Release 2.5.0/ Update ExternalResources to HERD (#1754)

* Update ExternalResources to HERD

* Update setup.py

* Update requirements.txt

* Update requirements-min.txt

* Update environment-ros3.yml

* Update CHANGELOG.md

* Update environment-ros3.yml

* Update run_tests.yml

* Update run_all_tests.yml

* Update run_tests.yml

* Update run_all_tests.yml

* Update run_all_tests.yml

* Update run_tests.yml

Author: mavaylon1

.github/workflows/run_all_tests.yml

@@ -108,6 +108,7 @@ jobs:
       - uses: actions/checkout@v3
         with:
           submodules: 'recursive'
+          fetch-depth: 0  # tags are required for versioneer to determine the version
 
       - name: Set up Python
         uses: actions/setup-python@v4
@@ -151,6 +152,7 @@ jobs:
       - uses: actions/checkout@v3
         with:
           submodules: 'recursive'
+          fetch-depth: 0  # tags are required for versioneer to determine the version
 
       - name: Set up Conda
         uses: conda-incubator/setup-miniconda@v2
@@ -207,6 +209,7 @@ jobs:
       - uses: actions/checkout@v3
         with:
           submodules: 'recursive'
+          fetch-depth: 0  # tags are required for versioneer to determine the version
 
       - name: Set up Conda
         uses: conda-incubator/setup-miniconda@v2
@@ -253,6 +256,7 @@ jobs:
       - uses: actions/checkout@v3
         with:
           submodules: 'recursive'
+          fetch-depth: 0  # tags are required for versioneer to determine the version
 
       - name: Set up Conda
         uses: conda-incubator/setup-miniconda@v2
@@ -278,4 +282,4 @@ jobs:
 
       - name: Run gallery ros3 tests
         run: |
-          python test.py --example-ros3
+          python test.py --example-ros3

.github/workflows/run_tests.yml

@@ -92,6 +92,7 @@ jobs:
       - uses: actions/checkout@v3
         with:
           submodules: 'recursive'
+          fetch-depth: 0  # tags are required for versioneer to determine the version
 
       - name: Set up Python
         uses: actions/setup-python@v4
@@ -184,6 +185,7 @@ jobs:
       - uses: actions/checkout@v3
         with:
           submodules: 'recursive'
+          fetch-depth: 0  # tags are required for versioneer to determine the version
 
       - name: Set up Conda
         uses: conda-incubator/setup-miniconda@v2
@@ -228,6 +230,7 @@ jobs:
       - uses: actions/checkout@v3
         with:
           submodules: 'recursive'
+          fetch-depth: 0  # tags are required for versioneer to determine the version
 
       - name: Set up Conda
         uses: conda-incubator/setup-miniconda@v2
@@ -271,6 +274,7 @@ jobs:
         uses: actions/checkout@v3
         with:
           submodules: 'recursive'
+          fetch-depth: 0  # tags are required for versioneer to determine the version
 
       - name: Set up Python
         uses: actions/setup-python@v4

CHANGELOG.md

@@ -1,10 +1,11 @@
 # PyNWB Changelog
 
-## PyNWB 2.5.0 (Upcoming)
+## PyNWB 2.5.0 (August 18, 2023)
 
 ### Enhancements and minor changes
 - Add `TimeSeries.get_timestamps()`. @bendichter [#1741](https://github.com/NeurodataWithoutBorders/pynwb/pull/1741)
 - Add `TimeSeries.get_data_in_units()`. @bendichter [#1745](https://github.com/NeurodataWithoutBorders/pynwb/pull/1745)
+- Updated `ExternalResources` name change to `HERD`, along with HDMF 3.9.0 being the new minimum. @mavaylon1 [#1754](https://github.com/NeurodataWithoutBorders/pynwb/pull/1754)
 
 ### Documentation and tutorial enhancements
 - Updated streaming tutorial to ensure code is run on tests and clarify text. @bendichter [#1760](https://github.com/NeurodataWithoutBorders/pynwb/pull/1760) @oruebel [#1762](https://github.com/NeurodataWithoutBorders/pynwb/pull/1762)

environment-ros3.yml

@@ -15,4 +15,4 @@ dependencies:
   - dandi==0.55.1  # NOTE: dandi does not support osx-arm64
   - fsspec==2023.6.0
   - requests==2.28.1
-  - aiohttp==3.8.3
+  - aiohttp==3.8.3

requirements-min.txt

@@ -1,6 +1,6 @@
 # minimum versions of package dependencies for installing PyNWB
 h5py==2.10  # support for selection of datasets with list of indices added in 2.10
-hdmf==3.8.0
+hdmf==3.9.0
 numpy==1.18
 pandas==1.1.5
 python-dateutil==2.7.3

requirements.txt

@@ -1,6 +1,6 @@
 # pinned dependencies to reproduce an entire development environment to use PyNWB
 h5py==3.8.0
-hdmf==3.8.0
+hdmf==3.9.0
 numpy==1.24.2
 pandas==2.0.0
 python-dateutil==2.8.2

setup.py

@@ -20,7 +20,7 @@
 
 reqs = [
     'h5py>=2.10',
-    'hdmf>=3.8.0',
+    'hdmf>=3.9.0',
     'numpy>=1.16',
     'pandas>=1.1.5',
     'python-dateutil>=2.7.3',

src/pynwb/__init__.py

@@ -216,12 +216,12 @@ class NWBHDF5IO(_HDF5IO):
             {'name': 'comm', 'type': "Intracomm", 'doc': 'the MPI communicator to use for parallel I/O',
              'default': None},
             {'name': 'driver', 'type': str, 'doc': 'driver for h5py to use when opening HDF5 file', 'default': None},
-            {'name': 'external_resources_path', 'type': str, 'doc': 'The path to the ExternalResources',
+            {'name': 'herd_path', 'type': str, 'doc': 'The path to the HERD',
              'default': None},)
     def __init__(self, **kwargs):
-        path, mode, manager, extensions, load_namespaces, file_obj, comm, driver, external_resources_path =\
+        path, mode, manager, extensions, load_namespaces, file_obj, comm, driver, herd_path =\
             popargs('path', 'mode', 'manager', 'extensions', 'load_namespaces',
-                    'file', 'comm', 'driver', 'external_resources_path', kwargs)
+                    'file', 'comm', 'driver', 'herd_path', kwargs)
         # Define the BuildManager to use
         if load_namespaces:
             if manager is not None:
@@ -251,7 +251,7 @@ def __init__(self, **kwargs):
                 manager = get_manager()
         # Open the file
         super().__init__(path, manager=manager, mode=mode, file=file_obj, comm=comm,
-                         driver=driver, external_resources_path=external_resources_path)
+                         driver=driver, herd_path=herd_path)
 
     @property
     def nwb_version(self):

src/pynwb/file.py

@@ -8,7 +8,7 @@
 import pandas as pd
 
 from hdmf.common import DynamicTableRegion, DynamicTable
-from hdmf.container import ExternalResourcesManager
+from hdmf.container import HERDManager
 from hdmf.utils import docval, getargs, get_docval, popargs, popargs_to_dict, AllowPositional
 
 from . import register_class, CORE_NAMESPACE
@@ -150,7 +150,7 @@ def __init__(self, **kwargs):
 
 
 @register_class('NWBFile', CORE_NAMESPACE)
-class NWBFile(MultiContainerInterface, ExternalResourcesManager):
+class NWBFile(MultiContainerInterface, HERDManager):
     """
     A representation of an NWB file.
     """

src/pynwb/resources.py

@@ -1,10 +1,14 @@
-from hdmf.common import ExternalResources as hdmf_ExternalResources
+from hdmf.common import HERD as hdmf_HERD
 from . import get_type_map as tm
 from hdmf.utils import docval, get_docval
 
 
-class ExternalResources(hdmf_ExternalResources):
-    @docval(*get_docval(hdmf_ExternalResources.__init__))
+class HERD(hdmf_HERD):
+    """
+    HDMF External Resources Data Structure.
+    A table for mapping user terms (i.e. keys) to resource entities.
+    """
+    @docval(*get_docval(hdmf_HERD.__init__))
     def __init__(self, **kwargs):
         kwargs['type_map'] = tm()
         super().__init__(**kwargs)