From 92aeee31d6adca0f1b44655cc3224289778bae49 Mon Sep 17 00:00:00 2001
From: ahmedk <karim.ahmed@xfel.eu>
Date: Tue, 21 Mar 2023 10:01:32 +0100
Subject: [PATCH] remove conf file
---
docs/source/conf.py | 609 --------------------------------------------
1 file changed, 609 deletions(-)
delete mode 100644 docs/source/conf.py
diff --git a/docs/source/conf.py b/docs/source/conf.py
deleted file mode 100644
index e48276188..000000000
--- a/docs/source/conf.py
+++ /dev/null
@@ -1,609 +0,0 @@
-#!/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:`âŒ`"]
-
- if num_skip > 0:
- rst[-1] += ":header-skipped:`âš `"
- 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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