GitLab

Add the parameters_file keyword to pcigale.ini and adapt the construction of the configuration dictionary while taking into account the fact that parameters_file may or may not be indicated.

Abstract the call to the parameters handler to allow for the creation of different handlers depending on how the parameters are provided, for instance either a systematic grid by giving then in pcigale.ini or through a file with each line providing a the parameters for a different model. The change is transparent to the rest of pcigale so it does not matter which handler is actually used.

If the list of analysed/saved physical properties is left empty in pcigale.ini, savefluxes saved all physical properties. This has been moved to the Configuration class and easily extended to the pdf_analysis module.

When the redshifts are not indicated in pcigale.ini, compute them from the input flux file when the configuration dictionary is returned rather than in the analysis module, which should not have to change the configuration.

When no dust emission module is used, pcigale genconf complains that no dust attenuation module is used. Correctly specify dust emission and not attenuation. Bug reported by Laure Ciesla.

Implement a simple verification of the list of modules to warn the user if some mandatory modules are missing.

First implementation of a script to list, add, remove, and plot the filters in the pcigale database. One or more filters can be added, removed, or plotted in one command.

Implement a priodic SFH module in replacement of the sfhcomb_constant and sfhcomb_delayed modules. The new module handles rectangular, delayed, and exponential star-forming episodes.

We rely on OrderedDict to keep the order of the parameters. However given the way the code is structured currently, there is really no reason for this. So let's just switch to the standard dictionary. This has two advantages. First the standard dictionary is much faster than OrderedDict (implemented in C rather than in pure python). Then, standard dictionaries are marshalable, which makes them usable as keys for other dictionaries.

Specify that encoding for pcigale.ini. Otherwise if a non-ASCII character is used it may work or crash depending on the computer. Now we encode everything in UTF-8, which will allow again to use these chracters in the description of the modules parameters.

Make the configuration file optional. This is particularly useful when only generating fluxes for instance. In the process the description of the input file has been clarified.

Check that the id and redshift columns are present in the input file. Freely inspired from an initial patch written by Denis.

Get rid of the parameters array. Rather we generate parameters on-on-fly. This is done using a new class ParameterHandlers, which handles the generation of parameters from a given 1D index. While at it, also do away with global variables. This allows to spawn processes rather than fork them. Even if it takes a little time to do the spawn, this allows to solves some deadlocks with libraries which do not support being used on both sides of a forked process. Overall these modifications makes startup faster (no need to compute the cache cleaning parameters beforehand) and the generation speed is also a few percent faster when the number of models is large enough to compensate for the relatively slow spaning time.

Implement partial cache clearing in order not to clog the memory with models that are not necessary anymore. This requires the proper computation of models that will not be used anymore. This is why we used ordered dictionaries to ensures that parameters are always considered in the same order.

glob is imported in the pcigale/session/configuration.py to allow its use in
the configuration file (with eval).

TODO: write a new configuration pattern to add several files with something
like "files *.fits".

Correction of a problem spotted by Médéric, basestring does not exists
in Python 3.

Make the source code more compatible with Python 3. As far as I understand the documentation, this should be harmless for Python 2.

Move the igmattenuation module and its LSST dependencies inside the psum
analysis module.
Remove the redshift_module and redshift_configuration parts of the
configuration file.

Making glob() available in session/configuration.py allows users of
savefluxes and sfhfromfile to use something like

filename = "eval glob('sfh*.fits')"
sfr_column = 2

to take the star formation history from several files.