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napari-hub-cli

Command line utilities for inspecting and validating plugins for the napari hub.

NOTE: the project is still under developement and this version is not yet deployed in Pypi.

Supported operating systems

The tool works on Linux and MacOS without issue. On Windows, the tool works without issue in the Windows Subsystem for Linux (WSL) but there is a known issue in Windows without WSL - the result from the plugin installation check is flaky. See this issue for more details.

To set up WSL, follow the instructions here. With WSL set up, you can run the tool from the WSL terminal following the instructions below.

Installation

First the repository needs to be cloned

git clone https://github.com/chanzuckerberg/napari-hub-cli.git
cd napari-hub-cli

As any python program, it is recommended to create a virtual env. You probably have your own and prefered method, here is a classical one using the venv module:

# inside the "napari-hub-cli" folder, where you cloned the repository
python -m venv --symlinks .venv
source .venv/bin/activate  # activating the virtual env

Once you activated the virtual env, you can install all the required dependencies and the tool this way using pip:

python -m pip install napari-hub-cli

Alternatively, you can also install the napari hub CLI directly from the cloned repository:

# inside the "napari-hub-cli" folder, where you cloned the repository
# and with virtual env activated
python -m pip install -e .

To check that the installation went well, this command prints the help menu

napari-hub-cli --help

Usage

Code quality checklist

The command used to create the Code quality checklist is

 napari-hub-cli check-quality /tmp/example-plugin

The intent of this utility is to check your plugin for code quality metrics listed described in the wiki. The checklist comes in two parts, first, a freeform metadata section, and second, a list of metrics that are checked as True/False.

Example output:

Code quality check from command line using the napari-hub-cli tool

Documentation checklist

The command used to create the Documentation checklist is

 napari-hub-cli check-metadata /tmp/example-plugin

The intent of this utility is to check your plugin for specific metadata in the napari-Hub recommended file locations. With this, it creates a Documentation checklist identifying if a plugin has the metadata listed in the wiki.

Example output:

Metadata check from command line using the napari-hub-cli tool

Citation

To create a citation file (CITATION.CFF) for your plugin run

 napari-hub-cli create-citation /tmp/example-plugin

This utility works by looking into:

  • GitHub Repository metadata
  • README.md

and creating a CITATION.CFF, a plain text file with human- and machine-readable citation information for software and datasets.

For citations to be parsed from the README.md these need to have either the APA(American Psychological Association) style or BibTex style format.

The CITATION.CFF file naming needs to be as it is, otherwise GitHub won't recognize it as a citation file.

The format for the CITATION.CFF is the following:

  • The first citation that appears references the software
  • The preffered citation, the one used in GitHub, references an article/publisher, preferring an article citation when both exist
  • when both article and publisher information exist, publisher information is written as a sub-reference

Citation references

Below you can find some examples of how to use the CITATION.CFF.

Referencing other work:

cff-version: 1.2.0
authors:
  - family-names: Druskat
    given-names: Stephan
message: "If you use this software, please cite it using these metadata."
references:
  - authors:
      - family-names: Spaaks
        given-names: "Jurriaan H."
    title: "The foundation of Research Software"
    type: software
  - authors:
      - family-names: Haines
        given-names: Robert
    title: "Ruby CFF Library"
    type: software
    version: 1.0
title: "My Research Software"

Credit Redirection:

cff-version: 1.2.0
authors:
  - family-names: Druskat
    given-names: Stephan
message: "If you use this software, please cite both the article from preferred-citation and the software itself."
preferred-citation:
  authors:
    - family-names: Druskat
      given-names: Stephan
  title: "Software paper about My Research Software"
  type: article
title: "My Research Software"

Some more information regarding .CFF can be found here.

Previewing your plugin's napari hub page

To view a preview of your plugin listing for the napari hub, we recommend using the napari hub preview page service.

Code of Conduct

This project adheres to the Contributor Covenant code of conduct. By participating, you are expected to uphold this code. Please report unacceptable behavior to [email protected].