ndx-guppy 0.1.0__tar.gz

ndx_guppy-0.1.0/.gitignore

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+# output NWB files
+*.nwb
+
+# generated docs
+docs/source/_format_auto_docs
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+.ruff_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+# Mac finder
+.DS_Store
+
+# VS Code
+.vscode/

ndx_guppy-0.1.0/.pre-commit-config.yaml

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+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.6.0
+    hooks:
+    -   id: check-yaml
+    -   id: end-of-file-fixer
+    -   id: trailing-whitespace
+-   repo: https://github.com/psf/black
+    rev: 24.4.2
+    hooks:
+    -   id: black
+        exclude: ^docs/

ndx_guppy-0.1.0/CHANGELOG.md

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+# Changelog for ndx-guppy
+
+# v0.1.0 (Upcoming)
+
+### Features
+Initial release of 10 new neurodata types representing the derived outputs of the GuPPy fiber-photometry tool (one NWB file per session):
+* `GuppyParameters` extends `LabMetaData` to hold the session-level GuPPy processing parameters.
+* `GuppyRecordingSitesTable` extends `DynamicTable` as the canonical registry of recording sites (one row per site, e.g. `dms`) that the derived products reference.
+* `GuppyEventsTable` extends `DynamicTable` as the registry of behavioral events GuPPy aligned to, with an optional ragged `DynamicTableRegion` into a merged core `EventsTable`.
+* `GuppyValidSignalIntervals` extends `TimeIntervals` to hold the valid (artifact-free) signal intervals per recording site.
+* `GuppyDerivedResponseSeries` extends `FiberPhotometryResponseSeries` to hold a derived trace (`control_fit`/`dff`/`z_score`), stamped with its `trace_type` and referencing its recording site.
+* `GuppyTransientsTable` extends `DynamicTable` to hold the detected transients.
+* `GuppyTransientSummaryTable` extends `DynamicTable` to hold per-condition transient summary statistics.
+* `GuppyPSTH` holds the peri-event PSTH for one (recording_site, trace_type, baseline) condition, concatenated across events.
+* `GuppyCrossCorrelation` holds the cross-correlation between a recording-site pair for one trace_type, concatenated across events.
+* `GuppyPeakAUC` holds the peak and area-under-the-curve metrics for one (recording_site, trace_type) condition, concatenated across events.
+
+### Fixes
+* Fixed the ruff and Sphinx CI jobs (import ordering and doc-autogen namespace registration; no schema changes) [PR #1](https://github.com/catalystneuro/ndx-guppy/pull/1).

ndx_guppy-0.1.0/LICENSE.txt

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+BSD 3-Clause License
+
+Copyright (c) 2026, Paul Adkisson-Floro
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

ndx_guppy-0.1.0/NEXTSTEPS.md

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+
+
+# Next Steps for ndx-guppy Extension for NWB
+
+## Creating Your Extension
+
+1. In a terminal, change directory into the new ndx-guppy directory: `cd ndx-guppy`
+
+2. Add any packages required by your extension to the `[project] dependencies` or `[project.optional-dependencies]` 
+section of `pyproject.toml`.
+
+3. Run `python -m pip install -e .` to install your new extension Python package
+and any other packages required to develop, document, and run your extension.
+
+4. Modify `src/spec/create_extension_spec.py` to define your extension.
+
+5. Run `python src/spec/create_extension_spec.py` to generate the
+`spec/ndx-guppy.namespace.yaml` and
+`spec/ndx-guppy.extensions.yaml` files.
+
+6. Define API classes for your new extension data types.
+
+    - As a starting point, `src/pynwb/ndx_guppy/__init__.py` includes an
+      example for how to use
+      the `pynwb.get_class` to generate a basic Python class for your new extension data
+      type. This class contains a constructor and properties for the new data type.
+    - Instead of using `pynwb.get_class`, you can define your own custom class for the
+      new type, which will allow you to customize the class methods, customize the
+      object mapping, and create convenience functions. See the
+      [Extending NWB tutorial](https://pynwb.readthedocs.io/en/stable/tutorials/general/extensions.html)
+      for more details.
+
+7. Define tests for your new extension data types in 
+`src/pynwb/ndx_guppy/tests` or `src/matnwb/tests`.
+A test for the example `TetrodeSeries` data type is provided as a reference and should be
+replaced or removed.
+
+     - Python tests should be runnable by executing [`pytest`](https://docs.pytest.org/en/latest/)
+     from the root of the extension directory. Use of PyNWB testing infrastructure from
+     `pynwb.testing` is encouraged (see
+     [documentation](https://pynwb.readthedocs.io/en/stable/pynwb.testing.html)).
+     - Creating both **unit tests** (e.g., testing initialization of new data type classes and
+     new functions) and **integration tests** (e.g., write the new data types to file, read
+     the file, and confirm the read data types are equal to the written data types) is
+     highly encouraged.
+     - By default, to aid with debugging, the project is configured NOT to run code coverage as
+     part of the tests.
+     Code coverage reporting is useful to help with creation of tests and report test coverage.
+     However, with this option enabled, breakpoints for debugging with pdb are being ignored.
+     To enable this option for code coverage reporting, uncomment out the following line in
+     your `pyproject.toml`: [line](https://github.com/nwb-extensions/ndx-template/blob/11ae225b3fd3934fa3c56e6e7b563081793b3b43/%7B%7B%20cookiecutter.namespace%20%7D%7D/pyproject.toml#L82-L83
+)
+
+7. (Optional) Define custom visualization widgets for your new extension data types in
+`src/pynwb/ndx_guppy/widgets` so that the visualizations can be displayed with
+[nwbwidgets](https://github.com/NeurodataWithoutBorders/nwbwidgets).
+You will also need to update the `vis_spec` dictionary in 
+`src/pynwb/ndx_guppy/widgets/__init__.py` so that
+nwbwidgets can find your custom visualizations.
+
+8. You may need to modify `pyproject.toml` and re-run `python -m pip install -e .` if you
+use any dependencies.
+
+9. Update the `CHANGELOG.md` regularly to document changes to your extension.
+
+
+## Documenting and Publishing Your Extension to the Community
+
+1. Install the latest release of hdmf_docutils: `python -m pip install hdmf-docutils`
+
+2. Start a git repository for your extension directory ndx-guppy
+ and push it to GitHub. You will need a GitHub account.
+    - Follow these directions:
+  https://help.github.com/en/articles/adding-an-existing-project-to-github-using-the-command-line
+
+3. Change directory into `docs`.
+
+4. Run `make html` to generate documentation for your extension based on the YAML files.
+
+5. Read `docs/README.md` for instructions on how to customize documentation for
+your extension.
+
+6. Modify `README.md` to describe this extension for interested developers.
+
+7. Add a license file. Permissive licenses should be used if possible. **A [BSD license](https://opensource.org/licenses/BSD-3-Clause) is recommended.**
+
+8. Update the `CHANGELOG.md` to document changes to your extension.
+
+8. Push your repository to GitHub. A default set of GitHub Actions workflows is set up to
+test your code on Linux, Windows, Mac OS, and Linux using conda; upload code coverage
+stats to codecov.io; check for spelling errors; check for style errors; and check for broken
+links in the documentation. For the code coverage workflow to work, you will need to
+set up the repo on codecov.io and uncomment the "Upload coverage to Codecov" step
+in `.github/workflows/run_coverage.yml`.
+
+8. Make a release for the extension on GitHub with the version number specified. e.g. if version is 0.1.0, then this page should exist: https://github.com/CatalystNeuro/ndx-guppy/releases/tag/0.1.0 . For instructions on how to make a release on GitHub see [here](https://help.github.com/en/github/administering-a-repository/creating-releases).
+
+9. Publish your updated extension on [PyPI](https://pypi.org/).
+    - Follow these directions: https://packaging.python.org/en/latest/tutorials/packaging-projects/
+    - You may need to modify `pyproject.toml`
+    - If your extension version is 0.1.0, then this page should exist: https://pypi.org/project/ndx-guppy/0.1.0
+
+   Once your GitHub release and `pyproject.toml` are ready, publishing on PyPI:
+    ```bash
+    python -m pip install --upgrade build twine
+    python -m build
+    twine upload dist/*
+    ```
+
+10. Go to https://github.com/nwb-extensions/staged-extensions and fork the
+repository.
+
+11. Clone the fork onto your local filesystem.
+
+12. Copy the directory `staged-extensions/example` to a new directory
+`staged-extensions/ndx-guppy`:
+
+    ```bash
+    cp -r staged-extensions/example staged-extensions/ndx-guppy
+    ```
+
+13. Edit `staged-extensions/ndx-guppy/ndx-meta.yaml`
+with information on where to find your NWB extension.
+    - The YAML file MUST contain a dict with the following keys:
+      - name: extension namespace name
+      - version: extension version
+      - src: URL for the main page of the public repository (e.g. on GitHub, BitBucket, GitLab) that contains the sources of the extension
+      - pip: URL for the main page of the extension on PyPI
+      - license: name of the license of the extension
+      - maintainers: list of GitHub usernames of those who will reliably maintain the extension
+    - You may copy and modify the following YAML that was auto-generated:
+
+      ```yaml
+      name: ndx-guppy
+      version: 0.1.0
+      src: https://github.com/CatalystNeuro/ndx-guppy
+      pip: https://pypi.org/project/ndx-guppy/
+      license: BSD-3-Clause
+      maintainers: 
+        - CatalystNeuro
+      ```
+
+14. Edit `staged-extensions/ndx-guppy/README.md`
+to add information about your extension. You may copy it from
+`ndx-guppy/README.md`.
+
+  ```bash
+  cp ndx-guppy/README.md staged-extensions/ndx-guppy/README.md
+  ```
+
+15. Add and commit your changes to Git and push your changes to GitHub.
+```
+cd staged-extensions
+git add ndx-guppy
+git commit -m "Add new catalog entry for ndx-guppy" .
+git push
+```
+
+16. Open a pull request. Building of your extension will be tested on Windows,
+Mac, and Linux. The technical team will review your extension shortly after
+and provide feedback and request changes, if any.
+
+17. When your pull request is merged, a new repository, called
+ndx-guppy-record will be created in the nwb-extensions
+GitHub organization and you will be added as a maintainer for that repository.
+
+
+## Updating Your Published Extension
+
+1. Update your ndx-guppy GitHub repository.
+
+2. Publish your updated extension on PyPI.
+
+3. Fork the ndx-guppy-record repository on GitHub.
+
+4. Open a pull request to test the changes automatically. The technical team
+will review your changes shortly after and provide feedback and request changes,
+if any.
+
+5. Your updated extension is approved.