,
help="Do not run as a cluster job")
+
+ parser.add_argument('--report-to', type=str,
+ help='Filename (and optionally path) for output report')
+
return parser
parser = make_initial_parser()
@@ -340,7 +344,6 @@ def concurrent_run(temp_path, nb, nbname, args, cparm=None, cval=None,
params = parameter_values(parms, **args)
new_nb = replace_definitions(nb, params, execute=False)
base_name = nbname.replace(".ipynb", "")
-
new_name = "{}_{}.ipynb".format(os.path.basename(base_name), suffix)
nbpath = "{}/{}".format(temp_path, new_name)
@@ -449,7 +452,9 @@ def run():
author = "anonymous"
if not version:
version = ""
-
+
+ title = title.rstrip()
+
run_uuid = uuid4()
# check that a modules field is present if we run concurrently
@@ -466,7 +471,20 @@ def run():
# create a temporary output directory to work in
run_tmp_path = "{}/slurm_tmp_{}".format(temp_path, run_uuid)
os.makedirs(run_tmp_path)
-
+
+ # Write all input parameters to rst file to be included to final report
+ parms = parameter_values(parms, **args)
+ with open("{}/slurm_tmp_{}/InputParameters.rst".format(temp_path, run_uuid), "w") as finfile:
+ finfile.write("Input Parameters \n")
+ finfile.write("================ \n")
+ for p in parms:
+ finfile.write("{} \n\n".format(p.comment))
+ finfile.write(".. parsed-literal::\n")
+ if p.type is str:
+ finfile.write(" {} = '{}' \n\n".format(p.name, p.value))
+ else:
+ finfile.write(" {} = {} \n\n".format(p.name, p.value))
+
# wait on all jobs to run and then finalize the run by creating a report from the notebooks
out_path = "{}/{}/{}/{}".format(report_path, detector.upper(), caltype.upper(), datetime.now().isoformat())
if try_report_to_output:
@@ -484,11 +502,16 @@ def run():
os.makedirs(out_path)
cmd = ('"from cal_tools.cal_tools import finalize; ' +
'finalize({{joblist}}, \'{run_path}\', \'{out_path}\', '+
- '\'{project}\', \'{calibration}\', \'{author}\', \'{version}\')"')
+ '\'{project}\', \'{calibration}\', \'{author}\', '
+ '\'{version}\', \'{report_to}\')"')
+ report_to = title.replace(" ","")
+ if args["report_to"] is not None:
+ report_to = args["report_to"]
+
fmtcmd = cmd.format(run_path=run_tmp_path, out_path=out_path,
project=title, calibration=title,
- author=author, version=version)
+ author=author, version=version, report_to=report_to)
joblist = []
if concurrency.get("parameter", None) is None:
diff --git a/xfel_calibrate/notebooks.py b/xfel_calibrate/notebooks.py
index 1b2d7ae1d784782f28b2e835dafec39fcebff63f..09f6e6f76a94dcbadee4fcd9c8ba0f8bba772527 100644
--- a/xfel_calibrate/notebooks.py
+++ b/xfel_calibrate/notebooks.py
@@ -96,7 +96,7 @@ notebooks = {
"notebook": "notebooks/Tutorial/calversion.ipynb",
"concurrency": {"parameter": "random_seed",
"default concurrency": None,
- "cluster cores": 32},
+ "cluster cores": 4},
},
},
}