[SyneRBI/SIRF-SuperBuild] Docker conda (PR #978)
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Kris Thielemans
Dec 1, 2025, 3:29:50 AM12/1/25
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Alternative to #946 with more conda.
I've dropped some commits, and added one that installs more conda packages and attempts to use them
You can view, comment on, or merge this pull request online at:
https://github.com/SyneRBI/SIRF-SuperBuild/pull/978
Commit Summary
- 0c5be02 fix conda hdf5: use cxx-compiler, boost, fftw3
- 179c79e fix siemens_to_ismrmrd build
- 08bf684 cil: numpy>=2
- 328a691 pip install cil
- 4dec1ea fix parallelproj openmp linking
- 9ec072d drop astra GPU
- 60604fe self-hosted conda channel for speed & reliability
- 68b18f9 build boost, use system fftw3
- 2b82cac revert boost to 1.85
- e78af31 bump STIR
- d7e8a64 minor CIL & Exercises fixes
- 9a4d1b0 fix missing packages
- b48690e TODO: REVERT: DEBUG: NOWARN
- 3954763 TODO: REVERT: DEBUGGING
- 6ac1f0b TODO: REVERT: skip tests for now
- c9b7ed7 use STIR of 28Nove2025
- f5b4c79 docker: use more conda
File Changes
(10 files)
- D .github/workflows/c-cpp.yml (183)
- M .github/workflows/docker.yml (2)
- M CMakeLists.txt (3)
- M Dockerfile (16)
- M SuperBuild/External_siemens_to_ismrmrd.cmake (2)
- M docker/build_system-ubuntu.sh (2)
- M docker/docker-stacks (2)
- M docker/requirements.yml (63)
- M docker/user_demos.sh (30)
- M version_config.cmake (15)
Patch Links:
- https://github.com/SyneRBI/SIRF-SuperBuild/pull/978.patch
- https://github.com/SyneRBI/SIRF-SuperBuild/pull/978.diff
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Kris Thielemans
Dec 1, 2025, 8:44:09 AM12/1/25
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KrisThielemans left a comment (SyneRBI/SIRF-SuperBuild#978)log doesn't say what's going on, but on my Ubuntu 16.04 (!) VM, I get
$ conda env create -n test -f docker/requirements.yml
Retrieving notices: done
Channels:
- conda-forge
- https://tomography.stfc.ac.uk/conda
- defaults
Platform: linux-64
Collecting package metadata (repodata.json): done
Solving environment: failed
LibMambaUnsatisfiableError: Encountered problems while solving:
- package armadillo-12.8.4-h4b5cfcf_1 requires liblapack >=3.9.0,<4.0a0, but none of the providers can be installed
Could not solve for environment specs
The following packages are incompatible
├─ armadillo 12.8.4** is installable and it requires
│ └─ liblapack >=3.9.0,<4.0a0 with the potential options
│ ├─ liblapack [3.11.0|3.9.0], which can be installed;
│ ├─ liblapack 3.9.0 would require
│ │ └─ libblas [3.9.0 10_mkl|3.9.0 11_linux64_mkl|...|3.9.0 9_mkl], which requires
│ │ └─ blas * mkl, which can be installed;
│ ├─ liblapack 3.9.0 would require
│ │ └─ libblas [3.9.0 4_mkl|3.9.0 5_mkl|3.9.0 6_mkl|3.9.0 7_mkl|3.9.0 8_mkl], which requires
│ │ ├─ blas * mkl, which can be installed;
│ │ └─ mkl >=2020.4,<2021.0a0 , which can be installed;
│ ├─ liblapack 3.11.0 would require
│ │ └─ libblas 3.11.0 0_h5875eb1_mkl, which requires
│ │ └─ blas 2.300 mkl, which can be installed;
│ ├─ liblapack 3.11.0 would require
│ │ └─ libblas 3.11.0 1_h5875eb1_mkl, which requires
│ │ └─ blas 2.301 mkl, which can be installed;
│ ├─ liblapack 3.11.0 would require
│ │ └─ libblas 3.11.0 2_h5875eb1_mkl, which requires
│ │ └─ blas 2.302 mkl, which can be installed;
│ ├─ liblapack 3.9.0 would require
│ │ └─ libblas 3.9.0 27_h2556b6b_mkl, which requires
│ │ └─ blas 2.127 mkl, which can be installed;
│ ├─ liblapack 3.9.0 would require
│ │ └─ libblas 3.9.0 28_h2556b6b_mkl, which requires
│ │ └─ blas 2.128 mkl, which can be installed;
│ ├─ liblapack 3.9.0 would require
│ │ └─ libblas 3.9.0 29_h2556b6b_mkl, which requires
│ │ └─ blas 2.129 mkl, which can be installed;
│ ├─ liblapack 3.9.0 would require
│ │ └─ libblas 3.9.0 30_h2556b6b_mkl, which requires
│ │ └─ blas 2.130 mkl, which can be installed;
│ ├─ liblapack 3.9.0 would require
│ │ └─ libblas 3.9.0 31_hfdb39a5_mkl, which requires
│ │ └─ blas 2.131 mkl, which can be installed;
│ ├─ liblapack 3.9.0 would require
│ │ └─ libblas 3.9.0 32_hfdb39a5_mkl, which requires
│ │ └─ blas 2.132 mkl, which can be installed;
│ ├─ liblapack 3.9.0 would require
│ │ └─ libblas 3.9.0 33_hfdb39a5_mkl, which requires
│ │ └─ blas 2.133 mkl, which can be installed;
│ ├─ liblapack 3.9.0 would require
│ │ └─ libblas 3.9.0 34_hfdb39a5_mkl, which requires
│ │ └─ blas 2.134 mkl, which can be installed;
│ ├─ liblapack 3.9.0 would require
│ │ └─ libblas [3.9.0 35_h5875eb1_mkl|3.9.0 35_hfdb39a5_mkl], which requires
│ │ └─ blas 2.135 mkl, which can be installed;
│ ├─ liblapack 3.9.0 would require
│ │ └─ libblas 3.9.0 36_h5875eb1_mkl, which requires
│ │ └─ blas 2.136 mkl, which can be installed;
│ ├─ liblapack 3.9.0 would require
│ │ └─ libblas 3.9.0 37_h5875eb1_mkl, which requires
│ │ └─ blas 2.137 mkl, which can be installed;
│ ├─ liblapack 3.9.0 would require
│ │ └─ libblas 3.9.0 38_h5875eb1_mkl, which requires
│ │ └─ blas 2.138 mkl, which can be installed;
│ └─ liblapack 3.9.0 would require
│ └─ libblas 3.9.0 39_h5875eb1_mkl, which requires
│ └─ blas 2.139 mkl, which can be installed;
├─ cil >=25 is installable and it requires
│ └─ numpy >=1.23,<2 with the potential options
│ ├─ numpy [1.23.1|1.23.3|...|2.3.1] would require
│ │ └─ blas * openblas but there are no viable options
│ │ ├─ blas [1.0|1.1|...|2.9] conflicts with any installable versions previously reported;
│ │ └─ blas [2.4|2.5|2.6|2.7] would require
│ │ └─ libblas [3.8.0 4_openblas|3.8.0 5_openblas|3.8.0 6_openblas|3.8.0 7_openblas], which requires
│ │ └─ openblas 0.3.5.* , which does not exist (perhaps a missing channel);
│ ├─ numpy [1.24.3|1.25.2|...|2.3.5] would require
│ │ └─ __glibc >=2.28,<3.0.a0 , which is missing on the system;
│ ├─ numpy [1.23.0|1.23.1|...|1.26.4], which can be installed;
│ ├─ numpy [1.23.1|1.23.3|...|1.26.4] would require
│ │ └─ blas 1.0 mkl, which conflicts with any installable versions previously reported;
│ ├─ numpy 1.23.3 would require
│ │ └─ numpy-base 1.23.3 py310h375b286_0, which does not exist (perhaps a missing channel);
│ └─ numpy 1.23.3 would require
│ └─ numpy-base 1.23.3 py310h8e6c178_0, which does not exist (perhaps a missing channel);
├─ libblas * *mkl is installable with the potential options
│ ├─ libblas 3.8.0 would require
│ │ └─ liblapack 3.8.0 4_mkl, which conflicts with any installable versions previously reported;
│ ├─ libblas 3.8.0 would require
│ │ └─ liblapack 3.8.0 10_mkl, which conflicts with any installable versions previously reported;
│ ├─ libblas 3.8.0 would require
│ │ └─ liblapack 3.8.0 11_mkl, which conflicts with any installable versions previously reported;
│ ├─ libblas 3.8.0 would require
│ │ └─ liblapack 3.8.0 12_mkl, which conflicts with any installable versions previously reported;
│ ├─ libblas 3.8.0 would require
│ │ └─ liblapack 3.8.0 13_mkl, which conflicts with any installable versions previously reported;
│ ├─ libblas 3.8.0 would require
│ │ └─ liblapack 3.8.0 14_mkl, which conflicts with any installable versions previously reported;
│ ├─ libblas 3.8.0 would require
│ │ └─ liblapack 3.8.0 15_mkl, which conflicts with any installable versions previously reported;
│ ├─ libblas 3.8.0 would require
│ │ └─ liblapack 3.8.0 16_mkl, which conflicts with any installable versions previously reported;
│ ├─ libblas 3.8.0 would require
│ │ └─ liblapack 3.8.0 18_mkl, which conflicts with any installable versions previously reported;
│ ├─ libblas 3.8.0 would require
│ │ └─ liblapack 3.8.0 19_mkl, which conflicts with any installable versions previously reported;
│ ├─ libblas 3.8.0 would require
│ │ └─ liblapack 3.8.0 20_mkl, which conflicts with any installable versions previously reported;
│ ├─ libblas 3.8.0 would require
│ │ └─ liblapack 3.8.0 21_mkl, which conflicts with any installable versions previously reported;
│ ├─ libblas 3.8.0 would require
│ │ └─ liblapack 3.8.0 5_mkl, which conflicts with any installable versions previously reported;
│ ├─ libblas 3.8.0 would require
│ │ └─ liblapack 3.8.0 6_mkl, which conflicts with any installable versions previously reported;
│ ├─ libblas 3.8.0 would require
│ │ └─ liblapack 3.8.0 7_mkl, which conflicts with any installable versions previously reported;
│ ├─ libblas 3.8.0 would require
│ │ └─ liblapack 3.8.0 8_mkl, which conflicts with any installable versions previously reported;
│ ├─ libblas 3.8.0 would require
│ │ └─ liblapack 3.8.0 9_mkl, which conflicts with any installable versions previously reported;
│ ├─ libblas 3.9.0, which can be installed (as previously explained);
│ ├─ libblas 3.9.0, which can be installed (as previously explained);
│ ├─ libblas 3.11.0, which can be installed (as previously explained);
│ ├─ libblas 3.11.0, which can be installed (as previously explained);
│ ├─ libblas 3.11.0, which can be installed (as previously explained);
│ ├─ libblas 3.9.0, which can be installed (as previously explained);
│ ├─ libblas 3.9.0, which can be installed (as previously explained);
│ ├─ libblas 3.9.0, which can be installed (as previously explained);
│ ├─ libblas 3.9.0, which can be installed (as previously explained);
│ ├─ libblas 3.9.0, which can be installed (as previously explained);
│ ├─ libblas 3.9.0, which can be installed (as previously explained);
│ ├─ libblas 3.9.0, which can be installed (as previously explained);
│ ├─ libblas 3.9.0, which can be installed (as previously explained);
│ ├─ libblas 3.9.0, which can be installed (as previously explained);
│ ├─ libblas 3.9.0, which can be installed (as previously explained);
│ ├─ libblas 3.9.0, which can be installed (as previously explained);
│ ├─ libblas 3.9.0, which can be installed (as previously explained);
│ └─ libblas 3.9.0, which can be installed (as previously explained);
└─ numpy >=2 is not installable because there are no viable options
├─ numpy [2.0.0|2.0.1|...|2.3.5] conflicts with any installable versions previously reported;
├─ numpy [2.0.0|2.0.1|...|2.3.1] would require
│ └─ blas 1.0 mkl, which conflicts with any installable versions previously reported;
├─ numpy [1.23.1|1.23.3|...|2.3.1], which cannot be installed (as previously explained);
├─ numpy 2.0.0 would require
│ ├─ blas 1.0 mkl, which conflicts with any installable versions previously reported;
│ └─ mkl >=2023.1.0,<2024.0a0 , which conflicts with any installable versions previously reported;
└─ numpy [1.24.3|1.25.2|...|2.3.5], which cannot be installed (as previously explained).
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