Merge branch 'staging' into 'master'

Bugfix: more consistent treatment of environment variables throughout container.

See merge request !7

.gitlab-ci.yml

@@ -48,6 +48,7 @@ config_stable:
     - bash containers/release/configure_release.sh
   artifacts:
     paths:
+      - config/spack-env.sh
       - config/eic-env.sh
       - config/Dockerfile
 config_unstable:
@@ -63,6 +64,7 @@ config_unstable:
     - bash containers/release/configure_release.sh
   artifacts:
     paths:
+      - config/spack-env.sh
       - config/eic-env.sh
       - config/Dockerfile
       
@@ -76,6 +78,7 @@ release_stable:
      - staging
   script:
      - cp config/Dockerfile containers/release/Dockerfile
+     - cp config/eic-env.sh containers/release/eic-env.sh
      - cd containers/release
      - make login
      - make release-cached
@@ -89,6 +92,7 @@ release_unstable:
      - staging
   script:
      - cp config/Dockerfile containers/release/Dockerfile
+     - cp config/eic-env.sh containers/release/eic-env.sh
      - cd containers/release
      - make login
      - make develop-cached

containers/release/Dockerfile.in

@@ -30,10 +30,6 @@ ENV DOCKERFILE_DISTRO=ubuntu          \
 COPY --from=builder /opt/spack-environment /opt/spack-environment
 COPY --from=builder /opt/software /opt/software
 COPY --from=builder /opt/view /opt/view
-COPY --from=builder /etc/profile.d/z10_spack_environment.sh /etc/profile.d/z10_spack_environment.sh
-## Setup fresh bashrc, useful for singularity
-COPY bashrc /etc/bash.bashrc
-COPY bashrc /root/.bashrc
 
 ## Symlink /opt/view to /usr/local
 ## Maybe in a future release we should install the view directly to /usr/local
@@ -46,7 +42,12 @@ RUN rm -rf /usr/local && ln -s /opt/view /usr/local
 ## eic-shell and environment scripts. Not strictly needed anymore now we auto-load
 ## the environment but still provided for backward compatibility (and documentation).
 COPY eic-shell /usr/local/bin/eic-shell
-COPY --from=builder /etc/profile.d/z10_spack_environment.sh /etc/eic-env.sh
+COPY eic-env.sh /etc/eic-env.sh
+COPY eic-env.sh /etc/profile.d/z10_eic-env.sh
+
+## Setup fresh bashrc, useful for singularity
+COPY bashrc /etc/bash.bashrc
+COPY bashrc /root/.bashrc
 
 ## make sure we have the entrypoints setup correctly
 ENTRYPOINT []

containers/release/configure_release.sh

@@ -7,18 +7,20 @@
 
 mkdir -p config
 
-## Extract the desired environment variables as defined by spack
-grep export /etc/profile.d/z10_spack_environment.sh | \
-  sed 's/export /    /' | \
-  sed 's/;$/ \\/' > config/eic-env.sh
+cp /etc/profile.d/z10_spack_environment.sh config/spack-env.sh
 
 ## ensure we also have /lib/x86_64-linux-gnu in our library path
 ## as it contains important ubuntu system libraries
-sed -i "s?LD_LIBRARY_PATH=?&/lib/x86_64-linux-gnu:?" config/eic-env.sh
+sed -i "s?LD_LIBRARY_PATH=?&/lib/x86_64-linux-gnu:?" config/spack-env.sh
 
 ## Spack sets the man-path, which stops bash from using the default man-path
 ## We can fix this by appending a trailing colon to MANPATH
-sed -i '/MANPATH/ s/ \\$/: \\/' config/eic-env.sh
+sed -i '/MANPATH/ s/;$/:;/' config/spack-env.sh
+
+## Extract the desired environment variables as defined by spack
+grep export config/spack-env.sh | \
+  sed 's/export /    /' | \
+  sed 's/;$/ \\/' > config/eic-env.sh
 
 ## create our release Dockerfile
 sed '/^@ENV@/r config/eic-env.sh' containers/release/Dockerfile.in | \