Fix showcase tutorial #101
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mikemhenry
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May 2, 2024
* spruce up CI * now test the rc * Fix choose_protocol.ipynb * Duplicate openmm_rbfe/OpenFE_showcase_1_RBFE_of_T4lysozyme.ipynb history in showcase/openfe_showcase.ipynb history. * shave and a haircut - 2 bits * Fix showcase tutorial (#101) * fix showcase notebook * small fixes * added some stuff from hannah pr * update ligand_networks_for_developers.ipynb for 1.0rc0 * update benchmark_demo.ipynb for 1.0rc0 * first stab at changing examples to tyk2 * more switches to tyk2 * Add TYK2 image, remove T4L references * Remove output * Remove atom mapping CLI stuff * show options atom mappers and ligand networks * more notebook changes * Add tyk2 figure and logo * more changes showcase notebook * Adress review comments * Addressing review comments * fix mapping * transformation inputs as bullet points * see if python 3.10 works * lets see which python versions will work * rerun ci * update url for showcase installer * unpin python version in env * remove cell merged in by mistake * see issue #138 * some small fixes for google colab * just test on python 3.10 * pull down inputs for showcase * drop osx for now * put inputs in correct location * updated with results, see issue #141 * skip running nbval on openfe gather cells at the end * fix url for download * update manual spec of default settings for openff bump this is now 2.1.1 in 1.0 of openfe * use fetch results for demoing gather * use fetch to pull in inputs * we can run more cells in CI, also added a note about it being a single edige * fix Analysis typo * pulled down wrong inputs * Added a hack for google colab --------- Co-authored-by: hannahbaumann <hbaumann@uci.edu> Co-authored-by: Hannah Baumann <43765638+hannahbaumann@users.noreply.github.com> Co-authored-by: richard gowers <richardjgowers@gmail.com> Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
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