Update requirements and release template

.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/

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 +1,7 @@
 # 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"
 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