wip

Dockerfile.backup

+ARG BUILDER_BASE_IMAGE=jupyter/tensorflow-notebook:2ce7c06a61a1
+FROM $BUILDER_BASE_IMAGE
+
+
+# ================================================================================
+# Linux applications and libraries
+# ================================================================================
+
+USER root
+
+ENV DEBIAN_FRONTEND noninteractive
+
+RUN apt update --yes \
+ && apt install --yes --quiet --no-install-recommends \
+    build-essential \
+   #  g++-10 \
+   #  gcc-10 \
+    cmake \
+    git \
+   #  libblas-dev \
+   #  liblapack-dev \
+    lsof \
+    libgsl-dev \
+ && apt clean \
+ && rm -rf /var/lib/apt/lists/*
+
+#  RUN update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-10 100 --slave /usr/bin/g++ g++ /usr/bin/g++-10 --slave /usr/bin/gcov gcov /usr/bin/gcov-10
+#  RUN update-alternatives --install /usr/bin/cpp cpp /usr/bin/cpp-10 100
+
+# ================================================================================
+#  QMMLPACK
+# ================================================================================
+
+
+WORKDIR /opt/qmmlpack
+COPY dependencies/qmmlpack .
+
+USER root
+ENV PYTHONPATH /opt/qmmlpack/python:$PYTHONPATH
+
+# Workaround: for the test TMPDIR has to be defined
+ENV TMPDIR "/tmp/"
+
+# Workaround: the build precess fails witout pytest installed
+USER ${NB_UID}
+RUN pip install --no-cache-dir \
+   pytest \
+ && fix-permissions "${CONDA_DIR}" \
+ && fix-permissions "/home/${NB_USER}"
+USER root
+
+RUN ./make --debug --verbose cpp --include-path /usr/include/gsl/ --library-path /usr/lib/
+
+RUN ./make --debug --verbose python --include-path /usr/include/gsl/ --library-path /usr/lib/
+
+RUN chown -R $NB_USER:$NB_GID $PWD
+USER $NB_USER
+
+#RUN make -v install
+#
+# # The CML_PLUGINS environment variable tells cmlkit to register the cscribe plugin, which provides the dscribe interface.
+# ENV CML_PLUGINS "cscribe"
+# ENV CML_DATASET_PATH $HOME/tutorials/data/cmlkit/
+
+# # ================================================================================
+# #  CMLKIT
+# # ================================================================================
+#
+# WORKDIR /opt/cmlkit
+#
+# COPY dependencies/cmlkit ./cmlkit
+# USER root
+# RUN pip install ./cmlkit
+
+# ================================================================================
+# Python environment
+# ================================================================================
+
+USER ${NB_UID}
+
+# RUN mamba install --yes \
+#         'numpy' \
+#         'pandas' \
+#         'hdbscan' \
+#         'scikit-learn' \
+#         'plotly' \
+#         'bokeh' \
+#         'matplotlib' \
+#         'ipywidgets' \
+#  && mamba clean --all -f -y \
+#  && fix-permissions "${CONDA_DIR}" \
+#  && fix-permissions "/home/${NB_USER}"
+
+
+# RUN pip install --no-cache-dir --index-url https://gitlab.mpcdf.mpg.de/api/v4/projects/2187/packages/pypi/simple \
+#         'nomad-lab' \
+#         'numpy' \
+#         'pandas' \
+#         'hdbscan' \
+#         'scikit-learn' \
+#         'plotly' \
+#         'bokeh' \
+#         'matplotlib' \
+#         'ipywidgets' \
+#         'jupyter_jsmol==2021.3.0' \
+#  && fix-permissions "${CONDA_DIR}" \
+#  && fix-permissions "/home/${NB_USER}"
+
+# # Install from the requirements.txt file
+# COPY --chown=${NB_UID}:${NB_GID} requirements.in /tmp/
+# RUN pip install --no-cache-dir --requirement /tmp/requirements.in \
+#  && fix-permissions "${CONDA_DIR}" \
+#  && fix-permissions "/home/${NB_USER}"
+
+# ================================================================================
+# Switch back to jovyan to avoid accidental container runs as root
+# ================================================================================
+
+USER ${NB_UID}
+WORKDIR ${HOME}
+
+COPY --chown=${NB_UID}:${NB_GID} data/ data/
+COPY --chown=${NB_UID}:${NB_GID} assets/ assets/
+COPY --chown=${NB_UID}:${NB_GID} krr4mat.ipynb .

requirements.in

 # pip-compile requirements.in -o requirements.txt
-tensorflow==1.13.1
-keras==2.2.4
-git+https://github.com/raghakot/keras-vis.git
-numpy==1.21.6
-scipy==1.2.3
-h5py==2.9.0
-matplotlib
-scikit-image==0.15.0
-protobuf~=3.20.0
-# pandas
-# scikit-image
-# scikit-learn
-
-# tensorflow-cpu==1.15.0
-# keras
-# keras-vis
-# numpy==1.21.6
-# scipy==1.2.3
-# matplotlib
-# scikit-image==0.15.0
-# protobuf~=3.20.0
-# Succesfull test of this tutorial was conducted for:
-# 'tensorflow==1.13.1', 'keras==2.2.4', 'numpy==1.16.4', 'scipy==1.1.0', 'matplotlib', 'pandas', 'seaborn', 'pymatgen==2020.3.13', 'sklearn'
+cscribe
+seaborn
\ No newline at end of file

setup.py

-import json
-from setuptools import setup, find_packages
-
-with open('metainfo.json') as file:
-    metainfo = json.load(file)
-
-setup(
-    name='krr4mat',
-    version='0.1',
-    author=', '.join(metainfo['authors']),
-    author_email=metainfo['email'],
-    url=metainfo['url'],
-    description=metainfo['title'],
-    long_description=metainfo['description'],
-    packages=find_packages(),
-    install_requires=['seaborn', 'cscribe'],
-)