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minimal-template

template repo

Install

the env.yml contains the line - -e . which installs the package in developer mode:

  1. optional: conda env create -f env.yml
  2. activate: conda activate mini_template

alternative install it in your existing environment::

  1. normal: python -m pip install . OR in developer mode:
  2. pip install -e . --user

How to use:

  • add some bullets here

FILES

short explanation of all files in the repo:

  • minimal_template/: folder contains [code, modules]
    • __init__: init file
  • tests/: folder contains test files
    • test_with_pytest.py: example file to test tesing via e.g. pytest
  • env.yml: YAML environment file than specifies dependencies from other packages
  • LICENSE: LICENSE File
  • pyproject.toml: contains dependencies and various settings (black, ruff, ...) for the project
  • README.md: the readme
  • setup.py: needed for install via pip

Dependencies

  • plotting related:
    • matplotlib: used for plotting
    • plotly: fast interactive plotting
  • jupyter notebook related:
    • ipykernel: to be able to load the environment in jupyterlab
    • jupyterlab: to run notebooks
    • jupyter_contrib_nbextensions: to enable "strip-notebook-output clean"
    • nbconvert: to enable "strip-notebook-output clean"
  • formatting + linting:
    • ruff
    • pylint
  • numpy: for numerical computations
  • pathlib: for a portable way to navigate file-systems
  • pandas: to use DataFrame objects
  • tabulate: to create tables

Explanation:

I will update the package the more I understand of the other template files and functions (poetry, tox vs. pytest, black)

  • the setup.py file is only needed for developer mode install
    • in fact the pyproject.toml contains a block [build-system] with some flit-stuff that should enable developer-mode somehow without setup.py file (read)

Developer notes

  • if the package depends on a custum package my_other_pack that you want to edit during development
    1. specify it in the env.yml file (so users have it in their env)
    2. when doing conda create -f env.yml it will get installed via pip (good for the users, bad for you since the path is somewhere in your env-directory)
    3. now reinstall with your local repo folder my_other_pack by:
      • activate environment conda env create -f env.yml
      • uninstall the package pip uninstall my_other_pack
      • change directory to your local installation cd /PATH/to/your/local/my_other_pack
      • pip-install it in editable mode: pip install -e . --user

Git settings

If you plan having jupyter-notebooks in your repository, place them in the ./notebooks folder. The below settings are inspired by this stackoverflow post

  • this folder contains the file ./notebooks/.gitattributes that will run at each add of an *.ipynb file the filter strip-notebook-output.
    • note that it will only remove the output for the git-commit BUT the output in your local notebook remains.
  • the filter strip-notebook-output needs to be defined in your local .git/config or global .gitconfig as:
[filter "strip-notebook-output"]
    clean = "jupyter nbconvert --ClearOutputPreprocessor.enabled=True --to=notebook --stdin --stdout --log-level=ERROR"
  • in order to run this you need to have the following packages installed
    • conda install -c conda-forge jupyter_contrib_nbextensions
    • conda install nbconvert