barronh / permm Goto Github PK

Traceback (most recent call last):
  File "/home/xin/miniconda3/envs/python37/lib/python3.8/tkinter/__init__.py", line 1883, in __call__
    return self.func(*args)
  File "/home/xin/miniconda3/envs/python37/lib/python3.8/site-packages/permm-1.0-py3.8.egg/permm/guis/SimpleTk.py", line 87, in execute
    getattr(self.mech, method)(**thiskwds)
  File "/home/xin/miniconda3/envs/python37/lib/python3.8/site-packages/permm-1.0-py3.8.egg/permm/core/Mechanism.py", line 597, in plot_rxns
    reactions = [(rxn.sum()[plot_spc], rxn) for rxn in reactions]
  File "/home/xin/miniconda3/envs/python37/lib/python3.8/site-packages/permm-1.0-py3.8.egg/permm/core/Mechanism.py", line 597, in <listcomp>
    reactions = [(rxn.sum()[plot_spc], rxn) for rxn in reactions]
AttributeError: 'str' object has no attribute 'sum'

['RXN_02', 'RXN_92', 'RXN_108']

    def _get_species(self, species_list):
        items = species_list.curselection()
        try: items = list(map(int, items))
        except: pass
        items = list(map(lambda i, d = self.species_objects: d[i], items))
        return items

Traceback (most recent call last):
  File "main.py", line 84, in <module>
    parse_and_run()
  File "main.py", line 28, in parse_and_run
    ifiles, pncoptions = pncparse(has_ofile = False, interactive = True, parser = pncparser, args = args.pseudonetcdf)
NameError: name 'args' is not defined

What steps will reproduce the problem?
1. Running permm with "python -m permm"

What is the expected output? What do you see instead?
Anything that's not an error, really...

What version of the product are you using? On what operating system?
Latest version as of June 2011, with Python 2.7.1+ on Ubuntu 11.04 86x64

Please provide any additional information below.

I followed the install instructions, installed NetCDF and HDF5 using Aptitude, 
installed PseudoNetCDF and NetCDF4.

I cannot seem to run Permm, no matter what I try, I get an error about 'permm' 
being a package.  For example, trying step 2 of the 
[http://code.google.com/p/permm/wiki/TutorialPlotGUI tutorial]:

matt@khea:permm-1.0rc$ python -m permm -g /tmp/cmaq.base
/usr/bin/python: No module named permm.__main__; 'permm' is a package and 
cannot be directly executed


The install seems to have gone fine:

matt@khea:permm-1.0rc$ sudo python setup.py install
running install
running build
running build_py
copying src/permm/netcdf.py -> build/lib.linux-x86_64-2.7/permm
running install_lib
copying build/lib.linux-x86_64-2.7/permm/netcdf.py -> 
/usr/local/lib/python2.7/dist-packages/permm
byte-compiling /usr/local/lib/python2.7/dist-packages/permm/netcdf.py to 
netcdf.pyc
running install_egg_info
Removing /usr/local/lib/python2.7/dist-packages/permm-1.0rc.egg-info
Writing /usr/local/lib/python2.7/dist-packages/permm-1.0rc.egg-info


Or, the verbose install log which is attached.

What steps will reproduce the problem?
1. Get pyPA output 
2. Use permm to create processes plot from pyPA output(such as test.mrg.nc)
3. Display the plot

What is the expected output? What do you see instead?
The unit of the secondary y-axis shows ppmV/time, it should be ppmV. The unit 
for the primary y-axis is missing.  

What version of the product are you using? On what operating system?
permm-1.0rc-py2.6

Please provide any additional information below.

None

It would be nice to be able to plot specific reactions based on reaction
number if known (e.g. plot_rxns(IRR_1, ...) ) as well as combine reactions
using a syntax similar to the mathematical processing for species (e.g. NOx
= NO + NO2, rxns_1 = IRR_1 + IRR_2) and be able to plot those as well (e.g.
plot_rxns(rxns_1, ...) ).

1. from permm.SpeciesGroup import Sepcies
2. OH = Species(names = ['OH'], stoic = [1])
3. print (-OH).exclude

What is the expected output?
False

What do you see instead?
0

This was an error in the reimplementation of Species from dict to object. 
I have made the update that fixes Species.