Merge branch 'bugfixes' into 'v0.8.1'

Bugfixes

See merge request !120

Dockerfile

@@ -19,10 +19,8 @@
 # The dockerfile is multistaged to use a fat, more convinient build image and
 # copy only necessities to a slim final image
 
-# We use stretch instead of slim to allow compoilation of some dependencies. We
-# do not bother to have an additional copy to a final slim image, because the space
-# savings are minimal
-FROM python:3.7-stretch as final
+# We use slim for the final image
+FROM python:3.7-slim as final
 
 # First built the GUI in a gui build image
 FROM node:latest as gui_build
@@ -34,10 +32,11 @@ COPY gui/yarn.lock /app/yarn.lock
 RUN yarn
 COPY gui /app
 RUN yarn run build
+# RUN yarn run --silent react-docgen src/components --pretty > react-docgen.out
 
 # Second, build all python stuff in a python build image
-FROM final
-RUN mkdir /app
+FROM python:3.7-stretch as build
+RUN mkdir /install
 
 # Install linux package dependencies
 RUN apt-get update
@@ -63,6 +62,10 @@ RUN pip install matid
 RUN pip install mdtraj
 RUN pip install mdanalysis
 
+# Make will be necessary to build the docs with sphynx
+RUN apt-get update && apt-get install -y make
+RUN apt-get update && apt-get install -y vim
+
 # Install pymolfile (required by some parsers)
 RUN git clone -b nomad-fair https://gitlab.mpcdf.mpg.de/nomad-lab/pymolfile.git
 WORKDIR /pymolfile/
@@ -70,24 +73,48 @@ RUN python3 setup.py install
 RUN rm -rf /pymolfile
 
 # Copy files and install nomad@FAIRDI
-WORKDIR /app
-COPY . /app
+WORKDIR /install
+COPY . /install
 RUN python setup.py compile
 RUN pip install .[all]
 RUN python setup.py sdist
 RUN cp dist/nomad-lab-*.tar.gz dist/nomad-lab.tar.gz
-
-WORKDIR /app/docs
+WORKDIR /install/docs
+# COPY --from=gui_build /app/react-docgen.out /install/docs
 RUN make html
-
-# Remove unnessesary files
-WORKDIR /app
 RUN \
     find /usr/local/lib/python3.7/ -name 'tests' ! -path '*/networkx/*' -exec rm -r '{}' + && \
     find /usr/local/lib/python3.7/ -name 'test' -exec rm -r '{}' + && \
     find /usr/local/lib/python3.7/site-packages/ -name '*.so' -print -exec sh -c 'file "{}" | grep -q "not stripped" && strip -s "{}"' \;
 
-# Setup directories, users, rights
+# Third, create a slim final image
+FROM final
+
+RUN apt-get update && apt-get install -y --no-install-recommends libgomp1 && apt-get install -y libmagic-dev curl
+
+# copy the sources for tests, coverage, qa, etc.
+COPY . /app
+WORKDIR /app
+# transfer installed packages from dependency stage
+COPY --from=build /usr/local/lib/python3.7/site-packages /usr/local/lib/python3.7/site-packages
+RUN echo "copy 1"
+# copy the meta-info, since it files are loaded via relative paths. TODO that should change.
+COPY --from=build /install/dependencies/nomad-meta-info /app/dependencies/nomad-meta-info
+RUN echo "copy 2"
+# copy the documentation, its files will be served by the API
+COPY --from=build /install/docs/.build /app/docs/.build
+RUN echo "copy 3"
+# copy the source distribution, its files will be served by the API
+COPY --from=build /install/dist /app/dist
+RUN echo "copy 4"
+# copy the nomad command
+COPY --from=build /usr/local/bin/nomad /usr/bin/nomad
+RUN echo "copy 5"
+# copy the gui
+RUN mkdir -p /app/gui
+COPY --from=gui_build /app/build /app/gui/build
+RUN echo "copy 6"
+
 RUN mkdir -p /app/.volumes/fs
 RUN useradd -ms /bin/bash nomad
 RUN chown -R nomad /app

gui/src/searchQuantities.json

@@ -212,7 +212,7 @@
       "cubic",
       "hexagonal",
       "monoclinic",
-      "orthorombic",
+      "orthorhombic",
       "tetragonal",
       "triclinic",
       "trigonal",