Updated formatting function for setting parser (try to get absolute path if file field)

.gitignore

 # Created by .ignore support plugin (hsz.mobi)
 .venv
-data/examples
-.idea
\ No newline at end of file
+.idea
+data/

ariaec/base.py

@@ -124,11 +124,14 @@ def format_str(string):
     elif re.search(r"^[\s\d-]+\.\d+\s*$", string):
         return float(string)
     elif re.search(r'^".+"$', string):
+        # remove " characters
         return string[1:-1]
     elif "," in string:
         return string.split(',')
     elif "+" in string:
         return string.split('+')
+    elif "/" in string and os.path.exists(string):
+        return os.path.abspath(string)
     elif re.search(r"[/\w]+", string):
         return string
     else:
@@ -154,7 +157,8 @@ def format_dict(indict):
     :return:
     """
     for key in indict:
-        indict[key] = format_str(indict[key])
+        if type(indict[key]) == str:
+            indict[key] = format_str(indict[key])
     return indict
 
 

ariaec/commands.py

@@ -8,6 +8,7 @@ import os
 import logging
 import argparse as argp
 
+from .base import format_dict
 from .ecsettings import AriaEcSettings
 from .maplot import AriaEcContactMap
 from .econverter import AriaEcBbConverter
@@ -203,7 +204,7 @@ class AriaEcCommand(object):
         parser.add_argument("--merge", nargs="+", dest="merge",
                             choices=self.contact_types,
                             help="Merge given contact types with other maps")
-        parser.add_argument("--filter", dest="nofilter", action="store_true",
+        parser.add_argument("--filter", dest="filter", action="store_true",
                             default=False, help="Use contact list filter "
                                                 "and top n contacts selection")
         parser.add_argument("--onlyreport", dest="onlyreport",
@@ -242,10 +243,11 @@ class AriaEcCommand(object):
             LOG.info("Updating settings with conf file")
             settings.load_config(self.args.conf_file)
         # Update settings associated to command section
-        LOG.info("Updating %s settings with args", self.args.command)
-        getattr(settings, self.args.command).args.update(self.args.__dict__)
+        LOG.info("Updating %s args settings", self.args.command)
+        getattr(settings, self.args.command).args.update(format_dict(self.args.__dict__))
+        LOG.debug(getattr(settings, self.args.command).args)
         if self.args.output_directory:
-            LOG.info("Updating output directory")
+            LOG.info("Updating output directory %s", self.args.output_directory)
             settings.infra = self.args.output_directory
         return settings
 

ariaec/ecsettings.py

@@ -72,6 +72,7 @@ class Settings(object):
         LOG.debug(config)
         for section in config.sections():
             if hasattr(self, section):
+                LOG.debug("Formatting items of %s section", section)
                 tmp = format_dict(dict(config.items(section)))
                 getattr(self, section).config.update(tmp)
                 LOG.debug("%s config updated", section)

ariaec/maplot.py

@@ -78,7 +78,11 @@ class AriaEcContactMap(object):
                 self.reftype = fo.filetype
                 self.refname = fo.filename if type(self.outprefix) != list \
                     else self.outprefix[idx]
-            if self.settings.contactmap.args.get("filter"):
+            if (self.settings.contactmap.args.get("filter") and idx != 0) or \
+                    (self.settings.contactmap.args.get("filter")
+                     and len(self.file_reader.filelist) == 1):
+                # Filtering all contactmap except the reference map
+                LOG.info("Filtering %s map", fo.filetype)
                 self.filter(fo.mapdict, fo.filetype, fo.contactlist,
                             self.protein, clashlist=fo.clashlist,
                             outprefix=self.outprefix[idx] if type(

ariaec/pdbqual.py

@@ -34,9 +34,9 @@ class AriaEcPdbqual(CommandProtocol):
         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"])
+        LOG.info(self.settings.pdbqual["output_directory"])
         QualityChecks.runChecks(
-            workingDirectory=os.path.abspath(
-                self.settings.pdbqual["output_directory"]),
+            workingDirectory=self.settings.pdbqual["output_directory"],
             trashDirectory=self.settings.pdbqual["trash_directory"],
             prosaOnOff=1 if self.settings.pdbqual["prosa"] else 0,
             procheckExe=self.settings.main["procheck_executable"],
@@ -52,8 +52,11 @@ 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")
+        LOG.info("Removing infile(s) in output directory %s", self.settings.pdbqual["output_directory"])
         [os.remove(
-            os.path.join(os.path.abspath(self.settings.pdbqual["output_directory"]),
+            os.path.join(self.settings.pdbqual["output_directory"],
                          os.path.basename(infile)))
-         for infile in self.settings.pdbqual["infiles"]]
+         for infile in self.settings.pdbqual["infiles"]
+         if os.path.exists(os.path.join(
+            self.settings.pdbqual["output_directory"],
+            os.path.basename(infile)))]

setup.py

@@ -55,8 +55,8 @@ class CleanCommand(Command):
                   './*.egg-info')
 
 
-with open('README.rst') as f:
-    long_description = f.read()
+# with open('README.rst') as f:
+#     long_description = f.read()
 
 # with open('LICENSE') as f:
 #     license = f.read()
@@ -72,7 +72,7 @@ setup(
     author="Allain Fabrice",
     author_email="fabrice.allain@pasteur.fr",
     description="ARIA Evolutive Contact toolbox",
-    long_description=long_description,
+    # long_description=long_description,
     # license="PSF",
     # keywords="hello world example examples",
     url="http://aria.pasteur.fr/",  # project home page
@@ -93,7 +93,6 @@ setup(
         'Programming Language :: Python :: 2.7',
         'Programming Language :: Python :: 3',
         'Programming Language :: Python :: 3.2',
-        'Programming Language :: Python :/home/raionic/Workspace/bis-aria/NEFparser/branches/fallain_branche/BMRB: 3.3',
         'Programming Language :: Python :: 3.4',
     ],
 
@@ -110,7 +109,8 @@ setup(
         'matplotlib'],
 
     install_requires=[
-        # 'configparser',     # TODO: add this requiirement only if python v2
+        'configparser',     # TODO: add this requiirement only if python v2
+        'Sphinx',
         'docutils>=0.3',
         'pandas',
         'seaborn',