Changes to parsim

Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

case.run(): Changed search order for executables. Case directory is searched before project bin directory, so that case excetutable has precedence.

Now uses pyDOE3, rather than pyDOE2, due to the use of deprecated libraries in the pyDOE2 code base.

This release is verified to work correctly with Python versions from 3.8 to 3.13, pyexpander versions from 1.9.x to 2.2.1.

Avoided use of pandas.DataFrame.append method, as this is deprecated in recent pandas versions.
Fixed issue with recent pyexpander versions (>=2.0). Now using keyword arguments in call to pyexpander.lib.expandFile. Works with both new and old pyexpander versions.
Use raw strings for regexp patterns, to avoid problems with escape sequences in recent versions of Python.
Parsim object info() methods had problems with info string escape sequences in recent versions of Python. Now corrected.
Fixed crash when saving parsim objects to disk: Starting with Python 3.10, the __getstate__ method now exists also for many “state-less” objects (like lists) and returns “None”. This is now handled correctly.
Now using pyDOE3 instead of pyDOE2, as pyDOE2 still uses the “imp” module, which was deprecated and removed in Python 3.12.
Fixed minor documentation issues.

Special parameters with parsim-related case information are available for macro expansion on case creation. They are also available as environent variables of the subprocesses started with the psm run command.

Implemented DOE scheme gsd (Generalized Subset Design), as available in pyDOE2 package. Allows reduced factorial designs with more than two levels.
With DOE scheme fracfact, the user can now define the reduced design either by a generator expression (option “gen”), or by the design resolution (option “res”).
Property-based getter functions in Case and Study classes now provide caselist, results and parameter info as pandas DataFrame or Series objects.
Study.collect() method now aggregates all collected results in a file “study.results” in the study directory. This file includes also cases with missing data (marked as “NaN”, pandas-style).
pyDOE2, numpy, scipy and pandas are now mandatory dependencies.
Constructor of Case class now handles colon-separated format <study>:<case> for cases inside studies. This simplifies use of the parsim Python API for working with results.
Examples of how to use the Python API for post-processing and data analysis.

Support for Python 2 has been removed!
Config option paramlist_upper_names has been removed (controlled optional automatic conversion of all parameter names to uppercase).

API changes in ParsimObjects (incl. subclasses Project, Study and Case), especially in constructors (__init__) and create() method. These changes makes the CLI command implementations shorter and easier to understand. Better checking of sane name and path arguments to constructor.