Separate environments #417
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Commits on Jan 26, 2024
Commits on Feb 5, 2024
Commits on Feb 15, 2024
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ignore DeprecationWarning and FutureWarning warnings in all internal/…
…external modules
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The utility used in OpenCADD (i.e. `opencadd.structure.core.Structure`) is just a wrapper around `MDAnalysis.Universe` with no added functionalities. Therefore, the `opencadd` dependency was removed and `MDAnalysis` was used directly instead, in order to avoid version pinning problems in `opencadd`.
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Suppress deprecation warnings in plip
plip has not updated its code with regard to new numpy versions, and thus the explicit casting `np.uint32(i)` in line 361 of `plip.basic.supplemental` (function `int32_to_negative`) throws thousands of warnings. These are suppressed here, as the warning suppression in our `util.__init__` is not catching these, probably due to setting of the logging level at the top of this module.
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The nootebook is re-run with the added environment. This caused some slight (numerical) changes (e.g. calculated binding affinities by `smina`, calculated interactions by `plip`) in the outputs, which were mentioned in the text. Therefore, the text was also edited to reflect the new results.
Commits on Feb 27, 2024
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CI: talktorial testing in python script
* talktorials are tested on shared environments * environments are placed in directory devtools * during testing the environment is created and all talktorials with that environment are run * talktorials and environments are connected in `devtools/test_configurations.yml`
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Commits on Feb 28, 2024
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Merge pull request #416 from AAriam/dev
Separate environment for T018
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