Bug Report: parseCalFile() has issue with root_numpy...?

Brief summary of issue

Parsing of a calibration file causes an exception. This was not an issue pre-packaging so I suspect perhaps there is still an issue with how root_numpy is installed on the machine.

Types of issue

[X] Bug report (report an issue with the code)
[ ] Feature request (request for change which adds functionality)

Expected Behavior

Parsing a calibration file should not cause an exception.

Current Behavior

(py2.7) [dorney@gem904qc8daq]/data/bigdisk/GEM-Data-Taking/GE11_QC8/GE11-X-S-CERN-0003/scurve% python
Python 2.7.5 (default, Apr 11 2018, 07:36:10) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-28)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> from gempython.gemplotting.utils.anautilities import parseCalFile
>>> parseCalFile("/data/bigdisk/GEM-Data-Taking/GE11_QC8/GE11-X-S-CERN-0003/scurve/calFile_GE11-X-S-CERN-0003.txt")
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/afs/cern.ch/user/d/dorney/scratch0/CMS_GEM/CMS_GEM_DAQ/venv/cc7/py2.7/lib/python2.7/site-packages/gempython/gemplotting/utils/anautilities.py", line 429, in parseCalFile
    array_CalData = rp.tree2array(tree=calTree, branches=list_bNames)
AttributeError: 'module' object has no attribute 'tree2array'

Doesn't throw an import error which is strange. The tree2array function was definitely in 4.7.2 my venv has 4.7.3 installed:

(py2.7) % which pip
~/scratch0/CMS_GEM/CMS_GEM_DAQ/venv/cc7/py2.7/bin/pip
(py2.7) % pip list | grep "root-numpy"
root-numpy                       4.7.3     
(py2.7) % pip list --user | grep "root-numpy"
(py2.7) %

This does not appear to be a problem with my venv since the user account on the qc8 machine gives the same problem:

[gemuser@gem904qc8daq 2018.06.01.04.39]$ anaUltraScurve.py -i SCurveData_trimdac0.root -c -f --calFile=/data/bigdisk/GEM-Data-Taking/GE11_QC8/GE11-X-S-CERN-0003/scurve/calFile_GE11-X-S-CERN-0003.txt
Analyzing: 'SCurveData_trimdac0.root'
mkdir: cannot create directory ‘SCurveData_trimdac0’: File exists
SysError in <TFile::TFile>: could not delete SCurveData_trimdac0/SCurveFitData.root (errno: 13) (Permission denied)
Traceback (most recent call last):
  File "/opt/cmsgemos/bin/anaUltraScurve.py", line 191, in <module>
    tuple_calInfo = parseCalFile(options.calFile)
  File "/usr/lib/python2.7/site-packages/gempython/gemplotting/utils/anautilities.py", line 429, in parseCalFile
    array_CalData = rp.tree2array(tree=calTree, branches=list_bNames)
AttributeError: 'module' object has no attribute 'tree2array'

Steps to Reproduce (for bugs)

Call anaUltraScurve.py -i SomeSCurveFile.root -f --calFile=$DATA_PATH/GE11-X-S-CERN-0003/scurve/calFile_GE11-X-S-CERN-0003.txt

Possible Solution (for bugs)

The internet seems to think this is due to multiple top-level imports as described here. However I could not find an instance in which root_numpy was imported at top level in anaUltraScurve.py or any of it's imports.

Context (for feature requests)

Cannot run calibrated analysis.

Your Environment

Version used: 1.0.0
Shell used: /bin/zsh

Trying the previous hack I had:

    pip uninstall --yes root-numpy
    cd /tmp
    git clone git://github.com/rootpy/root_numpy.git
    cd root_numpy
    python setup.py install
    cd /data/bigdisk/GEM-Data-Taking/GE11_QC8/GE11-X-S-CERN-0003/trim/z4.000000/2018.06.01.04.39
    anaUltraScurve.py -i SCurveData_trimdac0.root -c -f --calFile=$DATA_PATH/GE11-X-S-CERN-0003/scurve/calFile_GE11-X-S-CERN-0003.txt

Now the calibration file is successfully parsed.

I think there is an issue with installation of the package. Specifically on a gem904 machine:

    mkdir -p <some/path>
    python -m virtualenv -p python --system-site-packages <some/path>
    . <some/path>/bin/activate
    python -m pip install -U importlib setuptools pip
    python -m pip install gempython_gemplotting-1.0.0.tar.gz

Does not ensure that root_numpy is properly present.

@jsturdy looks like another issue we need to follow-up on. Removing the "bug" tag since it is not an issue with the software.

Is it an issue with 4.7.3 of root_numpy? (seems unlikely if the git installed method worked)
When installing gemplotting does the output print any information about checking for and installing root_numpy?

Making a new venv:

source $BUILD_HOME/setup_gemdaq.sh -w -c 0.3.1 -g 1.0.0 -G 5 -v 2.0.0 -V 3 -p $PWD/venv_test 2>&1 | tee venvLog.log

Then when installing gemplotting relevant output from venvLog.log is:

python -m pip install gempython_gemplotting-1.0.0.tar.gz
Processing ./gempython_gemplotting-1.0.0.tar.gz
Requirement already satisfied: root_numpy in /usr/lib64/python2.7/site-packages (from gempython-gemplotting==1.0.0) (4.7.3)
Requirement already satisfied: numpy<1.15,>1.7 in /usr/lib64/python2.7/site-packages (from gempython-gemplotting==1.0.0) (1.7.1)
Building wheels for collected packages: gempython-gemplotting
  Running setup.py bdist_wheel for gempython-gemplotting: started
  Running setup.py bdist_wheel for gempython-gemplotting: finished with status 'done'
  Stored in directory: /afs/cern.ch/user/d/dorney/.cache/pip/wheels/93/1c/13/b26f22301c4d62fc111e81bc48d1946cccc94e8877b9c86daa
Successfully built gempython-gemplotting
xstatic-jquery-ui 1.12.0.1 requires XStatic-jQuery, which is not installed.
sphinxcontrib-spelling 2.3.0 requires PyEnchant>=1.6.5, which is not installed.
pyramid 1.5.6 requires WebOb>=1.3.1, which is not installed.
sphinx-rtd-theme 0.1.8 has requirement sphinx>=1.3, but you'll have sphinx 1.1.3 which is incompatible.
rtslib-fb 2.1.63 has requirement pyudev>=0.16.1, but you'll have pyudev 0.15 which is incompatible.
ipapython 4.5.4 has requirement dnspython>=1.15, but you'll have dnspython 1.12.0 which is incompatible.
Installing collected packages: gempython-gemplotting
  Found existing installation: gempython-gemplotting 1.0.0
    Not uninstalling gempython-gemplotting at /usr/lib/python2.7/site-packages, outside environment /home/dorney/venv_test/cc7/py2.7
    Can't uninstall 'gempython-gemplotting'. No files were found to uninstall.
Successfully installed gempython-gemplotting-1.0.0

Which makes a check on root-numpy:

Requirement already satisfied: root_numpy in /usr/lib64/python2.7/site-packages (from gempython-gemplotting==1.0.0) (4.7.3)

However issue persists:

% anaUltraScurve.py -i SomeSCurveFile.root -f --calFile=$DATA_PATH/GE11-X-S-CERN-0003/scurve/calFile_GE11-X-S-CERN-0003.txt
Analyzing: 'SomeSCurveFile.root'
Traceback (most recent call last):
  File "/home/dorney/venv_test/cc7/py2.7/lib/python2.7/site-packages/gempython/scripts/anaUltraScurve.py", line 191, in <module>
    tuple_calInfo = parseCalFile(options.calFile)
  File "/home/dorney/venv_test/cc7/py2.7/lib/python2.7/site-packages/gempython/gemplotting/utils/anautilities.py", line 429, in parseCalFile
    array_CalData = rp.tree2array(tree=calTree, branches=list_bNames)
AttributeError: 'module' object has no attribute 'tree2array'

I don't think the issue is with 4.7.3 of root-numpy but with how the package is being installed. I am not sure it's effectively installed:

% pip uninstall --yes root-numpy 
Not uninstalling root-numpy at /usr/lib64/python2.7/site-packages, outside environment /home/dorney/venv_test/cc7/py2.7
Can't uninstall 'root-numpy'. No files were found to uninstall.

Then attempting to install root-numpy using the hack above works. Trying to run anaUltraScurve.py works without issue:

    cd /data/bigdisk/GEM-Data-Taking/GE11_QC8/GE11-X-S-CERN-0003/trim/z4.000000/2018.06.01.04.39
    anaUltraScurve.py -i SCurveData_trimdac0.root -c -f --calFile=$DATA_PATH/GE11-X-S-CERN-0003/scurve/calFile_GE11-X-S-CERN-0003.txt

Processed no problem =/

What about

python -m pip install -I gempython_gemplotting-1.0.0.tar.gz

i.e., force reinstalling packages (though not sure about dependencies...)

Also, you have a typo:

pip uninstall --yes root-numpy

should be

pip uninstall --yes root_numpy

Installing with:

python -m pip install -I gempython_gemplotting-1.0.0.tar.gz

Has seemed to resolve the issue with rp.tree2array(...) not being found. However it also seems that the version of root-numpy that was installed on gem904qc8daq was installed against root 5.43.Y while ROOT 6.12/04 is installed on the machine:

%     anaUltraScurve.py -i SCurveData_trimdac0.root -c -f --calFile=$DATA_PATH/GE11-X-S-CERN-0003/scurve/calFile_GE11-X-S-CERN-0003.txt
Analyzing: 'SCurveData_trimdac0.root'
mkdir: cannot create directory ‘SCurveData_trimdac0’: File exists
Traceback (most recent call last):
  File "/home/dorney/venv_test/cc7/py2.7/lib/python2.7/site-packages/gempython/scripts/anaUltraScurve.py", line 191, in <module>
    tuple_calInfo = parseCalFile(options.calFile)
  File "/home/dorney/venv_test/cc7/py2.7/lib/python2.7/site-packages/gempython/gemplotting/utils/anautilities.py", line 419, in parseCalFile
    import root_numpy as rp #note need root_numpy-4.7.2 (may need to run 'pip install root_numpy --upgrade')
  File "/usr/lib64/python2.7/site-packages/ROOT.py", line 318, in _importhook
    return _orig_ihook( name, *args, **kwds )
  File "/home/dorney/venv_test/cc7/py2.7/lib/python2.7/site-packages/root_numpy/__init__.py", line 51, in <module>
    from ._tree import (
  File "/usr/lib64/python2.7/site-packages/ROOT.py", line 318, in _importhook
    return _orig_ihook( name, *args, **kwds )
  File "/home/dorney/venv_test/cc7/py2.7/lib/python2.7/site-packages/root_numpy/_tree.py", line 6, in <module>
    from . import _librootnumpy
  File "/usr/lib64/python2.7/site-packages/ROOT.py", line 318, in _importhook
    return _orig_ihook( name, *args, **kwds )
ImportError: libCore.so.5.34: cannot open shared object file: No such file or directory

See last line:

ImportError: libCore.so.5.34: cannot open shared object file: No such file or directory

Is this a potential issue with setupMachine.sh maybe not taking the correct package version of root-numpy?

Not sure, but let's decouple these issues:

It seems that the pip install -I package didn't reinstall dependencies, e.g., root_numpy
System version of root_numpy needs to be tracked down, i.e., why is it asking for some root5 bindings...

After you tried to build the root_numpy rpm by hand it seems like a version bound to root5 is still being installed when setting up a venv.

I tried with a fresh venv and still obtained:

(py2.7) [dorney@gem904qc8daq]~/scratch0/CMS_GEM/CMS_GEM_DAQ%     cd /data/bigdisk/GEM-Data-Taking/GE11_QC8/GE11-X-S-CERN-0003/trim/z4.000000/2018.06.01.04.39
(py2.7) [dorney@gem904qc8daq]/data/bigdisk/GEM-Data-Taking/GE11_QC8/GE11-X-S-CERN-0003/trim/z4.000000/2018.06.01.04.39%     anaUltraScurve.py -i SCurveData_trimdac0.root -c -f --calFile=$DATA_PATH/GE11-X-S-CERN-0003/scurve/calFile_GE11-X-S-CERN-0003.txt 
Analyzing: 'SCurveData_trimdac0.root'
mkdir: cannot create directory ‘SCurveData_trimdac0’: File exists
Traceback (most recent call last):
  File "/afs/cern.ch/user/d/dorney/scratch0/CMS_GEM/CMS_GEM_DAQ/venv/cc7/py2.7/lib/python2.7/site-packages/gempython/scripts/anaUltraScurve.py", line 189, in <module>
    tuple_calInfo = parseCalFile(options.calFile)
  File "/afs/cern.ch/user/d/dorney/scratch0/CMS_GEM/CMS_GEM_DAQ/venv/cc7/py2.7/lib/python2.7/site-packages/gempython/gemplotting/utils/anautilities.py", line 419, in parseCalFile
    import root_numpy as rp #note need root_numpy-4.7.2 (may need to run 'pip install root_numpy --upgrade')
  File "/usr/lib64/python2.7/site-packages/ROOT.py", line 318, in _importhook
    return _orig_ihook( name, *args, **kwds )
  File "/afs/cern.ch/user/d/dorney/scratch0/CMS_GEM/CMS_GEM_DAQ/venv/cc7/py2.7/lib/python2.7/site-packages/root_numpy/__init__.py", line 51, in <module>
    from ._tree import (
  File "/usr/lib64/python2.7/site-packages/ROOT.py", line 318, in _importhook
    return _orig_ihook( name, *args, **kwds )
  File "/afs/cern.ch/user/d/dorney/scratch0/CMS_GEM/CMS_GEM_DAQ/venv/cc7/py2.7/lib/python2.7/site-packages/root_numpy/_tree.py", line 6, in <module>
    from . import _librootnumpy
  File "/usr/lib64/python2.7/site-packages/ROOT.py", line 318, in _importhook
    return _orig_ihook( name, *args, **kwds )
ImportError: libCore.so.5.34: cannot open shared object file: No such file or directory

Below is the venv setup.

`venv` setup

(py2.7) [dorney@gem904qc8daq]~/scratch0/CMS_GEM/CMS_GEM_DAQ% source setup_gemdaq.sh -c 0.3.1 -v 2.0.0 -V 3 -p $PWD/venv 
Already using interpreter /usr/bin/python
New python executable in /afs/cern.ch/user/d/dorney/scratch0/CMS_GEM/CMS_GEM_DAQ/venv/cc7/py2.7/bin/python
Installing setuptools, pip, wheel...done.
Requirement already up-to-date: importlib in /afs/cern.ch/user/d/dorney/.local/lib/python2.7/site-packages (1.0.4)
Requirement already up-to-date: setuptools in ./venv/cc7/py2.7/lib/python2.7/site-packages (39.2.0)
Requirement already up-to-date: pip in ./venv/cc7/py2.7/lib/python2.7/site-packages (10.0.1)
xstatic-jquery-ui 1.12.0.1 requires XStatic-jQuery, which is not installed.
sphinxcontrib-spelling 2.3.0 requires PyEnchant>=1.6.5, which is not installed.
pyramid 1.5.6 requires WebOb>=1.3.1, which is not installed.
sphinx-rtd-theme 0.1.8 has requirement sphinx>=1.3, but you'll have sphinx 1.1.3 which is incompatible.
rtslib-fb 2.1.63 has requirement pyudev>=0.16.1, but you'll have pyudev 0.15 which is incompatible.
ipapython 4.5.4 has requirement dnspython>=1.15, but you'll have dnspython 1.12.0 which is incompatible.
cp /afs/cern.ch/user/s/sturdy/public/cmsgemos_gempython-0.3.1.tar.gz .
python -m pip install cmsgemos_gempython-0.3.1.tar.gz --no-deps
Processing ./cmsgemos_gempython-0.3.1.tar.gz
Building wheels for collected packages: cmsgemos-gempython
  Running setup.py bdist_wheel for cmsgemos-gempython ... done
  Stored in directory: /afs/cern.ch/user/d/dorney/.cache/pip/wheels/33/e4/f0/e0ad3108a73ad75c2385987f6d2e37cc72fe034eb77451ebcb
Successfully built cmsgemos-gempython
Installing collected packages: cmsgemos-gempython
  Found existing installation: cmsgemos-gempython 0.3.1
    Not uninstalling cmsgemos-gempython at /usr/lib/python2.7/site-packages, outside environment /afs/cern.ch/user/d/dorney/scratch0/CMS_GEM/CMS_GEM_DAQ/venv/cc7/py2.7
    Can't uninstall 'cmsgemos-gempython'. No files were found to uninstall.
Successfully installed cmsgemos-gempython-0.3.1
wget https://github.com/cms-gem-daq-project/vfatqc-python-scripts/releases/download/v2.0.0-dev3/gempython_vfatqc-2.0.0.tar.gz
--2018-06-06 21:52:22--  https://github.com/cms-gem-daq-project/vfatqc-python-scripts/releases/download/v2.0.0-dev3/gempython_vfatqc-2.0.0.tar.gz
Resolving github.com (github.com)... 192.30.253.113, 192.30.253.112
Connecting to github.com (github.com)|192.30.253.113|:443... connected.
HTTP request sent, awaiting response... 302 Found
Location: https://github-production-release-asset-2e65be.s3.amazonaws.com/58535542/c83e9b00-5393-11e8-8c23-c1df69e3a595?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20180606%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20180606T195223Z&X-Amz-Expires=300&X-Amz-Signature=7e8a3b875f200935f054dd5481d39005b9a237b04e433618dcf4c2475575e781&X-Amz-SignedHeaders=host&actor_id=0&response-content-disposition=attachment%3B%20filename%3Dgempython_vfatqc-2.0.0.tar.gz&response-content-type=application%2Foctet-stream [following]
--2018-06-06 21:52:23--  https://github-production-release-asset-2e65be.s3.amazonaws.com/58535542/c83e9b00-5393-11e8-8c23-c1df69e3a595?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20180606%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20180606T195223Z&X-Amz-Expires=300&X-Amz-Signature=7e8a3b875f200935f054dd5481d39005b9a237b04e433618dcf4c2475575e781&X-Amz-SignedHeaders=host&actor_id=0&response-content-disposition=attachment%3B%20filename%3Dgempython_vfatqc-2.0.0.tar.gz&response-content-type=application%2Foctet-stream
Resolving github-production-release-asset-2e65be.s3.amazonaws.com (github-production-release-asset-2e65be.s3.amazonaws.com)... 52.216.228.104
Connecting to github-production-release-asset-2e65be.s3.amazonaws.com (github-production-release-asset-2e65be.s3.amazonaws.com)|52.216.228.104|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 21077 (21K) [application/octet-stream]
Saving to: ‘gempython_vfatqc-2.0.0.tar.gz’

100%[====================================================================================================================================================================================================>] 21,077      --.-K/s   in 0.1s    

2018-06-06 21:52:24 (196 KB/s) - ‘gempython_vfatqc-2.0.0.tar.gz’ saved [21077/21077]

python -m pip install gempython_vfatqc-2.0.0.tar.gz
Processing ./gempython_vfatqc-2.0.0.tar.gz
Requirement already satisfied: root_numpy in /usr/lib64/python2.7/site-packages (from gempython-vfatqc==2.0.0) (4.7.3)
Requirement already satisfied: numpy<1.15,>1.7 in /usr/lib64/python2.7/site-packages (from gempython-vfatqc==2.0.0) (1.7.1)
Building wheels for collected packages: gempython-vfatqc
  Running setup.py bdist_wheel for gempython-vfatqc ... done
  Stored in directory: /afs/cern.ch/user/d/dorney/.cache/pip/wheels/44/ce/e5/a4216b1bcd56625ab745c31a36a9fd96b28d95d770f518a2c6
Successfully built gempython-vfatqc
xstatic-jquery-ui 1.12.0.1 requires XStatic-jQuery, which is not installed.
sphinxcontrib-spelling 2.3.0 requires PyEnchant>=1.6.5, which is not installed.
pyramid 1.5.6 requires WebOb>=1.3.1, which is not installed.
sphinx-rtd-theme 0.1.8 has requirement sphinx>=1.3, but you'll have sphinx 1.1.3 which is incompatible.
rtslib-fb 2.1.63 has requirement pyudev>=0.16.1, but you'll have pyudev 0.15 which is incompatible.
ipapython 4.5.4 has requirement dnspython>=1.15, but you'll have dnspython 1.12.0 which is incompatible.
Installing collected packages: gempython-vfatqc
  Found existing installation: gempython-vfatqc 2.0.0
    Not uninstalling gempython-vfatqc at /usr/lib/python2.7/site-packages, outside environment /afs/cern.ch/user/d/dorney/scratch0/CMS_GEM/CMS_GEM_DAQ/venv/cc7/py2.7
    Can't uninstall 'gempython-vfatqc'. No files were found to uninstall.
Successfully installed gempython-vfatqc-2.0.0

Then installing gem-plotting-tools from an rpm I built myself:

(py2.7) [dorney@gem904qc8daq]~/scratch0/CMS_GEM/CMS_GEM_DAQ% python -m pip install -I gem-plotting-tools/rpm/gempython_gemplotting-1.0.0.tar.gz
Processing ./gem-plotting-tools/rpm/gempython_gemplotting-1.0.0.tar.gz
Collecting root_numpy (from gempython-gemplotting==1.0.0)
Collecting numpy<1.15,>1.7 (from gempython-gemplotting==1.0.0)
  Using cached https://files.pythonhosted.org/packages/05/7d/df63c9d42eb4485e79b61a054ba5db7c8efb830d29504d4fa849cf80eb01/numpy-1.14.4-cp27-cp27mu-manylinux1_x86_64.whl
Building wheels for collected packages: gempython-gemplotting
  Running setup.py bdist_wheel for gempython-gemplotting ... done
  Stored in directory: /afs/cern.ch/user/d/dorney/.cache/pip/wheels/13/ae/43/56ae2398e13083ccc7fe4823acca0b7bd6abe30924a94ae2d1
Successfully built gempython-gemplotting
xstatic-jquery-ui 1.12.0.1 requires XStatic-jQuery, which is not installed.
sphinxcontrib-spelling 2.3.0 requires PyEnchant>=1.6.5, which is not installed.
pyramid 1.5.6 requires WebOb>=1.3.1, which is not installed.
sphinx-rtd-theme 0.1.8 has requirement sphinx>=1.3, but you'll have sphinx 1.1.3 which is incompatible.
rtslib-fb 2.1.63 has requirement pyudev>=0.16.1, but you'll have pyudev 0.15 which is incompatible.
ipapython 4.5.4 has requirement dnspython>=1.15, but you'll have dnspython 1.12.0 which is incompatible.
Installing collected packages: root-numpy, numpy, gempython-gemplotting
Successfully installed gempython-gemplotting-1.0.0 numpy-1.14.4 root-numpy-4.7.3

Based on discussion in ops meeting I have tried:

[gemuser@gem904qc8daq tmp]$ python
Python 2.7.5 (default, Apr 11 2018, 07:36:10) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-28)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> from gempython.gemplotting.utils.anautilities import parseCalFile
>>> parseCalFile("/data/bigdisk/GEM-Data-Taking/GE11_QC8/GE11-X-S-CERN-0003/scurve/calFile_GE11-X-S-CERN-0003.txt")
TTree::SetCacheSizeAux:0: RuntimeWarning: A TTreeCache could not be created because the TTree has no file
(array([-0.2692    , -0.238106  , -0.25319999, -0.27678299, -0.28      ,
        1.        , -0.29872099, -0.246732  , -0.244578  , -0.24450199,
       -0.27260301, -0.25      ,  1.        , -0.25592199, -0.26756299,
       -0.25104499, -0.242985  , -0.24558499, -0.27000001, -0.27000001,
       -0.274398  , -0.26885599, -0.25      , -0.238913  ]), array([ 66.01625061,  58.06386948,  62.37217331,  68.10211945,
        69.41000366,   0.        ,  73.83969116,  60.39213943,
        60.1219101 ,  60.58520889,  66.92677307,  61.65999985,
         0.        ,  62.92581558,  66.06646729,  61.58579636,
        59.49411774,  60.52045441,  66.87999725,  66.62999725,
        67.62643433,  66.5633316 ,  61.54000092,  58.32714844]))

So indeed the system version of root-numpy has no issue. Trying on a dummy venv:

% source $BUILD_HOME/setup_gemdaq.sh -c 0.3.1 -g 1.0.0 -G 5 -p $PWD/venv_test 2>&1 | tee venvTestLog.log
% source $BUILD_HOME/setup_gemdaq.sh -p $PWD/venv_test 
source /home/dorney/venv_test/cc7/py2.7/bin/activate
(py2.7) % python                                              
Python 2.7.5 (default, Apr 11 2018, 07:36:10) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-28)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> from gempython.gemplotting.utils.anautilities import parseCalFile
>>> parseCalFile("/data/bigdisk/GEM-Data-Taking/GE11_QC8/GE11-X-S-CERN-0003/scurve/calFile_GE11-X-S-CERN-0003.txt")
TTree::SetCacheSizeAux:0: RuntimeWarning: A TTreeCache could not be created because the TTree has no file
(array([-0.2692    , -0.238106  , -0.25319999, -0.27678299, -0.28      ,
        1.        , -0.29872099, -0.246732  , -0.244578  , -0.24450199,
       -0.27260301, -0.25      ,  1.        , -0.25592199, -0.26756299,
       -0.25104499, -0.242985  , -0.24558499, -0.27000001, -0.27000001,
       -0.274398  , -0.26885599, -0.25      , -0.238913  ]), array([ 66.01625061,  58.06386948,  62.37217331,  68.10211945,
        69.41000366,   0.        ,  73.83969116,  60.39213943,
        60.1219101 ,  60.58520889,  66.92677307,  61.65999985,
         0.        ,  62.92581558,  66.06646729,  61.58579636,
        59.49411774,  60.52045441,  66.87999725,  66.62999725,
        67.62643433,  66.5633316 ,  61.54000092,  58.32714844]))

So it seems to work now.

Looks like my old venv somehow kept some knowledge of the old root-numpy version in which root 5 bindings were used. Probably a carry over.

Closing this issue.

cms-gem-daq-project / gem-plotting-tools