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The optionally saved spectra in the pdf_analysis and savefluxes modules were saved in the VO-table format. The most important downside is that it is very slow to write to, which proves to be a major bottleneck in the computing speed. To overcome this issue, we rather save the spectra using the FITS formation. Instead of having one file containing the spectra (including the various components) and the SFH in a single file, now we have one file for the spectra and one file for the SFH.

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.

Better handle the case where one of the redshift is 0 to correct the physical properties for a possible offset between the observed and the model redshifts.

Correct the mass-dependent physical quantities for the difference between the redshift of the model and the redshift of the observation. Because the former is rounded to 2 decimal places, there can be a redshift difference of 0.005 (if CIGALE computes the list of redshifts itself). This can lead to differences of more than 0.35 dex at z=0.01 for instance.

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

In the presence of upper limits, correct the scaling factor of the models to the observations before computing the χ², not after.

When stripping the _log suffix of a variable names, let's just remove the last four characters instead of relying on strip(), which can have nasty side effects.

When estimating a parameter in log, these were not scaled appropriately and taken in log when saving the related PDF

When estimating a parameter in log, these were not scaled appropriately and taken in log when saving the related χ²

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.

Assign the fluxes to the correct array. For some reason I was sure I corrected that before committing the changes last Friday.

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

Introduce the possibility of saving only specific output parameters with savefluxes. This should accelerate the computation while reducing memory usage.

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.

Handle the case where we do not know the redshift to estimate the physical parameters by taking all models at all redshifts. This means that in effect pcigale can also act as a photo-z code now on.

Now that we leave the models with NaN fluxes, the scaling factors and χ² may be NaN too. Handle this case.

Avoid multiply the array by a scalar once rather than twice. It makes the computation quite a bit faster.