Since running in a working directory with a space in will fail somewhere, fail instantly

xia2 / xia2

An expert system for automated reduction of X-ray diffraction data from macromolecular crystals

https://xia2.github.io/

BSD 3-Clause "New" or "Revised" License

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Since running in a working directory with a space in will fail somewhere, fail instantly #114

Open graeme-winter opened 7 years ago

graeme-winter commented 7 years ago

Get this error

-------------------- Preparing DEFAULT ---------------------
Status: error "Pointless failed: /tmp/tmpmpUXYW/ABD2Lg.hkl does not exist"
Please send the contents of xia2.txt, xia2.error and xia2-debug.txt to:
xia2.support@gmail.com

From this run

[gw56@cs04r-sc-com99-01 working_dir with_space]$ less xia2.txt 
Environment configuration...
Python => /dls/science/users/gw56/svn/cctbx/build/../base/bin/python2.7
CCTBX => /dls/science/users/gw56/svn/cctbx/modules
CCP4 => /dls_sw/apps/ccp4/64/7.0/update35/ccp4-7.0
CLIBD => /dls_sw/apps/ccp4/64/7.0/update35/ccp4-7.0/lib/data
CCP4_SCR => /tmp/tmpmpUXYW
Starting directory: /tmp/working_dir with_space
Working directory: /tmp/working_dir with_space
Free space:        192.12 GB
Host: cs04r-sc-com99-01
Contact: xia2.support@gmail.com
XIA2 0.5.275-g5c7e5d5
DIALS 1.dev.1312-gdf7f1bb
CCP4 7.0.035

graeme-winter commented 7 years ago

Quoting the input does not help... ultimately this is a bug in pointless.

Reporting now

graeme-winter commented 7 years ago

Will fail soon now with

Environment configuration...
Python => /dls/science/users/gw56/svn/cctbx/build/../base/bin/python2.7
CCTBX => /dls/science/users/gw56/svn/cctbx/modules
CCP4 => /dls_sw/apps/ccp4/64/7.0/update35/ccp4-7.0
CLIBD => /dls_sw/apps/ccp4/64/7.0/update35/ccp4-7.0/lib/data
CCP4_SCR => /tmp/tmpArD5te
Starting directory: /tmp/bug report
Working directory: /tmp/bug report
Error setting up xia2 environment: Space in working directory (https://github.com/xia2/xia2/issues/114)
Please send the contents of xia2.txt, xia2.error and xia2-debug.txt to:
xia2.support@gmail.com

graeme-winter commented 4 years ago

This is not a problem now for pipeline=dials -> remove if that is the case?

graeme-winter commented 4 years ago

In /Users/graeme/data/LCY_15_15_2/Space the Final Frontier/Working Area I could run xia2 ../The\ Data/ just fine without the check -> be smarter

graeme-winter commented 4 years ago

XDS does not like, but could work around with softlinks?

Grey-Area index :) $ cat 2_xds_INIT.log 

 ***** XDS ***** (VERSION Mar 15, 2019  BUILT=20191211)  14-May-2020
 Author: Wolfgang Kabsch
 Copy licensed until 30-Sep-2020 to
  academic users for non-commercial applications   
 No redistribution.

  !!! ERROR !!! INVALID "NAME_TEMPLATE_OF_DATA_FRAMES="

stale[bot] commented 3 years ago

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