Merge pull request #32 from catalystneuro/update_template

Minor update to use latest template

.github/workflows/run_all_tests.yml

@@ -61,19 +61,20 @@ jobs:
         if: ${{ matrix.requirements == 'minimum' }}
         run: |
           python -m pip install -r requirements-min.txt -r requirements-dev.txt
-          python -m pip install -e .
+          python -m pip install .
 
       - name: Install run requirements (pinned)
         if: ${{ matrix.requirements == 'pinned' }}
         run: |
           python -m pip install -r requirements-dev.txt
-          python -m pip install -e .
+          python -m pip install .
 
       - name: Install run requirements (upgraded)
         if: ${{ matrix.requirements == 'upgraded' }}
         run: |
           python -m pip install -r requirements-dev.txt
-          python -m pip install -U -e .
+          # force upgrade of all dependencies to latest versions within allowed range
+          python -m pip install -U --upgrade-strategy eager .
 
       - name: Run tests
         run: |
@@ -146,19 +147,19 @@ jobs:
         if: ${{ matrix.requirements == 'minimum' }}
         run: |
           python -m pip install -r requirements-min.txt -r requirements-dev.txt
-          python -m pip install -e .
+          python -m pip install .
 
       - name: Install run requirements (pinned)
         if: ${{ matrix.requirements == 'pinned' }}
         run: |
           python -m pip install -r requirements-dev.txt
-          python -m pip install -e .
+          python -m pip install .
 
       - name: Install run requirements (upgraded)
         if: ${{ matrix.requirements == 'upgraded' }}
         run: |
           python -m pip install -r requirements-dev.txt
-          python -m pip install -U -e .
+          python -m pip install -U --upgrade-strategy eager .
 
       - name: Run tests
         run: |

.github/workflows/run_coverage.yml

@@ -40,14 +40,12 @@ jobs:
 
       - name: Install package
         run: |
-          python -m pip install -e .  # must install in editable mode for coverage to find sources
+          python -m pip install .
           python -m pip list
 
       - name: Run tests and generate coverage report
         run: |
-          pytest --cov
-          python -m coverage xml  # codecov uploader requires xml format
-          python -m coverage report -m
+          pytest --cov --cov-report=xml --cov-report=term # codecov uploader requires xml format
 
       # TODO uncomment after setting up repo on codecov.io
       # - name: Upload coverage to Codecov

.github/workflows/validate_schema.yml

@@ -0,0 +1,25 @@
+name: Validate schema
+
+on:
+  push:
+  pull_request:
+  workflow_dispatch:
+
+jobs:
+  validate:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python 3.12
+      uses: actions/setup-python@v4
+      with:
+        python-version: "3.12"
+    - name: Install HDMF
+      run: |
+        pip install hdmf
+    - name: Download latest nwb schema language specification
+      run: |
+        curl -L https://raw.githubusercontent.com/NeurodataWithoutBorders/nwb-schema/dev/nwb.schema.json -o nwb.schema.json
+    - name: Validate schema specification
+      run: |
+        validate_hdmf_spec spec -m nwb.schema.json

pyproject.toml

@@ -43,44 +43,42 @@ dependencies = [
 # "Discussions" = "https://github.com/organization/package/discussions"
 # "Changelog" = "https://github.com/organization/package/blob/main/CHANGELOG.md"
 
-[tool.hatch.build]
-include = [
-    "src/pynwb",
-    "spec/ndx-fiber-photometry.extensions.yaml",
-    "spec/ndx-fiber-photometry.namespace.yaml",
-]
-exclude = [
-    "src/pynwb/tests",
-]
-
+# Include only the source code under `src/pynwb/ndx_fiber_photometry` and the spec files under `spec`
+# in the wheel.
 [tool.hatch.build.targets.wheel]
 packages = [
     "src/pynwb/ndx_fiber_photometry",
     "spec"
 ]
 
+# Rewrite the path to the `spec` directory to `{{ cookiecutter.py_pkg_name }}/spec`.
+# `{{ cookiecutter.py_pkg_name }}/__init__.py` will look there first for the spec files.
+# The resulting directory structure within the wheel will be:
+# {{ cookiecutter.py_pkg_name }}/
+# ├── __init__.py
+# ├── spec
+# └── widgets
 [tool.hatch.build.targets.wheel.sources]
 "spec" = "ndx_fiber_photometry/spec"
 
+# The source distribution includes everything in the package except for the `src/matnwb` directory and
+# git and github-related files.
 [tool.hatch.build.targets.sdist]
-include = [
-    "src/pynwb",
-    "spec/ndx-fiber-photometry.extensions.yaml",
-    "spec/ndx-fiber-photometry.namespace.yaml",
-    "docs",
+exclude = [
+    ".git*",
+    "src/matnwb",
 ]
-exclude = []
 
 [tool.pytest.ini_options]
-# uncomment below to run pytest with code coverage reporting. NOTE: breakpoints may not work
+# uncomment below to run pytest always with code coverage reporting. NOTE: breakpoints may not work
 # addopts = "--cov --cov-report html"
 
 [tool.codespell]
 skip = "htmlcov,.git,.mypy_cache,.pytest_cache,.coverage,*.pdf,*.svg,venvs,.tox,hdmf-common-schema,./docs/_build/*,*.ipynb"
 
 [tool.coverage.run]
 branch = true
-source = ["src/pynwb"]
+source = ["ndx_fiber_photometry"]
 
 [tool.coverage.report]
 exclude_lines = [
@@ -94,7 +92,7 @@ preview = true
 exclude = ".git|.mypy_cache|.tox|.venv|venv|.ipynb_checkpoints|_build/|dist/|__pypackages__|.ipynb|docs/"
 
 [tool.ruff]
-select = ["E", "F", "T100", "T201", "T203"]
+lint.select = ["E", "F", "T100", "T201", "T203"]
 exclude = [
   ".git",
   ".tox",
@@ -105,9 +103,9 @@ exclude = [
 ]
 line-length = 120
 
-[tool.ruff.per-file-ignores]
+[tool.ruff.lint.per-file-ignores]
 "src/pynwb/ndx_fiber_photometry/__init__.py" = ["E402", "F401"]
 "src/spec/create_extension_spec.py" = ["T201"]
 
-[tool.ruff.mccabe]
+[tool.ruff.lint.mccabe]
 max-complexity = 17

requirements-dev.txt

@@ -5,7 +5,7 @@ codespell==2.2.6
 coverage==7.4.4
 hdmf==3.14.2
 hdmf-docutils==0.4.7
-nwbwidgets==0.11.3
+# nwbwidgets==0.11.3
 pre-commit==3.5.0
 pynwb==2.8.1
 pytest==8.1.1

src/pynwb/ndx_fiber_photometry/__init__.py

@@ -31,15 +31,9 @@
 EdgeOpticalFilter = get_class("EdgeOpticalFilter", "ndx-fiber-photometry")
 FiberPhotometry = get_class("FiberPhotometry", "ndx-fiber-photometry")
 from .fiber_photometry import FiberPhotometryTable
+
 FiberPhotometryResponseSeries = get_class("FiberPhotometryResponseSeries", "ndx-fiber-photometry")
 CommandedVoltageSeries = get_class("CommandedVoltageSeries", "ndx-fiber-photometry")
 
-
-# NOTE: `widgets/tetrode_series_widget.py` adds a "widget"
-# attribute to the TetrodeSeries class. This attribute is used by NWBWidgets.
-# Delete the `widgets` subpackage or the `tetrode_series_widget.py` module
-# if you do not want to define a custom widget for your extension neurodata
-# type.
-
 # Remove these functions from the package
 del load_namespaces, get_class

src/pynwb/ndx_fiber_photometry/fiber_photometry.py

@@ -3,13 +3,15 @@
 
 FiberPhotometryTable = get_class("FiberPhotometryTable", "ndx-fiber-photometry")
 
+
 @docval(
-    {'name': 'region', 'type': list, 'doc': 'the indices of the FiberPhotometryTable'},
-    {'name': 'description', 'type': str, 'doc': 'a brief description of what these table entries represent'},
+    {"name": "region", "type": list, "doc": "the indices of the FiberPhotometryTable"},
+    {"name": "description", "type": str, "doc": "a brief description of what these table entries represent"},
 )
 def create_fiber_photometry_table_region(self, **kwargs):
-    region, description = popargs('region', 'description', kwargs)
-    name = 'fiber_photometry_table_region'
+    region, description = popargs("region", "description", kwargs)
+    name = "fiber_photometry_table_region"
     return super(FiberPhotometryTable, self).create_region(name=name, region=region, description=description)
 
-FiberPhotometryTable.create_fiber_photometry_table_region = create_fiber_photometry_table_region
+
+FiberPhotometryTable.create_fiber_photometry_table_region = create_fiber_photometry_table_region