Update ctapipe to 0.12.0, gammapy 0.19, pyirf 0.6

[maxnoe]

Needs a new release of ctapipe_io_lst, until that is done, this is in draft mode.

It seems changes are again not large, so me might want to update already.

[rlopezcoto]

ctapipe_io_lst v0.12 was already released and included in lstchain, anything else missing?

[rlopezcoto]

sorry, I just saw the pending PR cta-observatory/ctapipe_io_lst#128, that would need to be merged and a new release of ctapipe_io_lst issued before moving on

[maxnoe]

This just updates and fixes tests along with removing subarray related IO functions that are now served using Subarray.{from,to}_hdf

[codecov]

Codecov Report

Merging #802 (865955a) into master (70bbb7c) will increase coverage by 0.12%.
The diff coverage is 100.00%.

@@            Coverage Diff             @@
##           master     #802      +/-   ##
==========================================
+ Coverage   83.71%   83.84%   +0.12%     
==========================================
  Files          76       76              
  Lines        5992     5916      -76     
==========================================
- Hits         5016     4960      -56     
+ Misses        976      956      -20     

Impacted Files	Coverage Δ
lstchain/calib/camera/calibration_calculator.py	89.65% <ø> (ø)
lstchain/calib/camera/flatfield.py	96.22% <ø> (ø)
lstchain/calib/camera/pedestals.py	95.60% <ø> (ø)
lstchain/io/tests/test_io.py	100.00% <ø> (ø)
lstchain/tools/lstchain_create_dl3_index_files.py	77.77% <ø> (ø)
lstchain/tools/lstchain_create_irf_files.py	90.16% <ø> (ø)
lstchain/visualization/plot_calib.py	100.00% <ø> (ø)
lstchain/io/io.py	73.00% <100.00%> (+0.46%)	⬆️
lstchain/reco/r0_to_dl1.py	93.71% <100.00%> (ø)
lstchain/scripts/tests/test_lstchain_scripts.py	99.58% <100.00%> (ø)

---

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[rlopezcoto]

it looks fine to me in general, I left a couple of comments and let's see if @FrancaCassol can have a look to the changes affecting the calibration code

[rlopezcoto]

there are still some conflicts to be solved, otherwise the PR looks good already

[maxnoe]

Ah sorry, I didn't catch that there were conflicts again.