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fixed one remaining wrong date in CHANGES #391

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Sep 4, 2024
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fixed one remaining wrong date in CHANGES #391

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153 changes: 81 additions & 72 deletions CHANGES
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Original file line number Diff line number Diff line change
Expand Up @@ -7,18 +7,17 @@ The rules for this file:
* entries are sorted newest-first.
* summarize sets of changes - don't reproduce every git log comment here.
* don't ever delete anything.
* keep the format consistent (79 char width, M/D/Y date format) and do not
use tabs but use spaces for formatting
* keep the format consistent (79 char width, MM/DD/YYYY date format) and do
not use tabs but use spaces for formatting
* accompany each entry with github issue/PR number (Issue #xyz)
* release numbers follow "Semantic Versioning" https://semver.org

------------------------------------------------------------------------------

08/24/2024 xiki-tempula

* 2.3.2

Changes:
Changes
- Remove Python 3.9 support (issue #389, PR #390).

Enhancements
Expand All @@ -29,7 +28,7 @@ Enhancements

* 2.3.1

Changes:
Changes
- alchemlyb adopts SPEC 0 (replaces NEP 29)
https://scientific-python.org/specs/spec-0000/

Expand All @@ -43,23 +42,29 @@ Fixes

Changes
- Default value for keyword argument `initial_nk` of the MBAR estimator was
changed to "BAR" (run an initial BAR calculation before MBAR) instead of
`None` (start from all zeros) as this change provides a sizable speedup (PR #357)
changed to "BAR" (run an initial BAR calculation before MBAR) instead of
`None` (start from all zeros) as this change provides a sizable speedup (PR
#357)

Enhancements
- `forward_backward_convergence` uses the bootstrap error when the statistical error
is too large. (PR #358)

- `forward_backward_convergence` uses the bootstrap error when the
statistical error is too large. (PR #358)
- `BAR` result is used as initial guess for `MBAR` estimator. (PR #357)
- `forward_backward_convergence` uses the result from the previous step as the initial guess for the next step. (PR #357)
- `forward_backward_convergence` uses the result from the previous step as
the initial guess for the next step. (PR #357)


04/06/2024 hl2500, xiki-tempula

* 2.2.0

Changes
- Require pandas >= 2.1 (PR #340)
- For pandas>=2.1, metadata will be loaded from the parquet file (issue #331, PR #340).
- add support for Python 3.12, remove Python 3.8 support (issue #341, PR #304).
- For pandas>=2.1, metadata will be loaded from the parquet file (issue #331,
PR #340).
- add support for Python 3.12, remove Python 3.8 support (issue #341, PR
#304).

Enhancements
- Add a TI estimator using gaussian quadrature to calculate the free energy.
Expand All @@ -70,8 +75,8 @@ Enhancements
doesn't have the same length (issue #337, PR #338)

Fixes
- data_fraction column in workflow.convergence won't be affected by the
unit conversion (issue #350, PR#319).
- data_fraction column in workflow.convergence won't be affected by the unit
conversion (issue #350, PR#319).


06/22/2023 xiki-tempula
Expand All @@ -81,15 +86,18 @@ Fixes
Changes
- ValueError raised if concatenated amber output file is passed to amber
parser (issue #315, PR #326).
- Change the % based string formatting to {} based string formatting (issue #323, PR #324).
- Change the % based string formatting to {} based string formatting (issue
#323, PR #324).
- Use loguru instead of logging for log (issue #301, PR #303).

Enhancements
- "Statistical inefficiency" is logged at debug level for equilibrium_detection
and statistical_inefficiency (issue #295, PR#325).
- Add a parser to read serialised pandas dataframe (parquet) (issue #316, PR#317).
- "Statistical inefficiency" is logged at debug level for
equilibrium_detection and statistical_inefficiency (issue #295, PR#325).
- Add a parser to read serialised pandas dataframe (parquet) (issue #316,
PR#317).
- workflow.ABFE allow parquet as input (issue #316, PR#317).
- Allow MBAR estimator to use bootstrap to compute error (issue #320, PR#322).
- Allow MBAR estimator to use bootstrap to compute error (issue #320,
PR#322).

Fixes
- Fix the case where visualisation.plot_convergence would fail when the final
Expand All @@ -105,9 +113,9 @@ DeprecationWarning
* 2.0.1

Fixes
- Fix the dE method in u_nk2series to use the difference between two
lambda columns instead of using the next lambda column or the previous
column for the last window (issue #299, PR #300).
- Fix the dE method in u_nk2series to use the difference between two lambda
columns instead of using the next lambda column or the previous column for
the last window (issue #299, PR #300).
- work around hanging tests on Mac M1 by using Path.glob instead of glob.glob
in ABFE workflow (issue #309, PR #310).

Expand All @@ -117,8 +125,8 @@ Fixes
* 2.0.0

Changes
- use pymbar 4 as backend; this release is incompatible with
pymbar 3.x (issue #207, PR #268, discussion #205).
- use pymbar 4 as backend; this release is incompatible with pymbar 3.x
(issue #207, PR #268, discussion #205).
- The default for keyword argument `method` in estimators.MBAR was changed
from "hybr" to "robust" (issue #207, PR #268).

Expand All @@ -132,32 +140,32 @@ Removals
equivalent functionality. (issue #284)


09/12/2022 DrDomenicoMarson, xiki-tempula, orbeckst
12/09/2022 DrDomenicoMarson, xiki-tempula, orbeckst

* 1.0.1

Fixes
- make workflow.ABFE handle 0 as input to forwrev instead of crashing
(issue #276, PR #282).
- make workflow.ABFE handle 0 as input to forwrev instead of crashing (issue
#276, PR #282).
- Remove most of the iloc in the tests (issue #202, PR #254).
- AMBER parser now raises ValueError when the initial simulation time
is not found (issue #272, PR #273).
- AMBER parser now raises ValueError when the initial simulation time is not
found (issue #272, PR #273).
- The regex in the AMBER parser now reads also 'field=value' pairs where
there are no spaces around the equal sign (issue #272, PR #273).
- Pre-processing function slicing will not drop NaN rows (issue
#274, PR #275).
- Pre-processing function slicing will not drop NaN rows (issue #274, PR
#275).

Deprecations
- deprecate AutoMBAR for removal in 2.0 because pymbar 4 already contains
equivalent functionality (issue #284, PR #285).

Internal Enhancements (do not affect API)
- Blackfy the codebase (PR #280).
- Refactor the test to make all the parsing done at conftest level
(issue #206, PR #278).
- Refactor the test to make all the parsing done at conftest level (issue
#206, PR #278).


10/31/2022 orbeckst, xiki-tempula, DrDomenicoMarson
10/31/2022 orbeckst, xiki-tempula, DrDomenicoMarson

* 1.0.0

Expand Down Expand Up @@ -217,15 +225,15 @@ Fixes
* 0.7.0

Changes
- Deployment to PyPI is now done automatically using github actions
(Issue #193)
- gmx parser now defaults to dropping NaN and corrupted lines (filter=True)
- Deployment to PyPI is now done automatically using github actions (Issue
#193)
- gmx parser now defaults to dropping NaN and corrupted lines (filter=True)
(#171, PR #183)
- remove broken .zip support from util.anyopen() (PR #197)

Enhancements
- Add filter function to gmx.extract to make it more robust (PR #183): can filter
incomplete/corrupted lines (#126, #171) with filter=True.
- Add filter function to gmx.extract to make it more robust (PR #183): can
filter incomplete/corrupted lines (#126, #171) with filter=True.
- Add support to util.anyopen() for taking filelike objects (PR #197)

Fixes
Expand All @@ -248,15 +256,15 @@ Enhancements
Various malformations of input files are detected, where lambdas do not
monotonically increase or decrease, or are inconsistent or missing.
- Convenience function for decorrelating u_nk and dHdl (PR #163).
- Time convergence function forward_backward_convergence
introduced and plot_convergence now takes dataframe from
forward_backward_convergence as input (PR #168).
- Time convergence function forward_backward_convergence introduced and
plot_convergence now takes dataframe from forward_backward_convergence as
input (PR #168).
- Automatic MBAR solver with fall back (issue #170, PR #172)

Fixes
- Subsampling now works with bounds and step (PR #167, issue #166).
- AMBER parser logger now always logs to alchemlyb.parsers.Amber
instead of the root logger (PR #173)
- AMBER parser logger now always logs to alchemlyb.parsers.Amber instead of
the root logger (PR #173)
- updated deprecated pandas aggregation, now using groupby(level).agg (#175)


Expand All @@ -269,10 +277,12 @@ Changes (not affecting code)
#159, issue #160, PR #161)

Fixes
- MBAR estimator now correctly passes max_iterations to pymbar.MBAR. (PR #162)
- MBAR estimator now correctly passes max_iterations to pymbar.MBAR. (PR
#162)
- docs (PR #157)
- visualisation.df_state.plot_dF_state() now correctly raises ValueError instead
of NameError when incorrect orientation keyword argument is supplied
- visualisation.df_state.plot_dF_state() now correctly raises ValueError
instead of NameError when incorrect orientation keyword argument is
supplied


08/01/2021 xiki-tempula, orbeckst
Expand All @@ -281,22 +291,20 @@ Fixes

Changes
- alchemlyb adopts NEP29
https://numpy.org/neps/nep-0029-deprecation_policy.html
to effectively only support the last 2-3 minor Python versions
- Removed support for Python 2.7 and 3.6 (issue #130, #140):
supported/tested Python versions are 3.7, 3.8, 3.9 on
Linux, macOS, and Windows
https://numpy.org/neps/nep-0029-deprecation_policy.html to effectively only
support the last 2-3 minor Python versions
- Removed support for Python 2.7 and 3.6 (issue #130, #140): supported/tested
Python versions are 3.7, 3.8, 3.9 on Linux, macOS, and Windows
- The scipy constant for gas constant is used for parsers instead of the
constants used by the corresponding MD engine (issue #125, PR #129).
This leads to small changes in results from GROMACS simulations in kT
compared to the previous releases, with a relative difference on the order
of 1e-7.
- Added unit-awareness: the base unit remains kT but dataframes need to
carry the unit and temperature in a DataFrame.attrs so that dataframes
can be easily converted to different energy units (issue #125)
constants used by the corresponding MD engine (issue #125, PR #129). This
leads to small changes in results from GROMACS simulations in kT compared
to the previous releases, with a relative difference on the order of 1e-7.
- Added unit-awareness: the base unit remains kT but dataframes need to carry
the unit and temperature in a DataFrame.attrs so that dataframes can be
easily converted to different energy units (issue #125)
- The parser outputs dataframe with metadata (issue #125, PR #129).
- Visualisation module will change the data according to input unit
(issue #125, PR #129).
- Visualisation module will change the data according to input unit (issue
#125, PR #129).
- Bump the minimum pandas version to 1.2 (issue #130, #140).

Enhancements
Expand Down Expand Up @@ -341,11 +349,11 @@ Changes
* 0.4.0

Enhancements
- Allow the dhdl from TI estimator to be separated for multiple lambda
(PR #121).
- Allow the dhdl from TI estimator to be separated for multiple lambda (PR
#121).
- Allow the convergence to be plotted. (PR #121)
- Allow automatic sorting and duplication removal during subsampling
(issue #118, PR #119).
- Allow automatic sorting and duplication removal during subsampling (issue
#118, PR #119).
- Allow statistical_inefficiency to work on multiindex series. (issue #116,
PR #117)
- Allow the overlap matrix of the MBAR estimator to be plotted. (issue #73,
Expand All @@ -372,8 +380,9 @@ Enhancements
Deprecations

Fixes
- added explicit `return_theta=True` for call to pymbar.MBAR.getFreeEnergyDifferences,
as this was happening prior to changes in `pymbar` without the explicit call
- added explicit `return_theta=True` for call to
pymbar.MBAR.getFreeEnergyDifferences, as this was happening prior to
changes in `pymbar` without the explicit call

Changes

Expand Down Expand Up @@ -411,8 +420,8 @@ Changes
First release

Features:

- Parsers for GROMACS, including reduced potentials and gradients.
- Subsampler functions for slicing, statitistical inefficiency, equilibration detection.
- Minimally functional estimators for MBAR, TI.
- high test coverage (works with data in alchemistry/alchemtests)
- Parsers for GROMACS, including reduced potentials and gradients.
- Subsampler functions for slicing, statitistical inefficiency, equilibration
detection.
- Minimally functional estimators for MBAR, TI.
- high test coverage (works with data in alchemistry/alchemtests)
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