Merge pull request #112 from helenkirk/casa65

CASA versions 6.4.4 to 6.5.4 (directory is called version-6.5)

science-containers/Dockerfiles/casa/version-6.5/Dockerfile

@@ -0,0 +1,90 @@
+FROM images.canfar.net/skaha/ubuntu:22.04
+
+#NB: the one CASA pipeline version within this range has a different naming
+# structure within the unpacked directories.  All of my attempts to deal with
+# this difference in a scriptable manner have failed (see commented out below)
+#Thus instead, please uncomment out the special CASA_RELEASE2 definition when
+# building the CASA pipeline version
+#idea below: if pipeline is in name, remove the -py* part, otherwise keep the same
+#RUN if [[ ${CASA_RELEASE}=*pipeline* ]]; then CASA_RELEASE2=${CASA_RELEASE%%-py*}; else CASA_RELEASE2=${CASA_RELEASE}; fi
+
+# setup all required env variables
+ARG CASA_RELEASE
+ENV CASA_RELEASE=${CASA_RELEASE}
+ENV PATH /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/opt/casa/bin
+
+ENV CASA_RELEASE2=${CASA_RELEASE}
+#uncomment out the line below *only* when building the pipeline version
+#ENV CASA_RELEASE2=casa-6.5.3-28-pipeline-2023.0.0.36
+#ENV CASA_RELEASE2=casa-6.5.4-9-pipeline-2023.1.0.124
+
+# unpack and move casa databundle to container
+ADD ${CASA_RELEASE}.tar.xz /opt/
+
+# chown because the untarred casa has wrong owner/group
+RUN chown -R root:root /opt/${CASA_RELEASE2} && \
+    ln -s /opt/${CASA_RELEASE2} /opt/casa
+
+
+## add the admit enhancement (issue #25)
+RUN mkdir /opt/admit
+ADD admit /opt/admit
+RUN cd /opt/admit && \
+    autoupdate && autoconf && ./configure --with-casa-root=/opt/${CASA_RELEASE2}
+
+# Allow runtime symlink creation to the casa-data-repository
+# Create a dangling symlink to casa-data-repository so that after deployment
+# the symlink will link to the actual casa-data-repository in storage.
+RUN mkdir -p /arc/projects/casa-data-repository && \
+    rm -rf /opt/${CASA_RELEASE2}/data && \
+    ln -s /arc/projects/casa-data-repository/ /opt/${CASA_RELEASE2}/data && \
+    chmod 777 /opt/${CASA_RELEASE2} && \
+    cd /opt/${CASA_RELEASE2} && \
+    REPLACED_DATA=`find lib -name __data__` && \
+    chmod 777 ${REPLACED_DATA}/.. && \
+    rm -rf ${REPLACED_DATA} && \
+    ln -s /arc/projects/casa-data-repository/ /opt/${CASA_RELEASE2}/${REPLACED_DATA} && \
+    rm -rf /arc
+
+##(below stuff commented out, was old code version)
+##RUN rm -rf /opt/${CASA_RELEASE%%-py*}/data
+###update for CASA6+, new directory for the leapsecond data
+###(in theory, might need to run something like below, but this causes other
+### install errors, presumably b/c of other files also in the lib directory)
+###RUN rm -rf /opt/${CASA_RELEASE%%-py*}/lib
+##RUN chmod 777 /opt/${CASA_RELEASE%%-py*}
+#
+#Add in analysisUtils package
+RUN mkdir /opt/casa/analysisUtils && \
+    cd /opt/casa/analysisUtils && \
+    wget ftp://ftp.cv.nrao.edu/pub/casaguides/analysis_scripts.tar && \ 
+    tar -xvf analysis_scripts.tar
+#(if above doesn't work, can manually download the package and add as below)
+#ADD ./analysis_scripts.tar /opt/casa/analysisUtils/
+#NB: the analysisUtils path is added to the CASA startup file in the init.sh script
+# (needs access to user's $HOME)
+
+
+##NEW for CASA6.*: explicitly add in astropy
+##Instructions here: https://casadocs.readthedocs.io/en/latest/notebooks/frequently-asked-questions.html
+RUN /opt/${CASA_RELEASE2}/bin/python3 -m pip install --upgrade pip && \
+    /opt/${CASA_RELEASE2}/bin/pip3 install astropy && \
+#also add astroquery (astroquery.readthedocs.io/en/latest/)
+    /opt/${CASA_RELEASE2}/bin/python3 -m pip install --pre astroquery[all]
+
+RUN mkdir /skaha
+ADD init.sh /skaha/
+
+# generate missing dbus uuid (issue #47)
+RUN dbus-uuidgen --ensure
+
+ADD nsswitch.conf /etc/
+
+WORKDIR /opt
+COPY extract-casaviewer.sh .
+ENV PYTHONPATH /opt/${CASA_RELEASE2}/lib/py/lib/python3.8/site-packages
+RUN bash extract-casaviewer.sh && rm extract-casaviewer.sh
+
+RUN chmod 777 -R /opt/squashfs-root /opt/squashfs-root/usr /opt/squashfs-root/usr/*
+
+CMD [ "/skaha/init.sh" ]

science-containers/Dockerfiles/casa/version-6.5/Makefile

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+#NB: before using, uncomment the particular version to be built
+#NB#2: the extract_casaviewer.sh script also needs to have the correct
+# casa version set at the top
+
+#pipeline NB: the directory structure is different than the regular versions:
+# the -py3.8 portion is not included when the file is untarred.  
+#***For this directory only, when building the pipeline version below, you
+# need to additionally uncomment out a line near the top of the Dockerfile
+# (noted clearly there)
+VERSIONS_PIPELINE = \
+#	casa-6.5.4-9-pipeline-2023.1.0.124-py3.8
+#	casa-6.5.3-28-pipeline-2023.0.0.36-py3.8 
+
+VERSIONS = \
+	casa-6.4.4-31-py3.8
+#	casa-6.5.0-15-py3.8
+#	casa-6.5.5-21-py3.8
+#	casa-6.5.2-26-py3.8
+#	casa-6.5.3-28-py3.8
+#	casa-6.5.1-23-py3.8
+#	casa-6.5.6-22-py3.8 #Incorporated in version-6.6 as the download is different
+
+DOCKER_REPO_BASE=images.canfar.net/casa-6/casa
+
+.PHONY: build clean run 
+
+all: build-pipeline build
+
+build-pipeline: 
+	@- $(foreach V,$(VERSIONS_PIPELINE), \
+                ./download.sh $(V) pipeline ; \
+                docker build --build-arg CASA_RELEASE=$(V) -t ${DOCKER_REPO_BASE}:$(V) .; \
+	)
+
+build: 
+	@- $(foreach V,$(VERSIONS), \
+                ./download.sh $(V) current ; \
+                docker build --build-arg CASA_RELEASE=$(V) -t ${DOCKER_REPO_BASE}:$(V) .; \
+	)
+
+clean-pipeline:
+	@- $(foreach V,$(VERSIONS_PIPELINE), \
+                docker rmi ${DOCKER_REPO_BASE}:$(V) ; \
+	)
+
+clean:
+	@- $(foreach V,$(VERSIONS), \
+                docker rmi ${DOCKER_REPO_BASE}:$(V) ; \
+	)
+
+clean-all: clean-pipeline clean 
+
+upload-pipeline: build-pipeline
+	@- $(foreach V,$(VERSIONS_PIPELINE), \
+                docker push ${DOCKER_REPO_BASE}:$(V) ; \
+	)
+
+upload: build
+	@- $(foreach V,$(VERSIONS), \
+                docker push ${DOCKER_REPO_BASE}:$(V) ; \
+	)
+
+upload-all: upload-pipeline upload