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Numpy 2.0 #1956

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Sep 4, 2024
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Numpy 2.0 #1956

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ebc887f
Update pyproject.toml
mavaylon1 Sep 4, 2024
04096d9
Update requirements-min.txt
mavaylon1 Sep 4, 2024
c0b481b
Update requirements.txt
mavaylon1 Sep 4, 2024
480dcf3
Update requirements-min.txt
mavaylon1 Sep 4, 2024
44ceef0
Update requirements-min.txt
mavaylon1 Sep 4, 2024
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Update requirements.txt
mavaylon1 Sep 4, 2024
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Update pyproject.toml
mavaylon1 Sep 4, 2024
81accd3
Update export.rst
mavaylon1 Sep 4, 2024
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Update export.rst
mavaylon1 Sep 4, 2024
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Update export.rst
mavaylon1 Sep 4, 2024
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Update CHANGELOG.md
mavaylon1 Sep 4, 2024
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Update docs/source/export.rst
stephprince Sep 4, 2024
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3 changes: 3 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -2,6 +2,9 @@

## PyNWB 2.8.2 (Upcoming)

### Enhancements and minor changes
- Added support for numpy 2.0. @mavaylon1 [#1956](https://github.com/NeurodataWithoutBorders/pynwb/pull/1956)

### Documentation and tutorial enhancements
- Added pre-release pull request instructions to release process documentation @stephprince [#1928](https://github.com/NeurodataWithoutBorders/pynwb/pull/1928)
- Added section on how to use the `family` driver in `h5py` for splitting data across multiple files @oruebel [#1949](https://github.com/NeurodataWithoutBorders/pynwb/pull/1949)
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10 changes: 4 additions & 6 deletions docs/source/export.rst
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Expand Up @@ -53,14 +53,12 @@ on the :py:class:`~pynwb.file.NWBFile` before exporting.

How do I create a copy of an NWB file with different data layouts (e.g., applying compression)?
---------------------------------------------------------------------------------------------------------
Use the `h5repack <https://support.hdfgroup.org/HDF5/doc/RM/Tools.html#Tools-Repack>`_ command line tool from the HDF5 Group.
See also this `h5repack tutorial <https://support.hdfgroup.org/HDF5/Tutor/cmdtooledit.html#chglayout>`_.
Use the `h5repack <https://docs.hdfgroup.org/hdf5/v1_14/_view_tools_edit.html>`_ command line tool from the HDF5 Group.


How do I create a copy of an NWB file with different controls over how links are treated and whether copies are deep or shallow?
---------------------------------------------------------------------------------------------------------------------------------
Use the `h5copy <https://support.hdfgroup.org/HDF5/doc/RM/Tools.html#Tools-Copy>`_ command line tool from the HDF5 Group.
See also this `h5copy tutorial <https://support.hdfgroup.org/HDF5/Tutor/cmdtooledit.html#copy>`_.
Use the `h5copy <https://docs.hdfgroup.org/hdf5/v1_14/_view_tools_edit.html>`_ command line tool from the HDF5 Group.


How do I generate new object IDs for a newly exported NWB file?
Expand Down Expand Up @@ -101,8 +99,8 @@ For example:
export_io.export(src_io=read_io, nwbfile=nwbfile, write_args={'link_data': False}) # copy linked datasets
# the written file will contain no links to external datasets

You can also the `h5copy <https://support.hdfgroup.org/HDF5/doc/RM/Tools.html#Tools-Copy>`_ command line tool \
from the HDF5 Group. See also this `h5copy tutorial <https://support.hdfgroup.org/HDF5/Tutor/cmdtooledit.html#copy>`_.
You can also the `h5copy <https://docs.hdfgroup.org/hdf5/v1_14/_view_tools_edit.html>`_ command line tool \
from the HDF5 Group.


How do I write a newly instantiated ``NWBFile`` to two different file paths?
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4 changes: 2 additions & 2 deletions pyproject.toml
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Expand Up @@ -34,8 +34,8 @@ classifiers = [
]
dependencies = [
"h5py>=2.10",
"hdmf>=3.14.0",
"numpy>=1.18, <2.0", # pin below 2.0 until HDMF supports numpy 2.0
"hdmf>=3.14.3",
"numpy>=1.18",
"pandas>=1.1.5",
"python-dateutil>=2.7.3",
]
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2 changes: 1 addition & 1 deletion requirements-min.txt
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@@ -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==3.14.0
hdmf==3.14.3
numpy==1.18
pandas==1.1.5
python-dateutil==2.7.3
4 changes: 2 additions & 2 deletions requirements.txt
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@@ -1,6 +1,6 @@
# pinned dependencies to reproduce an entire development environment to use PyNWB
h5py==3.11.0
hdmf==3.14.0
numpy==1.26.4
hdmf==3.14.3
numpy==2.1.1
pandas==2.2.2
python-dateutil==2.9.0.post0
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