Initial commit from ndx-template

.gitignore

@@ -1,3 +1,12 @@
+# output NWB files
+*.nwb
+
+# generated docs
+docs/source/_format_auto_docs
+
+# copied spec files
+src/pynwb/ndx_hed/spec/*.yaml
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]
@@ -50,6 +59,7 @@ coverage.xml
 .hypothesis/
 .pytest_cache/
 cover/
+.ruff_cache/
 
 # Translations
 *.mo
@@ -158,3 +168,6 @@ cython_debug/
 #  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

CHANGELOG.md

@@ -0,0 +1 @@
+# Changelog for ndx-hed

LICENSE.txt

@@ -0,0 +1,29 @@
+BSD 3-Clause License
+
+Copyright (c) 2023, Ryan Ly, Oliver Ruebel, Kay Robbins
+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.

NEXTSTEPS.md

@@ -0,0 +1,158 @@
+
+
+# Next Steps for ndx-hed Extension for NWB
+
+## Creating Your Extension
+
+1. In a terminal, change directory into the new ndx-hed directory: `cd ndx-hed`
+
+2. Add any packages required by your extension to the `dependencies` key in `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-hed.namespace.yaml` and
+`spec/ndx-hed.extensions.yaml` files.
+
+6. Define API classes for your new extension data types.
+
+    - As a starting point, `src/pynwb/__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/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.
+
+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-hed
+ 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. 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/rly/ndx-hed/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-hed/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-hed`:
+
+    ```bash
+    cp -r staged-extensions/example staged-extensions/ndx-hed
+    ```
+
+13. Edit `staged-extensions/ndx-hed/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-hed
+      version: 0.1.0
+      src: https://github.com/rly/ndx-hed
+      pip: https://pypi.org/project/ndx-hed/
+      license: BSD-3
+      maintainers: 
+        - rly
+        - oruebel
+        - VisLab
+      ```
+
+14. Edit `staged-extensions/ndx-hed/README.md`
+to add information about your extension. You may copy it from
+`ndx-hed/README.md`.
+
+  ```bash
+  cp ndx-hed/README.md staged-extensions/ndx-hed/README.md
+  ```
+
+15. Add and commit your changes to Git and push your changes to GitHub.
+```
+cd staged-extensions
+git add ndx-hed
+git commit -m "Add new catalog entry for ndx-hed" .
+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-hed-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-hed GitHub repository.
+
+2. Publish your updated extension on PyPI.
+
+3. Fork the ndx-hed-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.

README.md

@@ -1,2 +1,15 @@
-# ndx-hed
-HED extensions for Neurodata Without Borders (nwb)
+# ndx-hed Extension for NWB
+
+Description of the extension
+
+## Installation
+
+
+## Usage
+
+```python
+
+```
+
+---
+This extension was created using [ndx-template](https://github.com/nwb-extensions/ndx-template).