prepare release 2.8.1 (#1927)

* Update CHANGELOG.md * Update pyproject.toml * update readme and requirements-doc.txt * fix yaml file path for configurator tutorial * update path to yaml in configuration tutorial * update path to yaml in configuration tutorial * update working dir for gallery tests * update channel number to stop transpose warning * update yaml file path in configuration tutorial * fix text section in configuration tutorial
NeurodataWithoutBorders · Jul 3, 2024 · d3ac4b9 · d3ac4b9
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,6 +1,6 @@
 # PyNWB Changelog
 
-## PyNWB 2.8.1 (Upcoming)
+## PyNWB 2.8.1 (July 3, 2024)
 
 ### Documentation and tutorial enhancements
 - Simplified the introduction to NWB tutorial. @rly [#1914](https://github.com/NeurodataWithoutBorders/pynwb/pull/1914)

diff --git a/README.rst b/README.rst
@@ -49,10 +49,10 @@ Overall Health
      :target: https://github.com/neurodatawithoutborders/pynwb/blob/dev/license.txt
      :alt: PyPI - License
 
-**Conda**
+**Conda Feedstock**
 
-.. image:: https://circleci.com/gh/conda-forge/pynwb-feedstock.svg?style=shield
-     :target: https://circleci.com/gh/conda-forge/pynwb-feedstock
+.. image:: https://dev.azure.com/conda-forge/feedstock-builds/_apis/build/status/pynwb-feedstock?branchName=main
+     :target: https://dev.azure.com/conda-forge/feedstock-builds/_build/latest?definitionId=5703&branchName=main
      :alt: Conda Feedstock Status
 
 NWB Format API

diff --git a/docs/gallery/general/plot_configurator.py b/docs/gallery/general/plot_configurator.py
@@ -55,6 +55,7 @@
 from pynwb import NWBFile, get_loaded_type_config, load_type_config, unload_type_config
 from pynwb.file import Subject
 
+####################################
 # How to use a Configuration file
 # -------------------------------
 # As mentioned prior, the first step after creating a configuration file is
@@ -69,7 +70,10 @@
 # the value of the fields are wrapped and then validated to see if it is a
 # permissible value in their respective :py:class:`~hdmf.term_set.TermSet`.
 
-dir_path = os.path.dirname(os.path.abspath("__file__"))
+try:
+    dir_path = os.path.dirname(os.path.abspath(__file__))  # when running as a .py
+except NameError:
+    dir_path = os.path.dirname(os.path.abspath("__file__"))  # when running as a script or notebook
 yaml_file = os.path.join(dir_path, 'nwb_gallery_config.yaml')
 load_type_config(config_path=yaml_file)
 

diff --git a/pyproject.toml b/pyproject.toml
@@ -9,7 +9,8 @@ authors = [
   { name="Ryan Ly", email="rly@lbl.gov" },
   { name="Oliver Ruebel", email="oruebel@lbl.gov" },
   { name="Ben Dichter", email="ben.dichter@gmail.com" },
-  { name="Matthew Avaylon", email="mavaylon@lbl.gov" }
+  { name="Matthew Avaylon", email="mavaylon@lbl.gov" },
+  { name="Stephanie Prince", email="smprince@lbl.gov" },
 ]
 description= "Package for working with Neurodata stored in the NWB format."
 readme = "README.rst"

diff --git a/requirements-doc.txt b/requirements-doc.txt
@@ -13,4 +13,7 @@ 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
+zarr<3  # limited to zarr<3 until hdmf-zarr resolves issues with zarr 3.0
+linkml-runtime==1.7.4; python_version >= "3.9"
+schemasheets==0.2.1; python_version >= "3.9"
+oaklib==0.5.32; python_version >= "3.9"
diff --git a/tests/unit/test_ecephys.py b/tests/unit/test_ecephys.py
@@ -118,7 +118,7 @@ def test_dimensions_warning(self):
 
     def test_get_data_in_units(self):
         samples = 100
-        channels = 2
+        channels = 5
         conversion = 10.0
         offset = 3.0
         channel_conversion = np.random.rand(channels)