On VM SIRF 2.2.0_py3, spyder3 fails to start with this error:
sirfuser@vagrant:~/devel/buildVM/sources/SIRF/examples/Python/PET/interactive$ spyder3
Traceback (most recent call last):
File "/usr/local/bin/spyder3", line 5, in <module>
from spyder.app.start import main
File "/usr/local/lib/python3.6/dist-packages/spyder/app/start.py", line 34, in <module>
from spyder.config.manager import CONF
File "/usr/local/lib/python3.6/dist-packages/spyder/config/manager.py", line 17, in <module>
from spyder.config.main import CONF_VERSION, DEFAULTS, NAME_MAP
File "/usr/local/lib/python3.6/dist-packages/spyder/config/main.py", line 19, in <module>
from spyder.config.fonts import MEDIUM, SANS_SERIF
File "/usr/local/lib/python3.6/dist-packages/spyder/config/fonts.py", line 14, in <module>
from spyder.config.utils import is_ubuntu
File "/usr/local/lib/python3.6/dist-packages/spyder/config/utils.py", line 17, in <module>
from spyder_kernels.utils import iofuncs
ModuleNotFoundError: No module named 'spyder_kernels'
________________________________
From: SYNERBI-DEVEL CCP SyneRBI Developers list <[log in to unmask]> on behalf of Edoardo Pasca - UKRI STFC <[log in to unmask]>
Sent: Friday, June 12, 2020 8:41:34 PM
To: [log in to unmask]
Subject: Re: SIRF 2.2.0
Hi
I’ve uploaded an updated VM for python3. Should you wish to try, it’s at the same place.
scp [log in to unmask]<mailto:[log in to unmask]>:"/home/sirfuser/SIRF\\ 2.2.0_py3.ova" ~/Desktop
Edo
From: SYNERBI-DEVEL CCP SyneRBI Developers list <[log in to unmask]> On Behalf Of Edoardo Pasca - UKRI STFC
Sent: 12 June 2020 09:59
To: [log in to unmask]
Subject: Re: SIRF 2.2.0
I found that it is CCPi-Regularisation-Toolkit (and possibly astra-toolkit, which isn’t built in this VM) that can’t find Cython as it’s been searched as cython, but on ubuntu18.04 the version for python3 is called cython3.
I modified the SuperBuild https://github.com/SyneRBI/SIRF-SuperBuild/tree/find_cython3 which should fix this.
Edo
From: Thielemans, Kris <[log in to unmask]<mailto:[log in to unmask]>>
Sent: 12 June 2020 07:37
To: Pasca, Edoardo (STFC,RAL,SC) <[log in to unmask]<mailto:[log in to unmask]>>; [log in to unmask]<mailto:[log in to unmask]>
Subject: RE: SIRF 2.2.0
Hi all
Given the comment you quote below, I think this will be premature to merge for 2.2. We can of course always release another VM afterwards.
Can we therefore concentrate on testing the python2 VM please? Sorry.
kris
From: Edoardo Pasca - UKRI STFC <[log in to unmask]<mailto:[log in to unmask]>>
Sent: 12 June 2020 07:27
To: Thielemans, Kris <[log in to unmask]<mailto:[log in to unmask]>>; [log in to unmask]<mailto:[log in to unmask]>
Subject: RE: SIRF 2.2.0
Hi
You find an updated py3 VM on the server. You can get it with
scp [log in to unmask]<mailto:[log in to unmask]>:"/home/sirfuser/SIRF\\ 2.2.0_py3.ova" ~/Desktop
Have a go at it.
Please notice https://github.com/SyneRBI/SyneRBI_VM/pull/170#issuecomment-642917253
Edo
From: SYNERBI-DEVEL CCP SyneRBI Developers list <[log in to unmask]<mailto:[log in to unmask]>> On Behalf Of Thielemans, Kris
Sent: 11 June 2020 18:18
To: [log in to unmask]<mailto:[log in to unmask]>
Subject: Re: SIRF 2.2.0
Could check python version from the jupyter prompt. I’ve never understood why the kernel is in the notebook and how it’s used (see all the nbstripout discussions).
Can someone else try this out as well please (once there’s a new version).
kris
From: SYNERBI-DEVEL CCP SyneRBI Developers list <[log in to unmask]<mailto:[log in to unmask]>> On Behalf Of Brown, Richard
Sent: 11 June 2020 18:09
To: [log in to unmask]<mailto:[log in to unmask]>
Subject: Re: SIRF 2.2.0
Hi,
After running update_VM.sh everything ran fine. I only ran the python PET ctest and two jupyer notebooks - the registration one and a PET one.
The only thing that I noticed is that in the top right of the jupyter notebook, when running the registration notebook, it correctly said the kernel was python3. However, when running the PET notebook, it said python2. That said, there wasn’t an error, so it must have been running the python3 kernel all the same.
Slightly confusing, but I guess the kernel reflects the python version that was used to write the notebook (I wrote the registration with python3, whereas PET notebooks were written with python2).
Rich
Research Associate in Medical Imaging Physics at University College London,
Institute of Nuclear Medicine, UCL Hospital, Tower 5,
235 Euston Road, London NW1 2BU, UK
On 11 Jun 2020, at 16:33, Edoardo Pasca - UKRI STFC <[log in to unmask]<mailto:[log in to unmask]>> wrote:
I just found that you need to install cython3
So, I’ll upload a new VM and let you know in due course.
Edo
From: SYNERBI-DEVEL CCP SyneRBI Developers list <[log in to unmask]<mailto:[log in to unmask]>> On Behalf Of Edoardo Pasca - UKRI STFC
Sent: 11 June 2020 16:25
To: [log in to unmask]<mailto:[log in to unmask]>
Subject: Re: SIRF 2.2.0
Ah, that’s my bad. I fixed installation problems as they came and then I run make directly from the buildVM directory. This means that update_VM.sh hasn’t run to the end and created all the env variables and links.
So, in the py3 machine one has to run update_VM.sh
I will create a VM from scratch
Edo
From: SYNERBI-DEVEL CCP SyneRBI Developers list <[log in to unmask]<mailto:[log in to unmask]>> On Behalf Of Brown, Richard
Sent: 11 June 2020 16:02
To: [log in to unmask]<mailto:[log in to unmask]>
Subject: Re: SIRF 2.2.0
Loading up terminal gives bash: "/home/sirfuser/.sirfrc: No such file or directory”.
Research Associate in Medical Imaging Physics at University College London,
Institute of Nuclear Medicine, UCL Hospital, Tower 5,
235 Euston Road, London NW1 2BU, UK
On 11 Jun 2020, at 14:55, Thielemans, Kris <[log in to unmask]<mailto:[log in to unmask]>> wrote:
Ok, great. It would have to come with a big warning that they have to use python3.
Did you try spyder? How does jupyter know which python to run?
Please have a look at the issue for other things
From: Edoardo Pasca - UKRI STFC <[log in to unmask]<mailto:[log in to unmask]>>
Sent: 11 June 2020 14:50
To: Thielemans, Kris <[log in to unmask]<mailto:[log in to unmask]>>; [log in to unmask]<mailto:[log in to unmask]>
Subject: RE: SIRF 2.2.0
Of course there’s a branch https://github.com/SyneRBI/SyneRBI_VM/tree/python3_build
I haven’t opened a PR as I wanted to test it worked first.
Basically I had:
* to append a 3 to all the apt installed python packages.
* to call pip3
* to pass -DPYVER:STRING=3 at cmake invocation https://github.com/SyneRBI/SyneRBI_VM/blob/python3_build/scripts/UPDATE.sh#L199
Edo
From: SYNERBI-DEVEL CCP SyneRBI Developers list <[log in to unmask]<mailto:[log in to unmask]>> On Behalf Of Thielemans, Kris
Sent: 11 June 2020 14:42
To: [log in to unmask]<mailto:[log in to unmask]>
Subject: Re: SIRF 2.2.0
Thanks Edo
I obviously agree that a python3 version would be best. Can you enlighten us what you changed? Is there a branch/PR?
See also https://github.com/SyneRBI/SyneRBI_VM/issues/122
> I noticed that in the MR-Joint-TV.ipynb it reads
> # currently ned to work around a small CIL bug for SIRF ImageData. Please ignore!
I of course can’t remember. Have a look at the work-around… In any case, that demo needs much more work.
Kris
From: SYNERBI-DEVEL CCP SyneRBI Developers list <[log in to unmask]<mailto:[log in to unmask]>> On Behalf Of Brown, Richard
Sent: 11 June 2020 14:27
To: [log in to unmask]<mailto:[log in to unmask]>
Subject: Re: SIRF 2.2.0
I’ll try the python3 version.
FYI because of the space in the filename, I had to scp like this: scp [log in to unmask]<mailto:[log in to unmask]>:"/home/sirfuser/SIRF\\ 2.2.0_py3.ova" ~/Desktop
Rich
Research Associate in Medical Imaging Physics at University College London,
Institute of Nuclear Medicine, UCL Hospital, Tower 5,
235 Euston Road, London NW1 2BU, UK
On 11 Jun 2020, at 13:54, Edoardo Pasca - UKRI STFC <[log in to unmask]<mailto:[log in to unmask]>> wrote:
I’ve uploaded to the same machine a VM running the software with python3
If you want to test them.
I think, in 2020, it’d be good to publish a VM with python3 rather than python2.
Edo
From: Pasca, Edoardo (STFC,RAL,SC) <[log in to unmask]<mailto:[log in to unmask]>>
Sent: 10 June 2020 22:03
To: Pasca, Edoardo (STFC,RAL,SC) <[log in to unmask]<mailto:[log in to unmask]>>; [log in to unmask]<mailto:[log in to unmask]>
Subject: RE: SIRF 2.2.0
Hi all,
I’ve tested the VM and it seems to me in good shape.
I’ve run ctest and some SIRF-Exercises.
I noticed that in the MR-Joint-TV.ipynb it reads
# currently ned to work around a small CIL bug for SIRF ImageData. Please ignore!
What’s the bug?
I’m uploading to STFC cloud machine 130.246.214.97 and it should be there in 30 min. In the home directory.
The user is sirfuser and if you want to know the password please send me a separate email.
Richard uses the machine regularly.
The latest bug I encountered is just demonstrating the fact that we shouldn’t distribute the software with python2. I’ll try to build a VM with python3
Edo
From: SYNERBI-DEVEL CCP SyneRBI Developers list <[log in to unmask]<mailto:[log in to unmask]>> On Behalf Of Edoardo Pasca - UKRI STFC
Sent: 10 June 2020 12:07
To: [log in to unmask]<mailto:[log in to unmask]>
Subject: Re: SIRF 2.2.0
Hi
Building the 2.2.0 VM from scratch exposed a new issue https://github.com/SyneRBI/SyneRBI_VM/issues/169
Due to an updated nbstripout which isn’t compatible with python2
I’m running the tests
Edo
From: SYNERBI-DEVEL CCP SyneRBI Developers list <[log in to unmask]<mailto:[log in to unmask]>> On Behalf Of Thielemans, Kris
Sent: 08 June 2020 15:35
To: [log in to unmask]<mailto:[log in to unmask]>
Subject: SIRF 2.2.0
Dear all
I’ve tagged and released SIRF 2.2.0 and the SuperBuild. There’s a few more things to do (https://github.com/SyneRBI/SIRF/issues/704), so no big announcements yet, but I thought I’d let you know. I’d like to thank you all for your input in this release and CCP SyneRBI software.
There’s a few PRs that were waiting for SIRF 2.2.0, so feel free to merge now.
I’m looking forward to the future! In fact, can we discuss future plans during our tcon on Friday? We need to get some (virtual) meetings/hackathons scheduled.
Thanks again
Kris
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