From 1c93f0ffddc93e582eb56c24355fe1171db53da5 Mon Sep 17 00:00:00 2001
From: Bansal Utkarsh <bansalutkarsh3@gmail.com>
Date: Fri, 16 Jun 2017 18:45:15 +0530
Subject: [PATCH 01/15] Add basic cache config

---
 .travis.yml | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/.travis.yml b/.travis.yml
index 66a56880381..049b2c6f0cc 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -9,6 +9,11 @@ branches:
 os:
   - linux
 
+cache:
+   pip: true
+   directories:
+       - $HOME/miniconda
+
 env:
   global:
     - secure: "f8EMSWeYC38elhpB4B/ddxlklEvQoycaxnt90Xw2tH/+ThdP1qteQ2vdgNFy1KL7Am/xnbrRhavI5K+ayfxJ93NoE2adaJ9f9aljXK+Oeu+buv5MVo2E2HhN9mX9opSSxiqGmnHIVYcdLP+1soIsDD78SGL7hB/u5nQ1aTzkbaM="

From 1d53dc3ca9a559eba691c5faec7280ae9ce829c7 Mon Sep 17 00:00:00 2001
From: Bansal Utkarsh <bansalutkarsh3@gmail.com>
Date: Fri, 16 Jun 2017 19:01:05 +0530
Subject: [PATCH 02/15] Drop miniconda cache

---
 .travis.yml | 2 --
 1 file changed, 2 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 049b2c6f0cc..c47a4c938a7 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -11,8 +11,6 @@ os:
 
 cache:
    pip: true
-   directories:
-       - $HOME/miniconda
 
 env:
   global:

From 590a4d098be3f2a078175b59190dd2d51fd2bcd2 Mon Sep 17 00:00:00 2001
From: Bansal Utkarsh <bansalutkarsh3@gmail.com>
Date: Fri, 16 Jun 2017 19:13:48 +0530
Subject: [PATCH 03/15] Install dependencies via pip

---
 .travis.yml | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index c47a4c938a7..8d6def89547 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -31,7 +31,7 @@ env:
     - CONDA_DEPENDENCIES="mmtf-python nose=1.3.7 mock six biopython networkx cython joblib nose-timer"
     - CONDA_ALL_DEPENDENCIES="mmtf-python nose=1.3.7 mock six biopython networkx cython joblib nose-timer matplotlib netcdf4 scikit-learn scipy seaborn coveralls clustalw=2.1"
     # Install griddataformats from PIP so that scipy is only installed in the full build (#1147)
-    - PIP_DEPENDENCIES='griddataformats'
+    - PIP_DEPENDENCIES='griddataformats mmtf-python nose=1.3.7 mock six biopython networkx cython joblib nose-timer'
     - CONDA_CHANNELS='biobuilds conda-forge'
     - CONDA_CHANNEL_PRIORITY=True
     - NUMPY_VERSION=stable
@@ -82,8 +82,9 @@ matrix:
 
 install:
   - git clone git://github.com/astropy/ci-helpers.git
-  - source ci-helpers/travis/setup_conda_$TRAVIS_OS_NAME.sh
+  # - source ci-helpers/travis/setup_conda_$TRAVIS_OS_NAME.sh
   # additional external tools (Issue #898) -- HOLE
+  - pip install $PIP_DEPENDENCIES
   - |
     if [[ $NAME == 'full' ]]; then \
         bash ./maintainer/install_hole.sh $TRAVIS_OS_NAME "${HOME}/${MDA_OPTPACKAGES}"; \

From ebfdc198247048d2e8c98d410547a5abd171f222 Mon Sep 17 00:00:00 2001
From: Bansal Utkarsh <bansalutkarsh3@gmail.com>
Date: Fri, 16 Jun 2017 19:17:13 +0530
Subject: [PATCH 04/15] Fix pip dependencies

---
 .travis.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index 8d6def89547..005a122410c 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -31,7 +31,7 @@ env:
     - CONDA_DEPENDENCIES="mmtf-python nose=1.3.7 mock six biopython networkx cython joblib nose-timer"
     - CONDA_ALL_DEPENDENCIES="mmtf-python nose=1.3.7 mock six biopython networkx cython joblib nose-timer matplotlib netcdf4 scikit-learn scipy seaborn coveralls clustalw=2.1"
     # Install griddataformats from PIP so that scipy is only installed in the full build (#1147)
-    - PIP_DEPENDENCIES='griddataformats mmtf-python nose=1.3.7 mock six biopython networkx cython joblib nose-timer'
+    - PIP_DEPENDENCIES='griddataformats mmtf-python nose==1.3.7 mock six biopython networkx cython joblib nose-timer'
     - CONDA_CHANNELS='biobuilds conda-forge'
     - CONDA_CHANNEL_PRIORITY=True
     - NUMPY_VERSION=stable

From d819894d5bffd07716721c9234f26f698e1ff681 Mon Sep 17 00:00:00 2001
From: Bansal Utkarsh <bansalutkarsh3@gmail.com>
Date: Fri, 16 Jun 2017 19:21:17 +0530
Subject: [PATCH 05/15] Setup virtual env

---
 .travis.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.travis.yml b/.travis.yml
index 005a122410c..6a1b6f28ecf 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -84,6 +84,8 @@ install:
   - git clone git://github.com/astropy/ci-helpers.git
   # - source ci-helpers/travis/setup_conda_$TRAVIS_OS_NAME.sh
   # additional external tools (Issue #898) -- HOLE
+  - virtualenv venv --system-site-packages
+  - source venv/bin/activate
   - pip install $PIP_DEPENDENCIES
   - |
     if [[ $NAME == 'full' ]]; then \

From d72d9843095387404307b8a6172a523e95b4e1e7 Mon Sep 17 00:00:00 2001
From: Bansal Utkarsh <bansalutkarsh3@gmail.com>
Date: Fri, 16 Jun 2017 19:23:59 +0530
Subject: [PATCH 06/15] Install virtualenv

---
 .travis.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.travis.yml b/.travis.yml
index 6a1b6f28ecf..494ee03b02d 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -80,6 +80,9 @@ matrix:
            CONDA_DEPENDENCIES=${CONDA_ALL_DEPENDENCIES}
            EVENT_TYPE='cron'
 
+before_install:
+    - sudo apt-get update python-virtualenv
+
 install:
   - git clone git://github.com/astropy/ci-helpers.git
   # - source ci-helpers/travis/setup_conda_$TRAVIS_OS_NAME.sh

From 3b54af057f07580398803ec0f7a8cd55a007a248 Mon Sep 17 00:00:00 2001
From: Bansal Utkarsh <bansalutkarsh3@gmail.com>
Date: Fri, 16 Jun 2017 19:25:55 +0530
Subject: [PATCH 07/15] Fix virtualenv install command

---
 .travis.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index 494ee03b02d..3fe60a33985 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -81,7 +81,7 @@ matrix:
            EVENT_TYPE='cron'
 
 before_install:
-    - sudo apt-get update python-virtualenv
+    - sudo apt-get install python-virtualenv
 
 install:
   - git clone git://github.com/astropy/ci-helpers.git

From 8bd2c25551896da593b8275f308106cfb19e4451 Mon Sep 17 00:00:00 2001
From: Bansal Utkarsh <bansalutkarsh3@gmail.com>
Date: Fri, 16 Jun 2017 19:35:05 +0530
Subject: [PATCH 08/15] Drop virtualenv, install dependencies using sudo

---
 .travis.yml | 6 +-----
 1 file changed, 1 insertion(+), 5 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 3fe60a33985..f65186b711b 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -80,16 +80,12 @@ matrix:
            CONDA_DEPENDENCIES=${CONDA_ALL_DEPENDENCIES}
            EVENT_TYPE='cron'
 
-before_install:
-    - sudo apt-get install python-virtualenv
 
 install:
   - git clone git://github.com/astropy/ci-helpers.git
   # - source ci-helpers/travis/setup_conda_$TRAVIS_OS_NAME.sh
   # additional external tools (Issue #898) -- HOLE
-  - virtualenv venv --system-site-packages
-  - source venv/bin/activate
-  - pip install $PIP_DEPENDENCIES
+  - sudo pip install $PIP_DEPENDENCIES
   - |
     if [[ $NAME == 'full' ]]; then \
         bash ./maintainer/install_hole.sh $TRAVIS_OS_NAME "${HOME}/${MDA_OPTPACKAGES}"; \

From e6b46c12c6934a2261b360f56c9bdab60f19402e Mon Sep 17 00:00:00 2001
From: Bansal Utkarsh <bansalutkarsh3@gmail.com>
Date: Fri, 16 Jun 2017 19:49:49 +0530
Subject: [PATCH 09/15] Ubuntu 14.04 might fix ssl problems

---
 .travis.yml | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/.travis.yml b/.travis.yml
index f65186b711b..3da7ff73b39 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -40,6 +40,8 @@ matrix:
   fast_finish: true
   include:
     - os : linux
+      dist: trusty
+      sudo: required
       env: NAME='minimal'
            PYTHON_VERSION=2.7
            SETUP_CMD='--with-memleak'
@@ -60,6 +62,8 @@ matrix:
            PIP_DEPENDENCIES=""
 
     - os: linux
+      dist: trusty
+      sudo: required
       env: NAME='full'
            SETUP_CMD='--with-coverage --cover-package MDAnalysis'
            CONDA_DEPENDENCIES=${CONDA_ALL_DEPENDENCIES}
@@ -85,6 +89,7 @@ install:
   - git clone git://github.com/astropy/ci-helpers.git
   # - source ci-helpers/travis/setup_conda_$TRAVIS_OS_NAME.sh
   # additional external tools (Issue #898) -- HOLE
+  - sudo pip install --upgrade-pip
   - sudo pip install $PIP_DEPENDENCIES
   - |
     if [[ $NAME == 'full' ]]; then \

From e4fdb2fe6035407e61b4e59dc9943ecbd9a693b4 Mon Sep 17 00:00:00 2001
From: Bansal Utkarsh <bansalutkarsh3@gmail.com>
Date: Fri, 16 Jun 2017 19:53:02 +0530
Subject: [PATCH 10/15] Fix upgrade pip command

---
 .travis.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index 3da7ff73b39..ade231c9f44 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -89,7 +89,7 @@ install:
   - git clone git://github.com/astropy/ci-helpers.git
   # - source ci-helpers/travis/setup_conda_$TRAVIS_OS_NAME.sh
   # additional external tools (Issue #898) -- HOLE
-  - sudo pip install --upgrade-pip
+  - sudo pip install --upgrade pip
   - sudo pip install $PIP_DEPENDENCIES
   - |
     if [[ $NAME == 'full' ]]; then \

From b5043d32963fa4e9f23697f640dd4c47f3ad1081 Mon Sep 17 00:00:00 2001
From: Bansal Utkarsh <bansalutkarsh3@gmail.com>
Date: Fri, 16 Jun 2017 19:59:38 +0530
Subject: [PATCH 11/15] Install lib-ssl

---
 .travis.yml | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index ade231c9f44..3682e271f0d 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -40,8 +40,6 @@ matrix:
   fast_finish: true
   include:
     - os : linux
-      dist: trusty
-      sudo: required
       env: NAME='minimal'
            PYTHON_VERSION=2.7
            SETUP_CMD='--with-memleak'
@@ -62,8 +60,6 @@ matrix:
            PIP_DEPENDENCIES=""
 
     - os: linux
-      dist: trusty
-      sudo: required
       env: NAME='full'
            SETUP_CMD='--with-coverage --cover-package MDAnalysis'
            CONDA_DEPENDENCIES=${CONDA_ALL_DEPENDENCIES}
@@ -86,6 +82,7 @@ matrix:
 
 
 install:
+  - sudo apt-get install libssl1.0.0
   - git clone git://github.com/astropy/ci-helpers.git
   # - source ci-helpers/travis/setup_conda_$TRAVIS_OS_NAME.sh
   # additional external tools (Issue #898) -- HOLE

From 7caeb99392c6570e7ad84ada442717eac63ec8fd Mon Sep 17 00:00:00 2001
From: Bansal Utkarsh <bansalutkarsh3@gmail.com>
Date: Sat, 17 Jun 2017 11:57:17 +0530
Subject: [PATCH 12/15] Undo all changes and use fork of ci-helpers

---
 .travis.yml | 15 ++++-----------
 1 file changed, 4 insertions(+), 11 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 3682e271f0d..476a65c781e 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -9,9 +9,6 @@ branches:
 os:
   - linux
 
-cache:
-   pip: true
-
 env:
   global:
     - secure: "f8EMSWeYC38elhpB4B/ddxlklEvQoycaxnt90Xw2tH/+ThdP1qteQ2vdgNFy1KL7Am/xnbrRhavI5K+ayfxJ93NoE2adaJ9f9aljXK+Oeu+buv5MVo2E2HhN9mX9opSSxiqGmnHIVYcdLP+1soIsDD78SGL7hB/u5nQ1aTzkbaM="
@@ -31,7 +28,7 @@ env:
     - CONDA_DEPENDENCIES="mmtf-python nose=1.3.7 mock six biopython networkx cython joblib nose-timer"
     - CONDA_ALL_DEPENDENCIES="mmtf-python nose=1.3.7 mock six biopython networkx cython joblib nose-timer matplotlib netcdf4 scikit-learn scipy seaborn coveralls clustalw=2.1"
     # Install griddataformats from PIP so that scipy is only installed in the full build (#1147)
-    - PIP_DEPENDENCIES='griddataformats mmtf-python nose==1.3.7 mock six biopython networkx cython joblib nose-timer'
+    - PIP_DEPENDENCIES='griddataformats'
     - CONDA_CHANNELS='biobuilds conda-forge'
     - CONDA_CHANNEL_PRIORITY=True
     - NUMPY_VERSION=stable
@@ -80,14 +77,10 @@ matrix:
            CONDA_DEPENDENCIES=${CONDA_ALL_DEPENDENCIES}
            EVENT_TYPE='cron'
 
-
 install:
-  - sudo apt-get install libssl1.0.0
-  - git clone git://github.com/astropy/ci-helpers.git
-  # - source ci-helpers/travis/setup_conda_$TRAVIS_OS_NAME.sh
+  - git clone git://github.com/utkbansal/ci-helpers
+  - source ci-helpers/travis/setup_conda_$TRAVIS_OS_NAME.sh
   # additional external tools (Issue #898) -- HOLE
-  - sudo pip install --upgrade pip
-  - sudo pip install $PIP_DEPENDENCIES
   - |
     if [[ $NAME == 'full' ]]; then \
         bash ./maintainer/install_hole.sh $TRAVIS_OS_NAME "${HOME}/${MDA_OPTPACKAGES}"; \
@@ -107,4 +100,4 @@ after_success:
   # can't use test here since this leads to travis fails even though the build passes
   - if [[ ${TRAVIS_PULL_REQUEST} == "false" ]] && [[ ${BUILD_DOCS} == "true" ]] && [[ ${TRAVIS_BRANCH} == ${GH_DOC_BRANCH} ]]; then
             bash ${TRAVIS_BUILD_DIR}/maintainer/deploy_docs.sh;
-    fi
+    fi
\ No newline at end of file

From d7b5c198e46eb873c7fc84a4416b045628e30309 Mon Sep 17 00:00:00 2001
From: Bansal Utkarsh <bansalutkarsh3@gmail.com>
Date: Sat, 17 Jun 2017 12:00:19 +0530
Subject: [PATCH 13/15] Add cache config

---
 .travis.yml | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/.travis.yml b/.travis.yml
index 476a65c781e..b3bf778132e 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -9,6 +9,11 @@ branches:
 os:
   - linux
 
+cache:
+   pip: true
+   directories:
+       - $HOME/miniconda
+
 env:
   global:
     - secure: "f8EMSWeYC38elhpB4B/ddxlklEvQoycaxnt90Xw2tH/+ThdP1qteQ2vdgNFy1KL7Am/xnbrRhavI5K+ayfxJ93NoE2adaJ9f9aljXK+Oeu+buv5MVo2E2HhN9mX9opSSxiqGmnHIVYcdLP+1soIsDD78SGL7hB/u5nQ1aTzkbaM="

From 74eb29690636a9ddc5d7379793564729a036cc13 Mon Sep 17 00:00:00 2001
From: Bansal Utkarsh <bansalutkarsh3@gmail.com>
Date: Sat, 17 Jun 2017 12:12:07 +0530
Subject: [PATCH 14/15] Use 'caching' branch of ci-helpers

---
 .travis.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.travis.yml b/.travis.yml
index b3bf778132e..9243f4f7b67 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -84,6 +84,7 @@ matrix:
 
 install:
   - git clone git://github.com/utkbansal/ci-helpers
+  - cd ci-helpers && git checkout caching && cd ..
   - source ci-helpers/travis/setup_conda_$TRAVIS_OS_NAME.sh
   # additional external tools (Issue #898) -- HOLE
   - |

From 3f4c53f10f184dacde7be4048efcbeaeccfe3c0e Mon Sep 17 00:00:00 2001
From: Bansal Utkarsh <bansalutkarsh3@gmail.com>
Date: Sat, 17 Jun 2017 12:15:21 +0530
Subject: [PATCH 15/15] Build on private Travis

---
 .travis.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.travis.yml b/.travis.yml
index 9243f4f7b67..e4b179b4450 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -5,6 +5,7 @@ branches:
   only:
     - master
     - develop
+    - travis-cache
 
 os:
   - linux