Updated df.applymap to df.map to silence FutureWarning

[ray-berkeley]

Small change to silence a FutureWarning that is thrown by newer versions of Pandas

[alisterburt]

Right on, thanks for the PR! Is this change backwards compatible or does it break with slightly older pandas versions? If the latter can you update the pandas requirement to >=the minimum version?

Once this is done I'll merge and push out a release, thanks again!!

[alisterburt]

Looks like the pandas version required is not released on 3.8 - I'm happy to drop 3.8 support here too and will remove it from the test matrix

[ray-berkeley]

Thanks for taking a look at it! I made the change you suggested to setup.cfg and verified it with a test install.

The pandas docs suggest that df.map() is backwards-compatible to 2.1.0–I was able to test it back to 2.1.1, but I get a separate error from pandas when trying to read a starfile using pandas 2.1.0 and python 3.11 or 3.9. I tried it with a few different starfiles and got a similar error.

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File ".../python3.9/site-packages/starfile/functions.py", line 26, in read
    parser = StarParser(filename, n_blocks_to_read=read_n_blocks)
  File ".../python3.9/site-packages/starfile/parser.py", line 40, in __init__
    self.parse_file()
  File ".../python3.9/site-packages/starfile/parser.py", line 51, in parse_file
    block_name, block = self._parse_data_block()
  File ".../python3.9/site-packages/starfile/parser.py", line 65, in _parse_data_block
    return block_name, self._parse_loop_block()
  File ".../python3.9/site-packages/starfile/parser.py", line 117, in _parse_loop_block
    df.columns = loop_column_names
  File ".../python3.9/site-packages/pandas/core/generic.py", line 6216, in __setattr__
    return object.__setattr__(self, name, value)
  File "properties.pyx", line 69, in pandas._libs.properties.AxisProperty.__set__
  File ".../python3.9/site-packages/pandas/core/generic.py", line 767, in _set_axis
    self._mgr.set_axis(axis, labels)
  File ".../python3.9/site-packages/pandas/core/internals/managers.py", line 227, in set_axis
    self._validate_set_axis(axis, new_labels)
  File ".../python3.9/site-packages/pandas/core/internals/base.py", line 85, in _validate_set_axis
    raise ValueError(
ValueError: Length mismatch: Expected axis has 25 elements, new values have 12 elements

[alisterburt]

@ray-berkeley tests are passing for me locally and in the test matrix on >3.8 - could you paste the contents of your file so I can double check it myself? Hopefully it's a local issue for you... if I don't hear back in a couple of days I'll merge here and if it breaks I'm sure I'll hear about it :-)

Thanks again for the PR!

[ray-berkeley]

Sure! Here's a minimal starfile that should reproduce the error. It only seems to be a problem with Pandas 2.1.0:

# version 30001

data_optics

loop_ 
_rlnOpticsGroup #1 
_rlnOpticsGroupName #2 
_rlnAmplitudeContrast #3 
_rlnBeamTiltX #4 
_rlnBeamTiltY #5 
_rlnSphericalAberration #6 
_rlnVoltage #7 
_rlnImagePixelSize #8 
_rlnMicrographOriginalPixelSize #9 
_rlnImageSize #10 
_rlnImageDimensionality #11 
_rlnOddZernike #12 
_rlnEvenZernike #13 
           1 opticsGroup1     0.100000     0.296532     -0.11369     2.700000   200.000000     2.240000     0.560000           96            2 [-0.512329168678,1.33476636873,-0.443026555711,0,0,1.04243806264] [1.46288490105,0.370363079954,2.44605608265,-1.89801788564,-3.14098732609,0.117745343458,1.03266007965,-0.841780044036,3.04355953351] 
           2 opticsGroup2     0.100000     -0.21438     0.161131     2.700000   200.000000     2.240000     0.560000           96            2 [0.709153648516,-0.955645680221,9.97627294315,0,0,-10.1434434973] [0.75276733627,0.837454240706,1.31038420099,-1.20886925188,-2.59055495481,0.265832972474,0.598879387485,-0.553876811671,-8.2646276172] 
           3 opticsGroup3     0.100000     0.143370     -0.14056     2.700000   200.000000     2.240000     0.566000           96            2 [-0.611693882648,1.08746776327,-0.504494994403,0,0,-3.2349096551] [1.54077504279,1.66789488846,2.58486712372,-7.62783630324,6.02593490545,0.589969463855,1.104075202,-2.89198279973,7.76718046708] 
 

# version 30001

data_particles

loop_ 
_rlnCoordinateX #1 
_rlnCoordinateY #2 
_rlnClassNumber #3 
_rlnAutopickFigureOfMerit #4 
_rlnAnglePsi #5 
_rlnImageName #6 
_rlnMicrographName #7 
_rlnCtfMaxResolution #8 
_rlnCtfFigureOfMerit #9 
_rlnDefocusU #10 
_rlnDefocusV #11 
_rlnDefocusAngle #12 
_rlnCtfBfactor #13 
_rlnCtfScalefactor #14 
_rlnPhaseShift #15 
_rlnGroupNumber #16 
_rlnAngleRot #17 
_rlnAngleTilt #18 
_rlnNormCorrection #19 
_rlnLogLikeliContribution #20 
_rlnMaxValueProbDistribution #21 
_rlnNrOfSignificantSamples #22 
_rlnRandomSubset #23 
_rlnBeamTiltClass #24 
_rlnOpticsGroup #25 
_rlnOriginXAngst #26 
_rlnOriginYAngst #27 
_rlnSphericalAberration #28 
  207.000000   207.000000            1     1.000000   -132.17428 000001@calibration_grid.mrcs Micrographs/calibration_grid/D1.mrc     2.634397     0.425778 13241.734375 13064.365234    -58.88372     0.000000     1.000000     0.000000            1    10.768136    56.799662     0.534664 25220.411190     0.514471           89            1            3            2     -4.34431     6.855688     2.700000 
  207.000000   363.000000            2     1.000000   -155.95937 000002@calibration_grid.mrcs Micrographs/calibration_grid/D2.mrc     2.634397     0.425778 13241.734375 13064.365234    -58.88372     0.000000     1.000000     0.000000            1   146.715904    51.023781     0.444846 25447.427149     0.457400          955            2            3            2     -4.34431     -2.10431     2.700000 
  207.000000   518.000000            2     1.000000   -142.54589 000003@calibration_grid.mrcs Micrographs/calibration_grid/D3.mrc     2.634397     0.425778 13241.734375 13064.365234    -58.88372     0.000000     1.000000     0.000000            1    90.926684    60.188403     0.446103 25403.345273     0.203695          440            1            3            2     -2.10431     -2.10431     2.700000 

[alisterburt]

thanks! this is working with the version of pandas that is currently installed in >=3.9 so I'll merge and recommend updating pandas if anyone has issues :-)

[ray-berkeley]

Sweet, thank you!