From de7f4747d30d7937aed553159986ea968826ee14 Mon Sep 17 00:00:00 2001 From: Ryan Ly Date: Tue, 11 Apr 2023 14:49:41 -0700 Subject: [PATCH] Prepare PyNWB 2.3.2 (#1672) --- CHANGELOG.md | 5 ++++- docs/gallery/general/add_remove_containers.py | 8 ++++---- requirements-dev.txt | 6 +++--- requirements-min.txt | 2 +- requirements.txt | 10 +++++----- setup.py | 10 +++++----- 6 files changed, 22 insertions(+), 19 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index bf2eb5ae9..e2386c47d 100644 --- 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 index 578d9a38c..26708f639 100644 --- 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 index 6ec6ae5ce..93968f3f9 100644 --- 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 index c45e99846..46a79dce0 100644 --- 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 index 0bfbd920f..def13b089 100644 --- 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 index 9c311efcf..d9ad4b8fa 100755 --- 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' ]