Merge branch 'master' into version1.0

Author: JuliaSprenger

doc/index.rst

@@ -10,9 +10,9 @@ odMLtables - Table-based editing of odML metadata collections
 Synopsis
 =========
 
-*odMLtables* is a tool to support working with metadata collections for electrophysiological data.
+*odMLtables* is a tool to support working with metadata collections for electrophysiological data and is described in detail in `Sprenger et al. (2019) odMLtables: A User-Friendly Approach for Managing Metadata of Neurophysiological Experiments`_.
 
-The odML_ file format and library API provides a means to store hierarchical metadata collections for electrophysiological data. Such collections typically consist of a large number of key-value pairs organized by a hierarchy of sections (see `Grewe et al, 2011, Frontiers in Neuroinformatics 5, 16`_). However, for editing and viewing metadata the use of standard spreadsheet software offering a flat tabular representation of a selected subset of metadata is desireable (cf., `Zehl et al, 2016, Frontiers in Neuroinformatics 10, 26`_). *odMLtables* provides a set of library functions as well as a graphical user interface that offers to swtich between hierarchical and flat representations of their metadata collection, and provides functions that assist in working with these files.
+The odML_ file format and library API provides a means to store hierarchical metadata collections for electrophysiological data. Such collections typically consist of a large number of key-value pairs organized by a hierarchy of sections (see `Grewe et al. (2011) Frontiers in Neuroinformatics 5:16`_). However, for editing and viewing metadata the use of standard spreadsheet software offering a flat tabular representation of a selected subset of metadata is desireable (cf., `Zehl et al. (2016) Frontiers in Neuroinformatics 10:26`_). *odMLtables* provides a set of library functions as well as a graphical user interface that offers to swtich between hierarchical and flat representations of their metadata collection, and provides functions that assist in working with these files.
 
 Currently, odMLtables supports:
 
@@ -43,9 +43,17 @@ Indices and tables
 * :ref:`search`
 
 
+Citation
+========
+If you are using *odMLtables* for your project please consider citing
+
+`Sprenger J, Zehl L, Pick J, Sonntag M, Grewe J, Wachtler T, Grün S and Denker M (2019) odMLtables: A User-Friendly Approach for Managing Metadata of Neurophysiological Experiments. Front. Neuroinform. 13:62. doi: 10.3389/fninf.2019.00062`_
+
+.. _`Sprenger et al. (2019) odMLtables: A User-Friendly Approach for Managing Metadata of Neurophysiological Experiments`: https://doi.org/10.3389/fninf.2019.00062
+.. _`Sprenger J, Zehl L, Pick J, Sonntag M, Grewe J, Wachtler T, Grün S and Denker M (2019) odMLtables: A User-Friendly Approach for Managing Metadata of Neurophysiological Experiments. Front. Neuroinform. 13:62. doi: 10.3389/fninf.2019.00062`: https://doi.org/10.3389/fninf.2019.00062
 .. _`odML`: http://www.g-node.org/projects/odml
-.. _`Grewe et al, 2011, Frontiers in Neuroinformatics 5, 16`: http://dx.doi.org/10.3389/fninf.2011.00016
-.. _`Zehl et al, 2016, Frontiers in Neuroinformatics 10, 26`: http://dx.doi.org/10.3389/fninf.2016.00026
+.. _`Grewe et al. (2011) Frontiers in Neuroinformatics 5:16`: http://dx.doi.org/10.3389/fninf.2011.00016
+.. _`Zehl et al. (2016) Frontiers in Neuroinformatics 10:26`: http://dx.doi.org/10.3389/fninf.2016.00026
 
 .. |date| date::
 .. |time| date:: %H:%M

odmltables/VERSION.txt

@@ -1 +1 @@
-1.0.0b3
+1.0.0

odmltables/compare_section_table.py

@@ -104,6 +104,8 @@ def load_from_file(self, load_from):
 
         """
         self._odmldoc = odml.load(load_from, show_warnings=self.show_odml_warnings)
+        # resolve links and includes
+        self._odmldoc.finalize()
 
     def choose_sections_startwith(self, startwith):
         """

odmltables/gui/compsectionpages.py

@@ -210,6 +210,8 @@ def initializePage(self):
 
         # load sections and properties from the selected file
         odmldoc = odml.load(self.settings.get_object("inputfilename"))
+        # resolve links and includes
+        odmldoc.finalize()
         for section in odmldoc.itersections():
             self.sections.append([section.name,
                                   section.get_path(),

odmltables/odml_table.py

@@ -124,6 +124,8 @@ def load_from_file(self, load_from):
 
         """
         doc = odml.load(load_from, show_warnings=self.show_odml_warnings)
+        # resolve links and includes
+        doc.finalize()
         self._odmldict = self.__create_odmldict(doc)
         self._docdict = self._create_documentdict(doc)
 

setup.py

@@ -1,3 +1,4 @@
+#!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
 import sys, os, glob
@@ -26,7 +27,7 @@
                   'installing the odmltables gui, eg. using "conda install -c anaconda '
                   '\'pyqt>=5\'"')
 
-VERSION = open('./odmltables/VERSION.txt', 'r').read()
+VERSION = open('./odmltables/VERSION.txt', 'r').read().strip()
 
 setup(
     name="odmltables",
@@ -56,14 +57,10 @@
     zip_safe=False,
     keywords=['odml', 'excel', 'metadata management'],
     # Extension('foo', ['foo.c'], include_dirs=['.']),
-    data_files=[
-                  # ('/usr/share/applications', ['odmltables.desktop']),
-                  # ('/usr/share/pixmaps', ['logo/odMLtables.png']),
-                  ('share/pixmaps', glob.glob(os.path.join("logo", "*"))),
-                  # ('share/pixmaps', ['logo/odMLtables.png']),
-                  ('.', ['odmltables/VERSION.txt',
-                         'requirements.txt',
-                         'requirements_doc.txt',
-                         'requirements_gui.txt',
-                         'requirements_test.txt'])]
-)
+    data_files=[('share/pixmaps', glob.glob(os.path.join("logo", "*"))),
+                ('.', ['odmltables/VERSION.txt',
+                       'requirements.txt',
+                       'requirements_doc.txt',
+                       'requirements_gui.txt',
+                       'requirements_test.txt'])]
+)