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niagads-pylib

a collection of python packages, classes, and utility functions in support of NIAGADS projects -ega comment

Documentation

see https://niagads.github.io/niagads-pylib

Requirements

  • python 3.10+

Installation

NOTE: add the --user flag to the pip3 or setup.py calls to install as a user or local package add #branch-name to the end of the URL to install from a specific branch

pip3 installation direct from GitHub:

  • latest stable / main branch
pip3 install git+https://github.com/NIAGADS/niagads-pylib.git
  • other branch
pip3 install git+https://github.com/NIAGADS/niagads-pylib.git#branch-name

python3 setup.py from local working version

git clone https://github.com/NIAGADS/niagads-pylib.git
cd niagads-pylib.git
python3 setup.py install

docker

  • Requires docker or docker desktop

NOTE: This is for NIAGADS organization members only at this time

If a member of NIAGADS, make a request to Emily G or Otto V to be added to the NIAGADS GitHub organization, and to be given pull access to the docker-repo. Next:

git clone https://github.com/NIAGADS/docker-repo.git
docker build --build-arg GID=$GID --pull --rm -f "docker-repo/dev-environments/pylib/Dockerfile" -t pylib:latest "docker-repo/dev-environments/pylib

${GID} is your group_id; this is for permissions if you need to run a script that requires mounting a volume and writing to the host (defaults to 1001)

use the --build-arg PYLIB_SOURCE to override the GitHub target (e.g., use your own fork or a branch other than main)

Example docker usage coming soon.

Contributing

Suggested working environment

suggest configuring autoDocstring to use google style comment blocks

  • create a python venv to facilitate testing scripts

Standard Operating Procedure

  • create your own fork (details coming soon)
  • make pull request to submit contribution

Coding Conventions

Naming

  • file names and directories should be in snake_case
  • function names should be in snake_case
  • variable names should be in lowerCamelCase
  • class names should be in UpperCamelCase
  • constants should be in UPPER_SNAKE_CASE

Documentation

All functions, classes and packages should have a doc-string. For non-inuitive or complex functions, please provide a summary description, a list of args, a description of the return value, and any raised exceptions. For simple functions (e.g., member getters and setters, no documentation is need or a simple summary doc string will suffice)

Logging

Please use logging to log script progress and debug statements. Details coming soon.

Classes

  • When definining classes, try to stick to the principles of Object Oriented Programming: Encapsulation, Data Abstraction, Polymorphism and Inheritence.

Especially Encapsulation:

  • all class variables should be private (protected if class using Inheritence and class has children)

    • private: variable only accessible within the class
      • naming: starts with __ (double underscore; e.g., __size)
    • protected: variable accesesible within class and any child classes
      • nameing: starts with _ (underscore; e.g., _size)

  • getters and setters methods should be defined to manipulate variable values

  • when creating class methods consider usage of functions and make functions private or protected if should not be directly accessed by the user (i.e., only used internally by the class) by prefixing with __ or _ as needed

  • all classes should have a public logger member variable

  • all classes should have a protected debug member variable

Scripts

Executable scripts can be added to the scripts directory. setup.py will also need to be updated. Details coming soon.

Other

  • use type hints when possible help the Pylance (the Python interpreter) provide better autocompletion examples

  • use enums to define variables limited to controlled vocabularies (see the enums utilities and the api_wrapper constants for examples)