update documentation and remove deprecated scripts (RosettaCommons#41)

* Update README.md
* add reference docker files
* add reference Docker files readme
* remove deprecated Conda setup and instructions
* remove PyRosetta deprecated build option and update readme

README.md

@@ -29,7 +29,15 @@ PyRosetta
 
 PyRosetta are Python bindings to the Rosetta library. These can be built from the Rosetta source code. 
 
-See <https://www.pyrosetta.org/> for more information about PyRosetta.
+See <https://www.pyrosetta.org> for more information about PyRosetta.
+
+Docker
+======
+
+Official Rosetta/PyRosetta images could be found at https://hub.docker.com/r/rosettacommons/rosetta. Both `serial` and `mpi` Rosetta builds provided as well as the number of PyRosetta builds including fully functional Jupyter setups with PyRosetta pre-installed and experimenta builds with `libtorch` and `tensorflow` integration. Please see https://hub.docker.com/r/rosettacommons/rosetta for more information.
+
+Various reference Docker files could be found in `rosetta/docker` dir.
+
 
 Developing Rosetta
 ==================

docker/README.md

@@ -0,0 +1,18 @@
+
+Rosetta/PyRosetta reference Docker recipes
+==========================================
+
+Collection of various recipes to serve as example for setting up Rosetta/PyRosetta build environment.
+Note that these recipes _does not actually clone/build Rosetta or PyRosetta_ and _only serve as examples_ to
+how-to setup build environments. When using this images you will need to mount already cloned Rosetta repository build commands:
+```
+# to build Rosetta
+cd rosetta/source && ./scons.py -j8 mode=release bin
+
+# to build PyRosetta
+cd rosetta/source/src/python/PyRosetta && python3 build.py -j8
+```
+
+* `alpine-3.9` absolutely minimal Rosetta build environment
+* `ubuntu-xx.xx` reference images for building Rosetta and PyRosetta
+* `ml` PyRosetta reference image to build PyRosetta with `libtorch` and `TensorFlow`  support

docker/rosetta-alpine-3.9.dockerfile

@@ -0,0 +1,18 @@
+# (c) Copyright Rosetta Commons Member Institutions.
+# (c) This file is part of the Rosetta software suite and is made available under license.
+# (c) The Rosetta software is developed by the contributing members of the Rosetta Commons.
+# (c) For more information, see http://www.rosettacommons.org. Questions about this can be
+# (c) addressed to University of Washington CoMotion, email: [email protected].
+
+## @author Sergey Lyskov
+
+FROM alpine:3.9
+
+RUN apk update
+RUN apk add mc python git bash build-base zlib-dev
+RUN apk add python3 cmake ninja
+RUN apk add libexecinfo-dev
+
+RUN apk add clang clang-dev
+
+ENTRYPOINT cd ~ && /bin/bash

docker/rosetta-ml.dockerfile

@@ -0,0 +1,47 @@
+# (c) Copyright Rosetta Commons Member Institutions.
+# (c) This file is part of the Rosetta software suite and is made available under license.
+# (c) The Rosetta software is developed by the contributing members of the Rosetta Commons.
+# (c) For more information, see http://www.rosettacommons.org. Questions about this can be
+# (c) addressed to University of Washington CoMotion, email: [email protected].
+
+## @author Sergey Lyskov
+
+
+FROM ubuntu:22.04
+
+# prevent any user interaction during install
+ENV DEBIAN_FRONTEND=noninteractive
+
+ENV LANG=C.UTF-8
+ENV LC_ALL=C.UTF-8
+
+RUN apt-get  -y update
+RUN apt-get -y install --no-install-recommends mc git curl wget unzip
+RUN apt-get -y install --no-install-recommends cmake ninja-build
+RUN apt-get -y install --no-install-recommends build-essential clang
+RUN apt-get -y install --no-install-recommends zlib1g-dev libssl-dev libbz2-dev libreadline-dev libsqlite3-dev liblzma-dev libffi-dev
+
+RUN apt-get -y install --no-install-recommends python3 python3-dev python3-numpy python3-setuptools python3-distutils python3-openssl python3-venv
+
+RUN apt-get -y install --no-install-recommends ca-certificates
+
+RUN apt-get -y install --no-install-recommends python-dev-is-python3
+
+
+# Download and extract TensorFlow
+RUN wget https://storage.googleapis.com/tensorflow/libtensorflow/libtensorflow-cpu-linux-x86_64-1.15.0.tar.gz
+RUN tar -xzf libtensorflow-cpu-linux-x86_64-1.15.0.tar.gz -C /usr/local && rm libtensorflow-cpu-linux-x86_64-1.15.0.tar.gz
+
+# Set environment variables for TensorFlow
+ENV LIBRARY_PATH=$LIBRARY_PATH:/usr/local/lib/
+ENV LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/lib/
+
+# Download and extract PyTorch
+RUN cd /root && wget https://download.pytorch.org/libtorch/cpu/libtorch-cxx11-abi-shared-with-deps-2.0.1%2Bcpu.zip -O libtorch.zip
+RUN cd /root && unzip libtorch.zip && rm libtorch.zip
+RUN cp -r /root/libtorch/* /usr/local && rm -rf /root/libtorch
+
+# setting up python
+RUN update-alternatives --install /usr/bin/python python /usr/bin/python3 1
+
+#RUN apt-get clean && rm -rf /var/lib/apt/lists/*

docker/rosetta-ubuntu-18.04.dockerfile

@@ -0,0 +1,32 @@
+# (c) Copyright Rosetta Commons Member Institutions.
+# (c) This file is part of the Rosetta software suite and is made available under license.
+# (c) The Rosetta software is developed by the contributing members of the Rosetta Commons.
+# (c) For more information, see http://www.rosettacommons.org. Questions about this can be
+# (c) addressed to University of Washington CoMotion, email: [email protected].
+
+## @author Sergey Lyskov
+
+FROM ubuntu:18.04
+
+
+# prevent any user interaction during install
+ENV DEBIAN_FRONTEND=noninteractive
+
+ENV LANG=C.UTF-8
+ENV LC_ALL=C.UTF-8
+
+RUN apt-get -y update
+RUN apt-get -y install --no-install-recommends mc git curl
+RUN apt-get -y install --no-install-recommends cmake ninja-build
+RUN apt-get -y install --no-install-recommends build-essential clang
+RUN apt-get -y install --no-install-recommends zlib1g-dev libssl-dev libbz2-dev libreadline-dev libsqlite3-dev liblzma-dev libffi-dev
+
+RUN apt-get -y install --no-install-recommends python2.7 python-dev
+RUN apt-get -y install --no-install-recommends python3 python3-dev python3-numpy python3-setuptools python3-distutils python3-openssl python3-venv
+
+RUN apt-get -y install --no-install-recommends clang-tidy
+RUN apt-get -y install --no-install-recommends ca-certificates
+
+RUN apt-get -y install --no-install-recommends
+
+#RUN apt-get clean && rm -rf /var/lib/apt/lists/*

docker/rosetta-ubuntu-20.04.dockerfile

@@ -0,0 +1,39 @@
+# (c) Copyright Rosetta Commons Member Institutions.
+# (c) This file is part of the Rosetta software suite and is made available under license.
+# (c) The Rosetta software is developed by the contributing members of the Rosetta Commons.
+# (c) For more information, see http://www.rosettacommons.org. Questions about this can be
+# (c) addressed to University of Washington CoMotion, email: [email protected].
+
+## @author Sergey Lyskov
+
+
+FROM ubuntu:20.04
+
+# prevent any user interaction during install
+ENV DEBIAN_FRONTEND=noninteractive
+
+ENV LANG=C.UTF-8
+ENV LC_ALL=C.UTF-8
+
+RUN apt-get -y update
+RUN apt-get -y install --no-install-recommends mc git curl
+RUN apt-get -y install --no-install-recommends cmake ninja-build
+RUN apt-get -y install --no-install-recommends build-essential clang
+RUN apt-get -y install --no-install-recommends zlib1g-dev libssl-dev libbz2-dev libreadline-dev libsqlite3-dev liblzma-dev libffi-dev
+
+RUN apt-get -y install --no-install-recommends python3 python3-dev python3-numpy python3-setuptools python3-distutils python3-openssl python3-venv
+
+RUN apt-get -y install --no-install-recommends clang-tidy
+RUN apt-get -y install --no-install-recommends ca-certificates
+
+RUN apt-get -y install --no-install-recommends python3-dev
+
+RUN apt-get -y install --no-install-recommends mpich mpi-default-dev
+
+# optional
+RUN apt-get -y install --no-install-recommends clang-format
+
+# setting up python
+RUN update-alternatives --install /usr/bin/python python /usr/bin/python3 1
+
+#RUN apt-get clean && rm -rf /var/lib/apt/lists/*

docker/rosetta-ubuntu-22.04.dockerfile

@@ -0,0 +1,42 @@
+# (c) Copyright Rosetta Commons Member Institutions.
+# (c) This file is part of the Rosetta software suite and is made available under license.
+# (c) The Rosetta software is developed by the contributing members of the Rosetta Commons.
+# (c) For more information, see http://www.rosettacommons.org. Questions about this can be
+# (c) addressed to University of Washington CoMotion, email: [email protected].
+
+## @author Sergey Lyskov
+
+
+FROM ubuntu:22.04
+
+# prevent any user interaction during install
+ENV DEBIAN_FRONTEND=noninteractive
+
+ENV LANG=C.UTF-8
+ENV LC_ALL=C.UTF-8
+
+RUN apt-get -y update
+RUN apt-get -y install --no-install-recommends mc git curl
+RUN apt-get -y install --no-install-recommends cmake ninja-build
+RUN apt-get -y install --no-install-recommends build-essential clang
+RUN apt-get -y install --no-install-recommends zlib1g-dev libssl-dev libbz2-dev libreadline-dev libsqlite3-dev liblzma-dev libffi-dev
+
+RUN apt-get -y install --no-install-recommends python3 python3-dev python3-numpy python3-setuptools python3-distutils python3-openssl python3-venv
+
+RUN apt-get -y install --no-install-recommends clang-tidy
+RUN apt-get -y install --no-install-recommends ca-certificates
+
+RUN apt-get -y install --no-install-recommends python-dev-is-python3
+
+RUN apt-get -y install --no-install-recommends mpich mpi-default-dev # mpi
+
+# optional
+RUN apt-get -y install --no-install-recommends clang-format
+
+# for Rosetta documentation build
+RUN apt-get -y install --no-install-recommends doxygen graphviz
+
+# setting up python
+RUN update-alternatives --install /usr/bin/python python /usr/bin/python3 1
+
+#RUN apt-get clean && rm -rf /var/lib/apt/lists/*