Improve the presentation of the sanity check and only do as at the end of the run so that sporadic messages are not displayed in individual blocks.

Do display the model counter twice when the numbers of models is a multiple of the printing frequency.

The counter can become a bottleneck when many parallel processes are running concurrently because of the lock to update it. To address this we implement a Counter class that only updates the counter periodically rather than at each iteration. The number of models actually computed at any moment is kept in a local counter.

Add ParameterManager as input to ObserbationsManagerPassbands class, this is use to separate the intensive properties to fit from the extensive and add them to the class. Modify pdf_analysis/__init__.py to call ParameterManager befor ObservationsManager

Implement an observations manager. For now it is mainly used as a simple container for the observations table but upcoming rearchitecturing will make full use of it.

Remove the TOLERANCE constant and replace it with 0. There is no good reason to have a tolerance and its value is quite arbitrary anyway.

Rename ParametersHandler to ParametersManager to be consistent with new managers that will come in the near future.

Move the backup_dir() function to the base class of the analysis modules as it makes sense for analysers to prepare the output directories.

As we loop over the bands to compute the χ², it is smarter that the bands are the slower varying index and the models the faster varying index. That way it is more likely that models at the correct redshift are prefetched into the cache.

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

Remove some variables used only once and that could be directly obtained from the configuration dictionary.

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.

Specify the types and the constraints of the input parameters for the SED creation modules and the analysis modules. Once validation is activated, the validation module will be able to infer the constraints from the specified information.

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.

Simplify the interface of the analysis modules as it is needlessly restrictive by forcing a precise list of parameters. Different modules do not necessarily need the same information and the need for different input parameters may emerge in the future. To make the interface future-proof, we simply pass the file containing the configuration file. Then each analysis module picks the data it needs from it.

Merge the output files into one. The parameters estimated from the PDF are prefixed with 'bayes' and those from the best fit with 'best'.

Médéric Boquien authored Dec 07, 2015 and Yannick Roehlly committed Dec 07, 2015

The detection of the '_log' suffix in variables and its removal to compute the models was overzealous. Fix this.

Revert the commit to re-apply it using git-flow hotfix.

This reverts commit d8fab1df.

The detection of the '_log' suffix in variables and its removal to compute the models was overzealous. Fix this.

Get rid of the array containing the redshifts of all the models. Now that we infer the redshift of individual models from the list of unique redshifts it is not needed anymore. This change saves 8 bytes per model. The code should be marginally faster too.