Changelog ========= Adapted from `keepachangelog.com `__ for org-mode. See the git commit log history for full details. .. _section-1: 1.1.0 - 2021-03-22 ------------------ - Fixes uninitialized discontinuities when not using boundary conditions in a ``ContigTree``. (Fixes: 10.gh\ :sub:`issue`) - Fixes mistake in the ``ContigTree.lineages`` function. (Fixes: 10.gh\ :sub:`issue`) - 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 the ``BaseMacroStateNetwork`` 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 the ``BaseMacroStateNetwork`` (and ``MacroStateNetwork``) classes. This generalizes and supercedes the use of the precomputed ``countsmat`` and ``probmat`` 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 the ``pre_cycle()`` is called without a platform. - Moves the ``set_loglevel`` function into ``wepy.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- The two attributes ``countsmat`` and ``probmat`` for ``(Base)MacroStateNetwork`` classes have been removed, and superceded by the ``edge_attribute_to_matrix`` method.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 from ``wepy.orchestration.cli`` to ``wepy.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. .. _section-2: 1.0.7 - 2020-11-12 ------------------ - Adds a check to make sure the ``platform`` for the ``runners.openmm.OpenMMRunner`` is a string and not an actual ``Platform`` object. - Fixes the :sub:`tranchecumulativepartition` function in the ``analysis.profiles`` module. - Pins version of ``h5py`` to less than version 3, which introduced breaking API changes. .. _section-3: 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). .. _section-4: 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. .. _section-5: 1.0.4 - 2020-08-27 ------------------ - Fixes the broken CLI interface. Moves it into the standard ``__main__.py`` module. .. _section-6: 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. .. _section-7: 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 .. _section-8: 1.0.1 - 2020-08-07 ------------------ This fixes an issue with the MacroStateNetwork that allows for different shapes of state assignment arrays. .. _section-9: 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 wepy\ :sub:`tools` 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 of ``openmm_systems`` fork Changes in rc2: - adds support for setting the OpenMM Platform at ``run_segment`` or in ``pre_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 in ``pre_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