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- 7 commits
- 27 files changed
- 5 contributors
Commits on Oct 2, 2024
Commits on Oct 6, 2024
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Parallel read and preprocess the data in ABFE workflow (#371)
- Use joblib to parallelise the read and preprocess in ABFE workflow - add joblib as dependency - new kwarg n_jobs=1 for run() (and read()/preprocess()); default is n_jobs=1, which maintains the previous behavior - add tests - update CHANGES (start 2.5.0)
Commits on Oct 16, 2024
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correct error in tutorial for plot_convergence() (#422)
The function plot_convergence() expects a pandas dataframe as the single argument in the current implementation, causing it to fail when passed 4 different lists as arguments instead. This edit corrects the tutorial to appropriately pass a single dataframe with the appropriate column names, resulting in code that successfully reproduces the example graph.
Commits on Oct 29, 2024
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* docs\conf.py line-too-long Made line shorter, its end wasn't readable * src\alchemlyb\visualisation\dF_state.py too-many-branches Function plot_dF_state had 42 branches, while it is recommended not to have more than 12. The function is structured with clear blocks by logic and documentation. I extracted methods to encapsulate the logical blocks, reducing complexity. * src\alchemlyb\workflows\abfe.py too-many-branches Both methods generate_result and estimate had a bit too many branches. I extracted methods to reduce complexity and make code clearer. * src\alchemlyb\parsing\namd.py too-many-branches Two functions, extract_u_nk and _get_lambdas had too many branches. Smaller functions were extracted. * src\alchemlyb\parsing\amber.py line-too-long Made two readable lines shorter * src\alchemlyb\parsing\util.py line-too-long Made a readable line shorter * src\alchemlyb\visualisation\ti_dhdl.py too-many-statements The function plot_ti_dhdl had 81 statements, while it is recommended not to have more than 50. I extracted few smaller functions, reducing the length and increasing structure. * Add default value for mnb in get_determine_orientation The value of mnb is not set in the case of landscape orientation. It was like that even before extracting get_determine_orientation. However, now that this is a separated function, the test fails due to returning an unset variable. This might detect a bigger bug regarding not setting it unintentionally. * Fix _fit_estimators extraction _fit_estimators fails on E UnboundLocalError: cannot access local variable 'u_nk' where it is not associated with a value Since the goal is to reduce branches I revert that and extract the more isolated check_estimators_availability instead * Revert "Fix _fit_estimators extraction" This reverts commit f017972. * Revert "Add default value for mnb in get_determine_orientation" This reverts commit a1ea9d9. * Revert "src\alchemlyb\visualisation\ti_dhdl.py too-many-statements" This reverts commit d2ed7fa. * Revert "src\alchemlyb\parsing\namd.py too-many-branches" This reverts commit 7ece0f8. * Revert "src\alchemlyb\workflows\abfe.py too-many-branches" This reverts commit ea1ecca. * Revert "src\alchemlyb\visualisation\dF_state.py too-many-branches" This reverts commit 3a311d4. --------- Co-authored-by: Zhiyi Wu <zwu@exscientia.ai>
Commits on Nov 14, 2024
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Add entropy and enthalpy (#406)
* Add enthalpy and entropy calculations * Add enthalpy and entropy calculations * Update tests for coverage * black * Add bootstrapping to BAR().fit(use_mbar=True) and adapt tests for code coverage * Update CHANGES * Update get_group syntax * Update method default in bar when use_mbar==True * Remove enthalpy/entropy for BAR * Address review comments * Update docstrings for units.py for the case of entropy values * Update entropy attribute name from delta_s to delta_sT * Undo irrelevant addition
Commits on Dec 18, 2024
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add badge and how to cite (#426)
* fix #415 * add badge and how to cite * add to readme * update docs
Commits on May 15, 2025
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