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  • v1.1.1   BETSE 1.1.1 (Nicer Nestor) released. Significant changes include: * Dependencies bumped: * setuptools >= 38.2.0. The same version of setuptools required by BETSEE is now required by BETSE, ensuring parity between the two codebases and avoiding painful dependency conflicts. For uniformity, this dependency is repeated in both the top-level "pyproject.toml" and "tox.ini" configuration files. * Issues resolved: * pypa/pip#6163 and pypa/pip#6434. This commit circumvents a countably infinite number of issues introduced by both pip 19.0.0 and 19.1.0 - all pertaining to PEP 517 and 518, which is to say "pyproject.toml". The mere existence of a "pyproject.toml" file fundamentally breaks pip in inexplicable and horrifying ways: a significantly worse state of affairs than the pre-PEP 517 and 518 days of setuptools yore. Say what you will of setuptools ("...so much hate"), but at least it sorta worked. The same cannot be said of recent pip versions, which absolutely do not work whatsoever. "Die, pip! Die!" Specifically: * pypa/pip#6163 resolved. All files and subdirectories of the project directory containing the top-level "setup.py" script are now safely registered to be importable modules and packages. Technically, this should not be needed. The current build framework (e.g., pip, setuptools) should implicitly guarantee this to be the case. Indeed, the obsolete setuptools-based "easy_install" script does so. Sadly, pip >= 19.0.0 fails to do so for projects defining a top-level "pyproject.toml" file. Although upstream purports to have resolved this, the most recent stable release of pip continues to suffer this. This is suffering. * pypa/pip#6434 resolved. The top-level "pyproject.toml" file now explicitly declares a default value for the "build-backend" key. Doing so safeguards backward compatibility with pip 19.1.0, which erroneously violated PEP 51{7,8} by failing to fallback to a sane default value in the absence of this key. If this key is left undeclared, pip 19.1.0 fails on attempting to perform an editable (i.e., developer-specific) installation of this project. * tox-dev/tox#765 resolved. "tox" bundles an obsolete version of "virtualenv" itself bundling obsolete versions of both "pip" and "setuptools", which obstructs sanity. Our "tox.ini" configuration resolves this issue by instructing "tox" to manually update both "setuptools" and "virtualenv" to their most recent stable releases. * Entry points (i.e., wrapper scripts) resolved. Specifically: * Windows-specific entry points installable. Entry points yet again install as expected under non-WSL Windows variants (i.e., vanilla, Cygwin Windows). * Dependency entry points preserved. Long-standing issues with a custom monkey patch applied by our top-level "setup.py" script at setuptools-based application installation time have now been resolved. Previously, this patch globally applied to all dependencies installed by "easy_install" (but neither "pip" nor "conda", which fortuitously remain unaffected). Now, this monkey patch only locally applies to this project and downstream consumers of this project (e.g., BETSEE). * Setuptools validation relaxed. Validation of the currently installed version of setuptools has been relaxed to accept recent non-standard version strings (e.g., "41.6.0.post20191029"). * Testing improved: * GitLab CI + "tox". Specifically: * Rewrote the top-level ".gitlab-ci.yml" file from the ground up to test both installation and runtime on all supported Python 3.x versions (rather than runtime on the most recent stable Python 3.x version) and leverage industry standards, including: * A test matrix exercising all official Python version-tagged Docker images rather than a single unofficial Python version-agnostic Docker image (i.e., "continuumio/anaconda3"). Non-slim images are currently preferred to slim variants with names suffixed by "-slim" (e.g., "python:3.8-slim"), as the latter fail to include C and C++ compilers required to build and install wheels for Python packages both lacking official wheels and containing mandatory C extensions (e.g., "psutil"). * The Python-specific "pip" and Debian-based "apt" package managers rather than the Anaconda-based "conda" package manager. An initial "apt" package cache is now explicitly created before attempting to install system-wide packages requiring this cache. * The high-level "tox" wrapper rather than the lower-level "pytest" test harness. * The standard "virtualenv" package rather than GitLab-CI internals for isolating test results between different Python 3.x versions. * YAML anchor-based key mapping interpolation rather than external scripts for resolving DRY between different Python 3.x versions. * Defined a top-level "tox.ini" configuration file, installing all optional runtime dependencies to maximize test coverage. * Removed the top-level "requirements-pip.txt" file, which was frankly superfluous. * Documentation revised: * Installation instructions rewritten. These instructions have been revised from the ground up for simplicity, consistency, and with an increased emphasis on the standard pip ecosystem rather than the increasingly non-standard Anaconda ecosystem. Specifically: * "README.rst" truncated. The top-level "README.rst" file now provides only minimal instructions for installing BETSE under the two most popular platform-agnostic package managers: pip (recommeded) and Anaconda. * "INSTALL.rst" added. A new "doc/rst/INSTALL.rst" file providing verbose platform-specific instructions for installing BETSE under each supported platform (i.e., Linux, macOS, Windows) as well as Git-based development and Docker-based containerization has now been added. * "INSTALL.md" obsoleted. The "doc/md/INSTALL.md" file has been removed in favor of the new "doc/rst/INSTALL.rst" file, whose underlying reStructuredText is significantly easier to maintain. * The sub-level "doc/rst/INSTALL.rst" file * pip-based editable installation. The top-level "README.rst" file now advises developers to leverage pip rather than setuptools when performing an editable installation of this project. * "setup.cfg"-based PyPI documentation. The top-level "setup.cfg" file now transcludes the contents of the top-level "README.rst" file, a substantial improvement over the prior code-based approach strewn throughout the codebase (e.g., "setup.py", "betse_setup.buputil"). * Extraneous files removed. All irrelevant image masks have now been pruned from the "doc/yaml/paper" subdirectory. Doing so reduces the filesize of release tarballs, minimizes the maintenance burden, and presumably eliminates bitrot. * Git maintenance: * pip directories untracked. All top-level pip-specific temporary directories (e.g., "pip-wheel-metadata") are now ignored with respect to Git tracking. * API generalized: * Renamed: * The "betse.util.path.command" subpackage to "betse.util.os.command". * The "betse.util.test.tests" submodule to "betse.util.test.tsttest". * Generalized the top-level py.test-specific "conftest.py" plugin: * Defined a new private _clean_imports() function to perform the following when the active Python interpreter is isolated to a venv (e.g., due to being exercised by "tox"): 1. If the top-level directory for this project is listed in the global list of all import directories (i.e., "sys.path"), remove this directory from this list. Doing so prevents this test session from accidentally importing from modules not isolated to this venv, including this project being tested. 2. If the first directory on this list is not isolated to this venv, raise an exception. This condition implies that modules will be imported from outside this venv, which entirely defeats the purpose of isolating tests with "tox" to a venv. 3. If the top-level "betse" package is not isolated to this venv, raise an exception. This condition implies that this project has been imported from outside this venv. * Refactored the pytest_sessionstart() hook run at test session startup to sanitize import directories by calling the newly defined _clean_imports() function. Specifically, if this session is isolated to a venv, this hook now removes all import directories not isolated to this venv from "sys.path" -- as required for sane "tox"-based testing. (See above.) * Generalized the top-level "setup.py" script: * Called the newly defined betse_setup.buputil.die_unless_setuptools_version_at_least() validator to ensure the currently installed version of setuptools satisfies all installation-time requirements. * Added a new "test" key-value pair to the setuptools-specific "extras_require" dictionary, enabling "tox" to install all mandatory testing requirements of this application without duplicating those requirements in the top-level "tox.ini" file. * Generalized the "betse.exceptions" submodule: * Defined new "BetseFunctionUnimplementedException", "BetseProcessException", and "BetseProcessNotFoundException" classes. * Renamed the "BetseOSShellEnvException" class to "BetseShellEnvException". * Generalized the "betse.metadeps" submodule: * Defined a new "SETUPTOOLS_VERSION_MIN" global, providing the minimum version of "setuptools" required at both install- and runtime. Previously, this global was inaccessibly hardcoded into the coarse-grained "RUNTIME_MANDATORY" global. * Generalized the "betse.lib.setuptools.command.supcommand" submodule: * Defined a new "SetuptoolsCommandDistributionTypes" global tuple of all distribution types commonly passed to methods called by the "setuptools.command.easy_install.easy_install" class, suitable for use in type checking. * Defined a new "betse.lib.setuptools.command.supcmdbuild" submodule, preserving the most critical of the contents of the prior implementation of the "betse_setup.bupbuild" submodule: * For safety, this submodule now safely monkey patches "easy_install" in an application-local manner. * For reusability, this submodule is now generically applicable to arbitrary applications -- including both BETSE and downstream consumers thereof (e.g., BETSEE). * Refactored the _scriptwriter_get_args_patched() class method to: * Accept any "ScriptWriter" or "VersionlessRequirement" instance as the passed "distribution" parameter. * Silently defer to the default ScriptWriter.get_args() method under non-WSL Windows variants (i.e., vanilla, Cygwin Windows). * Generalized the "betse.util.cli.cliabc" submodule: * Improved the CLIABC._options_top() method to print human-readable version specifiers when the "-V" and "--version" options are passed, complete with optional human-readable codename (e.g., "BETSE 1.1.0 (Nice Nestor)"). * Defined a new "betse.util.os.process" subpackage: * Defined a new "betse.util.os.process.prctest" submodule: * Defined a new is_process_command() tester, returning true only if the parent process of the active Python interpreter is running an external command with the passed basename. This function currently requires the optional "psutil" dependency -- but could theoretically be expanded with platform-specific implementations circumventing this requirement. * Generalized the "betse.util.os.shell.shellenv" submodule: * Refactored the to_str() converter in terms of the mappings.to_str_flat() converter. * Defined a new "betse.util.py.module.pyimport" submodule: * Renamed the prior betse.util.py.pys.add_import_dirname() function to register_dir() for brevity and clarity. * Defined a new to_str_modules_imported_name() converter, returning a human-readable string of the fully-qualified names of all previously imported modules. * Defined a new "betse.util.py.pyvenv" submodule: * Defined a new is_venv() tester, returning true only if the active Python interpreter is isolated to a venv. * Defined a new get_system_prefix() getter, returning the absolute dirname of the top-level directory containing the system-wide Python interpreter. * Generalized the "betse.util.type.cls.classes" submodule: * Revised the die_unless_subclass() docstring to note that all classes are considered to be subclasses of themselves within the context of this function, complete with a minimal length example (MLE) demonstrating this. * Generalized the "betse.util.type.iterable.mapping.mappings" submodule: * Defined a new to_str_flat() converter, flattening the passed string-keyed and -valued dictionary into a human-readable string. * Refactored the "betse_setup.bupbuild" submodule to defer to the new "betse.lib.setuptools.command.supcmdbuild" submodule. * Generalized the "betse.lib.setuptools.command.supcmdtest" submodule: * Refactored the "test" subclass to inherit the test suite-specific "setuptools.command.test.test" superclass rather than the generic "setuptools.Command" superclass. * Generalized the "betse.util.path.dirs" submodule: * Renamed for disambiguity: * copy() to copy_dir(). * copy_into_dir() to copy_dir_into_dir(). * Defined a new die_if_subdir() function, raising an exception if the second passed directory is a subdirectory of the first passed directory. * Defined a new is_subdir() function, returning true if the second passed directory is a subdirectory of the first passed directory. * Defined a new remove_dir() function, recursively removing the passed directory after logging a warning and waiting several seconds for user intervention. * Revised docstrings for various existing functions. * Generalized the "betse.util.path.files" submodule: * Renamed for disambiguity: * remove() to remove_file(). * remove_if_found() to remove_file_if_found(). * Generalized the "betse.util.path.paths" submodule: * Renamed for disambiguity: * move() to move_path(). * Defined a new remove_path() function, either recursively removing the passed path if a directory or non-recursively removing this path if a file. * Generalized the "betse.util.type.obj.objtest" submodule: * Defined a new die_unless_is() validator, raising an exception if any passed object is not identical to every passed object. * Refactored the "betse_setup.bupbuild" submodule to defer to the new "betse.lib.setuptools.command.supcmdbuild" submodule. * Generalized the "betse_setup.buputil" submodule: * Minimized this submodule to the smallest set of requisite functions required by the top-level "setup.py" script. * Defined a new die_unless_setuptools_version_at_least() validator, copied verbatim from the "betsee.beuputil" submodule. * Generalized the die_unless_setuptools_version_at_least() function to use the general-purpose "distutils.version.LooseVersion" class rather than the strict "distutils.version.StrictVersion" class. * Debugged the "betse_test.func.sim.test_sim" submodule: * Improved the test_cli_sim_compat() functional test to squelch (i.e., silence) warnings emitted by matplotlib during this test. Specifically, interactive visualizations are now disabled during this test by enabling the "betse_cli_sim_compat" fixture to overwrite the old simulation configuration required by this test. (Bituminous arbiter delicately dangles the provocative invocation!)
  • v1.1.0   BETSE 1.1.0 (Nice Nestor) released. Significant changes include: * "--headless" option. The "betse" command now accepts a "--headless" option, permitting both end users and our test suite alike to explicitly enable headless operation. While the codebase did already detect most headless environments and thus automatically enable headless operation as needed, permitting interested parties to do so sanitizes numerous use cases. * Backward compatibility guarantee extended to BETSE >= 0.5.0. BETSE now guarantees backward compatibility with simulation configurations supported by relatively recent versions of BETSE (i.e., BETSE 0.5.0 and newer). * PyYAML -> ruamel.yaml >= 0.15.24 required. BETSE now requires the comment- and whitespace-preserving "ruamel.yaml" YAML roundtripper rather than the antiquated PyYAML parser. Inadequacies in the Python installation ecosystem (e.g., setuptools, wheels) prevent BETSE from permissively accepting one of several different YAML implementations at installation time. Since "ruamel.yaml" is the superset of all YAML implementations, BETSE 1.1.0 officially drops PyYAML in favour of "ruamel.yaml". * YAML 1.1 -> 1.2. All bundled YAML files have been trivially bumped from compliance with YAML 1.1 to 1.2 (i.e., the most recent YAML standard), resolving numerous valid complaints from "ruamel.yaml" at load time. To preserve backward compatibility with prior YAML-formatted simulation configuration files, files compliant with YAML 1.1 are implicitly interpreted as compliant with YAML 1.2 instead. * Mandatory dependencies bumped: * numpy >= 1.13.0. A recent version of numpy is now required, due to our widespread usage of the optional "axis" keyword argument passed to the numpy.unique() function first introduced by numpy 1.13.0. Doing so resolves a recent spate of CI failures in Windows-ish AppVeyor pipelines. * py.test >= 3.7.0. A recent version of py.test is now required, which introduced a new "package" scope for fixtures. This scope is required to efficiently initialize and deinitialize application metadata singletons for unit tests. * Deprecation warnings resolved: * A deprecation from the "betse" script wrapper. * A deprecation from the numpy.unique() function on failing to explicitly pass the "axis" keyword argument. * Numpy optimization detection. To improve detection of optimized Numpy installations (i.e., of a "numpy" package linked against a multithreaded BLAS implementation), application startup preferentially detects whether the active Python interpreter is managed by any of the following, in which case Numpy is guaranteed to be optimized: * The "conda" package manager. * The modern Gentoo Linux scientific stack (i.e., "eselect-ldso"). * Problematic matplotlib backends blacklisted (i.e., prohibited): * Unconditionally blacklisted all Qt 4-specific matplotlib backends (e.g., "Qt4Agg", "Qt4cairo"). The Qt Company ceased maintenance of Qt 4 in 2015, implying Qt 4 to be insecure, fragile, and largely unavailable. * Conditionally blacklisted all Qt 5-specific matplotlib backends (e.g., "Qt5Agg", "Qt5cairo") under headless environments. When headless, these backends reliably cause Qt 5 to silently fail with a segmentation fault. * Logging improvements: * Logfile rotation race conditions resolved. A long-standing issue inviting race conditions between multiple processes contending for write access to rotational logfiles has now been resolved, thanks to intrepid end user Edward Ned Harvey at the Levin Lab. Thanks a metric ton, Ed! * Logfile closure. Open logfile handles are now guaranteeably closed in a platform-portable manner at application shutdown, resolving Windows-specific "ResourceWarning: unclosed file" warnings. Namely: * The application metadata singleton is now unconditionally deinitialized at application shutdown (even in the event of fatal exceptions). * Our default logging configuration now removes all existing handlers from the root logger and close all open file handles maintained by those handlers at both initialization and deinitialization time. * Testing improvements: * "${DISPLAY}" squelched. The X.org-specific "${DISPLAY}" environment variable is now squelched during testing, resolving functional test failures. * Windows-specific warnings logged as informational non-warnings, a crude workaround to prevent PowerShell from erroneously raising non-human-readable exceptions on the first write to standard error. (Why!?) * "--export-sim-conf-dir" removed. The awkward "--export-sim-conf-dir" option previously accepted by our test suite has been obsoleted. * Our AppVeyor configuration now: * Locally resolves conda/conda#8836, a recent Windows-specific Anaconda change significantly breaking backward compatibility with most existing AppVeyor configurations -- including ours. To do so, the base Anaconda environment is now explicitly activated in an early-time manner. * Activates its "conda" environment via the "activate" command rather than the "conda activate" subcommand, which appears to be non-functional. * Coerces high-level PowerShell stream objects produced by running the "py.test" command into low-level strings. If omitted, PowerShell insanely interprets the first write to stderr as a non-human-readable exception. * Our GitLab-CI Runner configuration now: * Caches both "conda" environments and packages to project-local directories, which should reduce redundant pipeline overhead. * Imports environment variables required for sane "conda" usage and, in particular, the recently introduced "conda activate" subcommand. * Has been streamlined for porting to downstream consumers (e.g., BETSEE): * Removed all disabled configuration pertaining to "pip". Leveraging "pip" from a Miniconda-based configuration is fundamentally wrong. * Printed application metadata before running the test suite via the new "--headless" option. * Documentation improvements: * Docstring revisions for numerous subclasses in the "betse.science.config.export.visual" submodule for accuracy. * API generalizations: * Renamed the prior: * "betse.metaapp" submodule to "betse.appmeta". * "betse.util.app.meta.metaappabc" submodule to "betse.util.app.meta.appmetaabc". * "betse.util.app.meta.appmetadep" submodule to "betse.util.app.meta.appmetamod". * "betse.util.app.meta.metaappton" submodule to "betse.util.app.meta.appmetaone". * "betse.util.io.log.logconfig" submodule to "betse.util.io.log.conf.logconf". * "betse.util.io.log.logformat" submodule to "betse.util.io.log.conf.logconfformat". * "betse.util.io.log.loghandle" submodule to "betse.util.io.log.conf.logconfhandle". * "betse_test.fixture.metaapper" submodule to "betse_test.fixture.initter". * Generalized the existing "betse.exceptions" submodule: * Defines new exception classes, including: * "BetseMappingKeyException". * "BetseLogRaceException", unique to the aforementioned log rotation race condition. * Generalized the existing "betse.metadata" submodule: * Replaced all references to the obsolete static "SCRIPT_BASENAME" global with the dynamic betse.util.app.meta.appmetaone.get_app_meta().package_name() property, which properly applies to downstream consumers (e.g., BETSEE). * Renamed the "GIT_TAG_OLDEST_BACKWARD_COMPATIBILITY" global to "GIT_TAG_COMPAT_OLDEST" for brevity. * Reverted this global to "v0.5.0", restoring guaranteeable backward compatibility with all simulation configurations from BETSE >= 0.5.0. * Generalized the existing "betse.lib.matplotlib.matplotlibs" submodule: * Defined a new MplConfig.logger() property, yielding Matplotlib's root logger object (i.e., "matplotlib"). * Optimized the existing "betse.lib.numpy.numpys" submodule: * Defined a new _is_blas_optimized_conda() tester, deferring to the newly defined betse.util.py.pys.is_conda() tester. * Optimized the existing is_blas_optimized() tester to preferentially call the _is_blas_optimized_conda() tester first, which is guaranteed to be both the most optimal and portable solution. * Streamlined the existing "betse.lib.setuptools.command.supcmdtest" submodule: * Removed the obsolete "test.export_sim_conf_dir" instance variable. * Generalized the existing "betse.lib.yaml.yamls" submodule: * Refactored the load() function to accept a new optional "yaml_version" parameter, overriding any version directive prefacing the passed YAML-formatted file. When passed such a parameter with a value other than "1.1" (e.g., "1.2"), this function temporarily ignores all non-fatal warnings emitted by "ruamel.yaml" specific to the YAML 1.1 specification. * Defined a new "betse.lib.yaml.abc.yamlfileabc" submodule: * Shifted the prior "betse.lib.yaml.abc.yamlabc.YamlFileABC" superclass into this submodule: * Defined a new copy() method, encapsulating the lower-level load() and save() methods for safe copying YAML-formatted files. * Generalized the load() method to accept variadic keyword arguments, passed as is to the betse.lib.yaml.yamls.load() function. * Generalized the save() method to accept two new optional parameters: * "is_conf_file_overwritable", the overwrite policy for the passed target file. * "conf_subdir_overwrite_policy", the overwrite policy for subdirectories of this file. * Defined a new "YamlFileDefaultABC" superclass defining: * An abstract conf_default_filename() class property, returning the absolute filename of the subclass-specific default YAML file (e.g., default simulation configuration). * A concrete copy_default() method, copying this file to the passed target filename. * Removed the "betse.science.config.confio" submodule. * Generalized the existing "betse.science.parameters" submodule: * Refactored the "Parameters" class: * To subclass the newly defined "YamlFileDefaultABC" subclass. * Refactored the load() method to override any version directive prefacing all YAML-formatted files loaded by this method with "1.2", preserving backward compatibility with prior simulation configuration files erroneously prefaced by the "%YAML 1.1" directive. * Replaced all prior calls to the betse.science.config.confio.write_default() function with calls to the save_default() method. * Generalized the existing "betse.science.math.mesh" submodule: * Improved the DECMesh.refine_mesh() method to log rather than merely print informational messages. * Generalized the existing "betse.util.app.meta.metaappabc" submodule: * Refactored the "AppMetaABC" superclass: * Defined a new deinit() method, deinitializing both this application metadata singleton and the current application. * Defined the following new properties: * module_metadata(), the subclass-specific application metadata submodule. * module_metadeps(), the subclass-specific application dependency metadata submodule. * test_package(), the root test package for the current application if found or raises an exception otherwise. * test_dirname(), the absolute dirname of that package's directory if found or raises an exception otherwise. * test_data_dirname(), the absolute dirname of that package's data subdirectory if found or raises an exception otherwise. * Replaced all prior references to the prior abstract betse.util.cli.cliabc._module_metadata() property to the new module_metadata() property and removed the former. * Generalized the existing "betse.util.app.meta.appmetamod" submodule: * Defined a new merge_module_metadeps() function: * Dynamically creating and returning a new application dependency metadata module with arbitrary name iteratively merged from the contents of all passed application dependency metadata modules. * Copying the "RequirementCommand" class globally defined by the first such module into the output module. * Generalized the existing "betse.util.app.meta.appmetaone" submodule: * Defined a new deinit() function, conditionally encapsulating the lower-level betse.util.app.meta.appmetaabc.AppMetaABC.deinit() method. * Generalized the "betse.util.cli.cliabc" submodule: * Refactored the _make_options_top() method into an "_options_top" property, preserving orthogonality with the existing "betse.util.cli.clicmdabc._subcommander_top" property. * Refactored the "_is_option_matplotlib_backend" boolean property into an "_matplotlib_backend_name_forced" string property, enabling subclasses to force initialization of a desired subclass-specific matplotlib backend. * Defined a new "betse.util.io.log.conf" subpackage. * Defined a new "betse.util.io.log.conf.logconfcls" submodule: * Shifted the prior "betse.util.io.log.logconfig.LogConfig" class to "LogConf" in this submodule. * Generalized the existing "betse.util.io.log.conf.logconf" submodule: * Defined a new deinit() function calling a new betse.util.io.log.conf.logconfcls.LogConf.deinit() method, deinitializing the initialized logging configuration and hence closing all open file handles associated with this configuration. * Improved the existing init() function to reduce to a noop rather than reinitialize a previously initialized logging configuration. * Generalized the existing "betse.util.io.log.conf.logconfhandle" submodule: * Refactored the .LogHandlerFileRotateSafe" subclass: * Revised class and method docstrings for clarity, including a recommendation that external callers manually pass the "--log-file" CLI option when running concurrent BETSE processes. * Refactored the _emit_safely() method to: * Accept a "self" parameter, a critical bug fix. * Sleep for 100ms rather than 50ms. * Print additional debug output to standard error documenting this method's automatic resolution process. * Raise a human-readable exception on exhausting all other options, including the same recommendation as documented in docstrings. * Generalized the existing "betse.util.io.log.logs" submodule: * Renamed the get() function to get_logger() for disambiguity. * Generalized the existing "betse.util.io.stdouts" submodule: * Repaired the output_lines() function, which suffered a critical (albeit trivial) defect. * Defined a new "betse.util.os.brand.linux" submodule: * Defined a new is_mir() tester, returning true only if the active Python interpreter is running under the Mir compositor. * Defined a new is_wayland() tester, returning true only if the active Python interpreter is running under the Wayland compositor. * Shifted the existing betse.util.os.is_linux() tester into this submodule. * Defined a new "betse.util.os.brand.macos" submodule: * Shifted the existing betse.util.os.is_macos() tester into this submodule. * Defined a new "betse.util.os.brand.posix" submodule: * Defined a new is_x11() tester, returning true only if the active Python interpreter is running under an X11 display server. * Shifted the existing betse.util.os.is_posix() tester into this submodule. * Generalized the existing "betse.util.os.brand.windows" submodule: * Defined a new is_version_10_or_newer() tester, returning true if the current platform is Windows >= 10. * Defined a new get_api_version() getter, returning the current low-level Windows API (WinAPI, Win32) version. * Shifted the is_windows(), is_windows_cygwin(), is_windows_vanilla(), and is_windows_wsl() testers from the existing "betse.util.os.brand.os" submodule into this submodule. * Generalized the existing "betse.util.os.displays" submodule: * Defined a new is_dpi_scaling() tester, returning true if the current platform natively supports high-DPI scaling. * Refactored the is_headless() tester to defer to the most recent call to the newly defined set_headless() function (if any). * Defined a new set_headless() setter, enabling callers to explicitly force headless operation and hence override the implicit detection of headless environments performed by the is_headless() tester. * Generalized the existing "betse.util.os.kernels" submodule: * Defined a new is_version_greater_than_or_equal_to() tester, enabling callers to trivially detect minimum kernel versions and hence the existence of platform features introduced by those versions. * Revises the get_version() getter to return the high-level Windows kernel version (e.g., "10.0.10240") rather than the low-level Windows API version (e.g., "6.2.9200"). * Generalized the existing "betse.util.os.shell.shellenv" submodule: * Defined a new to_str() function, returning a human-readable string of all environment variables defined by the host shell environment. * Generalized the existing "betse.util.py.module.pymodname" submodule: * Defined a new make_module() function, enabling callers to dynamically generate new in-memory modules containing arbitrary module attributes. * Generalized the existing "betse.util.py.module.pymodule" submodule: * Defining a new is_module() tester, returning true only if the passed object is a module. * Generalized the existing "betse.util.type.obj.objects" submodule: * Refactoring the get_attr() getter to embed the fully-qualified name of the passed module when passed a module in raised exceptions. * Generalized the existing "betse.util.py.pys" submodule: * Defined a new is_conda() tester, returning true if the active Python interpreter is managed by conda. For debuggability, this metadata is now logged when the "info" subcommand is run. * Defined a new "betse.util.test.pytest.fixture" subpackage: * Defined a new "betse.util.test.pytest.fixture.pytfixture" submodule: * Defined a new monkeypatch_session() fixture, generalizing the standard function-scope "monkeypatch" fixture to session scope. * Generalized the existing "betse.util.test.pytest.pytests" submodule: * Defined a new output() function, printing the passed objects to standard output in a format consistent with that of standard "py.test" messages. * Generalized the existing "betse.util.type.iterable.iterables" submodule: * Defined a new to_str() function, synthesizing a human-readable prettified string of the passed iterable. * Improves the existing to_iterable() converter to behave as expected when passed an input generator. * Defined a new "betse.util.type.iterable.iteriter" submodule: * Defined a new iter_pairs() iterator, creating and returning a new iterable of all possible pairs of items in the passed iterable. * Defined a new iter_combinations() iterator, creating and returning a new iterable of all possible k-combinations of items in the passed iterable. * Generalized the existing "betse.util.type.iterable.mapping.mappings" submodule: * Defined a new die_unless_keys_unique() function, raising an exception unless no passed dictionaries collide (i.e., contain the same key). * Defined a new is_keys_unique() tester, returning true only if no passed dictionaries collide. * Defined a new iter_keys_ascending() iterator, returning an iterable of all keys of the passed dictionary in ascending order (typically, lexicographic). * Removed the unused (and largely useless) format_map() function, now superceded by the newly defined betse.util.type.iterable.iterables.to_str() function. * Defined a new "betse.util.type.iterable.mapping.mapmerge" submodule: * Shifted the betse.util.type.iterable.mapping.mappings.merge_maps() function into this submodule. * Defined a new "MergeCollisionPolicy" enumeration type whose members each describe a different type of key collision merger policy (i.e., strategy for merging keys shared by one or more mappings). * Refactored the merge_maps() function to: * Merge arbitrarily many dictionaries under any key collision policy. * Behave as expected when passed a non-sequence of input mappings. * Defer to the newly defined betse.util.type.iterable.mapping.maptest.die_if_maps_collide() validator. * Defined a new "betse.util.type.iterable.mapping.maptest" submodule: * Shifted all testing and exception handling logic from the "betse.util.type.iterable.mapping.mappings" submodule into this submodule. * Renamed the following functions for orthogonality: * die_unless_keys_equal() to die_unless_maps_keys_equal(). * die_unless_keys_unique() to die_unless_maps_keys_unique(). * is_key() to has_keys(). * is_keys_equal() to is_maps_keys_equal(). * is_keys_unique() to is_maps_keys_unique(). * Defined a new die_unless_has_keys() validator, raising an exception unless the passed mappings contains all passed keys. * Replaced the largely useless die_unless_maps_keys_unique() validator with a new die_if_maps_collide() validator, raising an exception only if no passed mappings collide. * Replaced the largely useless is_maps_keys_unique() tester with a new is_maps_collide() tester, returning true only if one or more passed mappings collide (i.e., contain key-value pairs containing the same keys but differing values). * Refactored the die_unless_maps_keys_unique() validator to improve the granularity of the exception message raised by this function, which now iteratively finds the exact set of key collisions in the passed dictionaries with the newly defined betse.util.type.iterable.iteriter.iter_pairs() iterator. * Refactored the has_keys() tester to accept a simple iterable of all keys to be tested rather than a variadic positional tuple of such keys. * Generalized the "betse.util.type.iterable.sequences" submodule: * Defined a new die_if_length_less_than() validator, raising an exception if the passed sequence contains less than the passed number of items. * Defined a new to_sequence() converter, converting the passed iterable into a sequence as needed. * Refactored the die_if_empty() validator to operate similarly to all other validators defined by this submodule. * Generalizes the "betse.util.type.iterable.mapping.maptest" submodule: * Refactored the is_maps_collide() tester to call the newly defined betse.util.type.iterable.sequences.die_if_length_less_than() and betse.util.type.iterable.set.sets.make_union() functions, thereby both simplifying and correcting the existing implementation. * Defined a new "betse.util.type.iterable.set" subpackage: * Shifted the existing "betse.util.type.iterable.sets" submodule to "betse.util.type.iterable.set.setcls" for disambiguity. * Defined a new "betse.util.type.iterable.set.sets" submodule: * Defined a new make_union() function, calculating the union of all items in arbitrarily many possibly non-set iterables. * Generalized the existing "betse.util.type.text.string.strs" submodule: * Refactored the get_prefix_preceding_char_or_none() getter: * Renamed this getter to get_prefix_or_none(). * Renamed the "char" parameter accepted by this getter to "anchor". * Added an optional "is_first" parameter to this getter, enabling callers to retrieve both greedy and non-greedy prefixes. * Streamlined the existing "betse_setup.buputil" submodule by removing extraneous functionality (e.g., die_unless_module(), is_module()). * Streamlined the existing "betse_test.conftest" submodule: * Removed all functionality pertaining to the ${DISPLAY} environment variable from the less robust and reusable pytest_configure() function in favour of the betse_test.fixture.initter.betse_autouse() fixture. * Removed the obsolete "EXPORT_SIM_CONF_DIRNAME" global. * Defined a new "betse_test.data" subdirectory embedding the default simulation configuration supplied by BETSE 0.5.0, enabling the betse_test.func.sim.test_sim.test_cli_sim_compat() functional test to fully exercise backward compatibility with this configuration. * Rewrote the "betse_test.fixture.initter" submodule: * Defined a new autouse package-scoped betse_init_package() fixture, intended to be imported by the "betse_test.unit.conftest" plugin to guarantee application initialization before unit testing. * Renamed the betse_meta_app() fixture to betse_autouse(), which now additionally unsets the ${DISPLAY} environment variable if set. * Moved the existing betse_test.conftest._init_app() and _deinit_app() functions into this submodule as init_app() and deinit_app() for importability elsewhere. * Generalized the existing "betse_test.fixture.simconf.simconfer" submodule: * Redefined the betse_sim_conf() fixture in terms of the lower-level betse_sim_conf_default() fixture. * Refactored the betse_sim_conf_compat() fixture to leverage the Git-hosted "betse_test/data/v0.5.0/yaml/sim_config.yaml" simulation configuration corresponding to the default configuration circa BETSE 0.5.0. * Generalized the existing "betse_test.fixture.simconf.simconfclser" submodule: * Refactored the "SimConfTestABC" superclass to initialize the application metadata singleton before saving a simulation configuration for the current functional test. * Refactored the "SimConfTestInternal" subclass to require general-purpose "src_conf_filename" and "trg_conf_filepath" filenames be passed on initialization. Previously, this subclass only accepted the latter and defaulted the former to the default simulation configuration file. * Generalized the existing "betse_test.fixture.simconf.simconfwrapper" submodule: * Refactored the "SimConfigTestWrapper" class: * Refactored the __init__() method to accept a high-level "Parameters" object rather than a low-level simulation configuration filename. * Removed a number of extraneous methods and properties (notably, the make_default() class method). * Generalized the existing "betse_test.func.fixture.clier" submodule: * Called the betse.util.app.meta.metaappabc.AppMetaABC.deinit() method before running each functional test. * Removed the obsolete "betse_test.func.sim.test_sim_export" submodule. * Generalized the existing "betse_test.func.sim.test_sim" submodule: * Removed all @skip decoration from the test_cli_sim_compat() test. * Defined a new "betse_test.unit.type.iterable.mapping.test_mapmerge" submodule, fully exercising the newly generalized betse.util.type.iterable.mapping.mapmerge.merge_maps() function (now featuring 667% more obscure Cthulhu mythos references). * Defined a new "betse_test.unit.app.meta.test_appmetamod" submodule, fully exercising the newly defined betse.util.app.meta.appmetamod.merge_module_metadeps() function. * Generalized the betse_test.unit.path.test_dirs.test_packages_init() unit test to exclude all data-specific directories from consideration, including both the "AppMetaABC.data_dirname" and "AppMetaABC.test_data_dirname" directories if found. * Generalized the existing betse_test.unit.type.iterable.test_iterables.test_to_iterable() unit test to exercise additional edge cases of that underlying function.
  • v1.0.0   BETSE 1.0.0 (Mighty Maxwell) released. Significant changes include: * Discrete exterior calculus (DEC). In the seed phase, BETSE now rigorously constructs the Voronoi diagrams and dual triangular meshes underlying all cell clusters according to DEC theory. DEC operators and methods are available for external use via the newly introduced "cells.mesh" object. * New "fast" and "full" solver types. BETSE can now work from an equivalent circuit model formalism (e.g. Hodgkin-Huxley based model of bioelectricity) using the new "fast" solver or from its original molecular view of bioelectricity using the "full" solver type. This allows users to tailor their computational perspective to the needs of their biophysical problem. * Expression profile read-in. BETSE can now read in expression levels from a user-defined expression configuration file for any custom-defined biomolecule, transporter, or channel. This allows different levels of a biomolecule, transporter, or channel to be specified on all of the user-defined tissue profiles of a BETSE model, where expression data can be sourced from experiments or experimental databases. * Single cell simulation. BETSE can now simulate a single cell, a feature requested for fast prototyping of certain simulations. * SVG model definition. In addition to the original bitmap method of defining cell cluster and tissue profiles, BETSE also allows use of Scalable Vector Graphics (SVG) files to define exact locations of cells in your cluster, with the fill colors of circles defined by these files now assigning the cell centred at that circle to the tissue profile associated with that color. * Mesh refinement. Optionally run a refinement algorithm on BETSE meshes to generate more computationally robust model geometries. * Modulator functions. Use a customizable modulator function (e.g. gradient along the x-axis) to modulate expression of custom biomolecules, transporters, or pumps. * Significant bugs resolved, including: * Gene regulatory network (GRN) equilibrium guarantees. Reactions and transporter rate expressions in user-defined GRNs now converge to the appropriate equilibrium constants. * Arrowhead size in exported visuals sanitized. Arrowheads in exported stream plots and animations are now sized appropriately rather than oversized. * Cation leak channels. * Deprecations and warnings resolved, including: * Deprecated usage of the "pytest.config" global. The betse_test.conftest.pytest_configure() hook now sets the "betse_test.conftest.EXPORT_SIM_CONF_DIRNAME" global to the value of the "--export-sim-conf-dirname" option, circumventing "pytest.config" entirely. * Deprecated usage of the yaml.load() function with no explicit "Loader". The betse.lib.yaml.yamls._load_pyyaml() function now dynamically calls whichever of the yaml.full_load() or yaml.load() functions are available for the current version of PyYAML, thus circumventing yaml.load() insecurities under newer PyYAML versions. * Simulation configuration improvements, including: * Nameable exports. A human-readable name (e.g., "Cell Cluster: Transmembrane Voltage") may now be associated with each pipelined export, including plots, animations, and CSV-formatted files. * Obsolete settings removed, including: * A vestigial block of intervention-specific settings. * Data descriptor encapsulation. Various settings derived from the currently open YAML-formatted simulation configuration file have now been refactored from low-level instance variables of the "betse.science.parameters.Parameters" class to high-level yaml_alias()-based data descriptors, enabling downstream consumers (e.g., the BETSEE GUI) to transparently propagate modifications to these settings back to this file. These include settings pertaining to: * Enumeration (i.e., indexation, numbering) of cells in the cell cluster. * Matplotlib colormap names. * Documentation improvements, including: * Tutorials. Official user- and developer-specific BETSE tutorials have now been added to the repository. A "Tutorials" subsection listing this documentation has also been the top-level "README.rst" file. * Simulation configuration settings, including: * Application-specific matplotlib colormaps. Our default YAML-formatted simulation configuration file now exhaustively lists the names of all available application-specific matplotlib colormaps. * Test suite improvements, including: * "py.test" exit code. The top-level "test" script now correctly reports the exact exit code reported by the "py.test" test suite. * Additional unit tests, including: * The "betse_test.unit.type.iterable.test_iterables" submodule, which now exercises the overly intricate and hence fragile betse.util.type.iterable.iterables.to_iterable() function. * Debuggability improvements, including: * Type validation debuggability. Wrapper functions synthesized by the @type_check decorator now sport the disambiguous name "__{func_name}_type_checked__" rather than the ambiguous name "func_type_checked". * API generalizations, including: * The "betse.science.pipe" subpackage, such that: * The existing SimPipeABC.iter_runners_conf() method is now constrained to strictly return indexable sequences rather than possibly non-indexable iterables, as external callers commonly require the former. * The new SimPipeABC.iter_runners_metadata_kind() method returns a sequence of the types of all runners declared by the current pipeline (in sorted lexicographic order). * The prior "SimPipeRunnerMetadata.name" instance variable has been renamed to "SimPipeRunnerMetadata.kind" for disambiguity with the unrelated "name" data descriptor of runner subconfigurations. * The "betse.lib.matplotlib.mplcolormap" submodule, which defines: * The iter_colormap_names() iterator, yielding the names of all currently registered matplotlib colormaps (in sorted lexicographic order). * The "betse.util.math.geometry.geopoint" submodule, whose is_point() function has been generalized to test whether coordinates of each passed point are strictly numeric or not. * The "betse.util.type.iterable.iterables" submodule, whose: * to_iterable() function has been generalized to optionally accept an "item_cls" parameter, which when non-None coerces all items of the returned iterable to instances of that parameter. * The "betse.util.type.iterable.iterget" submodule, whose: * Newly defined get_item_first() and get_item_first_or_sentinel() functions retrieve the first items from arbitrarily many iterables. * get_item_str_uniquified() has been generalized to optionally implicitly synthesize default string values for non-compliant items, as needed for preserving backward compatibility. * The "betse.util.type.iterable.itersort" submodule, whose: * _sort_iterable() function has been optimized for the common case of generators and generator comprehensions. * The "betse.util.type.iterable.itertest" submodule, whose: * is_items_unique() function has been: * Generalized to support iterables not satisfying the "collections.abc.Sized" protocol (e.g., generators). * Optimized to induce best-case time complexity in the average case. * The "betse.util.type.iterable.mapping.mappings" submodule, which defines: * A pair of related die_unless_keys_equal() and is_keys_equal() functions, efficiently validating and testing whether the passed set of dictionaries all contain the exact same keys. * The "betse.util.type.iterable.sequences" submodule, which defines: * The get_index() function, enabling callers to retrieve items with arbitrary indices from arbitrary sequences in a manner guaranteed to raise human-readable exceptions on failure. * The "betse.util.type.obj.objects" submodule, whose: * get_method() function has been renamed to get_callable(). * get_method_or_none() function has been renamed to get_callable_or_none(). * "method_name" parameters accepted by both of the aforementioned functions have been renamed to "callable_name". * The "betse.util.type.text.string.strjoin" submodule, which defines: * A new join_iterable_as_conjunction_double_quoted() function implicitly coercing all items of the passed iterable to strings. * The "betse.util.type.types" submodule, which now defines: * The special "MethodWrapperType" type, formerly available only under Python >= 3.7 as "types.MethodWrapperType". * A "ContainerTypes" type supporting both standard Python containers and Numpy arrays, replacing the prior "ContainerType" type not supporting Numpy arrays. * A "SequenceStandardTypes" tuple of all standard sequence types (i.e., "list", "tuple"). * Significantly fewer obsolete testers and asserters, which have now been permanently removed in favour of the @type_check decorator.
  • v0.9.2   BETSE 0.9.2 (Luckiest Levin) released. Significant changes include: * Downstream data dirname issues resolved. Previously, downstream consumers (e.g., the BETSEE GUI) were erroneously required to recreate rather than share the default simulation configuration provided by the BETSE codebase. This has now been resolved, reducing unseemly Don't Repeat Yourself (DRY). * Gene regulatory network (GRN) pathname issues resolved. Specifically, the "gene regulatory network settings/gene regulatory network config" setting in YAML-formatted simulation configuration files has now been generalized to be relative to the directory containing those files. * Resource consumption reduced. Matplotlib-based figures, graphs, plots, and animations are now properly destroyed on completion, substantially reducing memory usage during long-running simulation exports. * Deprecation warnings eliminated. The codebase now complies with all upstream deprecations, including breaking NumPy, py.test, and Python changes. Notably, NumPy >= 1.16 has deprecated the passing of arbitrary iterables to the np.column_stack() function, which now requires strict sequences: FutureWarning: arrays to stack must be passed as a "sequence" type such as list or tuple. Support for non-sequence iterables such as generators is deprecated as of NumPy 1.16 and will raise an error in the future. Since converting non-sequence iterables to sequences is trivial (ignoring the obvious edge case of infinite generators, which much like the legendary Pokemon of yore appear not to exist in the wild), NumPy developers chose poorly when they chose to explicitly break rather than implicitly resolve this non-issue. Thanks for generating more meaningless boilerplate, NumPy. * Significant continuous integration (CI) improvements, including: * Conda-forge-centric testing. All CI host environments (i.e., GitLab-CI, AppVeyor) now install all mandatory and optional application dependencies from the open-source volunteer "conda-forge" channel rather than the closed-source proprietary "anaconda" channel. Doing so better mimics real-world installation environments and enables us to begin exercising optional dependencies (e.g., FFmpeg, NetworkX, PyDot). * Early-time logging verbosity increased. To simplify testing maintenance, Early-time logging verbosity increased has now been increased during tests. * CI-specific decorators added. The new betse.util.test.pytest.mark.pytskip.skip_if_ci_gitlab() decorator skips the decorated test or fixture if GitLab-CI is currently hosting these tests. * The following previously failing tests have been corrected: * The test_packages_init() unit test, which is now conditionally skipped under GitLab-CI by the aforementioned decorator. GitLab-CI no longer clones this repository correctly, erroneously preserving empty subdirectories no longer tracked by git. While usually innocuous, empty subdirectories trigger false negatives from this unit test. Since this test succeeds both locally and under AppVeyor, GitLab-CI's misconfigured git checkout policy inexplicably remains the culprit. * The test_c_* pair of unit tests, which erupted into incoherent flames due to inappropriate assumptions about the internal structure of NumPy. NumPy 1.16.0 unified the prior public "numpy.core.multiarray" and "numpy.core.umath" C extensions into a new private "numpy.core._multiarray_umath" C extension. * The pivotal test_cli_sim_compat() functional test, which has now been reenabled in a manner seemingly incompatible with recent py.test changes. Since this test safeguards backward compatibility with respect to our YAML-based simulation configuration format, enabling this test is critical to long-term joy. * Installation-time improvements, including: * Substantial "setup.py" streamlining. The contents of our topmost setuptools-based installation script now reflect those of their counterpart in the BETSEE GUI -- which is to say, this script has been compacted into a fairly minimal line length. * "betse.metadata.PYTHON_VERSION_MINOR_MAX" addition. This integer global specifies the maximum minor stable version of the Python 3.x mainline, as required by this "setup.py" streamlining. * "betse_setup.buputil" streamlining. This submodule collects miscellaneous utility functions required only at BETSE installation. This submodule has now been reduced in length, reducing our maintenance burden. * Significant internal API improvements, including: * Application API creation. The new "betse.util.app" subpackage now provides: * The prior "betse.util.meta" subpackage, which has been subsumed under "betse.util.app.meta" for maintainability. * Application pathname API creation. The new "betse.util.app.apppath" submodule enables callers to query the absolute pathnames of application-relative paths regardless of application installation specifics (e.g., setuptools-based egg, frozen application). * Application initialization API centralized. The existing "betse.util.app.meta.metaappabc.MetaAppABC" superclass now centralizes all application initialization logic into a single coherent object-oriented API previously distributed throughout the codebase as a cacophony of incoherent procedural APIs not reusable by downstream consumers. This includes: * The "MetaAppABC" constructor, which now guarantees the current application to be completely initialized excluding third-party dependencies (e.g., NumPy, SciPy), whose initialization must necessarily be deferred until later in the application startup process. This constructor now entirely obsoletes the prior "betse.ignition" API. * The MetaAppABC.init_libs() method, which now initializes third-party dependencies (e.g., NumPy, SciPy) in a user-configurable manner late in the application startup process. This method now obsoletes a significant portion of the existing "betse.lib.libs" API. * The MetaAppABC.init_libs_if_needed() method, which efficiently simplifies the aforementioned process on behalf of low-level automation (e.g., dark voodoo in the "betse.science.__init__" module). * Application metadata singleton API creation. The new "betse.util.app.meta.metaappton" submodule centralizes all logic concerning the application metadata singleton previously residing in the "betse.metaapp" submodule. * Bitwise API creation. The new "betse.util.type.numeric.bits" submodule now provides general-purpose bit and bit field functionality, including an is_bit_on() function implementing a standard bit field testing routine. * Matplotlib Figure API creation. The new "betse.lib.matplotlib.mplfigure" submodule defines critical functionality for reliably closing matplotlib figures, a prevalent "pain point" in most matplotlib-based applications. * Testing API creation. The new "betse.util.test" subpackage now defines testing-specific APIs, including: * The new "betse.util.test.tests" submodule, defining general-purpose test suite functionality. This includes the is_testing() tester, enabling the codebase itself to query whether or not it is currently being tested. * The new "betse.util.test.tstci" submodule, defining CI-specific functionality. This includes one tester for each well-known CI host (e.g., is_ci_gitlab() for GitLab-CI), returning true only when the active Python interpreter is exercising tests on that host. * The new py.test API. The BETSE-specific and hence non-reusable "betse_test.util" subpackage has been moved to the BETSE-agnostic and hence reusable "betse.util.test.pytest" subpackage, enabling reuse by downstream consumers (e.g., BETSEE). * Class API generalizations. The "betse.util.type.cls.classes" submodule now defines a host of new general-purpose getter functions, including: * get_name_qualified(), obtaining the fully-qualified name of the passed class. The implementation proved highly non-trivial, due to common edge cases (e.g., classes with no or poorly defined modules). * get_module_name_qualified_or_none(), obtaining the fully-qualified name of the module defining the passed class if any or "None" otherwise. * Module API generalizations. A new "betse.util.py.module" subpackage has been created, replacing the prior "betse.util.py.pymodule" submodule. This subpackage provides the following new submodules: * "betse.util.py.module.pymodname", providing lookup facilities both to and from fully-qualified module names and their corresponding module objects. * "betse.util.py.module.pymodule", providing generic module handling. * "betse.util.py.module.pypackage", providing generic package handling -- notably, the get_object_type_package_root() function returning the root package transitively defining any arbitrary object's class. * String API generalizations. The existing "betse.util.type.text.strs" submodule now defines a holy trifecta of "get_prefix_preceding_char"-prefixed functions, enabling callers to obtain the prefix preceding any character in arbitrary strings. * Obsolete subdirectories removed, including: * The long-broken "doc/examples" subdirectory, whose code snippets have all non-working for at least several major application revisions. While documentation in and of itself is commendable, bad documentation is readily worse than no documentation. * The long-unused "betse/data/yamale" subdirectory.
  • v0.9.1   BETSE 0.9.1 (Luckier Levin) released. Significant changes include: * Cell boundary search radius increased, improving simulation stability in worst-case spatial layouts for user-defined cell clusters. * MetaAppABC API added. The new object-oriented "betse.metaapp" submodule replaces the prior procedural "betse.pathtree" submodule, enabling inheritance-fueled reuse from downstream consumers (e.g., BETSEE). The MetaAppABC API is intended to eventually encompass all general-purpose functionality required.to implement BETSE-like applications -- including application initialization, dependency resolution and initialization, and a nominal command-line interface (CLI). * Git API generalized. The new betse.util.path.gits.get_package_worktree_dirname_or_none() function queries whether a given top-level Python package is in Git-based development mode. * Numpy API generalized. The new betse.lib.numpy.nparray.get_subarray_indices() function efficiently yields the indices of all items of one Numpy array residing in another. * Path API generalized. The new high-level betse.util.files.copy_overwritable() function, wrapping the existing lower-level betse.util.files.copy() function for the common case of silently overwriting arbitrary target files. * String API generalized to support substantially enhanced truncation operations in the "betse.util.type.text.strs" submodule, including: * The new high-level truncate() function, truncating strings to caller-defined barriers (e.g., maximum length, terminal substring) and then replacing the truncated suffixes with arbitrary strings (e.g., ellipses). * The new replace_suffix_prefixed() function, prematurely truncating strings on impermissible substrings (e.g., newline). * The existing remove_suffix_with_prefix() function reduced to a one-liner, a substantial optimization preventing this function from erroneously raising exceptions in edge cases both common and uncommon. * The existing betse.util.type.text.regexes.die_unless_replace_substrs_line() function, now truncating internally raised exception messages for readability. * Version API generalized. The formerly mostly empty "betse.util.type.numeric.versions" submodule has been substantially improved, despite the inability of the setuptools-bundled "pkg_resources" API to preserve backward compatibility across stable releases. Our version API now portably allows versions in any of several formats (i.e., string, tuple, or setuptools-specific "Version" or "LegacyVersion" objects) to be reliably compared. PEP 440-compliant versions (e.g., "5.9.0") and PEP 440-uncompliant versions (e.g., "5.9.0~a1") are explicitly supported. * Version API tested. Unit tests fully exercising all edge cases of the "betse.util.type.numeric.versions" submodule have been added.
  • v0.9.0   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.
  • v0.8.4   BETSE 0.8.4 (Kindlier Kaufmann) released. Significant changes include: * Default time step for the cutting event reverted to 0.0 s (i.e., the initial time step). While this and prior releases technically permit the cutting event to occur at subsequent time steps, doing so currently results in fatal exceptions during the "betse plot sim" phase and hence is highly discouraged. This issue will be permanently resolved in the next stable release of BETSE - to be released shortly.
  • v0.8.3   BETSE 0.8.3 (Kindly Kaufmann) released. Significant changes include: * Dill >= 0.2.8 fundamentally broke backward compatibility by renaming the public "dill.dill" submodule to "dill._dill". This stable release restores compatibility with dill >= 0.2.3, including dill >= 0.2.8. * Mapping API marginally optimized. The betse.util.type.mapping.mappings.is_keys() function has been renamed for generality to is_key() and has now been optimized for the common edge case of testing key containment for a single key.
  • v0.8.2   BETSE 0.8.2 (Kindest Kaufmann) released. Significant changes include: * Segmentation fault handling. Developer-friendly tracebacks are now printed to standard error on fatal segmentation faults (i.e., low-level memory access violations by the active Python process). * Mapping API generalized. The "betse.util.type.mapping.mappings" API has been marginally improved with a bevy of convenience functions pertaining to efficient dictionary key removal.
  • v0.8.1   BETSE 0.8.1 (Kinder Kaufmann) released. This corrective re-release of the BETSE 0.8.0 bump amends a minor (albeit significant) oversight in our installation routine for "bare" Python environments (i.e., having no current NumPy installation). In short, there's largely nothing to see here.
  • v0.8.0   BETSE 0.8.0 (Kind Kaufmann) released. Significant changes include: * Official Anaconda release. This is the first major release of BETSE to officially support our new conda-forge-hosted Anaconda package at: https://anaconda.org/conda-forge/betse * Installation instructions simplified. Installation instructions in our front-facing "README.rst" documentation have been substantially simplified to reflect our official Anaconda release. * Fast simulation solver added. As an efficient alternative to the usual full simulation solver, the newly developed fast solver implements a less space- and time-intensive formalism for simulating a subset of bioelectric phenomena. Specifically, the fast solver leverages the well-known equivalent circuit model to simulate core bioelectricity optionally coupled to a gene regulatory network (GRN). As a crude heuristic, cursory inspection shows the fast solver to be approximately 500—2000% faster than the full solver. Bioelectric phenomena supported by the fast solver includes: * Transmembrane potential (Vmem). * Voltage-sensitive gap junctions. * Intracellular currents and fields. All other bioelectric phenomena should be assumed to be unsupported. * Microtubule density maps and initial-condition alignment maps. These maps are user-defined image mask files permitting any simulation to preconfigure various properties pertaining to microtubules for that simulation's cell cluster. * Morris-Lecar ion channels. Ion channels based on the Morris-Lecar formalism (including a so-called "slow" Morris-Lecar channel) have now been added. * Biomolecule degradation activation and inhibition. Degradation of arbitrary biomolecules in gene regulatory networks (GRN) may now be configured via customary activation and inhibition relations. * Surgical interventions generalized. Cell clusters may now be surgically cut at any arbitrary time step of a simulation. Previously, surgical cuts were only supported at the first time step. * "sim-grn" dynamic cutting support. The "betse sim-grn" subcommand simulating a gene regulatory network (GRN) isolated from bioelectric phenomena now supports all standard surgical interventions. * Extracellular matrix (ECM) handling finalized. Main electrophysiological properties of our standard planarian model have now been successfully matched to experimental observation (e.g., as compiled by several prominent planarian theses), validating our handling of the extracellular matrix (ECM). These properties include: * Transepithelial potential (TEP) level. * Transepithelial potential (TEP) under an applied exogenous field. * Current magnitude and direction. * Lloyd's Voronoi mesh optimization. The pseudo-random Voronoi mesh underlying each cell cluster has now been optimized using Lloyd's algorithm, improving simulation accuracy and substantially reducing the likelihood of mesh errors inducing computational instabilities. * Realistic cell polarizability algorithm. An improved algorithm for simulating the polarizability of cells has now been implemented. * Microtubule Gaussian-noise distribution. Microtubules may now be distributed according to a proper Gaussian-noise distribution. * Numerous locomotion issues resolved, including: * Mass conservation issues in motor protein transport. * Gap junction-isolated profiles. * Microtubule transport. * Laplacians, including: * Cell-grid Laplacians. * Voronoi grid Laplacians. * Comma-separated value (CSV) file exports pipelined. CSV files are now exported via our standard pipeline infrastructure much like all other exports (e.g., plots, animations), enabling the "plot init" and "plot sim" subcommands to trivially support the fast solver. * Seed exports generalized. All exports previously created via only the "betse plot seed" subcommand are now general-purpose exports created via all plotting subcommands (e.g., both the "betse plot init" and "betse plot sim" subcommands). These exports includes: * "cluster_mask" for the all-cells image mask defining the cell cluster shape. * "diffusion_extra" for final all-cells extracellular diffusion weights (logarithm-scaled). Ignored if extracellular spaces are disabled. * "gj_connectivity" for the all-cells gap junction connectivity network. * "gj_permeability" for final all-cells gap junction relative permeabilities. * "tissue_cuts" for all-cells tissue and cut profiles. * Simulation configuration file documentation improved. To simplify usage, the configuration file now documents all simulation features required by each type of export -- which usually means the full solver. * Simulation configuration creation generalized. Simulation configurations created by the "betse config" subcommand now ignore all existing files in target subdirectories (e.g., "geo/"), permitting users to create multiple configurations in the same directory. * Simulation runner callback API. The new "betse.science.phase.phasecallbacks" class hierarchy provides a general-purpose mechanism for interested callers (notably, the BETSEE GUI) to register low-level callbacks with instances of the high-level "SimRunner" class responsible for running simulation subcommands and hence phases. Currently, these callbacks include methods to receive periodic updates on simulation progress. The three principal simulation subcommands (i.e., seed, initialization, and simulation) now inform callers of incremental progress with respect to work performed. * Simulation runner API generalized. The SimRunner.__init__() method now accepts a "Parameters" object rather than a simulation configuration filename, enabling callers (notably, the BETSEE GUI) to reconfigure simulation parameters in-memory without writing changes back to disk. * Simulation phase API sanitized. The "Simulator.dyna" and "SimPhase.dyna" tissue handlers are now synonyms rather than duplicates of one another, improving sanity throughout the codebase. Although the former has been temporarily preserved, all code requiring a tissue handler should now use the canonical "phase.dyna" object. * Script API removed. The "betse.script" subpackage has been removed. This API had begun to unsafely bit-rot, had remained unused by end users for several years, and could no longer be reasonably maintained. It is dead. * REPL API disabled. The "betse.cli.repl" API has been moved to "betse.util.cli.repl" and temporarily disabled until further notice. This API had also begun to unsafely bit-rot, but could yield tangible benefit at some future date. This API has been preserved in cold storage until it can be resuscitated by a future development effort. It isn't dead; it's merely sleeping for eternity. * Simulation phase requirements API generalized. The existing "betse.science.phase.require" subpackage has been refactored to leverage immutable sets, permitting two or more lower-level simulation phase requirements to be readily composed into a high-level simulation phase requirement. * KDTree -> cKDTree optimization. For efficiency, all prior usage of the pure-Python "KDTree" class has been refactored to leverage the C-based "cKDTree" class instead. The latter is a drop-in replacement for the former commonly providing speedups in kd-tree queries of up to 4000%. Doing so also permits all kd-tree instances to be trivially pickled. * Numpy array validation API. The new "betse.lib.numpy.nptest" submodule now provides optimized routines for testing and validating Numpy arrays -- notably, whether a given array contains one or more Not-a-Number (NaN) values or not. * Numpy-based image loading API improved. The existing "betse.lib.pil.pilnumpy" submodule deserializing arbitrary image files into Numpy arrays has now resolved a critical defect pertaining to signed versus unsigned data types, reducing the likelihood of computational errors on the resulting Numpy arrays. * Simulation phase enumerations isolated. For maintainability, the central "betse.science.phase.phasecls.SimPhaseKind" enumeration has been shifted into the newly created "betse.science.phase.phaseenum" submodule. * @log_time_seconds decorator. All simulation subcommand methods (e.g., betse.science.simrunner.SimRunner.seed()) are now decorated by the new @log_time_seconds decorator defined by the new "betse.util.type.decorator.decprof" submodule, logging wall clock time in fractional seconds consumed by each such subcommand. * @abstractproperty decorator de-deprecated. Python >= 3.3 deprecated the @abc.abstractproperty decorator, for unwise and frankly incomprehensible reasons. This release locally reverts this deprecation by restoring the @abstractproperty decorator in perpetuity under the rubric of the "betse.util.type.decorators.deccls" submodule. * @type_check decorator generalized. The @type_check decorator widely used throughout the codebase to perform type checking of callable parameters now supports tuple annotations containing both class objects and fully-qualified classnames, finally finalizing this decorator. * Matplotlib >= 2.2.0 compatibility. Matplotlib 2.2.0, the most recently released version of matplotlib as of this writing, accidentally broke backward compatibility in a horrifying manner. The long-standing public "matplotlib.verbose" API was removed in favour of the standard "logging" API -- a dramatic upheaval so terrifying it even broke PyCharm. This release permanently resolves the breakage on our end by dynamically detecting the current version of matplotlib at runtime such that: * For matplotlib >= 2.2.0, matplotlib logging is configured via the standard "logging" API. * For matplotlib < 2.2.0, matplotlib logging is configured via the non-standard "matplotlib.verbose" API. Since this API is now deprecated and expected to be properly removed in six months, this API is only safely accessible under older versions of matplotlib. * Test suite expanded. Continuous integration (CI) now exercises most simulation features with comprehensive tests, including: * Fast simulation solver. * The "betse sim-grn" subcommand simulating a gene regulatory network (GRN) isolated from bioelectric phenomena. Exercised features include: * Piggybacking onto an uninitialized, unsimulated cell cluster. * Piggybacking onto an initialized, unsimulated cell cluster. * Piggybacking onto an initialized, simulated cell cluster. * Restarting from the last time step of a prior GRN run. * Project logo adopted. The official logo for this release of BETSE is an aesthetic flat icon bundled with Maxim Kulikov's Noun Project-hosted "Cows" collection, kindly released under the permissive BSD-compatible CC BY 3.0 license.
  • v0.7.0   BETSE 0.7.0 (Jamboree Jackson) released. Significant changes include: * Dynamic ion channels significantly rewritten. Backward compatibility-breaking changes include: * *OBSOLETE YAML CONFIGURATION SECTION REMOVED.* Users are encouraged to switch to the existing gene regulatory network (GRN) formalism, which provides more reliable dynamic channels support. See the "channels" subsection of the "general network" section in the default YAML file. * Pump- and channel-specific electroosmosis removed. Users are encouraged to switch to the existing gene regulatory network (GRN) formalism, which provides more reliable electroosmosis support. * Configuration changed from conductivity to membrane diffusion constants, improving consistency with the remainder of the BETSE codebase. * Endoplasmic reticulum (ER) calcium dynamics removed entirely. * All existing CaV channels renamed for clarity. (Requested by Cassandra.) * Multiple new CaV channels added. (Requested by Cassandra.) These include: * N-type CaV 2.2 channel. * Channel API generalized for external use outside of BETSE (e.g., Jupyter). * Z-offset support in modulator functions. (Requested by Micah Brodskey.) * Simulation time updates solved with the backward (implicit) Euler method. * Gap junctions modelled with the Goldman-Hodgkin-Katz (GHK) flux equation. * Negative concentrations causing "non-conservative" instabilities detected during simulation, triggering human-readable fatal exceptions. * Positive concentrations updated properly via dynamic dictionaries. * "show cells: False" plot output aesthetically improved. (Caveat: this option now assumes convert rather than concave cell cluster shapes.) * Voronoi grid construction slightly improved. * Setuptools >= 38.0.0 compatibility resolved, permitting BETSE to be portably installed under all setuptools versions. Setuptools >= 38.0.0 broke backward compatibility by prohibiting unordered iterables (e.g., sets) in prominent "setup.py" parameters that previously accepted such iterables. *sigh* * Image I/O API created. The new "betse.lib.pil" subpackage aggregates all functionality specific to Pillow, the PIL-compatible fork serving as this application's low-level image processing framework. * Expression alias API sanitized, raising human-readable exceptions on erroneous access to expression alias values. * Directory API sanitized, raising human-readable exceptions from recursive directory functions. * Object API sanitized, permitting object attributes and methods to be dynamically accessed in a "safe" sentinel-based manner. * YAML API generalized, enabling all YAML (sub)configurations to be loaded and unloaded in a general-purpose manner.
  • v0.6.1   BETSE 0.6.1 (Illuminous Ito) released. Significant changes include: * Trivial woes in the prior release resolved, including: * Permission issues during "pip3"-based installation. * Rendering issues during reStructuredText (reST) to HTML conversion on PyPI. * Release instructions improved to avert these woes in the future.
  • v0.6.0   BETSE 0.6.0 (Illustrious Ito) released. Significant changes include: * Core bioelectric features significantly improved, including: * Cell polarizability. * Charge balance in gene regulatory networks. * Electroosmotic flow, leveraging a new electric field formalism operating on free charge. * Extracellular currents. * Extracellular fields, now "...100% consistent with Maxwell's Equations to produce long-range electric fields in conjunction with (and balancing) ion currents resulting from Nernst-Planck electrodiffusive transport." * Fluid flow. * Flux transfer between the environment and cell cluster. * Microtubule alignment. * Modulator functions. * pH (i.e., hydrogen cations). * Voltage-gated calcium channels (e.g., CaV). * Voltage-gated potassium channels (e.g., Kv). * Gene regulatory network (GRN) features added, including: * Piggybacking, permitting GRNs to be efficiently simulated over previously simulated simulations without inefficiently resimulating underlying physics. * Network optimizer, permitting gene regulatory networks to be efficiently optimized in isolation. * Substances may now be transmembrane components subject to electrophoretic or electroosmotic forces acting from the extracellular space. * Substances may now leverage electrophoretic mobility instead of calculating Einstein's coefficient, intended for larger macromolecules exhibiting low diffusion but significant mobility (in which case the Einstein coefficient is an unsuitable estimate of mobility). * Substance smoothing reduced significantly (i.e., from 1:2 to 1:100). * "betse sim-brn" subcommand removed, obsoleted in entirety by the "betse sim-grn" subcommand simulating gene regulatory networks. * Two-dimensional Cartesian geometry primitives added, including: * Cell cluster (and hence Voronoi diagram) boundaries resected via the well-known Sutherland-Hodgman polygon clipping algorithm. * Point-line intersection (i.e., intersection of two lines). * Point-vector spatiality (i.e., whether arbitrary points reside to the right or left of arbitrary vectors). * Matplotlib backend detection significantly improved. Specifically, the Qt 5-based "Qt5Agg" backend is now BETSE's preferred backend under all recent releases of matplotlib (i.e., matplotlib >= 2.0.0). Under older releases of matplotlib, the obsolete Tcl/Tk-based "TkAgg" backend remains our preferred backend for stability. * Transparency automatically enabled in all animation images and video for all file formats supporting transparency (e.g., PNG). * Large-scale refactoring of simulation features for downstream use by BETSEE (the Qt 5-based BETSE GUI), including: * Spatial settings (e.g., cell lattice type, computational grid size, physical world size). * Temporal settings (e.g., time step, sampling rate). * Cut profiles. * Ion profiles. * Tissue profiles. * Object-YAML mapping (OYM) API generalized into the "betse.lib.yaml" subpackage, providing an elegant pure-Python solution (driven by data descriptors) to transparently mapping between in-memory high-level Python objects and on-disk low-level YAML files. * Backward compatibility API generalized into the new "betse.science.config.confcompat" and "betse.science.simulate.simcompat" submodules. * CLI API generalized into the new "betse.util.cli" subpackage, eliminating excess boilerplate in downstream CLI applications. * Current working directory (CWD) API generalized into the new "betse.util.os.shell.shelldir" submodule. * Enumeration API generalized into the new "betse.util.type.enums" submodule. * Exception handling API generalized into the new ""betse.util.io.ioexceptions" submodule. * Float API generalized, providing both validation and conversion of floating point numbers in either decimal or scientific notation. * Pathname API generalized into the new "betse.util.path.pathnames" submodule. * Textual APIs (e.g., raw string, regular expression, version specifier) generalized into the new "betse.util.type.text" subpackage. * Matplotlib colormap API generalized into the new "betse.lib.matplotlib.mplcolormap" subpackage. * Recursive file and directory mtime (modification time) discovery, providing efficient inspection and comparison of filesystem contents. * Sane default dictionary implementation now provided by the new "betse.util.type.mapping.mapcls.DefaultDict" class. * Matplotlib >= 1.5.0 now required. * Matplotlib >= 2.0.0 now supported. * SciPy >= 1.0.0 now supported. Specifically, the third-party image processing framework Pillow is now leveraged in lieu of the now-deprecated scipy.misc.imread() function for low-level image I/O. * Nominal "ruamel.yaml" compatibility. While we have yet to officially flip the switch on this alternate Python YAML implementation, BETSE now (in theory) supports roundtripped I/O via "ruamel.yaml". * Python 3.6 officially supported. * Python 3.6 support exercised with Windows-based AppVeyor CI. * New functional tests exercising: * Backward compatibility with all simulation configurations and pickled files produced by BETSE >= 0.5.0. * Our default simulation configuration.
  • v0.5.2   BETSE 0.5.2 (Happiest Hodgkin) released. This interim point release is both a 0.6.0 release candidate and now the oldest version for which backward compatibility is intended to be preserved, superceding the recent 0.5.1 release in that respect. Since this point release is principally required to validate backward compatibility by functional tests locally referencing the corresponding Git tag (i.e., "v0.5.2"), no release notes are provided. See the following 0.6.0 release for proper release notes. For similar reasons, no PyPI tarball or third-party packages are intended to be produced for this (possibly unstable) point release.
  • v0.5.1   BETSE 0.5.1 (Happier Hodgkin) released. This interim point release is both a 0.6.0 release candidate and the oldest version for which backward compatibility is intended to be preserved. Since this point release is principally required to validate backward compatibility by functional tests locally referencing the corresponding Git tag (i.e., "v0.5.1"), no release notes are provided. See the following 0.6.0 release for proper release notes. For similar reasons, no PyPI tarball or third-party packages are intended to be produced for this (possibly unstable) point release.
  • v0.5.0   BETSE 0.5.0 (Happy Hodgkin) released.
  • v0.4.1   BETSE 0.4.1 (Gladder Galvani) released.
  • v0.4.0   BETSE 0.4.0 (Glad Galvani).
  • v0.3.0   BETSE 0.3.0 official release.
    d7687e75 · BETSE 0.3.0 stabilized. ·