Prefix logger.warning messages with "WARNING:"

[dagewa]

This is a way of prefixing warning messages and thus make them stand out from general information messages in a consistent way. Draft for comments whether we want this kind of behaviour. This is for #1034.

[dagewa]

Preference is for coloured output to stdout. There is something for this in dlstbx But what about the log file - should we still do this in order to make warning messages stand out from general info?

[dagewa]

Following merge of #1057, this has been updated to only change the log file formatting. I agree with previous comments that colouring is preferable for console output. To that end, @Anthchirp can we get ColorStreamHandler in DIALS rather than locked up in dlstbx?

[Anthchirp]

Alternative suggestion:

If level >= warning then
   print "WARN: log message"
         "WARN: continuation"
else
   print "time: log message"
         "      continuation"

[Anthchirp]

is ElapsedFormatter still an appropriate name then?

[dagewa]

not really... any ideas?

[dagewa]

DialsLogfileFormatter?

[dagewa]

Alternative suggestion:

If level >= warning then
   print "WARN: log message"
         "WARN: continuation"
else
   print "time: log message"
         "      continuation"

Yes, that would highlight the warnings even better

[dagewa]

Example dials.index.log looks like this

  15.1: Using d_min_step 0.0
        
        Indexed crystal models:
        model 1 (19129 reflections):
        Crystal:
            Unit cell: (39.133, 41.884, 42.125, 90.132, 90.331, 90.320)
            Space group: P 1
            U matrix:  {{-0.1301,  0.5373,  0.8333},
                        {-0.9831,  0.0395, -0.1789},
                        {-0.1290, -0.8425,  0.5231}}
            B matrix:  {{ 0.0256,  0.0000,  0.0000},
                        { 0.0001,  0.0239,  0.0000},
                        { 0.0001,  0.0001,  0.0237}}
            A = UB:    {{-0.0031,  0.0129,  0.0198},
                        {-0.0251,  0.0009, -0.0042},
                        {-0.0033, -0.0201,  0.0124}}
        +------------+-------------+---------------+-------------+
        |   Imageset |   # indexed |   # unindexed | % indexed   |
        |------------+-------------+---------------+-------------|
        |          0 |       19129 |          6120 | 75.8%       |
        +------------+-------------+---------------+-------------+
        
        ################################################################################
        Starting refinement (macro-cycle 1)
        ################################################################################
        
  WARN: scan_varying=True not supported in indexing: setting scan_varying=False
  15.2: 
        Summary statistics for 19079 observations matched to predictions:
        +-------------------+--------+----------+---------+---------+--------+
        |                   |    Min |       Q1 |     Med |      Q3 |    Max |
        |-------------------+--------+----------+---------+---------+--------|
        | Xc - Xo (mm)      | -2.275 |   -0.396 | -0.2784 | -0.1821 | 0.5358 |
        | Yc - Yo (mm)      | -8.963 |  -0.1303 | 0.08766 |  0.2477 |  5.783 |
        | Phic - Phio (deg) | -15.38 | -0.05332 |  0.1556 |  0.3972 |  18.92 |
        | X weights         |  290.2 |    386.3 |   397.7 |   403.7 |  405.6 |
        | Y weights         |  296.6 |    386.6 |   396.9 |   403.3 |  405.6 |
        | Phi weights       |  11.11 |    11.97 |      12 |      12 |     12 |
        +-------------------+--------+----------+---------+---------+--------+
        
        Detecting centroid outliers using the Tukey algorithm
        2872 reflections have been flagged as outliers
        16207 reflections remain in the manager
        
        Summary statistics for 16207 observations matched to predictions:
        +-------------------+---------+----------+---------+---------+--------+
        |                   |     Min |       Q1 |     Med |      Q3 |    Max |
        |-------------------+---------+----------+---------+---------+--------|
        | Xc - Xo (mm)      |  -0.811 |  -0.3524 | -0.2596 | -0.1738 | 0.1512 |
        | Yc - Yo (mm)      |  -1.347 | -0.06906 | 0.09531 |  0.2317 |  1.436 |
        | Phic - Phio (deg) | -0.8908 | -0.02024 |    0.16 |  0.3807 |   1.24 |
        | X weights         |   290.2 |    389.3 |   399.4 |   404.1 |  405.6 |
        | Y weights         |   302.8 |    389.2 |   398.8 |   403.8 |  405.6 |
        | Phi weights       |   11.11 |    11.97 |   11.99 |      12 |     12 |
        +-------------------+---------+----------+---------+---------+--------+
        
  15.3: There are 16 parameters to refine against 9000 reflections in 3 dimensions