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Commit 886fe413 authored by Karim Ahmed's avatar Karim Ahmed
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remove conf file

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#!/usr/bin/env python3
# -*- coding: utf-8 -*-
#
# European XFEL Offline Calibration documentation build configuration file, created by
# sphinx-quickstart on Sun Jun 10 17:32:30 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.
import glob
# 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('.'))
import os
import shutil
import sys
import textwrap
from datetime import datetime
from subprocess import Popen, check_output
from textwrap import dedent, indent
from uuid import uuid4
import nbformat
import tabulate
from dateutil.parser import parse
from lxml import etree
from nbconvert import RSTExporter
# generate the list of available notebooks
from xfel_calibrate import notebooks
# -- 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.todo',
'sphinx.ext.mathjax',
'sphinx.ext.ifconfig',
'sphinx.ext.viewcode',
]
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']
# 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 = 'European XFEL Offline Calibration'
copyright = '2018, The European XFEL Detector Group'
author = 'The European XFEL Detector Group'
# 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 = '1.0'
# The full version, including alpha/beta/rc tags.
release = '1.0'
# 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 = []
# 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 = True
# -- 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'
# 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 = 'European XFEL Offline Calibration v1.0'
# 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 = 'EuropeanXFELOfflineCalibrationdoc'
# -- 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, 'EuropeanXFELOfflineCalibration.tex', 'European XFEL Offline Calibration Documentation',
'The European XFEL Detector Group', 'manual', True),
]
# 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, 'europeanxfelofflinecalibration', 'European XFEL Offline Calibration 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, 'EuropeanXFELOfflineCalibration', 'European XFEL Offline Calibration Documentation',
author, 'EuropeanXFELOfflineCalibration', '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}
# first install pandoc if necessary, this is mainly meant for the RTD builds
try:
from nbconvert.utils.pandoc import check_pandoc_version
check_pandoc_version()
print("Pandoc was found!")
except:
print("Installing Pandoc!")
from subprocess import check_call
pandoc_url = "https://github.com/jgm/pandoc/releases/download/2.2.1/pandoc-2.2.1-1-amd64.deb"
pandoc_pack = "pandoc-2.2.1-1-amd64.deb"
check_call(["wget", pandoc_url])
check_call(["dpkg", "-i", pandoc_pack])
rst_exporter = RSTExporter()
with open("available_notebooks.rst", "w") as f:
f.write(dedent("""
.. _available_notebooks:
Available Notebooks
===================
The following notebooks are currently integrated into the European XFEL
Offline Calibration tool chain.
"""))
for detector in sorted(notebooks.notebooks.keys()):
# Avoid having test notebooks in detector notebooks documentations.
if "TEST" in detector.upper():
continue
values = notebooks.notebooks[detector]
f.write("{}\n".format(detector))
f.write("{}\n".format("-"*len(detector)))
f.write("\n")
for caltype in sorted(values.keys()):
data = values[caltype]
nbpath = os.path.abspath("{}/../../../{}".format(__file__, data["notebook"]))
with open(nbpath, "r") as nf:
nb = nbformat.read(nf, as_version=4)
def first_markdown_cell(nb):
for cell in nb.cells:
if cell.cell_type == 'markdown':
return cell
mdcell = first_markdown_cell(nb)
nb.cells = [mdcell] # we only want this single cell
body, _ = rst_exporter.from_notebook_node(nb)
adjusted = []
# adjust titles
for line in body.split("\n"):
if line.startswith("=="):
line = line.replace("=", "+")
if line.startswith("--"):
line = line.replace("-", "~")
adjusted.append(line)
f.write("\n".join(adjusted))
f.write("\n")
f.write("To invoke this notebook and display help use:\n\n")
f.write(".. code-block:: bash\n\n")
f.write(" xfel-calibrate {} {} --help\n\n".format(detector, caltype))
f.write("The full parameter list of this notebook (with defaults is): \n\n")
f.write(".. code-block:: bash\n\n")
nb_help = ["xfel-calibrate", detector, caltype, "--help"]
output = check_output(nb_help).decode('utf8')
f.write(indent(output.replace("DETECTOR", detector).replace("TYPE", caltype), " "*4))
f.write("\n\n")
# add test results
test_artefact_dir = os.path.realpath("../../tests/legacy/artefacts")
def xml_to_rst_report(xml, git_tag, reports=[]):
e = etree.fromstring(xml.encode())
rst = [""]
rst += ["Test execution for {test_name} on {ex_date}"]
test_name, ex_date = e.get("name").split("-")
ex_date = parse(ex_date)
rst[-1] = rst[-1].format(test_name=test_name, ex_date=ex_date)
rst += ["="*len(rst[-1])]
rst += [""]
num_tests = e.get("tests")
num_err = int(e.get("errors"))
num_fail = int(e.get("failures"))
num_skip = int(e.get("skipped"))
# create a summary header
if num_err + num_fail == 0:
rst += [":header-passed:`✓`"]
else:
rst += [":header-failed:`❌`"]
if num_skip > 0:
rst[-1] += ":header-skipped:`⚠`"
rst += [""]
# give a summary
rst += [":Git tag: {git_tag}".format(git_tag=git_tag)]
rst += [":Tests: {num_tests}".format(num_tests=num_tests)]
rst += [":Errors: {num_err}".format(num_err=num_err)]
rst += [":Failures: {num_fail}".format(num_fail=num_fail)]
rst += [":Skipped: {num_skip}".format(num_skip=num_skip)]
rst += [":Duration: {duration}s".format(duration=e.get("time"))]
for rname, rpath in reports:
rst += [":Report: `{} <{}>`_".format(rname, rpath)]
rst += [""]
# now the details
rst += ["Detailed Results"]
rst += ["-"*len(rst[-1])]
rst += [""]
detailed_failures = []
rows = []
for child in e:
if child.tag != "testcase":
continue
name = child.get("name")
extime = child.get("time")
status = ":passed:`passed`"
msg = ""
etype = ""
if len(child): # children are pressent so test failed or skipped
detail = child[0]
etype = detail.get("type")
msg = detail.get("message")
if etype == "skip":
status = ":skipped:`skipped`"
else:
status= ":failed:`failed`"
detailed_failures.append((name, detail.text))
msg = "\n".join(textwrap.wrap(msg, 20))
row = [status, name, etype, msg, extime ]
rows.append(row)
header = ["Result", "Test", "Error", "Message", "Duration (s)"]
tblrst = tabulate.tabulate(rows, headers=header, tablefmt="rst")
rst += tblrst.split("\n")
rst += [""]
for test, report in detailed_failures:
rst += ["Failure report for: {}".format(test)]
rst += ["~"*len(rst[-1])]
rst += [""]
rst += [".. code-block:: python"]
rst += textwrap.indent(report, " "*4).split("\n")
rst += [""]
do_console = False
for child in e:
if child.tag == "system-out" and len(child.text.strip()):
do_console = True
break
if do_console:
# console output
rst += ["Console Output"]
rst += ["-"*len(rst[-1])]
rst += [""]
for child in e:
if child.tag != "system-out":
continue
rst += [".. code-block:: console"]
rst += textwrap.indent(child.text, " "*4).split("\n")
return "\n".join(rst)
def sorted_dir(folder):
def getmtime(name):
path = os.path.join(folder, name)
return os.path.getmtime(path)
sort = sorted(os.listdir(folder), key=getmtime, reverse=True)
return [(s, datetime.fromtimestamp(getmtime(s))) for s in sort]
header = """
Test Results
++++++++++++
Results are organized by git commit, and sorted descending by date.
Contents:
.. toctree::
:maxdepth: 2
"""
if not os.path.exists("./test_rsts"):
os.makedirs("./test_rsts")
with open("test_results.rst", "w") as f:
f.write(header)
for commit, modtime in sorted_dir(test_artefact_dir):
with open("./test_rsts/{}.rst".format(commit), "w") as fr:
rst = [".. include:: roles.rst"]
rst += [""]
rst += ["{} - {}".format(commit[:8], modtime)]
rst += ["+"*len(rst[-1])]
rst += [""]
fr.write("\n".join(rst))
# copy reports
pdfs = glob.glob("{}/{}/*/*.pdf".format(test_artefact_dir, commit))
if not os.path.exists("./_static/reports/{}".format(commit)):
os.makedirs("./_static/reports/{}".format(commit))
reports = {}
for pdf in pdfs:
ppath = "{}/{}.pdf".format(commit, uuid4())
shutil.copyfile(pdf, "./_static/reports/{}".format(ppath))
rloc = pdf.split("/")[-2]
rlist = reports.get(rloc, [])
rname = os.path.basename(pdf).split(".")[0]
rlist.append((rname, "../_static/reports/{}".format(ppath)))
reports[rloc] = rlist
xmls = glob.glob("{}/{}/*/TEST*.xml".format(test_artefact_dir, commit))
for xml in xmls:
rloc = xml.split("/")[-2]
with open(xml, "r") as xf:
xs = xf.read()
rst = xml_to_rst_report(xs, commit, reports=reports.get(rloc, []))
fr.write(rst)
f.write(" test_rsts/{}\n".format(commit))
def setup(app):
app.add_stylesheet('css/test_decorators.css')
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