Changelog¶
Adapted from keepachangelog.com for org-mode.
See the git commit log history for full details.
1.1.0 - 2021-03-22¶
Fixes uninitialized discontinuities when not using boundary conditions in a
ContigTree
. (Fixes: 10.ghissue)Fixes mistake in the
ContigTree.lineages
function. (Fixes: 10.ghissue)Adds an option to account for discontinuities in
ContigTree.lineages
.Fixes the
WepyHDF5.observable_field_names
function.Fixes the
ContigTreeProfiler
functions for partitioning FE profiles into tranches:_tranche_cumulative_partitions
Fixes the setting of continuations in
ContigTree
initialization.Fixes computation of
ContigTreeProfiler.fe_profile_all
.Fix the arguments to the mapped function in
MacroStateNetwork.node_fields_map
Removed all implicit file opening in
MacroStateNetwork
except for in theBaseMacroStateNetwork
constructor. This allows for parallel processing.Improves calculations of transition counts when constructing
BaseMacroStateNetwork
objects. Now instead of only calculating the “weighted counts” for edges the “unweighted counts” are also calculated and the full set of transition sample weights are also saved as edge attributes. This change in interface is the reason for the breakages and regressions, see below.Addition of the
edge_attribute_to_matrix
to theBaseMacroStateNetwork
(andMacroStateNetwork
) classes. This generalizes and supercedes the use of the precomputedcountsmat
andprobmat
attributes. And makes the source-to-sink orientation of the matrix explicit and user controlled.Addition of edge attribute getting methods similar to the node ones:
get_edge_attribute
,get_edge_attributes
,get_edges_attributes
.Fixes the setting of the platform in the
OpenMMRunner
when thepre_cycle()
is called without a platform.Moves the
set_loglevel
function intowepy.util.util
thus making it a general purpose function rather than a helper to the orchestration CLI (see breakages, but we don’t expect anyone to have used this and is minor).
Breakages¶
The two attributes
countsmat
andprobmat
for(Base)MacroStateNetwork
classes have been removed, and superceded by theedge_attribute_to_matrix
method.The values of the columns of the nodes and edges dataframe have changed. They no longer have the ‘Weight’ column, which was for support of gephi tables, and was too tight a coupling. The edges dataframe will no longer have the ‘transition probability’ or ‘type’ columns. The latter for similar reasons and the former because this value is no longer calculated.
The
set_loglevel
function was removed fromwepy.orchestration.cli
towepy.util.util
, risk of breaking other peoples code is low (we can put a stub in for backwards compatibility if needed).
Regression¶
As stated in the Growth items, a potentially large amount of transition sample weights are stored in the
BaseMacroStateNetwork
object now.
1.0.7 - 2020-11-12¶
Adds a check to make sure the
platform
for therunners.openmm.OpenMMRunner
is a string and not an actualPlatform
object.Fixes the tranchecumulativepartition function in the
analysis.profiles
module.Pins version of
h5py
to less than version 3, which introduced breaking API changes.
1.0.6 - 2020-09-28¶
Fixes the
WepyHDF5.get_trace_field
function.Previously I had implemented a chunking strategy to improve performance for situations with very long traces. This has a bug somewhere in it. For the time being we have just reverted this optimization to the naive (but correct) approach. If an optimized version is introduced it will be made explicit (either in the
get_trace_field
call, or as a wrapper or separate method).
1.0.5 - 2020-09-14¶
Work around fix for final snapshot in orchestrator being deleted if it is the same hash as the last checkpoint snapshot.
1.0.4 - 2020-08-27¶
Fixes the broken CLI interface. Moves it into the standard
__main__.py
module.
1.0.3 - 2020-08-19¶
This fixes an issue with the MacroStateNetwork that allows for
different shapes of state assignment arrays. This was previously an issue but did not completely solve the issue.
1.0.2 - 2020-08-13¶
Fixes too-large chunk size when copying observable run data to other files in
WepyHDF5.copy_run_slice
Improves docstrings for the MacroStateNetwork methods
1.0.1 - 2020-08-07¶
This fixes an issue with the MacroStateNetwork that allows for different shapes of state assignment arrays.
1.0.0 - 2020-08-04¶
Changes in rc6:
adds feature to make weighted transition counts from simulation data. This was also made the way that the MacroStateNetwork calculates the counts and transition probabilities matrices.
Fixed initialization errors in the TaskMapper which would cause a zombie job.
Fixed implementation of the CPU Task process for OpenMM.
Fixed sim maker details in wepytools
Changes in rc5:
adds simulation monitoring via prometheus (or whatever) as a feature
Changes in rc4:
fixes bugs introduced to work mappers from rc2
Changes in rc3:
removed integration with
openmmtools.testsystems
in favor ofopenmm_systems
fork
Changes in rc2:
adds support for setting the OpenMM Platform at
run_segment
or inpre_cycle
add support for parametrizing apparatus components (runner, resampler, or BC) in the orchestration
Configuration
object.Fixes
wepy_tools.sim_makers
for no longer default arguments for resamplers.minor bugfixes found during testing.
Changes in rc1:
fixes bug in WorkerMapper
1.0.0rc1 - 2020-04-09¶
Changes in rc2:
adds support for setting the OpenMM Platform at
run_segment
or inpre_cycle
add support for parametrizing apparatus components (runner, resampler, or BC) in the orchestration
Configuration
object.Fixes
wepy_tools.sim_makers
for no longer default arguments for resamplers.minor bugfixes found during testing.
Changes in rc1:
fixes bug in WorkerMapper
1.0.0rc0¶
Prehistory