Commit 3696334e authored by Fabrice Allain's avatar Fabrice Allain
Browse files

Added sphinx documentation files generated with sphinx-apidoc

parent 994315ae
......@@ -123,6 +123,8 @@ def format_str(string):
return int(string)
elif re.search(r"^[\s\d-]+\.\d+\s*$", string):
return float(string)
elif re.search(r'^".+"$', string):
return string[1:-1]
elif "," in string:
return string.split(',')
elif "+" in string:
......
No preview for this file type
No preview for this file type
......@@ -89,7 +89,7 @@ nd_alpha: 1.0
; --------------------------- ARIA XML parameters ---------------------------- #
runid: 1
cpus: 100
host_command: sbatch --cores-per-socket=10 -o /baycells/home/fallain/slurm.errors
host_command: "srun --begin=now+2hour -Q touch done & sbatch --cores-per-socket=10 -o /baycells/home/fallain/slurm.errors"
host_executable: /baycells/home/bardiaux/bin/cns1.21_aria_logn_linux_x86_64_intel.exe
temp_root: data/examples/out/setup/tmp
parameter_definition: automatic
......@@ -185,7 +185,7 @@ diversityvalue:
L:
[pdbqual]
trash_directory:
trash_directory: /tmp
prosa: False
skip_prefix: fitted
csh_executable: csh
\ No newline at end of file
csh_executable: csh
......@@ -31,7 +31,9 @@ class AriaEcPdbqual(CommandProtocol):
"""
LOG.info("Starting quality runs with %s file(s)", self.settings.pdbqual["infiles"])
LOG.info("Copying file(s) to output directory")
[shutil.copy(infile, self.settings.pdbqual["output_directory"]) for infile in self.settings.pdbqual["infiles"]]
for infile in self.settings.pdbqual["infiles"]:
if os.path.abspath(infile) != os.path.abspath(self.settings.pdbqual["output_directory"]):
shutil.copy(infile, self.settings.pdbqual["output_directory"])
QualityChecks.runChecks(
workingDirectory=os.path.abspath(
self.settings.pdbqual["output_directory"]),
......@@ -50,3 +52,8 @@ class AriaEcPdbqual(CommandProtocol):
LOG.info("%s generated",
os.path.join(self.settings.pdbqual["output_directory"],
QualityChecks.FILENAME_REPORT))
LOG.info("Removing infile(s) in output directory")
[os.remove(
os.path.join(os.path.abspath(self.settings.pdbqual["output_directory"]),
os.path.basename(infile)))
for infile in self.settings.pdbqual["infiles"]]
No preview for this file type
# Makefile for Sphinx documentation
#
# You can set these variables from the command line.
SPHINXOPTS =
SPHINXBUILD = sphinx-build
PAPER =
BUILDDIR = _build
# Internal variables.
PAPEROPT_a4 = -D latex_paper_size=a4
PAPEROPT_letter = -D latex_paper_size=letter
ALLSPHINXOPTS = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
# the i18n builder cannot share the environment and doctrees with the others
I18NSPHINXOPTS = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
.PHONY: help
help:
@echo "Please use \`make <target>' where <target> is one of"
@echo " html to make standalone HTML files"
@echo " dirhtml to make HTML files named index.html in directories"
@echo " singlehtml to make a single large HTML file"
@echo " pickle to make pickle files"
@echo " json to make JSON files"
@echo " htmlhelp to make HTML files and a HTML help project"
@echo " qthelp to make HTML files and a qthelp project"
@echo " applehelp to make an Apple Help Book"
@echo " devhelp to make HTML files and a Devhelp project"
@echo " epub to make an epub"
@echo " epub3 to make an epub3"
@echo " latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
@echo " latexpdf to make LaTeX files and run them through pdflatex"
@echo " latexpdfja to make LaTeX files and run them through platex/dvipdfmx"
@echo " text to make text files"
@echo " man to make manual pages"
@echo " texinfo to make Texinfo files"
@echo " info to make Texinfo files and run them through makeinfo"
@echo " gettext to make PO message catalogs"
@echo " changes to make an overview of all changed/added/deprecated items"
@echo " xml to make Docutils-native XML files"
@echo " pseudoxml to make pseudoxml-XML files for display purposes"
@echo " linkcheck to check all external links for integrity"
@echo " doctest to run all doctests embedded in the documentation (if enabled)"
@echo " coverage to run coverage check of the documentation (if enabled)"
@echo " dummy to check syntax errors of document sources"
.PHONY: clean
clean:
rm -rf $(BUILDDIR)/*
.PHONY: html
html:
$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
@echo
@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
.PHONY: dirhtml
dirhtml:
$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
@echo
@echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
.PHONY: singlehtml
singlehtml:
$(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
@echo
@echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
.PHONY: pickle
pickle:
$(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
@echo
@echo "Build finished; now you can process the pickle files."
.PHONY: json
json:
$(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
@echo
@echo "Build finished; now you can process the JSON files."
.PHONY: htmlhelp
htmlhelp:
$(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp
@echo
@echo "Build finished; now you can run HTML Help Workshop with the" \
".hhp project file in $(BUILDDIR)/htmlhelp."
.PHONY: qthelp
qthelp:
$(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp
@echo
@echo "Build finished; now you can run "qcollectiongenerator" with the" \
".qhcp project file in $(BUILDDIR)/qthelp, like this:"
@echo "# qcollectiongenerator $(BUILDDIR)/qthelp/ariaec.qhcp"
@echo "To view the help file:"
@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/ariaec.qhc"
.PHONY: applehelp
applehelp:
$(SPHINXBUILD) -b applehelp $(ALLSPHINXOPTS) $(BUILDDIR)/applehelp
@echo
@echo "Build finished. The help book is in $(BUILDDIR)/applehelp."
@echo "N.B. You won't be able to view it unless you put it in" \
"~/Library/Documentation/Help or install it in your application" \
"bundle."
.PHONY: devhelp
devhelp:
$(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
@echo
@echo "Build finished."
@echo "To view the help file:"
@echo "# mkdir -p $$HOME/.local/share/devhelp/ariaec"
@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/ariaec"
@echo "# devhelp"
.PHONY: epub
epub:
$(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
@echo
@echo "Build finished. The epub file is in $(BUILDDIR)/epub."
.PHONY: epub3
epub3:
$(SPHINXBUILD) -b epub3 $(ALLSPHINXOPTS) $(BUILDDIR)/epub3
@echo
@echo "Build finished. The epub3 file is in $(BUILDDIR)/epub3."
.PHONY: latex
latex:
$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
@echo
@echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
@echo "Run \`make' in that directory to run these through (pdf)latex" \
"(use \`make latexpdf' here to do that automatically)."
.PHONY: latexpdf
latexpdf:
$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
@echo "Running LaTeX files through pdflatex..."
$(MAKE) -C $(BUILDDIR)/latex all-pdf
@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
.PHONY: latexpdfja
latexpdfja:
$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
@echo "Running LaTeX files through platex and dvipdfmx..."
$(MAKE) -C $(BUILDDIR)/latex all-pdf-ja
@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
.PHONY: text
text:
$(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text
@echo
@echo "Build finished. The text files are in $(BUILDDIR)/text."
.PHONY: man
man:
$(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man
@echo
@echo "Build finished. The manual pages are in $(BUILDDIR)/man."
.PHONY: texinfo
texinfo:
$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
@echo
@echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo."
@echo "Run \`make' in that directory to run these through makeinfo" \
"(use \`make info' here to do that automatically)."
.PHONY: info
info:
$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
@echo "Running Texinfo files through makeinfo..."
make -C $(BUILDDIR)/texinfo info
@echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo."
.PHONY: gettext
gettext:
$(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale
@echo
@echo "Build finished. The message catalogs are in $(BUILDDIR)/locale."
.PHONY: changes
changes:
$(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
@echo
@echo "The overview file is in $(BUILDDIR)/changes."
.PHONY: linkcheck
linkcheck:
$(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck
@echo
@echo "Link check complete; look for any errors in the above output " \
"or in $(BUILDDIR)/linkcheck/output.txt."
.PHONY: doctest
doctest:
$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
@echo "Testing of doctests in the sources finished, look at the " \
"results in $(BUILDDIR)/doctest/output.txt."
.PHONY: coverage
coverage:
$(SPHINXBUILD) -b coverage $(ALLSPHINXOPTS) $(BUILDDIR)/coverage
@echo "Testing of coverage in the sources finished, look at the " \
"results in $(BUILDDIR)/coverage/python.txt."
.PHONY: xml
xml:
$(SPHINXBUILD) -b xml $(ALLSPHINXOPTS) $(BUILDDIR)/xml
@echo
@echo "Build finished. The XML files are in $(BUILDDIR)/xml."
.PHONY: pseudoxml
pseudoxml:
$(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml
@echo
@echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml."
.PHONY: dummy
dummy:
$(SPHINXBUILD) -b dummy $(ALLSPHINXOPTS) $(BUILDDIR)/dummy
@echo
@echo "Build finished. Dummy builder generates no files."
# Sphinx build info version 1
# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
config: 6a7fc801f3b652c72ff1539653a227f7
tags: 645f666f9bcd5a90fca523b33c5a78b7
ariaec.test package
===================
Module contents
---------------
.. automodule:: ariaec.test
:members:
:undoc-members:
:show-inheritance:
ariaec package
==============
Subpackages
-----------
.. toctree::
ariaec.test
Submodules
----------
ariaec.base module
------------------
.. automodule:: ariaec.base
:members:
:undoc-members:
:show-inheritance:
ariaec.commands module
----------------------
.. automodule:: ariaec.commands
:members:
:undoc-members:
:show-inheritance:
ariaec.econverter module
------------------------
.. automodule:: ariaec.econverter
:members:
:undoc-members:
:show-inheritance:
ariaec.ecsettings module
------------------------
.. automodule:: ariaec.ecsettings
:members:
:undoc-members:
:show-inheritance:
ariaec.maplot module
--------------------
.. automodule:: ariaec.maplot
:members:
:undoc-members:
:show-inheritance:
ariaec.ndconv module
--------------------
.. automodule:: ariaec.ndconv
:members:
:undoc-members:
:show-inheritance:
ariaec.pdbqual module
---------------------
.. automodule:: ariaec.pdbqual
:members:
:undoc-members:
:show-inheritance:
ariaec.protein module
---------------------
.. automodule:: ariaec.protein
:members:
:undoc-members:
:show-inheritance:
ariaec.protmap module
---------------------
.. automodule:: ariaec.protmap
:members:
:undoc-members:
:show-inheritance:
ariaec.reader module
--------------------
.. automodule:: ariaec.reader
:members:
:undoc-members:
:show-inheritance:
ariaec.setup module
-------------------
.. automodule:: ariaec.setup
:members:
:undoc-members:
:show-inheritance:
Module contents
---------------
.. automodule:: ariaec
:members:
:undoc-members:
:show-inheritance:
.. ariaec documentation master file, created by
sphinx-quickstart on Wed Sep 21 10:51:54 2016.
You can adapt this file completely to your liking, but it should at least
contain the root `toctree` directive.
Welcome to ariaec's documentation!
==================================
Contents:
.. toctree::
:maxdepth: 2
ariaec
Indices and tables
==================
* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`
ariaec
======
.. toctree::
:maxdepth: 4
ariaec
@import url("basic.css");
/* -- page layout ----------------------------------------------------------- */
body {
font-family: 'goudy old style', 'minion pro', 'bell mt', Georgia, 'Hiragino Mincho Pro', serif;
font-size: 17px;
background-color: #fff;
color: #000;
margin: 0;
padding: 0;
}
div.document {
width: 940px;
margin: 30px auto 0 auto;
}
div.documentwrapper {
float: left;
width: 100%;
}
div.bodywrapper {
margin: 0 0 0 220px;
}
div.sphinxsidebar {
width: 220px;
font-size: 14px;
line-height: 1.5;
}
hr {
border: 1px solid #B1B4B6;
}
div.body {
background-color: #fff;
color: #3E4349;
padding: 0 30px 0 30px;
}
div.body > .section {
text-align: left;
}
div.footer {
width: 940px;
margin: 20px auto 30px auto;
font-size: 14px;
color: #888;
text-align: right;
}
div.footer a {
color: #888;
}
p.caption {
font-family: inherit;
font-size: inherit;
}
div.relations {
display: none;
}
div.sphinxsidebar a {
color: #444;
text-decoration: none;
border-bottom: 1px dotted #999;
}
div.sphinxsidebar a:hover {
border-bottom: 1px solid #999;
}
div.sphinxsidebarwrapper {
padding: 18px 10px;
}
div.sphinxsidebarwrapper p.logo {
padding: 0;
margin: -10px 0 0 0px;
text-align: center;
}
div.sphinxsidebarwrapper h1.logo {
margin-top: -10px;
text-align: center;
margin-bottom: 5px;
text-align: left;
}
div.sphinxsidebarwrapper h1.logo-name {
margin-top: 0px;
}
div.sphinxsidebarwrapper p.blurb {
margin-top: 0;
font-style: normal;
}
div.sphinxsidebar h3,
div.sphinxsidebar h4 {
font-family: 'Garamond', 'Georgia', serif;
color: #444;
font-size: 24px;
font-weight: normal;
margin: 0 0 5px 0;
padding: 0;
}
div.sphinxsidebar h4 {
font-size: 20px;
}
div.sphinxsidebar h3 a {
color: #444;
}
div.sphinxsidebar p.logo a,
div.sphinxsidebar h3 a,
div.sphinxsidebar p.logo a:hover,