Welcome to Coordinator Data Tasks’s documentation!

Contents:

Coordinator Data Tasks

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A python-based command line utility to automate some of the most common data tasks faced by the Clinical Coordinators.

Features

  • left joins on multiple columns
  • smart loading of *.xls, *.xlsx, *.csv, *.csv.gz files

Credits

This package was created with Cookiecutter and the xguse/cookiecutter-pypackage project template which is based on audreyr/cookiecutter-pypackage.

Installation

Stable release

To install Coordinator Data Tasks, run this command in your terminal:

$ pip install coordinator_data_tasks

This is the preferred method to install Coordinator Data Tasks, as it will always install the most recent stable release.

If you don’t have pip installed, this Python installation guide can guide you through the process.

From sources

The sources for Coordinator Data Tasks can be downloaded from the Github repo.

You can either clone the public repository:

$ git clone git://github.com/xguse/coordinator_data_tasks

Or download the tarball:

$ curl  -OL https://github.com/xguse/coordinator_data_tasks/tarball/master

Once you have a copy of the source, you can install it with:

$ python setup.py install

Usage

From the command line

data_tasks --help

As a library

To use Coordinator Data Tasks in a project:

import coordinator_data_tasks

Source Code Documentation

coordinator_data_tasks package

Subpackages

coordinator_data_tasks.commands package
Submodules
coordinator_data_tasks.commands.left_join module
Module contents
coordinator_data_tasks.utils package
Submodules
coordinator_data_tasks.utils.errors module

Provide error classes for coordinator_data_tasks.

exception coordinator_data_tasks.utils.errors.DataTasksError[source]

Bases: Exception

Base error class for data_tasks.

exception coordinator_data_tasks.utils.errors.NoResult[source]

Bases: coordinator_data_tasks.utils.errors.DataTasksError

Raise when an iteration has nothing to return, but normally would.

exception coordinator_data_tasks.utils.errors.NotImplementedYet(msg=None)[source]

Bases: NotImplementedError, coordinator_data_tasks.utils.errors.DataTasksError

Raise when a section of code that has been left for another time is asked to execute.

__init__(msg=None)[source]

Set up the Exception.

exception coordinator_data_tasks.utils.errors.ValidationError[source]

Bases: coordinator_data_tasks.utils.errors.DataTasksError

Raise when a validation/sanity check comes back with unexpected value.

coordinator_data_tasks.utils.loaders module
coordinator_data_tasks.utils.recoders module

Provide functions to recode a dataframe column.

Each function should be in a form that can be handed to df[column_name].apply(func).

coordinator_data_tasks.utils.recoders.recode_dates(x)[source]

Return x recast as datetime[ns], or NaT.

Module contents

Submodules

coordinator_data_tasks.cli module

coordinator_data_tasks.coordinator_data_tasks module

Main module.

Module contents

Top-level package for Coordinator Data Tasks.

Contributing

Contributions are welcome, and they are greatly appreciated! Every little bit helps, and credit will always be given.

You can contribute in many ways:

Types of Contributions

Report Bugs

Report bugs at https://github.com/ScottSnapperLab/coordinator_data_tasks/issues.

If you are reporting a bug, please include:

  • Your operating system name and version.
  • Any details about your local setup that might be helpful in troubleshooting.
  • Detailed steps to reproduce the bug.

Fix Bugs

Look through the GitHub issues for bugs. Anything tagged with “bug” and “help wanted” is open to whoever wants to implement it.

Implement Features

Look through the GitHub issues for features. Anything tagged with “enhancement” and “help wanted” is open to whoever wants to implement it.

Write Documentation

Coordinator Data Tasks could always use more documentation, whether as part of the official Coordinator Data Tasks docs, in docstrings, or even on the web in blog posts, articles, and such.

Submit Feedback

The best way to send feedback is to file an issue at https://github.com/ScottSnapperLab/coordinator_data_tasks/issues.

If you are proposing a feature:

  • Explain in detail how it would work.
  • Keep the scope as narrow as possible, to make it easier to implement.
  • Remember that this is a volunteer-driven project, and that contributions are welcome :)

Get Started!

Ready to contribute? Here’s how to set up coordinator_data_tasks for local development.

  1. Fork the coordinator_data_tasks repo on GitHub.

  2. Clone your fork locally:

    $ git clone git@github.com:your_name_here/coordinator_data_tasks.git

  3. Install your local copy into a conda environment. Assuming you have conda installed, this is how you set up your fork for local development:

    $ cd coordinator_data_tasks/
$ make install

  4. Create a branch for local development:

    $ git checkout -b name-of-your-bugfix-or-feature

    Now you can make your changes locally.

  5. When you’re done making changes, check that your changes pass flake8, the tests, and that the docs build successfully, including testing other Python versions with tox:

    $ make test-all

  6. Commit your changes and push your branch to GitHub:

    $ git add .
$ git commit -m "Your detailed description of your changes."
$ git push origin name-of-your-bugfix-or-feature

  7. Submit a pull request through the GitHub website.

Pull Request Guidelines

Before you submit a pull request, check that it meets these guidelines:

  1. The pull request should include tests.
  2. If the pull request adds functionality, the docs should be updated. Put your new functionality into a function with a docstring, and add the feature to the list in README.rst.
  3. The pull request should work for Python 3.6. Check https://travis-ci.org/ScottSnapperLab/coordinator_data_tasks/pull_requests and make sure that the tests pass for all supported Python versions.

Tips

To run a subset of tests:

$ py.test tests.test_coordinator_data_tasks

Credits

Development Lead

Contributors

None yet. Why not be the first?

History

v0.0.5 / 2017-10-25

  • updated docs
  • Makefile: pull-req-check aliased to test-all
  • flake8
  • make test-all now tests docs build

v0.0.4 / 2017-10-25

  • travis tests now passing
  • changed pypi deploy target to 3.7
  • utils/loaders.py: added file (smart table loaders)
  • track some xls files for tests

v0.0.3 / 2017-10-24

  • Makefile: experimenting with install structure
  • test_coordinator_data_tasks.py: removed useless test
  • cli.py: added join subcommands
  • requirements.dev.pip.txt: mypy lives here now
  • docs/index.rst: fixed too few == under title
  • docs/conf.py: upgraded auto-build code
  • left_join.py: more log entries
  • moved recommonmark req to requirements.pip.txt
  • got tox to work
  • Makefile: experimenting with install structure
  • MANIFEST.in: add req files to allow tox to work
  • flake8
  • removed setup and test specific req files
  • README.rst: fixed badge address errors
  • fix repo in travis ci setup

v0.0.2 / 2017-10-23

  • prelim tests
  • allow from coordinator_data_tasks import commands
  • travis ci setup

v0.0.1 / 2017-10-23

  • setup.py: update metadata (language support)
  • configure tox
  • Makefile: formatting
  • Makefile: py.test -> pytest
  • setup.py: pick up reqs from req.txt files
  • setup.cfg: ignore some errors
  • Makefile: upgraded help, supported conda install
  • requirements.dev.txt: unpin for now
  • added commands pkg
  • added utils pkg
  • added extra requirements subfiles (pip,setup,etc)
  • ignore binary document extentions
  • ignore vscode and mypy_cache

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