python-intermediate-development

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As mentioned in #268, the lack of a way to easily install the project repo in a virtual environment makes it quite difficult to navigate some aspects of the course,...

bielsnohr

PEP8 specifies that imports should be put at the top of a Python file: https://peps.python.org/pep-0008/#imports Therefore, linters will complain for the tests explained in [Episode 2, Section 2, "Scaling Up...

bielsnohr

Additional section on continuous integration/continuous deployment?

7

Hey, We recently taught a workshop using this material see https://github.com/carpentries-incubator/python-intermediate-development/issues/159 . We organized an additional morning on continuous integration/continuous deployment. We added the section to the material in our...

svenvanderburg

running pytest for test_models.py fails

2

Running `pytest tests/test_models.py` from python-intermediate-inflammation directory fails and raises a ModuleNotFoundError: No module named 'inflammation' error I have tried to run it from the inflammation directory but it still doesn't...

bioinfwithjudith

In episode 4 of section 1 ("Collaborative Software Development Using Git and GitHub"), the term "working directory" is used when describing the file space where the git project is checked...

bielsnohr

Virtual Environments and Conda

5

A good number of learners are using Conda as their Python, and have expressed concern over using pip and virtualenvs. As far as I know you can just do `python...

smangham

In `Diagnosing Issues and Improving Robustness`, in the test `test_patient_normalise`, `npt.assert_almost_equal` is used to compare the actual and expected results. However, [it is recommended](https://numpy.org/doc/stable/reference/generated/numpy.testing.assert_almost_equal.html) to instead use `npt.assert_allclose`. This is...

p-j-smith

Checking an error is raised by a test

2

In the `Defensive Programming` section, there is a test for `patient_normalise` that checks a `ValueError` is raised when negative values are passed to the function: ```py with pytest.raises(raises): npt.assert_almost_equal(patient_normalise(np.array(test)), np.array(expected),...

p-j-smith

Adjust the advice given for running linter on CI

2

Currently the course recommends using a `--fail-under` score for the linting: > Note we need to add `--fail-under=0` otherwise the builds will fail if we don’t get a ‘perfect’ score...

thomaskileyukaea

anenadic