Prepare 6.1.0 release (#1516)

Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

Author: rly

.github/workflows/check_sphinx_links.yml

@@ -25,7 +25,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@ece7cb06caefa5fff74198d8649806c4678c61a1  # v6.3.0
         with:
-          python-version: '3.13'  # TODO: Update to 3.14 when linkml and its deps support 3.14
+          python-version: '3.14'
 
       - name: Install Sphinx dependencies and package
         run: |

.github/workflows/run_all_tests.yml

@@ -98,14 +98,15 @@ jobs:
       fail-fast: false
       matrix:
         include:
-          # TODO: Update to 3.14 when linkml and its deps support 3.14
           - { name: linux-gallery-python3.10-minimum               , test-tox-env: gallery-py310-minimum             , python-ver: "3.10", os: ubuntu-latest }
-          - { name: linux-gallery-python3.13-upgraded-optional     , test-tox-env: gallery-py313-upgraded-optional   , python-ver: "3.13", os: ubuntu-latest }
-          - { name: linux-gallery-python3.13-prerelease-optional   , test-tox-env: gallery-py313-prerelease-optional , python-ver: "3.13", os: ubuntu-latest }
+          - { name: linux-gallery-python3.14-upgraded-optional     , test-tox-env: gallery-py314-upgraded-optional   , python-ver: "3.14", os: ubuntu-latest }
+          - { name: linux-gallery-python3.14-prerelease-optional   , test-tox-env: gallery-py314-prerelease-optional , python-ver: "3.14", os: ubuntu-latest }
           - { name: windows-gallery-python3.10-minimum             , test-tox-env: gallery-py310-minimum             , python-ver: "3.10", os: windows-latest }
-          - { name: windows-gallery-python3.13-upgraded-optional   , test-tox-env: gallery-py313-upgraded-optional   , python-ver: "3.13", os: windows-latest }
-          - { name: windows-gallery-python3.13-prerelease-optional , test-tox-env: gallery-py313-prerelease-optional , python-ver: "3.13", os: windows-latest }
+          - { name: windows-gallery-python3.14-upgraded-optional   , test-tox-env: gallery-py314-upgraded-optional   , python-ver: "3.14", os: windows-latest }
+          - { name: windows-gallery-python3.14-prerelease-optional , test-tox-env: gallery-py314-prerelease-optional , python-ver: "3.14", os: windows-latest }
           - { name: macos-gallery-python3.10-minimum               , test-tox-env: gallery-py310-minimum             , python-ver: "3.10", os: macos-15-intel }
+          # numcodecs==0.15.1 (pulled in by the zarr optional extra) has no Python 3.14 wheel and cannot be
+          # built on macos-latest, so the optional gallery tests stay on 3.13 there. See https://github.com/hdmf-dev/hdmf/pull/1367
           - { name: macos-gallery-python3.13-upgraded-optional     , test-tox-env: gallery-py313-upgraded-optional   , python-ver: "3.13", os: macos-latest }
           - { name: macos-gallery-python3.13-prerelease-optional   , test-tox-env: gallery-py313-prerelease-optional , python-ver: "3.13", os: macos-latest }
     steps:

.github/workflows/run_coverage.yml

@@ -34,7 +34,7 @@ jobs:
           - { os: macos-latest  , opt_req: false }
     env:  # used by codecov-action
       OS: ${{ matrix.os }}
-      PYTHON: '3.13'  # TODO: Update to 3.14 when linkml and its deps support 3.14
+      PYTHON: '3.14'
     steps:
       - name: Checkout repo with submodules
         uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0  # v7.0.0

.github/workflows/run_tests.yml

@@ -86,11 +86,10 @@ jobs:
       fail-fast: false
       matrix:
         include:
-          # TODO: Update to 3.14 when linkml and its deps support 3.14
           - { name: linux-gallery-python3.10-minimum             , test-tox-env: gallery-py310-minimum           , python-ver: "3.10", os: ubuntu-latest }
-          - { name: linux-gallery-python3.13-upgraded-optional   , test-tox-env: gallery-py313-upgraded-optional , python-ver: "3.13", os: ubuntu-latest }
+          - { name: linux-gallery-python3.14-upgraded-optional   , test-tox-env: gallery-py314-upgraded-optional , python-ver: "3.14", os: ubuntu-latest }
           - { name: windows-gallery-python3.10-minimum           , test-tox-env: gallery-py310-minimum           , python-ver: "3.10", os: windows-latest }
-          - { name: windows-gallery-python3.13-upgraded-optional , test-tox-env: gallery-py313-upgraded-optional , python-ver: "3.13", os: windows-latest }
+          - { name: windows-gallery-python3.14-upgraded-optional , test-tox-env: gallery-py314-upgraded-optional , python-ver: "3.14", os: windows-latest }
     steps:
       - name: Checkout repo with submodules
         uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0  # v7.0.0

.readthedocs.yaml

@@ -8,7 +8,7 @@ version: 2
 build:
   os: ubuntu-24.04
   tools:
-    python: '3.13'  # TODO: Update to 3.14 when linkml and its deps support 3.14
+    python: '3.14'
   jobs:
     install:
       - python -m pip install --upgrade pip

CHANGELOG.md

@@ -1,20 +1,20 @@
 # HDMF Changelog
 
-## HDMF 6.0.3 (Upcoming)
-
-### Breaking changes
-- Removed the `file` argument from `HERD.add_ref` and `HERD.add_ref_termset`. The file is now always resolved automatically from the container's parent hierarchy, so a reference can only be added to a container that has already been added to a file. This enforces that an external reference cannot be attached to a container that is not yet in a file. Callers passing `file=...` to these methods should remove that argument and ensure the container has been added to its file first. @bendichter
+## HDMF 6.1.0 (June 25, 2026)
 
 ### Enhancements
-- Accept pandas `Series` and `ExtensionArray` (including `StringArray` and `ArrowStringArray`) as `data` in `Data` and its subclasses (e.g., `VectorData`), normalizing to numpy at construction. This restores compatibility with pandas 3.0, where DataFrame string columns are PyArrow-backed by default and previously failed HDMF's type validation. Inputs containing missing values (`pd.NA`/`NaN`) raise an informative `TypeError` rather than silently failing at HDF5 write time. The `pandas<3` cap has been lifted from the dependency pin. @rly [#1384](https://github.com/hdmf-dev/hdmf/issues/1384)
+- Accept pandas `Series` and `ExtensionArray` (including `StringArray` and `ArrowStringArray`) as `data` in `Data` and its subclasses (e.g., `VectorData`), normalizing to numpy at construction. This restores compatibility with pandas 3.0, where DataFrame string columns are PyArrow-backed by default and previously failed HDMF's type validation. Inputs containing missing values (`pd.NA`/`NaN`) raise an informative `TypeError` rather than silently failing at HDF5 write time. The `pandas<3` cap has been lifted from the dependency pin. @rly [#1469](https://github.com/hdmf-dev/hdmf/pull/1469)
 - Added a `HERD`-specific `__repr__` and `_repr_html_` that surface the references as a flattened table, so a `HERD` (especially one read back from a file) no longer appears empty in its default display. @rly [#1510](https://github.com/hdmf-dev/hdmf/pull/1510)
 - `HERD.add_ref` now defaults `key` to the value of a scalar string `attribute` when `key` is not provided, removing the redundant argument in the common case. @rly [#1511](https://github.com/hdmf-dev/hdmf/pull/1511)
 - `HERD.add_ref` no longer warns when an `entity_uri` is provided for an already-existing `entity_id` and the URI matches the stored one. The entity tables are normalized, so re-passing the same `entity_uri` (common when annotating many objects or files with the same entity) is harmless; a warning is now emitted only when a *different* `entity_uri` is provided, in which case the existing URI is kept. @bendichter [#1513](https://github.com/hdmf-dev/hdmf/pull/1513)
 
 ### Changed
+- Removed the `file` argument from `HERD.add_ref` and `HERD.add_ref_termset`. The file is now always resolved automatically from the container's parent hierarchy, so a reference can only be added to a container that has already been added to a file. This enforces that an external reference cannot be attached to a container that is not yet in a file. This is technically a breaking change, but the `file` argument was not yet used publicly. @bendichter [#1512](https://github.com/hdmf-dev/hdmf/pull/1512)
 - Refactored `HERD` internals. The object lookup now identifies an object by its file together with its object_id, relative_path, and field, so a shared object_id across files (e.g. a copied, modified file) resolves to the correct object instead of colliding. @rly [#1515](https://github.com/hdmf-dev/hdmf/pull/1515)
 
 ### Internal improvements
+- Minor `HERD` internal cleanups: removed a dead assignment and hoisted the files dataframe construction. @rly [#1507](https://github.com/hdmf-dev/hdmf/pull/1507)
+- Switched the release pipeline to PyPI OIDC trusted publishing and the `gh` CLI, and now build the GitHub release notes from the changelog. @rly [#1517](https://github.com/hdmf-dev/hdmf/pull/1517)
 - Hardened the GitHub Actions CI: added least-privilege `permissions` blocks, pinned actions to commit SHAs (or immutable release tags), deduplicated the test setup into a composite action, passed untrusted inputs through environment variables, and added a zizmor security audit of the workflows. @rly [#1518](https://github.com/hdmf-dev/hdmf/pull/1518)
 
 ### Fixed

tox.ini

@@ -52,9 +52,9 @@ commands =
 [testenv:pytest-py{313,314}-prerelease-optional]
 
 # minimum envs use uv with --resolution lowest-direct to install the lowest
-# compatible versions of direct dependencies. These are defined explicitly
-# (rather than using factor matching in [testenv]) because gallery-minimum
-# needs to resolve docs deps together with project deps to avoid incompatibilities.
+# compatible versions of the project's direct dependencies. These are defined
+# explicitly (rather than using factor matching in [testenv]) because gallery-minimum
+# installs the docs group as well and needs to control how those deps are resolved.
 [testenv:pytest-py310-minimum]
 skip_install = True
 dependency_groups = test
@@ -67,9 +67,15 @@ skip_install = True
 dependency_groups = test
 commands_pre =
     python -m pip install uv
-    python -m uv pip install --resolution lowest-direct --group docs -e .
+    # install the documentation dependencies at their latest compatible versions
+    python -m uv pip install --group docs -e .
+    # then resolve the project's own (direct) dependencies down to their minimum supported versions
+    python -m uv pip install --resolution lowest-direct -e .
 
-# TODO: Update to 3.14 when linkml and its deps support 3.14
+[testenv:gallery-py314-upgraded-optional]
+[testenv:gallery-py314-prerelease-optional]
+# py313 optional gallery envs are used on macos-latest, where numcodecs 0.15.1
+# (pulled in by the zarr extra) has no 3.14 wheel and cannot be built.
 [testenv:gallery-py313-upgraded-optional]
 [testenv:gallery-py313-prerelease-optional]