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2311a2f2d9
* add more checks * make precommit manual * apply formatting to pyproject.toml * add TODO * remove unneeded, add a few more * add ruff, but turn everything off * add openfe known first party * format highest-level files * first half of openfe protocols * second half of openfe protocols * openfe protocols formatting, with alyssa's fmt skips * add ruff formatter to precommit * fmt: off all vendored _rfe_utils code * addressing review comments * format openfe/utils * format openfe/setup * first batch of cli formatting * second batch of cli formatting * formatting the rest of openfecli commands * format openfecli/parameters * format openfe/storage * run precommit * Update openfecli/commands/gather.py Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com> * update example notebooks branch for v1.7.0 docs changes (#1615) * bump example notebooks branch * add ipykernel to env * roll back to fixing septop branch * i dont think we want ipykernel * bump to tmp_fix_docs branch * point to branch revert-237-v1.7_cookbooks * point to latest example notebooks release * remove colab button, point to updated example notebooks, reorg landing page (#1618) * remove colab button from example notebooks in docs * point to example notebooks 2025.10.2 * replace 'try' with CLI --------- Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
43 lines
1.5 KiB
Python
43 lines
1.5 KiB
Python
"""Plugins for the ``fetch`` command"""
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from openfecli.fetching import URLFetcher, PkgResourceFetcher
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_EXAMPLE_NB_BASE = "https://raw.githubusercontent.com/OpenFreeEnergy/ExampleNotebooks/main/"
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RBFE_SHOWCASE = URLFetcher(
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resources=[
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(_EXAMPLE_NB_BASE + "openmm_rbfe/inputs/", "181L_mod_capped_protonated.pdb"),
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(_EXAMPLE_NB_BASE + "openmm_rbfe/inputs/", "Jnk1_ligands.sdf"),
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(_EXAMPLE_NB_BASE + "openmm_rbfe/inputs/", "benzene.sdf"),
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(_EXAMPLE_NB_BASE + "openmm_rbfe/inputs/", "ligands.sdf"),
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(_EXAMPLE_NB_BASE + "openmm_rbfe/inputs/", "styrene.sdf"),
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],
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short_name="rbfe-showcase",
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short_help="Inputs needed for the RBFE Showcase Notebook",
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section="hidden",
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requires_ofe=(0, 9, 1),
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).plugin
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RBFE_TUTORIAL = URLFetcher(
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resources=[
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(_EXAMPLE_NB_BASE + "rbfe_tutorial/", "tyk2_ligands.sdf"),
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(_EXAMPLE_NB_BASE + "rbfe_tutorial/", "tyk2_protein.pdb"),
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(_EXAMPLE_NB_BASE + "rbfe_tutorial/", "cli_tutorial.md"),
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(_EXAMPLE_NB_BASE + "rbfe_tutorial/", "rbfe_python_tutorial.ipynb"),
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],
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short_name="rbfe-tutorial",
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short_help="CLI and Python tutorial on relative binding free energies",
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section="Tutorials",
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requires_ofe=(0, 7, 0),
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).plugin
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RBFE_TUTORIAL_RESULTS = PkgResourceFetcher(
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resources=[
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("openfecli.tests.data", "rbfe_results.tar.gz"),
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],
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short_name="rbfe-tutorial-results",
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short_help="Results package to follow-up the rbfe-tutorial",
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section="Tutorials",
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requires_ofe=(0, 7, 5),
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).plugin
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