Fix release workflow and prepare 3.10.0 release

.github/PULL_REQUEST_TEMPLATE/release.md

@@ -2,18 +2,19 @@ Prepare for release of HDMF [version]
 
 ### Before merging:
 - [ ] Major and minor releases: Update package versions in `requirements.txt`, `requirements-dev.txt`,
-  `requirements-doc.txt`, `requirements-min.txt`, `requirements-opt.txt`, `environment-ros3.yml`, and `setup.py` as needed
+  `requirements-doc.txt`, `requirements-opt.txt`, and `environment-ros3.yml` to the latest versions,
+  and update dependency ranges in `pyproject.toml` and minimums in `requirements-min.txt` as needed
 - [ ] Check legal file dates and information in `Legal.txt`, `license.txt`, `README.rst`, `docs/source/conf.py`,
   and any other locations as needed
-- [ ] Update `setup.py` as needed
+- [ ] Update `pyproject.toml` as needed
 - [ ] Update `README.rst` as needed
 - [ ] Update `src/hdmf/common/hdmf-common-schema` submodule as needed. Check the version number and commit SHA manually
 - [ ] Update changelog (set release date) in `CHANGELOG.md` and any other docs as needed
 - [ ] Run tests locally including gallery tests, and inspect all warnings and outputs
   (`pytest && python test_gallery.py`)
 - [ ] Run PyNWB tests locally including gallery and validation tests, and inspect all warnings and outputs
   (`cd pynwb; python test.py -v > out.txt 2>&1`)
-- [ ] Test docs locally by going into the `docs` directory and running the following: `make clean && make html`
+- [ ] Test docs locally and inspect all warnings and outputs `cd docs; make clean && make html`
 - [ ] Push changes to this PR and make sure all PRs to be included in this release have been merged
 - [ ] Check that the readthedocs build for this PR succeeds (build latest to pull the new branch, then activate and
   build docs for new branch): https://readthedocs.org/projects/hdmf/builds/

CHANGELOG.md

@@ -1,5 +1,13 @@
 # HDMF Changelog
 
+## HDMF 3.10.0 (October 3, 2023)
+
+Since version 3.9.1 should have been released as 3.10.0 but failed to release on PyPI and conda-forge, this release
+will increase the minor version number to 3.10.0. See the 3.9.1 release notes below for new features.
+
+### Bug fixes
+- Fixed issue with testing and deployment of releases. @rly [#957](https://github.com/hdmf-dev/hdmf/pull/957)
+
 ## HDMF 3.9.1 (September 29, 2023)
 
 ### Enhancements
@@ -20,7 +28,7 @@
 - Updated `add_ref_termset` to add all instances of `TermSet` within a given root container. @mavaylon1 [#935](https://github.com/hdmf-dev/hdmf/pull/935)
 - Added Dynamic Enumerations and Schemasheets support to `TermSet`. @mavaylon1 [#923](https://github.com/hdmf-dev/hdmf/pull/923)
 - Updated `HERD` to support user defined file name for the `HERD` zip file. @mavaylon1 [#941](https://github.com/hdmf-dev/hdmf/pull/941)
-- Added method `Containter.set_data_io`, which wraps an existing data field in a `DataIO`. @bendichter [#938](https://github.com/hdmf-dev/hdmf/pull/938)
+- Added method `Container.set_data_io`, which wraps an existing data field in a `DataIO`. @bendichter [#938](https://github.com/hdmf-dev/hdmf/pull/938)
 
 ## HDMF 3.8.1 (July 25, 2023)
 

docs/CONTRIBUTING.rst

@@ -90,7 +90,7 @@ Style Guides
 Python Code Style Guide
 ^^^^^^^^^^^^^^^^^^^^^^^
 
-Before you create a Pull Request, make sure you are following the PEP8_ style guide. .
+Before you create a Pull Request, make sure you are following the HDMF style guide.
 To check whether your code conforms to the HDMF style guide, simply run the ruff_ tool in the project's root
 directory. ``ruff`` will also sort imports automatically and check against additional code style rules.
 

environment-ros3.yml

@@ -5,11 +5,11 @@ channels:
   - defaults
 dependencies:
   - python==3.11
-  - h5py==3.8.0
-  - matplotlib==3.7.1
-  - numpy==1.24.3
-  - pandas==2.0.1
+  - h5py==3.9.0
+  - matplotlib==3.8.0
+  - numpy==1.26.0
+  - pandas==2.1.1
   - python-dateutil==2.8.2
-  - pytest==7.3.1
-  - pytest-cov==4.0.0
+  - pytest==7.4.2
+  - pytest-cov==4.1.0
   - setuptools

requirements-dev.txt

@@ -2,12 +2,12 @@
 # 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==23.3.0
-codespell==2.2.4
-coverage==7.2.5
-pre-commit==3.3.1
-pytest==7.3.1
-pytest-cov==4.0.0
+black==23.9.1
+codespell==2.2.6
+coverage==7.3.2
+pre-commit==3.4.0
+pytest==7.4.2
+pytest-cov==4.1.0
 python-dateutil==2.8.2
-ruff==0.0.265
-tox==4.5.1
+ruff==0.0.292
+tox==4.11.3

requirements-opt.txt

@@ -1,7 +1,8 @@
 # pinned dependencies that are optional. used to reproduce an entire development environment to use HDMF
-tqdm==4.65.0
-zarr==2.14.2
-linkml-runtime==1.5.5; python_version >= "3.9"
-schemasheets==0.1.23; python_version >= "3.9"
-oaklib==0.5.12; python_version >= "3.9"
+tqdm==4.66.1
+zarr==2.16.1
+linkml-runtime==1.6.0; python_version >= "3.9"
+schemasheets==0.1.24; python_version >= "3.9"
+oaklib==0.5.20; python_version >= "3.9"
+pydantic==1.10.13  # linkml-runtime 1.6.0 and related packages require pydantic<2
 pyyaml==6.0.1; python_version >= "3.9"

requirements.txt

@@ -1,8 +1,8 @@
 # pinned dependencies to reproduce an entire development environment to use HDMF
 h5py==3.9.0
 importlib-resources==6.0.0; python_version < "3.9"  # TODO: remove when minimum python version is 3.9
-jsonschema==4.18.4
-numpy==1.25.1
-pandas==2.0.3
-ruamel.yaml==0.17.32
-scipy==1.11.1
+jsonschema==4.19.1
+numpy==1.26.0
+pandas==2.1.1
+ruamel.yaml==0.17.33
+scipy==1.11.3

test_gallery.py

@@ -33,6 +33,8 @@ def _import_from_file(script):
     "and is not guaranteed to maintain backward compatibility"
 )
 
+pydantic_warning_re = ("Support for class-based `config` is deprecated, use ConfigDict instead.")
+
 
 def run_gallery_tests():
     global TOTAL, FAILURES, ERRORS
@@ -70,6 +72,13 @@ def run_gallery_tests():
                     message=_numpy_warning_re,
                     category=RuntimeWarning,
                 )
+                warnings.filterwarnings(
+                    # this warning is triggered when some linkml dependency like curies uses pydantic in a way that
+                    # will be deprecated in the future
+                    "ignore",
+                    message=pydantic_warning_re,
+                    category=DeprecationWarning,
+                )
                 _import_from_file(script)
         except (ImportError, ValueError) as e:
             if "linkml" in str(e) and sys.version_info < (3, 9):