[GRASS-dev] PYTHONPATH question

cmbarton · July 27, 2008, 9:52pm

Any idea why the following PYTHONPATH in my .profile works fine for GRASS finding packages like MatPlotLib and a version with the site-packages entry last does not?

PYTHONPATH=“/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages:/Library/Frameworks/Python.framework/Versions/2.5/lib/python25.zip:/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5:/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/plat-darwin:/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/plat-mac:/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/plat-mac/lib-scriptpackages:/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/lib-tk:/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/lib-dynload:”$PYTHONPATH

I had to modify this from the one that the Mac Python installation sets to put site-packages first. The Python interpreter has no problem with the path either way. Does something in the grass Python parser stop reading this path if it hits non-existent directories?

Michael

C. Michael Barton, Professor of Anthropology
Director of Graduate Studies
School of Human Evolution & Social Change
Center for Social Dynamics & Complexity
Arizona State University

Phone: 480-965-6262
Fax: 480-965-7671
www: <www.public.asu.edu/~cmbarton>

Glynn_Clements1 · July 27, 2008, 11:01pm

Michael Barton wrote:

Any idea why the following PYTHONPATH in my .profile works fine for
GRASS finding packages like MatPlotLib and a version with the site-
packages entry last does not?

PYTHONPATH="/Library/Frameworks/Python.framework/Versions/2.5/lib/
python2.5/site-packages:/Library/Frameworks/Python.framework/Versions/
2.5/lib/python25.zip:/Library/Frameworks/Python.framework/Versions/2.5/
lib/python2.5:/Library/Frameworks/Python.framework/Versions/2.5/lib/
python2.5/plat-darwin:/Library/Frameworks/Python.framework/Versions/
2.5/lib/python2.5/plat-mac:/Library/Frameworks/Python.framework/
Versions/2.5/lib/python2.5/plat-mac/lib-scriptpackages:/Library/
Frameworks/Python.framework/Versions/2.5/lib/python2.5/lib-tk:/Library/
Frameworks/Python.framework/Versions/2.5/lib/python2.5/lib-
dynload:"$PYTHONPATH

Why do you have all of your Python system directories in PYTHONPATH?
Those should already be in sys.path.

FWIW, on Gentoo, the only directory which is added to PYTHONPATH by
the OS configuration is /usr/lib/portage/pym ("portage" is Gentoo's
package manager, and it's written mainly in Python).

I suggest completely unsetting PYTHONPATH, and seeing what problems
(if any) that causes.

I had to modify this from the one that the Mac Python installation
sets to put site-packages first. The Python interpreter has no problem
with the path either way. Does something in the grass Python parser
stop reading this path if it hits non-existent directories?

No.

--
Glynn Clements <glynn@gclements.plus.com>

cmbarton · July 27, 2008, 11:39pm

On Jul 27, 2008, at 4:01 PM, Glynn Clements wrote:

Michael Barton wrote:

Any idea why the following PYTHONPATH in my .profile works fine for
GRASS finding packages like MatPlotLib and a version with the site-
packages entry last does not?

PYTHONPATH="/Library/Frameworks/Python.framework/Versions/2.5/lib/
python2.5/site-packages:/Library/Frameworks/Python.framework/Versions/
2.5/lib/python25.zip:/Library/Frameworks/Python.framework/Versions/2.5/
lib/python2.5:/Library/Frameworks/Python.framework/Versions/2.5/lib/
python2.5/plat-darwin:/Library/Frameworks/Python.framework/Versions/
2.5/lib/python2.5/plat-mac:/Library/Frameworks/Python.framework/
Versions/2.5/lib/python2.5/plat-mac/lib-scriptpackages:/Library/
Frameworks/Python.framework/Versions/2.5/lib/python2.5/lib-tk:/Library/
Frameworks/Python.framework/Versions/2.5/lib/python2.5/lib-
dynload:"$PYTHONPATH

Why do you have all of your Python system directories in PYTHONPATH?
Those should already be in sys.path.

FWIW, on Gentoo, the only directory which is added to PYTHONPATH by
the OS configuration is /usr/lib/portage/pym ("portage" is Gentoo's
package manager, and it's written mainly in Python).

I suggest completely unsetting PYTHONPATH, and seeing what problems
(if any) that causes.

Interesting. This was something the Mac Python installation puts in, though I can tell it not to do so. If I unset this, Python works fine from a terminal and importing in the Python interpreter works fine too.

BUT, there are problems in GRASS because Init.sh now sets $PYTHONPATH to $GISBASE/etc. This is fine for grass.py, but it causes problems accessing anything else in site-packages. Here is the result of running one of the MatPlotLib demo scripts.

GRASS 7.0.svn (Spearfish60_test):~ > histogram_mpldemo.py
Traceback (most recent call last):
File "/Applications/Grass/GRASS-7.0.app/Contents/MacOS/scripts/histogram_mpldemo.py", line 94, in <module>
import matplotlib
ImportError: No module named matplotlib

It's looking for matplotlib in $GISBASE/etc now.

Michael

Glynn_Clements1 · July 28, 2008, 12:19am

Michael Barton wrote:

>> Any idea why the following PYTHONPATH in my .profile works fine for
>> GRASS finding packages like MatPlotLib and a version with the site-
>> packages entry last does not?
>>
>> PYTHONPATH="/Library/Frameworks/Python.framework/Versions/2.5/lib/
>> python2.5/site-packages:/Library/Frameworks/Python.framework/
>> Versions/
>> 2.5/lib/python25.zip:/Library/Frameworks/Python.framework/Versions/
>> 2.5/
>> lib/python2.5:/Library/Frameworks/Python.framework/Versions/2.5/lib/
>> python2.5/plat-darwin:/Library/Frameworks/Python.framework/Versions/
>> 2.5/lib/python2.5/plat-mac:/Library/Frameworks/Python.framework/
>> Versions/2.5/lib/python2.5/plat-mac/lib-scriptpackages:/Library/
>> Frameworks/Python.framework/Versions/2.5/lib/python2.5/lib-tk:/
>> Library/
>> Frameworks/Python.framework/Versions/2.5/lib/python2.5/lib-
>> dynload:"$PYTHONPATH
>
> Why do you have all of your Python system directories in PYTHONPATH?
> Those should already be in sys.path.
>
> FWIW, on Gentoo, the only directory which is added to PYTHONPATH by
> the OS configuration is /usr/lib/portage/pym ("portage" is Gentoo's
> package manager, and it's written mainly in Python).
>
> I suggest completely unsetting PYTHONPATH, and seeing what problems
> (if any) that causes.

Interesting. This was something the Mac Python installation puts in,
though I can tell it not to do so. If I unset this, Python works fine
from a terminal and importing in the Python interpreter works fine too.

BUT, there are problems in GRASS because Init.sh now sets $PYTHONPATH
to $GISBASE/etc. This is fine for grass.py, but it causes problems
accessing anything else in site-packages. Here is the result of
running one of the MatPlotLib demo scripts.

GRASS 7.0.svn (Spearfish60_test):~ > histogram_mpldemo.py
Traceback (most recent call last):
File "/Applications/Grass/GRASS-7.0.app/Contents/MacOS/scripts/
histogram_mpldemo.py", line 94, in <module>
import matplotlib
ImportError: No module named matplotlib

It's looking for matplotlib in $GISBASE/etc now.

Any directories in PYTHONPATH should be in addition to the Python
system directories, not instead of them.

What do you get from:

import sys
print '\n'.join(sys.path)
?

When you say that you can tell the Mac Python installer not to set
PYTHONPATH, do you know if does something else instead?

Is "python" the actual executable, or is it a front-end script?

I'm wondering whether python is being invoked with the -S switch,
which suppresses the automatic "import site" (which causes
site-packages to be added to sys.path, along with any subdirectories
referenced by any site-packages/*.pth files).

--
Glynn Clements <glynn@gclements.plus.com>

cmbarton · July 28, 2008, 12:40am

On Jul 27, 2008, at 5:19 PM, Glynn Clements wrote:

Michael Barton wrote:

I suggest completely unsetting PYTHONPATH, and seeing what problems

(if any) that causes.

Interesting. This was something the Mac Python installation puts in,
though I can tell it not to do so. If I unset this, Python works fine
from a terminal and importing in the Python interpreter works fine too.

BUT, there are problems in GRASS because Init.sh now sets $PYTHONPATH
to $GISBASE/etc. This is fine for grass.py, but it causes problems
accessing anything else in site-packages. Here is the result of
running one of the MatPlotLib demo scripts.

GRASS 7.0.svn (Spearfish60_test):~ > histogram_mpldemo.py
Traceback (most recent call last):
  File "/Applications/Grass/GRASS-7.0.app/Contents/MacOS/scripts/
histogram_mpldemo.py", line 94, in <module>
    import matplotlib
ImportError: No module named matplotlib

It's looking for matplotlib in $GISBASE/etc now.

Any directories in PYTHONPATH should be in addition to the Python
system directories, not instead of them.

What do you get from:

  import sys
  print '\n'.join(sys.path)
?

/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/setuptools-0.6c8-py2.5.egg
/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/Dabo-0.8.3-py2.5.egg
/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/setuptools-0.6c8-py2.5.egg
/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/ipython-0.8.4-py2.5.egg
/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/numpy-1.1.0-py2.5-macosx-10.3-i386.egg
/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/matplotlib-0.98.1-py2.5-macosx-10.3.egg
/Applications/Grass/GRASS-7.0.app/Contents/MacOS/etc/python
/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages
/usr/local/lib/wxPython-unicode-2.8.8.1/lib/python2.5/site-packages
/usr/local/lib/wxPython-unicode-2.8.8.1/lib/python2.5/site-packages/wx-2.8-mac-unicode
/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/lib-dynload
/usr/local/lib/wxPython-unicode-2.8.8.1/lib/python2.5
/Library/Frameworks/Python.framework/Versions/2.5/lib/python25.zip
/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5
/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/plat-darwin
/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/plat-mac
/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/plat-mac/lib-scriptpackages
/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/lib-tk

When you say that you can tell the Mac Python installer not to set
PYTHONPATH, do you know if does something else instead?

No. It simply has an option (default, but can turn off) to modify .profile.

Is "python" the actual executable, or is it a front-end script?

/usr/bin/python and /usr/local/bin/python are symlinks to /Library/Frameworks/.../python2.5, which is an executable. I've checked and this is the only "python" in my path

I'm wondering whether python is being invoked with the -S switch,
which suppresses the automatic "import site" (which causes
site-packages to be added to sys.path, along with any subdirectories
referenced by any site-packages/*.pth files).

I don't think so. It works fine when just calling the python interpreter from the shell. I think the issue is now just down to the fact that Init.sh creates a $PYTHONPATH that has $GISBASE/etc/python. Once this is created, the python side of g.parser only looks for modules to import in $PYTHONPATH. If I just invoke python from the GRASS shell to start the interpreter, there is no problem importing matplotlib or anything else. It's only having parsing import matplotlib when it's in a script. This is an improvement over previous complications. I really appreciate your help.

Michael

--
Glynn Clements <glynn@gclements.plus.com>

Glynn_Clements1 · July 28, 2008, 1:53am

Michael Barton wrote:

>>>> I suggest completely unsetting PYTHONPATH, and seeing what problems
>>> (if any) that causes.
>>
>> Interesting. This was something the Mac Python installation puts in,
>> though I can tell it not to do so. If I unset this, Python works fine
>> from a terminal and importing in the Python interpreter works fine
>> too.
>>
>> BUT, there are problems in GRASS because Init.sh now sets $PYTHONPATH
>> to $GISBASE/etc. This is fine for grass.py, but it causes problems
>> accessing anything else in site-packages. Here is the result of
>> running one of the MatPlotLib demo scripts.
>>
>> GRASS 7.0.svn (Spearfish60_test):~ > histogram_mpldemo.py
>> Traceback (most recent call last):
>> File "/Applications/Grass/GRASS-7.0.app/Contents/MacOS/scripts/
>> histogram_mpldemo.py", line 94, in <module>
>> import matplotlib
>> ImportError: No module named matplotlib
>>
>> It's looking for matplotlib in $GISBASE/etc now.
>
> Any directories in PYTHONPATH should be in addition to the Python
> system directories, not instead of them.
>
> What do you get from:
>
> import sys
> print '\n'.join(sys.path)
> ?

/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/setuptools-0.6c8-py2.5.egg
/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/Dabo-0.8.3-py2.5.egg
/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/setuptools-0.6c8-py2.5.egg
/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/ipython-0.8.4-py2.5.egg
/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/numpy-1.1.0-py2.5-macosx-10.3-i386.egg
/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/matplotlib-0.98.1-py2.5-macosx-10.3.egg
/Applications/Grass/GRASS-7.0.app/Contents/MacOS/etc/python
/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages
/usr/local/lib/wxPython-unicode-2.8.8.1/lib/python2.5/site-packages
/usr/local/lib/wxPython-unicode-2.8.8.1/lib/python2.5/site-packages/wx-2.8-mac-unicode
/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/lib-dynload
/usr/local/lib/wxPython-unicode-2.8.8.1/lib/python2.5
/Library/Frameworks/Python.framework/Versions/2.5/lib/python25.zip
/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5
/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/plat-darwin
/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/plat-mac
/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/plat-mac/lib-scriptpackages
/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/lib-tk

Is this for a configuration which works, or which doesn't work?

I note that GRASS' etc/python directory is there.

> I'm wondering whether python is being invoked with the -S switch,
> which suppresses the automatic "import site" (which causes
> site-packages to be added to sys.path, along with any subdirectories
> referenced by any site-packages/*.pth files).

I don't think so. It works fine when just calling the python
interpreter from the shell. I think the issue is now just down to the
fact that Init.sh creates a $PYTHONPATH that has $GISBASE/etc/python.
Once this is created, the python side of g.parser only looks for
modules to import in $PYTHONPATH. If I just invoke python from the
GRASS shell to start the interpreter, there is no problem importing
matplotlib or anything else. It's only having parsing import
matplotlib when it's in a script. This is an improvement over previous
complications. I really appreciate your help.

Is there any pattern to which modules will import and which won't?

I notice that matplotlib is a .egg file. I don't have any of these on
my system (I do have a bunch of .egg-info files, which are just plain
text), probably because Gentoo builds everything from source.

--
Glynn Clements <glynn@gclements.plus.com>

cmbarton · July 28, 2008, 3:11am

On Jul 27, 2008, at 6:53 PM, Glynn Clements wrote:

Is there any pattern to which modules will import and which won't?

All the paths in sys.path are valid. AFAICT, everything works without $PYTHONPATH in all cases EXCEPT in a script running under the GRASS parser.

Michael

I notice that matplotlib is a .egg file. I don't have any of these on
my system (I do have a bunch of .egg-info files, which are just plain
text), probably because Gentoo builds everything from source.

Glynn_Clements1 · July 28, 2008, 12:44pm

Michael Barton wrote:

> Is there any pattern to which modules will import and which won't?

All the paths in sys.path are valid.

That isn't what I asked.

Which modules will import, and which won't? Presumably "sys" imports
(that's built into Python)? What about "os"?

Is it just the modules in site-packages, or the "system" modules as
well?

AFAICT, everything works without $PYTHONPATH in all cases EXCEPT in
a script running under the GRASS parser.

So what changes before and after g.parser?

In the scripts which I have seen so far, the imports are at the top
level, so they will be executed on both occasions. I can't think of
any reason why an import would fail when the script is run initially
but then work when the script is re-invoked from g.parser.

Can you add commands to print sys.argv and sys.path (and, if you can
import "os", os.environ) to the top of the script, and see what is
changing before and after g.parser.

--
Glynn Clements <glynn@gclements.plus.com>

cmbarton · July 28, 2008, 5:13pm

On Jul 28, 2008, at 5:44 AM, Glynn Clements wrote:

Michael Barton wrote:

Is there any pattern to which modules will import and which won't?

All the paths in sys.path are valid.

That isn't what I asked.

Which modules will import, and which won't? Presumably "sys" imports
(that's built into Python)? What about "os"?

Is it just the modules in site-packages, or the "system" modules as
well?

System modules import fine. It's just site-packages modules

AFAICT, everything works without $PYTHONPATH in all cases EXCEPT in
a script running under the GRASS parser.

So what changes before and after g.parser?

In the scripts which I have seen so far, the imports are at the top
level, so they will be executed on both occasions. I can't think of
any reason why an import would fail when the script is run initially
but then work when the script is re-invoked from g.parser.

Can you add commands to print sys.argv and sys.path (and, if you can
import "os", os.environ) to the top of the script, and see what is
changing before and after g.parser.

I'm not sure I understand. The structure is a 'standard GRASS script' for Python.

##################################

#!/usr/bin/python

GRASS doc area

GUI description area

most import statements (this is where it stops with an import from site-packages; the 'system' modules import fine)

def Main(): (i.e., the first procedure called by the parser line)

other procedures

if __name__ == "__main__":
options, flags = grass.parser()
main()

##################################

This works fine if I type the following on at the GRASS command prompt before executing

PYTHONPATH="/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages"$PYTHONPATH

I thought I'd show you how setting PYTHONPATH in Init.sh was causing the trouble, but discovered something that seems a bit odd. I tried unsetting PYTHONPATH and got the same results as before.

GRASS 7.0.svn (Spearfish60_test):~ > $PYTHONPATH
bash: /Applications/Grass/GRASS-7.0.app/Contents/MacOS/etc/python:: No such file or directory
GRASS 7.0.svn (Spearfish60_test):~ > export PYTHONPATH=""
GRASS 7.0.svn (Spearfish60_test):~ > $PYTHONPATH
GRASS 7.0.svn (Spearfish60_test):~ >
GRASS 7.0.svn (Spearfish60_test):~ > histogram_mpldemo.py
Traceback (most recent call last):
File "/Applications/Grass/GRASS-7.0.app/Contents/MacOS/scripts/histogram_mpldemo.py", line 93, in <module>
import matplotlib
ImportError: No module named matplotlib

If I start Python from the GRASS command prompt, sys.path is as before and $PYTHONPATH is unset. So what is setting the search path for Python modules now?

Michael

Glynn_Clements1 · July 29, 2008, 1:36pm

Michael Barton wrote:

>> AFAICT, everything works without $PYTHONPATH in all cases EXCEPT in
>> a script running under the GRASS parser.
>
> So what changes before and after g.parser?
>
> In the scripts which I have seen so far, the imports are at the top
> level, so they will be executed on both occasions. I can't think of
> any reason why an import would fail when the script is run initially
> but then work when the script is re-invoked from g.parser.
>
> Can you add commands to print sys.argv and sys.path (and, if you can
> import "os", os.environ) to the top of the script, and see what is
> changing before and after g.parser.

I'm not sure I understand. The structure is a 'standard GRASS script'
for Python.

##################################

#!/usr/bin/python

At this point, put:

  import sys
  print sys.argv
  print sys.path

import os
print os.environ

When you run the script, you should get two lots of output, one from
before g.parser, one from when the script is re-invoked. Unless
g.parser is never being invoked in the first place.

This works fine if I type the following on at the GRASS command prompt
before executing

PYTHONPATH="/Library/Frameworks/Python.framework/Versions/2.5/lib/
python2.5/site-packages"$PYTHONPATH

There ought to be a colon between the literal and $PYTHONPATH.

I thought I'd show you how setting PYTHONPATH in Init.sh was causing
the trouble, but discovered something that seems a bit odd. I tried
unsetting PYTHONPATH and got the same results as before.

GRASS 7.0.svn (Spearfish60_test):~ > $PYTHONPATH
bash: /Applications/Grass/GRASS-7.0.app/Contents/MacOS/etc/python:: No
such file or directory

To print a variable, use "echo", e.g. "echo $PYTHONPATH". If you just
type "$PYTHONPATH", the shell will try to execute its value as a
command.

GRASS 7.0.svn (Spearfish60_test):~ > export PYTHONPATH=""
GRASS 7.0.svn (Spearfish60_test):~ > $PYTHONPATH
GRASS 7.0.svn (Spearfish60_test):~ >
GRASS 7.0.svn (Spearfish60_test):~ > histogram_mpldemo.py
Traceback (most recent call last):
File "/Applications/Grass/GRASS-7.0.app/Contents/MacOS/scripts/
histogram_mpldemo.py", line 93, in <module>
import matplotlib
ImportError: No module named matplotlib

If I start Python from the GRASS command prompt, sys.path is as before
and $PYTHONPATH is unset. So what is setting the search path for
Python modules now?

Unless it's started with the -S switch, the Python interpreter
performs an automatic "import site". This module adds the
site-packages directory to sys.path; it also adds each subdirectory
which is named in one fo the site-packages/*.pth files.

http://docs.python.org/lib/module-site.html

It shoudn't be necessary for PYTHONPATH to be set unless you need to
use modules which aren't installed in Python's lib directory.

Are any of the other PYTHON* environment variables set? If
$PYTHONSTARTUP is set, that could cause an interactive interpreter to
behave differently from a script.

You could try starting python with and without the -S flag, printing
sys.path in each case. It's possible that there's some oddity in your
setup that is causing site.py to misbehave.

--
Glynn Clements <glynn@gclements.plus.com>

cmbarton · July 29, 2008, 4:22pm

Glynn,

See below...

On Jul 29, 2008, at 6:36 AM, Glynn Clements wrote:

Michael Barton wrote:

AFAICT, everything works without $PYTHONPATH in all cases EXCEPT in
a script running under the GRASS parser.

So what changes before and after g.parser?

In the scripts which I have seen so far, the imports are at the top
level, so they will be executed on both occasions. I can't think of
any reason why an import would fail when the script is run initially
but then work when the script is re-invoked from g.parser.

Can you add commands to print sys.argv and sys.path (and, if you can
import "os", os.environ) to the top of the script, and see what is
changing before and after g.parser.

I'm not sure I understand. The structure is a 'standard GRASS script'
for Python.

##################################

#!/usr/bin/python

At this point, put:

  import sys
  print sys.argv
  print sys.path

  import os
  print os.environ

GRASS 7.0.svn (Spearfish60_test):~ > histogram_mpldemo.py

********* sys.argv ***********

/Applications/Grass/GRASS-7.0.app/Contents/MacOS/scripts/histogram_mpldemo.py

********* sys.path ***********

/Applications/Grass/GRASS-7.0.app/Contents/MacOS/scripts
/Library/Python/2.5/site-packages/GDAL-1.5.2-py2.5-macosx-10.5-i386.egg
/Applications/Grass/GRASS-7.0.app/Contents/MacOS/etc/python
/Users/cmbarton
/usr/local/lib/wxPython-unicode-2.8.8.1/lib/python2.5/site-packages
/usr/local/lib/wxPython-unicode-2.8.8.1/lib/python2.5/site-packages/wx-2.8-mac-unicode
/System/Library/Frameworks/Python.framework/Versions/2.5/lib/python25.zip
/System/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5
/System/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/plat-darwin
/System/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/plat-mac
/System/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/plat-mac/lib-scriptpackages
/System/Library/Frameworks/Python.framework/Versions/2.5/Extras/lib/python
/System/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/lib-tk
/System/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/lib-dynload
/Library/Python/2.5/site-packages
/usr/local/lib/wxPython-unicode-2.8.8.1/lib/python2.5
/System/Library/Frameworks/Python.framework/Versions/2.5/Extras/lib/python/PyObjC

********* os.environ ***********

_
HISTFILE
GRASS_FONT
GRASS_HTML_BROWSER
TERM_PROGRAM_VERSION
CVS_RSH
GRASS_SH
USER
HOME
PATH
GRASS_GNUPLOT
DISPLAY
TERM_PROGRAM
LANG
GRASS_ADDON_PATH
TERM
Apple_PubSub_Socket_Render
INFOPATH
SHLVL
SECURITYSESSIONID
GRASS_PAGER
HISTSIZE
EDITOR
MANPATH
GISBASE
CVSROOT
TK_LIBRARY
GRASS_PERL
PYTHONPATH
SSH_AUTH_SOCK
GRASS_HTML_BROWSER_MACOSX
TCL_LIBRARY
DYLD_LIBRARY_PATH
PWD
SHELL
GRASS_XTERM
GRASS_ADDON_ETC
GRASS_OS_STARTUP
TMPDIR
PERL5LIB
GRASS_LD_LIBRARY_PATH
GRASS_PROJSHARE
GRASS_PYTHON
__CF_USER_TEXT_ENCODING
GRASS_WISH
GISRC
GRASS_TCLSH
GRASS_VERSION
GRASS_FONT_CAP
LOGNAME
GIS_LOCK
COMMAND_MODE
Traceback (most recent call last):
File "/Applications/Grass/GRASS-7.0.app/Contents/MacOS/scripts/histogram_mpldemo.py", line 104, in <module>
import matplotlib
ImportError: No module named matplotlib
GRASS 7.0.svn (Spearfish60_test):~ >

.

This works fine if I type the following on at the GRASS command prompt
before executing

PYTHONPATH="/Library/Frameworks/Python.framework/Versions/2.5/lib/
python2.5/site-packages"$PYTHONPATH

There ought to be a colon between the literal and $PYTHONPATH.

Typo in the email. It is usually there.

Unless it's started with the -S switch, the Python interpreter
performs an automatic "import site". This module adds the
site-packages directory to sys.path; it also adds each subdirectory
which is named in one fo the site-packages/*.pth files.

site — Site-specific configuration hook — Python 3.12.7 documentation

It shoudn't be necessary for PYTHONPATH to be set unless you need to
use modules which aren't installed in Python's lib directory.

Are any of the other PYTHON* environment variables set? If
$PYTHONSTARTUP is set, that could cause an interactive interpreter to
behave differently from a script.

Not that I've set anywhere. $PYTHONSTARTUP is not set.

You could try starting python with and without the -S flag, printing
sys.path in each case. It's possible that there's some oddity in your
setup that is causing site.py to misbehave.

with -S does not have any site-packages; without -S has site-packages. See below.

GRASS 7.0.svn (Spearfish60_test):~ > python
Python 2.5.2 (r252:60911, Feb 22 2008, 07:57:53)
[GCC 4.0.1 (Apple Computer, Inc. build 5363)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import sys
>>> print '\n'.join(sys.path)

/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/Dabo-0.8.3-py2.5.egg
/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/setuptools-0.6c8-py2.5.egg
/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/ipython-0.8.4-py2.5.egg
/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages
/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/numpy-1.1.0-py2.5-macosx-10.3-i386.egg
/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/matplotlib-0.98.1-py2.5-macosx-10.3.egg
/Applications/Grass/GRASS-7.0.app/Contents/MacOS/etc/python
/Users/cmbarton
/usr/local/lib/wxPython-unicode-2.8.8.1/lib/python2.5/site-packages
/usr/local/lib/wxPython-unicode-2.8.8.1/lib/python2.5/site-packages/wx-2.8-mac-unicode
/Library/Frameworks/Python.framework/Versions/2.5/lib/python25.zip
/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5
/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/plat-darwin
/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/plat-mac
/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/plat-mac/lib-scriptpackages
/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/lib-tk
/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/lib-dynload
/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages
/usr/local/lib/wxPython-unicode-2.8.8.1/lib/python2.5

GRASS 7.0.svn (Spearfish60_test):~ > python -S
Python 2.5.2 (r252:60911, Feb 22 2008, 07:57:53)
[GCC 4.0.1 (Apple Computer, Inc. build 5363)] on darwin
>>> import sys
>>> print '\n'.join(sys.path)

/Applications/Grass/GRASS-7.0.app/Contents/MacOS/etc/python

/Library/Frameworks/Python.framework/Versions/2.5/lib/python25.zip
/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/
/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/plat-darwin
/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/plat-mac
/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/plat-mac/lib-scriptpackages
/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/lib-tk
/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/lib-dynload
>>>

William_Kyngesburye · July 29, 2008, 4:37pm

On Jul 29, 2008, at 11:22 AM, Michael Barton wrote:

GRASS 7.0.svn (Spearfish60_test):~ > histogram_mpldemo.py

********* sys.argv ***********

/Applications/Grass/GRASS-7.0.app/Contents/MacOS/scripts/histogram_mpldemo.py

********* sys.path ***********

/Applications/Grass/GRASS-7.0.app/Contents/MacOS/scripts
/Library/Python/2.5/site-packages/GDAL-1.5.2-py2.5-macosx-10.5-i386.egg
/Applications/Grass/GRASS-7.0.app/Contents/MacOS/etc/python
/Users/cmbarton
/usr/local/lib/wxPython-unicode-2.8.8.1/lib/python2.5/site-packages
/usr/local/lib/wxPython-unicode-2.8.8.1/lib/python2.5/site-packages/wx-2.8-mac-unicode
/System/Library/Frameworks/Python.framework/Versions/2.5/lib/python25.zip
/System/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5
/System/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/plat-darwin
/System/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/plat-mac
/System/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/plat-mac/lib-scriptpackages
/System/Library/Frameworks/Python.framework/Versions/2.5/Extras/lib/python
/System/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/lib-tk
/System/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/lib-dynload
/Library/Python/2.5/site-packages
/usr/local/lib/wxPython-unicode-2.8.8.1/lib/python2.5
/System/Library/Frameworks/Python.framework/Versions/2.5/Extras/lib/python/PyObjC

Traceback (most recent call last):
File "/Applications/Grass/GRASS-7.0.app/Contents/MacOS/scripts/histogram_mpldemo.py", line 104, in <module>
import matplotlib
ImportError: No module named matplotlib
GRASS 7.0.svn (Spearfish60_test):~ >

[coming out of lurking on this one]

It looks like, when run from a python script in GRASS, you're getting the system python.

Yet, when you run python itself from GRASS, you get the python.org Python. What is the shebang line (first line) in your python script, it may be pointing to the system python?

On Jul 27, 2008, at 7:40 PM, Michael Barton wrote:

Is "python" the actual executable, or is it a front-end script?

/usr/bin/python and /usr/local/bin/python are symlinks to /Library/Frameworks/.../python2.5, which is an executable. I've checked and this is the only "python" in my path

/usr/bin/python should be a symlink to the SYSTEM python.

-----
William Kyngesburye <kyngchaos*at*kyngchaos*dot*com>
http://www.kyngchaos.com/

"Oh, look, I seem to have fallen down a deep, dark hole. Now what does that remind me of? Ah, yes - life."

- Marvin

cmbarton · July 29, 2008, 4:54pm

On Jul 29, 2008, at 9:37 AM, William Kyngesburye wrote:

[coming out of lurking on this one]

It looks like, when run from a python script in GRASS, you're getting the system python.

Yet, when you run python itself from GRASS, you get the python.org Python. What is the shebang line (first line) in your python script, it may be pointing to the system python?

On Jul 27, 2008, at 7:40 PM, Michael Barton wrote:

Is "python" the actual executable, or is it a front-end script?

/usr/bin/python and /usr/local/bin/python are symlinks to /Library/Frameworks/.../python2.5, which is an executable. I've checked and this is the only "python" in my path

/usr/bin/python should be a symlink to the SYSTEM python.

Weird. When I do 'show original' for /usr/bin/python, it shows as a symlink to

/System/Library/Frameworks/Python.framework/Versions/2.5/bin/python

...which is a symlink to /System/Library/Frameworks/Python.framework/Versions/2.5/bin/python2.5

BUT, if I start it...

cmb-MBP-2:~ cmbarton$ python
Python 2.5.2 (r252:60911, Feb 22 2008, 07:57:53)
[GCC 4.0.1 (Apple Computer, Inc. build 5363)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>>
cmb-MBP-2:~ cmbarton$ /usr/bin/python
Python 2.5.1 (r251:54863, Jan 17 2008, 19:35:17)
[GCC 4.0.1 (Apple Inc. build 5465)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> ^D
cmb-MBP-2:~ cmbarton$ /usr/bin/python2.5
Python 2.5.1 (r251:54863, Jan 17 2008, 19:35:17)
[GCC 4.0.1 (Apple Inc. build 5465)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>>
cmb-MBP-2:~ cmbarton$ /usr/local/bin/python
Python 2.5.2 (r252:60911, Feb 22 2008, 07:57:53)
[GCC 4.0.1 (Apple Computer, Inc. build 5363)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>>

So it IS the shebang at the top.

So what to do to make this work?

#!/usr/bin/env python ???

This works on my Mac. Does it work for others?

Michael

cmbarton · July 29, 2008, 4:59pm

On Jul 29, 2008, at 9:54 AM, Michael Barton wrote:

On Jul 29, 2008, at 9:37 AM, William Kyngesburye wrote:

[coming out of lurking on this one]

It looks like, when run from a python script in GRASS, you're getting the system python.

Yet, when you run python itself from GRASS, you get the python.org Python. What is the shebang line (first line) in your python script, it may be pointing to the system python?

On Jul 27, 2008, at 7:40 PM, Michael Barton wrote:

Is "python" the actual executable, or is it a front-end script?

/usr/bin/python and /usr/local/bin/python are symlinks to /Library/Frameworks/.../python2.5, which is an executable. I've checked and this is the only "python" in my path

/usr/bin/python should be a symlink to the SYSTEM python.

Weird. When I do 'show original' for /usr/bin/python, it shows as a symlink to

/System/Library/Frameworks/Python.framework/Versions/2.5/bin/python

...which is a symlink to /System/Library/Frameworks/Python.framework/Versions/2.5/bin/python2.5

Note that when I do a 'show original' for both symlinks /usr/bin/python and /usr/local/bin/python, they both go to the same place:

/System/Library/Frameworks/Python.framework/Versions/2.5/bin/python

But one calls the System 2.5.1 and the other one calls the MacPython 2.5.2

Michael

William_Kyngesburye1 · July 29, 2008, 5:10pm

On Jul 29, 2008, at 11:59 AM, Michael Barton wrote:

On Jul 29, 2008, at 9:54 AM, Michael Barton wrote:

Weird. When I do 'show original' for /usr/bin/python, it shows as a symlink to

/System/Library/Frameworks/Python.framework/Versions/2.5/bin/python

...which is a symlink to /System/Library/Frameworks/Python.framework/Versions/2.5/bin/python2.5

Note that when I do a 'show original' for both symlinks /usr/bin/python and /usr/local/bin/python, they both go to the same place:

/System/Library/Frameworks/Python.framework/Versions/2.5/bin/python

But one calls the System 2.5.1 and the other one calls the MacPython 2.5.2

Michael

By "show original", do you mean right-click->show original in the Finder?

What about:

ls -l /usr/bin/python
ls -l /usr/local/bin/python

-----
William Kyngesburye <kyngchaos*at*kyngchaos*dot*com>
http://www.kyngchaos.com/

"Oh, look, I seem to have fallen down a deep, dark hole. Now what does that remind me of? Ah, yes - life."

- Marvin

cmbarton · July 29, 2008, 5:15pm

On Jul 29, 2008, at 10:10 AM, William Kyngesburye wrote:

On Jul 29, 2008, at 11:59 AM, Michael Barton wrote:

On Jul 29, 2008, at 9:54 AM, Michael Barton wrote:

Weird. When I do 'show original' for /usr/bin/python, it shows as a symlink to

/System/Library/Frameworks/Python.framework/Versions/2.5/bin/python

...which is a symlink to /System/Library/Frameworks/Python.framework/Versions/2.5/bin/python2.5

Note that when I do a 'show original' for both symlinks /usr/bin/python and /usr/local/bin/python, they both go to the same place:

/System/Library/Frameworks/Python.framework/Versions/2.5/bin/python

But one calls the System 2.5.1 and the other one calls the MacPython 2.5.2

Michael

By "show original", do you mean right-click->show original in the Finder?

Yup

What about:

ls -l /usr/bin/python
ls -l /usr/local/bin/python

cmb-MBP-2:~ cmbarton$ ls -l /usr/bin/python
lrwxr-xr-x 1 root wheel 72 May 9 15:32 /usr/bin/python -> ../../System/Library/Frameworks/Python.framework/Versions/2.5/bin/python
cmb-MBP-2:~ cmbarton$ ls -l /usr/local/bin/python
lrwxr-xr-x 1 root wheel 68 May 9 23:07 /usr/local/bin/python - > ../../../Library/Frameworks/Python.framework/Versions/2.5/bin/python
cmb-MBP-2:~ cmbarton$

-----
William Kyngesburye <kyngchaos*at*kyngchaos*dot*com>
http://www.kyngchaos.com/

"Oh, look, I seem to have fallen down a deep, dark hole. Now what does that remind me of? Ah, yes - life."

- Marvin

William_Kyngesburye · July 29, 2008, 5:16pm

On Jul 29, 2008, at 11:54 AM, Michael Barton wrote:

So it IS the shebang at the top.

So what to do to make this work?

#!/usr/bin/env python ???

This works on my Mac. Does it work for others?

Are those ??? literally in the shebang? I don't know the finer details of env, but that doesn't look right. Try removing them:

#!/usr/bin/env python

-----
William Kyngesburye <kyngchaos*at*kyngchaos*dot*com>
http://www.kyngchaos.com/

"We are at war with them. Neither in hatred nor revenge and with no particular pleasure I shall kill every ___ I can until the war is over. That is my duty."

"Don't you even hate 'em?"

"What good would it do if I did? If all the many millions of people of the allied nations devoted an entire year exclusively to hating the ____ it wouldn't kill one ___ nor shorten the war one day."

<Ha, ha> "And it might give 'em all stomach ulcers."

- Tarzan, on war

cmbarton · July 29, 2008, 5:19pm

On Jul 29, 2008, at 10:16 AM, William Kyngesburye wrote:

On Jul 29, 2008, at 11:54 AM, Michael Barton wrote:

So it IS the shebang at the top.

So what to do to make this work?

#!/usr/bin/env python ???

This works on my Mac. Does it work for others?

Are those ??? literally in the shebang? I don't know the finer details of env, but that doesn't look right. Try removing them:

#!/usr/bin/env python

No. The ??? was just me questioning if I should use that format.

Michael

William_Kyngesburye · July 29, 2008, 5:34pm

On Jul 29, 2008, at 12:15 PM, Michael Barton wrote:

cmb-MBP-2:~ cmbarton$ ls -l /usr/bin/python
lrwxr-xr-x 1 root wheel 72 May 9 15:32 /usr/bin/python -> ../../System/Library/Frameworks/Python.framework/Versions/2.5/bin/python
cmb-MBP-2:~ cmbarton$ ls -l /usr/local/bin/python
lrwxr-xr-x 1 root wheel 68 May 9 23:07 /usr/local/bin/python -> ../../../Library/Frameworks/Python.framework/Versions/2.5/bin/python
cmb-MBP-2:~ cmbarton$

They're each pointing to the right python.

#!/usr/bin/env python

No. The ??? was just me questioning if I should use that format.

So, it should work, and run Mac Python. Or did you not have that there before, and *now* it's working?

-----
William Kyngesburye <kyngchaos*at*kyngchaos*dot*com>
http://www.kyngchaos.com/

"Mon Dieu! but they are all alike. Cheating, murdering, lying, fighting, and all for things that the beasts of the jungle would not deign to possess - money to purchase the effeminate pleasures of weaklings. And yet withal bound down by silly customs that make them slaves to their unhappy lot while firm in the belief that they be the lords of creation enjoying the only real pleasures of existence....

- the wisdom of Tarzan

cmbarton · July 29, 2008, 5:42pm

On Jul 29, 2008, at 10:34 AM, William Kyngesburye wrote:

On Jul 29, 2008, at 12:15 PM, Michael Barton wrote:

cmb-MBP-2:~ cmbarton$ ls -l /usr/bin/python
lrwxr-xr-x 1 root wheel 72 May 9 15:32 /usr/bin/python -> ../../System/Library/Frameworks/Python.framework/Versions/2.5/bin/python
cmb-MBP-2:~ cmbarton$ ls -l /usr/local/bin/python
lrwxr-xr-x 1 root wheel 68 May 9 23:07 /usr/local/bin/python -> ../../../Library/Frameworks/Python.framework/Versions/2.5/bin/python
cmb-MBP-2:~ cmbarton$

They're each pointing to the right python.

Looking more closely, one is in...

/Library/Frameworks/Python.framework/Versions/2.5/bin/python

and the other is in...

/System/Library/Frameworks/Python.framework/Versions/2.5/bin/python

Is one of these a System Python, or has MacPython shifted where it installs?

Michael

#!/usr/bin/env python

No. The ??? was just me questioning if I should use that format.

So, it should work, and run Mac Python. Or did you not have that there before, and *now* it's working?

-----
William Kyngesburye <kyngchaos*at*kyngchaos*dot*com>
http://www.kyngchaos.com/

"Mon Dieu! but they are all alike. Cheating, murdering, lying, fighting, and all for things that the beasts of the jungle would not deign to possess - money to purchase the effeminate pleasures of weaklings. And yet withal bound down by silly customs that make them slaves to their unhappy lot while firm in the belief that they be the lords of creation enjoying the only real pleasures of existence....

- the wisdom of Tarzan