Initial commit

.github/workflows/add-to-dashboard.yml

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+name: Add Issue or Pull Request to Dashboard
+
+on:
+  issues:
+    types:
+      - opened
+  pull_request:
+    types:
+      - opened
+
+jobs:
+  add-to-project:
+    name: Add issue or pull request to project
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/[email protected]
+        with:
+          project-url: https://github.com/orgs/catalystneuro/projects/3
+          github-token: ${{ secrets.PROJECT_TOKEN }}

.github/workflows/auto-publish.yml

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+# This workflow will upload a Python Package using Twine when a release is created
+# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
+
+# For the template repo, we simply won't specify a PYPI token. We also won't do any actual releases.
+# For your actual conversion project using this template, add the PYPI_API_TOKEN to your secrets.
+
+name: Upload Package to PyPI
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install wheel
+      - name: Build package
+        run: |
+          python setup.py sdist bdist_wheel
+      - name: pypi-publish
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          verbose: true
+          user: __token__
+          password: ${{ secrets.PYPI_API_TOKEN }}

.github/workflows/test-install.yml

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+
+name: Installation
+on:
+  workflow_dispatch:
+  schedule:
+    - cron: "0 0 1 * *"  # First day of the month
+
+jobs:
+  run:
+    name: Installation on (${{ matrix.os }} with Python ${{ matrix.python-version }})
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: ["ubuntu-latest", "macos-latest", "windows-latest"]
+        python-version: ["3.8", "3.9", "3.10"]
+    steps:
+    - uses: actions/checkout@v3
+    - run: git fetch --prune --unshallow --tags
+    - name: Setup Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install pip
+      run: |
+        python -m pip install --upgrade pip
+        pip3 install packaging
+    - name: Install package
+      run: pip install -e .
+    - name: Test module load
+      run: python -c "import cohen_lab_to_nwb"
+

.gitignore

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+# 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/
+pip-wheel-metadata/
+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/
+
+# 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
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.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
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder repo_name settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# vscode
+.vscode/*
+.vscode/settings.json
+.vscode/tasks.json
+.vscode/launch.json
+.vscode/extensions.json
+*.code-workspace
+
+# pycharm
+.idea/*
+
+# Local History for Visual Studio Code
+.history/
+
+#Mac
+.DS_Store
+
+# NWB files
+**.nwb

.pre-commit-config.yaml

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+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.2.0
+    hooks:
+    -   id: check-yaml
+    -   id: end-of-file-fixer
+    -   id: trailing-whitespace
+-   repo: https://github.com/psf/black
+    rev: 22.8.0
+    hooks:
+    -   id: black
+        exclude: ^docs/

LICENSE

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+MIT License
+
+Copyright (c) 2020 CatalystNeuro
+
+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 *.yml
+include *.json
+include *.txt

README.md

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+# cohen-lab-to-nwb
+NWB conversion scripts for Cohen lab data to the [Neurodata Without Borders](https://nwb-overview.readthedocs.io/) data format.
+
+
+## Installation
+## Basic installation
+
+You can install the latest release of the package with pip:
+
+```
+pip install cohen-lab-to-nwb
+```
+
+We recommend that you install the package inside a [virtual environment](https://docs.python.org/3/tutorial/venv.html). A simple way of doing this is to use a [conda environment](https://docs.conda.io/projects/conda/en/latest/user-guide/concepts/environments.html) from the `conda` package manager ([installation instructions](https://docs.conda.io/en/latest/miniconda.html)). Detailed instructions on how to use conda environments can be found in their [documentation](https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html).
+
+### Running a specific conversion
+Once you have installed the package with pip, you can run any of the conversion scripts in a notebook or a python file:
+
+https://github.com/catalystneuro/cohen-lab-to-nwb//tree/main/src/AbbyLeung/AbbyLeung_convert_session.py
+
+
+
+
+## Installation from Github
+Another option is to install the package directly from Github. This option has the advantage that the source code can be modifed if you need to amend some of the code we originally provided to adapt to future experimental differences. To install the conversion from GitHub you will need to use `git` ([installation instructions](https://github.com/git-guides/install-git)). We also recommend the installation of `conda` ([installation instructions](https://docs.conda.io/en/latest/miniconda.html)) as it contains all the required machinery in a single and simple instal
+
+From a terminal (note that conda should install one in your system) you can do the following:
+
+```
+git clone https://github.com/catalystneuro/cohen-lab-to-nwb
+cd cohen-lab-to-nwb
+conda env create --file make_env.yml
+conda activate cohen-lab-to-nwb-env
+```
+
+This creates a [conda environment](https://docs.conda.io/projects/conda/en/latest/user-guide/concepts/environments.html) which isolates the conversion code from your system libraries.  We recommend that you run all your conversion related tasks and analysis from the created environment in order to minimize issues related to package dependencies.
+
+Alternatively, if you want to avoid conda altogether (for example if you use another virtual environment tool) you can install the repository with the following commands using only pip:
+
+```
+git clone https://github.com/catalystneuro/cohen-lab-to-nwb
+cd cohen-lab-to-nwb
+pip install -e .
+```
+
+Note:
+both of the methods above install the repository in [editable mode](https://pip.pypa.io/en/stable/cli/pip_install/#editable-installs).
+
+### Running a specific conversion
+To run a specific conversion, you might need to install first some conversion specific dependencies that are located in each conversion directory:
+```
+pip install -r src/cohen_lab_to_nwb/AbbyLeung/AbbyLeung_requirements.txt
+```
+
+You can run a specific conversion with the following command:
+```
+python src/cohen_lab_to_nwb/AbbyLeung/AbbyLeung_convert_session.py
+```
+
+## Repository structure
+Each conversion is organized in a directory of its own in the `src` directory:
+
+    cohen-lab-to-nwb/
+    ├── LICENSE
+    ├── make_env.yml
+    ├── pyproject.toml
+    ├── README.md
+    ├── requirements.txt
+    ├── setup.py
+    └── src
+        ├── cohen_lab_to_nwb
+        │   ├── conversion_directory_1
+        │   └── AbbyLeung
+        │       ├── AbbyLeung_behaviorinterface.py
+        │       ├── AbbyLeung_convert_session.py
+        │       ├── AbbyLeung_metadata.yml
+        │       ├── AbbyLeung_nwbconverter.py
+        │       ├── AbbyLeung_requirements.txt
+        │       ├── AbbyLeung_notes.md
+
+        │       └── __init__.py
+        │   ├── conversion_directory_b
+
+        └── __init__.py
+
+ For example, for the conversion `AbbyLeung` you can find a directory located in `src/cohen-lab-to-nwb/AbbyLeung`. Inside each conversion directory you can find the following files:
+
+* `AbbyLeung_convert_sesion.py`: this script defines the function to convert one full session of the conversion.
+* `AbbyLeung_requirements.txt`: dependencies specific to this conversion.
+* `AbbyLeung_metadata.yml`: metadata in yaml format for this specific conversion.
+* `AbbyLeung_behaviorinterface.py`: the behavior interface. Usually ad-hoc for each conversion.
+* `AbbyLeung_nwbconverter.py`: the place where the `NWBConverter` class is defined.
+* `AbbyLeung_notes.md`: notes and comments concerning this specific conversion.
+
+The directory might contain other files that are necessary for the conversion but those are the central ones.

make_env.yml

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+name: cohen_lab_to_nwb_env
+channels:
+- conda-forge
+- defaults
+dependencies:
+- python>=3.9
+- pip
+- pip:
+  - -e .  # This calls the setup and therefore requirements minimal