PoPy v1.2.3 released
Popy v1.2.3 is a micro release containing mainly bug fixes but also some minor changes to the suite of tools and solvers offered by PoPy.
Improvements
- Option to specify the delimiter of the data file (e.g., a semicolon).
- Option to display a progress bar when iterating over individuals.
- Shortcut functions for the PREPROCESS block, making it easier to read Nonmem data files and to debug.
- Access to alternative Levenberg-Marquardt methods (e.g., the Trust Region Reflective algorithm) that may be more stable.
- Templating facility for config files whereby you can use ${ENVVAR} and PoPy will automatically substitute environment variable ENVVAR into the script.
- New "PRED_vs_TIME" and "{PRED}_vs_TIME" plot types that plot only predictions, without observation points.
- Faster "leastsq" r[X] optimization.
- A fail() function to the PREPROCESS to stop PoPy on demand during preprocessing.
- Access to initial states within the DERIVATIVES block via the s0[X] notation.
- Added output of random effect covariances as a correlation matrix.
- The *= operator is now accepted in DERIVATIVES.
Bug Fixes
- Initializing a state within a condition without an "else:" clause no longer leaves the state uninitialized (and unrecognized entirely).
- A zero bioavailability no longer causes the code to crash when there are multiple doses.
- The *= compound operator is now accepted in the DERIVATIVES for a single compartment (but not for directed flows between two compartments).
- TABLE now has access to the c[X] input data and supports the PREPROCESS block so that non-standard input data doesn't fail.
- FITSUM now processes non-standard input data without needing a PREPROCESS block.
- Expressions evaluating to log(0) now give an error to the user rather than generating unrunnable code.
- Bug in Solution file's "fx_opt_types_path" corrected so Solutions can be copied directly between folders.
- Closing the console window in Windows 7 now forcibly terminates all processes in the current PoPy run.
- You can now have an empty list for some covariates (e.g., t[DOSE]).
- Pseudocode that evaluates to log(0) now raises an exception rather then generating unrunnable code.
- Data files with "." or "-" as aliases for zero are now converted much earlier to avoid problems downstream.
- PREPROCESS is now propagated to all scripts where it might be necessary/useful.