Prepare for release of PyNWB 2.8.0 (#1910)

.readthedocs.yaml

@@ -25,6 +25,7 @@ formats: all
 python:
   install:
     - requirements: requirements-doc.txt
+    - requirements: requirements-opt.txt
     - requirements: requirements.txt
 
 # Optionally include all submodules

CHANGELOG.md

@@ -8,7 +8,7 @@
 - Exposed `aws_region` to `NWBHDF5IO`. @rly [#1903](https://github.com/NeurodataWithoutBorders/pynwb/pull/1903)
 
 ### Bug fixes
-- Revert changes in PyNWB 2.7.0 that allow datetimes without a timezone and without a time while issues with DANDI upload are resolved. @rly [#1908](https://github.com/NeurodataWithoutBorders/pynwb/pull/1908)
+- Revert changes in PyNWB 2.7.0 that allow datetimes without a timezone and without a time while issues with DANDI upload of NWB files missing timezone are resolved. @rly [#1908](https://github.com/NeurodataWithoutBorders/pynwb/pull/1908)
 
 ## PyNWB 2.7.0 (May 2, 2024)
 

docs/gallery/domain/ecephys.py

@@ -16,7 +16,7 @@
 It is recommended to cover :ref:`basics` before this tutorial.
 
 .. note:: It is recommended to check if your source data is supported by
-  `NeuroConv Extracellular Electrophysiology Gallery <https://neuroconv.readthedocs.io/en/main/conversion_examples_gallery/conversion_example_gallery.html#extracellular-electrophysiology>`_.
+  `NeuroConv Extracellular Electrophysiology Gallery <https://neuroconv.readthedocs.io/en/main/conversion_examples_gallery/#extracellular-electrophysiology>`_.
   If it is supported, it is recommended to use NeuroConv to convert your data.
 
 The following examples will reference variables that may not be defined within the block they are used in. For

docs/gallery/domain/ophys.py

@@ -15,7 +15,7 @@
 It is recommended to cover :ref:`basics` before this tutorial.
 
 .. note:: It is recommended to check if your source data is supported by
-  `NeuroConv Optical Physiology Gallery <https://neuroconv.readthedocs.io/en/main/conversion_examples_gallery/conversion_example_gallery.html#optical-physiology>`_.
+  `NeuroConv Optical Physiology Gallery <https://neuroconv.readthedocs.io/en/main/conversion_examples_gallery/#optical-physiology>`_.
   If it is supported, it is recommended to use NeuroConv to convert your data.
 
 The following examples will reference variables that may not be defined within the block they are used in. For

environment-ros3.yml

@@ -9,8 +9,8 @@ dependencies:
   - hdmf==3.14.0
   - matplotlib==3.8.0
   - numpy==1.26.4
-  - pandas==2.2.1
-  - python-dateutil==2.8.2
+  - pandas==2.2.2
+  - python-dateutil==2.9.0
   - setuptools
   - pytest==7.4.3 # This is for the upcoming pytest update
   - dandi==0.60.0  # NOTE: dandi does not support osx-arm64
@@ -19,4 +19,4 @@ dependencies:
   - aiohttp==3.9.3
   - pip
   - pip:
-    - remfile==0.1.9
+    - remfile==0.1.11

requirements-dev.txt

@@ -2,11 +2,11 @@
 # compute coverage, and create test environments. note that depending on the version of python installed, different
 # versions of requirements may be installed due to package incompatibilities.
 #
-black==24.3.0
-codespell==2.2.6
-coverage==7.3.2
-pytest==7.4.3
-isort==5.12.0
-pytest-cov==4.1.0
-tox==4.11.3
-ruff==0.1.3
+black==24.4.2
+codespell==2.3.0
+coverage==7.5.3
+pytest==8.2.1
+isort==5.13.2
+pytest-cov==5.0.0
+tox==4.15.0
+ruff==0.4.6

requirements-doc.txt

@@ -13,3 +13,4 @@ lxml  # used by dataframe_image when using the matplotlib backend
 hdf5plugin
 dandi>=0.46.6
 hdmf-zarr
+zarr<2.18.0  # limited until hdmf-zarr 0.8.0 is released to resolve issues with zarr>=2.18.0

requirements.txt

@@ -2,5 +2,5 @@
 h5py==3.11.0
 hdmf==3.14.0
 numpy==1.26.4
-pandas==2.2.1
+pandas==2.2.2
 python-dateutil==2.9.0.post0