[SyneRBI/SIRF-SuperBuild] Updated modules in find_package command for Python3 (PR #933)
NicoleJurjew
You can view, comment on, or merge this pull request online at:
https://github.com/SyneRBI/SIRF-SuperBuild/pull/933
Commit Summary
- 5963dbd Updated updated modules in find_package command for Python3
File Changes
(1 file)
- M SuperBuild.cmake (14)
Patch Links:
- https://github.com/SyneRBI/SIRF-SuperBuild/pull/933.patch
- https://github.com/SyneRBI/SIRF-SuperBuild/pull/933.diff
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Kris Thielemans
https://cmake.org/cmake/help/latest/module/FindPythonInterp.html deprecated since 3.12, while we require 3.16.2.
Current change is minimal. We probably should pass Python_EXECUTABLE as opposed to PYTHON_EXECUTABLE to dependencies, but this needs a check which ones we use. Probably easiest to pass both. I think we should no longer attempt to pass include and other paths, and let CMake sort it out.
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Kris Thielemans
@KrisThielemans commented on this pull request.
In SuperBuild.cmake:
> @@ -47,7 +47,7 @@ endif() # Find CUDA option(DISABLE_CUDA "Disable CUDA" OFF) if (NOT DISABLE_CUDA) - find_package(CUDA) + find_package(CUDAToolkit REQUIRED)⬇️ Suggested change
- find_package(CUDAToolkit REQUIRED) + find_package(CUDA)
While this is needed, let's do it in another PR, as both of these could create discussions.
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Kris Thielemans
@KrisThielemans pushed 1 commit.
- 50805ce revert change in finding CUDA
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Kris Thielemans
> if (PYTHONLIBS_FOUND)
message(STATUS "Found PYTHON_INCLUDE_DIRS=${PYTHON_INCLUDE_DIRS}")
message(STATUS "Found PYTHON_LIBRARIES=${PYTHON_LIBRARIES}")
endif()
# Set destinations for Python files
- set (BUILD_PYTHON ${PYTHONLIBS_FOUND})
+ set (BUILD_PYTHON = ${Python3_FOUND})
⬇️ Suggested change
- set (BUILD_PYTHON = ${Python3_FOUND})
+ set (BUILD_PYTHON ${Python3_FOUND})
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Kris Thielemans
@KrisThielemans pushed 1 commit.
- 1fabcc0 correct typo
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Kris Thielemans
Need to update how we look for cython I guess
[100%] Generating build/timestamp
Traceback (most recent call last):
File "/home/runner/work/SIRF-SuperBuild/SIRF-SuperBuild/build/builds/TomoPhantom/build/Wrappers/Python/setup.py", line 19, in <module>
from Cython.Distutils import build_ext
ModuleNotFoundError: No module named 'Cython'
gmake[5]: *** [Wrappers/Python/CMakeFiles/PythonWrapper.dir/build.make:76: Wrappers/Python/build/timestamp] Error 1
gmake[4]: *** [CMakeFiles/Makefile2:157: Wrappers/Python/CMakeFiles/PythonWrapper.dir/all] Error 2
gmake[3]: *** [Makefile:136: all] Error 2
gmake[2]: *** [CMakeFiles/TomoPhantom.dir/build.make:86: builds/TomoPhantom/stamp/TomoPhantom-build] Error 2
gmake[1]: *** [CMakeFiles/Makefile2:755: CMakeFiles/TomoPhantom.dir/all] Error 2
This error is different from why I saw in #932 but it's possible that @NicoleJurjew only saw the Tomophantom error when using this branch I guess.
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NicoleJurjew
With the suggested changes, the PYTHONPATH isn't exported correctly.
I think some changes need to be done here, as well:
https://github.com/SyneRBI/SIRF-SuperBuild/blob/5f1a7f498bf6f41551c19eb53798b5d33af43eec/SuperBuild.cmake#L366C1-L386C8
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Kris Thielemans
that's a bit strange. What is the content of env_sirf.sh etc then? Can you just do a
message(STATUS "PYTHON_EXECUTABLE=${PYTHON_EXECUTABLE}")
before those statement to check what it is?
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NicoleJurjew
This is the content of env_sirf.sh:
grafik.png (view on web)
Where will that message be written to then? Thanks!
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Edoardo Pasca
See also #313
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Casper da Costa-Luis
@casperdcl pushed 4 commits.
- 30905f4 Updated updated modules in find_package command for Python3
- ebcc4ac revert change in finding CUDA
- b6da241 correct typo
- 3f09077 cmake: FindPython3
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Casper da Costa-Luis
@casperdcl pushed 2 commits.
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Casper da Costa-Luis
casperdcl left a comment (SyneRBI/SIRF-SuperBuild#933)Looks like a gadgetron build error related to https://groups.google.com/g/linux.debian.bugs.dist/c/JpHAw3GY0Bk
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Kris Thielemans
KrisThielemans left a comment (SyneRBI/SIRF-SuperBuild#933)This was all discussed in #937. I've contributed a PR to Gadgetron. However, moving on with Gadgetron created a lot of other problems. So @paskino and I decided to wait with that, and just fix Ubuntu 22.04. This is done in #943. So suggestion therefore is to finish #943, merge it, and merge that back on here.
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Kris Thielemans
@KrisThielemans commented on this pull request.
Did you check if the dependencies indeed accept Python3_EXECUTABLE. In any case, I'm fairly sure this needs to be Python_EXECUTABLE. Easiest might be to pass both of course, although that's a bit ugly.
Also, in SIRF and STIR, we have a "backwards compatible" line to set Python_EXECUTABLE if PYTHON_EXECUTABLE is set. Maybe no longer need it?
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Kris Thielemans
KrisThielemans left a comment (SyneRBI/SIRF-SuperBuild#933)@casperdcl I've merged #943.
Note that we'll also need to update CHANGES.md here.
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Casper da Costa-Luis
@casperdcl pushed 5 commits.
- 25e7ece Updated updated modules in find_package command for Python3
- 698cafb revert change in finding CUDA
- 4f27200 correct typo
- 5e5aa82 cmake: FindPython3
- 15b6504 cmake: fix hints
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Casper da Costa-Luis
@casperdcl commented on this pull request.
On SuperBuild.cmake:
technically
find_package |
-D hint |
|---|---|
Python3 |
Python3_EXECUTABLE |
Python |
Python_EXECUTABLE |
so perhaps we could just use Python without the 3-suffix everywhere?
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Casper da Costa-Luis
@casperdcl pushed 1 commit.
- 4960efe Python3_EXCUTABLE => Python_EXECUTABLE
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Kris Thielemans
@KrisThielemans requested changes on this pull request.
In SuperBuild.cmake:
> @@ -431,7 +431,7 @@ if (WIN32) endif() if (PYTHONINTERP_FOUND)⬇️ Suggested change
- if (PYTHONINTERP_FOUND) + if (Python_EXECUTABLE)
In SuperBuild/External_NiftyPET.cmake:
> + -DPython_EXECUTABLE=${NiftyPET_PYTHON_EXECUTABLE}
+ -DPython3_Executable=${NiftyPET_PYTHON_EXECUTABLE}
note that we are stuck to NiftyPET 2. Are you sure this is ok?
In VirtualBox/scripts/UPDATE_functions.sh:
> @@ -185,7 +185,8 @@ SuperBuild_install(){
-DDEVEL_BUILD="$DEVEL_BUILD" \
-DNIFTYREG_USE_CUDA=OFF\
-DBUILD_CIL=ON\
- -DPYTHON_EXECUTABLE="$PYTHON_EXECUTABLE"\
+ -DPython_EXECUTABLE="$PYTHON_EXECUTABLE"\
+ -DPython3_EXECUTABLE="$PYTHON_EXECUTABLE"\
⬇️ Suggested change
- -DPython3_EXECUTABLE="$PYTHON_EXECUTABLE"\
This isn't necessary for our own SB.
In SuperBuild/External_ROOT.cmake:
> + -DPython_EXECUTABLE:FILE=${Python_EXECUTABLE}
+ -DPython3_EXECUTABLE:FILE=${Python_EXECUTABLE}
⬇️ Suggested change
- -DPython_EXECUTABLE:FILE=${Python_EXECUTABLE}
- -DPython3_EXECUTABLE:FILE=${Python_EXECUTABLE}
+ ${PYTHONLIBS_CMAKE_ARGS}
In SuperBuild.cmake:
> message(STATUS "Python version ${PYTHON_VERSION_STRING}")
endif()
-
- find_package(PythonLibs 3)
-
+
if (PYTHONLIBS_FOUND)
Python_*, and different conditional
In SuperBuild.cmake:
> CONDA: do nothing")
set_property(CACHE PYTHON_STRATEGY PROPERTY STRINGS PYTHONPATH SETUP_PY CONDA)
endif()
# set PYTHONLIBS_CMAKE_ARGS to be used in the ExternalProject_add calls
# note: Find_package(PythonLibs) takes PYTHON_INCLUDE_DIR and PYTHON_LIBRARY as input
- set (PYTHONLIBS_CMAKE_ARGS -DPYTHON_EXECUTABLE:FILEPATH=${PYTHON_EXECUTABLE})
+ set (PYTHONLIBS_CMAKE_ARGS
+ -DPython_EXECUTABLE:FILEPATH=${Python_EXECUTABLE}
+ -DPython3_EXECUTABLE:FILEPATH=${Python_EXECUTABLE})
if (EXISTS "${PYTHON_INCLUDE_DIR}")
Python, not PYTHON
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Casper da Costa-Luis
@casperdcl commented on this pull request.
In SuperBuild/External_NiftyPET.cmake:
> + -DPython_EXECUTABLE=${NiftyPET_PYTHON_EXECUTABLE}
+ -DPython3_Executable=${NiftyPET_PYTHON_EXECUTABLE}
Any reason why? Current NiftyPET is Python3 only.
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Casper da Costa-Luis
@casperdcl commented on this pull request.
In VirtualBox/scripts/UPDATE_functions.sh:
> @@ -185,7 +185,8 @@ SuperBuild_install(){
-DDEVEL_BUILD="$DEVEL_BUILD" \
-DNIFTYREG_USE_CUDA=OFF\
-DBUILD_CIL=ON\
- -DPYTHON_EXECUTABLE="$PYTHON_EXECUTABLE"\
+ -DPython_EXECUTABLE="$PYTHON_EXECUTABLE"\
+ -DPython3_EXECUTABLE="$PYTHON_EXECUTABLE"\
I was hesitant just in case people use the new UPDATE_functions.sh on an old SB version.
Hopefully a niche problem, though, so will remove this line.
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Kris Thielemans
KrisThielemans left a comment (SyneRBI/SIRF-SuperBuild#933)There seem to be 2 different Python versions used in the CIL install, resulting in the cil not being found at import. There are 2 causes for this.
For the SB, CMake finds a surprising version (which is then passed on)
Found Python: /opt/hostedtoolcache/Python/3.10.12/x64/bin/python3.10 (found version "3.10.12") found components: Interpreter Development Development.Module Development.Embed
Found Python_EXECUTABLE=/opt/hostedtoolcache/Python/3.10.12/x64/bin/python3.10
The CMake strategy for selecting a python version is still far too complicated/error-prone. I suggest therefore to explicitly set
Python_EXECUTABLE=which python` in the Action.
In addition, it looks like the CIL version that is being built (I only checked with DEVEL_BUILD=OFF) uses old-style:
-- Found PythonLibs: /usr/lib/x86_64-linux-gnu/libpython3.10.so (found version "3.10.12")
-- Found PYTHON_EXECUTABLE=/home/runner/virtualenv/bin/python
I think therefore we need to add PYTHON_EXECUTABLE to the PYTHONLIBS_CMAKE_ARGS variable. That's safest in any case.
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Kris Thielemans
@KrisThielemans commented on this pull request.
In VirtualBox/scripts/UPDATE_functions.sh:
> @@ -185,7 +185,8 @@ SuperBuild_install(){
-DDEVEL_BUILD="$DEVEL_BUILD" \
-DNIFTYREG_USE_CUDA=OFF\
-DBUILD_CIL=ON\
- -DPYTHON_EXECUTABLE="$PYTHON_EXECUTABLE"\
+ -DPython_EXECUTABLE="$PYTHON_EXECUTABLE"\
+ -DPython3_EXECUTABLE="$PYTHON_EXECUTABLE"\
oh, right. This is on the VM. Sorry. Let's leave this in then.
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Kris Thielemans
@KrisThielemans commented on this pull request.
In VirtualBox/scripts/UPDATE_functions.sh:
> @@ -185,7 +185,8 @@ SuperBuild_install(){
-DDEVEL_BUILD="$DEVEL_BUILD" \
-DNIFTYREG_USE_CUDA=OFF\
-DBUILD_CIL=ON\
- -DPYTHON_EXECUTABLE="$PYTHON_EXECUTABLE"\
+ -DPython_EXECUTABLE="$PYTHON_EXECUTABLE"\
+ -DPython3_EXECUTABLE="$PYTHON_EXECUTABLE"\
Certainly as on GHA, CMake found the wrong python...
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Kris Thielemans
@KrisThielemans commented on this pull request.
In SuperBuild/External_NiftyPET.cmake:
> + -DPython_EXECUTABLE=${NiftyPET_PYTHON_EXECUTABLE}
+ -DPython3_Executable=${NiftyPET_PYTHON_EXECUTABLE}
We currently only use NiftyPET via STIR, but that all happens on the C++ front. NiftyPET3 no longer has the appropriate libraries, and I have no energy for it.
See UCL/STIR#1294 to jog your memory :-)
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Kris Thielemans
@KrisThielemans commented on this pull request.
In SuperBuild/External_NiftyPET.cmake:
> + -DPython_EXECUTABLE=${NiftyPET_PYTHON_EXECUTABLE}
+ -DPython3_Executable=${NiftyPET_PYTHON_EXECUTABLE}
It could be worthwile wrapping NiftyPET in CIL instead, but it's nowhere on my (our?) list of priorities.
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Casper da Costa-Luis
@casperdcl pushed 1 commit.
- 9e2e844 misc fixes
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Casper da Costa-Luis
@casperdcl pushed 1 commit.
- c4bacd6 misc fixes
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Kris Thielemans
KrisThielemans left a comment (SyneRBI/SIRF-SuperBuild#933)ModuleNotFoundError: No module named 'Cython'
when building TomoPhantom. Not sure why this happens now? Wrong python used? TBH, We shouldn't really build TomoPhantom as part of our CI I think. @paskino ?
Run actions/upload-artifact@v4
with:
name: build_log_files-ubuntu-22.04-gcc9-Release-DEVEL=OFF
...
Error: Failed to CreateArtifact: Received non-retryable error: Failed request: (409) Conflict: an artifact with this name already exists on the workflow run
I guess we have a problem with the naming somewhere.
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Casper da Costa-Luis
@casperdcl pushed 1 commit.
- f5489e6 potential TomoPhantom build fix
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Casper da Costa-Luis
@casperdcl pushed 1 commit.
- 2e56611 potential TomoPhantom build fix
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Casper da Costa-Luis
@casperdcl pushed 1 commit.
- 9fa54cf fix TomoPhantom build deps
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Casper da Costa-Luis
casperdcl left a comment (SyneRBI/SIRF-SuperBuild#933)TomoPhantom v2.0.0 (and also the slightly more recent v3.0) doesn't specify build deps. Its setup.py needs Cython & numpy. Adding them to the build step works.
Current test failures due to lack of CIL deps... CIL:scripts/requirements-test.yml are not included in CIL:pyproject.toml and I think they should be.
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Casper da Costa-Luis
@casperdcl pushed 1 commit.
- 3d3fc3f hardcode CIL deps
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Kris Thielemans
@KrisThielemans commented on this pull request.
In SuperBuild.cmake:
> CONDA: do nothing")
set_property(CACHE PYTHON_STRATEGY PROPERTY STRINGS PYTHONPATH SETUP_PY CONDA)
endif()
# set PYTHONLIBS_CMAKE_ARGS to be used in the ExternalProject_add calls
- # note: Find_package(PythonLibs) takes PYTHON_INCLUDE_DIR and PYTHON_LIBRARY as input
- set (PYTHONLIBS_CMAKE_ARGS -DPYTHON_EXECUTABLE:FILEPATH=${PYTHON_EXECUTABLE})
- if (EXISTS "${PYTHON_INCLUDE_DIR}")
- set (PYTHONLIBS_CMAKE_ARGS ${PYTHONLIBS_CMAKE_ARGS}
- -DPYTHON_INCLUDE_DIR:PATH=${PYTHON_INCLUDE_DIR})
- endif()
- if (EXISTS "${PYTHON_LIBRARY}")
+ set (PYTHONLIBS_CMAKE_ARGS
+ -DPython_EXECUTABLE:FILEPATH=${Python_EXECUTABLE}
+ -DPython3_EXECUTABLE:FILEPATH=${Python_EXECUTABLE}
+ -DPYTHON_EXECUTABLE:FILEPATH=${Python_EXECUTABLE})
+ if (Python_Development_FOUND)
we require it, so no extra if
In SuperBuild.cmake:
> + -DPython_INCLUDE_DIRS=${Python_INCLUDE_DIRS}
+ -DPython_LIBRARIES=${Python_LIBRARIES}
+ -DPYTHON_INCLUDE_DIR=${Python_INCLUDE_DIRS}
+ -DPYTHON_LIBRARY=${Python_LIBRARIES})
I don't think we should be setting the *DIRS and *LIBRARIES variables, only the "singular" ones, as they are the input ones, while the "plural" variables are the output. (It could go wrong when there are multiple directories in the "plural" variables).
That means though that we should only set those if the input ones are set.
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Casper da Costa-Luis
@casperdcl pushed 1 commit.
- ed81a12 hardcode CIL deps
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Casper da Costa-Luis
@casperdcl pushed 1 commit.
- 74fd9cb hardcode CIL deps
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Kris Thielemans
KrisThielemans left a comment (SyneRBI/SIRF-SuperBuild#933)For the SB, CMake finds a surprising version (which is then passed on)
Found Python: /opt/hostedtoolcache/Python/3.10.12/x64/bin/python3.10 (found version "3.10.12") found components: Interpreter Development Development.Module Development.Embed Found Python_EXECUTABLE=/opt/hostedtoolcache/Python/3.10.12/x64/bin/python3.10
The CMake strategy for selecting a python version is still far too complicated/error-prone. I suggest therefore to explicitly set
Python_EXECUTABLE=${which python}in the Action.
This is still the case, hence the failures.
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Casper da Costa-Luis
@casperdcl pushed 1 commit.
- 2fc3591 fix FindPython hints
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Casper da Costa-Luis
@casperdcl pushed 1 commit.
- 3569455 fix FindPython hints
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Casper da Costa-Luis
@casperdcl pushed 1 commit.
- 72b5111 fix FindPython hints
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Casper da Costa-Luis
@casperdcl pushed 1 commit.
- cd45e61 fix env vars for cmake FindPython
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Casper da Costa-Luis
casperdcl left a comment (SyneRBI/SIRF-SuperBuild#933)Ah I finally understood; you don't want to use the system Python.
TL;DR we need to unset the cmake helpers defined by https://github.com/actions/setup-python/blob/main/docs/advanced-usage.md#environment-variables
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Kris Thielemans
KrisThielemans left a comment (SyneRBI/SIRF-SuperBuild#933)Ah I finally understood; you don't want to use the system Python.
TL;DR we need to unset the cmake helpers defined by
actions/setup-python.
pretty confusing... I don't care which python is being used here, but obviously we should always use the same. As we seem to be using setup-python with pip, and then create a venv, we should be using that one. I guess that's what you did now, so ... great.
Sadly, some zenodo download issues ATM.
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Kris Thielemans
@KrisThielemans approved this pull request.
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Kris Thielemans
@KrisThielemans commented on this pull request.
oh. still need to update CHANGES.md!
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Casper da Costa-Luis
Merged #933 into master.
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Kris Thielemans
KrisThielemans left a comment (SyneRBI/SIRF-SuperBuild#933)Success! Thanks @casperdcl . however, can you now have a different PR to update CHANGES.md, saying that we've switched to FindPython (maybe a link), and that they should use Python_EXECUTABLE or any other variables as indicated in the CMake doc? (Sorry, I shouldn't have approved the PR :-))
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Casper da Costa-Luis
casperdcl left a comment (SyneRBI/SIRF-SuperBuild#933)Already updated the changelog; feel free to update further
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Kris Thielemans
KrisThielemans left a comment (SyneRBI/SIRF-SuperBuild#933)Sorry. Confused. Which changelog?
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Casper da Costa-Luis
casperdcl left a comment (SyneRBI/SIRF-SuperBuild#933)https://github.com/SyneRBI/SIRF-SuperBuild/blob/master/CHANGES.md
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