Add dataset to store list of software that produced a file (#1924)

Co-authored-by: Ryan Ly <[email protected]>

CHANGELOG.md

@@ -4,7 +4,8 @@
 
 ### Enhancements and minor changes
 - Added support for NWB schema 2.8.0:
-  - Removed `SpatialSeries.bounds` field that was not functional. This will be fixed in a future release. @rly [#1907](https://github.com/NeurodataWithoutBorders/pynwb/pull/1907), 
+  - Removed `SpatialSeries.bounds` field that was not functional. This will be fixed in a future release. @rly [#1907](https://github.com/NeurodataWithoutBorders/pynwb/pull/1907), [#1996](https://github.com/NeurodataWithoutBorders/pynwb/pull/1996)
+  - Added support for `NWBFile.was_generated_by` field. @stephprince [#1924](https://github.com/NeurodataWithoutBorders/pynwb/pull/1924)
 
 ## PyNWB 2.8.3 (Upcoming)
 

src/pynwb/file.py

@@ -261,6 +261,7 @@ class NWBFile(MultiContainerInterface, HERDManager):
                      'slices',
                      'source_script',
                      'source_script_file_name',
+                     'was_generated_by',
                      'data_collection',
                      'surgery',
                      'virus',
@@ -339,6 +340,8 @@ class NWBFile(MultiContainerInterface, HERDManager):
              'doc': 'Script file used to create this NWB file.', 'default': None},
             {'name': 'source_script_file_name', 'type': str,
              'doc': 'Name of the source_script file', 'default': None},
+            {'name': 'was_generated_by', 'type': 'array_data',
+             'doc': 'List of software package names and versions used to generate this NWB File.', 'default': None},
             {'name': 'data_collection', 'type': str,
              'doc': 'Notes about data collection and analysis.', 'default': None},
             {'name': 'surgery', 'type': str,
@@ -448,6 +451,7 @@ def __init__(self, **kwargs):
             'slices',
             'source_script',
             'source_script_file_name',
+            'was_generated_by',
             'surgery',
             'virus',
             'stimulus_notes',

src/pynwb/io/file.py

@@ -97,6 +97,7 @@ def __init__(self, spec):
                             'session_id',
                             'slices',
                             'source_script',
+                            'was_generated_by',
                             'stimulus',
                             'surgery',
                             'virus']

tests/integration/hdf5/test_nwbfile.py

@@ -42,6 +42,7 @@ def setUp(self):
                                session_id='007',
                                slices='noslices',
                                source_script='nosources',
+                               was_generated_by=[('nosoftware', '0.0.0')],
                                surgery='nosurgery',
                                virus='novirus',
                                source_script_file_name='nofilename')
@@ -128,6 +129,7 @@ def build_nwbfile(self):
                                  virus='a virus',
                                  source_script='noscript',
                                  source_script_file_name='nofilename',
+                                 was_generated_by=[('nosoftware', '0.0.0')],
                                  stimulus_notes='test stimulus notes',
                                  data_collection='test data collection notes',
                                  keywords=('these', 'are', 'keywords'))
@@ -176,6 +178,32 @@ def build_nwbfile(self):
         self.nwbfile.experimenter = ('experimenter1', 'experimenter2')
 
 
+class TestWasGeneratedByConstructorRoundtrip(TestNWBFileIO):
+    """ Test that a list of software packages / versions in a constructor is written to and read from file """
+
+    def build_nwbfile(self):
+        description = 'test nwbfile was_generated_by'
+        identifier = 'TEST_was_generated_by'
+        self.nwbfile = NWBFile(session_description=description,
+                               identifier=identifier,
+                               session_start_time=self.start_time,
+                               was_generated_by=[('software1', '0.1.0'),
+                                                 ('software2', '0.2.0'),
+                                                 ('software3', '0.3.0')],)
+
+class TestWasGeneratedBySetterRoundtrip(TestNWBFileIO):
+    """ Test that a single tuple of software versions packages in a setter is written to and read from file """
+
+    def build_nwbfile(self):
+        description = 'test nwbfile was_generated_by'
+        identifier = 'TEST_was_generated_by'
+        self.nwbfile = NWBFile(session_description=description,
+                               identifier=identifier,
+                               session_start_time=self.start_time)
+        self.nwbfile.was_generated_by = [('software1', '0.1.0'),
+                                         ('software2', '0.2.0'),
+                                         ('software3', '0.3.0')]
+
 class TestPublicationsConstructorRoundtrip(TestNWBFileIO):
     """ Test that a list of multiple publications in a constructor is written to and read from file """
 

tests/unit/test_file.py

@@ -42,6 +42,7 @@ def setUp(self):
                                virus='a virus',
                                source_script='noscript',
                                source_script_file_name='nofilename',
+                               was_generated_by=[('nosoftware', '0.0.0')],
                                stimulus_notes='test stimulus notes',
                                data_collection='test data collection notes',
                                keywords=('these', 'are', 'keywords'))
@@ -61,6 +62,7 @@ def test_constructor(self):
         self.assertEqual(self.nwbfile.related_publications, ('my pubs',))
         self.assertEqual(self.nwbfile.source_script, 'noscript')
         self.assertEqual(self.nwbfile.source_script_file_name, 'nofilename')
+        self.assertEqual(self.nwbfile.was_generated_by, [('nosoftware', '0.0.0')])
         self.assertEqual(self.nwbfile.keywords, ('these', 'are', 'keywords'))
         self.assertEqual(self.nwbfile.timestamps_reference_time, self.ref_time)