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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>
21 lines
866 B
Python
21 lines
866 B
Python
import click
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from plugcli.params import Option
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N_PROTOCOL_REPEATS = Option(
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"--n-protocol-repeats",
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type=click.INT,
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help="Number of independent repeat(s) to be run per execution of a transformation using the ``openfe quickrun`` command.\n\n"
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"For example:\n\n ``--n-protocol-repeats=3`` means ``openfe quickrun`` will execute 3 repeats in serial.\n\n"
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" ``--n-protocol-repeats=1`` means ``openfe quickrun`` will execute only 1 repeat per call, "
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"which allows for individual repeats to be submitted in parallel by calling ``openfe quickrun`` on the same input JSON file multiple times.",
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)
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NCORES = Option("-n", "--n-cores", help="Number of cores to use for multiprocessing.")
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OVERWRITE = Option(
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"--overwrite-charges",
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is_flag=True,
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default=False,
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help="Overwrite any partial charges present in the input molecules.",
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)
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