Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Feature/refactor kinship print to write #43

Open
wants to merge 47 commits into
base: develop
Choose a base branch
from
Open

Feature/refactor kinship print to write #43

wants to merge 47 commits into from

Commits on Aug 20, 2024

  1. add pandas to dockerfile

    @ellendejong
    ellendejong committed Aug 20, 2024
    Configuration menu
    Copy the full SHA
    73e7f37 View commit details
    Browse the repository at this point in the history

  2. refactor kinship: use pandas and add user friendly message if kinship… 

    … check fails
    @ellendejong
    ellendejong committed Aug 20, 2024
    Configuration menu
    Copy the full SHA
    4d22c20 View commit details
    Browse the repository at this point in the history

Commits on Aug 27, 2024

  1. Install CustomModules as package to enable import of utils

    @ellendejong
    ellendejong committed Aug 27, 2024
    Configuration menu
    Copy the full SHA
    9059f93 View commit details
    Browse the repository at this point in the history

  2. add non_empty_existing_path to utils

    @ellendejong
    ellendejong committed Aug 27, 2024
    Configuration menu
    Copy the full SHA
    658a832 View commit details
    Browse the repository at this point in the history

  3. Move parse_ped to utils and add unit tests

    @ellendejong
    ellendejong committed Aug 27, 2024
    Configuration menu
    Copy the full SHA
    0e9d1f7 View commit details
    Browse the repository at this point in the history

  4. add utils and remove unused imports

    @ellendejong
    ellendejong committed Aug 27, 2024
    Configuration menu
    Copy the full SHA
    c56a676 View commit details
    Browse the repository at this point in the history

  5. use non_empty_existing_path in argparser

    @ellendejong
    ellendejong committed Aug 27, 2024
    Configuration menu
    Copy the full SHA
    2857d93 View commit details
    Browse the repository at this point in the history

  6. fix quote issues

    @ellendejong
    ellendejong committed Aug 27, 2024
    Configuration menu
    Copy the full SHA
    3b7909f View commit details
    Browse the repository at this point in the history

  7. add pytest

    @ellendejong
    ellendejong committed Aug 27, 2024
    Configuration menu
    Copy the full SHA
    16abdac View commit details
    Browse the repository at this point in the history

  8. add docstrings to check_kinship

    @ellendejong
    ellendejong committed Aug 27, 2024
    Configuration menu
    Copy the full SHA
    677032f View commit details
    Browse the repository at this point in the history

  9. add docstring to non_empty_existing_path

    @ellendejong
    ellendejong committed Aug 27, 2024
    Configuration menu
    Copy the full SHA
    0d7c4d1 View commit details
    Browse the repository at this point in the history

  10. add docstring parse_ped

    @ellendejong
    ellendejong committed Aug 27, 2024
    Configuration menu
    Copy the full SHA
    c5c9d13 View commit details
    Browse the repository at this point in the history

  11. resolve flake8 warnings and errors.

    @ellendejong
    ellendejong committed Aug 27, 2024
    Configuration menu
    Copy the full SHA
    0d10f6e View commit details
    Browse the repository at this point in the history

Commits on Sep 20, 2024

  1. add pyproject custommodules

    @ellendejong
    ellendejong committed Sep 20, 2024
    Configuration menu
    Copy the full SHA
    0e6a209 View commit details
    Browse the repository at this point in the history

  2. Instead of using util functions, duplicate function in tool.

    @ellendejong
    ellendejong committed Sep 20, 2024
    Configuration menu
    Copy the full SHA
    96f0bba View commit details
    Browse the repository at this point in the history

  3. add poetry project

    @ellendejong
    ellendejong committed Sep 20, 2024
    Configuration menu
    Copy the full SHA
    f4b5d49 View commit details
    Browse the repository at this point in the history

  4. Add github workflows kinship lint and test

    @ellendejong
    ellendejong committed Sep 20, 2024
    Configuration menu
    Copy the full SHA
    2a7d6ac View commit details
    Browse the repository at this point in the history

  5. Change python version

    @ellendejong
    ellendejong committed Sep 20, 2024
    Configuration menu
    Copy the full SHA
    bcffc89 View commit details
    Browse the repository at this point in the history

  6. Add missing dependencies using poetry

    @ellendejong
    ellendejong committed Sep 20, 2024
    Configuration menu
    Copy the full SHA
    407e569 View commit details
    Browse the repository at this point in the history

  7. add dependency pytest-datadir

    @ellendejong
    ellendejong committed Sep 20, 2024
    Configuration menu
    Copy the full SHA
    81ea36e View commit details
    Browse the repository at this point in the history

  8. remove custommodules install as package in readme

    @ellendejong
    ellendejong committed Sep 20, 2024
    Configuration menu
    Copy the full SHA
    1d7f5dc View commit details
    Browse the repository at this point in the history

  9. remove init in custommodules

    @ellendejong
    ellendejong committed Sep 20, 2024
    Configuration menu
    Copy the full SHA
    e22c2d6 View commit details
    Browse the repository at this point in the history

  10. revert parse_ped pytest in utils, will be added to dev via another br… 

    …anch
    @ellendejong
    ellendejong committed Sep 20, 2024
    Configuration menu
    Copy the full SHA
    79cd433 View commit details
    Browse the repository at this point in the history

Commits on Sep 23, 2024

  1. typo - vs _

    @ellendejong
    ellendejong committed Sep 23, 2024
    Configuration menu
    Copy the full SHA
    4fc6e20 View commit details
    Browse the repository at this point in the history

  2. open file in parse_ped

    @ellendejong
    ellendejong committed Sep 23, 2024
    Configuration menu
    Copy the full SHA
    1e05063 View commit details
    Browse the repository at this point in the history

Commits on Sep 27, 2024

  1. add on push

    @ellendejong
    ellendejong committed Sep 27, 2024
    Configuration menu
    Copy the full SHA
    b185b49 View commit details
    Browse the repository at this point in the history

  2. add working dir to ruff

    @ellendejong
    ellendejong committed Sep 27, 2024
    Configuration menu
    Copy the full SHA
    f5965ca View commit details
    Browse the repository at this point in the history

Commits on Oct 4, 2024

  1. Filter paths as list

    @ellendejong
    ellendejong committed Oct 4, 2024
    Configuration menu
    Copy the full SHA
    7e47f74 View commit details
    Browse the repository at this point in the history

  2. add poetry group dev dependencies

    @ellendejong
    ellendejong committed Oct 4, 2024
    Configuration menu
    Copy the full SHA
    b8d54cd View commit details
    Browse the repository at this point in the history

  3. Add author

    @ellendejong
    ellendejong committed Oct 4, 2024
    Configuration menu
    Copy the full SHA
    dcf41b4 View commit details
    Browse the repository at this point in the history

  4. add Authors

    @ellendejong
    ellendejong committed Oct 4, 2024
    Configuration menu
    Copy the full SHA
    986175e View commit details
    Browse the repository at this point in the history

  5. poetry group dev dependencies

    @ellendejong
    ellendejong committed Oct 4, 2024
    Configuration menu
    Copy the full SHA
    2066991 View commit details
    Browse the repository at this point in the history

Commits on Oct 7, 2024

  1. revert changes

    @ellendejong
    ellendejong committed Oct 7, 2024
    Configuration menu
    Copy the full SHA
    2c309fe View commit details
    Browse the repository at this point in the history

  2. Use poetry to install dependencies in docker file.

    @ellendejong
    ellendejong committed Oct 7, 2024
    Configuration menu
    Copy the full SHA
    2bd6ec0 View commit details
    Browse the repository at this point in the history

  3. Increase poetry tool version.

    @ellendejong
    ellendejong committed Oct 7, 2024
    Configuration menu
    Copy the full SHA
    11c12bf View commit details
    Browse the repository at this point in the history

  4. Change function name read_kinship to read_and_modify_kinship

    @ellendejong
    ellendejong committed Oct 7, 2024
    Configuration menu
    Copy the full SHA
    35f45ed View commit details
    Browse the repository at this point in the history

  5. Delete poetry.lock and pyproject.toml from CustomModules dir

    @ellendejong
    ellendejong committed Oct 7, 2024
    Configuration menu
    Copy the full SHA
    c7f01aa View commit details
    Browse the repository at this point in the history

  6. Add final else.

    @ellendejong
    ellendejong committed Oct 7, 2024
    Configuration menu
    Copy the full SHA
    fd7492a View commit details
    Browse the repository at this point in the history

  7. Add 'validate' to function name.

    @ellendejong
    ellendejong committed Oct 7, 2024
    Configuration menu
    Copy the full SHA
    b67849b View commit details
    Browse the repository at this point in the history

  8. Add try-except when reading ped file.

    @ellendejong
    ellendejong committed Oct 7, 2024
    Configuration menu
    Copy the full SHA
    479d897 View commit details
    Browse the repository at this point in the history

  9. Use 'is' in type comparisons

    @ellendejong
    ellendejong committed Oct 7, 2024
    Configuration menu
    Copy the full SHA
    eb4ab75 View commit details
    Browse the repository at this point in the history

Commits on Oct 9, 2024

  1. Run pytest with poetry.

    @ellendejong
    ellendejong committed Oct 9, 2024
    Configuration menu
    Copy the full SHA
    18b7a19 View commit details
    Browse the repository at this point in the history

  2. Specify github action poetry version.

    @ellendejong
    ellendejong committed Oct 9, 2024
    Configuration menu
    Copy the full SHA
    3d80afa View commit details
    Browse the repository at this point in the history

  3. Dockerfile; poetry installation in its own isolated venv

    @ellendejong
    ellendejong committed Oct 9, 2024
    Configuration menu
    Copy the full SHA
    d6c3c02 View commit details
    Browse the repository at this point in the history

  4. Add VIRTUAL_ENV.

    @ellendejong
    ellendejong committed Oct 9, 2024
    Configuration menu
    Copy the full SHA
    0d3af94 View commit details
    Browse the repository at this point in the history

Commits on Oct 11, 2024

  1. use pip3

    @ellendejong
    ellendejong committed Oct 11, 2024
    Configuration menu
    Copy the full SHA
    da15079 View commit details
    Browse the repository at this point in the history

  2. Remove setuptools.

    @ellendejong
    ellendejong committed Oct 11, 2024
    Configuration menu
    Copy the full SHA
    3f4ef68 View commit details
    Browse the repository at this point in the history