Thanks!

Probably best to put this in the python 3 PR of SyneRBI_VM. However, we've given up on the python3 VM for now anyway... Does the python2 VM work ok?

kris

> -----Original Message-----
> From: SYNERBI-DEVEL CCP SyneRBI Developers list <SYNERBI-
> [log in to unmask]> On Behalf Of Evgueni Ovtchinnikov - UKRI STFC
> Sent: 15 June 2020 15:23
> To: [log in to unmask]
> Subject: Re: SIRF 2.2.0
> 
> On VM SIRF 2.2.0_py3, spyder3 fails to start with this error:
> 
> sirfuser@vagrant:~/devel/buildVM/sources/SIRF/examples/Python/PET/intera
> ctive$ 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 <SYNERBI-
> [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/SI
> RF\\ 2.2.0_py3.ova" ~/Desktop
> 
> Edo
> 
> From: SYNERBI-DEVEL CCP SyneRBI Developers list <SYNERBI-
> [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]>>; SYNERBI-
> [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]>>; SYNERBI-
> [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/SI
> RF\\ 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 <SYNERBI-
> [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:SYNERBI-
> [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 <SYNERBI-
> [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:SYNERBI-
> [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 <SYNERBI-
> [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:SYNERBI-
> [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 <SYNERBI-
> [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:SYNERBI-
> [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]>>; SYNERBI-
> [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 <SYNERBI-
> [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:SYNERBI-
> [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 <SYNERBI-
> [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:SYNERBI-
> [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/SI
> RF\\ 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]>>; SYNERBI-
> [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 <SYNERBI-
> [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:SYNERBI-
> [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 <SYNERBI-
> [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:SYNERBI-
> [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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