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 kind_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/
+
+-   repo: https://github.com/codespell-project/codespell
+    rev: v2.3.0
+    hooks:
+    - id: codespell
+      additional_dependencies:
+        - tomli
+
+-   repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.6.9
+    hooks:
+    - id: ruff
+      args: [ --fix ]

MANIFEST.in

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+include *.yml
+include *.json
+include *.txt

README.md

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 # kind-lab-to-nwb
-NWB Conversion project for the Kind lab.
+NWB conversion scripts for Kind 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 kind-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/kind-lab-to-nwb//tree/main/src/arc_ecephys_2024/convert_session.py
+
+Copy or download this file run the script with the following command:
+
+```
+python 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 modified 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 install.
+
+From a terminal (note that conda should install one in your system) you can do the following:
+
+```
+git clone https://github.com/catalystneuro/kind-lab-to-nwb
+cd kind-lab-to-nwb
+conda env create --file make_env.yml
+conda activate kind_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/kind-lab-to-nwb
+cd kind-lab-to-nwb
+pip install --editable .
+```
+
+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
+If the project has more than one conversion, you can install the requirements for a specific conversion with the following command:
+```
+pip install --editable .[arc_ecephys_2024]
+```
+
+You can run a specific conversion with the following command:
+```
+python src/kind_lab_to_nwb/arc_ecephys_2024/convert_session.py
+```
+
+## Repository structure
+Each conversion is organized in a directory of its own in the `src` directory:
+
+    kind-lab-to-nwb/
+    ├── LICENSE
+    ├── make_env.yml
+    ├── pyproject.toml
+    ├── README.md
+    ├── requirements.txt
+    ├── setup.py
+    └── src
+        ├── kind_lab_to_nwb
+        │   └── arc_ecephys_2024
+        │       ├── notes.md
+        │       ├── behaviorinterface.py
+        │       ├── convert_session.py
+        │       ├── metadata.yml
+        │       ├── nwbconverter.py
+        │       ├── notes.md
+        │       └── __init__.py
+        │   ├── conversion_directory_b
+
+        └── __init__.py
+
+For example, for the conversion `arc_ecephys_2024` you can find a directory located in `src/kind-lab-to-nwb/arc_ecephys_2024`.
+Inside each conversion directory you can find the following files:
+
+
+* `convert_sesion.py`: this script defines the function to convert one full session of the conversion.
+* `metadata.yml`: metadata in yaml format for this specific conversion.
+* `behaviorinterface.py`: the behavior interface. Usually ad-hoc for each conversion.
+* `nwbconverter.py`: the place where the `NWBConverter` class is defined.
+* `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: kind_lab_to_nwb_env
+channels:
+- conda-forge
+- defaults
+dependencies:
+- python>=3.11
+- pip
+- pip:
+  - --editable .  # This calls the setup and therefore requirements minimal