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Commit aa52736a authored by Mikhail Karnevskiy's avatar Mikhail Karnevskiy
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Merge branch 'feat/manual_titlepage' into 'master' 

Add title page. Modify conf.py.

See merge request detectors/pycalibration!68
parents eeb57d91 da728d61
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1 merge request!68Add title page. Modify conf.py.
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cal_tools/cal_tools/conf_latex.patch deleted 100644 → 0
+ 0
− 10
View file @ eeb57d91
--- 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
cal_tools/cal_tools/conf_latex.py deleted 100644 → 0
+ 0
− 347
View file @ eeb57d91
#!/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}
cal_tools/cal_tools/conf_orig.py deleted 100644 → 0
+ 0
− 346
View file @ eeb57d91
#!/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}
cal_tools/cal_tools/tools.py
+ 128
− 90
View file @ aa52736a
import argparse
from collections import OrderedDict from collections import OrderedDict
import copy from glob import glob
import glob from importlib.machinery import SourceFileLoader
from jinja2 import Template from os import chdir, listdir, makedirs, path, remove, stat
import os from os.path import isdir, isfile, splitext
from os.path import isfile, isdir, splitext
from queue import Queue from queue import Queue
import re from shutil import copy, copytree, move, rmtree
import shutil from subprocess import CalledProcessError, check_call, check_output
from subprocess import Popen, PIPE, check_output, check_call from textwrap import dedent
import textwrap
from time import sleep from time import sleep
import time
from uuid import uuid4 from jinja2 import Template
import tabulate
from xfel_calibrate import settings
def atoi(text): def atoi(text):
''' """
Convert string to integer is possible Convert string to integer is possible
:param text: string to be converted :param text: string to be converted
:return: integer value or input string :return: integer value or input string
''' """
return int(text) if text.isdigit() else text return int(text) if text.isdigit() else text
def natural_keys(text): def natural_keys(text):
''' """
Decompose string to list of integers and sub-strings Decompose string to list of integers and sub-strings
''' """
return [ atoi(c) for c in re.split(r'(\d+)', text) ] return [atoi(c) for c in re.split(r'(\d+)', text)]
def combine_report(run_path, calibration): def combine_report(run_path, calibration):
sphinx_path = "{}/sphinx_rep".format(os.path.abspath(run_path)) sphinx_path = "{}/sphinx_rep".format(path.abspath(run_path))
os.makedirs(sphinx_path) makedirs(sphinx_path)
direntries = os.listdir(run_path) direntries = listdir(run_path)
direntries.sort(key=natural_keys) direntries.sort(key=natural_keys)
for entry in direntries: for entry in direntries:
...@@ -72,7 +72,7 @@ def combine_report(run_path, calibration): ...@@ -72,7 +72,7 @@ def combine_report(run_path, calibration):
gfile.write("\n\n") gfile.write("\n\n")
if isdir("{}/{}".format(run_path, entry)): if isdir("{}/{}".format(run_path, entry)):
shutil.copytree("{}/{}".format(run_path, entry), "{}/{}".format(sphinx_path, entry)) copytree("{}/{}".format(run_path, entry), "{}/{}".format(sphinx_path, entry))
return sphinx_path return sphinx_path
...@@ -91,20 +91,20 @@ def prepare_plots(run_path, threshold=1000000): ...@@ -91,20 +91,20 @@ def prepare_plots(run_path, threshold=1000000):
:param threshold: Max svg file size (in bytes) to be converted to pdf :param threshold: Max svg file size (in bytes) to be converted to pdf
""" """
print('Convert svg to pdf and png') print('Convert svg to pdf and png')
run_path = os.path.abspath(run_path) run_path = path.abspath(run_path)
rst_files = glob.glob('{}/*rst'.format(run_path)) rst_files = glob('{}/*rst'.format(run_path))
for rst_file in rst_files: for rst_file in rst_files:
rst_file_name = os.path.basename(rst_file) rst_file_name = path.basename(rst_file)
rst_file_name = os.path.splitext(rst_file_name)[0] rst_file_name = path.splitext(rst_file_name)[0]
svg_files = glob.glob( svg_files = glob(
'{}/{}_files/*svg'.format(run_path, rst_file_name)) '{}/{}_files/*svg'.format(run_path, rst_file_name))
for f_path in svg_files: for f_path in svg_files:
f_name = os.path.basename(f_path) f_name = path.basename(f_path)
f_name = os.path.splitext(f_name)[0] f_name = path.splitext(f_name)[0]
if (os.stat(f_path)).st_size < threshold: if (stat(f_path)).st_size < threshold:
check_call(["svg2pdf", "{}".format(f_path)], shell=False) check_call(["svg2pdf", "{}".format(f_path)], shell=False)
new_ext = 'pdf' new_ext = 'pdf'
else: else:
...@@ -127,7 +127,7 @@ def make_timing_summary(run_path, joblist): ...@@ -127,7 +127,7 @@ def make_timing_summary(run_path, joblist):
:param joblist: List of slurm jobs :param joblist: List of slurm jobs
""" """
print('Prepare timing summary') print('Prepare timing summary')
run_path = os.path.abspath(run_path) run_path = path.abspath(run_path)
pars_vals = [] pars_vals = []
pars = 'JobID,Elapsed,Suspended' pars = 'JobID,Elapsed,Suspended'
pars_name = pars.split(',') pars_name = pars.split(',')
...@@ -136,10 +136,10 @@ def make_timing_summary(run_path, joblist): ...@@ -136,10 +136,10 @@ def make_timing_summary(run_path, joblist):
out = check_output(['sacct', '-j', job, out = check_output(['sacct', '-j', job,
'--format={}'.format(pars)], '--format={}'.format(pars)],
shell=False) shell=False)
l = str(out).split('\\n') lines = str(out).split('\\n')
# loop over output lines, skip first two lines with header. # loop over output lines, skip first two lines with header.
for line in l[2:]: for line in lines[2:]:
s = line.split() s = line.split()
if len(s) == len(pars_name): if len(s) == len(pars_name):
pars_vals.append(s) pars_vals.append(s)
...@@ -154,65 +154,87 @@ def make_timing_summary(run_path, joblist): ...@@ -154,65 +154,87 @@ def make_timing_summary(run_path, joblist):
{{ line }} {{ line }}
{%- endfor %} {%- endfor %}
''') ''')
import tabulate
with open("{}/timing_summary.rst".format(run_path), "w+") as gfile: with open("{}/timing_summary.rst".format(run_path), "w+") as gfile:
table = tabulate.tabulate(pars_vals, tablefmt='latex', table = tabulate.tabulate(pars_vals, tablefmt='latex',
headers=pars_name) headers=pars_name)
gfile.write(textwrap.dedent(tmpl.render(table=table.split('\n')))) gfile.write(dedent(tmpl.render(table=table.split('\n'))))
def make_report(run_path, tmp_path, out_path, project, author, version, report_to): def make_report(run_path, tmp_path, out_path, project, author, version,
run_path = os.path.abspath(run_path) report_to):
report_path, report_name = os.path.split(report_to) """
Create calibration report (pdf file)
Automatically generated report document results, produced by
jupyter-notebooks.
:param run_path: Path to sphinx run directory
:param tmp_path: Run path of the slurm job
:param out_path: Output directory for report.
Overwritten if path to report is given in `report_to`
:param project: Project title
:param author: Author of the notebook
:param version: Version of the notebook
:param report_to: Name or path of the report file
"""
run_path = path.abspath(run_path)
report_path, report_name = path.split(report_to)
if report_path != '': if report_path != '':
out_path = report_path out_path = report_path
try: try:
import subprocess check_call(["sphinx-quickstart",
subprocess.check_call(["sphinx-quickstart", "--quiet",
"--quiet", "--project='{}'".format(project),
"--project='{}'".format(project), "--author='{}'".format(author),
"--author='{}'".format(author), "-v", str(version),
"-v", str(version), "--suffix=.rst",
"--suffix=.rst", "--master=index",
"--master=index", "--ext-intersphinx",
"--ext-intersphinx", "--ext-mathjax",
"--ext-mathjax", "--makefile",
"--makefile", "--no-batchfile", run_path])
"--no-batchfile", run_path])
# now conf.py exists in temp folder, so add latex options to remove empty pages except CalledProcessError:
patch_path = "{}".format(os.path.abspath(os.path.dirname(__file__))) raise Exception("Failed to run sphinx-quickbuild. Is sphinx installed?"
patch_file = ("{}/conf_latex.patch".format(patch_path)) "Generated simple index.rst instead")
try:
subprocess.check_call(["patch",
"{}/sphinx_rep/conf.py".format(tmp_path),
patch_file])
except:
print("Patching latex conf failed")
try: # quickbuild went well we need to edit the index.rst and conf.py files
module_path = "{}".format(path.abspath(path.dirname(__file__)))
subprocess.check_call(["sed", conf = SourceFileLoader("conf",
"-i", "{}/conf.py".format(run_path)).load_module()
"-e", l_var = [v for v in dir(conf) if not v.startswith('__')]
"s/{}.tex/{}.tex/g".format(project.replace(" ", ""), report_name),
"{}/sphinx_rep/conf.py".format(tmp_path)], shell=False)
except:
print("SEDing tex failed")
except subprocess.CalledProcessError: with open("{}/conf.py.tmp".format(run_path), "w") as mf:
raise Exception("Failed to run sphinx-quickbuild. Is sphinx installed?" latex_elements = {'extraclassoptions': ',openany, oneside',
"Generated simple index.rst instead") 'maketitle': r'\input{titlepage.tex.txt}'}
mf.write("latex_elements = {}\n".format(latex_elements))
mf.write("latex_logo = '{}/{}'\n".format(module_path,
settings.logo_path))
mf.write("latex_additional_files = ['titlepage.tex.txt']\n")
# quickbuild went well we need to edit the index file for var in l_var:
from shutil import move if var in ['latex_elements', 'latex_logo',
'latex_additional_files']:
direntries = os.listdir(run_path) continue
tmpl = '{} = {}\n'
v = getattr(conf, var, None)
if isinstance(v, str):
tmpl = '{} = "{}"\n'
mf.write(tmpl.format(var, v))
remove("{}/conf.py".format(run_path))
move("{}/conf.py.tmp".format(run_path), "{}/conf.py".format(run_path))
direntries = listdir(run_path)
files_to_handle = [] files_to_handle = []
for entry in direntries: for entry in direntries:
if isfile("{}/{}".format(run_path, entry)): if isfile("{}/{}".format(run_path, entry)):
name, ext = splitext("{}".format(entry)) name, ext = splitext("{}".format(entry))
if ext == ".rst" and "index" not in name: if ext == ".rst" and "index" not in name:
files_to_handle.append(name.strip()) files_to_handle.append(name.strip())
...@@ -228,29 +250,44 @@ def make_report(run_path, tmp_path, out_path, project, author, version, report_t ...@@ -228,29 +250,44 @@ def make_report(run_path, tmp_path, out_path, project, author, version, report_t
''') ''')
with open("{}/index.rst".format(run_path), "w+") as mf: with open("{}/index.rst".format(run_path), "w+") as mf:
mf.write(textwrap.dedent(index_tmp.render(keys=files_to_handle))) mf.write(dedent(index_tmp.render(keys=files_to_handle)))
# finally call the make scripts # finally call the make scripts
os.chdir(run_path) chdir(run_path)
try: try:
import subprocess check_call(["make", "latexpdf"])
subprocess.check_call(["make", "latexpdf"])
except subprocess.CalledProcessError: except CalledProcessError:
print("Failed to make pdf documentation") print("Failed to make pdf documentation")
print("Temp files will not be deleted and "+ print("Temp files will not be deleted and " +
"can be inspected at: {}".format(run_path)) "can be inspected at: {}".format(run_path))
return return
print("Moving report to final location: {}".format(out_path)) print("Moving report to final location: {}".format(out_path))
for f in glob.glob(r'{}/_build/latex/*.pdf'.format(run_path)): for f in glob(r'{}/_build/latex/*.pdf'.format(run_path)):
print(f) copy(f, out_path)
shutil.copy(f, out_path)
print("Removing temporary files at: {}".format(tmp_path)) print("Removing temporary files at: {}".format(tmp_path))
shutil.rmtree(tmp_path) rmtree(tmp_path)
def make_titlepage(sphinx_path, project, data_path):
"""
Create title page for report using template
:param sphinx_path: path to sphinx run directory
:param project: title of the project
:param data_path: path to input data sample used for notebook
"""
module_path = "{}".format(path.abspath(path.dirname(__file__)))
with open('{}/titlepage.tmpl'.format(module_path)) as file_:
title_tmp = Template(file_.read())
with open("{}/titlepage.tex.txt".format(sphinx_path), "w+") as mf:
mf.write(dedent(title_tmp.render(project=project,
data_path=data_path)))
def finalize(joblist, finaljob, run_path, out_path, project, calibration, def finalize(joblist, finaljob, run_path, out_path, project, calibration,
author, version, report_to): author, version, report_to, data_path='Unknown'):
print("Waiting on jobs to finish: {}".format(joblist)) print("Waiting on jobs to finish: {}".format(joblist))
while True: while True:
...@@ -267,6 +304,7 @@ def finalize(joblist, finaljob, run_path, out_path, project, calibration, ...@@ -267,6 +304,7 @@ def finalize(joblist, finaljob, run_path, out_path, project, calibration,
prepare_plots(run_path) prepare_plots(run_path)
make_timing_summary(run_path, joblist+[str(finaljob)]) make_timing_summary(run_path, joblist+[str(finaljob)])
sphinx_path = combine_report(run_path, calibration) sphinx_path = combine_report(run_path, calibration)
make_titlepage(sphinx_path, project, data_path)
make_report(sphinx_path, run_path, out_path, project, author, version, make_report(sphinx_path, run_path, out_path, project, author, version,
report_to) report_to)
...@@ -317,7 +355,7 @@ def map_modules_from_files(filelist, file_inset, quadrants, modules_per_quad): ...@@ -317,7 +355,7 @@ def map_modules_from_files(filelist, file_inset, quadrants, modules_per_quad):
if file_infix in file: if file_infix in file:
module_files[name].put(file) module_files[name].put(file)
total_sequences += 1 total_sequences += 1
total_file_size += os.path.getsize(file) total_file_size += path.getsize(file)
return module_files, mod_ids, total_sequences, total_file_size return module_files, mod_ids, total_sequences, total_file_size
...@@ -328,19 +366,19 @@ def gain_map_files(in_folder, runs, sequences, file_inset, quadrants, modules_pe ...@@ -328,19 +366,19 @@ def gain_map_files(in_folder, runs, sequences, file_inset, quadrants, modules_pe
gain_mapped_files = OrderedDict() gain_mapped_files = OrderedDict()
for gain, run in runs.items(): for gain, run in runs.items():
ginfolder = "{}/{}".format(in_folder, run) ginfolder = "{}/{}".format(in_folder, run)
dirlist = os.listdir(ginfolder) dirlist = listdir(ginfolder)
file_list = [] file_list = []
for entry in dirlist: for entry in dirlist:
#only h5 file #only h5 file
abs_entry = "{}/{}".format(ginfolder, entry) abs_entry = "{}/{}".format(ginfolder, entry)
if os.path.isfile(abs_entry) and os.path.splitext(abs_entry)[1] == ".h5": if path.isfile(abs_entry) and path.splitext(abs_entry)[1] == ".h5":
if sequences is None: if sequences is None:
file_list.append(abs_entry) file_list.append(abs_entry)
else: else:
for seq in sequences: for seq in sequences:
if "{:05d}.h5".format(seq) in abs_entry: if "{:05d}.h5".format(seq) in abs_entry:
file_list.append(os.path.abspath(abs_entry)) file_list.append(path.abspath(abs_entry))
mapped_files, mod_ids, seq, fs = map_modules_from_files(file_list, file_inset, mapped_files, mod_ids, seq, fs = map_modules_from_files(file_list, file_inset,
quadrants, modules_per_quad) quadrants, modules_per_quad)
......
cal_tools/cal_tools/xfel.pdf 0 → 100644
+ 0
− 0
View file @ aa52736a
File added
cal_tools/setup.py
+ 0
− 1
View file @ aa52736a
...@@ -4,7 +4,6 @@ setup( ...@@ -4,7 +4,6 @@ setup(
name='calTools', name='calTools',
version='0.1', version='0.1',
packages=['cal_tools',], packages=['cal_tools',],
package_data={'': ['conf_latex.patch']},
url='', url='',
license='(c) European XFEL GmbH', license='(c) European XFEL GmbH',
author='Steffen Hauf', author='Steffen Hauf',
......
xfel_calibrate/settings.py
+ 3
− 0
View file @ aa52736a
...@@ -24,6 +24,9 @@ report_path = "{}/calibration_reports/".format(os.getcwd()) ...@@ -24,6 +24,9 @@ report_path = "{}/calibration_reports/".format(os.getcwd())
# Also try to output the report to an out_folder defined by the notebook # Also try to output the report to an out_folder defined by the notebook
try_report_to_output = True try_report_to_output = True
# logo file for calibration report (located in cal_tools/cal_tools)
logo_path = "xfel.pdf"
# the command to run this concurrently. It is prepended to the actual call # the command to run this concurrently. It is prepended to the actual call
sprof = os.environ.get("XFELCALSLURM", "exfel") sprof = os.environ.get("XFELCALSLURM", "exfel")
launcher_command = "sbatch -t 24:00:00 --mem 500G --requeue --output {temp_path}/slurm-%j.out" launcher_command = "sbatch -t 24:00:00 --mem 500G --requeue --output {temp_path}/slurm-%j.out"
......
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