Drillcore Transformations

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  • Transforms measurements from drillcores.

  • Supports alpha, beta and gamma measurements.

  • Supports .csv and .xlsx files.

  • Supports adding the column names of your data files to a custom-built config.ini file for each user.

  • TODO: Convention support

  • Currently supported convention explanation found in Documentation and Help

  • Documentation and Help: https://drillcore-transformations.readthedocs.io.

Running tests

To run pytest in currently installed environment:

poetry run pytest

To run full extensive test suite:

poetry run doit
# Add -n <your-cpu-core-count> to execute tasks in parallel
# E.g.
poetry run doit -n 8 -v 0
# -v 0 is added to limit verbosity to mininum (optional)
# doit makes sure tasks are run in the correct order
# E.g. if a task uses a requirements.txt file that other task produces
# the producer is run first even with parallel execution

Formatting and linting

Formatting & linting:

poetry run doit pre_commit
poetry run doit lint

Building docs

Docs can be built locally to test that ReadTheDocs can also build them:

poetry run doit docs

doit usage

To list all available commands from dodo.py:

poetry run doit list


Development dependencies for drillcore_transformations include:

  • poetry

    • Used to handle Python package dependencies.

    # Use poetry run to execute poetry installed cli tools such as invoke,
    # nox and pytest.
    poetry run <cmd>
  • doit

    • A general task executor that is a replacement for a Makefile

    • Understands task dependencies and can run tasks in parallel even while running them in the order determined from dependencies between tasks. E.g. requirements.txt is a requirement for running tests and therefore the task creating requirements.txt will always run before the test task.

    # Tasks are defined in dodo.py
    # To list doit tasks from command line
    poetry run doit list
    # To run all tasks in parallel (recommended before pushing and/or
    # committing)
    # 8 is the number of cpu cores, change as wanted
    # -v 0 sets verbosity to very low. (Errors will always still be printed.)
    poetry run doit -n 8 -v 0
  • nox

    • nox is a replacement for tox. Both are made to create reproducible Python environments for testing, making docs locally, etc.

    # To list available nox sessions
    # Sessions are defined in noxfile.py
    poetry run nox --list
  • copier

    • copier is a project templater. Many Python projects follow a similar framework for testing, creating documentations and overall placement of files and configuration. copier allows creating a template project (e.g. https://github.com/nialov/nialov-py-template) which can be firstly cloned as the framework for your own package and secondly to pull updates from the template to your already started project.

    # To pull copier update from github/nialov/nialov-py-template
    poetry run copier update
  • pytest

    • pytest is a Python test runner. It is used to run defined tests to check that the package executes as expected. The defined tests in ./tests contain many regression tests (done with pytest-regressions) that make it almost impossible to add features to drillcore_transformations that changes the results of functions and methods.

    # To run tests implemented in ./tests directory and as doctests
    # within project itself:
    poetry run pytest
  • coverage

    # To check coverage of tests
    # (Implemented as nox session!)
    poetry run nox --session test_pip
  • sphinx

    • Creates documentation from files in ./docs_src.

    # To create documentation
    # (Implemented as nox session!)
    poetry run nox --session docs

Big thanks to all maintainers of the above packages!



Copyright © 2020, Nikolas Ovaskainen.


Module documentation for developers

References and Credits

Big thanks to PhD Jussi Mattila for his Brittle Structures course at the University of Turku, code snippets and tips for the development of this module and for handing over sample materials for testing.