chore: restructure dockerfile for build performance and caching (#154)

SwissDataScienceCenter · Dec 23, 2022 · c83a1b1 · c83a1b1
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diff --git a/R-minimal/Dockerfile b/R-minimal/Dockerfile
@@ -3,6 +3,31 @@
 ARG RENKU_BASE_IMAGE=renku/renkulab-r:4.2.0-0.13.1
 FROM ${RENKU_BASE_IMAGE}
 
+########################################################
+#        Renku install section - do not edit           #
+
+# RENKU_VERSION determines the version of the renku CLI
+# that will be used in this image. To find the latest version,
+# visit https://pypi.org/project/renku/#history.
+ARG RENKU_VERSION={{ __renku_version__ | default("2.0.0") }}
+
+# Install renku from pypi or from github if a dev version
+RUN if [ -n "$RENKU_VERSION" ] ; then \
+        source .renku/venv/bin/activate ; \
+        currentversion=$(renku --version) ; \
+        if [ "$RENKU_VERSION" != "$currentversion" ] ; then \
+            pip uninstall renku -y ; \
+            gitversion=$(echo "$RENKU_VERSION" | sed -n "s/^[[:digit:]]\+\.[[:digit:]]\+\.[[:digit:]]\+\(rc[[:digit:]]\+\)*\(\.dev[[:digit:]]\+\)*\(+g\([a-f0-9]\+\)\)*\(+dirty\)*$/\4/p") ; \
+            if [ -n "$gitversion" ] ; then \
+                pip install --force "git+https://github.com/SwissDataScienceCenter/renku-python.git@$gitversion" ;\
+            else \
+                pip install --force renku==${RENKU_VERSION} ;\
+            fi \
+        fi \
+    fi
+#             End renku install section                #
+########################################################
+
 # Uncomment and adapt if code is to be included in the image
 # COPY src /code/src
 
@@ -24,28 +49,3 @@ RUN R -f /tmp/install.R
 # install the python dependencies
 COPY requirements.txt /tmp/
 RUN pip3 install -r /tmp/requirements.txt
-
-# RENKU_VERSION determines the version of the renku CLI
-# that will be used in this image. To find the latest version,
-# visit https://pypi.org/project/renku/#history.
-ARG RENKU_VERSION={{ __renku_version__ | default("1.6.0") }}
-
-########################################################
-# Do not edit this section and do not add anything below
-
-# Install renku from pypi or from github if it's a dev version
-RUN if [ -n "$RENKU_VERSION" ] ; then \
-        source .renku/venv/bin/activate ; \
-        currentversion=$(renku --version) ; \
-        if [ "$RENKU_VERSION" != "$currentversion" ] ; then \
-            pip uninstall renku -y ; \
-            gitversion=$(echo "$RENKU_VERSION" | sed -n "s/^[[:digit:]]\+\.[[:digit:]]\+\.[[:digit:]]\+\(rc[[:digit:]]\+\)*\(\.dev[[:digit:]]\+\)*\(+g\([a-f0-9]\+\)\)*\(+dirty\)*$/\4/p") ; \
-            if [ -n "$gitversion" ] ; then \
-                pip install --force "git+https://github.com/SwissDataScienceCenter/renku-python.git@$gitversion" ;\
-            else \
-                pip install --force renku==${RENKU_VERSION} ;\
-            fi \
-        fi \
-    fi
-
-########################################################
diff --git a/bioc-minimal/Dockerfile b/bioc-minimal/Dockerfile
@@ -2,6 +2,32 @@
 # to swap this image for the latest version available
 FROM renku/renkulab-bioc:RELEASE_3_15-0.13.1
 
+########################################################
+#        Renku install section - do not edit           #
+
+# RENKU_VERSION determines the version of the renku CLI
+# that will be used in this image. To find the latest version,
+# visit https://pypi.org/project/renku/#history.
+ARG RENKU_VERSION={{ __renku_version__ | default("2.0.0") }}
+
+# Install renku from pypi or from github if a dev version
+RUN if [ -n "$RENKU_VERSION" ] ; then \
+        source .renku/venv/bin/activate ; \
+        currentversion=$(renku --version) ; \
+        if [ "$RENKU_VERSION" != "$currentversion" ] ; then \
+            pip uninstall renku -y ; \
+            gitversion=$(echo "$RENKU_VERSION" | sed -n "s/^[[:digit:]]\+\.[[:digit:]]\+\.[[:digit:]]\+\(rc[[:digit:]]\+\)*\(\.dev[[:digit:]]\+\)*\(+g\([a-f0-9]\+\)\)*\(+dirty\)*$/\4/p") ; \
+            if [ -n "$gitversion" ] ; then \
+                pip install --force "git+https://github.com/SwissDataScienceCenter/renku-python.git@$gitversion" ;\
+            else \
+                pip install --force renku==${RENKU_VERSION} ;\
+            fi \
+        fi \
+    fi
+#             End renku install section                #
+########################################################
+
+
 # Uncomment and adapt if code is to be included in the image
 # COPY src /code/src
 
@@ -23,28 +49,3 @@ RUN R -f /tmp/install.R
 # install the python dependencies
 COPY requirements.txt /tmp/
 RUN pip3 install -r /tmp/requirements.txt
-
-# RENKU_VERSION determines the version of the renku CLI
-# that will be used in this image. To find the latest version,
-# visit https://pypi.org/project/renku/#history.
-ARG RENKU_VERSION={{ __renku_version__ | default("1.6.0") }}
-
-########################################################
-# Do not edit this section and do not add anything below
-
-# Install renku from pypi or from github if it's a dev version
-RUN if [ -n "$RENKU_VERSION" ] ; then \
-        source .renku/venv/bin/activate ; \
-        currentversion=$(renku --version) ; \
-        if [ "$RENKU_VERSION" != "$currentversion" ] ; then \
-            pip uninstall renku -y ; \
-            gitversion=$(echo "$RENKU_VERSION" | sed -n "s/^[[:digit:]]\+\.[[:digit:]]\+\.[[:digit:]]\+\(rc[[:digit:]]\+\)*\(\.dev[[:digit:]]\+\)*\(+g\([a-f0-9]\+\)\)*\(+dirty\)*$/\4/p") ; \
-            if [ -n "$gitversion" ] ; then \
-                pip install --force "git+https://github.com/SwissDataScienceCenter/renku-python.git@$gitversion" ;\
-            else \
-                pip install --force renku==${RENKU_VERSION} ;\
-            fi \
-        fi \
-    fi
-
-########################################################
diff --git a/julia-minimal/Dockerfile b/julia-minimal/Dockerfile
@@ -3,6 +3,31 @@
 ARG RENKU_BASE_IMAGE=renku/renkulab-julia:1.7.1-0.13.1
 FROM ${RENKU_BASE_IMAGE}
 
+########################################################
+#        Renku install section - do not edit           #
+
+# RENKU_VERSION determines the version of the renku CLI
+# that will be used in this image. To find the latest version,
+# visit https://pypi.org/project/renku/#history.
+ARG RENKU_VERSION={{ __renku_version__ | default("2.0.0") }}
+
+# Install renku from pypi or from github if a dev version
+RUN if [ -n "$RENKU_VERSION" ] ; then \
+        source .renku/venv/bin/activate ; \
+        currentversion=$(renku --version) ; \
+        if [ "$RENKU_VERSION" != "$currentversion" ] ; then \
+            pip uninstall renku -y ; \
+            gitversion=$(echo "$RENKU_VERSION" | sed -n "s/^[[:digit:]]\+\.[[:digit:]]\+\.[[:digit:]]\+\(rc[[:digit:]]\+\)*\(\.dev[[:digit:]]\+\)*\(+g\([a-f0-9]\+\)\)*\(+dirty\)*$/\4/p") ; \
+            if [ -n "$gitversion" ] ; then \
+                pip install --force "git+https://github.com/SwissDataScienceCenter/renku-python.git@$gitversion" ;\
+            else \
+                pip install --force renku==${RENKU_VERSION} ;\
+            fi \
+        fi \
+    fi
+#             End Renku install section                #
+########################################################
+
 # Uncomment and adapt if code is to be included in the image
 # COPY src /code/src
 
@@ -19,38 +44,13 @@ FROM ${RENKU_BASE_IMAGE}
 
 # install the python dependencies
 COPY requirements.txt environment.yml /tmp/
-RUN conda env update -q -f /tmp/environment.yml && \
+RUN mamba env update -q -f /tmp/environment.yml && \
     /opt/conda/bin/pip install -r /tmp/requirements.txt && \
-    conda clean -y --all && \
-    conda env export -n "root"
+    mamba clean -y --all && \
+    mamba env export -n "root"
 
 # download and precompile any libaries to speed up startup time
 COPY Project.toml Manifest.toml /tmp/
 RUN mkdir /tmp/julia-pkg && \
     cp /tmp/Project.toml /tmp/Manifest.toml /tmp/julia-pkg/ && \
     julia -e'using Pkg; Pkg.activate("/tmp/julia-pkg/"); Pkg.instantiate(); Pkg.precompile()'
-
-# RENKU_VERSION determines the version of the renku CLI
-# that will be used in this image. To find the latest version,
-# visit https://pypi.org/project/renku/#history.
-ARG RENKU_VERSION={{ __renku_version__ | default("1.6.0") }}
-
-########################################################
-# Do not edit this section and do not add anything below
-
-# Install renku from pypi or from github if it's a dev version
-RUN if [ -n "$RENKU_VERSION" ] ; then \
-        source .renku/venv/bin/activate ; \
-        currentversion=$(renku --version) ; \
-        if [ "$RENKU_VERSION" != "$currentversion" ] ; then \
-            pip uninstall renku -y ; \
-            gitversion=$(echo "$RENKU_VERSION" | sed -n "s/^[[:digit:]]\+\.[[:digit:]]\+\.[[:digit:]]\+\(rc[[:digit:]]\+\)*\(\.dev[[:digit:]]\+\)*\(+g\([a-f0-9]\+\)\)*\(+dirty\)*$/\4/p") ; \
-            if [ -n "$gitversion" ] ; then \
-                pip install --force "git+https://github.com/SwissDataScienceCenter/renku-python.git@$gitversion" ;\
-            else \
-                pip install --force renku==${RENKU_VERSION} ;\
-            fi \
-        fi \
-    fi
-
-########################################################
diff --git a/minimal/Dockerfile b/minimal/Dockerfile
@@ -3,6 +3,31 @@
 ARG RENKU_BASE_IMAGE=renku/renkulab-py:3.9-0.13.1
 FROM ${RENKU_BASE_IMAGE}
 
+########################################################
+#        Renku install section - do not edit           #
+
+# RENKU_VERSION determines the version of the renku CLI
+# that will be used in this image. To find the latest version,
+# visit https://pypi.org/project/renku/#history.
+ARG RENKU_VERSION={{ __renku_version__ | default("2.0.0") }}
+
+# Install renku from pypi or from github if a dev version
+RUN if [ -n "$RENKU_VERSION" ] ; then \
+        source .renku/venv/bin/activate ; \
+        currentversion=$(renku --version) ; \
+        if [ "$RENKU_VERSION" != "$currentversion" ] ; then \
+            pip uninstall renku -y ; \
+            gitversion=$(echo "$RENKU_VERSION" | sed -n "s/^[[:digit:]]\+\.[[:digit:]]\+\.[[:digit:]]\+\(rc[[:digit:]]\+\)*\(\.dev[[:digit:]]\+\)*\(+g\([a-f0-9]\+\)\)*\(+dirty\)*$/\4/p") ; \
+            if [ -n "$gitversion" ] ; then \
+                pip install --force "git+https://github.com/SwissDataScienceCenter/renku-python.git@$gitversion" ;\
+            else \
+                pip install --force renku==${RENKU_VERSION} ;\
+            fi \
+        fi \
+    fi
+#             End renku install section                #
+########################################################
+
 # Uncomment and adapt if code is to be included in the image
 # COPY src /code/src
 
@@ -28,28 +53,3 @@ FROM ${RENKU_BASE_IMAGE}
 #    /opt/conda/bin/pip install -r /tmp/requirements.txt && \
 #    conda clean -y --all && \
 #    conda env export -n "root"
-
-# RENKU_VERSION determines the version of the renku CLI
-# that will be used in this image. To find the latest version,
-# visit https://pypi.org/project/renku/#history.
-ARG RENKU_VERSION={{ __renku_version__ | default("1.6.0") }}
-
-########################################################
-# Do not edit this section and do not add anything below
-
-# Install renku from pypi or from github if it's a dev version
-RUN if [ -n "$RENKU_VERSION" ] ; then \
-        source .renku/venv/bin/activate ; \
-        currentversion=$(renku --version) ; \
-        if [ "$RENKU_VERSION" != "$currentversion" ] ; then \
-            pip uninstall renku -y ; \
-            gitversion=$(echo "$RENKU_VERSION" | sed -n "s/^[[:digit:]]\+\.[[:digit:]]\+\.[[:digit:]]\+\(rc[[:digit:]]\+\)*\(\.dev[[:digit:]]\+\)*\(+g\([a-f0-9]\+\)\)*\(+dirty\)*$/\4/p") ; \
-            if [ -n "$gitversion" ] ; then \
-                pip install --force "git+https://github.com/SwissDataScienceCenter/renku-python.git@$gitversion" ;\
-            else \
-                pip install --force renku==${RENKU_VERSION} ;\
-            fi \
-        fi \
-    fi
-
-########################################################
diff --git a/python-minimal/Dockerfile b/python-minimal/Dockerfile
@@ -3,36 +3,16 @@
 ARG RENKU_BASE_IMAGE=renku/renkulab-py:3.9-0.13.1
 FROM ${RENKU_BASE_IMAGE}
 
-# Uncomment and adapt if code is to be included in the image
-# COPY src /code/src
 
-# Uncomment and adapt if your R or python packages require extra linux (ubuntu) software
-# e.g. the following installs apt-utils and vim; each pkg on its own line, all lines
-# except for the last end with backslash '\' to continue the RUN line
-#
-# USER root
-# RUN apt-get update && \
-#    apt-get install -y --no-install-recommends \
-#    apt-utils \
-#    vim
-# USER ${NB_USER}
-
-# install the python dependencies
-COPY requirements.txt environment.yml /tmp/
-RUN conda env update -q -f /tmp/environment.yml && \
-    /opt/conda/bin/pip install -r /tmp/requirements.txt && \
-    conda clean -y --all && \
-    conda env export -n "root"
+########################################################
+#        Renku install section - do not edit           #
 
 # RENKU_VERSION determines the version of the renku CLI
 # that will be used in this image. To find the latest version,
 # visit https://pypi.org/project/renku/#history.
-ARG RENKU_VERSION={{ __renku_version__ | default("1.6.0") }}
-
-########################################################
-# Do not edit this section and do not add anything below
+ARG RENKU_VERSION={{ __renku_version__ | default("2.0.0") }}
 
-# Install renku from pypi or from github if it's a dev version
+# Install renku from pypi or from github if a dev version
 RUN if [ -n "$RENKU_VERSION" ] ; then \
         source .renku/venv/bin/activate ; \
         currentversion=$(renku --version) ; \
@@ -46,5 +26,26 @@ RUN if [ -n "$RENKU_VERSION" ] ; then \
             fi \
         fi \
     fi
-
+#             End renku install section                #
 ########################################################
+
+# Uncomment and adapt if code is to be included in the image
+# COPY src /code/src
+
+# Uncomment and adapt if your R or python packages require extra linux (ubuntu) software
+# e.g. the following installs apt-utils and vim; each pkg on its own line, all lines
+# except for the last end with backslash '\' to continue the RUN line
+#
+# USER root
+# RUN apt-get update && \
+#    apt-get install -y --no-install-recommends \
+#    apt-utils \
+#    vim
+# USER ${NB_USER}
+
+# install the python dependencies
+COPY requirements.txt environment.yml /tmp/
+RUN mamba env update -q -f /tmp/environment.yml && \
+    /opt/conda/bin/pip install -r /tmp/requirements.txt && \
+    mamba clean -y --all && \
+    mamba env export -n "root"