* 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
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Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
* add pandas construction
* removing csv writer
* replicating original behavior
* add rich table
* split into function
* make names clearer
* adding adjustments from rebase
* put it in a box
* adding tsv flag
* update tests to use tsv flag
* add smoke test for pretty print
* adding file creation test
* adding news item
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Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com>
* print message to stderr when no valid results files are found
* fix check
* move check into main function to keep single responsibility
* fix cmet test bug
* adding test
* reorg for clarity
* moving try/except into function for clarity
* reorg data parsing for clarity
* remove unused function
* add try/except to pass through info about failed edges
* updating tests for new expected failed simulation checking behavior
* pass through for raw and ddg
* pass through failures for dgs
* remove unused import
* adding a missing check
* docstrings
* cleaning up logic
* cleaning up logic
* docstrings and formatting
* fixing conditionals bug
* more docstrings
* make 'name' a tuple for consistency
* make functions private
* updating output statement for clarity (hopefully)
* remove unused dg raw expected output
* adding comment description
* updating tests
* cleaning up test to not use tmp dir
* only use non-None legs for deciding whether to do rbfe/rhfe
* fix typo
* pass empty list instead of None through to ddg
* add cmet data
* add assert success tests - still need output validation
* light reordering for clarity
* adding pytest regressions
* don't include stderr in file regression
* making output more legible
* switch from runtime error to exit(1)
* add missing complex legs test
* adding regressoin tsvs to manifest
* reordering functions for clarity
* updating tests
* adding test for disconnected network
* updating warning message, not throwing error for now
* updating tests for missing runs
* add disconnected network check
* switch from NaN to Error
* removing unused regression files
* fixing typo
* adding test coverage
* fix typo
* adding news entry
* updates to cli from_json
* replacing dump instances with to_json
* Remove unnecessary imports of JSON_HANDLER
* addressing review
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Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com>
Co-authored-by: David L. Dotson <dotsdl@gmail.com>
* adding output for failed edges
* adding print statements, tests don't pass yet because of extra output
* remove straggler
* Update openfecli/commands/gather.py
Co-authored-by: Josh Horton <Josh.Horton@newcastle.ac.uk>
* comment out exception check temporarily
* adding exception check back (test data was wrong)
* adding tests in progress
* trying different mocking
* adding unit tests
* cleaning up
* updating zenodo doi to use correct parallel rbfe dataset
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Co-authored-by: Josh Horton <Josh.Horton@newcastle.ac.uk>
* add type annotations
* use assert_click_success
* rename set_vals to leg_types for clarity
* formatting stdout whitespace for clarity
* formatting output to handle multiple legs in a clearer way
* docstring
* adding news item
* updating test match strings
* simplify legs error message
* updating tests for new error handling
* add docstrings
* Revert "add docstrings"
This reverts commit 6ae5d1d33492c78a95ace4dcc0ef3890c03e2318.
* adding fixture
* whitespace fixes
* added (failing) test for parallel results data
* add back all report types into testing
* include serial and paralell in paramterize
* adding support for raw output type
* expose uncertainty and estimate functions to gather
* pass dGs through - works but isn't pretty
* remove todo
* updating changelog
* updating changelog
* Update openfe/protocols/openmm_rfe/equil_rfe_methods.py
Co-authored-by: Hannah Baumann <43765638+hannahbaumann@users.noreply.github.com>
* fix type hint
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Co-authored-by: Hannah Baumann <43765638+hannahbaumann@users.noreply.github.com>
* update rbfe_results.tar.gz for new settings schema
* re-enable test_gather tests
* devscript for updating rbfe_results.tar.gz
* cli: gather: rework raw gather to work off protocol_result dict
this allows us to later deduplicate and remove the unit_results key from results dicts
* cli: gather: update expected gather results
current raw results are only one replicate, should probably have multiple repeats to test raw output
* cli: gather: use \t escape code in gather raw test
could instead normalise the whitespace to be more permissive...
* Apply suggestions from code review
Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com>
* rerun ci
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Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com>
