add docker

docker/Dockerfile

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+########################################################################
+# Pynamical Dockerfile
+# License: MIT, see full license in LICENSE.txt
+# Web: https://github.com/gboeing/pynamical
+#
+# Build an image from the dockerfile:
+# >>> docker build -t gboeing/pynamical .
+#
+# Push the built image to hub so others can pull/run it:
+# >>> docker tag gboeing/pynamical gboeing/pynamical:v0.0.0
+# >>> docker login
+# >>> docker push gboeing/pynamical
+#
+# Run bash in this container and export final conda environment to a yml file:
+# >>> docker run --rm -it -u 0 --name pynamical -v %cd%:/home/jovyan/work gboeing/pynamical /bin/bash
+# >>> conda env export -n base > /home/jovyan/work/environment.yml
+#
+# Run jupyter lab in this container:
+# >>> docker run --rm -it --name pynamical -p 8888:8888 -v %cd%:/home/jovyan/work gboeing/pynamical
+#
+# Stop/delete all local docker containers/images:
+# >>> docker stop $(docker ps -aq)
+# >>> docker rm $(docker ps -aq)
+# >>> docker rmi $(docker images -q)
+########################################################################
+
+FROM jupyter/base-notebook
+LABEL maintainer="Geoff Boeing <g.boeing@northeastern.edu>"
+
+# symlink and permissions
+USER root
+RUN ln -s /opt/conda/bin/jupyter /usr/local/bin
+USER $NB_UID
+
+# configure conda and install packages in one RUN to keep image tidy
+RUN conda config --set show_channel_urls true && \
+    conda config --prepend channels conda-forge && \
+    conda update --override-channels -c conda-forge --yes -n base conda && \
+    conda update --override-channels -c conda-forge --yes --all && \
+    conda install --override-channels -c conda-forge --yes pynamical && \
+    conda clean --yes --all && \
+    conda info --all && \
+    conda list
+
+# launch notebook in the local working directory that we mount
+WORKDIR /home/jovyan/work
+
+# set default command to launch when container is run
+CMD ["jupyter", "lab", "--no-browser", "--NotebookApp.token=''", "--NotebookApp.password=''"]
+
+# to test, import pynamical and print its version
+RUN python -c "import pynamical; print(pynamical.__version__)"

docker/readme.md

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+# Pynamical Docker Image
+
+First, install [docker](https://www.docker.com/). 
+
+The pynamical docker container image and usage instructions are available on [docker hub](https://hub.docker.com/r/gboeing/pynamical).

docker/windows-env/create-windows-environment.bat

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+CALL conda update conda -n base --yes
+CALL conda deactivate
+CALL conda env remove -n pyn --yes
+CALL conda create -n pyn -c conda-forge --strict-channel-priority --file "../../requirements.txt" --file "../../requirements-dev.txt" --file "requirements-more.txt" --yes
+CALL conda activate pyn
+CALL python -m ipykernel install --user
+CALL conda clean --all --yes
+CALL conda env export > environment-windows.yml

docker/windows-env/environment-windows.yml

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+name: pyn
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - alabaster=0.7.12=py_0
+  - asn1crypto=0.24.0=py36_1003
+  - atomicwrites=1.3.0=py_0
+  - attrs=19.1.0=py_0
+  - babel=2.6.0=py_1
+  - backcall=0.1.0=py_0
+  - blas=1.1=openblas
+  - bleach=3.1.0=py_0
+  - bottleneck=1.2.1=py36h452e1ab_1001
+  - ca-certificates=2018.11.29=ha4d7672_0
+  - certifi=2018.11.29=py36_1000
+  - cffi=1.12.2=py36hfa6e2cd_0
+  - chardet=3.0.4=py36_1003
+  - colorama=0.4.1=py_0
+  - coverage=4.5.2=py36hfa6e2cd_1001
+  - coveralls=1.5.1=py_0
+  - cryptography=2.5=py36h74b6da3_1
+  - cycler=0.10.0=py_1
+  - cython=0.29.6=py36h6538335_0
+  - decorator=4.3.2=py_0
+  - defusedxml=0.5.0=py_1
+  - docopt=0.6.2=py_1
+  - docutils=0.14=py36_1001
+  - entrypoints=0.3=py36_1000
+  - freetype=2.9.1=h5db478b_1005
+  - icu=58.2=vc14_0
+  - idna=2.8=py36_1000
+  - imagesize=1.1.0=py_0
+  - ipykernel=5.1.0=py36h39e3cac_1002
+  - ipython=7.3.0=py36h39e3cac_0
+  - ipython_genutils=0.2.0=py_1
+  - jedi=0.13.3=py36_0
+  - jinja2=2.10=py_1
+  - jpeg=9c=hfa6e2cd_1001
+  - jsonschema=3.0.1=py36_0
+  - jupyter_client=5.2.4=py_3
+  - jupyter_core=4.4.0=py_0
+  - jupyterlab=0.35.4=py36_0
+  - jupyterlab_server=0.2.0=py_0
+  - kiwisolver=1.0.1=py36he980bc4_1002
+  - libflang=5.0.0=h6538335_20180525
+  - libpng=1.6.36=h7602738_1000
+  - libsodium=1.0.16=h2fa13f4_1001
+  - libtiff=4.0.10=h016b793_1002
+  - llvm-meta=5.0.0=0
+  - llvmlite=0.24.0=py36_1
+  - m2w64-gcc-libgfortran=5.3.0=6
+  - m2w64-gcc-libs=5.3.0=7
+  - m2w64-gcc-libs-core=5.3.0=7
+  - m2w64-gmp=6.1.0=2
+  - m2w64-libwinpthread-git=5.0.0.4634.697f757=2
+  - markupsafe=1.1.1=py36hfa6e2cd_0
+  - matplotlib=3.0.3=py36_0
+  - matplotlib-base=3.0.3=py36h3e3dc42_0
+  - mistune=0.8.4=py36hfa6e2cd_1000
+  - more-itertools=4.3.0=py36_1000
+  - msys2-conda-epoch=20160418=1
+  - nbconvert=5.4.1=py_2
+  - nbformat=4.4.0=py_1
+  - nodejs=11.10.0=0
+  - notebook=5.7.5=py36_0
+  - numba=0.39.0=py36h830ac7b_0
+  - numexpr=2.6.9=py36h6538335_1000
+  - numpy=1.16.2=py36_blas_openblash442142e_0
+  - olefile=0.46=py_0
+  - openblas=0.3.3=h535eed3_1001
+  - openmp=5.0.0=vc14_1
+  - openssl=1.0.2r=hfa6e2cd_0
+  - packaging=19.0=py_0
+  - pandas=0.24.1=py36h6538335_0
+  - pandoc=2.6=1
+  - pandocfilters=1.4.2=py_1
+  - parso=0.3.4=py_0
+  - pickleshare=0.7.5=py36_1000
+  - pillow=5.4.1=py36h9a613e6_1000
+  - pip=19.0.3=py36_0
+  - pluggy=0.9.0=py_0
+  - prometheus_client=0.6.0=py_0
+  - prompt_toolkit=2.0.9=py_0
+  - py=1.8.0=py_0
+  - pycparser=2.19=py_0
+  - pygments=2.3.1=py_0
+  - pynamical=0.2.1=py_0
+  - pyopenssl=19.0.0=py36_0
+  - pyparsing=2.3.1=py_0
+  - pyqt=5.6.0=py36h764d66f_1008
+  - pyrsistent=0.14.11=py36hfa6e2cd_0
+  - pysocks=1.6.8=py36_1002
+  - pytest=4.3.0=py36_0
+  - python=3.6.7=he025d50_1004
+  - python-dateutil=2.8.0=py_0
+  - pytz=2018.9=py_0
+  - pywinpty=0.5.5=py36_1000
+  - pyyaml=3.13=py36hfa6e2cd_1001
+  - pyzmq=18.0.1=py36he418aac_0
+  - qt=5.6.2=h2639256_8
+  - requests=2.21.0=py36_1000
+  - send2trash=1.5.0=py_0
+  - setuptools=40.8.0=py36_0
+  - sip=4.18.1=py36h6538335_1000
+  - six=1.12.0=py36_1000
+  - snowballstemmer=1.2.1=py_1
+  - sphinx=1.8.4=py36_0
+  - sphinxcontrib-websupport=1.1.0=py_1
+  - sqlite=3.26.0=hfa6e2cd_1000
+  - terminado=0.8.1=py36_1001
+  - testpath=0.4.2=py36_1000
+  - tk=8.6.9=hfa6e2cd_1000
+  - tornado=6.0.1=py36hfa6e2cd_0
+  - traitlets=4.3.2=py36_1000
+  - urllib3=1.24.1=py36_1000
+  - vc=14=0
+  - vs2015_runtime=14.0.25420=0
+  - wcwidth=0.1.7=py_1
+  - webencodings=0.5.1=py_1
+  - wheel=0.33.1=py36_0
+  - win_inet_pton=1.1.0=py36_0
+  - wincertstore=0.2=py36_1002
+  - winpty=0.4.3=4
+  - xz=5.2.4=h2fa13f4_1001
+  - yaml=0.1.7=hfa6e2cd_1001
+  - zeromq=4.2.5=he025d50_1006
+  - zlib=1.2.11=h2fa13f4_1004
+  - zstd=1.3.3=vc14_1
+prefix: C:\Anaconda\envs\pyn
+

docker/windows-env/requirements-more.txt

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+bottleneck
+cython
+jupyterlab
+nodejs
+numexpr
+pillow
+pip
+pynamical
+python == 3.*