GitLab

Clarify that if the parameters are given through a file, then the pdf_analysis module should not be used.

With the new sanity check of the input parameters, cigale did not handle the fact that the redshift could be given in the parameters file. Now this is handled properly.

The name creation_modules is a bit vague. For more clarity and consistency we rather use sed_modules now

Homogenise savefluxes and pdf_analysis for the variables/analysed_variables keyword in pcigale.ini. We adopt the former as it is more compact and applies correctly to both modules.

Change the vague column_list keyword in pcigale.ini to bands. This will require the user to rebuild their pcigale.ini but that is necessary for the validation anyway so that is the right moment to do so.

Pratical implementation of the validation of the parameters. The patch is quite long as it has a direct effect on the structure of the configuration dictionary. The validation has the advantage of automatically convert the parameters to the right type. Therefore rather than building a dictionary ourselves, we rather use the ready-made dictionary from ConfigObj. Because the names of the sections are not the same, quite a bit of code had to be adapted. Finally, note that the validation file containing the specification of each variable, pcigale.ini.spec, is created while building the pcigale.ini file. Also because it is needed to convert the data to the right type, one cannot run cigale without a correct validation file.

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.