#123 Package mne-cpp
Opened 3 years ago by ankursinha. Modified 7 months ago


Metadata Update from @mhough:
- Issue assigned to mhough

3 years ago

@mhough - as soon as your review submission for this is approved in principle, I will request that you be added to the packagers group as a neuro-sig co-maintainer. Does that sound OK?

Absolutely. Sounds good.

This is a more complicated package than I think I should start with. Using the Qt5 system libs and the latest stable branch, the instructions to build specify using the QtCreator app which is available in Fedora 29. Following the instructions at the link below:

http://wiki.mne-cpp.org/index.php/Compile_the_MNE-CPP_source_code

cd mne-cpp
qtcreator mne-cpp.pro

does bring up the QtCreator gui but I am hunting around to follow the instructions currently.

Ah, yikes---one never knows how hard they'll be until one begins to package them XD.

Maybe start with something python based? They're generally easier and we have a template spec to aid with packaging too (check the files section of this repo).

I think I was also just getting tired and just not familiar with the Qt framework really. I decided to ignore the build instructions and followed DSI-Studio's instructions which just use

qmake-qt5 ../
cd mne-cpp/
make

which seems to properly produce the binaries without errors. I will check with upstream and see if there are any concerns about building this way and see if they have any additional command line instructions I can use in lieu of their Qt-creator instructions.

Here is the test dataset that I am using for all the non-DICOM testing as it has MEG, EEG, DWI, MRI and FMRI data. It is also used by SPM and mne-python.

https://legacy.openfmri.org/dataset/ds000117/

That's great. There are lots of scenarios where we cannot use upstream's instructions. It's why packagers are expected to have knowledge of the build projects (Cmake/autotools/..) so that they can use other correct ways of building the software.

The user-end testing is welcome, but that is not going to be enough. Upstreams must have their own exhaustive tests. Our user-end testing cannot replace those. We can work with upstreams to improve their testing, of course (we've done this in multiple cases already).

Hey there. I am working on MNE-CPP. Happy to help.

Hi @lorenze : welcome to NeuroFedora!

Are you on the MNE-CPP development team?

Great! As you see from the comments above, @mhough began working on packaging it for Fedora and has made some progress. Would you maybe have the time to co-maintain the package with us in Fedora? This requires:

  • writing the initial spec and srpm
  • getting it reviewed (to check for correctness and best practices)
  • updating it from time to time when a new version comes out

As a developer, you'd already have the required skills, and we can help you navigate the Fedora side of things (mostly the processes and infrastructure).

Unfortunately, I do not have enough time at the moment to contribute the whole package. However, I am interested in seeing MNE-CPP in NeuroFedora. Let me see if I can find someone in our team who is able to spend more time on this than myself.

Thank you. That would be most useful. We'll keep working on it in the meantime.

Hello - I work with Lorenze who commented above, and per his request have looked at building mne-cpp. I've had some success building it with qmake and make on fc28 after installing some qt5 packages. Did you have in mind creating an mne-cpp rpm ?

Hello - I work with Lorenze who commented above, and per his request have looked at building mne-cpp. I've had some success building it with qmake and make on fc28 after installing some qt5 packages. Did you have in mind creating an mne-cpp rpm ?

Hello @buildeng: yes, it is on our list, but currently our list is quite long so we're not sure when we'll get to it. Would you, by any chance, like to make the rpm and maintain it in Fedora? The main work is only the initial packaging and review. We'll be happy to help you navigate the process and the tools that are needed to provide mne-cpp in Fedora.

I'd be happy to start the process of trying to package up what the mne-cpp developers currently have in their dev tree; maybe you could suggest some preferred links to the packaging tools, docs, etc. Thanks in advance for any info.

That sounds great, @buildeng. I've put some links up on this page to get people started with packaging:

https://fedoraproject.org/wiki/User:Ankursinha/PackagerSponsor

You could start there, and e-mail me to clarify any issues you run into? How does that sound? We can help you with the rpm(s), and we can sponsor you to the packager group when the time comes too.

Thanks very much,
Ankur

@buildeng hello: how is this going? Is there anything we can help with?

(We've added you to the pagure group now so you can modify tickets and so on)

Metadata Update from @ankursinha:
- Issue assigned to buildeng (was: mhough)

3 years ago

Metadata Update from @ankursinha:
- Issue untagged with: S: Needs packaging
- Issue tagged with: S: WIP

3 years ago

After reading some docs, I started to create a spec file that can download the source and compile it using make from Qt5. But after talking to developers it seems they would prefer a binary only rpm for a release. Is this acceptable?

... should have said "qmake" and not make.

After reading some docs, I started to create a spec file that can download the source and compile it using make from Qt5. But after talking to developers it seems they would prefer a binary only rpm for a release. Is this acceptable?

So, do they want that users only have access to a binary? If that is so, that's fine. While we build from source, end-users only receive the binary rpms from the repos (they can also fetch the sources, but that is not part of the general set up).

If upstream only wants users to use the binary they provide, that's a problem. As you'll see in the packaging guidelines at https://docs.fedoraproject.org/en-US/packaging-guidelines/ , all software included in Fedora must be built from source. This is to ensure that:

  • it is built correctly (which will be inspected in the review)
  • it functions correctly on the Fedora environment (the build environment---which is the development tool chain, versions of libraries and so on---mirrors the environment users will have when they use Fedora, so rpms built on our build environment will function exactly in the same way on user systems).
  • the binaries that upstream builds may be tested in their environment, but unless they are tested on each fedora release the way our packaging pipleline does it, there is no guarantee that they will work in the same way. (In general, that is not the best practice for using software on multiple platforms IMO.)

To update, I have a prototype spec file that does a source build and creates a binary rpm file via rpmbuild on CentOS7 (which is currently their linux reference platform). I have just reviewed the binary rpm install with developers and need to make some changes w.r.t newer versions of Qt and adding some files to be installed. Once I have something dev approves for CentOS7 I can follow up again on fc28.

if it builds on CentOS7, there's a good chance it'll build on Fedora as well. I'd target rawhide first, since that's the platform new packages are added too. Once it builds there, we can work on F30 and F29 (F28 will be EOL in a month now that F30 was released).

You can use mock to test your builds on different Fedora etc releases, or COPR too:

https://fedoraproject.org/wiki/Using_Mock_to_test_package_builds
https://copr.fedorainfracloud.org/

I updated my fc28 VM, and ran the mock command "mock -v mne-cpp-master-1.0.fc28.src.rpm " to build the source RPM (which exited with status 0). I also ran the dnf command w/o the BuildRequires packages installed to see if everything would get installed (and all the installs worked), i.e., "sudo dnf builddep mne-cpp.spec". If you would like to get an idea of what is currently in the spec file, you can get it from the URL below. I can remove the ifdef/comments for redhat (CentOS7), further test, edit, cleanup etc. as you like.
https://drive.google.com/file/d/1RWNkZSyL93U0tRcxLWcZpYfl9LOkVwd0/view?usp=sharing

If you submit if for review, one of us can review it and sponsor you @buildeng . What do you think?

https://fedoraproject.org/wiki/Join_the_package_collection_maintainers

It looks like I can use COPR to allow review of the spec file and source RPM?

Yes. You can use any build service to test your spec/srpm, and you can make them available however you want (if COPR provides a link to the spec and srpm, that will work too). The only requirement is that it must go through the review process. So from this step on now, I think:

https://fedoraproject.org/wiki/Join_the_package_collection_maintainers#Upload_Your_Package

Here is a recent example of the python-elephant review:
https://bugzilla.redhat.com/show_bug.cgi?id=1651824

Hey @buildeng : any updates here? Would you be able to pursue this, otherwise please let us know and we'll unassign it so it's free for someone else to take up. Cheers

Please keep assigned for now as working in updates. Thanks for the links which I will review.

Since we are not yet at release 1.0, there is no online source or binary archive to download. I can fetch the source via a tag from GitHub, but my understanding is I am not allowed in the spec file to do checkouts from git (via a tag), e.g., in the prep section to create the Source0 archive (though this works). Please advise.

@buildeng: the packaging guidelines have no prohibition on using tags. Just download the tarball corresponding to the tag from github. See https://docs.fedoraproject.org/en-US/packaging-guidelines/Versioning/#_snapshots for details how to specify the Version.

I see multiple tags for the project, so this latest one is completely fine to package, for example:

https://github.com/mne-tools/mne-cpp/releases/tag/v0.1.9

As far as we're concerned, there's no difference between tags and releases. "Releases" are a GitHub concept, but git (the tool) only does tags.

https://stackoverflow.com/a/18512221/375067

Thanks for the previous feedback on tags. There is actually an archive corresponding to the latest tag which I did not see - so my bad.

I tried a koji build with the spec file you can see with the link below, but it failed.
https://drive.google.com/file/d/1KQjq0vyhF_hHtypCruIHc1Kt00wIWx7v/view?usp=sharing
Wondering if the BuildRequires conditions for Qt, gcc are an issue.

What was the build failure please?

(The spec has multiple bits where it does not follow the Fedora packaging guidelines, so it'll take some tweaking before it'll be ready for submission.)

It looks like it failed for some architectures that I would not expect it to build for. I don't expect it to build for anything except fedora 32, ubuntu 18,20, and centos8 (x86_64) right now.

$ koji build --scratch rawhide mne-cpp-0.1.9-0.fc32.src.rpm
Uploading srpm: mne-cpp-0.1.9-0.fc32.src.rpm
[====================================] 100% 00:00:08 26.91 MiB 3.10 MiB/sec
Created task: 79055485
Task info: https://koji.fedoraproject.org/koji/taskinfo?taskID=79055485
Watching tasks (this may be safely interrupted)...
79055485 build (rawhide, mne-cpp-0.1.9-0.fc32.src.rpm): free
79055485 build (rawhide, mne-cpp-0.1.9-0.fc32.src.rpm): free -> open (buildvm-s390x-22.s390.fedoraproject.org)
79055486 rebuildSRPM (noarch): open (buildvm-s390x-22.s390.fedoraproject.org)
79055486 rebuildSRPM (noarch): open (buildvm-s390x-22.s390.fedoraproject.org) -> closed
0 free 1 open 1 done 0 failed
79055560 buildArch (mne-cpp-0.1.9-0.fc36.src.rpm, armv7hl): open (buildvm-a32-25.iad2.fedoraproject.org)
79055561 buildArch (mne-cpp-0.1.9-0.fc36.src.rpm, i686): free
79055564 buildArch (mne-cpp-0.1.9-0.fc36.src.rpm, ppc64le): free
79055562 buildArch (mne-cpp-0.1.9-0.fc36.src.rpm, x86_64): free
79055565 buildArch (mne-cpp-0.1.9-0.fc36.src.rpm, s390x): free
79055563 buildArch (mne-cpp-0.1.9-0.fc36.src.rpm, aarch64): open (buildvm-a64-32.iad2.fedoraproject.org)
79055565 buildArch (mne-cpp-0.1.9-0.fc36.src.rpm, s390x): free -> open (buildvm-s390x-21.s390.fedoraproject.org)
79055561 buildArch (mne-cpp-0.1.9-0.fc36.src.rpm, i686): free -> open (buildvm-x86-10.iad2.fedoraproject.org)
79055562 buildArch (mne-cpp-0.1.9-0.fc36.src.rpm, x86_64): free -> open (buildvm-x86-07.iad2.fedoraproject.org)
79055564 buildArch (mne-cpp-0.1.9-0.fc36.src.rpm, ppc64le): free -> open (buildvm-ppc64le-08.iad2.fedoraproject.org)
79055561 buildArch (mne-cpp-0.1.9-0.fc36.src.rpm, i686): open (buildvm-x86-10.iad2.fedoraproject.org) -> FAILED: BuildError: error
building package (arch i686), mock exited with status 30; see root.log for more information
Relevant logs:
https://kojipkgs.fedoraproject.org//work/tasks/5561/79055561/mock_output.log
https://kojipkgs.fedoraproject.org//work/tasks/5561/79055561/hw_info.log
https://kojipkgs.fedoraproject.org//work/tasks/5561/79055561/state.log
https://kojipkgs.fedoraproject.org//work/tasks/5561/79055561/build.log
https://kojipkgs.fedoraproject.org//work/tasks/5561/79055561/root.log
0 free 6 open 1 done 1 failed
79055560 buildArch (mne-cpp-0.1.9-0.fc36.src.rpm, armv7hl): open (buildvm-a32-25.iad2.fedoraproject.org) -> FAILED: BuildError: er
ror building package (arch armv7hl), mock exited with status 30; see root.log for more information
Relevant logs:
https://kojipkgs.fedoraproject.org//work/tasks/5560/79055560/mock_output.log
https://kojipkgs.fedoraproject.org//work/tasks/5560/79055560/hw_info.log
https://kojipkgs.fedoraproject.org//work/tasks/5560/79055560/state.log
https://kojipkgs.fedoraproject.org//work/tasks/5560/79055560/build.log
https://kojipkgs.fedoraproject.org//work/tasks/5560/79055560/root.log
0 free 5 open 1 done 2 failed
79055564 buildArch (mne-cpp-0.1.9-0.fc36.src.rpm, ppc64le): open (buildvm-ppc64le-08.iad2.fedoraproject.org) -> closed
0 free 4 open 2 done 2 failed
79055562 buildArch (mne-cpp-0.1.9-0.fc36.src.rpm, x86_64): open (buildvm-x86-07.iad2.fedoraproject.org) -> closed
0 free 3 open 3 done 2 failed
79055565 buildArch (mne-cpp-0.1.9-0.fc36.src.rpm, s390x): open (buildvm-s390x-21.s390.fedoraproject.org) -> closed
0 free 2 open 4 done 2 failed
79055563 buildArch (mne-cpp-0.1.9-0.fc36.src.rpm, aarch64): open (buildvm-a64-32.iad2.fedoraproject.org) -> closed
0 free 1 open 5 done 2 failed
79055485 build (rawhide, mne-cpp-0.1.9-0.fc32.src.rpm): open (buildvm-s390x-22.s390.fedoraproject.org) -> FAILED: BuildError: error
building package (arch armv7hl), mock exited with status 30; see root.log for more information
0 free 0 open 5 done 3 failed

79055485 build (rawhide, mne-cpp-0.1.9-0.fc32.src.rpm) failed

If upstream does not support architectures, they can be excluded but tracker tickets etc. need to be opened to make sure we know what packages and why they don't build on whatever architectures

https://docs.fedoraproject.org/en-US/packaging-guidelines/#_architecture_build_failures

Fedora 32 is now EOL. If we want this in Fedora, we'll be targeting Fedora 36, which is currently "rawhide". (New packages get added to rawhide first, and optionally to current Fedora releases, which are 34 and 35 at the moment)

this is the file list from one of the arches where it passed:

drwxr-xr-x  /opt/mne-cpp-0.1.9/bin
drwxr-xr-x  /opt/mne-cpp-0.1.9/bin/MNE-sample-data
-rw-r--r--  /opt/mne-cpp-0.1.9/bin/MNE-sample-data/README.md
-rw-r--r--  /opt/mne-cpp-0.1.9/bin/MNE-sample-data/download_sample_data.html
-rwxr-xr-x  /opt/mne-cpp-0.1.9/bin/ex_averaging
-rwxr-xr-x  /opt/mne-cpp-0.1.9/bin/ex_cancel_noise
-rwxr-xr-x  /opt/mne-cpp-0.1.9/bin/ex_clustered_inverse_mne
-rwxr-xr-x  /opt/mne-cpp-0.1.9/bin/ex_clustered_inverse_mne_raw
-rwxr-xr-x  /opt/mne-cpp-0.1.9/bin/ex_clustered_inverse_pwl_rap_music_raw
-rwxr-xr-x  /opt/mne-cpp-0.1.9/bin/ex_clustered_inverse_rap_music_raw
-rwxr-xr-x  /opt/mne-cpp-0.1.9/bin/ex_compute_forward
-rwxr-xr-x  /opt/mne-cpp-0.1.9/bin/ex_connectivity
-rwxr-xr-x  /opt/mne-cpp-0.1.9/bin/ex_connectivity_comparison
-rwxr-xr-x  /opt/mne-cpp-0.1.9/bin/ex_connectivity_performance
-rwxr-xr-x  /opt/mne-cpp-0.1.9/bin/ex_coreg
-rwxr-xr-x  /opt/mne-cpp-0.1.9/bin/ex_disp
-rwxr-xr-x  /opt/mne-cpp-0.1.9/bin/ex_disp_3D
-rwxr-xr-x  /opt/mne-cpp-0.1.9/bin/ex_evoked_grad_amp
-rwxr-xr-x  /opt/mne-cpp-0.1.9/bin/ex_fiff_io
-rwxr-xr-x  /opt/mne-cpp-0.1.9/bin/ex_filtering
-rwxr-xr-x  /opt/mne-cpp-0.1.9/bin/ex_find_evoked
-rwxr-xr-x  /opt/mne-cpp-0.1.9/bin/ex_fs_surface
-rwxr-xr-x  /opt/mne-cpp-0.1.9/bin/ex_histogram
-rwxr-xr-x  /opt/mne-cpp-0.1.9/bin/ex_hpiFit
-rwxr-xr-x  /opt/mne-cpp-0.1.9/bin/ex_interpolation
-rwxr-xr-x  /opt/mne-cpp-0.1.9/bin/ex_inverse_mne
-rwxr-xr-x  /opt/mne-cpp-0.1.9/bin/ex_inverse_mne_raw
-rwxr-xr-x  /opt/mne-cpp-0.1.9/bin/ex_inverse_pwl_rap_music
-rwxr-xr-x  /opt/mne-cpp-0.1.9/bin/ex_inverse_rap_music
-rwxr-xr-x  /opt/mne-cpp-0.1.9/bin/ex_make_inverse_operator
-rwxr-xr-x  /opt/mne-cpp-0.1.9/bin/ex_make_layout
-rwxr-xr-x  /opt/mne-cpp-0.1.9/bin/ex_read_bem
-rwxr-xr-x  /opt/mne-cpp-0.1.9/bin/ex_read_epochs
-rwxr-xr-x  /opt/mne-cpp-0.1.9/bin/ex_read_evoked
-rwxr-xr-x  /opt/mne-cpp-0.1.9/bin/ex_read_fwd
-rwxr-xr-x  /opt/mne-cpp-0.1.9/bin/ex_read_fwd_disp_3D
-rwxr-xr-x  /opt/mne-cpp-0.1.9/bin/ex_read_raw
-rwxr-xr-x  /opt/mne-cpp-0.1.9/bin/ex_read_write_raw
-rwxr-xr-x  /opt/mne-cpp-0.1.9/bin/ex_roi_clustered_inverse_pwl_rap_music
-rwxr-xr-x  /opt/mne-cpp-0.1.9/bin/ex_spectral
-rwxr-xr-x  /opt/mne-cpp-0.1.9/bin/ex_st_clustered_inverse_pwl_rap_music
-rwxr-xr-x  /opt/mne-cpp-0.1.9/bin/ex_tf_plot
drwxr-xr-x  /opt/mne-cpp-0.1.9/bin/mne-cpp-test-data
-rwxr-xr-x  /opt/mne-cpp-0.1.9/bin/mne_analyze
drwxr-xr-x  /opt/mne-cpp-0.1.9/bin/mne_analyze_plugins
-rwxr-xr-x  /opt/mne-cpp-0.1.9/bin/mne_analyze_plugins/libannotationmanager.so
-rwxr-xr-x  /opt/mne-cpp-0.1.9/bin/mne_analyze_plugins/libaveraging.so
-rwxr-xr-x  /opt/mne-cpp-0.1.9/bin/mne_analyze_plugins/libchannelselection.so
-rwxr-xr-x  /opt/mne-cpp-0.1.9/bin/mne_analyze_plugins/libcontrolmanager.so
-rwxr-xr-x  /opt/mne-cpp-0.1.9/bin/mne_analyze_plugins/libcoregistration.so
-rwxr-xr-x  /opt/mne-cpp-0.1.9/bin/mne_analyze_plugins/libdataloader.so
-rwxr-xr-x  /opt/mne-cpp-0.1.9/bin/mne_analyze_plugins/libdatamanager.so
-rwxr-xr-x  /opt/mne-cpp-0.1.9/bin/mne_analyze_plugins/libdipolefit.so
-rwxr-xr-x  /opt/mne-cpp-0.1.9/bin/mne_analyze_plugins/libfiltering.so
-rwxr-xr-x  /opt/mne-cpp-0.1.9/bin/mne_analyze_plugins/librawdataviewer.so
-rwxr-xr-x  /opt/mne-cpp-0.1.9/bin/mne_analyze_plugins/libsourcelocalization.so
-rwxr-xr-x  /opt/mne-cpp-0.1.9/bin/mne_analyze_plugins/libview3d.so
-rwxr-xr-x  /opt/mne-cpp-0.1.9/bin/mne_anonymize
-rwxr-xr-x  /opt/mne-cpp-0.1.9/bin/mne_dipole_fit
-rwxr-xr-x  /opt/mne-cpp-0.1.9/bin/mne_edf2fiff
-rwxr-xr-x  /opt/mne-cpp-0.1.9/bin/mne_forward_solution
-rwxr-xr-x  /opt/mne-cpp-0.1.9/bin/mne_rt_server
drwxr-xr-x  /opt/mne-cpp-0.1.9/bin/mne_rt_server_plugins
-rwxr-xr-x  /opt/mne-cpp-0.1.9/bin/mne_rt_server_plugins/libfiffsimulator.so
-rwxr-xr-x  /opt/mne-cpp-0.1.9/bin/mne_scan
drwxr-xr-x  /opt/mne-cpp-0.1.9/bin/mne_scan_plugins
-rwxr-xr-x  /opt/mne-cpp-0.1.9/bin/mne_scan_plugins/libaveraging.so
-rwxr-xr-x  /opt/mne-cpp-0.1.9/bin/mne_scan_plugins/libbabymeg.so
-rwxr-xr-x  /opt/mne-cpp-0.1.9/bin/mne_scan_plugins/libcovariance.so
-rwxr-xr-x  /opt/mne-cpp-0.1.9/bin/mne_scan_plugins/libfiffsimulator.so
-rwxr-xr-x  /opt/mne-cpp-0.1.9/bin/mne_scan_plugins/libftbuffer.so
-rwxr-xr-x  /opt/mne-cpp-0.1.9/bin/mne_scan_plugins/libhpi.so
-rwxr-xr-x  /opt/mne-cpp-0.1.9/bin/mne_scan_plugins/libnatus.so
-rwxr-xr-x  /opt/mne-cpp-0.1.9/bin/mne_scan_plugins/libneuronalconnectivity.so
-rwxr-xr-x  /opt/mne-cpp-0.1.9/bin/mne_scan_plugins/libnoisereduction.so
-rwxr-xr-x  /opt/mne-cpp-0.1.9/bin/mne_scan_plugins/librtcmne.so
-rwxr-xr-x  /opt/mne-cpp-0.1.9/bin/mne_scan_plugins/librtfwd.so
-rwxr-xr-x  /opt/mne-cpp-0.1.9/bin/mne_scan_plugins/libwritetofile.so
drwxr-xr-x  /opt/mne-cpp-0.1.9/bin/resources
drwxr-xr-x  /opt/mne-cpp-0.1.9/bin/resources/general
drwxr-xr-x  /opt/mne-cpp-0.1.9/bin/resources/general/2DLayouts
-rw-r--r--  /opt/mne-cpp-0.1.9/bin/resources/general/2DLayouts/CTF-275.lout
-rw-r--r--  /opt/mne-cpp-0.1.9/bin/resources/general/2DLayouts/Vectorview-all.lout
-rw-r--r--  /opt/mne-cpp-0.1.9/bin/resources/general/2DLayouts/Vectorview-grad.lout
-rw-r--r--  /opt/mne-cpp-0.1.9/bin/resources/general/2DLayouts/Vectorview-mag.lout
-rw-r--r--  /opt/mne-cpp-0.1.9/bin/resources/general/2DLayouts/babymeg-mag-inner-layer.lout
-rw-r--r--  /opt/mne-cpp-0.1.9/bin/resources/general/2DLayouts/babymeg-mag-outer-layer.lout
-rw-r--r--  /opt/mne-cpp-0.1.9/bin/resources/general/2DLayouts/babymeg-mag-ref.lout
-rw-r--r--  /opt/mne-cpp-0.1.9/bin/resources/general/2DLayouts/magnesWH3600.lout
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A few issues here because Fedora follows the FHS:

https://docs.fedoraproject.org/en-US/packaging-guidelines/#_filesystem_layout

  • we don't use /opt at all
  • lots of things that are not binaries are going to /bin. These should go into %_datadir, which is /usr/share/ on Fedora
  • all the shared objects should go into /usr/lib{,64}
  • docs go into /usr/share/doc../

I haven't looked at the spec or the build logs yet to do a full review yet.

In trying to reverse engineer what the installed list of <absolute path>/<file names> should look like from the file system guidelines, I have tentatively come up with the list below.

All binaries are under /bin (and not /usr/bin or /usr/local/bin), all libs are under /usr/lib64, and all non-ELF files are under /usr/share/mne-cpp (assuming it is OK to have an mne-cpp subdir under /usr/share).

There are only 6 core mne-cpp binaries - if installed under /bin, they would read as:
/bin/mne_analyze
/bin/mne_anonymize
/bin/mne_dipole_fit
/bin/mne_edf2fiff
/bin/mne_rt_server
/bin/mne_scan

The other binaries are test binaries, i.e., named mne_test and examples of programming, i.e., named mne_ex that can be run to see how the applications work. But I gather it is not allowed to have an mne-cpp specific subdir as /bin/mne-cpp with the 6 core binaries at that top level and then child subdirs to break out the test and exmaple binaries, i.e., /bin/mne-cpp/{test,examples}.

Please advise.

/bin/mne_analyze
/bin/mne_anonymize
/bin/mne_dipole_fit
/bin/mne_edf2fiff
/bin/mne_ex_averaging
/bin/mne_ex_cancel_noise
/bin/mne_ex_clustered_inverse_mne
/bin/mne_ex_clustered_inverse_mne_raw
/bin/mne_ex_clustered_inverse_pwl_rap_music_raw
/bin/mne_ex_clustered_inverse_rap_music_raw
/bin/mne_ex_compute_forward
/bin/mne_ex_connectivity
/bin/mne_ex_connectivity_comparison
/bin/mne_ex_connectivity_performance
/bin/mne_ex_coreg
/bin/mne_ex_disp
/bin/mne_ex_disp_3D
/bin/mne_ex_evoked_grad_amp
/bin/mne_ex_fiff_io
/bin/mne_ex_filtering
/bin/mne_ex_find_evoked
/bin/mne_ex_fs_surface
/bin/mne_ex_histogram
/bin/mne_ex_hpiFit
/bin/mne_ex_interpolation
/bin/mne_ex_inverse_mne
/bin/mne_ex_inverse_mne_raw
/bin/mne_ex_inverse_pwl_rap_music
/bin/mne_ex_inverse_rap_music
/bin/mne_ex_make_inverse_operator
/bin/mne_ex_make_layout
/bin/mne_ex_read_bem
/bin/mne_ex_read_epochs
/bin/mne_ex_read_evoked
/bin/mne_ex_read_fwd
/bin/mne_ex_read_fwd_disp_3D
/bin/mne_ex_read_raw
/bin/mne_ex_read_write_raw
/bin/mne_ex_roi_clustered_inverse_pwl_rap_music
/bin/mne_ex_spectral
/bin/mne_ex_st_clustered_inverse_pwl_rap_music
/bin/mne_ex_tf_plot
/bin/mne_forward_solution
/bin/mne_rt_server
/bin/mne_scan
/bin/mne_test_coregistration
/bin/mne_test_dipole_fit
/bin/mne_test_edf2fiff_rwr
/bin/mne_test_fiff_coord_trans
/bin/mne_test_fiff_cov
/bin/mne_test_fiff_digitizer
/bin/mne_test_fiff_mne_types_io
/bin/mne_test_fiff_rwr
/bin/mne_test_filtering
/bin/mne_test_geometryinfo
/bin/mne_test_hpiFit
/bin/mne_test_interpolation
/bin/mne_test_mne_anonymize
/bin/mne_test_mne_forward_solution
/bin/mne_test_mne_msh_display_surface_set
/bin/mne_test_mne_project_to_surface
/bin/mne_test_spectral_connectivity
/usr/lib64/libanShared.so.0.1.9
/usr/lib64/libannotationmanager.so
/usr/lib64/libaveraging.so
/usr/lib64/libbabymeg.so
/usr/lib64/libchannelselection.so
/usr/lib64/libcontrolmanager.so
/usr/lib64/libcoregistration.so
/usr/lib64/libcovariance.so
/usr/lib64/libdataloader.so
/usr/lib64/libdatamanager.so
/usr/lib64/libdipolefit.so
/usr/lib64/libfiffsimulator.so
/usr/lib64/libfiltering.so
/usr/lib64/libftbuffer.so
/usr/lib64/libhpi.so
/usr/lib64/libmnecppCommunication.so.0.1.9
/usr/lib64/libmnecppConnectivity.so.0.1.9
/usr/lib64/libmnecppDisp.so.0.1.9
/usr/lib64/libmnecppDisp3D.so.0.1.9
/usr/lib64/libmnecppFiff.so.0.1.9
/usr/lib64/libmnecppFs.so.0.1.9
/usr/lib64/libmnecppFwd.so.0.1.9
/usr/lib64/libmnecppInverse.so.0.1.9
/usr/lib64/libmnecppMne.so.0.1.9
/usr/lib64/libmnecppRtProcessing.so.0.1.9
/usr/lib64/libmnecppUtils.so.0.1.9
/usr/lib64/libnatus.so
/usr/lib64/libneuronalconnectivity.so
/usr/lib64/libnoisereduction.so
/usr/lib64/librawdataviewer.so
/usr/lib64/librtcmne.so
/usr/lib64/librtfwd.so
/usr/lib64/libscDisp.so.0.1.9
/usr/lib64/libscMeas.so.0.1.9
/usr/lib64/libscShared.so.0.1.9
/usr/lib64/libsourcelocalization.so
/usr/lib64/libview3d.so
/usr/lib64/libwritetofile.so
/usr/share/mne-cpp/
/usr/share/mne-cpp/doc/
/usr/share/mne-cpp/doc/doxygen/
/usr/share/mne-cpp/doc/doxygen/DoxygenLayout.xml
/usr/share/mne-cpp/doc/doxygen/MNE-CPP_Doxygen_Logo.svg
/usr/share/mne-cpp/doc/doxygen/about.md
/usr/share/mne-cpp/doc/doxygen/mne-cpp_doxyfile
/usr/share/mne-cpp/doc/gh-pages/
/usr/share/mne-cpp/doc/gh-pages/README.md
/usr/share/mne-cpp/doc/gh-pages/_config.yml
/usr/share/mne-cpp/doc/gh-pages/cite.md
/usr/share/mne-cpp/doc/gh-pages/contact.md
/usr/share/mne-cpp/doc/gh-pages/favicon.ico
/usr/share/mne-cpp/doc/gh-pages/feature_catalogue.md
/usr/share/mne-cpp/doc/gh-pages/images/
/usr/share/mne-cpp/doc/gh-pages/images/1280px-EEGoSportsGUI.jpg
/usr/share/mne-cpp/doc/gh-pages/images/BrainAMP_GUI.jpg
/usr/share/mne-cpp/doc/gh-pages/images/EEGoSportsImpedanceWidget.jpg
/usr/share/mne-cpp/doc/gh-pages/images/GUSBampGUI.jpg
/usr/share/mne-cpp/doc/gh-pages/images/analyze/
/usr/share/mne-cpp/doc/gh-pages/images/analyze/mne_an_1.png
/usr/share/mne-cpp/doc/gh-pages/images/analyze/mne_an_2.png
/usr/share/mne-cpp/doc/gh-pages/images/analyze/mne_an_annotationmanager_1.png
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/usr/share/mne-cpp/doc/gh-pages/images/analyze/mne_an_dip1.png
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/usr/share/mne-cpp/doc/gh-pages/images/analyze/mne_an_filter_3.png
/usr/share/mne-cpp/doc/gh-pages/images/analyze/mne_an_rawdataviewer_1.png
/usr/share/mne-cpp/doc/gh-pages/images/analyze/mne_an_scaling1.png
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/usr/share/mne-cpp/resources/general/styles/rc/line_horizontal_disabled.png
/usr/share/mne-cpp/resources/general/styles/rc/line_horizontal_disabled@2x.png
/usr/share/mne-cpp/resources/general/styles/rc/line_horizontal_focus.png
/usr/share/mne-cpp/resources/general/styles/rc/line_horizontal_focus@2x.png
/usr/share/mne-cpp/resources/general/styles/rc/line_horizontal_pressed.png
/usr/share/mne-cpp/resources/general/styles/rc/line_horizontal_pressed@2x.png
/usr/share/mne-cpp/resources/general/styles/rc/line_vertical.png
/usr/share/mne-cpp/resources/general/styles/rc/line_vertical@2x.png
/usr/share/mne-cpp/resources/general/styles/rc/line_vertical_disabled.png
/usr/share/mne-cpp/resources/general/styles/rc/line_vertical_disabled@2x.png
/usr/share/mne-cpp/resources/general/styles/rc/line_vertical_focus.png
/usr/share/mne-cpp/resources/general/styles/rc/line_vertical_focus@2x.png
/usr/share/mne-cpp/resources/general/styles/rc/line_vertical_pressed.png
/usr/share/mne-cpp/resources/general/styles/rc/line_vertical_pressed@2x.png
/usr/share/mne-cpp/resources/general/styles/rc/radio_checked.png
/usr/share/mne-cpp/resources/general/styles/rc/radio_checked@2x.png
/usr/share/mne-cpp/resources/general/styles/rc/radio_checked_disabled.png
/usr/share/mne-cpp/resources/general/styles/rc/radio_checked_disabled@2x.png
/usr/share/mne-cpp/resources/general/styles/rc/radio_checked_focus.png
/usr/share/mne-cpp/resources/general/styles/rc/radio_checked_focus@2x.png
/usr/share/mne-cpp/resources/general/styles/rc/radio_checked_pressed.png
/usr/share/mne-cpp/resources/general/styles/rc/radio_checked_pressed@2x.png
/usr/share/mne-cpp/resources/general/styles/rc/radio_unchecked.png
/usr/share/mne-cpp/resources/general/styles/rc/radio_unchecked@2x.png
/usr/share/mne-cpp/resources/general/styles/rc/radio_unchecked_disabled.png
/usr/share/mne-cpp/resources/general/styles/rc/radio_unchecked_disabled@2x.png
/usr/share/mne-cpp/resources/general/styles/rc/radio_unchecked_focus.png
/usr/share/mne-cpp/resources/general/styles/rc/radio_unchecked_focus@2x.png
/usr/share/mne-cpp/resources/general/styles/rc/radio_unchecked_pressed.png
/usr/share/mne-cpp/resources/general/styles/rc/radio_unchecked_pressed@2x.png
/usr/share/mne-cpp/resources/general/styles/rc/toolbar_move_horizontal.png
/usr/share/mne-cpp/resources/general/styles/rc/toolbar_move_horizontal@2x.png
/usr/share/mne-cpp/resources/general/styles/rc/toolbar_move_horizontal_disabled.png
/usr/share/mne-cpp/resources/general/styles/rc/toolbar_move_horizontal_disabled@2x.png
/usr/share/mne-cpp/resources/general/styles/rc/toolbar_move_horizontal_focus.png
/usr/share/mne-cpp/resources/general/styles/rc/toolbar_move_horizontal_focus@2x.png
/usr/share/mne-cpp/resources/general/styles/rc/toolbar_move_horizontal_pressed.png
/usr/share/mne-cpp/resources/general/styles/rc/toolbar_move_horizontal_pressed@2x.png
/usr/share/mne-cpp/resources/general/styles/rc/toolbar_move_vertical.png
/usr/share/mne-cpp/resources/general/styles/rc/toolbar_move_vertical@2x.png
/usr/share/mne-cpp/resources/general/styles/rc/toolbar_move_vertical_disabled.png
/usr/share/mne-cpp/resources/general/styles/rc/toolbar_move_vertical_disabled@2x.png
/usr/share/mne-cpp/resources/general/styles/rc/toolbar_move_vertical_focus.png
/usr/share/mne-cpp/resources/general/styles/rc/toolbar_move_vertical_focus@2x.png
/usr/share/mne-cpp/resources/general/styles/rc/toolbar_move_vertical_pressed.png
/usr/share/mne-cpp/resources/general/styles/rc/toolbar_move_vertical_pressed@2x.png
/usr/share/mne-cpp/resources/general/styles/rc/toolbar_separator_horizontal.png
/usr/share/mne-cpp/resources/general/styles/rc/toolbar_separator_horizontal@2x.png
/usr/share/mne-cpp/resources/general/styles/rc/toolbar_separator_horizontal_disabled.png
/usr/share/mne-cpp/resources/general/styles/rc/toolbar_separator_horizontal_disabled@2x.png
/usr/share/mne-cpp/resources/general/styles/rc/toolbar_separator_horizontal_focus.png
/usr/share/mne-cpp/resources/general/styles/rc/toolbar_separator_horizontal_focus@2x.png
/usr/share/mne-cpp/resources/general/styles/rc/toolbar_separator_horizontal_pressed.png
/usr/share/mne-cpp/resources/general/styles/rc/toolbar_separator_horizontal_pressed@2x.png
/usr/share/mne-cpp/resources/general/styles/rc/toolbar_separator_vertical.png
/usr/share/mne-cpp/resources/general/styles/rc/toolbar_separator_vertical@2x.png
/usr/share/mne-cpp/resources/general/styles/rc/toolbar_separator_vertical_disabled.png
/usr/share/mne-cpp/resources/general/styles/rc/toolbar_separator_vertical_disabled@2x.png
/usr/share/mne-cpp/resources/general/styles/rc/toolbar_separator_vertical_focus.png
/usr/share/mne-cpp/resources/general/styles/rc/toolbar_separator_vertical_focus@2x.png
/usr/share/mne-cpp/resources/general/styles/rc/toolbar_separator_vertical_pressed.png
/usr/share/mne-cpp/resources/general/styles/rc/toolbar_separator_vertical_pressed@2x.png
/usr/share/mne-cpp/resources/general/styles/rc/transparent.png
/usr/share/mne-cpp/resources/general/styles/rc/transparent@2x.png
/usr/share/mne-cpp/resources/general/styles/rc/transparent_disabled.png
/usr/share/mne-cpp/resources/general/styles/rc/transparent_disabled@2x.png
/usr/share/mne-cpp/resources/general/styles/rc/transparent_focus.png
/usr/share/mne-cpp/resources/general/styles/rc/transparent_focus@2x.png
/usr/share/mne-cpp/resources/general/styles/rc/transparent_pressed.png
/usr/share/mne-cpp/resources/general/styles/rc/transparent_pressed@2x.png
/usr/share/mne-cpp/resources/general/styles/rc/window_close.png
/usr/share/mne-cpp/resources/general/styles/rc/window_close@2x.png
/usr/share/mne-cpp/resources/general/styles/rc/window_close_disabled.png
/usr/share/mne-cpp/resources/general/styles/rc/window_close_disabled@2x.png
/usr/share/mne-cpp/resources/general/styles/rc/window_close_focus.png
/usr/share/mne-cpp/resources/general/styles/rc/window_close_focus@2x.png
/usr/share/mne-cpp/resources/general/styles/rc/window_close_pressed.png
/usr/share/mne-cpp/resources/general/styles/rc/window_close_pressed@2x.png
/usr/share/mne-cpp/resources/general/styles/rc/window_grip.png
/usr/share/mne-cpp/resources/general/styles/rc/window_grip@2x.png
/usr/share/mne-cpp/resources/general/styles/rc/window_grip_disabled.png
/usr/share/mne-cpp/resources/general/styles/rc/window_grip_disabled@2x.png
/usr/share/mne-cpp/resources/general/styles/rc/window_grip_focus.png
/usr/share/mne-cpp/resources/general/styles/rc/window_grip_focus@2x.png
/usr/share/mne-cpp/resources/general/styles/rc/window_grip_pressed.png
/usr/share/mne-cpp/resources/general/styles/rc/window_grip_pressed@2x.png
/usr/share/mne-cpp/resources/general/styles/rc/window_minimize.png
/usr/share/mne-cpp/resources/general/styles/rc/window_minimize@2x.png
/usr/share/mne-cpp/resources/general/styles/rc/window_minimize_disabled.png
/usr/share/mne-cpp/resources/general/styles/rc/window_minimize_disabled@2x.png
/usr/share/mne-cpp/resources/general/styles/rc/window_minimize_focus.png
/usr/share/mne-cpp/resources/general/styles/rc/window_minimize_focus@2x.png
/usr/share/mne-cpp/resources/general/styles/rc/window_minimize_pressed.png
/usr/share/mne-cpp/resources/general/styles/rc/window_minimize_pressed@2x.png
/usr/share/mne-cpp/resources/general/styles/rc/window_undock.png
/usr/share/mne-cpp/resources/general/styles/rc/window_undock@2x.png
/usr/share/mne-cpp/resources/general/styles/rc/window_undock_disabled.png
/usr/share/mne-cpp/resources/general/styles/rc/window_undock_disabled@2x.png
/usr/share/mne-cpp/resources/general/styles/rc/window_undock_focus.png
/usr/share/mne-cpp/resources/general/styles/rc/window_undock_focus@2x.png
/usr/share/mne-cpp/resources/general/styles/rc/window_undock_pressed.png
/usr/share/mne-cpp/resources/general/styles/rc/window_undock_pressed@2x.png
/usr/share/mne-cpp/resources/general/styles/styles.qrc
/usr/share/mne-cpp/resources/general/surf2bem/
/usr/share/mne-cpp/resources/general/surf2bem/icos.fif
/usr/share/mne-cpp/resources/mne_rt_server/
/usr/share/mne-cpp/resources/mne_rt_server/plugins/
/usr/share/mne-cpp/resources/mne_rt_server/plugins/fiffsimulator/
/usr/share/mne-cpp/resources/mne_rt_server/plugins/fiffsimulator/FiffSimulation.cfg
/usr/share/mne-cpp/resources/mne_rt_server/plugins/fiffsimulator/fiffsimulator.json
/usr/share/mne-cpp/resources/mne_rt_server/plugins/plugin.cfg
/usr/share/mne-cpp/resources/mne_scan/
/usr/share/mne-cpp/resources/mne_scan/plugins/
/usr/share/mne-cpp/resources/mne_scan/plugins/FiffSimulator/
/usr/share/mne-cpp/resources/mne_scan/plugins/FiffSimulator/VectorViewSimLayout.xml
/usr/share/mne-cpp/resources/mne_scan/plugins/FiffSimulator/inputFile.txt
/usr/share/mne-cpp/resources/mne_scan/plugins/babymeg/
/usr/share/mne-cpp/resources/mne_scan/plugins/babymeg/both.bad
/usr/share/mne-cpp/resources/mne_scan/plugins/babymeg/compensator.fif
/usr/share/mne-cpp/resources/mne_scan/plugins/babymeg/header.fif
/usr/share/mne-cpp/resources/mne_scan/plugins/noisereduction/
/usr/share/mne-cpp/resources/mne_scan/plugins/noisereduction/SPHARA/
/usr/share/mne-cpp/resources/mne_scan/plugins/noisereduction/SPHARA/BabyMEG_SPHARA_InvEuclidean_Inner.txt
/usr/share/mne-cpp/resources/mne_scan/plugins/noisereduction/SPHARA/BabyMEG_SPHARA_InvEuclidean_Outer.txt
/usr/share/mne-cpp/resources/mne_scan/plugins/noisereduction/SPHARA/Current_SPHARA_EEG.txt
/usr/share/mne-cpp/resources/mne_scan/plugins/noisereduction/SPHARA/Duke64Dry.txt
/usr/share/mne-cpp/resources/mne_scan/plugins/noisereduction/SPHARA/Vectorview_SPHARA_InvEuclidean_Grad.txt
/usr/share/mne-cpp/resources/mne_scan/plugins/noisereduction/SPHARA/Vectorview_SPHARA_InvEuclidean_Mag.txt
/usr/share/mne-cpp/resources/mne_scan/plugins/tmsi/
/usr/share/mne-cpp/resources/mne_scan/plugins/tmsi/loc_files/
/usr/share/mne-cpp/resources/mne_scan/plugins/tmsi/loc_files/Lorenz-Duke128-28-11-2013.elc
/usr/share/mne-cpp/resources/mne_scan/plugins/tmsi/loc_files/standard.elc
/usr/share/mne-cpp/resources/mne_scan/plugins/tmsi/loc_files/standard_waveguard128.elc
/usr/share/mne-cpp/resources/mne_scan/plugins/tmsi/loc_files/standard_waveguard256.elc
/usr/share/mne-cpp/resources/mne_scan/plugins/tmsi/loc_files/standard_waveguard32.elc
/usr/share/mne-cpp/resources/mne_scan/plugins/tmsi/loc_files/standard_waveguard64.elc
/usr/share/mne-cpp/resources/mne_scan/plugins/tmsi/loc_files/standard_waveguard8.elc
/usr/share/mne-cpp/sample-sata/
/usr/share/mne-cpp/sample-sata/README.md
/usr/share/mne-cpp/sample-sata/download_sample_data.html

So, Fedora follows the Filesystem hierarchy standard quite strictly:

https://www.pathname.com/fhs/pub/fhs-2.3.html

and we define macros for these common paths:

https://docs.fedoraproject.org/en-US/packaging-guidelines/RPMMacros/#macros_installation

So, all the user executable files go into /usr/bin, the libraries go into /usr/lib{,64} (/usr/lib on 32 bit systems and /usr/lib64 on 64 bit systems.

All your architecture independent data does go into %_datadir, which is /usr/share/ under a new folder specific to the package, so /usr/share/mne-cpp is perfectly fine.

The documentation usually goes into a folder under %_docdir, which is /usr/share/doc. However note that we avoid building sphinx docs etc. nowadays because they bundle javascript and fonts and it's a real pain to unbundle all that. So I tend to not package the docs or their sources---most folks can access them online anyway.

For the other executables etc., there are two options:

  • executables that are not to be used by users, like test executables, can be run during the build to run tests, but then don't need to be included in the package---they can be excluded from the file list using something like %exclude %{_bindir}/mne*test
  • example executables can be shipped, but in a different mne-cpp-examples sub package. This way, the main package has the necessary files, a -doc sub package has any documentation that you wish to ship, and an -examples sub-package can have the examples. The latter two can be installed by users when they need them.

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