Initial commit

.gitattributes

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+*.rst            whitespace=tab-in-indent conflict-marker-size=79

.gitignore

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+# output NWB files
+*.nwb
+
+# generated docs
+docs/source/_format_auto_docs
+
+# copied spec files
+src/pynwb/ndx_microscopy/spec/*.yaml
+
+# 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/
+*.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/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# 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/
+
+# Mac finder
+.DS_Store

LICENSE.txt

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+MIT License
+
+Copyright (c) 2023 Cody Baker and Alessandra Trapani
+
+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 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.

MANIFEST.in

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+include LICENSE.txt
+include README.md
+include requirements.txt
+
+include spec/*.yaml
+
+recursive-include tests *
+recursive-exclude * __pycache__
+recursive-exclude * *.py[co]
+
+recursive-include docs *.css *.rst conf.py conf_doc_autogen.py Makefile make.bat README.md

NEXTSTEPS.md

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+
+
+# Next Steps for ndx-microscopy Extension for NWB
+
+## Creating Your Extension
+
+1. In a terminal, change directory into the new ndx-microscopy directory.
+
+2. Add any packages required by your extension to `requirements.txt` and `setup.py`.
+
+3. Run `python -m pip install -r requirements.txt -r requirements-dev.txt` to install the `pynwb` package
+and any other packages required to install, develop, and document 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-microscopy.namespace.yaml` and
+`spec/ndx-microscopy.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 get 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
+      [https://pynwb.readthedocs.io/en/stable/tutorials/general/extensions.html](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 `setup.py` and re-run `python setup.py install` if you
+use any dependencies.
+
+
+## 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-microscopy
+ 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. 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/CodyCBakerPhD/ndx-microscopy/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/tutorials/packaging-projects/
+    - You may need to modify `setup.py`
+    - If your extension version is 0.1.0, then this page should exist: https://pypi.org/project/ndx-microscopy/0.1.0
+
+   Once your GitHub release and ``setup.py`` are ready, publishing on PyPI:
+    ```bash
+    python setup.py sdist bdist_wheel
+    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-microscopy`:
+
+    ```bash
+    cp -r staged-extensions/example staged-extensions/ndx-microscopy
+    ```
+
+13. Edit `staged-extensions/ndx-microscopy/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-microscopy
+      version: 0.1.0
+      src: https://github.com/CodyCBakerPhD/ndx-microscopy
+      pip: https://pypi.org/project/ndx-microscopy/
+      license: MIT
+      maintainers: 
+        - CodyCBakerPhD
+      ```
+
+14. Edit `staged-extensions/ndx-microscopy/README.md`
+to add information about your extension. You may copy it from
+`ndx-microscopy/README.md`.
+
+  ```bash
+  cp ndx-microscopy/README.md staged-extensions/ndx-microscopy/README.md
+  ```
+
+15. Add and commit your changes to Git and push your changes to GitHub.
+```
+cd staged-extensions
+git add ndx-microscopy
+git commit -m "Add new catalog entry for ndx-microscopy" .
+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-microscopy-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-microscopy GitHub repository.
+
+2. Publish your updated extension on PyPI.
+
+3. Fork the ndx-microscopy-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

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+# ndx-microscopy Extension for NWB
+
+Description of the extension
+
+## Installation
+
+
+## Usage
+
+```python
+
+```
+
+---
+This extension was created using [ndx-template](https://github.com/nwb-extensions/ndx-template).