[cctbxbb] iotbx.merging_statistics test failing: data file removed from phenix_regression

richard.gildea at diamond.ac.uk richard.gildea at diamond.ac.uk
Fri Jan 6 08:02:54 PST 2017 

Hi Tom,

Thanks for the quick response!

To run this specific test:

$ libtbx.python $(libtbx.find_in_repositories iotbx/regression/tst_merging_statistics.py)

The test also uses the file phenix_regression/wizards/unmerged.mtz which I guess was also removed with the same commit?

$ grep phenix_regression $(libtbx.find_in_repositories iotbx/regression/tst_merging_statistics.py)
  if (not libtbx.env.has_module("phenix_regression")) :
    print "phenix_regression not configured, skipping."
    relative_path="phenix_regression/wizards/p9_se_w2.sca",
    relative_path="phenix_regression/harvesting/unmerged.sca",
    relative_path="phenix_regression/harvesting/refine.mtz",
    relative_path="phenix_regression/reflection_files/i_anomalous.mtz",
    relative_path="phenix_regression/wizards/unmerged.mtz",
    relative_path="phenix_regression/reflection_files/AUTOMATIC_DEFAULT_scaled_unmerged_WAVE1.mtz",

$ libtbx.find_in_repositories phenix_regression/wizards/unmerged.mtz
Sorry: libtbx.find_in_repositories: cannot locate "phenix_regression/wizards/unmerged.mtz"

The other files still seem to be present in phenix_regression.

Cheers,

Richard

Dr Richard Gildea
Data Analysis Scientist
Tel: +441235 77 8078

Diamond Light Source Ltd.
Diamond House
Harwell Science & Innovation Campus
Didcot
Oxfordshire
OX11 0DE

________________________________________
From: Terwilliger, Thomas Charles [terwilliger at lanl.gov]
Sent: 06 January 2017 15:57
To: Gildea, Richard (DLSLtd,RAL,LSCI); cctbxbb at phenix-online.org
Cc: Terwilliger, Thomas Charles
Subject: Re: iotbx.merging_statistics test failing: data file removed from phenix_regression

Hi Richard,
Thanks for pointing that out!  I'll fix it. Yes, I deleted that file when I moved all the small files in phenix_regression/wizards/ into sub-directories.  I made the mistake of assuming that only wizards/ regression tests used files in the wizards/ directory (I should have run all the cctbx regression tests to make sure).
All the best,
Tom T
________________________________________
From: richard.gildea at diamond.ac.uk <richard.gildea at diamond.ac.uk>
Sent: Friday, January 6, 2017 8:51 AM
To: cctbxbb at phenix-online.org; Terwilliger, Thomas Charles
Subject: iotbx.merging_statistics test failing: data file removed from phenix_regression

Hi all,

The test for iotbx.merging_statistics has recently started failing as a result of one of the files it uses for testing being deleted, phenix_regression/wizards/p9_se_w2.sca:

https://github.com/cctbx/cctbx_project/blob/master/iotbx/regression/tst_merging_statistics.py#L17

Would it be possible to restore this file to phenix_regression so that the test will pass?


$ svn log -r r3879 -v

------------------------------------------------------------------------

r3879 | terwill | 2016-12-29 02:48:15 +0000 (Thu, 29 Dec 2016) | 1 line

Changed paths:

   D /trunk/wizards/000README

   D /trunk/wizards/4c5q.pdb

   D /trunk/wizards/ATP.pdb

   D /trunk/wizards/MM-all.tgz

   D /trunk/wizards/NAD.pdb

   D /trunk/wizards/PARAMS_1.eff

   D /trunk/wizards/a2u-data.mtz

   D /trunk/wizards/a2u-sigmaa.mtz

   D /trunk/wizards/a2u.sca

   D /trunk/wizards/a2u_short.pdb

   D /trunk/wizards/anb.pdb

   D /trunk/wizards/autosol_unmerged_False.std

   D /trunk/wizards/autosol_unmerged_True.std

   D /trunk/wizards/autosol_unmerged_p9.std

   D /trunk/wizards/bad_model.pdb

   D /trunk/wizards/check.xyz

   D /trunk/wizards/check_multiple_input_files_042908.tgz

   D /trunk/wizards/check_multiple_input_files_062608.tgz

   D /trunk/wizards/check_multiple_input_files_070508.tgz

   D /trunk/wizards/check_multiple_input_files_2011-03-03.tgz

   D /trunk/wizards/check_multiple_input_files_2011-06-29.tgz

   D /trunk/wizards/check_multiple_input_files_2011-11-04.tgz

   D /trunk/wizards/clean.com

   D /trunk/wizards/cocn.cif

   D /trunk/wizards/coords.pdb

   D /trunk/wizards/coords1.ali

   D /trunk/wizards/coords1.mtz

   D /trunk/wizards/coords1.pdb

   D /trunk/wizards/coords_A001.pdb

   D /trunk/wizards/coords_rna.pdb

   D /trunk/wizards/coords_rna_gap.pdb

   D /trunk/wizards/data_for_commands_in_doc.tgz

   D /trunk/wizards/find_all_ligands.eff

   D /trunk/wizards/find_all_ligands.standard

   D /trunk/wizards/find_ncs_ncs.standard

   D /trunk/wizards/find_ncs_resolve.standard

   D /trunk/wizards/fobs.mtz

   D /trunk/wizards/fobs_std.mtz

   D /trunk/wizards/fobs_std_edit.mtz

   D /trunk/wizards/gene-5.pdb

   D /trunk/wizards/generate.com

   D /trunk/wizards/get_cc_mtz_mtz.standard

   D /trunk/wizards/get_cc_mtz_pdb.standard

   D /trunk/wizards/ha.pdb

   D /trunk/wizards/ha_lig.pdb

   D /trunk/wizards/ha_perfect.pdb

   D /trunk/wizards/ha_perfect_2.pdb

   D /trunk/wizards/hipip.pdb

   D /trunk/wizards/hipip_2.sca

   D /trunk/wizards/hipip_shortseq.dat

   D /trunk/wizards/ignore.dat

   D /trunk/wizards/inf.sca

   D /trunk/wizards/ki.sca

   D /trunk/wizards/ligand.pdb

   D /trunk/wizards/mad.eff

   D /trunk/wizards/mad.mtz

   D /trunk/wizards/map_coeffs.mtz

   D /trunk/wizards/map_coeffs_1.mtz

   D /trunk/wizards/map_coeffs_2.mtz

   D /trunk/wizards/map_to_object.standard

   D /trunk/wizards/maps_only.standard

   D /trunk/wizards/mir.eff

   D /trunk/wizards/mlt.mtz

   D /trunk/wizards/mlt_gap.pdb

   D /trunk/wizards/mlt_regression.tgz

   D /trunk/wizards/mol1.pdb

   D /trunk/wizards/mol2.pdb

   D /trunk/wizards/mr_rosetta.eff

   D /trunk/wizards/mult_regr.tgz

   D /trunk/wizards/multi.pdb

   D /trunk/wizards/multi.pdb.mtz

   D /trunk/wizards/my_autobuild.eff

   D /trunk/wizards/my_automr.eff

   D /trunk/wizards/my_autosol.eff

   D /trunk/wizards/my_ligand.pdb

   D /trunk/wizards/my_ligandfit.eff

   D /trunk/wizards/my_target.pdb

   D /trunk/wizards/native.sca

   D /trunk/wizards/noligand.mtz

   D /trunk/wizards/omit_lig_results.list

   D /trunk/wizards/omit_regr.tgz

   D /trunk/wizards/p.pdb

   D /trunk/wizards/p21.sym

   D /trunk/wizards/p9-seq.dat

   D /trunk/wizards/p9-sites.xyz

   D /trunk/wizards/p9_ha.pdb

   D /trunk/wizards/p9_se_w2.sca

   D /trunk/wizards/part_mlt.pdb

   D /trunk/wizards/partial.pdb

   D /trunk/wizards/partial_refine_001.pdb

   D /trunk/wizards/partial_refine_001_map_coeffs.mtz

   D /trunk/wizards/peak.sca

   D /trunk/wizards/perfect.mtz

   D /trunk/wizards/perfect_rna.mtz

   D /trunk/wizards/phaser_1_offset.mtz

   D /trunk/wizards/pt.sca

   D /trunk/wizards/quick_clashlist.standard

   D /trunk/wizards/random.pdb

   D /trunk/wizards/random_0.7_mlt.mtz

   D /trunk/wizards/resolve_1_offset.mtz

   D /trunk/wizards/rna.seq

   D /trunk/wizards/run_multi.eff

   D /trunk/wizards/run_multi_new.eff

   D /trunk/wizards/seq.dat

   D /trunk/wizards/seq1.dat

   D /trunk/wizards/seq2.dat

   D /trunk/wizards/seq_mlt.dat

   D /trunk/wizards/short_seq.standard

   D /trunk/wizards/side.pdb

   D /trunk/wizards/sir_sad.eff

   D /trunk/wizards/sites_mlt.pdb

   D /trunk/wizards/smiles.dat

   D /trunk/wizards/solve.setup

   D /trunk/wizards/start.pdb

   D /trunk/wizards/starting_map.mtz

   D /trunk/wizards/test3.gz

   D /trunk/wizards/test9.gz

   D /trunk/wizards/test_ampl_int_autobuild.tgz

   D /trunk/wizards/test_labels_1.std

   D /trunk/wizards/test_labels_2.std

   D /trunk/wizards/test_labels_3.std

   D /trunk/wizards/test_missing.std

   D /trunk/wizards/test_multi.tgz

   D /trunk/wizards/test_ncs.standard

   D /trunk/wizards/test_ncs_find_ncs.standard

   D /trunk/wizards/test_ncs_lc.pdb

   D /trunk/wizards/test_resno.std

   D /trunk/wizards/test_resno.tgz

   D /trunk/wizards/unmerged.mtz

   D /trunk/wizards/w1.sca

   D /trunk/wizards/w1_rna.sca

   D /trunk/wizards/w2.sca


remove unneeded files

------------------------------------------------------------------------

Cheers,

Richard

Dr Richard Gildea
Data Analysis Scientist
Tel: +441235 77 8078

Diamond Light Source Ltd.
Diamond House
Harwell Science & Innovation Campus
Didcot
Oxfordshire
OX11 0DE

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