Merge pull request #186 from Autodesk/simplify-build

Simplify and speed up build

.coveragerc

@@ -1,8 +1,6 @@
 [paths]
 source =
   moldesign
-  */site-packages/moldesign
-  */dist-packages/moldesign
 
 
 [run]

.gitignore

@@ -15,7 +15,7 @@ __pycache__
 .coverage
 .coverage.*
 codeship.aes
-tokens
+*-tokens
 moldesign/_static_data/components.ci*
 moldesign/_static_data/aa-variants-v1.ci*
 tmp

DockerMakefiles/DockerMake.yml

@@ -1,103 +1,21 @@
 _SOURCES_:
-  - CLI.yml
-  - Libraries.yml
   - Moldesign.yml
-  - NWChem.yml
-  - PySCF.yml
-  - PythonTools.yml
-  - SymMol.yml
+  - Environments.yml
 
 
 _ALL_:
-  - ambertools
-  - opsin
-  - symmol
-  - nwchem
   - moldesign_complete
   - moldesign_complete_py2
   - moldesign_minimal
   - moldesign_minimal_py2
   - moldesign_notebook
-  - nwchem_build
-  - openblas
-  - pyscf_build
 
 
 ##################################################
 # Base image definitions
 base:
   FROM: debian:jessie
 
-buildbase:
-  description: |
-    Well-outfitted image for building binaries. Rather than deploying this huge image,
-    binaries should be built here then copied into smaller deployment images
-  requires:
-    - base
-  build: |
-    RUN apt-get update
-    RUN apt-get install -y \
-          autoconf        \
-          automake        \
-          build-essential \
-          cmake           \
-          cmake-curses-gui\
-          csh             \
-          doxygen         \
-          gfortran        \
-          git             \
-          libatlas-dev    \
-          libblas-dev     \
-          libbz2-dev      \
-          libcr-dev       \
-          libfftw3-dev    \
-          libhdf5-dev     \
-          liblapack-dev   \
-          libnetcdf-dev   \
-          libopenmpi-dev  \
-          libpng12-dev    \
-          libpython-dev   \
-          libtool         \
-          mercurial       \
-          mpich2          \
-          mpich2-doc      \
-          patch           \
-          pkg-config      \
-          python          \
-          python-numpy    \
-          python-pip      \
-          python-scipy    \
-          python-tornado  \
-          python-yaml     \
-          python-zmq      \
-          subversion      \
-          swig            \
-          tcsh            \
-          vim             \
-          wget            \
-          zip
-    ENV TERM=dumb
-    RUN echo '#!/bin/bash' > /usr/local/bin/cleanapt \
-      && chmod +x /usr/local/bin/cleanapt
-
-
-deploybase:
-  description: lightweight image for deployment of CLI binaries
-  requires:
-    - base
-  build_directory: buildfiles/deploybase
-  build: |
-    ADD cleanapt /usr/local/bin
-    RUN chmod +x /usr/local/bin/cleanapt
-    RUN apt-get update \
-      && apt-get install -y --no-install-recommends \
-        ca-certificates \
-        git \
-        vim \
-        wget \
-      && cleanapt
-
-
 miniconda:
   FROM: continuumio/miniconda3:4.3.11
   build: |
@@ -109,21 +27,21 @@ miniconda_py2:
    RUN conda install -c anaconda zlib
 
 
-
 deploy_requirements:
   build_directory: buildfiles/deploybase
   build: |
     ADD cleanapt /usr/local/bin
     RUN chmod +x /usr/local/bin/cleanapt
     RUN conda install -qy numpy scipy pyyaml
 
-python_deploy_base_py2:
-  requires:
-     - miniconda_py2
-     - deploy_requirements
 
-python_deploy_base:
+python_deploy:
   requires:
     - miniconda
     - deploy_requirements
 
+
+python_deploy_py2:
+  requires:
+     - miniconda_py2
+     - deploy_requirements

DockerMakefiles/Environments.yml

@@ -0,0 +1,54 @@
+# This file defines environments for MDT to be installed in
+
+_SOURCES_:
+ - PySCF.yml
+
+notebook:
+ requires:
+  - python_deploy
+ build_directory: buildfiles/notebook/
+ build: |
+    RUN conda install -yq matplotlib jupyter ipywidgets nbformat
+    ENTRYPOINT /run_notebook.sh
+    EXPOSE 8888
+    RUN mkdir /notebooks
+    WORKDIR /notebooks
+    COPY run_notebook.sh /run_notebook.sh
+
+
+complete_env_base:
+ requires:
+  - deploy_requirements
+  - pyscf_mixin
+ description: All of the external python chemistry libraries in one place
+ build: |
+   RUN apt-get update \
+    && apt-get install -y libpng12-dev \
+    && cleanapt
+   RUN conda install -qy -c openbabel openbabel=2.4.1 \
+    && conda install -qy -c omnia \
+           biopython=1.68 \
+           openmm=7.1.1 \
+           parmed=2.7.3 \
+           pdbfixer=1.4 \
+    && conda install -qy -c bioconda opsin
+
+
+
+
+complete_env:
+ requires:
+  - python_deploy
+  - complete_env_base
+
+
+complete_env_py2:
+ requires:
+  - python_deploy_py2
+  - complete_env_base
+
+
+complete_notebook_env:
+ requires:
+  - notebook
+  - complete_env_base