wip: remove physics dependencies; update packages

README.md

@@ -43,6 +43,9 @@ Environment in this image has all packages the same with only stable Kwant being
 
 
 ## Building and installing python codes
+
+**NOTE:** this functionality is being dropped - latest image that comes with it is tagged as `2018.5`.
+
 Code development process can be simplified by working in reproducible environments, like docker container.
 For this purpose I added a volume ``/src`` and convenient scripts (build and test) in ``/usr/local`` directory that can be executed through ``docker run command``.
 These scripts allow to easy build and install (in development mode) python source code into the ``base`` environment.

kwant/Dockerfile

-FROM rafalskolasinski/science:latest
+FROM rafalskolasinski/science:2018.5
 
 LABEL maintainer="Rafal Skolasinski <r.j.skolasinski@gmail.com>"
 

science/Dockerfile

@@ -9,35 +9,29 @@ RUN apt-get update && apt-get install --yes openssh-client
 
 # Add environment file
 RUN mkdir /environments
-COPY environment.yml build.conf /environments/
+COPY environment.yml /environments/
 
 # Create the main research environment
-RUN conda env update -n base -f /environments/environment.yml && \
-    pip install xyzpy==0.2.5 tqdm==4.28.1 && \
+RUN conda install --yes conda-forge::conda=4.7.5 && \
+    conda env update -n base -f /environments/environment.yml && \
+    pip install xyzpy==0.3.1 tqdm==4.32.2 && \
     conda clean -tipsy
 
 # Enable jupyter extension
 ARG NODE_OPTIONS=--max-old-space-size=4096
-RUN jupyter nbextension enable --py widgetsnbextension --sys-prefix && \
-    jupyter nbextension enable --py plotlywidget --sys-prefix && \
-    jupyter labextension install nbdime-jupyterlab && \
+RUN jupyter labextension install nbdime-jupyterlab && \
     jupyter labextension install @pyviz/jupyterlab_pyviz && \
     jupyter labextension install @jupyter-widgets/jupyterlab-manager@0.38 --no-build && \
-    jupyter labextension install plotlywidget@0.5.2  --no-build && \
-    jupyter labextension install jupyterlab-chart-editor@1.0 --no-build && \
-    jupyter labextension install @jupyterlab/plotly-extension@0.18.1  --no-build && \
-    jupyter lab build
+    jupyter labextension install plotlywidget@0.11.0  --no-build && \
+    jupyter labextension install @jupyterlab/plotly-extension@0.18.2  --no-build && \
+    jupyter labextension install jupyterlab-chart-editor@1.1 --no-build && \
+    jupyter lab build && \
+    jupyter nbextension enable --py widgetsnbextension --sys-prefix && \
+    jupyter nbextension enable --py plotlywidget --sys-prefix
 
 # Fix permissions (required when following the base image)
 RUN fix-permissions $HOME && \
     fix-permissions $CONDA_DIR
 
-# Add scripts and place for building source codes
-VOLUME /src
-
-ADD scripts/set.build.conf.sh /usr/local/bin/set.build.conf
-ADD scripts/build.sh /usr/local/bin/build
-ADD scripts/test.sh /usr/local/bin/test
-
 # Switch back to jovyan to avoid accidental container runs as root
 USER $NB_UID

science/build.conf

-[mumps]
-include_dirs = PREFIX/include
-library_dirs = PREFIX/lib
-libraries = zmumps mumps_common pord metis esmumps scotch scotcherr mpiseq gfortran openblas
-extra_link_args = -Wl,-rpath=PREFIX/lib

science/environment.yml

 name: science
 dependencies:
-  - conda-forge::python=3.6.6
+  - conda-forge::python=3.7.1
 
   # misc tools
-  - conda-forge::nbdime=1.0.2
+  - conda-forge::nbdime=1.0.6
 
   # main scientific packages
-  - conda-forge::scipy=1.1.0
-  - conda-forge::numpy=1.15.4
-
-  - conda-forge::kwant=1.3.3
-  - conda-forge::sympy=1.1.1
-  - conda-forge::adaptive=0.7.0
+  - conda-forge::scipy=1.3.0
+  - conda-forge::numpy=1.16.4
+  - conda-forge::adaptive=0.8.1
 
   # data analysis, visulation and serialisation
-  - conda-forge::matplotlib=3.0.2
-  - conda-forge::plotly=3.4.2
-  - conda-forge::holoviews=1.10.9
-  - conda-forge::xarray=0.11.0
-  - conda-forge::pandas=0.23.4
+  - conda-forge::matplotlib=3.1.1
+  - conda-forge::plotly=3.10.0
+  - conda-forge::holoviews=1.12.3
+  - conda-forge::xarray=0.12.2
+  - conda-forge::pandas=0.24.2
   - conda-forge::deepdish=0.3.4
 
-  # parallel computation
-  - conda-forge::ipyparallel=6.2.3
-  - conda-forge::hpc05=v1.30
-
-  # kwant build depenendencies (required for kwant environment)
-  - conda-forge::mumps=5.1.2
-  - conda-forge::lapack=3.6.1
-  - conda-forge::cython=0.29.1
-  - conda-forge::gcc=4.8.5
-
-  # libgfortran : make sure all dependencies are installed
-  - conda-forge::libgfortran=3.0.0
-  - conda-forge::libgfortran-ng=7.2.0
-
   # various packages that handle codes installed from sources
-  - conda-forge::pytest=4.0.1
-  - conda-forge::pytest-cov=2.6.0
+  - conda-forge::pytest=5.0.0
+  - conda-forge::pytest-cov=2.7.1
   - conda-forge::pytest-flakes=4.0.0
   - conda-forge::line_profiler=2.1.2
 
   # scikit packages
-  - conda-forge::scikit-learn=0.20.1
-  - conda-forge::scikit-image=0.14.1
+  - conda-forge::scikit-learn=0.21.2
+  - conda-forge::scikit-image=0.15.0
 
   # machine-learning packages
   - conda-forge::keras=2.2.4
-  - conda-forge::tensorflow=1.10.0
-
-  # semicon
-  - pip:
-    - git+https://gitlab.kwant-project.org/semicon/semicon.git@v0.2.0
+  - conda-forge::tensorflow=1.13.1

science/scripts/build.sh

-#!/bin/bash
-
-set -e
-
-cd /src
-source activate base
-
-python setup.py build $@
-pip install -e .

science/scripts/set.build.conf.sh

-#!/bin/bash
-
-source activate base
-
-cp /environments/build.conf /src
-sed -i -e "s:PREFIX:$CONDA_PREFIX:g" /src/build.conf

science/scripts/test.sh

-#!/bin/bash
-
-set -e
-
-cd /src
-source activate base
-
-py.test $@