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Desire to run Analysis in same python interpreter as CING #251

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
In order to use the data structures pyRpf generates it would be nice to have 
Tim's Analysis run in the same python interpreter. This should be possible 
according to Tim & Wayne by editing the Makefile and recompiling Analysis.

/Users/jd/workspace35/ccpnmr/ccpnmr2.1/c

What I need is an example environment.txt specific for the python2.6 from mac 
ports.

This is the diff with the original:

jd:stella/c/ diff environment.txt.bak environment.txt
0a1
> # edited by JFD
105c106
< SHARED_FLAGS = -L/Users/jd/workspace35/ccpnmr/python2.5/lib -bundle 
-bundle_loader /Users/jd/workspace35/ccpnmr/python2.5/bin/python2.5

---
> #SHARED_FLAGS = -L/Users/jd/workspace35/ccpnmr/python2.5/lib -bundle 
-bundle_loader /Users/jd/workspace35/ccpnmr/python2.5/bin/python2.5
109a111,113
> # JFD mods to: 
> SHARED_FLAGS = 
-L/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib -bundle 
-bundle_loader \
>                  
/opt/local/Library/Frameworks/Python.framework/Versions/2.6/bin/python2.6
136c140,142
< TCL_DIR = /Users/jd/workspace35/ccpnmr/tcl8.5

---
> #TCL_DIR = /Users/jd/workspace35/ccpnmr/tcl8.5
> # JFD mods to:
> TCL_DIR = /opt/local/lib/tcl8.5
137a144
> # JFD ABSENT, same for the TK below
143c150,152
< TK_DIR = /Users/jd/workspace35/ccpnmr/tk8.5

---
> #TK_DIR = /Users/jd/workspace35/ccpnmr/tk8.5
> # JFD mods to:
> TK_DIR = /opt/local/lib/tk8.5
150,151c159,164
< PYTHON_DIR = /Users/jd/workspace35/ccpnmr/python2.5
< PYTHON_INCLUDE_FLAGS = -I$(PYTHON_DIR)/include/python2.5

---
> #PYTHON_DIR = /Users/jd/workspace35/ccpnmr/python2.5
> # JFD mods to:
> PYTHON_DIR = /opt/local/Library/Frameworks/Python.framework/Versions/2.6
> #PYTHON_INCLUDE_FLAGS = -I$(PYTHON_DIR)/include/python2.5
> # JFD mods to:
> PYTHON_INCLUDE_FLAGS = -I$(PYTHON_DIR)/include/python2.6

Original issue reported on code.google.com by jurge...@gmail.com on 17 Jun 2010 at 11:46

GoogleCodeExporter commented 9 years ago 
Ideally, I would like to be able to run the unit test at:
http://code.google.com/p/cing/source/browse/trunk/cing/python/cing/PluginCode/te
st/test_Analysis.py

Original comment by jurge...@gmail.com on 17 Jun 2010 at 11:48

GoogleCodeExporter commented 9 years ago 
The unit test output:

==> Importing data from Ccpn project "1brv_cs_pk_2mdl"
Non-standard (residues and their) atoms added:
GLU : [ 189]
DEBUG: Residue.addDihedralD1: skipping residue <Residue HISH159> because of 
missing atoms
DEBUG: Residue.addDihedralD1: skipping residue <Residue GLN160> because of 
missing atoms
DEBUG: and so on for a total of 13 messages
==> Molecule 1brv: No potential disulfide bridged residues found
Calculating rmsd's (residues: 158-189, models: 0-1)
==> Ccpn molecule '1brv' imported
==> CCPN ShiftList 'brsvg.prot' imported from CCPN Nmr project '1brv'
==> CING (pseudo-)atom with resonances updated numbering 149
WARNING: CCPN peak '<ccp.nmr.Nmr.Peak ['1brv', 3, 1, 11, 546]>' missing both 
volume and height
==> PeakList 'NOESY_brsvg_sparky_11' imported from CCPN Nmr project '1brv'
==> Ccpn project imported
CcpNmr Analysis Version 2.1. Release 3 (Copyright 2003-2009 CCPN)
Distribution created Tue Feb 16 17:09:23 2010

If you use CcpNmr Analysis, please quote the following reference:

Wim F. Vranken, Wayne Boucher, Tim J. Stevens, Rasmus H. Fogh, Anne 
Pajon, Miguel Llinas, Eldon L. Ulrich, John L. Markley, John Ionides
and Ernest D. Laue (2005). The CCPN Data Model for NMR Spectroscopy: 
Development of a Software Pipeline. Proteins 59, 687 - 696.

For program documentation the CCPN wiki site is located at:
http://sites.google.com/site/ccpnwiki/Home/documentation/ccpnmr-software

For help and support visit the mailing list at:
http://www.jiscmail.ac.uk/ccpnmr

For Python API documentation, tutorials and CCPN web applications visit:
http://www.ccpn.ac.uk/

EXCEPTION CAUGHT: Traceback (most recent call last):
  File "/Users/jd/workspace35/cing/python/cing/PluginCode/Analysis.py", line 42, in initAnalysis
    self.app.initProject(self.project)
  File "/Users/jd/workspace35/ccpnmr/ccpnmr2.1/python/ccpnmr/analysis/Analysis.py", line 287, in initProject
    self.initTopObjects(project)
  File "/Users/jd/workspace35/ccpnmr/ccpnmr2.1/python/ccpnmr/analysis/Analysis.py", line 222, in initTopObjects
    if not project.currentInstrumentStore:
  File "/Users/jd/workspace35/cing/python/cing/Libs/NTutils.py", line 1269, in __getattr__
    raise AttributeError( '"%s" not found.' % attr )
AttributeError: "currentInstrumentStore" not found.

ERROR: Analysis crashed when starting the non-GUI version
Starting cing.PluginCode.Analysis#runRpf
Peaklists: [[<ccp.nmr.Nmr.PeakList ['1brv', 3, 1, 11]>]]
DEBUG: Using ensemble: <ccp.molecule.MolStructure.StructureEnsemble 
[<ccp.molecule.MolSystem.MolSystem ['1brv']>, 2]> 
DEBUG: Using peakList.dataSource.name: brsvg_sparky with tolerance: 
[[<ccp.nmr.Nmr.FreqDataDim ['1brv', 3, 1, 1]>, 0.050000000000000003, 1, 
0.050000000000000003], [<ccp.nmr.Nmr.FreqDataDim ['1brv', 3, 1, 2]>, 
0.050000000000000003, 1, 0.050000000000000003]]
Getting resonance-resonance possible peak assignments within tolerances
Peak List NOESY:brsvg_sparky:11
Peak <ccp.nmr.Nmr.Peak ['1brv', 3, 1, 11, 546]> does not have a peakDim1.value
  Time taken: 0.345909118652
Getting resonance-resonance NOE distances
Ensemble 2
  Time taken: 0.161898851395
Calculating scores and making CCPN validation objects
E
======================================================================
ERROR: Skip until project has been improved; looks like peaks without CS are 
found.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/jd/workspace35/cing/python/cing/PluginCode/test/test_Analysis.py", line 64, in testAnalysisRpf
    diagonalExclusion=DEFAULT_DIAGONAL_EXCLUSION_SHIFT
  File "/Users/jd/workspace35/cing/python/cing/PluginCode/Analysis.py", line 115, in runRpf
    verbose=cing.verbosity==cing.verbosityDebug)
  File "/Users/jd/workspace35/cing/python/cing/Scripts/Analysis/PyRPF.py", line 1769, in calcRPF
    peakListM = predictMissingPeaks(peakList, shiftsMissingPeaks, progressBar)
  File "/Users/jd/workspace35/cing/python/cing/Scripts/Analysis/PyRPF.py", line 1931, in predictMissingPeaks
    syntheticPeakList = getSyntheticMissingPeaksList(peakList)
  File "/Users/jd/workspace35/cing/python/cing/Scripts/Analysis/PyRPF.py", line 1908, in getSyntheticMissingPeaksList
    analysisPeakList = getAnalysisPeakList(syntheticPeakList)
  File "/Users/jd/workspace35/ccpnmr/ccpnmr2.1/python/ccpnmr/analysis/core/Util.py", line 339, in getAnalysisPeakList
    symbol = getPeakListSymbol(peakList)
  File "/Users/jd/workspace35/ccpnmr/ccpnmr2.1/python/ccpnmr/analysis/core/Util.py", line 848, in getPeakListSymbol
    application = peakList.root.application
AttributeError: 'MemopsRoot' object has no attribute 'application'

----------------------------------------------------------------------
Ran 1 test in 10.251s

FAILED (errors=1)

Original comment by jurge...@gmail.com on 17 Jun 2010 at 11:51

GoogleCodeExporter commented 9 years ago 
Oeps, sorry, I should have shown how far I got with the compile.
Alan, do you have Analysis under macport's python?

jd:stella/~/ cdf
/Users/jd/workspace35/ccpnmr/ccpnmr2.1/c
jd:stella/c/ make realclean
cd memops/global && make realclean
rm -f *.o
rm -f *.so
cd ccp/structure && make realclean
rm -f *.o
rm -f *.so
cd ccpnmr/analysis && make realclean
rm -f *.o
rm -f *.so
cd ccpnmr/clouds && make realclean
rm -f *.o
rm -f *.so
cd ccpnmr/dynamics && make realclean
/bin/sh: line 0: cd: ccpnmr/dynamics: No such file or directory
make: *** [dynamics_realclean] Error 1
jd:stella/c/ make 
cd memops/global && make
cc  -O -fPIC -DDO_NOT_HAVE_MALLOC  -c utility.c
cc  -O -fPIC -DDO_NOT_HAVE_MALLOC  
-I/opt/local/Library/Frameworks/Python.framework/Versions/2.6/include/python2.6 
-c python_util.c
python_util.c: In function ‘valid_py_object’:
python_util.c:54: warning: passing argument 1 of ‘equal_strings’ discards 
qualifiers from pointer target type
python_util.c:54: warning: passing argument 2 of ‘equal_strings’ discards 
qualifiers from pointer target type
cc  -O -fPIC -DDO_NOT_HAVE_MALLOC  -c hash_list.c
cc  -O -fPIC -DDO_NOT_HAVE_MALLOC  -c hash_table.c
cc  -O -fPIC -DDO_NOT_HAVE_MALLOC  -c mem_cache.c
cc  -O -fPIC -DDO_NOT_HAVE_MALLOC  -c mutex.c
cc  -O -fPIC -DDO_NOT_HAVE_MALLOC  
-I/opt/local/Library/Frameworks/Python.framework/Versions/2.6/include/python2.6 
-c py_mem_cache.c
cc  -O -fPIC -DDO_NOT_HAVE_MALLOC  -c block_file.c
cc  -O -fPIC -DDO_NOT_HAVE_MALLOC  -c shape_file.c
cc  -O -fPIC -DDO_NOT_HAVE_MALLOC  -c int_array.c
cc  -O -fPIC -DDO_NOT_HAVE_MALLOC  
-I/opt/local/Library/Frameworks/Python.framework/Versions/2.6/include/python2.6 
-c py_block_file.c
cc  -O -fPIC -DDO_NOT_HAVE_MALLOC  
-I/opt/local/Library/Frameworks/Python.framework/Versions/2.6/include/python2.6 
-c py_shape_file.c
cc  -O -fPIC -L/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib 
-bundle -bundle_loader 
/opt/local/Library/Frameworks/Python.framework/Versions/2.6/bin/python2.6 -o 
BlockFile.so utility.o python_util.o hash_list.o hash_table.o mem_cache.o 
mutex.o py_mem_cache.o block_file.o shape_file.o int_array.o py_block_file.o 
py_shape_file.o  
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      _get_python_float_array in python_util.o
      _get_python_float_alloc_array in python_util.o
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ld: symbol(s) not found
collect2: ld returned 1 exit status
make[1]: *** [BlockFile.so] Error 1
make: *** [global] Error 2

Original comment by jurge...@gmail.com on 17 Jun 2010 at 12:00

GoogleCodeExporter commented 9 years ago 
Well, I see the problem. What you may try is to compare with my 
environment.txt, done for Fink.

Original comment by alanwil...@gmail.com on 29 Jun 2010 at 10:48

Attachments:

GoogleCodeExporter commented 9 years ago

Original comment by jurge...@gmail.com on 10 Nov 2010 at 1:13