adding diagonal/blockdiagonal functionalities, round 2

[tgiani]

Here as agreed I implement again the same things as in PR #438

[tgiani]

There s something I don t understand. If I define the function theory_diagonal_covmat as

def theory_diagonal_covmat(theory_covmat_singleprocess,experiments_index):
    """Returns theory covmat with only diagonal values"""
    s = theory_covmat_singleprocess.values
    # Initialise array of zeros and set precision to same as FK tables
    s_diag = np.zeros((len(s),len(s)), dtype=np.float32)
    np.fill_diagonal(s_diag, np.diag(s))
    df = pd.DataFrame(s_diag, index=experiments_index, columns=experiments_index)
    return df

which is just as in the same way as in #438, I get the following error

[CRITICAL]: Bug in setup-fit ocurred. Please report it.
Traceback (most recent call last):
  File "/scratch/nnpdfgit/nnpdf/validphys2/src/validphys/scripts/vp_setupfit.py", line 181, in run
    super().run()
  File "/scratch/nnpdfgit/nnpdf/validphys2/src/validphys/app.py", line 143, in run
    super().run()
  File "/scratch/anaconda2/envs/nnpdf/lib/python3.7/site-packages/reportengine/app.py", line 359, in run
    rb.execute_sequential()
  File "/scratch/anaconda2/envs/nnpdf/lib/python3.7/site-packages/reportengine/resourcebuilder.py", line 168, in execute_sequential
    perform_final=self.perform_final)
  File "/scratch/anaconda2/envs/nnpdf/lib/python3.7/site-packages/reportengine/resourcebuilder.py", line 175, in get_result
    fres =  function(**kwdict)
  File "/scratch/nnpdfgit/nnpdf/validphys2/src/validphys/results.py", line 184, in experiment_result_table_no_table
    data_result = DataResult(loaded_exp)
TypeError: __init__() missing 2 required positional arguments: 'covmat' and 'sqrtcovmat'

which I was no getting before. Does anyone know why?
Btw I ve changed the definition of theory_diagonal_covmat to use theory_block_diag_covmat instead of theory_covmat_singleprocess and in this way the crash is not happening

[tgiani]

@RosalynLP I ve added also your commit where you changed the names of the functions. Please check if I ve done something stupid

[Zaharid]

This bug was introduced in #427 and is being addressed by #447.

cc @wilsonmr

[RosalynLP]

@tgiani looks sensible to me :)

[Zaharid]

@tgiani You should be able to rebase this on top of master and get it to work.

[Zaharid]

Please add a docstring here explaining what everything does. Also mention the existence of the flag in the corresponding section of guide.

[Zaharid]

@tgiani I have described the options explicitly, so that it is possible to use this by reading the documentation. I have also run a formatting tool to fix various whitespace errors.

[Zaharid]

Hello, this is @Zaharid's automated QA script. Please note it is highly experimental. I ran pylint on your changes and found some new issues.

On validphys2/src/validphys/config.py, pylint has reported the following new issues:

• Line 706: Unused argument 'use_thcovmat_in_sampling'
• Line 707: Unused argument 'use_thcovmat_in_fitting'

On validphys2/src/validphys/theorycovariance/construction.py, pylint has reported the following new issues:

• Line 67: Unused argument 'theoryids'
• Line 68: Unused argument 'fivetheories'
• Line 78: Unused argument 'fivetheories'
• Line 78: Line too long (109/100)
• Line 464: Trailing whitespace
• Line 488: Trailing whitespace
• Line 523: Trailing whitespace

[Zaharid]

Please fix the formatting errors in construction.py.

[tgiani]

@Zaharid Uhm do you mean

Line 464: Trailing whitespace
Line 488: Trailing whitespace
Line 523: Trailing whitespace

from your automated script?

[Zaharid]

Yes, and also "line too long".

[Zaharid]

Hello, this is @Zaharid's automated QA script. Please note it is highly experimental. I ran pylint on your changes and found some new issues.

On validphys2/src/validphys/config.py, pylint has reported the following new issues:

• Line 706: Unused argument 'use_thcovmat_in_sampling'
• Line 707: Unused argument 'use_thcovmat_in_fitting'

On validphys2/src/validphys/theorycovariance/construction.py, pylint has reported the following new issues:

• Line 67: Unused argument 'theoryids'
• Line 68: Unused argument 'fivetheories'
• Line 79: Unused argument 'fivetheories'