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CHANGELOG.md

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Changelog

Release 2.2 (October 2023)

Package

  • Migrated from Python 2.7 to Python 3.9+ (Python modules & Python/C API).
  • Migrated from NUPACK 3 to NUPACK 4, while still using thermodynamic models compatible with NUPACK 3.
  • Updated the Python package definition, simplified the installation and adapted the instructions.
  • Dropped the dependence on the environment variable $NUPACKHOME.
  • Created an Apptainer container for fully reproducible development and deployment. For reproducible debugging, there is also a container variant including debug builds of Python and Multistrand, which are pre-configured with GDB and Valgrind.
  • Updated the tutorial scripts (tutorials/under_the_hood/) and corresponding Jupyter notebooks (tutorials/under_the_hood_notebooks/).
  • Updated, refactored and improved the test suite. Some of the small tutorials are now executed as part of the test suite.

Functionality

  • Updated the NUPACK thermodynamic parameters to dna04/rna99.
  • Updated the default kinetic parameters in EnergyOptions (C++) to match the parameter preset Options.JSDefault() (Python).
  • Tied the formerly static EnergyModel (C++) instance as a dynamic attribute to an Options (Python) object. This enables different SimSystem (Python) objects to reuse the same EnergyModel instance sequentially if created from the same Options object (i.e., to avoid re-parsing the same NUPACK parameter file), as well as to use different EnergyModel instances concurrently otherwise (e.g., for varying environment conditions or kinetic parameters). Henceforth, serialising an Options object requires a call to Options.free_sim_system().
  • Enabled deterministic trajectory replays starting mid-way, using Options.restart_from_checkpoint().
  • Improved utility.printTrajectory(), which is now normalized w.r.t. strand-level cyclic permutations and able to report PRNG seeds.
  • Consolidated and extended SimSystem.stateInfo() (formerly initialInfo()) to accept states other than the initial state, to list both uni- and bimolecular moves, to print the adjacent secondary structure for each move, and to use consistent formatting that allows for efficient parsing.
  • Introduced the utils.thermo module, which wraps the updated NUPACK utility functions (e.g., Boltzmann sampling, disabling coaxial stacking in thermodynamic model, adjusting concentration units in ensemble free energy).
  • Defined repeatedly used physical constants (e.g., Boltzmann, Celsius to Kelvin) in the options and utils.thermo modules.
  • Enabled toggling simulator debug traces from the Python runtime via Options.verbosity, i.e., without recompiling the C++ extension.
  • Improved the reliability of MergeSim (Python) by switching from the standard library module multiprocessing to the multiprocess package, and by using spawn for concurrency in order to properly isolate NUPACK utilities.
  • Added an exception in MergeSim when the user-defined OptionsFactory is not deterministic (up to Boltzmann sampling of initial states), or if it is not consistent with the MergeSimSettings.

Internals

  • Consolidated the C++ extension module based on the new treatment of SimSystem and Options.
  • Relocated code which was previously inside assertions, in order to enable compilation with NDEBUG.
  • Resolved a number of compiler warnings.
  • Introduced const expressions for better compile time optimization.
  • Introduced BaseType, which replaces the previous char encoding of primary structure, in order to improve maintainability.
  • Enforced a global ordering over strand objects, by preventing Strand.id and ComplementaryStrand.id from overlapping.
  • Stopped computing transition types when they are not used in the kinetic model (rate_method != 'Arrhenius').
  • Added SimTimer.seed as an external buffer for the Libc PRNG, in order to track the full random variable state during trajectory sampling.
  • Prevented repeated intermediate prints when using multiprocess in MergeSim.
  • Cleaned up print statements.
  • Removed several obsolete code sections.

Bug fixes

Python

  • Corrected swapped dimensions in the parameter preset Options.DNA23Arrhenius().
  • Added explicit type casts, type checks and overflow checks in the Options interface, in order to guard against type errors that could crash the Python/C API.

C++

  • Fixed some missing return statements which caused segmentation faults.
  • Fixed a reference counting bug which previously mangled Complex objects, leading to a crash when accessing a Complex post simulation.
  • Removed some redundant memory management calls at the Python/C interface.
  • Corrected undefined behavior related to loop indexing vs. array indexing.
  • Corrected undefined behavior related to printing adjacent loops.
  • Caught illegal initial structures that would cause undefined behavior.
  • Fixed nondeterministic behavior in Arrhenius model simulations due to uninitialized memory.

Release 2.1 (May 2018)

  • Moved to c++11 standard.
  • Reworked c++ internals: new files, classes, structs, enums, consts and various tostrings added. For example: struct BaseCount instead of int[] for storing exposed bases in a complex or loop. Settings imported from Python are now cached.
  • Many files that were no longer relevant or not working are now removed. Multistrand no longer supports the ViennaRNA thermodynamic model.
  • Tests of long-run equilibrium and equivalence of the energy model (w.r.t. NUPACK) are now working.
  • SimSystem object now supports .initialInfo(), which prints the internal representation of the initial state (also see tutorials/misc/inspection.py).
  • Fixed a bug (pointer comparison) that prevented deterministic execution.
  • Fixed a bug that required the user to rename parameter files when simulating RNA.
  • Multistrand now ships with convenience classes for multithreading (interface/concurrent.py -- various demos, for example tutorials/misc/computeAnnealRate.py).
  • Multistrand will now complain when the user does not explicitly set the uni- and bi-molecular rate constants, before setting them automatically (as before). Default parameterization is provided in multistrand.utils.
  • Multistrand now prints a warning when no initial moves are available in first step mode.
  • Multistrand now prints a warning when the simulation time is exceeded, but no stopping condition is met (provided they are set).
  • Multistrand now creates a logfile (multistrandRun.log) containing some of the simulation details. This file is overwritten each time a simulation is started.
  • Now supports buffer conditions (see f.a.q.).
  • Updated documentation.
  • Updated the installation guidelines.
  • Removed unused code from the installation files.
  • Added case study files for hybridization (tutorials/hybridization_casestudy).
  • Added a case study on leak rates (tutorials/leak_casestudy).
  • Added a function that generates a unique (hashable) value for each visited state (see tutorials/misc/uniqueID.py).
  • Added a commandline utility (and tutorial file) to compute hybridization rates (tutorials/misc/computeAnnealRate.py).
  • Convenience functions for standard experimental setups are available in multistrand.experiment (for example multistrand.experiment.hybridization(multistrand.Options(), string:sequence) -- also see tutorials/misc/computeAnnealRate.py).

(Aug 2017)

  • Expanding the leak case study (Mirnank Sharma), added FirstStepLeak object to handle leak simulations in concurrent.py (FD and MS).
  • A macOS bugfix.
  • Added error messages for object initialization (Mirnank Sharma).
  • Added compute folder for (commandline) utility in tutorials/.
  • Removed unused code in Make files and initialization routine.
  • Added files for simulating Machinek-Turberfield mismatch paper.

(Jul 2017)

  • Added support for nupack 3.2.1

Known issues

  • Because multithreading is handled outside the C++ core, error messages print once for each thread.