remove CIL if BUILD_CIL=ON

CHANGES.md

@@ -2,6 +2,8 @@
 
 ## vx.x.x
 - Adds CCPi-Regularisation-Toolkit as prerequisite for CIL and reinstate unit tests
+- Docker:
+  - Handle BUILD_CIL correctly and not install CIL from conda if BUILD_CIL=ON
 - CMake:
   - only pass through `OpenMP*LIBRARY` variables if set, and add OpenMP_iomp_LIBRARY to the list (for Intel compiler)
 - Updated Versions:

Dockerfile

@@ -21,12 +21,16 @@ RUN bash /opt/scripts/build_system-ubuntu.sh
 
 # SIRF python deps
 ARG BUILD_GPU=0
+ARG BUILD_CIL="OFF"
 COPY docker/requirements.yml /opt/scripts/
 # https://jupyter-docker-stacks.readthedocs.io/en/latest/using/common.html#conda-environments
 # https://github.com/TomographicImaging/CIL/blob/master/Dockerfile
 RUN if test "$BUILD_GPU" != 0; then \
   sed -ri 's/^(\s*)#\s*(- \S+.*#.*GPU.*)$/\1\2/' /opt/scripts/requirements.yml; \
  fi \
+ && if test "$BUILD_CIL" != 0; then \
+  sed -r -i -e '/^\s*- (cil).*/d' /opt/scripts/requirements.yml; \
+ fi \
  && conda config --env --set channel_priority strict \
  && for ch in defaults ccpi intel conda-forge; do conda config --env --add channels $ch; done \
  && mamba env update -n base -f /opt/scripts/requirements.yml \
@@ -66,7 +70,8 @@ ARG USE_NiftyPET="OFF"
 ARG BUILD_siemens_to_ismrmrd="ON"
 ARG BUILD_pet_rd_tools="ON"
 ARG Gadgetron_USE_CUDA="ON"
-ARG BUILD_CIL="OFF"
+# BUILD_CIL is defined in the previous stage
+ARG BUILD_CIL
 ARG EXTRA_BUILD_FLAGS=""
 
 # build, install in /opt/SIRF-SuperBuild/{INSTALL,sources/SIRF}, test (if RUN_CTEST)
@@ -110,6 +115,7 @@ COPY --from=build --link --chown=${NB_USER} /opt/SIRF-SuperBuild/INSTALL/ /opt/S
 #COPY --from=build --link /opt/conda/ /opt/conda/
 
 # install {SIRF-Exercises,CIL-Demos}
+ARG BUILD_CIL
 COPY docker/user_demos.sh /opt/scripts/
 RUN BUILD_CIL="${BUILD_CIL}" bash /opt/scripts/user_demos.sh \
  && fix-permissions /opt/SIRF-Exercises /opt/CIL-Demos "${CONDA_DIR}" /home/${NB_USER}