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CHANGELOG
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CHANGELOG
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thermotools changelog
=====================
Version 0.1.0 (Alpha):
- Providing WHAM + dTRAM
Version 0.1.1 (Alpha):
- Fixing include error for _wham.h
Version 0.1.2 (Alpha):
- Adding Travis-CI
- Relaxing unreasonably strict test case for WHAM
- Python 3 compatibility
- Adding unit tests for dTRAM
Version 0.1.3 (Alpha):
- Refactoring subpackages and function names
- Implemented BAR with logsumexp
- Updated docstrings
Version 0.1.4 (Alpha):
- Adding and refactoring unit tests
- Refactoring dTRAM
- Placing normalisation into iterate_fi
- Adding placeholders for TRAM/xTRAM
Version 0.1.5 (Alpha):
- Changing f_K_i to be b_K_i + f_i in dTRAM/WHAM
- Adding MBAR
- Refactoring WHAM/dTRAM
- Adding self-consistent iteration functions to pyx files in WHAM/MBAR/dTRAM
Version 0.1.6 (Alpha):
- Fixing MANIFEST.in
Version 0.1.7 (Alpha):
- Fixing docstrings
- Adding util module for counting state visits and transitions
- Adding msmtools (>=1.1) and scipy (>=0.11) dependencies
Version 0.1.8 (Alpha):
- Fixing float argument for range()
- Refactoring API
- Adding function to restrict samples and state sequence to a set of conf states
Version 0.1.9 (Alpha): [broken]
- Changing bias_energy_sequence axes in util's sample restriction function
- Minor changes in util's transition count function
- Replacing lse module by additional functions in util module
- Fix missing break statement in dTRAM estimation
- Making dTRAM prior available on Python level
- Adding loglikelihood/increment tracking to WHAM/dTRAM
- WHAM/dTRAM code cleanup
Version 0.1.10 (Alpha): [broken]
- Replace _MS_VER-dependent check by a defined check for INFINITY and NAN in _util.h
- Adding a callback to WHAM and dTRAM
- Refactoring continuous integration
Version 0.1.11 (Alpha): [broken on Windows]
- Fixing MANIFEST.in for building source distribution
Version 0.1.12 (Alpha):
- Fixing Windows-related bug
Version 0.1.13 (Alpha):
- Adding tags to estimators' C functions to allow reusing code
- Adding util function to compute bias energies from umbrella sampling
Version 0.1.14 (Alpha):
- Collect convergence information under save_convergence_info instead of err_out and lll_out
- Adding bias averaging function
Version 0.2.0 (Beta):
- Use ttrajs, dtrajs instead of the 2D dtraj argument in state_counts() and count_matrices()
- New feature: the state-continuous TRAM estimator
Version 0.2.1 (Beta):
- New feature: TRAMMBAR, an extension of the TRAM estimator
Version 0.2.2 (Beta):
- Fixes spurious division by zero warning
Version 0.2.3 (Beta):
- Dropping support for numpy<1.10 on conda
- Requires msmtools>=1.1.3
- New feature: mbar.estimate_therm_energies() computes only the thermodynamic free energies
- Fixes: self-consistency check in cset
- Removes several misleading warnings
Version 0.2.4 (Beta):
- Allow periodicity when computing umbrella sampling bias energies
Version 0.2.5 (Beta):
- Fix MSC-related problems
Version 0.2.6 (Beta):
- New and better algorithm ("reversible_pathways") for detecting the ergodically connected set of Markov states
- Changed meaning of "post_hoc_RE" and "BAR_variance" algorithms.
They used to be stricter versions of "summed_count_matrix", now they are based on "reversible_pathways".
Upcoming:
-