Prepare PyNWB 2.3.2 (#1672)

rly · web-flow · commit de7f4747d30d · 2023-04-11T14:49:41.000-07:00
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,6 +1,6 @@
 # PyNWB Changelog
 
-## PyNWB 2.3.2 (Upcoming)
+## PyNWB 2.3.2 (April 10, 2023)
 
 ### Enhancements and minor changes
 - Fixed typos and added codespell GitHub action to check spelling in the future. @yarikoptic [#1648](https://github.com/NeurodataWithoutBorders/pynwb/pull/1648)
@@ -10,10 +10,13 @@
 - Add tutorial for optogenetics. @bendichter [#1657](https://github.com/NeurodataWithoutBorders/pynwb/pull/1657)
 - Update testing of gallery examples and disable testing of the allensdk tutorial.
   [#1680](https://github.com/NeurodataWithoutBorders/pynwb/pull/1680)
+- Updated tutorials to follow best practices. @bendichter [#1656](https://github.com/NeurodataWithoutBorders/pynwb/pull/1656)
 
 ### Bug fixes
+- Fixed bug when initializing ``OnePhotonSeries`` with no value for ``binning``. @bendichter [#1660](https://github.com/NeurodataWithoutBorders/pynwb/pull/1660)
 - Fixed bug in ``NWBHDF5IO.nwb_version`` property to support files written by third-party software with a fixed-length ``nwb_version`` attribute. @oruebel [#1669](https://github.com/NeurodataWithoutBorders/pynwb/pull/1669)
 - Fixed search bar and missing jquery in ReadTheDocs documentation. @rly [#1671](https://github.com/NeurodataWithoutBorders/pynwb/pull/1671)
+- Requires [HDMF 3.5.4](https://github.com/hdmf-dev/hdmf/releases/tag/3.5.4) which includes bug fixes. @rly [#1672](https://github.com/NeurodataWithoutBorders/pynwb/pull/1672)
 - Fixed issue with deprecated pkg_resources. @rly [#1678](https://github.com/NeurodataWithoutBorders/pynwb/pull/1678)
 
 ## PyNWB 2.3.1 (February 24, 2023)
diff --git a/docs/gallery/general/add_remove_containers.py b/docs/gallery/general/add_remove_containers.py
@@ -46,7 +46,7 @@
 
     # create a TimeSeries and add it to the file under the acquisition group
     data = list(range(100, 200, 10))
-    timestamps = np.arange(10, dtype=np.float)
+    timestamps = np.arange(10, dtype=float)
     test_ts = TimeSeries(
         name="test_timeseries", data=data, unit="m", timestamps=timestamps
     )
@@ -112,7 +112,7 @@
     session_start_time=datetime.datetime.now(datetime.timezone.utc),
 )
 data1 = list(range(100, 200, 10))
-timestamps1 = np.arange(10, dtype=np.float)
+timestamps1 = np.arange(10, dtype=float)
 test_ts1 = TimeSeries(
     name="test_timeseries1", data=data1, unit="m", timestamps=timestamps1
 )
@@ -123,7 +123,7 @@
     name="behavior", description="processed behavioral data"
 )
 data2 = list(range(100, 200, 10))
-timestamps2 = np.arange(10, dtype=np.float)
+timestamps2 = np.arange(10, dtype=float)
 test_ts2 = TimeSeries(
     name="test_timeseries2", data=data2, unit="m", timestamps=timestamps2
 )
@@ -141,7 +141,7 @@
 
     # add a new TimeSeries to the behavior processing module
     data3 = list(range(100, 200, 10))
-    timestamps3 = np.arange(10, dtype=np.float)
+    timestamps3 = np.arange(10, dtype=float)
     test_ts3 = TimeSeries(
         name="test_timeseries3", data=data3, unit="m", timestamps=timestamps3
     )
diff --git a/requirements-dev.txt b/requirements-dev.txt
@@ -7,12 +7,12 @@ codecov==2.1.12
 codespell==2.2.4
 coverage==7.2.2
 flake8==6.0.0; python_version >= "3.8"
-flake8==5.0.4; python_version == "3.8"
+flake8==5.0.4; python_version < "3.8"
 flake8-debugger==4.1.2
 flake8-print==5.0.0
 isort==5.12.0; python_version >= "3.8"
-isort==5.11.5; python_version == "3.8"
+isort==5.11.5; python_version < "3.8"
 pytest==7.1.2
 pytest-cov==4.0.0
 tox==4.4.8; python_version >= "3.8"
-tox==3.28.0; python_version == "3.8"
+tox==3.28.0; python_version < "3.8"
diff --git a/requirements-min.txt b/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==3.5.1
+hdmf==3.5.4
 numpy==1.16
 pandas==1.1.5
 python-dateutil==2.7.3
diff --git a/requirements.txt b/requirements.txt
@@ -1,9 +1,9 @@
 # pinned dependencies to reproduce an entire development environment to use PyNWB
 h5py==3.7.0
-hdmf==3.5.1
-numpy==1.23.3;python_version>='3.8'
-numpy==1.21.5;python_version<'3.8'  # note that numpy 1.22 dropped python 3.7 support
-pandas==1.5.0;python_version>='3.8'
-pandas==1.3.5;python_version<'3.8'  # note that pandas 1.4 dropped python 3.7 support
+hdmf==3.5.4
+numpy==1.23.3; python_version >= "3.8"
+numpy==1.21.5; python_version < "3.8"  # note that numpy 1.22 dropped python 3.7 support
+pandas==1.5.0; python_version >= "3.8"
+pandas==1.3.5; python_version < "3.8"  # note that pandas 1.4 dropped python 3.7 support
 python-dateutil==2.8.2
 setuptools==65.5.1
diff --git a/setup.py b/setup.py
@@ -19,11 +19,11 @@
 schema_dir = 'nwb-schema/core'
 
 reqs = [
-    'h5py>=2.10,<4',
-    'hdmf>=3.5.1,<4',
-    'numpy>=1.16,<1.24',
-    'pandas>=1.1.5,<2',
-    'python-dateutil>=2.7.3,<3',
+    'h5py>=2.10',
+    'hdmf>=3.5.4',
+    'numpy>=1.16',
+    'pandas>=1.1.5',
+    'python-dateutil>=2.7.3',
     'setuptools'
 ]
 

Original file line number	Diff line number	Diff line change
`@@ -46,7 +46,7 @@`
`46`	`46`
`47`	`47`	`# create a TimeSeries and add it to the file under the acquisition group`
`48`	`48`	`data = list(range(100, 200, 10))`
`49`		`- timestamps = np.arange(10, dtype=np.float)`
	`49`	`+ timestamps = np.arange(10, dtype=float)`
`50`	`50`	`test_ts = TimeSeries(`
`51`	`51`	`name="test_timeseries", data=data, unit="m", timestamps=timestamps`
`52`	`52`	`)`
`@@ -112,7 +112,7 @@`
`112`	`112`	`session_start_time=datetime.datetime.now(datetime.timezone.utc),`
`113`	`113`	`)`
`114`	`114`	`data1 = list(range(100, 200, 10))`
`115`		`-timestamps1 = np.arange(10, dtype=np.float)`
	`115`	`+timestamps1 = np.arange(10, dtype=float)`
`116`	`116`	`test_ts1 = TimeSeries(`
`117`	`117`	`name="test_timeseries1", data=data1, unit="m", timestamps=timestamps1`
`118`	`118`	`)`
`@@ -123,7 +123,7 @@`
`123`	`123`	`name="behavior", description="processed behavioral data"`
`124`	`124`	`)`
`125`	`125`	`data2 = list(range(100, 200, 10))`
`126`		`-timestamps2 = np.arange(10, dtype=np.float)`
	`126`	`+timestamps2 = np.arange(10, dtype=float)`
`127`	`127`	`test_ts2 = TimeSeries(`
`128`	`128`	`name="test_timeseries2", data=data2, unit="m", timestamps=timestamps2`
`129`	`129`	`)`
`@@ -141,7 +141,7 @@`
`141`	`141`
`142`	`142`	`# add a new TimeSeries to the behavior processing module`
`143`	`143`	`data3 = list(range(100, 200, 10))`
`144`		`- timestamps3 = np.arange(10, dtype=np.float)`
	`144`	`+ timestamps3 = np.arange(10, dtype=float)`
`145`	`145`	`test_ts3 = TimeSeries(`
`146`	`146`	`name="test_timeseries3", data=data3, unit="m", timestamps=timestamps3`
`147`	`147`	`)`