Commit 9dcd63b1 authored by Markus Scheidgen's avatar Markus Scheidgen
Browse files

Merge branch '42-parsers' into 'v0.8.1'

Adds the missing parsers

See merge request !117
parents 6677d66e 158402ee
Pipeline #76116 passed with stages
in 18 minutes and 38 seconds
......@@ -5,6 +5,7 @@
**/*.pyc
**/NOMAD.egg-info
.*env/
.pyenv*/
.pytest_cache
.vscode/
.volumes/
......
.DS_Store
.*env/
.pyenv*/
.pytest/
.python-version
.ipynb_checkpoints/
......
......@@ -96,7 +96,7 @@ tests:
install_tests:
stage: test
image: python:3.6
image: python:3.7
before_script:
- git submodule sync
- git submodule update --init --jobs=4
......
......@@ -155,3 +155,39 @@
[submodule "dependencies/parsers/eels"]
path = dependencies/parsers/eels
url = https://github.com/markus1978/eels.git
[submodule "dependencies/parsers/namd"]
path = dependencies/parsers/namd
url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-namd.git
[submodule "dependencies/parsers/charmm"]
path = dependencies/parsers/charmm
url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-charmm.git
[submodule "dependencies/parsers/dftbplus"]
path = dependencies/parsers/dftbplus
url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-dftb-plus.git
[submodule "dependencies/parsers/asap"]
path = dependencies/parsers/asap
url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-asap.git
[submodule "dependencies/parsers/fplo"]
path = dependencies/parsers/fplo
url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-fplo.git
[submodule "dependencies/parsers/mopac"]
path = dependencies/parsers/mopac
url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-mopac.git
[submodule "dependencies/parsers/amber"]
path = dependencies/parsers/amber
url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-amber.git
[submodule "dependencies/parsers/gromacs"]
path = dependencies/parsers/gromacs
url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-gromacs.git
[submodule "dependencies/parsers/gromos"]
path = dependencies/parsers/gromos
url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-gromos.git
[submodule "dependencies/parsers/lammps"]
path = dependencies/parsers/lammps
url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-lammps.git
[submodule "dependencies/parsers/openkim"]
path = dependencies/parsers/openkim
url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-openkim.git
[submodule "dependencies/parsers/tinker"]
path = dependencies/parsers/tinker
url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-tinker.git
......@@ -19,8 +19,10 @@
# The dockerfile is multistaged to use a fat, more convinient build image and
# copy only necessities to a slim final image
# We use slim for the final image
FROM python:3.6-slim as final
# 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
# First built the GUI in a gui build image
FROM node:latest as gui_build
......@@ -32,11 +34,15 @@ 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 python:3.6-stretch as build
RUN mkdir /install
FROM final
RUN mkdir /app
# Install linux package dependencies
RUN apt-get update
RUN apt-get install -y --no-install-recommends libgomp1
RUN apt-get install -y libmagic-dev curl vim make cmake swig libnetcdf-dev
# Install some specific dependencies necessary for the build process
RUN pip install --upgrade pip
......@@ -54,55 +60,33 @@ RUN pip install scikit-learn==0.20.2
RUN pip install ase==3.19.0
RUN pip install Pint
RUN pip install matid
RUN pip install mdtraj==1.9.1
RUN pip install mdanalysis==0.16.2
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/
RUN python3 setup.py install
RUN rm -rf /pymolfile
# Copy files and install nomad@FAIRDI
WORKDIR /install
COPY . /install
WORKDIR /app
COPY . /app
RUN python setup.py compile
RUN pip install .[all]
RUN python setup.py sdist
WORKDIR /install/docs
# COPY --from=gui_build /app/react-docgen.out /install/docs
RUN make html
RUN \
find /usr/local/lib/python3.6/ -name 'tests' ! -path '*/networkx/*' -exec rm -r '{}' + && \
find /usr/local/lib/python3.6/ -name 'test' -exec rm -r '{}' + && \
find /usr/local/lib/python3.6/site-packages/ -name '*.so' -print -exec sh -c 'file "{}" | grep -q "not stripped" && strip -s "{}"' \;
# 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
WORKDIR /app/docs
RUN make html
# copy the sources for tests, coverage, qa, etc.
COPY . /app
# Remove unnessesary files
WORKDIR /app
# transfer installed packages from dependency stage
COPY --from=build /usr/local/lib/python3.6/site-packages /usr/local/lib/python3.6/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 \
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
RUN mkdir -p /app/.volumes/fs
RUN useradd -ms /bin/bash nomad
RUN chown -R nomad /app
......
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