BETSE 0.9.0 (Lucky Levin) released.
Significant changes include:
* Python >= 3.5 required. In accordance with the looming end-of-life
(EOL) of Python 3.4, BETSE now strictly requires at least Python 3.5.
* Single-cell plots added. The following two single-cell plots may now
be added to both the initialization and simulation export pipelines:
* "ion_calcium_er", plotting all calcium (i.e., Ca2+) ion
concentrations for the endoplasmic reticulum of the single cell
indexed by the current simulation configuration over all sampled
time steps.
* "voltage_membrane_er", plotting all transmembrane voltages across
the endoplasmic reticulum of the single cell indexed by the current
simulation configuration over all sampled time steps.
* Deprecation warnings resolved. Deprecation warnings emitted by
py.test >= 3.1.0, Python >= 3.6, and recent versions of Numpy have
been summarily squelched.
* Simulation callbacks substantially improved, improving UX
responsiveness in downstream consumers (e.g., BETSEE). Specifically:
* Seed progress granularized. Progress for the seed phase is now
reported in a more granular (i.e., fine-grained) manner.
* Export progress. Progress on exporting CSV files, plots, and
animations from both the initialization export (i.e., "betse plot
init") and simulation export (i.e., "betse plot sim") phases is now
reported in a highly granular manner.
* Callbacks API generalized. Specifically, in the
"betse.util.type.call.callbacks" submodule:
* The new CallbacksBC.progress_stated() callback enables source
callables to notify sink callbacks of arbitrary human-readable
strings informing end users of the current state of progress. As
semantic sugar, the existing CallbacksBC.progressed_next()
callback has been augmented to accept the same strings.
* The new CallbacksABC.progressed_last() callback enables source
callables to safely iterate progress, improving robustness and
maintainability.
* Simulation variables streamlined. Specifically:
* All core simulation pathname variables now reside in the central
"Parameters" class rather than distributed across both that and the
"Cells" and "Simulator" classes, reducing logic across the codebase.
* The obsolete "Parameters.total_time_accelerated" variable has been
removed.
* All but one reference to the obsolete "Parameters._run_sim" boolean
have been removed in lieu of the "SimPhase.kind" enumeration.
* The obsolete Parameters.set_time_profile() method has been
refactored into the SimPhase._init_kludge_time() method.
* The "Parameters.init_tsteps" and "Parameters.sim_tsteps" variables
are now unconditionally defined rather than only conditionally
defined when the SimPhase._init_kludge_time() method is called.
* Matplotlib API sanitized. The antiquated
"betse.lib.matplotlib.matplotlibs" submodule now complies with the
modern Matplotlib API in a robust manner. Specifically:
* Headless Qt blacklisted. The default "Qt5Agg" backend is now
blacklisted when the current process is headless, preventing
Matplotlib from silently terminating this process.
* Visualization API improved. The "betse.science.visual.visabc"
submodule has been improved to preferentially leverage the
object-oriented Matplotlib API over the procedural "pyplot" API
where feasible, reducing unexpected exceptions from backends.
* Installation sanitized. Specifically:
* The top-level "MANIFEST.in" file now explicitly includes and
excludes all installation-time paths as appropriate.
* The top-level "setup.py" script now conforms to the more succinct
and hence saner approach of downstream consumers (e.g., BETSEE).
* Descriptor API added. The new "betse.util.type.descriptor.descs"
submodule defines general-purpose descriptors, including the
@classproperty_readonly and @abstractclassproperty_readonly decorators
implementing concrete and abstract read-only class properties
respectively.
* Iterable subpackage added. The new "betse.util.type.iterable"
subpackage now aggregates all subpackages pertaining to container
datatypes (e.g., iterables, queues, sequences). Specifically:
* Queue API added. The new "betse.util.type.iterable.queues" submodule
now aggregates queue-centric functionality, including the efficient
popping of multiple items from the head of a queue.
* Tuple API added. The new "betse.util.type.iterable.tuples" submodule
now aggregates tuple-centric functionality, including the efficient
creation of named tuple subclasses.
* CLI API generalized. The
"betse.util.cli.clicmdabc.CLISubcommandableABC" abstract base class
now helpfully provides a sane implementation of the abstract
_help_epilog() property, simplifying subclass implementation.
* Class decorator API generalized. The new
@betse.util.type.decorator.abstractclassmethod decorator trivially
enables definition of abstract class methods.
* Enumeration API generalized. The new
betse.util.type.enums.get_member_from_value() function expands the
functionality provided by the existing
betse.util.type.enums.get_member_from_name() function to enumeration
member values.
* Objects API generalized. The "betse.util.type.obj.objects" submodule
has been improved to:
* Enable callers to pass both classes and tuples of classes to
relevant submodule functions (e.g., die_if_instance()).
* Provide additional general-purpose getters for dynamically
retrieving arbitrary object attributes.
* Threading API generalized. The "betse.util.py.pythread" submodule now
provides quasi-portable functionality for validating whether the
active Python interpreter leverages a Global Interpreter Lock (GIL).
* Weak reference API generalized. The betse.util.py.pyref.refer_weak()
function now transparently creates weak references to bound methods,
which require special handling to avoid subtle race conditions.
* Module API shifted. The prior "betse.util.type.modules" submodule has
now been renamed to "betse.util.py.pymodule" for orthogonality.
* Continuous integration (CI) test suite improved. Specifically:
* Default simulation test expanded. The "betse_cli_sim_default"
functional test now exercise all simulation subcommands (i.e., seed,
initialization, and simulation) rather than merely the seed and
initialization subcommands, reducing the likelihood of edge-case
computational instabilities.
* Reference documentation improved. Specifically:
* Project badges (i.e., flat images synopsizing project health) have
been externalized from our front-facing "README.rst" document into
corresponding GitLab-aware project settings, improving both badge
visibility and aesthetics.
* The betse.util.py.pyref.proxy_weak() function docstring has been
significantly revised in accordance with the actual behaviour of the
underlying weakref.proxy() function.