Change log

Version 0.4.1

Released on 2011-12-02.

Miscellaneous improvements:

• validate both import and simulation files, i.e. detect bad structure and invalid and missing keywords.
• improved error messages (both during import and the simulation), by stripping any information that is not useful to the user. For some messages, we only have a line number and column left, this is not ideal but should be better than before. The technical details are written to a file (error.log) instead.
• improved “incoherent alignment data” error message when loading an alignment file by changing the wording and adding the path of the file with the error.
• reorganised bundle files so that there is no confusion between directories for Notepad++ and those of liam2.
• tweaked Notepad++ configuration:
  • added explore command as F7
  • removed more unnecessary features.

Fixes:

• disallowed using one2many links like many2one (it was never intended this was and produced wrong results).
• fixed groupby with a scalar expression (it does not make much sense, but it is better to return the result than to fail).
• re-enabled the code to show the expressions containing errors where possible (in addition to the error message). This was accidentally removed in a previous version).
• fixed usage to include the ‘explore’ command.

Version 0.4.0

Released on 2011-11-25.

New features:

• added grpgini function.
• added grpmedian function.
• implemented filter argument in grpsum().
• implemented N-dimensional alignment (alignment can be done on more than two variables/dimensions in the same file).
• added keyword arguments to csv():
  • ‘fname’ to allow defining the exact name of the csv file.
  • ‘mode’ to allow appending to a csv file instead of overwriting it.
• reworked csv() function to support several arguments, like show. It also supports non-table arguments.
• added ‘skip_shows’ simulation option, to make all show() functions do nothing.
• allowed expressions in addition to variable names in alignment files.
• added keyword arguments to dump():
  • ‘missing’ to convert nans into the given value.
  • ‘header’ to determine whether column names should be in the dump or not.
• improved import functionality:
  • compression is now configurable.
  • any csv file can be transposed, not just globals.
  • globals fields can be selected, renamed and inverted like in normal entities.
• added “explore” command to the main executable, to launch the interactive console on a completed simulation without re-simulating it.

Miscellaneous improvements:

• expressions do not need to be quoted anymore.
• reverted init to old semantic: it happens in “start_period - 1”, so that lag(variable_set_in_init) works even for the first period.
• purge all local variables after each process to lower memory usage.
• allowed the result of new() to not be stored in a variable.
• allowed using temporary variables in matching() function.
• added a tolerance of 1e-6 to the sum of choice’s probabilities to be equal 1.0
• added explicit message about alignment over and underflows.
• nicer display for small (< 5ms) and large (>= 1 hour) timings.
• improved error message on missing parenthesis around operands of boolean operators.
• improved error message on duplicate fields.
• improved error message when a variable which is not computed yet is used.
• added more information to the console log:
  • number of individuals at the start and end of each period.
  • more stats at the end of the simulation.
• excluded unused components in the executable to make it smaller.

Fixes:

• fixed logit_regr(align=float).
• fixed grpavg(bool, filter=cond).
• fixed groupby(a, b, c, expr=grpsum(d), percent=True).
• fixed having several grpavg with a filter argument in the same expression.
• fixed calling the main executable without argument (simply display usage).
• fixed dump with (some kind of) aggregate values in combination with a filter.
• fixed void data source.

Version 0.3.0

Released on 2011-06-29.

New features:

• added ability to import csv files directly with the main executable.

Miscellaneous improvements:

• made periodic globals optional.
• improved a few sections of the documentation.

Fixes:

• fixed non-assignment “actions” in interactive console (csv, remove, ...).
• fixed error_var argument to cont_regr, clip_regr and log_regr.

Version 0.2.1

Released on 2011-06-20.

Miscellaneous improvements:

• simplified and cleaned up the demonstration models.
• improved the error message when a link points to an unknown entity.
• the evaluator creates fewer internal temporary variables in some cases.

Fixes:

• added log and exp to the list of available functions (they were already implemented but not usable because of that).
• fixed log_regr, cont_regr and clip_regr which were comparing their result with 0.5 (like logit_regr when there is no alignment).
• fixed new() function, which created individuals correctly but in some cases returned values which did not correspond to the ids of the newly created individuals, due to a bug in numpy.

Version 0.2

Released on 2011-06-07.

New features:

• added support for retrospective simulation (ie simulating periods for which we already have some data): at the start of each simulated period, if there is any data in the input file for that period, it is “merged” with the result of the last simulated period. If there is any conflict, the data in the input file has priority.

• added “clone” function which creates new individuals by copying all fields from their “origin” individuals, except for the fields which are given a value manually.

• added breakpoint function, which launches the interactive console during a simulation. Two more console commands are available in that mode:

  • “s(tep)” to execute the next process
  • “r(esume)” to resume normal execution

  The breakpoint function takes an optional period argument so that it triggers only for that specific period.

• added “tsum” function, which sums an expression over the whole lifetime of individuals. It returns an integer when summing integer or boolean expressions, and a float for float expressions.

• implemented using the value of a periodic global at a specific period. That period can be either a constant (eg “MINR[2005]”) or an expression (eg “MINR[period - 10]” or “MINR[year_of_birth + 20]”)

• added “trunc” function which takes a float expression and returns an int (dropping everything after the decimal point)

Miscellaneous improvements:

• made integer division (int / int) return floats. eg 1/2 = 0.5 instead of 0.

• processes which do not return any value (csv and show) do not need to be named anymore when they are inside of a procedure.

• the array used to run the first period is constructed by merging the individuals present in all previous periods.

• print timing for sub-processes in procedures. This is quite verbose but makes debugging performance problems/regressions easier.

• made error messages more understandable in some cases.

• manually flush the “console” output every time we write to it, not only within the interactive console, as some environments (namely when using the notepad++ bundle) do not flush the buffer themselves.

• disable compression of the output/simulation file, as it hurts performance quite a bit (the simulation time can be increased by more than 60%). Previously, it was using the same compression settings as the input file.

• allowed align() to work on a constant. eg:

  align(0.0, fname='al_p_dead_m.csv')
  

• made the “tavg” function work with boolean and float expressions in addition to integer expressions

• allowed links to be used in expression given in the “new” function to initialise the fields of the new individuals.

• using “__parent__” in the new() function is no longer necessary.

• made the “init” section optional (it was never intended to be mandatory).

• added progress bar for copying table.

• optimised some parts for speed, making the whole simulation roughly as fast as 0.1 even though more work is done.

Fixes:

• fixed “tavg” function:
  • the result was wrong because the number of values (used in the division) was one less than it should.
  • it yielded “random” values when some individuals were present in a past period, but not in the current period.
• fixed “duration” function:
  • it crashed when a past period contained no individuals.
  • it yielded “random” values when some individuals were present in a past period, but not in the current period.
• fixed “many2one” links returning seemingly random values instead of “missing” when they were pointing to an individual which was not present anymore (usually because the individual was dead).
• fixed min/max functions.
• fields which are not given an explicit value in new() are initialised to missing, instead of 0.
• the result of the new() function (which returns the id of the newly created individuals) is now -1 (instead of 0) for parents which are not in the filter.
• fixed some expressions crashing when used within a lag.
• fixed the progress bar to display correctly even when there are only very few iterations.

Version 0.1

First semi-public release, released on 2011-02-24.