Add type hints and tests to analysis package

.github/workflows/python-tests.yml

@@ -0,0 +1,33 @@
+# This workflow will install Python dependencies, run tests and lint with a single version of Python
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
+
+name: Python Tests
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    branches: [ "main" ]
+
+permissions:
+  contents: read
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Install uv
+      uses: astral-sh/setup-uv@v5
+      with:
+        enable-cache: true
+        cache-dependency-glob: "uv.lock"
+    - name: Set up Python
+      run: uv python install
+    - name: Install the project
+      run: uv sync --extra dev
+    - name: Run tests  
+      run: uv run pytest tests
+

.gitignore

@@ -14,4 +14,5 @@ dist
 Notebooks
 notebooks
 
+.vscode
 .spyproject

CHANGELOG.md

@@ -1,5 +1,21 @@
 # `open-ephys-python-tools` Changelog
 
+## Unreleased
+
+- Dropped support for Python < 3.9
+- Refactoring without new functionality or API changes
+  - The `Continuous` and `Spike` classes of the three formats now have an explicit interface
+    (i.e. abstract parent class) and have been renamed to `BinaryContinuous`, `BinarySpike` etc.
+  - The metadata of `Continuous` and `Spike` in the analysis package now are typed dataclasses
+    instead of `dict` objects . This makes accessing metadata more reliable.
+  - Type hints have been added to the `analysis` package.
+  - Automated tests for reading Binary, NWB and OpenEphys data formats have been added.
+  - Added a `RecordingFormat` enum for the three formats
+  - Added a JSON schema for validating oebin files
+  - Added a `uv.lock` file for reproducible development environments.
+- `BinaryContinuous` and `BinarySpike` now have `__str__` methods to give an overview over
+  their contents.
+
 ## 0.1.4
 
 - Include `source_processor_id` and `source_processor_name` when writing .oebin file

LICENSE

@@ -1,7 +1,17 @@
-Copyright 2020 Open Ephys
+Copyright 2020-2025 Open Ephys
 
-Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
+Permission is hereby granted, free of charge, to any person obtaining a copy of this
+software and associated documentation files (the "Software"), to deal in the Software
+without restriction, including without limitation the rights to use, copy, modify, merge,
+publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons
+to whom the Software is furnished to do so, subject to the following conditions:
 
-The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
+The above copyright notice and this permission notice shall be included in all copies or
+substantial portions of the Software.
 
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED,
+INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR
+PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE
+FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
+OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.

pyproject.toml

@@ -5,29 +5,29 @@ build-backend = "setuptools.build_meta"
 [project]
 name = "open-ephys-python-tools"
 description = "Software tools for interfacing with the Open Ephys GUI"
-license = {text = "MIT"}
-requires-python = ">=3.7"
+license = { text = "MIT" }
+requires-python = ">=3.9"
 classifiers = [
     "Programming Language :: Python :: 3",
     "License :: OSI Approved :: MIT License",
-    "Operating System :: OS Independent"
+    "Operating System :: OS Independent",
 ]
 readme = "README.md"
 
 dynamic = ["version"]
 
-dependencies = [
-    'numpy',
-    'pandas',
-    'h5py',
-    'zmq',
-    'requests'
-]
+dependencies = ['numpy', 'pandas', 'h5py', 'zmq', 'requests']
 
 [tool.setuptools.packages.find]
 where = ["src"]
 
 [tool.setuptools.dynamic]
-version = {attr = "open_ephys.__version__"}
-
+version = { attr = "open_ephys.__version__" }
 
+[dependency-groups]
+dev = [
+    "black>=25.1.0",
+    "jsonschema>=4.23.0",
+    "mypy>=1.15.0",
+    "pytest>=8.3.5",
+]

src/open_ephys/__init__.py

@@ -1 +1 @@
-__version__ = "0.1.13"
+__version__ = "0.2.0-dev"

src/open_ephys/analysis/README.md

@@ -72,7 +72,7 @@ Each `continuous` object has four properties:
 - `samples` - a `numpy.ndarray` that holds the actual continuous data with dimensions of samples x channels. For Binary, NWB, and Kwik format, this will be a memory-mapped array (i.e., the data will only be loaded into memory when specific samples are accessed).
 - `sample_numbers` - a `numpy.ndarray` that holds the sample numbers since the start of acquisition. This will have the same size as the first dimension of the `samples` array
 - `timestamps` - a `numpy.ndarray` that holds global timestamps (in seconds) for each sample, assuming all data streams were synchronized in this recording. This will have the same size as the first dimension of the `samples` array
-- `metadata` - a `dict` containing information about this data, such as the ID of the processor it originated from.
+- `metadata` - a `ContinousMetadata` dataclass containing information about this data, such as the ID of the processor it originated from.
 
 Because the memory-mapped samples are stored as 16-bit integers in arbitrary units, all analysis should be done on a scaled version of these samples. To load the samples scaled to microvolts, use the `get_samples()` method:
 
@@ -124,7 +124,7 @@ If spike data has been saved by your Record Node (i.e., there is a Spike Detecto
 - `sample_numbers` - `numpy.ndarray` of sample indices (one per spikes)
 - `timestamps` - `numpy.ndarray` of global timestamps (in seconds)
 - `clusters` - `numpy.ndarray` of cluster IDs for each spike (default cluster = 0)
-- `metadata` - `dict` with metadata about each electrode
+- `metadata` - `SpikeMetadata` dataclass with metadata about each electrode
 
 ## Synchronizing timestamps