Conversion from nose to pytest#2516

Merged

rwest merged 88 commits intoReactionMechanismGenerator:mainfrom

Aug 9, 2023

Commits on Aug 9, 2023

Instruct Docker, Github Actions, and users to use 'for_rmg' branch of RMS.
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remove deprecated rule from makefile phony list

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move testing files to test dir

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MOVE arkane tests, move database test

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move and rename files not following the naming convention

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fix conflicting test file names

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black formatting for all test files

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delete unnecessary name main statements

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manually switch testdatabase to assert from yield generator

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yet more name conflicts and pytest warnings

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remove nosetest asserts with nose2pytest

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remove external software folder - no longer relevant bc of conda

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use bare assert statements (pytest style)

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delete unmaintained requirements file

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update makefile, run all tests at once to avoid double aggregation time

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multiple co-dependent changes, see extended description

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tests running, but not passing. Ran Black

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fix skippable tests

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update the default filepath for `test_data` to its new location

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rename setup_class and teardown_class

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run tests in parallel, remove unnecessary run files

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yet more setUp -> setup_class etc.

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parallel test execution does not work with Julia and pytest

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fix use of np.float and np.bool

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consolidate test_data directories

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Fix np.int warning, by converting np.int into int

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Tiny fix to some setup_class and setup_method methods.

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Fix how file paths are detected in some tests.

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Fix gaussian executable detection in gaussianTest

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Use test-all target in Makefile during CI testing (and include database)

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Fix file path detection in some tests.

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Fix a couple more unit tests, and setup_class to setup_method

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Removed spurious '\' from some test database comments.

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more hacks for pytest compat, remove deprecated methods

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all tests running, fix numpy types compilation issue

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Import HinderedRotor2D etc. from torsions. all tests running, fix numpy types compilation issue

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remove unittest self.fail syntax, fix more tests, remove more dep meths

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multiple, see ext

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fix pytest-check install issue

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fix failed julia import warning

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Some changes that look like undoing previous changes.

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increased test verbosity for debuggin

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remove deprecated methods from docs

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remove gas phase warning - so much output it crashes runner

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fix gitignore for example dir - explicitly include some examples/arkane folders

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resolve #2489

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Configure pytest to use coverage (and other pytest config)

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more test patches, arkane test was basically killing itself after run

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more patches for failing arkane tests, fix coverage

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yet more deprecated documentation

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yet more and more test patches - changed coverage settings

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final patches for fixing codecov, some np.float warnings

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update outdated rule in makefile

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combine tests which were reliant on shared global state

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update makefile rule (don't run coverage) and .gitignore

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fix implicit global state dependence in failing tests

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skip the most dysfunctional tests

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remove windows batch files we can't use anymore

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Remove windows .bat files from examples folders
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skip the failing Toluene_Hindered_Rotor_SemiClassicalND example in arkane

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initial review comments - see ext

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Q2DTor - see ext.

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Convert some float to np.float64 in arkane/statmech.py

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Convert setup_class to setup_method in arrheniusTest
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Disable a few lines in examples/arkane/species/thermo_demo
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pytest requires skip reason to be a kwarg

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fix incorrect use of self in hinderedrotor2d test

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another useful option for running tests in `pytest.ini`

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Fix calcPath to calc_path in arkane and toluene example.
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Black formatting and fixing line endings in an example.
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update makefile rule for unit tests

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Adding another example output file to the .gitignore
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fix bad nosetest rounding conversion

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Rename Toulene examples folders to Toluene.
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Fix TestHinderedRotor2D tests
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Install Q2DTor in unit test workflow
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Remove the hack that lets julia step fail in the CI workflow
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Fix a typo in a comment.
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Convert .format() into f-string
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Fixing Q2DTor paths.
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Convert a few stragling np.float64 into float
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Replace deprecated np.float alias with float.
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Arkane tests skips examples that aren't actual inputs.
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Updating VSCode debug config test instructions for developers.
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Updated developer documentation about debugging tests.
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Added developer documentation about testing in VSCode.
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A comment in the pytest.ini about running tests in parallel.
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Added a test result to .gitignore
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