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janelia-flyem / gala

Automatic segmentation of electron microscopy volumes
BSD 3-Clause "New" or "Revised" License
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No module named gala #38

Closed jaimebayes closed 9 years ago

jaimebayes commented 9 years ago

Hi, I installed gala into two machines (win8 & ubuntu). Apparently it was correctly installed. But when I try to run the examples into test folder, it sends this message:

python test_agglo.py ImportError: No module named gala

I included gala folder into PATH (win8) and .profile file (ubuntu), but this happens on both systems. so what I did wrong? what I have to do to run it?

thanks, jaime

jni commented 9 years ago

Hi Jaime,

What do you mean by "apparently it was correctly installed"? What were your installation steps?

Python packages have specific installation conventions. For example, you don't want to set PATH but PYTHONPATH.

When you download gala, you will need to do one of the following:

After installing it correctly, you should be able to run the examples...

Let me know if this fixes your issue!

jaimebayes commented 9 years ago

Hi Juan,

I mean with "apparently" that it never show any error message, but it didnt show "gala package was correctly installed" either. But I guess it is correctly installed.

I did the second option you suggested, but when I try to run examples it says "module gala not found"

C:\Users\Jaime\gala-master\tests>python test_agglo.py Traceback (most recent call last): File "test_agglo.py", line 8, in from gala import agglo ImportError: No module named gala

What else I can try?

Jaime

On Sun, Nov 23, 2014 at 6:54 AM, Juan Nunez-Iglesias < notifications@github.com> wrote:

Hi Jaime,

What do you mean by "apparently it was correctly installed"? What were your installation steps?

Python packages have specific installation conventions. For example, you don't want to set PATH but PYTHONPATH.

When you download gala, you will need to do one of the following:

  • to run locally, type "python build_ext -i" from the gala project root directory. Then add the root directory to your PYTHONPATH, for example, "export PYTHONPATH=$PYTHONPATH:/home/jaime/Download/gala"
  • "sudo python setup.py install" from the project root directory. This will install gala into your system Python installation.
  • if you use an environment management tool such as conda http://conda.pydata.org/docs/ (which I highly recommend), you can just type "python setup.py install".

After installing it correctly, you should be able to run the examples...

Let me know if this fixes your issue!

— Reply to this email directly or view it on GitHub https://github.com/janelia-flyem/gala/issues/38#issuecomment-64115378.

Jaime Lopez Carvajal

jni commented 9 years ago

Haha you can try option 3, installing the complete Anaconda distribution, which as I mentioned is highly recommended. =)

At any rate, what's the output of option 2? I expect that there were some errors that you ignored. =) In fact I'm not sure "sudo" works in Windows...

jaimebayes commented 9 years ago

Hi Juan,

Under win8 system, I erase previous gala installation, and try option 3 using console:

C:\Anaconda\Lib\site-packages>pip install gala Downloading/unpacking gala

Installing collected packages: gala

Successfully installed gala Cleaning up...

After that, I figure out that it doesnt exist test directory, just other directories named features and testdata, so where can I find the files to run the test you suggest on page? (BTW: testdata not contain them)

thank you, Jaime

On Mon, Nov 24, 2014 at 6:55 PM, Juan Nunez-Iglesias < notifications@github.com> wrote:

Haha you can try option 3, installing the complete Anaconda distribution http://continuum.io/downloads, which as I mentioned is highly recommended. =)

At any rate, what's the output of option 2? I expect that there were some errors that you ignored. =) In fact I'm not sure "sudo" works in Windows...

— Reply to this email directly or view it on GitHub https://github.com/janelia-flyem/gala/issues/38#issuecomment-64287357.

Jaime Lopez Carvajal

jni commented 9 years ago

Hey Jaime,

unfortunately, the version of gala installed by pip is quite old. I intend to update it around mid-December. In the meantime, you should download the version here on github and use "python setup.py install". It should work when you have Anaconda.

Juan.

jaimebayes commented 9 years ago

Hi Juan,

I have Anaconda install some time ago. I download the github version, and use inside gala directory: python setup.py install it sends this error:

c:/mingw/bin/../lib/gcc/mingw32/4.8.1/../../../../mingw32/bin/ld.exe: build\temp .win-amd64-2.7\Release\gala\optimized.o: bad reloc address 0x0 in section `.data ' collect2.exe: error: ld returned 1 exit status error: command 'c:\MinGW\bin\gcc.exe' failed with exit status 1

I'm using msysgit running on Windows8.

Jaime

On Tue, Nov 25, 2014 at 8:01 PM, Juan Nunez-Iglesias < notifications@github.com> wrote:

Hey Jaime,

unfortunately, the version of gala installed by pip is quite old. I intend to update it around mid-December. In the meantime, you should download the version here on github and use "python setup.py install". It should work when you have Anaconda.

Juan.

— Reply to this email directly or view it on GitHub https://github.com/janelia-flyem/gala/issues/38#issuecomment-64499379.

Jaime Lopez Carvajal

jni commented 9 years ago

Hey,

You mentioned you had an Ubuntu machine. Can you try to get it working there first? To be honest, gala has never been tested on Windows and I myself don't have a Windows machine to troubleshoot. It looks like some kind of incompatibility with your compiler, but again, I just have no idea... =\

Juan.

jni commented 9 years ago

@jaimebayes did you ever manage to get gala working?

jaimebayes commented 9 years ago

Yeah, Juan, I just got permissions to folder using chown -T jaimebayes ./*

thanks, Juan

On Tue, Feb 17, 2015 at 3:52 AM, Juan Nunez-Iglesias < notifications@github.com> wrote:

@jaimebayes https://github.com/jaimebayes did you ever manage to get gala working?

— Reply to this email directly or view it on GitHub https://github.com/janelia-flyem/gala/issues/38#issuecomment-74635228.

Jaime Lopez Carvajal

jni commented 9 years ago

Awesome, thanks for letting me know. Sorry that I couldn't be more helpful with the Windows install!