From ebd9d0adb1d096b5afc968b2c3be879860785f2c Mon Sep 17 00:00:00 2001
From: yeganer <yeganer@gmx.de>
Date: Thu, 31 Aug 2017 10:24:56 +0200
Subject: [PATCH 1/6] Add travis caching

---
 .travis.yml              | 175 ++++++++++++++++++++++-----------------
 travis/before_install.sh |  19 +++++
 2 files changed, 119 insertions(+), 75 deletions(-)
 create mode 100644 travis/before_install.sh

diff --git a/.travis.yml b/.travis.yml
index edce95dfdc3..f4098e19605 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -1,96 +1,121 @@
-os:
-  - linux
-language: python
+# We set the language to c because python isn't supported on the MacOS X nodes
+# on Travis. However, the language ends up being irrelevant anyway, since we
+# install Python ourselves using conda.
+language: c
 
-python:
-    - 2.7
+os:
+    - linux
 
-virtualenv:
-  system_site_packages: true
+# Setting sudo to false opts in to Travis-CI container-based builds.
+sudo: false
 
-cache:
-  apt: true
+# The apt packages below are needed for sphinx builds. A full list of packages
+# that can be included can be found here:
+#
+# https://github.com/travis-ci/apt-package-whitelist/blob/master/ubuntu-precise
 
-sudo: false
+addons:
+    apt:
+        packages:
+            -clang
 
 env:
     global:
-        - COMPILER=gcc
-        - PANDAS_VERSION=0.16
-        - ASTROPY_USE_SYSTEM_PYTEST=1
+
+        # The following versions are the 'default' for tests, unless
+        # overridden underneath. They are defined here in order to save having
+        # to repeat them for all configurations.
+        - PYTHON_VERSION=2.7
+        - NUMPY_VERSION=stable
+        - ASTROPY_VERSION=stable
+        - MAIN_CMD='python setup.py'
         - SETUP_CMD='test'
-        - TEST_MODE='normal'
+        - PIP_DEPENDENCIES=''
+        - EVENT_TYPE='pull_request push'
+
+
+        # For this package-template, we include examples of Cython modules,
+        # so Cython is required for testing. If your package does not include
+        # Cython code, you can set CONDA_DEPENDENCIES=''
+        - CONDA_DEPENDENCIES='Cython'
+
+        # List other runtime dependencies for the package that are available as
+        # pip packages here.
+        # - PIP_DEPENDENCIES=''
+
+        # Conda packages for affiliated packages are hosted in channel
+        # "astropy" while builds for astropy LTS with recent numpy versions
+        # are in astropy-ci-extras. If your package uses either of these,
+        # add the channels to CONDA_CHANNELS along with any other channels
+        # you want to use.
+        - CONDA_CHANNELS='astropy-ci-extras astropy'
+
+        # If there are matplotlib or other GUI tests, uncomment the following
+        # line to use the X virtual framebuffer.
+        # - SETUP_XVFB=True
+        - COMPILER=gcc
+
         - TARDIS_REF_DATA_URL='https://github.com/tardis-sn/tardis-refdata.git'
-        - MINICONDA_URL='http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh'
-        - SAVE_COVERAGE=false
+        - ASTROPY_USE_SYSTEM_PYTEST=1
+        - COMPILER=gcc
 
-matrix:
-    include:
-        - python: 2.7
-          env:
-            - COMPILER=gcc
-            - SETUP_CMD='test --coverage --args="--tardis-refdata=$HOME/tardis-refdata/"'
-            - TEST_MODE='spectrum'
-            - SAVE_COVERAGE=true
-
-        - python: 2.7
-          env:
-            - COMPILER=clang
-            - SETUP_CMD='test --args="--tardis-refdata=$HOME/tardis-refdata/"'
-            - TEST_MODE='spectrum'
+    matrix:
+        # Make sure that egg_info works without dependencies
+        # - PYTHON_VERSION=2.7 SETUP_CMD='egg_info'
+        # - PYTHON_VERSION=3.4 SETUP_CMD='egg_info'
+        # - PYTHON_VERSION=3.5 SETUP_CMD='egg_info'
+        # - PYTHON_VERSION=3.6 SETUP_CMD='egg_info'
+        - COMPILER=clang
 
-        - os: osx
-          language: generic
-          env:
-            - COMPILER=clang
-            - SETUP_CMD='test --args="--tardis-refdata=$HOME/tardis-refdata/"'
-            - TEST_MODE='spectrum'
-            - MINICONDA_URL='http://repo.continuum.io/miniconda/Miniconda2-latest-MacOSX-x86_64.sh'
+matrix:
 
+    # Don't wait for allowed failures
+    fast_finish: true
 
-        - python: 2.7
+    include:
+        # Try MacOS X
+        - os: osx
           env: SETUP_CMD='test'
 
-addons:
-  apt:
-    packages:
-    - clang
-
-
-
-
-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
-    - 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 fetch origin pull/3/head:carsus-ref; fi
-    - if [[ $TEST_MODE == 'spectrum' ]]; then git checkout carsus-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 $TRAVIS_BUILD_DIR; fi
+        # Do a coverage test.
+        - os: linux
+          env: SETUP_CMD='test --coverage --args="--tardis-refdata=$HOME/tardis-refdata/"'
+
+        - os: linux
+          env: SETUP_CMD='conda env create -f tardis_env27.yml'
 
 install:
-   - cd $TRAVIS_BUILD_DIR
-   - conda env create -f tardis_env27.yml
-   - source activate tardis
+
+    # We now use the ci-helpers package to set up our testing environment.
+    # This is done by using Miniconda and then using conda and pip to install
+    # dependencies. Which dependencies are installed using conda and pip is
+    # determined by the CONDA_DEPENDENCIES and PIP_DEPENDENCIES variables,
+    # which should be space-delimited lists of package names. See the README
+    # in https://github.com/astropy/ci-helpers for information about the full
+    # list of environment variables that can be used to customize your
+    # environment. In some cases, ci-helpers may not offer enough flexibility
+    # in how to install a package, in which case you can have additional
+    # commands in the install: section below.
+
+    - git clone git://github.com/yeganer/ci-helpers.git
+    - source ci-helpers/travis/setup_conda.sh
+    - source travis/before_install.sh
+
+    # As described above, using ci-helpers, you should be able to set up an
+    # environment with dependencies installed using conda and pip, but in some
+    # cases this may not provide enough flexibility in how to install a
+    # specific dependency (and it will not be able to install non-Python
+    # dependencies). Therefore, you can also include commands below (as
+    # well as at the start of the install section or in the before_install
+    # section if they are needed before setting up conda) to install any
+    # other dependencies.
 
 script:
-    - echo CC=$COMPILER python setup.py $SETUP_CMD
-    - CC=$COMPILER python setup.py $SETUP_CMD
+   - echo CC=$COMPILER $MAIN_CMD $SETUP_CMD
+   - CC=$COMPILER $MAIN_CMD $SETUP_CMD
 
 after_success:
-    - if [[ "$SAVE_COVERAGE" = true ]]; then coveralls; fi
-
-after_failure:
-    - cat /home/travis/.pip/pip.log
+    # If coveralls.io is set up for this package, uncomment the line below.
+    # The coveragerc file may be customized as needed for your package.
+    # - if [[ $SETUP_CMD == *coverage* ]]; then coveralls --rcfile='packagename/tests/coveragerc'; fi
+    - if [[ $SETUP_CMD == *coverage* ]]; then coveralls; fi
diff --git a/travis/before_install.sh b/travis/before_install.sh
new file mode 100644
index 00000000000..bb6b9575c7b
--- /dev/null
+++ b/travis/before_install.sh
@@ -0,0 +1,19 @@
+conda env create -f tardis_env27.yml
+source activate tardis
+if [[ $SETUP_CMD == *coverage* ]]; then 
+    conda install -c conda-forge git-lfs=2.2.1 -y
+    git lfs install --skip-smudge
+    git clone $TARDIS_REF_DATA_URL $HOME/tardis-refdata
+    cd $HOME/tardis-refdata
+
+    # Checkout PR version, not master
+    git fetch origin pull/3/head:carsus-ref
+    git checkout carsus-ref
+
+    # Pull the files
+    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
+fi

From 516e24169de4fe9f389534895c67f38810fe6994 Mon Sep 17 00:00:00 2001
From: yeganer <yeganer@gmx.de>
Date: Thu, 31 Aug 2017 10:42:49 +0200
Subject: [PATCH 2/6] Fix type in apt 'clang' dependency

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

diff --git a/.travis.yml b/.travis.yml
index f4098e19605..452d5eb3a68 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -16,8 +16,7 @@ sudo: false
 
 addons:
     apt:
-        packages:
-            -clang
+        packages: clang
 
 env:
     global:
@@ -57,7 +56,6 @@ env:
 
         - TARDIS_REF_DATA_URL='https://github.com/tardis-sn/tardis-refdata.git'
         - ASTROPY_USE_SYSTEM_PYTEST=1
-        - COMPILER=gcc
 
     matrix:
         # Make sure that egg_info works without dependencies
@@ -65,6 +63,7 @@ env:
         # - PYTHON_VERSION=3.4 SETUP_CMD='egg_info'
         # - PYTHON_VERSION=3.5 SETUP_CMD='egg_info'
         # - PYTHON_VERSION=3.6 SETUP_CMD='egg_info'
+        - COMPILER=gcc
         - COMPILER=clang
 
 matrix:

From 4e719e1541241c31a7db9a5bcef1e3ecf79d1ed8 Mon Sep 17 00:00:00 2001
From: yeganer <yeganer@gmx.de>
Date: Thu, 31 Aug 2017 11:10:57 +0200
Subject: [PATCH 3/6] Run the full test via build matrix

---
 .travis.yml | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 452d5eb3a68..03779978696 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -58,13 +58,15 @@ env:
         - ASTROPY_USE_SYSTEM_PYTEST=1
 
     matrix:
+        - COMPILER=gcc
+        - COMPILER=clang
+        - SETUP_CMD='test'
+        - SETUP_CMD='test --coverage --args="--tardis-refdata=$HOME/tardis-refdata/"'
         # Make sure that egg_info works without dependencies
         # - PYTHON_VERSION=2.7 SETUP_CMD='egg_info'
         # - PYTHON_VERSION=3.4 SETUP_CMD='egg_info'
         # - PYTHON_VERSION=3.5 SETUP_CMD='egg_info'
         # - PYTHON_VERSION=3.6 SETUP_CMD='egg_info'
-        - COMPILER=gcc
-        - COMPILER=clang
 
 matrix:
 
@@ -80,9 +82,6 @@ matrix:
         - os: linux
           env: SETUP_CMD='test --coverage --args="--tardis-refdata=$HOME/tardis-refdata/"'
 
-        - os: linux
-          env: SETUP_CMD='conda env create -f tardis_env27.yml'
-
 install:
 
     # We now use the ci-helpers package to set up our testing environment.

From eac566ad65fe73a92c727312f589cdd954bbb0f9 Mon Sep 17 00:00:00 2001
From: yeganer <yeganer@gmx.de>
Date: Thu, 31 Aug 2017 11:15:26 +0200
Subject: [PATCH 4/6] Enable caching

---
 .travis.yml              | 5 +++++
 travis/before_install.sh | 9 ++++++---
 2 files changed, 11 insertions(+), 3 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 03779978696..6e29ebe81e3 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -18,6 +18,11 @@ addons:
     apt:
         packages: clang
 
+cache:
+    directories:
+        - $HOME/miniconda
+        - $HOME/tardis-refdata
+
 env:
     global:
 
diff --git a/travis/before_install.sh b/travis/before_install.sh
index bb6b9575c7b..67c1840ad75 100644
--- a/travis/before_install.sh
+++ b/travis/before_install.sh
@@ -1,12 +1,15 @@
 conda env create -f tardis_env27.yml
 source activate tardis
-if [[ $SETUP_CMD == *coverage* ]]; then 
+
+if [[ $SETUP_CMD == *coverage* ]]; then
     conda install -c conda-forge git-lfs=2.2.1 -y
     git lfs install --skip-smudge
-    git clone $TARDIS_REF_DATA_URL $HOME/tardis-refdata
+    if [ ! -d "$HOME/tardis-refdata" ]; then
+        git clone $TARDIS_REF_DATA_URL $HOME/tardis-refdata
+    fi
     cd $HOME/tardis-refdata
 
-    # Checkout PR version, not master
+    # Checkout PR version of tardis-refdata, not master
     git fetch origin pull/3/head:carsus-ref
     git checkout carsus-ref
 

From 64c30bc427f6f131c15b7bd7d35fa81e2fa94a09 Mon Sep 17 00:00:00 2001
From: yeganer <yeganer@gmx.de>
Date: Fri, 8 Sep 2017 08:29:34 +0200
Subject: [PATCH 5/6] Include setup helper scripts in tardis

We can't use an external repository because we are hacking the scripts
heavily to work with a conda environment file instead of defining the
dependencies with environment variables in .travis.yml.
---
 .travis.yml                 |  3 +-
 travis/before_install.sh    |  3 --
 travis/setup_conda.sh       | 62 +++++++++++++++++++++++++++++++++++++
 travis/setup_conda_linux.sh | 23 ++++++++++++++
 travis/setup_conda_osx.sh   | 30 ++++++++++++++++++
 5 files changed, 116 insertions(+), 5 deletions(-)
 create mode 100755 travis/setup_conda.sh
 create mode 100755 travis/setup_conda_linux.sh
 create mode 100755 travis/setup_conda_osx.sh

diff --git a/.travis.yml b/.travis.yml
index 6e29ebe81e3..d41a2fbd476 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -100,8 +100,7 @@ install:
     # in how to install a package, in which case you can have additional
     # commands in the install: section below.
 
-    - git clone git://github.com/yeganer/ci-helpers.git
-    - source ci-helpers/travis/setup_conda.sh
+    - source travis/setup_conda.sh
     - source travis/before_install.sh
 
     # As described above, using ci-helpers, you should be able to set up an
diff --git a/travis/before_install.sh b/travis/before_install.sh
index 67c1840ad75..0d4d8a5df62 100644
--- a/travis/before_install.sh
+++ b/travis/before_install.sh
@@ -1,6 +1,3 @@
-conda env create -f tardis_env27.yml
-source activate tardis
-
 if [[ $SETUP_CMD == *coverage* ]]; then
     conda install -c conda-forge git-lfs=2.2.1 -y
     git lfs install --skip-smudge
diff --git a/travis/setup_conda.sh b/travis/setup_conda.sh
new file mode 100755
index 00000000000..8c93ccf6f5d
--- /dev/null
+++ b/travis/setup_conda.sh
@@ -0,0 +1,62 @@
+#!/bin/bash
+
+# Note to the future: keep the conda scripts separate for each OS because many
+# packages call ci-helpers with:
+#
+#   source ci-helpers/travis/setup_conda_$TRAVIS_OS_NAME.sh
+#
+# The present script was added later.
+
+if [[ $DEBUG == True ]]; then
+    set -x
+fi
+
+# First check: if the build should be run at all based on the event type
+
+if [[ ! -z $EVENT_TYPE ]]; then
+    for event in $EVENT_TYPE; do
+        if [[ $TRAVIS_EVENT_TYPE = $event ]]; then
+            allow_to_build=True
+        fi
+    done
+    if [[ $allow_to_build != True ]]; then
+        travis_terminate 0
+    fi
+fi
+
+# Second check: if any of the custom tags are used to skip the build
+
+TR_SKIP="\[(skip travis|travis skip)\]"
+DOCS_ONLY="\[docs only|build docs\]"
+
+# Travis doesn't provide the commit message of the top of the branch for
+# PRs, only the commit message of the merge. Thus this ugly workaround is
+# needed for now.
+
+if [[ $TRAVIS_PULL_REQUEST == false ]]; then
+    COMMIT_MESSAGE=${TRAVIS_COMMIT_MESSAGE}
+else
+    COMMIT_MESSAGE=$(git show -s $TRAVIS_COMMIT_RANGE | awk 'BEGIN{count=0}{if ($1=="Author:") count++; if (count==1) print $0}')
+fi
+
+# Skip build if the commit message contains [skip travis] or [travis skip]
+# Remove workaround once travis has this feature natively
+# https://github.com/travis-ci/travis-ci/issues/5032
+
+if [[ ! -z $(echo ${COMMIT_MESSAGE} | grep -E "${TR_SKIP}") ]]; then
+    echo "Travis was requested to be skipped by the commit message, exiting."
+    travis_terminate 0
+elif [[ ! -z $(echo ${COMMIT_MESSAGE} | grep -E "${DOCS_ONLY}") ]]; then
+    if [[ $SETUP_CMD != *build_docs* ]] && [[ $SETUP_CMD != *build_sphinx* ]]; then
+        echo "Only docs build was requested by the commit message, exiting."
+        travis_terminate 0
+    fi
+fi
+
+echo "==================== Starting executing ci-helpers scripts ====================="
+
+source travis/setup_conda_$TRAVIS_OS_NAME.sh;
+
+echo "================= Returning executing local .travis.yml script ================="
+
+set +x
diff --git a/travis/setup_conda_linux.sh b/travis/setup_conda_linux.sh
new file mode 100755
index 00000000000..fd41caef75b
--- /dev/null
+++ b/travis/setup_conda_linux.sh
@@ -0,0 +1,23 @@
+#!/bin/bash
+
+# Install conda
+# http://conda.pydata.org/docs/travis.html#the-travis-yml-file
+echo ls -la $HOME/miniconda
+ls -la $HOME/miniconda
+if [ ! "$(ls -A $HOME/miniconda)" ]; then
+    echo "Cache is empty, installing miniconda and test environment."
+    # Control will enter here if $HOME/miniconda is empty.
+    rm -r $HOME/miniconda
+    wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh
+    bash miniconda.sh -b -p $HOME/miniconda
+
+    export PATH="$HOME/miniconda/bin:$PATH"
+
+    hash -r
+
+    conda env create -f tardis_env27.yml
+else
+    export PATH="$HOME/miniconda/bin:$PATH"
+fi
+
+source activate tardis
diff --git a/travis/setup_conda_osx.sh b/travis/setup_conda_osx.sh
new file mode 100755
index 00000000000..ee88e8cd5c9
--- /dev/null
+++ b/travis/setup_conda_osx.sh
@@ -0,0 +1,30 @@
+#!/bin/bash
+
+# Workaround for https://github.com/travis-ci/travis-ci/issues/6307, which
+# caused the following error on MacOS X workers:
+#
+# /Users/travis/build.sh: line 109: shell_session_update: command not found
+#
+rvm get head
+
+# Install conda
+# http://conda.pydata.org/docs/travis.html#the-travis-yml-file
+echo ls -la $HOME/miniconda
+ls -la $HOME/miniconda
+if [ ! "$(ls -A $HOME/miniconda)" ]; then
+    echo "Cache is empty, installing miniconda and test environment."
+    # Control will enter here if $HOME/miniconda is empty.
+    rm -r $HOME/miniconda
+    # Control will enter here if $HOME/miniconda doesn't exist.
+    wget https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -O miniconda.sh
+
+    export PATH="$HOME/miniconda/bin:$PATH"
+
+    hash -r
+
+    conda env create -f tardis_env27.yml
+else
+    export PATH="$HOME/miniconda/bin:$PATH"
+fi
+
+source activate tardis

From ce6c76feeacfa2e1386f0af5bd68265f9b8665be Mon Sep 17 00:00:00 2001
From: yeganer <yeganer@gmx.de>
Date: Fri, 8 Sep 2017 10:40:14 +0200
Subject: [PATCH 6/6] Test for empty directory, not if it exists

---
 travis/before_install.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/travis/before_install.sh b/travis/before_install.sh
index 0d4d8a5df62..5775915e1a2 100644
--- a/travis/before_install.sh
+++ b/travis/before_install.sh
@@ -1,7 +1,7 @@
 if [[ $SETUP_CMD == *coverage* ]]; then
     conda install -c conda-forge git-lfs=2.2.1 -y
     git lfs install --skip-smudge
-    if [ ! -d "$HOME/tardis-refdata" ]; then
+    if [ ! "$(ls -A $HOME/tardis-refdata)" ]; then
         git clone $TARDIS_REF_DATA_URL $HOME/tardis-refdata
     fi
     cd $HOME/tardis-refdata