From fd1fe529b4521f742c73cf16e02d604cabaa0630 Mon Sep 17 00:00:00 2001
From: Wolfgang Kerzendorf <wkerzendorf@gmail.com>
Date: Thu, 23 Aug 2018 14:46:33 +0200
Subject: [PATCH 01/17] add caching

---
 .travis.yml                     | 24 ++++++++----------------
 ci-helpers/install_miniconda.sh | 11 +++++++++++
 2 files changed, 19 insertions(+), 16 deletions(-)
 create mode 100644 ci-helpers/install_miniconda.sh

diff --git a/.travis.yml b/.travis.yml
index 02c7e281865..2509fe6969d 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -10,6 +10,13 @@ virtualenv:
 
 cache:
   apt: true
+  directories:
+    - $HOME/miniconda
+addons:
+  apt:
+    packages:
+    - clang
+    - gdb
 
 sudo: true
 
@@ -52,24 +59,9 @@ matrix:
         - python: 2.7
           env: SETUP_CMD='test'
 
-addons:
-  apt:
-    packages:
-    - clang
-    - gdb
-
-
-
-
 before_install:
     # We do this to make sure we get the dependencies so pip works below
-    - export PYTHONIOENCODING=UTF8
-    - wget $MINICONDA_URL -O miniconda.sh
-    - chmod +x miniconda.sh
-    - bash miniconda.sh -b -p $HOME/miniconda
-    - export PATH=$HOME/miniconda/bin:$PATH
-    - hash -r
-    - conda update --yes conda
+    - source ci-helpers/install_miniconda.sh
     - if [[ $TEST_MODE == 'spectrum' ]]; then conda install -c conda-forge git-lfs=2.2.1 -y; fi
     - if [[ $TEST_MODE == 'spectrum' ]]; then git lfs install --skip-smudge; fi
     - if [[ $TEST_MODE == 'spectrum' ]]; then git clone $TARDIS_REF_DATA_URL $HOME/tardis-refdata; fi
diff --git a/ci-helpers/install_miniconda.sh b/ci-helpers/install_miniconda.sh
new file mode 100644
index 00000000000..e0f7b7d57cb
--- /dev/null
+++ b/ci-helpers/install_miniconda.sh
@@ -0,0 +1,11 @@
+export PYTHONIOENCODING=UTF8
+if test -e $HOME/miniconda/bin; then
+     echo "miniconda already installed.";
+else
+    wget $MINICONDA_URL -O miniconda.sh
+    chmod +x miniconda.sh
+    bash miniconda.sh -b -p $HOME/miniconda
+    export PATH=$HOME/miniconda/bin:$PATH
+    hash -r
+    conda update --yes conda
+fi
\ No newline at end of file

From 5c1a8a0a3eeef4a44cf2fdf9527c615210e86ead Mon Sep 17 00:00:00 2001
From: Wolfgang Kerzendorf <wkerzendorf@gmail.com>
Date: Thu, 23 Aug 2018 14:52:02 +0200
Subject: [PATCH 02/17] remove cached miniconda

---
 ci-helpers/install_miniconda.sh | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/ci-helpers/install_miniconda.sh b/ci-helpers/install_miniconda.sh
index e0f7b7d57cb..ccc7275308f 100644
--- a/ci-helpers/install_miniconda.sh
+++ b/ci-helpers/install_miniconda.sh
@@ -1,11 +1,17 @@
 export PYTHONIOENCODING=UTF8
 if test -e $HOME/miniconda/bin; then
-     echo "miniconda already installed.";
+    echo "miniconda already installed.";
+    export PATH=$HOME/miniconda/bin:$PATH
+    hash -r
+    #conda update --yes conda
+
 else
     wget $MINICONDA_URL -O miniconda.sh
     chmod +x miniconda.sh
+    rm -r $HOME/miniconda
     bash miniconda.sh -b -p $HOME/miniconda
+
     export PATH=$HOME/miniconda/bin:$PATH
     hash -r
     conda update --yes conda
-fi
\ No newline at end of file
+fi

From ef04184f271b8c92476fad04508d749b8fb7e18c Mon Sep 17 00:00:00 2001
From: Wolfgang Kerzendorf <wkerzendorf@gmail.com>
Date: Thu, 23 Aug 2018 14:58:01 +0200
Subject: [PATCH 03/17] swap coveralls for codecov

---
 tardis_env27.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tardis_env27.yml b/tardis_env27.yml
index 5a6b337f99d..314bf1b122f 100644
--- a/tardis_env27.yml
+++ b/tardis_env27.yml
@@ -34,12 +34,12 @@ dependencies:
 - requests=2.9.1
 - docopt=0.6.2
 - pytest-cov=2.2.1
+- codecov
 
 - pip:
   - sphinx_bootstrap_theme
   - sphinxcontrib-bibtex
   - sphinxcontrib-tikz
-  - coveralls
   - pytest-html==1.10.0
   - dokuwiki
   - dot2tex

From 2f319b1dd3a42acd60db072496642ca54b2a47da Mon Sep 17 00:00:00 2001
From: Wolfgang Kerzendorf <wkerzendorf@gmail.com>
Date: Thu, 23 Aug 2018 14:58:25 +0200
Subject: [PATCH 04/17] adding new ci helper

---
 ci-helpers/install_tardis_env.sh | 3 +++
 1 file changed, 3 insertions(+)
 create mode 100644 ci-helpers/install_tardis_env.sh

diff --git a/ci-helpers/install_tardis_env.sh b/ci-helpers/install_tardis_env.sh
new file mode 100644
index 00000000000..de347ff7bbe
--- /dev/null
+++ b/ci-helpers/install_tardis_env.sh
@@ -0,0 +1,3 @@
+export PYTHONIOENCODING=UTF8
+if test -e $HOME/miniconda/envs/tardis; then
+    echo "TARDIS env already installed.";

From 076bfbe6d00476594edad6055d0a4672371415bc Mon Sep 17 00:00:00 2001
From: Wolfgang Kerzendorf <wkerzendorf@gmail.com>
Date: Thu, 23 Aug 2018 15:00:15 +0200
Subject: [PATCH 05/17] caching tardis env

---
 .travis.yml                      | 5 +----
 ci-helpers/install_tardis_env.sh | 7 ++++++-
 2 files changed, 7 insertions(+), 5 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 2509fe6969d..d865ccd1be2 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -80,10 +80,7 @@ before_install:
 
 
 install:
-   - cd $TRAVIS_BUILD_DIR
-   - conda env create -f tardis_env27.yml
-   - source activate tardis
-   - conda install -y -c conda-forge codecov
+   - source ci-helpers/install_tardis_env.sh
    #trouble with building due to segfault at cython (https://github.com/cython/cython/issues/2199)
    #remove if we can get normal cython through conda
    - git clone https://github.com/cython/cython
diff --git a/ci-helpers/install_tardis_env.sh b/ci-helpers/install_tardis_env.sh
index de347ff7bbe..f32e170792c 100644
--- a/ci-helpers/install_tardis_env.sh
+++ b/ci-helpers/install_tardis_env.sh
@@ -1,3 +1,8 @@
-export PYTHONIOENCODING=UTF8
+cd $TRAVIS_BUILD_DIR
 if test -e $HOME/miniconda/envs/tardis; then
     echo "TARDIS env already installed.";
+else
+   conda env create -f tardis_env27.yml
+fi
+
+source activate tardis
\ No newline at end of file

From d70a8933256f6c9f10b62c1610cea0897b3d4f99 Mon Sep 17 00:00:00 2001
From: Wolfgang Kerzendorf <wkerzendorf@gmail.com>
Date: Thu, 23 Aug 2018 15:35:32 +0200
Subject: [PATCH 06/17] add refdata to caching

---
 .travis.yml                        | 34 ++++++++++--------------------
 ci-helpers/fetch_reference_data.sh | 16 ++++++++++++++
 tardis_env27.yml                   |  3 ++-
 3 files changed, 29 insertions(+), 24 deletions(-)
 create mode 100644 ci-helpers/fetch_reference_data.sh

diff --git a/.travis.yml b/.travis.yml
index d865ccd1be2..5136b0b014e 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -8,10 +8,6 @@ python:
 virtualenv:
   system_site_packages: true
 
-cache:
-  apt: true
-  directories:
-    - $HOME/miniconda
 addons:
   apt:
     packages:
@@ -27,23 +23,24 @@ env:
         - ASTROPY_USE_SYSTEM_PYTEST=1
         - SETUP_CMD='test'
         - TEST_MODE='normal'
-        - TARDIS_REF_DATA_URL='https://github.com/tardis-sn/tardis-refdata.git'
+        - REF_DATA_HOME=$HOME/tardis-refdata
         - MINICONDA_URL='http://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh'
         - SAVE_COVERAGE=false
+        - GIT_LFS_SKIP_SMUDGE=1
 
 matrix:
     include:
         - python: 2.7
           env:
             - COMPILER=gcc
-            - SETUP_CMD='test --coverage --args="--tardis-refdata=$HOME/tardis-refdata/"'
+            - SETUP_CMD='test --coverage --args="--tardis-refdata=$REF_DATA_HOME"'
             - TEST_MODE='spectrum'
             - SAVE_COVERAGE=true
 
         - python: 2.7
           env:
             - COMPILER=clang
-            - SETUP_CMD='test --args="--tardis-refdata=$HOME/tardis-refdata/"'
+            - SETUP_CMD='test --args="--tardis-refdata=$REF_DATA_HOME"'
             - TEST_MODE='spectrum'
 
 #trouble with osx building due to segfault at cython (https://github.com/cython/cython/issues/2199)
@@ -51,32 +48,23 @@ matrix:
           language: generic
           env:
             - COMPILER=clang
-            - SETUP_CMD='test --args="--tardis-refdata=$HOME/tardis-refdata/"'
+            - SETUP_CMD='test --args="--tardis-refdata=$REF_DATA_HOME"'
             - TEST_MODE='spectrum'
             - MINICONDA_URL='http://repo.continuum.io/miniconda/Miniconda2-latest-MacOSX-x86_64.sh'
 
 
         - python: 2.7
           env: SETUP_CMD='test'
+cache:
+  apt: true
+  directories:
+    - $HOME/miniconda
+    - $REF_DATA_HOME
+
 
 before_install:
     # We do this to make sure we get the dependencies so pip works below
     - source ci-helpers/install_miniconda.sh
-    - if [[ $TEST_MODE == 'spectrum' ]]; then conda install -c conda-forge git-lfs=2.2.1 -y; fi
-    - if [[ $TEST_MODE == 'spectrum' ]]; then git lfs install --skip-smudge; fi
-    - if [[ $TEST_MODE == 'spectrum' ]]; then git clone $TARDIS_REF_DATA_URL $HOME/tardis-refdata; fi
-    - if [[ $TEST_MODE == 'spectrum' ]]; then cd $HOME/tardis-refdata; fi
-    # Use the following to get the ref-data from the master; 
-    - if [[ $TEST_MODE == 'spectrum' ]]; then git fetch origin; fi
-    - if [[ $TEST_MODE == 'spectrum' ]]; then git checkout origin/master; fi
-    # Use the following to get the ref-data from a specific pull request; 
-    # - if [[ $TEST_MODE == 'spectrum' ]]; then git fetch origin pull/11/head:thomson-ref; fi
-    # - if [[ $TEST_MODE == 'spectrum' ]]; then git checkout thomson-ref; fi
-    - if [[ $TEST_MODE == 'spectrum' ]]; then git lfs pull --include="atom_data/kurucz_cd23_chianti_H_He.h5" origin; fi
-    - if [[ $TEST_MODE == 'spectrum' ]]; then git lfs pull --include="atom_data/chianti_He.h5" origin; fi
-    - if [[ $TEST_MODE == 'spectrum' ]]; then git lfs pull --include="plasma_reference/" origin; fi
-    - if [[ $TEST_MODE == 'spectrum' ]]; then git lfs pull --include="unit_test_data.h5" origin; fi
-    - if [[ $TEST_MODE == 'spectrum' ]]; then cd $TRAVIS_BUILD_DIR; fi
 
 
 install:
diff --git a/ci-helpers/fetch_reference_data.sh b/ci-helpers/fetch_reference_data.sh
new file mode 100644
index 00000000000..41cf39d09a7
--- /dev/null
+++ b/ci-helpers/fetch_reference_data.sh
@@ -0,0 +1,16 @@
+git lfs install
+
+if test -e $REF_DATA_HOME; then
+    git clone https://github.com/tardis-sn/tardis-refdata.git $REF_DATA_HOME
+else
+    cd $REF_DATA_HOME
+    # Use the following to get the ref-data from the master;
+    git fetch origin
+    checkout origin/master
+    # Use the following to get the ref-data from a specific pull request
+    #git fetch origin pull/11/head:thomson-ref
+    git lfs pull --include="atom_data/kurucz_cd23_chianti_H_He.h5" origin
+    git lfs pull --include="atom_data/chianti_He.h5" origin
+    git lfs pull --include="plasma_reference/" origin
+    git lfs pull --include="unit_test_data.h5" origin
+    cd $TRAVIS_BUILD_DIR
diff --git a/tardis_env27.yml b/tardis_env27.yml
index 314bf1b122f..de11427d97e 100644
--- a/tardis_env27.yml
+++ b/tardis_env27.yml
@@ -35,7 +35,8 @@ dependencies:
 - docopt=0.6.2
 - pytest-cov=2.2.1
 - codecov
-
+#testing requirements
+- git-lfs=2.4
 - pip:
   - sphinx_bootstrap_theme
   - sphinxcontrib-bibtex

From aed3f80ceed5d935ee145da6bd08c6b5925df61e Mon Sep 17 00:00:00 2001
From: Wolfgang Kerzendorf <wkerzendorf@gmail.com>
Date: Thu, 23 Aug 2018 15:38:42 +0200
Subject: [PATCH 07/17] fetch reference data

---
 .travis.yml                        | 1 +
 ci-helpers/fetch_reference_data.sh | 1 -
 2 files changed, 1 insertion(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index 5136b0b014e..a382b360c09 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -65,6 +65,7 @@ cache:
 before_install:
     # We do this to make sure we get the dependencies so pip works below
     - source ci-helpers/install_miniconda.sh
+    - source ci-helpers/fetch_reference_data.sh
 
 
 install:
diff --git a/ci-helpers/fetch_reference_data.sh b/ci-helpers/fetch_reference_data.sh
index 41cf39d09a7..d2ccafd4815 100644
--- a/ci-helpers/fetch_reference_data.sh
+++ b/ci-helpers/fetch_reference_data.sh
@@ -1,5 +1,4 @@
 git lfs install
-
 if test -e $REF_DATA_HOME; then
     git clone https://github.com/tardis-sn/tardis-refdata.git $REF_DATA_HOME
 else

From ebd95a2ffb9d9e75ca6692dc28c87d881b394ce9 Mon Sep 17 00:00:00 2001
From: Wolfgang Kerzendorf <wkerzendorf@gmail.com>
Date: Thu, 23 Aug 2018 15:41:59 +0200
Subject: [PATCH 08/17] ref data avail

---
 ci-helpers/fetch_reference_data.sh | 25 +++++++++++++------------
 1 file changed, 13 insertions(+), 12 deletions(-)

diff --git a/ci-helpers/fetch_reference_data.sh b/ci-helpers/fetch_reference_data.sh
index d2ccafd4815..4090d7ffe23 100644
--- a/ci-helpers/fetch_reference_data.sh
+++ b/ci-helpers/fetch_reference_data.sh
@@ -1,15 +1,16 @@
 git lfs install
 if test -e $REF_DATA_HOME; then
-    git clone https://github.com/tardis-sn/tardis-refdata.git $REF_DATA_HOME
+    echo "Ref data available"
 else
-    cd $REF_DATA_HOME
-    # Use the following to get the ref-data from the master;
-    git fetch origin
-    checkout origin/master
-    # Use the following to get the ref-data from a specific pull request
-    #git fetch origin pull/11/head:thomson-ref
-    git lfs pull --include="atom_data/kurucz_cd23_chianti_H_He.h5" origin
-    git lfs pull --include="atom_data/chianti_He.h5" origin
-    git lfs pull --include="plasma_reference/" origin
-    git lfs pull --include="unit_test_data.h5" origin
-    cd $TRAVIS_BUILD_DIR
+    git clone https://github.com/tardis-sn/tardis-refdata.git $REF_DATA_HOME
+cd $REF_DATA_HOME
+# Use the following to get the ref-data from the master;
+git fetch origin
+git checkout origin/master
+# Use the following to get the ref-data from a specific pull request
+#git fetch origin pull/11/head:thomson-ref
+git lfs pull --include="atom_data/kurucz_cd23_chianti_H_He.h5" origin
+git lfs pull --include="atom_data/chianti_He.h5" origin
+git lfs pull --include="plasma_reference/" origin
+git lfs pull --include="unit_test_data.h5" origin
+cd $TRAVIS_BUILD_DIR

From 0e6cf07e3c5a45b0d6b87e129c6ecaaefebfb2e2 Mon Sep 17 00:00:00 2001
From: Wolfgang Kerzendorf <wkerzendorf@gmail.com>
Date: Thu, 23 Aug 2018 15:58:42 +0200
Subject: [PATCH 09/17] remove the fetch reference data caching - to be done in
 next PR

---
 .travis.yml                        | 20 ++++++++++++++++++--
 ci-helpers/fetch_reference_data.sh |  8 ++++----
 2 files changed, 22 insertions(+), 6 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index a382b360c09..0c8d8cda8ad 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -59,13 +59,29 @@ cache:
   apt: true
   directories:
     - $HOME/miniconda
-    - $REF_DATA_HOME
+    #- $REF_DATA_HOME
 
 
 before_install:
     # We do this to make sure we get the dependencies so pip works below
     - source ci-helpers/install_miniconda.sh
-    - source ci-helpers/fetch_reference_data.sh
+    - if [[ $TEST_MODE == 'spectrum' ]]; then conda install -c conda-forge git-lfs=2.2.1 -y; fi
+    - if [[ $TEST_MODE == 'spectrum' ]]; then git lfs install --skip-smudge; fi
+    - if [[ $TEST_MODE == 'spectrum' ]]; then git clone $TARDIS_REF_DATA_URL $HOME/tardis-refdata; fi
+    - if [[ $TEST_MODE == 'spectrum' ]]; then cd $HOME/tardis-refdata; fi
+# Use the following to get the ref-data from the master;
+    - if [[ $TEST_MODE == 'spectrum' ]]; then git fetch origin; fi
+    - if [[ $TEST_MODE == 'spectrum' ]]; then git checkout origin/master; fi
+# Use the following to get the ref-data from a specific pull request;
+# - if [[ $TEST_MODE == 'spectrum' ]]; then git fetch origin pull/11/head:thomson-ref; fi
+# - if [[ $TEST_MODE == 'spectrum' ]]; then git checkout thomson-ref; fi
+    - if [[ $TEST_MODE == 'spectrum' ]]; then git lfs pull --include="atom_data/kurucz_cd23_chianti_H_He.h5" origin; fi
+    - if [[ $TEST_MODE == 'spectrum' ]]; then git lfs pull --include="atom_data/chianti_He.h5" origin; fi
+    - if [[ $TEST_MODE == 'spectrum' ]]; then git lfs pull --include="plasma_reference/" origin; fi
+    - if [[ $TEST_MODE == 'spectrum' ]]; then git lfs pull --include="unit_test_data.h5" origin; fi
+    - if [[ $TEST_MODE == 'spectrum' ]]; then cd $TRAVIS_BUILD_DIR; fi
+
+#- source ci-helpers/fetch_reference_data.sh
 
 
 install:
diff --git a/ci-helpers/fetch_reference_data.sh b/ci-helpers/fetch_reference_data.sh
index 4090d7ffe23..a9ded82dbd2 100644
--- a/ci-helpers/fetch_reference_data.sh
+++ b/ci-helpers/fetch_reference_data.sh
@@ -9,8 +9,8 @@ git fetch origin
 git checkout origin/master
 # Use the following to get the ref-data from a specific pull request
 #git fetch origin pull/11/head:thomson-ref
-git lfs pull --include="atom_data/kurucz_cd23_chianti_H_He.h5" origin
-git lfs pull --include="atom_data/chianti_He.h5" origin
-git lfs pull --include="plasma_reference/" origin
-git lfs pull --include="unit_test_data.h5" origin
+git lfs pull --include="atom_data/kurucz_cd23_chianti_H_He.h5" origin/master
+git lfs pull --include="atom_data/chianti_He.h5" origin/master
+git lfs pull --include="plasma_reference/" origin/master
+git lfs pull --include="unit_test_data.h5" origin/master
 cd $TRAVIS_BUILD_DIR

From 44460c56f1886cadecb053bcc9c3a43e4dfe0173 Mon Sep 17 00:00:00 2001
From: Wolfgang Kerzendorf <wkerzendorf@gmail.com>
Date: Thu, 23 Aug 2018 16:21:14 +0200
Subject: [PATCH 10/17] update ref_data_home

---
 .travis.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 0c8d8cda8ad..44068a34906 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -67,8 +67,8 @@ before_install:
     - source ci-helpers/install_miniconda.sh
     - if [[ $TEST_MODE == 'spectrum' ]]; then conda install -c conda-forge git-lfs=2.2.1 -y; fi
     - if [[ $TEST_MODE == 'spectrum' ]]; then git lfs install --skip-smudge; fi
-    - if [[ $TEST_MODE == 'spectrum' ]]; then git clone $TARDIS_REF_DATA_URL $HOME/tardis-refdata; fi
-    - if [[ $TEST_MODE == 'spectrum' ]]; then cd $HOME/tardis-refdata; fi
+    - if [[ $TEST_MODE == 'spectrum' ]]; then git clone https://github.com/tardis-sn/tardis-refdata.git $REF_DATA_HOME; fi
+    - if [[ $TEST_MODE == 'spectrum' ]]; then cd $REF_DATA_HOME; fi
 # Use the following to get the ref-data from the master;
     - if [[ $TEST_MODE == 'spectrum' ]]; then git fetch origin; fi
     - if [[ $TEST_MODE == 'spectrum' ]]; then git checkout origin/master; fi

From 88edc63753efc1617c8912a439afe257f906d030 Mon Sep 17 00:00:00 2001
From: Wolfgang Kerzendorf <wkerzendorf@gmail.com>
Date: Thu, 30 Aug 2018 15:34:11 +0200
Subject: [PATCH 11/17] update comments from unoebauer

---
 .travis.yml                        | 3 ++-
 ci-helpers/fetch_reference_data.sh | 1 +
 ci-helpers/install_miniconda.sh    | 1 +
 ci-helpers/install_tardis_env.sh   | 2 ++
 4 files changed, 6 insertions(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index 44068a34906..2e18cd542b4 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -24,6 +24,7 @@ env:
         - SETUP_CMD='test'
         - TEST_MODE='normal'
         - REF_DATA_HOME=$HOME/tardis-refdata
+        - REF_DATA_GITHUBURL = https://github.com/tardis-sn/tardis-refdata.git
         - MINICONDA_URL='http://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh'
         - SAVE_COVERAGE=false
         - GIT_LFS_SKIP_SMUDGE=1
@@ -67,7 +68,7 @@ before_install:
     - source ci-helpers/install_miniconda.sh
     - if [[ $TEST_MODE == 'spectrum' ]]; then conda install -c conda-forge git-lfs=2.2.1 -y; fi
     - if [[ $TEST_MODE == 'spectrum' ]]; then git lfs install --skip-smudge; fi
-    - if [[ $TEST_MODE == 'spectrum' ]]; then git clone https://github.com/tardis-sn/tardis-refdata.git $REF_DATA_HOME; fi
+    - if [[ $TEST_MODE == 'spectrum' ]]; then git clone $REF_DATA_GITHUBURL $REF_DATA_HOME; fi
     - if [[ $TEST_MODE == 'spectrum' ]]; then cd $REF_DATA_HOME; fi
 # Use the following to get the ref-data from the master;
     - if [[ $TEST_MODE == 'spectrum' ]]; then git fetch origin; fi
diff --git a/ci-helpers/fetch_reference_data.sh b/ci-helpers/fetch_reference_data.sh
index a9ded82dbd2..9002286ca2b 100644
--- a/ci-helpers/fetch_reference_data.sh
+++ b/ci-helpers/fetch_reference_data.sh
@@ -1,3 +1,4 @@
+#!/usr/bin/env bash
 git lfs install
 if test -e $REF_DATA_HOME; then
     echo "Ref data available"
diff --git a/ci-helpers/install_miniconda.sh b/ci-helpers/install_miniconda.sh
index ccc7275308f..399323e61ad 100644
--- a/ci-helpers/install_miniconda.sh
+++ b/ci-helpers/install_miniconda.sh
@@ -1,3 +1,4 @@
+#!/usr/bin/env bash
 export PYTHONIOENCODING=UTF8
 if test -e $HOME/miniconda/bin; then
     echo "miniconda already installed.";
diff --git a/ci-helpers/install_tardis_env.sh b/ci-helpers/install_tardis_env.sh
index f32e170792c..a2efe4582b0 100644
--- a/ci-helpers/install_tardis_env.sh
+++ b/ci-helpers/install_tardis_env.sh
@@ -1,6 +1,8 @@
+#!/usr/bin/env bash
 cd $TRAVIS_BUILD_DIR
 if test -e $HOME/miniconda/envs/tardis; then
     echo "TARDIS env already installed.";
+    # Also check for tardis_env27.yml change
 else
    conda env create -f tardis_env27.yml
 fi

From 3d5b44460c33184673e519204e894593f16ecd6f Mon Sep 17 00:00:00 2001
From: Wolfgang Kerzendorf <wkerzendorf@gmail.com>
Date: Thu, 30 Aug 2018 16:00:36 +0200
Subject: [PATCH 12/17] update refdata path

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

diff --git a/.travis.yml b/.travis.yml
index 81e21cc701c..2c7f61a8757 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -68,7 +68,7 @@ before_install:
     - source ci-helpers/install_miniconda.sh
     - if [[ $TEST_MODE == 'spectrum' ]]; then conda install -c conda-forge git-lfs=2.2.1 -y; fi
     - if [[ $TEST_MODE == 'spectrum' ]]; then git lfs install --skip-smudge; fi
-    - if [[ $TEST_MODE == 'spectrum' ]]; then git clone $REF_DATA_GITHUBURL $REF_DATA_HOME; fi
+    - if [[ $TEST_MODE == 'spectrum' ]]; then git clone $REF_DATA_GITHUBURL $HOME; fi
     - if [[ $TEST_MODE == 'spectrum' ]]; then cd $REF_DATA_HOME; fi
 # Use the following to get the ref-data from the master;
     - if [[ $TEST_MODE == 'spectrum' ]]; then git fetch origin; fi

From ae8b654562dcf683bfbbefdefced2c161b6b3cb3 Mon Sep 17 00:00:00 2001
From: Wolfgang Kerzendorf <wkerzendorf@gmail.com>
Date: Thu, 30 Aug 2018 16:07:47 +0200
Subject: [PATCH 13/17] add single quotes

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

diff --git a/.travis.yml b/.travis.yml
index 2c7f61a8757..46f37a1dd7c 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -24,7 +24,7 @@ env:
         - SETUP_CMD='test'
         - TEST_MODE='normal'
         - REF_DATA_HOME=$HOME/tardis-refdata
-        - REF_DATA_GITHUBURL = https://github.com/tardis-sn/tardis-refdata.git
+        - REF_DATA_GITHUBURL = 'https://github.com/tardis-sn/tardis-refdata.git'
         - MINICONDA_URL='http://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh'
         - SAVE_COVERAGE=false
         - GIT_LFS_SKIP_SMUDGE=1

From 7c7a171e2ecb4384a667918f5925ea4bbccc3add Mon Sep 17 00:00:00 2001
From: Wolfgang Kerzendorf <wkerzendorf@gmail.com>
Date: Thu, 30 Aug 2018 16:08:17 +0200
Subject: [PATCH 14/17] remove git lfs from separate install

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

diff --git a/.travis.yml b/.travis.yml
index 46f37a1dd7c..9d0b65ab88d 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -66,7 +66,7 @@ cache:
 before_install:
     # We do this to make sure we get the dependencies so pip works below
     - source ci-helpers/install_miniconda.sh
-    - if [[ $TEST_MODE == 'spectrum' ]]; then conda install -c conda-forge git-lfs=2.2.1 -y; fi
+    #- if [[ $TEST_MODE == 'spectrum' ]]; then conda install -c conda-forge git-lfs=2.2.1 -y; fi
     - if [[ $TEST_MODE == 'spectrum' ]]; then git lfs install --skip-smudge; fi
     - if [[ $TEST_MODE == 'spectrum' ]]; then git clone $REF_DATA_GITHUBURL $HOME; fi
     - if [[ $TEST_MODE == 'spectrum' ]]; then cd $REF_DATA_HOME; fi

From 8c3a24678c91bcefc1113384b2de7ab5c1f928a1 Mon Sep 17 00:00:00 2001
From: Wolfgang Kerzendorf <wkerzendorf@gmail.com>
Date: Thu, 30 Aug 2018 16:14:58 +0200
Subject: [PATCH 15/17] update clone refdata

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

diff --git a/.travis.yml b/.travis.yml
index 9d0b65ab88d..d90a132d2e2 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -68,6 +68,7 @@ before_install:
     - source ci-helpers/install_miniconda.sh
     #- if [[ $TEST_MODE == 'spectrum' ]]; then conda install -c conda-forge git-lfs=2.2.1 -y; fi
     - if [[ $TEST_MODE == 'spectrum' ]]; then git lfs install --skip-smudge; fi
+    - echo git clone $REF_DATA_GITHUBURL $REF_DATA_HOME
     - if [[ $TEST_MODE == 'spectrum' ]]; then git clone $REF_DATA_GITHUBURL $HOME; fi
     - if [[ $TEST_MODE == 'spectrum' ]]; then cd $REF_DATA_HOME; fi
 # Use the following to get the ref-data from the master;

From c9afcb715d3fca329daee4ae2a7352730654446a Mon Sep 17 00:00:00 2001
From: Wolfgang Kerzendorf <wkerzendorf@gmail.com>
Date: Thu, 30 Aug 2018 16:27:09 +0200
Subject: [PATCH 16/17] remove space after equal

---
 .travis.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index d90a132d2e2..2403a65a9a0 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -24,7 +24,7 @@ env:
         - SETUP_CMD='test'
         - TEST_MODE='normal'
         - REF_DATA_HOME=$HOME/tardis-refdata
-        - REF_DATA_GITHUBURL = 'https://github.com/tardis-sn/tardis-refdata.git'
+        - REF_DATA_GITHUBURL='https://github.com/tardis-sn/tardis-refdata.git'
         - MINICONDA_URL='http://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh'
         - SAVE_COVERAGE=false
         - GIT_LFS_SKIP_SMUDGE=1
@@ -69,7 +69,7 @@ before_install:
     #- if [[ $TEST_MODE == 'spectrum' ]]; then conda install -c conda-forge git-lfs=2.2.1 -y; fi
     - if [[ $TEST_MODE == 'spectrum' ]]; then git lfs install --skip-smudge; fi
     - echo git clone $REF_DATA_GITHUBURL $REF_DATA_HOME
-    - if [[ $TEST_MODE == 'spectrum' ]]; then git clone $REF_DATA_GITHUBURL $HOME; fi
+    - if [[ $TEST_MODE == 'spectrum' ]]; then git clone $REF_DATA_GITHUBURL $REF_DATA_HOME; fi
     - if [[ $TEST_MODE == 'spectrum' ]]; then cd $REF_DATA_HOME; fi
 # Use the following to get the ref-data from the master;
     - if [[ $TEST_MODE == 'spectrum' ]]; then git fetch origin; fi

From 27732bf8c307e700564c330956985d3c2b5f92f5 Mon Sep 17 00:00:00 2001
From: Wolfgang Kerzendorf <wkerzendorf@gmail.com>
Date: Thu, 30 Aug 2018 16:44:45 +0200
Subject: [PATCH 17/17] update travis yaml

---
 .travis.yml                      | 10 ----------
 ci-helpers/install_tardis_env.sh |  7 +++++++
 2 files changed, 7 insertions(+), 10 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 2403a65a9a0..9266d788cc0 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -53,9 +53,6 @@ matrix:
             - TEST_MODE='spectrum'
             - MINICONDA_URL='http://repo.continuum.io/miniconda/Miniconda2-latest-MacOSX-x86_64.sh'
 
-
-        - python: 2.7
-          env: SETUP_CMD='test'
 cache:
   apt: true
   directories:
@@ -88,13 +85,6 @@ before_install:
 
 install:
    - source ci-helpers/install_tardis_env.sh
-   #trouble with building due to segfault at cython (https://github.com/cython/cython/issues/2199)
-   #remove if we can get normal cython through conda
-   - git clone https://github.com/cython/cython
-   - cd cython
-   - git checkout c485b1b77264c3c75d090a3c526de24966830d42
-   - CFLAGS="$CFLAGS -D CYTHON_CLINE_IN_TRACEBACK=0" python setup.py install
-   - cd ..
 
 script:
     - echo CC=$COMPILER python setup.py $SETUP_CMD
diff --git a/ci-helpers/install_tardis_env.sh b/ci-helpers/install_tardis_env.sh
index a2efe4582b0..3851d30b218 100644
--- a/ci-helpers/install_tardis_env.sh
+++ b/ci-helpers/install_tardis_env.sh
@@ -5,6 +5,13 @@ if test -e $HOME/miniconda/envs/tardis; then
     # Also check for tardis_env27.yml change
 else
    conda env create -f tardis_env27.yml
+   #trouble with building due to segfault at cython (https://github.com/cython/cython/issues/2199)
+   #remove if we can get normal cython through conda
+   git clone https://github.com/cython/cython
+   cd cython
+   git checkout c485b1b77264c3c75d090a3c526de24966830d42
+   CFLAGS="$CFLAGS -D CYTHON_CLINE_IN_TRACEBACK=0" python setup.py install
+   cd ..
 fi
 
 source activate tardis
\ No newline at end of file