Merge branch 'dev' into dependabot/github_actions/actions/add-to-proj…

…ect-1.0.1

.github/workflows/run_all_tests.yml

@@ -197,7 +197,7 @@ jobs:
         run: |
           tox -e wheelinstall --installpkg dist/*.tar.gz
 
-  run-gallery-ros3-tests:
+  run-ros3-tests:
     name: ${{ matrix.name }}
     runs-on: ${{ matrix.os }}
     defaults:
@@ -210,9 +210,9 @@ jobs:
       fail-fast: false
       matrix:
         include:
-          - { name: linux-gallery-python3.12-ros3   , python-ver: "3.12", os: ubuntu-latest }
-          - { name: windows-gallery-python3.12-ros3 , python-ver: "3.12", os: windows-latest }
-          - { name: macos-gallery-python3.12-ros3   , python-ver: "3.12", os: macos-latest }
+          - { name: linux-python3.12-ros3   , python-ver: "3.12", os: ubuntu-latest }
+          - { name: windows-python3.12-ros3 , python-ver: "3.12", os: windows-latest }
+          - { name: macos-python3.12-ros3   , python-ver: "3.12", os: macos-latest }
     steps:
       - name: Checkout repo with submodules
         uses: actions/checkout@v4

.github/workflows/run_coverage.yml

@@ -70,3 +70,58 @@ jobs:
           file: ./coverage.xml
         env:
           CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+
+  run-ros3-coverage:
+    name: ${{ matrix.name }}
+    runs-on: ${{ matrix.os }}
+    defaults:
+      run:
+        shell: bash -l {0}  # necessary for conda
+    concurrency:
+      group: ${{ github.workflow }}-${{ github.ref }}-${{ matrix.name }}
+      cancel-in-progress: true
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - { name: linux-python3.12-ros3  , python-ver: "3.12", os: ubuntu-latest }
+    steps:
+      - name: Checkout repo with submodules
+        uses: actions/checkout@v4
+        with:
+          submodules: 'recursive'
+          fetch-depth: 0  # tags are required to determine the version
+
+      - name: Set up Conda
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          auto-update-conda: true
+          activate-environment: ros3
+          environment-file: environment-ros3.yml
+          python-version: ${{ matrix.python-ver }}
+          channels: conda-forge
+          auto-activate-base: false
+          mamba-version: "*"
+
+      - name: Install run dependencies
+        run: |
+          pip install .
+          pip list
+
+      - name: Conda reporting
+        run: |
+          conda info
+          conda config --show-sources
+          conda list --show-channel-urls
+
+      - name: Run ros3 tests  # TODO include gallery tests after they are written
+        run: |
+          pytest --cov --cov-report=xml --cov-report=term tests/unit/test_io_hdf5_streaming.py
+
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v4
+        with:
+          fail_ci_if_error: true
+          file: ./coverage.xml
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/run_tests.yml

@@ -209,7 +209,7 @@ jobs:
               --token ${{ secrets.BOT_GITHUB_TOKEN }} \
               --re-upload
 
-  run-gallery-ros3-tests:
+  run-ros3-tests:
     name: ${{ matrix.name }}
     runs-on: ${{ matrix.os }}
     defaults:
@@ -222,7 +222,7 @@ jobs:
       fail-fast: false
       matrix:
         include:
-          - { name: linux-gallery-python3.12-ros3  , python-ver: "3.12", os: ubuntu-latest }
+          - { name: linux-python3.12-ros3  , python-ver: "3.12", os: ubuntu-latest }
     steps:
       - name: Checkout repo with submodules
         uses: actions/checkout@v4

.gitignore

@@ -12,6 +12,8 @@
 /docs/source/hdmf*.rst
 /docs/gallery/*.hdf5
 /docs/gallery/*.sqlite
+/docs/gallery/expanded_example_dynamic_term_set.yaml
+/docs/gallery/schemasheets/nwb_static_enums.yaml
 
 # Auto-generated files after running tutorials
 mylab.*.yaml

.pre-commit-config.yaml

@@ -1,7 +1,7 @@
 # NOTE: run `pre-commit autoupdate` to update hooks to latest version
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v4.6.0
     hooks:
     -   id: check-yaml
     -   id: end-of-file-fixer
@@ -18,7 +18,7 @@ repos:
 #     hooks:
 #     -   id: black
 -   repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.3.3
+    rev: v0.4.4
     hooks:
     -   id: ruff
 # -   repo: https://github.com/econchick/interrogate

CHANGELOG.md

@@ -1,12 +1,26 @@
 # HDMF Changelog
 
-## HDMF 3.14.0 (Upcoming)
+## HDMF 3.14.1 (Upcoming)
+
+### Bug fixes
+- Excluded unnecessary artifacts from sdist and wheel. @rly [#1119](https://github.com/hdmf-dev/hdmf/pull/1119)
+- Fixed issue with resolving attribute specs that have the same name at different levels of a spec hierarchy.
+  @rly [#1122](https://github.com/hdmf-dev/hdmf/pull/1122)
+
+## HDMF 3.14.0 (May 20, 2024)
 
 ### Enhancements
 - Updated `_field_config` to take `type_map` as an argument for APIs. @mavaylon1 [#1094](https://github.com/hdmf-dev/hdmf/pull/1094)
 - Added `TypeConfigurator` to automatically wrap fields with `TermSetWrapper` according to a configuration file. @mavaylon1 [#1016](https://github.com/hdmf-dev/hdmf/pull/1016)
 - Updated `TermSetWrapper` to support validating a single field within a compound array. @mavaylon1 [#1061](https://github.com/hdmf-dev/hdmf/pull/1061)
 - Updated testing to not install in editable mode and not run `coverage` by default. @rly [#1107](https://github.com/hdmf-dev/hdmf/pull/1107)
+- Add `post_init_method` parameter when generating classes to perform post-init functionality, i.e., validation. @mavaylon1 [#1089](https://github.com/hdmf-dev/hdmf/pull/1089)
+- Exposed `aws_region` to `HDF5IO` and downstream passes to `h5py.File`. @codycbakerphd [#1040](https://github.com/hdmf-dev/hdmf/pull/1040)
+- Exposed `progress_bar_class` to the `GenericDataChunkIterator` for more custom control over display of progress while iterating. @codycbakerphd [#1110](https://github.com/hdmf-dev/hdmf/pull/1110)
+- Updated loading, unloading, and getting the `TypeConfigurator` to support a `TypeMap` parameter. @mavaylon1 [#1117](https://github.com/hdmf-dev/hdmf/pull/1117)
+
+### Bug Fixes
+- Fixed `TermSetWrapper` warning raised during the setters. @mavaylon1 [#1116](https://github.com/hdmf-dev/hdmf/pull/1116)
 
 ## HDMF 3.13.0 (March 20, 2024)
 
@@ -541,7 +555,7 @@ the fields (i.e., when the constructor sets some fields to fixed values). @rly
   Each sub-table is itself a DynamicTable that is aligned with the main table by row index. Each subtable
   defines a sub-category in the main table effectively creating a table with sub-headings to organize columns.
   @oruebel (#551)
-- Add tutoral for new `AlignedDynamicTable` type. @oruebel (#571)
+- Add tutorial for new `AlignedDynamicTable` type. @oruebel (#571)
 - Equality check for `DynamicTable` now also checks that the name and description of the table are the same. @rly (#566)
 
 ### Internal improvements