This repo serves as a generic template generator for all conversion projects undertaken by the CatalystNeuro team. The project is based and shares the structure of our generic template and extends it further by means of cookiecutter to auto-generate the rest of the configuration.
Install the latest cookiecutter version if you haven't installed it yet:
pip install -U cookiecutter
Then, use the following cookiecutter command to generate a CatalystNeuro conversion project structure:
cookiecutter https://github.com/catalystneuro/cookiecutter-my-lab-to-nwb-template
This will ask some questions that determine the project structure as in the following example:
lab [Lab Name]: Eric Kandel
repo_name [eric-kandel-lab-to-nwb]:
conversion_name [embargo2002a]: brenda_milner_2022
Where the lab usually corresponds to the principal investigator name, repo_name is the name of the github repositry and conversion_name is the name of the specific conversion to be carried out.
Leave the prompt unanswered (blank) to accept the default suggestion in square brackets (e.g. repo name will be assigned the value of eric-kandel-lab-to-nwb as the space is left blank). We suggest to use the name of the author plus the year for the conversion name (as it is done for conversion_name agove.)
For conversions concerning data under embargo we suggest a name following the pattern described in the brackets (i.e. embargo22a). The general form is embargo{year}{letter} where year is the year of the conversion and letter can be a, b, c, etc. in case there is more than one conversion that year.
After the questions in the prompt are answered as above, cookiecutter generates a directory with the following structure:
eric-kandel-lab-to-nwb/
├── LICENSE
├── make_env.yml
├── pyproject.toml
├── README.md
├── requirements.txt
├── setup.py
└── src
├── eric_kandel_lab_to_nwb
│ └── brenda_milner_2022
│ ├── brenda_milner_2022behaviorinterface.py
│ ├── brenda_milner_2022_convert_session.py
│ ├── brenda_milner_2022_metadata.yml
│ ├── brenda_milner_2022nwbconverter.py
│ ├── brenda_milner_2022_requirements.txt
│ └── __init__.py
└── __init__.py
You can then modify this to suit the particular needs of the ongoing conversion.
The last step is to create an empty repo with the same name as the generated directory from our team github account and just fill the contents with the ones in the directory generated by cookiecuter.
For new repos, an extra step of allowing the black auto-commit CI bot may have to be enabled at: https://results.pre-commit.ci/
To enable the pre-commit hook locally use the two following steps:
pip install pre-commit
pre-commit install
The .pre-commit-config.yaml is already included in the repository.