Use doc-building CI scripts from msmbuilder

.travis.yml

@@ -5,6 +5,7 @@ addons:
     sources:
     - ubuntu-toolchain-r-test
     packages:
+      # Why are these needed?
       - g++
       - gfortran
       - valgrind
@@ -13,29 +14,32 @@ addons:
       - gcc-multilib
 
 install:
-  - source devtools/travis-ci/install.sh
-  - export PYTHONUNBUFFERED=true
-  - export CC=gcc
-  - export CXX=g++
+  - source devtools/travis-ci/install_miniconda.sh
+  - source devtools/travis-ci/install_sparta.sh
+  - source devtools/travis-ci/install_ppm.sh
+  # Why is colli_r needed?
+  - conda config --add channels omnia colli_r
 
 script:
-  - conda config --add channels omnia
-  - conda update -qy conda-build
-  - conda build -q devtools/conda-recipe
+  conda build --quiet devtools/conda-recipe
+  && devtools/travis-ci/build_docs.sh
 
 env:
   matrix:
-    - CONDA_PY=27  CONDA_NPY=17
-    - CONDA_PY=27  CONDA_NPY=19
-    - CONDA_PY=34  CONDA_NPY=19
-    - CONDA_PY=35  CONDA_NPY=1.10
+    - CONDA_PY=2.7  CONDA_NPY=1.7
+    - CONDA_PY=2.7  CONDA_NPY=1.10
+    - CONDA_PY=3.4  CONDA_NPY=1.9
+    - CONDA_PY=3.5  CONDA_NPY=1.10
 
-  global:
-    # encrypted AWS_ACCESS_KEY_ID and AWS_SECRET_ACCESS_KEY to push documentation to S3
-    - secure: "qrbibHwlbXBTq+8h1DC1plyUcl67qwn5yr4UYILdk9WsBhPdNT0ObpRUOcFDW/YM9RDfcOvx7Ruq/OPhvlVCg1C+Lj01kSx3vHxYCxFJVyN7iiD9oI/xzFUc6guvYF9O8um2+QE1ZI70yffGJGT7MZUQNUBnKchqvV3uIeSOqw4="
-    - secure: "Y4deQNbKXm0dTth0VoR59wEPYr0dNmp4Np+GDnJofwL+HKQ/w3dTrM3PQOV3bZ2w7WV2gAdtOv8MMUjdFYyyB+GS1wIZa4XbXchGNJr/lljvT3OP579ZwSLAowjEFFR6hidFDfMcR4D7KzTnoCIe9odXrZplI6l0M4OL1agki84="
-    # encrypted ANACONDA_TOKEN for push of dev package to binstar
-    - secure: "Fk6rmrCd4fnzkowd//FD9lI0bR3oNy1G2WjSke/1UiLtdZyCegiP0y0qcU5EIfEOoNk3NudM44RmPTHjqUMC7oS3tFI7SUBVUAyW34WOtTlOEaEBAzTDwfWhl6PLZNiXmZd75knjCyL6xJif4VwNT02VuMoR3ZchWG27ALpThwM="
-
-after_success:
-  - source devtools/travis-ci/after_sucess.sh
+deploy:
+  - provider: s3
+    access_key_id:
+      secure: "ZJrGD3DMlnokMNL2IAro43fdILptst27+UNH1tcma5NFSXGYRpUYAk+uFdjtj5WR2bi0g81UFmsGd421SfDzJe9WY+zcNlBTNlushi0+8KOTXBVr38n8z03mUMz2wnGTYmOg5z0kBHQ+xBVuX9Hz9FM9CVbWZczCWpTTiem35W4="
+    secret_access_key:
+      secure: "lEpUy2/GD2PnpBcv1KV2qt5mzRPbe4hPJwqlCuYDYvLFLMTrl+v5d+R8IyZ1KMX5eRBTPdP2i2sVbyRH/rwCaeRl6btYcsLWmpydfovPP7KyL3dlSWxtquOZCi0wfjlK7H5RwZHUb0870XhdPrAPT04plbiqVHzlSqBhfVTbHB0="
+    bucket: "mdtraj.org"
+    skip_cleanup: true
+    local_dir: docs/_deploy/
+    on:
+      branch: master
+      condition: "$CONDA_PY = 3.5"

devtools/travis-ci/build_docs.sh

@@ -0,0 +1,27 @@
+#!/bin/bash
+
+# Print each line, exit on error
+set -ev
+
+# Install the built package
+conda create --yes -n docenv python=$CONDA_PY
+source activate docenv
+conda install -yq --use-local mdtraj-dev
+
+# TODO: Use conda
+# sphinx_rtd_theme's latest releases are not available
+# neither is msmb_theme
+# neither is sphinx > 1.3.1 (fix #1892 autodoc problem)
+pip install -I sphinx==1.3.5 sphinx_rtd_theme==0.1.9 msmb_theme==1.2.0
+
+# Install doc requirements
+conda install --yes --file doc/requirements.txt
+
+# Make docs
+cd docs && make html && cd -
+
+# Move the docs into a versioned subdirectory
+python devtools/ci/set_doc_version.py
+
+# Prepare versions.json
+python devtools/ci/update_versions_json.py

devtools/travis-ci/install_miniconda.sh

@@ -0,0 +1,15 @@
+#!/bin/bash
+MINICONDA=Miniconda3-latest-Linux-x86_64.sh
+MINICONDA_MD5=$(curl -s http://repo.continuum.io/miniconda/ | grep -A3 $MINICONDA | sed -n '4p' | sed -n 's/ *<td>\(.*\)<\/td> */\1/p')
+wget http://repo.continuum.io/miniconda/$MINICONDA
+if [[ $MINICONDA_MD5 != $(md5sum $MINICONDA | cut -d ' ' -f 1) ]]; then
+    echo "Miniconda MD5 mismatch"
+    exit 1
+fi
+bash $MINICONDA -b
+rm -f $MINICONDA
+
+export PATH=$HOME/miniconda3/bin:$PATH
+
+conda update -yq conda
+conda install --yq conda-build jinja2

devtools/travis-ci/install_ppm.sh

@@ -0,0 +1,18 @@
+#!/bin/bash
+
+# Install ppm for NMR chemical shift predicition
+MDTRAJ_DIR=`pwd`
+mkdir -p $HOME/external
+cd $HOME/external
+wget http://mdtraj.org/travis-ci-cache/ppm_linux_64.exe
+chmod a+x ppm_linux_64.exe
+REFERENCE_MD5="f3cb5681bd2769cdcfc77fe17c563ee4"
+RECEIVED_MD5=$(md5sum ppm_linux_64.exe | cut -d " " -f 1)
+if [ $REFERENCE_MD5 != $RECEIVED_MD5 ]; then
+    echo "ppm_linux_64.exe md5 mismatch"
+    exit 1
+fi
+
+export PATH=`pwd`:$PATH
+# go back to the original directory we were in
+cd $MDTRAJ_DIR

devtools/travis-ci/install_sparta.sh

@@ -0,0 +1,23 @@
+#!/bin/bash
+
+# Install SPARTA+ for NMR chemical shift predicition
+MDTRAJ_DIR=`pwd`
+mkdir -p $HOME/external
+cd $HOME/external
+wget http://mdtraj.org/travis-ci-cache/sparta+.tar.Z
+REFERENCE_MD5="d4293336254f5696221db0edcc57cfed"
+RECEIVED_MD5=$(md5sum sparta+.tar.Z | cut -d " " -f 1)
+if [ $REFERENCE_MD5 != $RECEIVED_MD5 ]; then
+    echo "sparta+.tar.Z md5 mismatch"
+    exit 1
+fi
+
+tar -xzf sparta+.tar.Z
+cd SPARTA+
+csh ./install.com
+export SPARTAP_DIR=`pwd`
+export SPARTA_DIR=`pwd`
+export PATH=`pwd`/bin:$PATH
+# go back to the original directory we were in
+cd $MDTRAJ_DIR
+

devtools/travis-ci/set_doc_version.py

@@ -0,0 +1,12 @@
+import os
+import shutil
+from mdtraj import version
+
+if version.release:
+    docversion = version.short_version
+else:
+    docversion = 'development'
+
+os.mkdir("doc/_deploy")
+shutil.copytree("doc/_build/html", "doc/_deploy/{docversion}"
+                .format(docversion=docversion))

devtools/travis-ci/update_versions_json.py

@@ -0,0 +1,23 @@
+import json
+from urllib.request import urlopen
+from mdtraj import version
+
+if not version.release:
+    print("This is not a release.")
+    exit(0)
+
+URL = 'http://www.msmbuilder.org'
+versions = json.load(urlopen(URL + '/versions.json'))
+
+# new release so all the others are now old
+for i in range(len(versions)):
+    versions[i]['latest'] = False
+
+versions.append({
+    'version': version.short_version,
+    'url': "{base}/{version}".format(base=URL, version=version.short_version),
+    'latest': True})
+
+with open("doc/_deploy/versions.json", 'w') as versionf:
+    json.dump(versions, versionf)
+