From ebc887f74a4ad92c6ab635ee3fcf252045ea82af Mon Sep 17 00:00:00 2001 From: Matthew Avaylon Date: Wed, 4 Sep 2024 10:51:15 -0700 Subject: [PATCH 01/12] Update pyproject.toml --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index befa3bb0f..29229f474 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -35,7 +35,7 @@ classifiers = [ dependencies = [ "h5py>=2.10", "hdmf>=3.14.0", - "numpy>=1.18, <2.0", # pin below 2.0 until HDMF supports numpy 2.0 + "numpy>=1.18", "pandas>=1.1.5", "python-dateutil>=2.7.3", ] From 04096d95482cb3f8d2853d535c48b03de2b6eab7 Mon Sep 17 00:00:00 2001 From: Matthew Avaylon Date: Wed, 4 Sep 2024 10:52:40 -0700 Subject: [PATCH 02/12] Update requirements-min.txt --- requirements-min.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements-min.txt b/requirements-min.txt index a047d81c7..b06c76c55 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==3.14.0 -numpy==1.18 +numpy==2.1.1 pandas==1.1.5 python-dateutil==2.7.3 From c0b481b274bf84d66db3878603f453457e8520fc Mon Sep 17 00:00:00 2001 From: Matthew Avaylon Date: Wed, 4 Sep 2024 10:52:57 -0700 Subject: [PATCH 03/12] Update requirements.txt --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 5b3c49ded..0bb87a875 100644 --- a/requirements.txt +++ b/requirements.txt @@ -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 +numpy==2.1.1 pandas==2.2.2 python-dateutil==2.9.0.post0 From 480dcf375501d6f57ead0ea73b962654354845c8 Mon Sep 17 00:00:00 2001 From: Matthew Avaylon Date: Wed, 4 Sep 2024 10:53:28 -0700 Subject: [PATCH 04/12] Update requirements-min.txt --- requirements-min.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements-min.txt b/requirements-min.txt index b06c76c55..a047d81c7 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==3.14.0 -numpy==2.1.1 +numpy==1.18 pandas==1.1.5 python-dateutil==2.7.3 From 44ceef059e66f367121059ae7d0b1331efab8152 Mon Sep 17 00:00:00 2001 From: Matthew Avaylon Date: Wed, 4 Sep 2024 10:56:11 -0700 Subject: [PATCH 05/12] Update requirements-min.txt --- requirements-min.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements-min.txt b/requirements-min.txt index a047d81c7..eef051b25 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==3.14.0 +hdmf==3.14.3 numpy==1.18 pandas==1.1.5 python-dateutil==2.7.3 From e27024a0fb570de1f5f428e9780161fbc4f15e75 Mon Sep 17 00:00:00 2001 From: Matthew Avaylon Date: Wed, 4 Sep 2024 10:56:28 -0700 Subject: [PATCH 06/12] Update requirements.txt --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 0bb87a875..27716cf5a 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,6 +1,6 @@ # pinned dependencies to reproduce an entire development environment to use PyNWB h5py==3.11.0 -hdmf==3.14.0 +hdmf==3.14.3 numpy==2.1.1 pandas==2.2.2 python-dateutil==2.9.0.post0 From 0d10e6dd5f76eddcec450f4b599ea9ac9cda7f6d Mon Sep 17 00:00:00 2001 From: Matthew Avaylon Date: Wed, 4 Sep 2024 10:56:47 -0700 Subject: [PATCH 07/12] Update pyproject.toml --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 29229f474..3ab85a4ae 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -34,7 +34,7 @@ classifiers = [ ] dependencies = [ "h5py>=2.10", - "hdmf>=3.14.0", + "hdmf>=3.14.3", "numpy>=1.18", "pandas>=1.1.5", "python-dateutil>=2.7.3", From 81accd3efcbf62d4227d338f0078ccf85d445edb Mon Sep 17 00:00:00 2001 From: Matthew Avaylon Date: Wed, 4 Sep 2024 11:13:36 -0700 Subject: [PATCH 08/12] Update export.rst --- docs/source/export.rst | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/docs/source/export.rst b/docs/source/export.rst index 490cd346e..35b893314 100644 --- a/docs/source/export.rst +++ b/docs/source/export.rst @@ -60,7 +60,6 @@ See also this `h5repack tutorial `_ command line tool from the HDF5 Group. -See also this `h5copy tutorial `_. How do I generate new object IDs for a newly exported NWB file? @@ -102,7 +101,7 @@ For example: # the written file will contain no links to external datasets You can also the `h5copy `_ command line tool \ -from the HDF5 Group. See also this `h5copy tutorial `_. +from the HDF5 Group. How do I write a newly instantiated ``NWBFile`` to two different file paths? From 5730fcba76903ff7d28ab91b8aaef735cfa8a247 Mon Sep 17 00:00:00 2001 From: Matthew Avaylon Date: Wed, 4 Sep 2024 11:18:41 -0700 Subject: [PATCH 09/12] Update export.rst --- docs/source/export.rst | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/docs/source/export.rst b/docs/source/export.rst index 35b893314..c83e870c1 100644 --- a/docs/source/export.rst +++ b/docs/source/export.rst @@ -53,13 +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 `_ command line tool from the HDF5 Group. -See also this `h5repack tutorial `_. +Use the h5repack `_ 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 `_ command line tool from the HDF5 Group. +Use the `h5copy `_ command line tool from the HDF5 Group. How do I generate new object IDs for a newly exported NWB file? From 205f43417c34312af1ba4f324f28691beca06a77 Mon Sep 17 00:00:00 2001 From: Matthew Avaylon Date: Wed, 4 Sep 2024 11:21:32 -0700 Subject: [PATCH 10/12] Update export.rst --- docs/source/export.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source/export.rst b/docs/source/export.rst index c83e870c1..fcd80a312 100644 --- a/docs/source/export.rst +++ b/docs/source/export.rst @@ -99,7 +99,7 @@ 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 `_ command line tool \ +You can also the `h5copy `_ command line tool \ from the HDF5 Group. From f468abd8ffaff78b22f704ffcf3ab48a0c6419f8 Mon Sep 17 00:00:00 2001 From: Matthew Avaylon Date: Wed, 4 Sep 2024 11:26:29 -0700 Subject: [PATCH 11/12] Update CHANGELOG.md --- CHANGELOG.md | 3 +++ 1 file changed, 3 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 82370cff4..5350d081f 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -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) From 4ee549ca8fe83afda0cf4a1a22305d7358eae8b2 Mon Sep 17 00:00:00 2001 From: Steph Prince <40640337+stephprince@users.noreply.github.com> Date: Wed, 4 Sep 2024 13:47:31 -0700 Subject: [PATCH 12/12] Update docs/source/export.rst --- docs/source/export.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source/export.rst b/docs/source/export.rst index fcd80a312..218184f9b 100644 --- a/docs/source/export.rst +++ b/docs/source/export.rst @@ -53,7 +53,7 @@ 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 `_ command line tool from the HDF5 Group. +Use the `h5repack `_ 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?