Added sphinx documentation files generated with sphinx-apidoc

ariaec/base.py

@@ -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:

ariaec/conf/aria_ec.ini

@@ -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

ariaec/pdbqual.py

@@ -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"]]

docs/Makefile

+# 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."

docs/_build/html/.buildinfo

+# 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

docs/_build/html/_sources/ariaec.test.txt

+ariaec.test package
+===================
+
+Module contents
+---------------
+
+.. automodule:: ariaec.test
+    :members:
+    :undoc-members:
+    :show-inheritance:

docs/_build/html/_sources/ariaec.txt

+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:

docs/_build/html/_sources/index.txt

+.. 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`
+

docs/_build/html/_sources/modules.txt

+ariaec
+======
+
+.. toctree::
+   :maxdepth: 4
+
+   ariaec

docs/_build/html/_static/alabaster.css

+
+
+
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+
+
+
+
+
+@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,