From 4f86b0d6c206488dc813644374f4ceb949c05b33 Mon Sep 17 00:00:00 2001
From: Vanessa Sochat <vsochat@stanford.edu>
Date: Fri, 1 Mar 2019 11:58:44 -0500
Subject: [PATCH 01/41] adding circleci to test

---
 .circleci/config.yml | 195 +++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 195 insertions(+)
 create mode 100644 .circleci/config.yml

diff --git a/.circleci/config.yml b/.circleci/config.yml
new file mode 100644
index 00000000..94e81806
--- /dev/null
+++ b/.circleci/config.yml
@@ -0,0 +1,195 @@
+# CircleCI build config to test different versions of Singuarity
+
+version: 2.1
+
+workflows:
+  version: 2
+  test:
+    jobs:
+      - test-singularity-3.1.0-python-3:
+          filters:
+            branches:
+              only: master
+      - test-singularity-3.1.0-python-2:
+          filters:
+            branches:
+              only: master
+      - test-singularity-2.6.1-python-2:
+          filters:
+            branches:
+              only: master
+      - test-singularity-2.6.1-python-3:
+          filters:
+            branches:
+              only: master
+
+
+setup: &setup
+  name: install setup
+  command: |
+     sudo apt-get update && \
+     sudo apt-get install -y wget git jq
+     sudo sed -i -e 's/^Defaults\tsecure_path.*$//' /etc/sudoers
+
+
+install_spython: &install_spython
+  name: install spython
+  command: |
+     $HOME/conda/bin/python setup.py install
+
+
+install_singularity_2: &install_singularity_2
+  name: install Singularity 2.6.1
+  command: |
+    which singularity &> /dev/null
+
+    if [ $? -eq 0 ]; then
+        echo "Singularity is installed."
+    else
+        sudo apt-get update && sudo apt-get -y install git \
+               build-essential \
+               libtool \
+               squashfs-tools \
+               autotools-dev \
+               libarchive-dev \
+               automake \
+               autoconf \
+               debootstrap \
+               yum \
+               uuid-dev \
+               libssl-dev \
+               python3-dev
+        wget https://github.com/sylabs/singularity/releases/download/2.6.1/singularity-2.6.1.tar.gz
+        tar -xzvf singularity-2.6.1.tar.gz
+        cd singularity-2.6.1 && ./autogen.sh && ./configure --prefix=/usr/local && make && sudo make install
+
+
+install_singularity_3: &install_singularity_3
+  name: install Singularity 3.1
+  command: | 
+    which singularity &> /dev/null
+
+    if [ $? -eq 0 ]; then
+        echo "Singularity is installed."
+        export GOPATH=/go
+        export PATH=$PATH:/usr/local/go/bin
+    else
+
+        sudo apt-get install -y build-essential \
+                                squashfs-tools \
+                                libtool \
+                                uuid-dev \
+                                libssl-dev \
+                                libgpgme11-dev \
+                                libseccomp-dev \
+                                pkg-config
+
+        # Install GoLang 
+        wget https://dl.google.com/go/go${GO_VERSION}.src.tar.gz && \
+        tar -C /usr/local -xzf go${GO_VERSION}.src.tar.gz 
+
+        export PATH=$PATH:/usr/local/go/bin && \
+            sudo mkdir -p /go && \
+            sudo chmod -R 7777 /go
+        export GOPATH=/go && \
+            go get -u github.com/golang/dep/cmd/dep && \
+            mkdir -p ${GOPATH}/src/github.com/sylabs && \
+            cd ${GOPATH}/src/github.com/sylabs && \
+            wget https://github.com/sylabs/singularity/releases/download/v${singularity_version}/singularity-${singularity_version}.tar.gz && \
+            tar -xzvf singularity-${singularity_version}.tar.gz && \
+            cd singularity && \
+            ./mconfig -p /usr/local && \
+            make -C builddir && \
+            sudo make -C builddir install
+    fi
+
+
+install_python_3: &install_python_3
+  name: install Python 3.5 dependencies
+  command: | 
+      ls $HOME
+      if [ ! -d "/home/circleci/conda" ]; then
+          wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
+          /bin/bash Miniconda3-latest-Linux-x86_64.sh -b -p $HOME/conda
+          export PATH=$HOME/conda/bin:$PATH
+          $HOME/conda/bin/python setup.py install
+       else
+           echo "Miniconda 3 is already installed, continuing to build."
+       fi
+
+install_python_2: &install_python_2
+  name: install Python 3.5 dependencies
+  command: | 
+      ls $HOME
+      if [ ! -d "/home/circleci/conda" ]; then
+          wget https://repo.anaconda.com/miniconda/Miniconda2-latest-Linux-x86_64.sh
+          /bin/bash Miniconda2-latest-Linux-x86_64.sh -b -p $HOME/conda
+          export PATH=$HOME/conda/bin:$PATH
+          $HOME/conda/bin/python setup.py install
+       else
+           echo "Miniconda 2 is already installed, continuing to build."
+       fi
+
+test_spython: &test_spython
+  name: Test Singularity Python
+  command: |
+        cd ~/repo
+        export PATH=$PATH:/opt/circleci/.pyenv/shims
+        $HOME/conda/bin/python -m unittest tests.test_client
+        $HOME/conda/bin/python -m unittest tests.test_utils
+
+
+jobs:
+  test-singularity-3.1.0-python-3:
+    machine: true
+    working_directory: ~/repo
+    steps:
+      - checkout
+      - run: *setup
+      - restore_cache:
+          keys:
+          - v1-dependencies
+      - run: *install_python_3
+      - run: *install_singularity_3
+      - run: *install_spython
+      - save_cache:
+          paths:
+            - /home/circleci/conda
+          key: v1-dependencies        
+      - run: *test_spython
+
+  test-singularity-3.1.0-python-2:
+    machine: true
+    working_directory: ~/repo
+    steps:
+      - checkout
+      - run: *setup
+      - restore_cache:
+          keys:
+          - v1-dependencies
+      - run: *install_python_2
+      - run: *install_singularity_3
+      - run: *install_spython
+      - save_cache:
+          paths:
+            - /home/circleci/conda
+          key: v1-dependencies        
+      - run: *test_spython
+
+  test-singularity-2.6.1-python-3:
+    machine: true
+    working_directory: ~/repo
+    steps:
+      - checkout
+      - run: *setup
+      - restore_cache:
+          keys:
+          - v1-dependencies
+      - run: *install_python_3
+      - run: *install_singularity_2
+      - run: *install_spython
+      - save_cache:
+          paths:
+            - /home/circleci/conda
+          key: v1-dependencies        
+      - run: *test_spython

From 4e32c7cee0a22781477e1614153bacf51a7ef0e3 Mon Sep 17 00:00:00 2001
From: Vanessa Sochat <vsochat@stanford.edu>
Date: Fri, 1 Mar 2019 12:00:47 -0500
Subject: [PATCH 02/41] adding circleci to test

---
 .circleci/config.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 94e81806..41973f88 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -23,7 +23,6 @@ workflows:
             branches:
               only: master
 
-
 setup: &setup
   name: install setup
   command: |

From 0cbbf3e817fb4652d763ff14ce1c06d60e51e48f Mon Sep 17 00:00:00 2001
From: Vanessa Sochat <vsochat@stanford.edu>
Date: Fri, 1 Mar 2019 12:14:22 -0500
Subject: [PATCH 03/41] adding circleci to test

---
 .circleci/config.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 41973f88..a81d008b 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -30,7 +30,6 @@ setup: &setup
      sudo apt-get install -y wget git jq
      sudo sed -i -e 's/^Defaults\tsecure_path.*$//' /etc/sudoers
 
-
 install_spython: &install_spython
   name: install spython
   command: |

From 90452943b2512fd65ba7e284042ee373cc39e82b Mon Sep 17 00:00:00 2001
From: Vanessa Sochat <vsochat@stanford.edu>
Date: Fri, 1 Mar 2019 12:29:00 -0500
Subject: [PATCH 04/41] adding circleci to test

---
 .circleci/config.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index a81d008b..a008e2ae 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -1,5 +1,4 @@
 # CircleCI build config to test different versions of Singuarity
-
 version: 2.1
 
 workflows:

From 5438e88baa7709e3b66ef27637573becb8ee1f0a Mon Sep 17 00:00:00 2001
From: Vanessa Sochat <vsochat@stanford.edu>
Date: Fri, 1 Mar 2019 12:41:40 -0500
Subject: [PATCH 05/41] adding circleci to test

---
 .circleci/config.yml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index a008e2ae..4d1559f7 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -8,19 +8,19 @@ workflows:
       - test-singularity-3.1.0-python-3:
           filters:
             branches:
-              only: master
+              ignore: master
       - test-singularity-3.1.0-python-2:
           filters:
             branches:
-              only: master
+              ignore: master
       - test-singularity-2.6.1-python-2:
           filters:
             branches:
-              only: master
+              ignore: master
       - test-singularity-2.6.1-python-3:
           filters:
             branches:
-              only: master
+              ignore: master
 
 setup: &setup
   name: install setup
@@ -59,7 +59,7 @@ install_singularity_2: &install_singularity_2
         wget https://github.com/sylabs/singularity/releases/download/2.6.1/singularity-2.6.1.tar.gz
         tar -xzvf singularity-2.6.1.tar.gz
         cd singularity-2.6.1 && ./autogen.sh && ./configure --prefix=/usr/local && make && sudo make install
-
+    fi
 
 install_singularity_3: &install_singularity_3
   name: install Singularity 3.1

From 17029a223635b034f7637ec5bb336e9896018072 Mon Sep 17 00:00:00 2001
From: Vanessa Sochat <vsochat@stanford.edu>
Date: Fri, 1 Mar 2019 12:43:29 -0500
Subject: [PATCH 06/41] adding circleci to test

---
 .circleci/config.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 4d1559f7..6ded0f8e 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -2,7 +2,6 @@
 version: 2.1
 
 workflows:
-  version: 2
   test:
     jobs:
       - test-singularity-3.1.0-python-3:

From a0fcca868b46b7446589ee7ebcd905c99d561b4c Mon Sep 17 00:00:00 2001
From: Vanessa Sochat <vsochat@stanford.edu>
Date: Fri, 1 Mar 2019 12:47:04 -0500
Subject: [PATCH 07/41] test

---
 .circleci/config.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 6ded0f8e..4d1559f7 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -2,6 +2,7 @@
 version: 2.1
 
 workflows:
+  version: 2
   test:
     jobs:
       - test-singularity-3.1.0-python-3:

From 9fa5aa801c5f47cdd651de3b74ed741542551808 Mon Sep 17 00:00:00 2001
From: Vanessa Sochat <vsochat@stanford.edu>
Date: Fri, 1 Mar 2019 12:49:17 -0500
Subject: [PATCH 08/41] test

---
 .circleci/config.yml | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 4d1559f7..6879cc8d 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -5,19 +5,19 @@ workflows:
   version: 2
   test:
     jobs:
-      - test-singularity-3.1.0-python-3:
+      - test-singularity-3-python-3:
           filters:
             branches:
               ignore: master
-      - test-singularity-3.1.0-python-2:
+      - test-singularity-3-python-2:
           filters:
             branches:
               ignore: master
-      - test-singularity-2.6.1-python-2:
+      - test-singularity-2-python-2:
           filters:
             branches:
               ignore: master
-      - test-singularity-2.6.1-python-3:
+      - test-singularity-2-python-3:
           filters:
             branches:
               ignore: master
@@ -137,7 +137,7 @@ test_spython: &test_spython
 
 
 jobs:
-  test-singularity-3.1.0-python-3:
+  test-singularity-3-python-3:
     machine: true
     working_directory: ~/repo
     steps:
@@ -155,7 +155,7 @@ jobs:
           key: v1-dependencies        
       - run: *test_spython
 
-  test-singularity-3.1.0-python-2:
+  test-singularity-3-python-2:
     machine: true
     working_directory: ~/repo
     steps:
@@ -173,7 +173,7 @@ jobs:
           key: v1-dependencies        
       - run: *test_spython
 
-  test-singularity-2.6.1-python-3:
+  test-singularity-2-python-3:
     machine: true
     working_directory: ~/repo
     steps:

From 9a7c665bd79410b75642222c88a5b124b278a16b Mon Sep 17 00:00:00 2001
From: Vanessa Sochat <vsochat@stanford.edu>
Date: Fri, 1 Mar 2019 12:50:15 -0500
Subject: [PATCH 09/41] test

---
 .circleci/config.yml | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 6879cc8d..f7e567da 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -190,3 +190,21 @@ jobs:
             - /home/circleci/conda
           key: v1-dependencies        
       - run: *test_spython
+
+  test-singularity-2-python-2:
+    machine: true
+    working_directory: ~/repo
+    steps:
+      - checkout
+      - run: *setup
+      - restore_cache:
+          keys:
+          - v1-dependencies
+      - run: *install_python_2
+      - run: *install_singularity_2
+      - run: *install_spython
+      - save_cache:
+          paths:
+            - /home/circleci/conda
+          key: v1-dependencies        
+      - run: *test_spython

From 70c2bd90f7af281c0b6c87808dfc77f9bbe17019 Mon Sep 17 00:00:00 2001
From: Vanessa Sochat <vsochat@stanford.edu>
Date: Fri, 1 Mar 2019 12:56:30 -0500
Subject: [PATCH 10/41] test

---
 .circleci/config.yml | 38 ++++++++++++++++----------------------
 1 file changed, 16 insertions(+), 22 deletions(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index f7e567da..f3b2f994 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -38,28 +38,22 @@ install_spython: &install_spython
 install_singularity_2: &install_singularity_2
   name: install Singularity 2.6.1
   command: |
-    which singularity &> /dev/null
-
-    if [ $? -eq 0 ]; then
-        echo "Singularity is installed."
-    else
-        sudo apt-get update && sudo apt-get -y install git \
-               build-essential \
-               libtool \
-               squashfs-tools \
-               autotools-dev \
-               libarchive-dev \
-               automake \
-               autoconf \
-               debootstrap \
-               yum \
-               uuid-dev \
-               libssl-dev \
-               python3-dev
-        wget https://github.com/sylabs/singularity/releases/download/2.6.1/singularity-2.6.1.tar.gz
-        tar -xzvf singularity-2.6.1.tar.gz
-        cd singularity-2.6.1 && ./autogen.sh && ./configure --prefix=/usr/local && make && sudo make install
-    fi
+    sudo apt-get update && sudo apt-get -y install git \
+           build-essential \
+           libtool \
+           squashfs-tools \
+           autotools-dev \
+           libarchive-dev \
+           automake \
+           autoconf \
+           debootstrap \
+           yum \
+           uuid-dev \
+           libssl-dev \
+           python3-dev
+    wget https://github.com/sylabs/singularity/releases/download/2.6.1/singularity-2.6.1.tar.gz
+    tar -xzvf singularity-2.6.1.tar.gz
+    cd singularity-2.6.1 && ./autogen.sh && ./configure --prefix=/usr/local && make && sudo make install
 
 install_singularity_3: &install_singularity_3
   name: install Singularity 3.1

From 93bfd4564c2a253d4629687893d689d44ef4682b Mon Sep 17 00:00:00 2001
From: Vanessa Sochat <vsochat@stanford.edu>
Date: Fri, 1 Mar 2019 13:01:11 -0500
Subject: [PATCH 11/41] testing

---
 .circleci/config.yml | 61 +++++++++++++++++++-------------------------
 1 file changed, 26 insertions(+), 35 deletions(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index f3b2f994..402ec4a8 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -58,41 +58,32 @@ install_singularity_2: &install_singularity_2
 install_singularity_3: &install_singularity_3
   name: install Singularity 3.1
   command: | 
-    which singularity &> /dev/null
-
-    if [ $? -eq 0 ]; then
-        echo "Singularity is installed."
-        export GOPATH=/go
-        export PATH=$PATH:/usr/local/go/bin
-    else
-
-        sudo apt-get install -y build-essential \
-                                squashfs-tools \
-                                libtool \
-                                uuid-dev \
-                                libssl-dev \
-                                libgpgme11-dev \
-                                libseccomp-dev \
-                                pkg-config
-
-        # Install GoLang 
-        wget https://dl.google.com/go/go${GO_VERSION}.src.tar.gz && \
-        tar -C /usr/local -xzf go${GO_VERSION}.src.tar.gz 
-
-        export PATH=$PATH:/usr/local/go/bin && \
-            sudo mkdir -p /go && \
-            sudo chmod -R 7777 /go
-        export GOPATH=/go && \
-            go get -u github.com/golang/dep/cmd/dep && \
-            mkdir -p ${GOPATH}/src/github.com/sylabs && \
-            cd ${GOPATH}/src/github.com/sylabs && \
-            wget https://github.com/sylabs/singularity/releases/download/v${singularity_version}/singularity-${singularity_version}.tar.gz && \
-            tar -xzvf singularity-${singularity_version}.tar.gz && \
-            cd singularity && \
-            ./mconfig -p /usr/local && \
-            make -C builddir && \
-            sudo make -C builddir install
-    fi
+    sudo apt-get install -y build-essential \
+                            squashfs-tools \
+                            libtool \
+                            uuid-dev \
+                            libssl-dev \
+                            libgpgme11-dev \
+                            libseccomp-dev \
+                            pkg-config
+
+    # Install GoLang 
+    wget https://dl.google.com/go/go${GO_VERSION}.src.tar.gz && \
+    tar -C /usr/local -xzf go${GO_VERSION}.src.tar.gz 
+
+    export PATH=$PATH:/usr/local/go/bin && \
+        sudo mkdir -p /go && \
+        sudo chmod -R 7777 /go
+    export GOPATH=/go && \
+        go get -u github.com/golang/dep/cmd/dep && \
+        mkdir -p ${GOPATH}/src/github.com/sylabs && \
+        cd ${GOPATH}/src/github.com/sylabs && \
+        wget https://github.com/sylabs/singularity/releases/download/v${singularity_version}/singularity-${singularity_version}.tar.gz && \
+        tar -xzvf singularity-${singularity_version}.tar.gz && \
+        cd singularity && \
+        ./mconfig -p /usr/local && \
+        make -C builddir && \
+        sudo make -C builddir install
 
 
 install_python_3: &install_python_3

From f117494e1d8ad6931f6aa96149134fe8bbdf3a54 Mon Sep 17 00:00:00 2001
From: Vanessa Sochat <vsochat@stanford.edu>
Date: Fri, 1 Mar 2019 13:04:20 -0500
Subject: [PATCH 12/41] testing

---
 .circleci/config.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 402ec4a8..01ce8064 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -78,8 +78,8 @@ install_singularity_3: &install_singularity_3
         go get -u github.com/golang/dep/cmd/dep && \
         mkdir -p ${GOPATH}/src/github.com/sylabs && \
         cd ${GOPATH}/src/github.com/sylabs && \
-        wget https://github.com/sylabs/singularity/releases/download/v${singularity_version}/singularity-${singularity_version}.tar.gz && \
-        tar -xzvf singularity-${singularity_version}.tar.gz && \
+        wget https://github.com/sylabs/singularity/releases/download/v3.1.0/singularity-3.1.0.tar.gz && \
+        tar -xzvf singularity-3.1.0.tar.gz && \
         cd singularity && \
         ./mconfig -p /usr/local && \
         make -C builddir && \

From 31f087ad6c038c90fa4278f362f243d833e2a47d Mon Sep 17 00:00:00 2001
From: Vanessa Sochat <vsochat@stanford.edu>
Date: Fri, 1 Mar 2019 13:06:00 -0500
Subject: [PATCH 13/41] testing

---
 .circleci/config.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 01ce8064..7c107525 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -116,6 +116,7 @@ test_spython: &test_spython
   name: Test Singularity Python
   command: |
         cd ~/repo
+        ls
         export PATH=$PATH:/opt/circleci/.pyenv/shims
         $HOME/conda/bin/python -m unittest tests.test_client
         $HOME/conda/bin/python -m unittest tests.test_utils

From b080dc9ee627e21e61ee00c8fb508b9be8c4a439 Mon Sep 17 00:00:00 2001
From: Vanessa Sochat <vsochat@stanford.edu>
Date: Fri, 1 Mar 2019 13:19:50 -0500
Subject: [PATCH 14/41] wrong pwd

---
 .circleci/config.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 7c107525..e6b39439 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -115,7 +115,7 @@ install_python_2: &install_python_2
 test_spython: &test_spython
   name: Test Singularity Python
   command: |
-        cd ~/repo
+        cd ~/repo/spython
         ls
         export PATH=$PATH:/opt/circleci/.pyenv/shims
         $HOME/conda/bin/python -m unittest tests.test_client

From d93f480ce6fab6919ec7bf8cf3b5c278b79408a3 Mon Sep 17 00:00:00 2001
From: Vanessa Sochat <vsochat@stanford.edu>
Date: Fri, 1 Mar 2019 13:29:34 -0500
Subject: [PATCH 15/41] go version missing

---
 .circleci/config.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index e6b39439..7368e4f8 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -68,8 +68,8 @@ install_singularity_3: &install_singularity_3
                             pkg-config
 
     # Install GoLang 
-    wget https://dl.google.com/go/go${GO_VERSION}.src.tar.gz && \
-    tar -C /usr/local -xzf go${GO_VERSION}.src.tar.gz 
+    wget https://dl.google.com/go/go1.11.5.src.tar.gz && \
+    tar -C /usr/local -xzf go1.11.5.src.tar.gz 
 
     export PATH=$PATH:/usr/local/go/bin && \
         sudo mkdir -p /go && \

From 23f0c927d2e04d0ad632f72f0ebde94239ae5e72 Mon Sep 17 00:00:00 2001
From: Vanessa Sochat <vsochat@stanford.edu>
Date: Fri, 1 Mar 2019 13:36:56 -0500
Subject: [PATCH 16/41] untar with sudo

---
 .circleci/config.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 7368e4f8..93effaab 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -69,7 +69,7 @@ install_singularity_3: &install_singularity_3
 
     # Install GoLang 
     wget https://dl.google.com/go/go1.11.5.src.tar.gz && \
-    tar -C /usr/local -xzf go1.11.5.src.tar.gz 
+    sudo tar -C /usr/local -xzf go1.11.5.src.tar.gz 
 
     export PATH=$PATH:/usr/local/go/bin && \
         sudo mkdir -p /go && \

From 7100130b4d9d1d1efbeaa46eb9411d5be3d9f450 Mon Sep 17 00:00:00 2001
From: Vanessa Sochat <vsochat@stanford.edu>
Date: Fri, 1 Mar 2019 14:11:18 -0500
Subject: [PATCH 17/41] untar with sudo

---
 .circleci/config.yml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 93effaab..05e66550 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -69,7 +69,9 @@ install_singularity_3: &install_singularity_3
 
     # Install GoLang 
     wget https://dl.google.com/go/go1.11.5.src.tar.gz && \
-    sudo tar -C /usr/local -xzf go1.11.5.src.tar.gz 
+    sudo mkdir -p /usr/local/go
+    cmhod -R 7777 /usr/local/go
+    tar -C /usr/local -xzf go1.11.5.src.tar.gz 
 
     export PATH=$PATH:/usr/local/go/bin && \
         sudo mkdir -p /go && \

From 4ccd0f04ddedc238b3ae6da794bfdbe33c30c313 Mon Sep 17 00:00:00 2001
From: Vanessa Sochat <vsochat@stanford.edu>
Date: Fri, 1 Mar 2019 14:12:42 -0500
Subject: [PATCH 18/41] untar with sudo

---
 .circleci/config.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 05e66550..00fcafd4 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -70,7 +70,7 @@ install_singularity_3: &install_singularity_3
     # Install GoLang 
     wget https://dl.google.com/go/go1.11.5.src.tar.gz && \
     sudo mkdir -p /usr/local/go
-    cmhod -R 7777 /usr/local/go
+    chmod -R 7777 /usr/local/go
     tar -C /usr/local -xzf go1.11.5.src.tar.gz 
 
     export PATH=$PATH:/usr/local/go/bin && \

From 0ce4bad74515535cad1586c67c890c5c2f5d55e9 Mon Sep 17 00:00:00 2001
From: Vanessa Sochat <vsochat@stanford.edu>
Date: Fri, 1 Mar 2019 14:14:52 -0500
Subject: [PATCH 19/41] go already instealled?

---
 .circleci/config.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 00fcafd4..ec340a37 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -70,7 +70,8 @@ install_singularity_3: &install_singularity_3
     # Install GoLang 
     wget https://dl.google.com/go/go1.11.5.src.tar.gz && \
     sudo mkdir -p /usr/local/go
-    chmod -R 7777 /usr/local/go
+    sudo rm -rf /usr/local/go
+    sudo chmod -R 7777 /usr/local/go
     tar -C /usr/local -xzf go1.11.5.src.tar.gz 
 
     export PATH=$PATH:/usr/local/go/bin && \

From 22d34f4f7f1a55d5c371c9a4be7d9610c32aa067 Mon Sep 17 00:00:00 2001
From: Vanessa Sochat <vsochat@stanford.edu>
Date: Fri, 1 Mar 2019 14:17:37 -0500
Subject: [PATCH 20/41] go already instealled?

---
 .circleci/config.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index ec340a37..81f28d5f 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -70,8 +70,8 @@ install_singularity_3: &install_singularity_3
     # Install GoLang 
     wget https://dl.google.com/go/go1.11.5.src.tar.gz && \
     sudo mkdir -p /usr/local/go
-    sudo rm -rf /usr/local/go
     sudo chmod -R 7777 /usr/local/go
+    ls /usr/local/go
     tar -C /usr/local -xzf go1.11.5.src.tar.gz 
 
     export PATH=$PATH:/usr/local/go/bin && \

From a35babc9e59fd32f1246278b0c6786e01c18c1d8 Mon Sep 17 00:00:00 2001
From: Vanessa Sochat <vsochat@stanford.edu>
Date: Fri, 1 Mar 2019 14:20:17 -0500
Subject: [PATCH 21/41] go already instealled?

---
 .circleci/config.yml | 9 +++------
 1 file changed, 3 insertions(+), 6 deletions(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 81f28d5f..b3003bad 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -68,13 +68,10 @@ install_singularity_3: &install_singularity_3
                             pkg-config
 
     # Install GoLang 
+    cd /tmp
     wget https://dl.google.com/go/go1.11.5.src.tar.gz && \
-    sudo mkdir -p /usr/local/go
-    sudo chmod -R 7777 /usr/local/go
-    ls /usr/local/go
-    tar -C /usr/local -xzf go1.11.5.src.tar.gz 
-
-    export PATH=$PATH:/usr/local/go/bin && \
+    tar -xzf go1.11.5.src.tar.gz 
+    export PATH=$PATH:/tmp/go/bin && \
         sudo mkdir -p /go && \
         sudo chmod -R 7777 /go
     export GOPATH=/go && \

From efc74f558deacbe42bb0b6207c4f735db3a7f657 Mon Sep 17 00:00:00 2001
From: Vanessa Sochat <vsochat@stanford.edu>
Date: Fri, 1 Mar 2019 14:24:35 -0500
Subject: [PATCH 22/41] using an older golang?

---
 .circleci/config.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index b3003bad..47f9f98e 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -71,9 +71,10 @@ install_singularity_3: &install_singularity_3
     cd /tmp
     wget https://dl.google.com/go/go1.11.5.src.tar.gz && \
     tar -xzf go1.11.5.src.tar.gz 
-    export PATH=$PATH:/tmp/go/bin && \
+    export PATH=/tmp/go/bin:$PATH && \
         sudo mkdir -p /go && \
         sudo chmod -R 7777 /go
+    which go
     export GOPATH=/go && \
         go get -u github.com/golang/dep/cmd/dep && \
         mkdir -p ${GOPATH}/src/github.com/sylabs && \

From 31a70baef72b3298e00e72e2e1d55925b5bfa0dd Mon Sep 17 00:00:00 2001
From: Vanessa Sochat <vsochat@stanford.edu>
Date: Fri, 1 Mar 2019 14:28:37 -0500
Subject: [PATCH 23/41] using an older golang?

---
 .circleci/config.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 47f9f98e..e35a1922 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -74,6 +74,7 @@ install_singularity_3: &install_singularity_3
     export PATH=/tmp/go/bin:$PATH && \
         sudo mkdir -p /go && \
         sudo chmod -R 7777 /go
+    sudo rm -rf /usr/local/go
     which go
     export GOPATH=/go && \
         go get -u github.com/golang/dep/cmd/dep && \

From a5f92d9053a9c080f6099b1061b6a7fa7e396034 Mon Sep 17 00:00:00 2001
From: Vanessa Sochat <vsochat@stanford.edu>
Date: Fri, 1 Mar 2019 14:31:42 -0500
Subject: [PATCH 24/41] using an older golang?

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

diff --git a/.circleci/config.yml b/.circleci/config.yml
index e35a1922..e5b2a006 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -69,11 +69,12 @@ install_singularity_3: &install_singularity_3
 
     # Install GoLang 
     cd /tmp
-    wget https://dl.google.com/go/go1.11.5.src.tar.gz && \
-    tar -xzf go1.11.5.src.tar.gz 
-    export PATH=/tmp/go/bin:$PATH && \
-        sudo mkdir -p /go && \
+    wget https://dl.google.com/go/go1.11.5.src.tar.gz
+    tar -xzf go1.11.5.src.tar.gz
+    export PATH=/tmp/go/bin:$PATH
+        sudo mkdir -p /go
         sudo chmod -R 7777 /go
+    which go
     sudo rm -rf /usr/local/go
     which go
     export GOPATH=/go && \

From ea3832300f1dfb67428e46d204881058a842ee8a Mon Sep 17 00:00:00 2001
From: Vanessa Sochat <vsochat@stanford.edu>
Date: Fri, 1 Mar 2019 14:34:59 -0500
Subject: [PATCH 25/41] using an older golang?

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

diff --git a/.circleci/config.yml b/.circleci/config.yml
index e5b2a006..d125a153 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -74,11 +74,10 @@ install_singularity_3: &install_singularity_3
     export PATH=/tmp/go/bin:$PATH
         sudo mkdir -p /go
         sudo chmod -R 7777 /go
-    which go
-    sudo rm -rf /usr/local/go
+    echo $PATH
     which go
     export GOPATH=/go && \
-        go get -u github.com/golang/dep/cmd/dep && \
+        /tmp/go/bin/go get -u github.com/golang/dep/cmd/dep && \
         mkdir -p ${GOPATH}/src/github.com/sylabs && \
         cd ${GOPATH}/src/github.com/sylabs && \
         wget https://github.com/sylabs/singularity/releases/download/v3.1.0/singularity-3.1.0.tar.gz && \

From 715abfada965af6c1d1eeb496938e3b9a1b5028b Mon Sep 17 00:00:00 2001
From: Vanessa Sochat <vsochat@stanford.edu>
Date: Fri, 1 Mar 2019 14:38:29 -0500
Subject: [PATCH 26/41] using an older golang?

---
 .circleci/config.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index d125a153..62911aa6 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -69,8 +69,11 @@ install_singularity_3: &install_singularity_3
 
     # Install GoLang 
     cd /tmp
+    echo ${PWD}
     wget https://dl.google.com/go/go1.11.5.src.tar.gz
     tar -xzf go1.11.5.src.tar.gz
+    echo $PWD
+    ls
     export PATH=/tmp/go/bin:$PATH
         sudo mkdir -p /go
         sudo chmod -R 7777 /go

From ed9a532e5d57d1764cfddfe69e9eca0e1119937f Mon Sep 17 00:00:00 2001
From: Vanessa Sochat <vsochat@stanford.edu>
Date: Fri, 1 Mar 2019 14:42:23 -0500
Subject: [PATCH 27/41] OMG DOWNLOADING WRONG ONE

---
 .circleci/config.yml | 7 ++-----
 1 file changed, 2 insertions(+), 5 deletions(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 62911aa6..9a4a459e 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -69,11 +69,8 @@ install_singularity_3: &install_singularity_3
 
     # Install GoLang 
     cd /tmp
-    echo ${PWD}
-    wget https://dl.google.com/go/go1.11.5.src.tar.gz
-    tar -xzf go1.11.5.src.tar.gz
-    echo $PWD
-    ls
+    wget https://dl.google.com/go/go1.11.5.linux-amd64.tar.gz
+    tar -xzf go1.11.5.linux-amd64.tar.gz
     export PATH=/tmp/go/bin:$PATH
         sudo mkdir -p /go
         sudo chmod -R 7777 /go

From 9d0c94a9ff6a1c1298a1774c06a0fde93955f49b Mon Sep 17 00:00:00 2001
From: Vanessa Sochat <vsochat@stanford.edu>
Date: Sat, 2 Mar 2019 10:16:17 -0500
Subject: [PATCH 28/41] testing orb in workflow

---
 .circleci/config.yml | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 9a4a459e..e6e62eab 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -1,6 +1,9 @@
 # CircleCI build config to test different versions of Singuarity
 version: 2.1
 
+orbs:
+  singularity: singularity/singularity@1.0.2
+
 workflows:
   version: 2
   test:
@@ -135,7 +138,9 @@ jobs:
           keys:
           - v1-dependencies
       - run: *install_python_3
-      - run: *install_singularity_3
+      - singularity/install_debian_3
+          go-version: 11.1.5
+          singularity-version: 3.1.0
       - run: *install_spython
       - save_cache:
           paths:

From b9f015c8fde38e4e7af368dfef612e03d9e0a48d Mon Sep 17 00:00:00 2001
From: Vanessa Sochat <vsochat@stanford.edu>
Date: Sat, 2 Mar 2019 10:17:11 -0500
Subject: [PATCH 29/41] testing orb in workflow

---
 .circleci/config.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index e6e62eab..36dc80fb 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -138,7 +138,7 @@ jobs:
           keys:
           - v1-dependencies
       - run: *install_python_3
-      - singularity/install_debian_3
+      - singularity/install_debian_3:
           go-version: 11.1.5
           singularity-version: 3.1.0
       - run: *install_spython

From b089bc9ab5d33fb123c95d344c08482c5cc80d05 Mon Sep 17 00:00:00 2001
From: Vanessa Sochat <vsochat@stanford.edu>
Date: Sat, 2 Mar 2019 10:19:06 -0500
Subject: [PATCH 30/41] testing orb in workflow

---
 .circleci/config.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 36dc80fb..554d890a 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -138,8 +138,9 @@ jobs:
           keys:
           - v1-dependencies
       - run: *install_python_3
-      - singularity/install_debian_3:
+      - singularity/install-go:
           go-version: 11.1.5
+      - singularity/debian-install-3:
           singularity-version: 3.1.0
       - run: *install_spython
       - save_cache:

From 9c4aebc1aec4c6b58aa11e7ebb30437ee995776c Mon Sep 17 00:00:00 2001
From: Vanessa Sochat <vsochat@stanford.edu>
Date: Sat, 2 Mar 2019 10:21:54 -0500
Subject: [PATCH 31/41] testing orb in workflow

---
 .circleci/config.yml | 68 ++++++--------------------------------------
 1 file changed, 9 insertions(+), 59 deletions(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 554d890a..2778ce73 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -37,60 +37,6 @@ install_spython: &install_spython
   command: |
      $HOME/conda/bin/python setup.py install
 
-
-install_singularity_2: &install_singularity_2
-  name: install Singularity 2.6.1
-  command: |
-    sudo apt-get update && sudo apt-get -y install git \
-           build-essential \
-           libtool \
-           squashfs-tools \
-           autotools-dev \
-           libarchive-dev \
-           automake \
-           autoconf \
-           debootstrap \
-           yum \
-           uuid-dev \
-           libssl-dev \
-           python3-dev
-    wget https://github.com/sylabs/singularity/releases/download/2.6.1/singularity-2.6.1.tar.gz
-    tar -xzvf singularity-2.6.1.tar.gz
-    cd singularity-2.6.1 && ./autogen.sh && ./configure --prefix=/usr/local && make && sudo make install
-
-install_singularity_3: &install_singularity_3
-  name: install Singularity 3.1
-  command: | 
-    sudo apt-get install -y build-essential \
-                            squashfs-tools \
-                            libtool \
-                            uuid-dev \
-                            libssl-dev \
-                            libgpgme11-dev \
-                            libseccomp-dev \
-                            pkg-config
-
-    # Install GoLang 
-    cd /tmp
-    wget https://dl.google.com/go/go1.11.5.linux-amd64.tar.gz
-    tar -xzf go1.11.5.linux-amd64.tar.gz
-    export PATH=/tmp/go/bin:$PATH
-        sudo mkdir -p /go
-        sudo chmod -R 7777 /go
-    echo $PATH
-    which go
-    export GOPATH=/go && \
-        /tmp/go/bin/go get -u github.com/golang/dep/cmd/dep && \
-        mkdir -p ${GOPATH}/src/github.com/sylabs && \
-        cd ${GOPATH}/src/github.com/sylabs && \
-        wget https://github.com/sylabs/singularity/releases/download/v3.1.0/singularity-3.1.0.tar.gz && \
-        tar -xzvf singularity-3.1.0.tar.gz && \
-        cd singularity && \
-        ./mconfig -p /usr/local && \
-        make -C builddir && \
-        sudo make -C builddir install
-
-
 install_python_3: &install_python_3
   name: install Python 3.5 dependencies
   command: | 
@@ -133,13 +79,12 @@ jobs:
     working_directory: ~/repo
     steps:
       - checkout
-      - run: *setup
       - restore_cache:
           keys:
           - v1-dependencies
       - run: *install_python_3
       - singularity/install-go:
-          go-version: 11.1.5
+          go-version: 1.11.5
       - singularity/debian-install-3:
           singularity-version: 3.1.0
       - run: *install_spython
@@ -159,7 +104,10 @@ jobs:
           keys:
           - v1-dependencies
       - run: *install_python_2
-      - run: *install_singularity_3
+      - singularity/install-go:
+          go-version: 1.11.5
+      - singularity/debian-install-3:
+          singularity-version: 3.1.0
       - run: *install_spython
       - save_cache:
           paths:
@@ -177,7 +125,8 @@ jobs:
           keys:
           - v1-dependencies
       - run: *install_python_3
-      - run: *install_singularity_2
+      - singularity/debian-install-2:
+          singularity-version: 2.6.1
       - run: *install_spython
       - save_cache:
           paths:
@@ -195,7 +144,8 @@ jobs:
           keys:
           - v1-dependencies
       - run: *install_python_2
-      - run: *install_singularity_2
+      - singularity/debian-install-2:
+          singularity-version: 2.6.1
       - run: *install_spython
       - save_cache:
           paths:

From 7fe9640e3a188bd40f2664d9ea8ed233bde9b81c Mon Sep 17 00:00:00 2001
From: Vanessa Sochat <vsochat@stanford.edu>
Date: Sat, 2 Mar 2019 10:40:00 -0500
Subject: [PATCH 32/41] try updated orb

---
 .circleci/config.yml | 12 +-----------
 1 file changed, 1 insertion(+), 11 deletions(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 2778ce73..583d6b5e 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -2,7 +2,7 @@
 version: 2.1
 
 orbs:
-  singularity: singularity/singularity@1.0.2
+  singularity: singularity/singularity@dev:alpha
 
 workflows:
   version: 2
@@ -25,13 +25,6 @@ workflows:
             branches:
               ignore: master
 
-setup: &setup
-  name: install setup
-  command: |
-     sudo apt-get update && \
-     sudo apt-get install -y wget git jq
-     sudo sed -i -e 's/^Defaults\tsecure_path.*$//' /etc/sudoers
-
 install_spython: &install_spython
   name: install spython
   command: |
@@ -99,7 +92,6 @@ jobs:
     working_directory: ~/repo
     steps:
       - checkout
-      - run: *setup
       - restore_cache:
           keys:
           - v1-dependencies
@@ -120,7 +112,6 @@ jobs:
     working_directory: ~/repo
     steps:
       - checkout
-      - run: *setup
       - restore_cache:
           keys:
           - v1-dependencies
@@ -139,7 +130,6 @@ jobs:
     working_directory: ~/repo
     steps:
       - checkout
-      - run: *setup
       - restore_cache:
           keys:
           - v1-dependencies

From 13a80611ed2f55f398b1c4edc214ca1af325ff7c Mon Sep 17 00:00:00 2001
From: Vanessa Sochat <vsochat@stanford.edu>
Date: Sat, 2 Mar 2019 11:13:08 -0500
Subject: [PATCH 33/41] updating version, removing travis dependencies

---
 .circleci/config.yml         |  2 +-
 .travis.yml                  | 24 ------------------------
 .travis/before_install       | 21 ---------------------
 .travis/script               |  4 ----
 CHANGELOG.md                 |  1 +
 spython/tests/test_client.py |  4 ++--
 spython/version.py           |  2 +-
 7 files changed, 5 insertions(+), 53 deletions(-)
 delete mode 100644 .travis.yml
 delete mode 100644 .travis/before_install
 delete mode 100644 .travis/script

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 583d6b5e..0d1cdab3 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -2,7 +2,7 @@
 version: 2.1
 
 orbs:
-  singularity: singularity/singularity@dev:alpha
+  singularity: singularity/singularity@1.0.3
 
 workflows:
   version: 2
diff --git a/.travis.yml b/.travis.yml
deleted file mode 100644
index bfad6304..00000000
--- a/.travis.yml
+++ /dev/null
@@ -1,24 +0,0 @@
-language: python
-
-sudo: true
-
-os: linux
-
-python:
-    - "2.7"
-    - "3.5"
-
-services:
-  - docker
-
-matrix:
-  allow_failures:
-    - python: "2.6"
-    - python: "3.5"
-
-before_install:
-  - sudo chmod u+x .travis/*
-  - /bin/bash .travis/before_install
-
-script:
-  - /bin/bash .travis/script
diff --git a/.travis/before_install b/.travis/before_install
deleted file mode 100644
index 9e81eb2d..00000000
--- a/.travis/before_install
+++ /dev/null
@@ -1,21 +0,0 @@
-#!/bin/bash
-
-sudo apt-get update && sudo apt-get install -y wget git build-essential squashfs-tools \
-                                                    libtool \
-                                                    autotools-dev \
-                                                    libarchive-dev \
-                                                    automake \
-                                                    autoconf \
-                                                    uuid-dev \
-                                                    libssl-dev
-
-
-sudo sed -i -e 's/^Defaults\tsecure_path.*$//' /etc/sudoers
-
-echo "PYTHON VERSION"
-which python
-
-python setup.py sdist && python setup.py install
-
-# Install Singularity (development)
-cd /tmp && git clone -b vault/release-2.6 https://github.com/singularityware/singularity.git && cd singularity && ./autogen.sh && ./configure --prefix=/usr/local && make && sudo make install
diff --git a/.travis/script b/.travis/script
deleted file mode 100644
index b16b7ee5..00000000
--- a/.travis/script
+++ /dev/null
@@ -1,4 +0,0 @@
-#!/bin/bash
-cd $TRAVIS_BUILD_DIR/spython
-python -m unittest tests.test_client
-python -m unittest tests.test_utils
diff --git a/CHANGELOG.md b/CHANGELOG.md
index b68da4b7..dbdbc1f0 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -17,6 +17,7 @@ The client here will eventually be released as "spython" (and eventually to
 singularity on pypi), and the versions here will coincide with these releases.
 
 ## [master](https://github.com/singularityhub/singularity-cli/tree/master)
+ - adding testing for 3.1.0 with Singularity Orbs (0.0.53)
  - instance stop all missing check for Singularity V3.+ (0.0.52)
  - fixing bug with instances list, name not taken into account (0.0.51)
  - additional of args to instance start commands (0.0.50)
diff --git a/spython/tests/test_client.py b/spython/tests/test_client.py
index a1ee5278..f8133c6a 100644
--- a/spython/tests/test_client.py
+++ b/spython/tests/test_client.py
@@ -31,10 +31,10 @@ def tearDown(self):
     def test_commands(self):
 
         print('Testing client.build command')
-        container = "%s/container.img" %(self.tmpdir)
+        container = "%s/container.sif" %(self.tmpdir)
 
         print("...Case 1: Build from docker uri")
-        created_container = self.cli.build('docker://ubuntu', 
+        created_container = self.cli.build('docker://busybox:1.30.1', 
                                            image=container,
                                            sudo=False)
         self.assertEqual(created_container, container)
diff --git a/spython/version.py b/spython/version.py
index 45621e95..280ce035 100644
--- a/spython/version.py
+++ b/spython/version.py
@@ -6,7 +6,7 @@
 # with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
 
 
-__version__ = "0.0.52"
+__version__ = "0.0.53"
 AUTHOR = 'Vanessa Sochat'
 AUTHOR_EMAIL = 'vsochat@stanford.edu'
 NAME = 'spython'

From 118f009c2ec00eb860a7da9a14b6382220170ba5 Mon Sep 17 00:00:00 2001
From: Vanessa Sochat <vsochat@stanford.edu>
Date: Sat, 2 Mar 2019 15:45:27 -0500
Subject: [PATCH 34/41] testing fixes

---
 CHANGELOG.md                 |  1 +
 spython/main/inspect.py      | 37 +++++++++++++++++++++++++++++-------
 spython/main/pull.py         | 15 +++++++++++++--
 spython/tests/test_client.py | 10 ++++------
 4 files changed, 48 insertions(+), 15 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index dbdbc1f0..151ae178 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -18,6 +18,7 @@ singularity on pypi), and the versions here will coincide with these releases.
 
 ## [master](https://github.com/singularityhub/singularity-cli/tree/master)
  - adding testing for 3.1.0 with Singularity Orbs (0.0.53)
+ - inspect returns parsed json on success, or full message / return code otherwise
  - instance stop all missing check for Singularity V3.+ (0.0.52)
  - fixing bug with instances list, name not taken into account (0.0.51)
  - additional of args to instance start commands (0.0.50)
diff --git a/spython/main/inspect.py b/spython/main/inspect.py
index 48935c50..bc2b02fd 100644
--- a/spython/main/inspect.py
+++ b/spython/main/inspect.py
@@ -5,21 +5,26 @@
 # Mozilla Public License, v. 2.0. If a copy of the MPL was not distributed
 # with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
 
+import json
 
 from spython.logger import bot
+from spython.utils import ( 
+    check_install, 
+    get_singularity_version, 
+    run_command
+)
 
-def inspect(self,image=None, json=True, app=None):
+def inspect(self, image=None, json=True, app=None, quiet=True):
     '''inspect will show labels, defile, runscript, and tests for an image
     
-
        Parameters
        ==========
-       image_path: path of image to inspect
+       image: path of image to inspect
        json: print json instead of raw text (default True)
+       quiet: Don't print result to the screen (default True)
        app: if defined, return help in context of an app
 
     '''
-    from spython.utils import check_install
     check_install()
 
     # No image provided, default to use the client's loaded image
@@ -31,12 +36,30 @@ def inspect(self,image=None, json=True, app=None):
         cmd = cmd + ['--app', app]
 
     options = ['e','d','l','r','hf','t']
+
+    # After Singularity 3.0, helpfile was changed to H from
+
+    if "version 3" in get_singularity_version():
+        options = ['e','d','l','r','H','t']
+
     [cmd.append('-%s' % x) for x in options]
 
     if json is True:
         cmd.append('--json')
 
     cmd.append(image)
-    output = self._run_command(cmd)
-    #self.println(output,quiet=self.quiet)    
-    return output
+    result = run_command(cmd, quiet=True)
+
+    if result['return_code'] == 0:
+        result = json.loads(result['message'][0])
+
+        # If labels included, try parsing to json
+
+        if 'labels' in result['attributes']:
+            labels = json.loads(result['attributes']['labels'])
+            result['attributes']['labels'] = labels
+
+        if not quiet:
+            print(json.dumps(result, indent=4))
+
+    return result
diff --git a/spython/main/pull.py b/spython/main/pull.py
index 12171818..af16ec9c 100644
--- a/spython/main/pull.py
+++ b/spython/main/pull.py
@@ -7,7 +7,7 @@
 
 
 from spython.logger import bot
-from spython.utils import stream_command
+from spython.utils import ( stream_command, get_singularity_version )
 import os
 import re
 import shutil
@@ -44,6 +44,10 @@ def pull(self,
 
     cmd = self._init_command('pull')
 
+    # If Singularity version > 3.0, we have sif format
+    if 'version 3' in get_singularity_version():
+        ext = 'sif'
+
     # No image provided, default to use the client's loaded image
     if image is None:
         image = self._get_uri()
@@ -74,7 +78,14 @@ def pull(self,
         
     # Only add name if we aren't naming by hash or commit
     if not name_by_commit and not name_by_hash:
-        cmd = cmd + ["--name", name]
+
+        # Regression Singularity 3.* onward, PULLFOLDER not honored
+        # https://github.com/sylabs/singularity/issues/2788
+        if pull_folder and 'version 3' in get_singularity_version():
+            pull_folder_name = os.path.join(pull_folder, os.path.basename(name))
+            cmd = cmd + ["--name", pull_folder_name]          
+        else:
+            cmd = cmd + ["--name", name]
 
     if force is True:
         cmd = cmd + ["--force"]
diff --git a/spython/tests/test_client.py b/spython/tests/test_client.py
index f8133c6a..a2652962 100644
--- a/spython/tests/test_client.py
+++ b/spython/tests/test_client.py
@@ -56,9 +56,9 @@ def test_commands(self):
         os.remove(image)
 
         print("...Case 2: Testing docker pull")
-        container = self.cli.pull("docker://ubuntu:14.04",
+        container = self.cli.pull("docker://busybox:1.30.1",
                                    pull_folder=self.tmpdir)
-        self.assertTrue("ubuntu:14.04" in container)
+        self.assertTrue("busybox:1.30.1" in container)
 
         print(container)
         self.assertTrue(os.path.exists(container))
@@ -69,11 +69,9 @@ def test_commands(self):
         self.assertTrue('bin\nboot\ndev' in result)
 
         print("Testing client.inspect command")
-        result = self.cli.inspect(container)
-        labels = json.loads(result)
-        self.assertTrue('data' in labels)     
-        os.remove(container)
+        labels = self.cli.inspect(container)
 
+        os.remove(container)
 
 
 if __name__ == '__main__':

From 22140b004ee75fdf43093bd9d7ea414746484408 Mon Sep 17 00:00:00 2001
From: Vanessa Sochat <vsochat@stanford.edu>
Date: Sat, 2 Mar 2019 15:48:50 -0500
Subject: [PATCH 35/41] container is changed

---
 spython/tests/test_client.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/spython/tests/test_client.py b/spython/tests/test_client.py
index a2652962..4f7bd9e2 100644
--- a/spython/tests/test_client.py
+++ b/spython/tests/test_client.py
@@ -66,7 +66,7 @@ def test_commands(self):
         print('Testing client.execute command')
         result = self.cli.execute(container,'ls /')
         print(result)
-        self.assertTrue('bin\nboot\ndev' in result)
+        self.assertTrue('tmp\nusr\nvar' in result)
 
         print("Testing client.inspect command")
         labels = self.cli.inspect(container)

From ae358568c98588525eef31fb048068ffb30d88e8 Mon Sep 17 00:00:00 2001
From: Vanessa Sochat <vsochat@stanford.edu>
Date: Sat, 2 Mar 2019 15:54:25 -0500
Subject: [PATCH 36/41] need to import json with different name

---
 spython/main/inspect.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/spython/main/inspect.py b/spython/main/inspect.py
index bc2b02fd..3231bee0 100644
--- a/spython/main/inspect.py
+++ b/spython/main/inspect.py
@@ -5,7 +5,7 @@
 # Mozilla Public License, v. 2.0. If a copy of the MPL was not distributed
 # with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
 
-import json
+import json as jsonp
 
 from spython.logger import bot
 from spython.utils import ( 
@@ -51,15 +51,15 @@ def inspect(self, image=None, json=True, app=None, quiet=True):
     result = run_command(cmd, quiet=True)
 
     if result['return_code'] == 0:
-        result = json.loads(result['message'][0])
+        result = jsonp.loads(result['message'][0])
 
         # If labels included, try parsing to json
 
         if 'labels' in result['attributes']:
-            labels = json.loads(result['attributes']['labels'])
+            labels = jsonp.loads(result['attributes']['labels'])
             result['attributes']['labels'] = labels
 
         if not quiet:
-            print(json.dumps(result, indent=4))
+            print(jsonp.dumps(result, indent=4))
 
     return result

From fc320d4e6e4705cd33d0a2101591b2f893e0de99 Mon Sep 17 00:00:00 2001
From: Vanessa Sochat <vsochat@stanford.edu>
Date: Sat, 2 Mar 2019 16:03:04 -0500
Subject: [PATCH 37/41] fixing labels

---
 spython/main/inspect.py | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/spython/main/inspect.py b/spython/main/inspect.py
index 3231bee0..e5e77cc5 100644
--- a/spython/main/inspect.py
+++ b/spython/main/inspect.py
@@ -54,10 +54,13 @@ def inspect(self, image=None, json=True, app=None, quiet=True):
         result = jsonp.loads(result['message'][0])
 
         # If labels included, try parsing to json
+        if "data" in result:
+            labels = result['data']['attributes'].get('labels', {})
 
-        if 'labels' in result['attributes']:
-            labels = jsonp.loads(result['attributes']['labels'])
-            result['attributes']['labels'] = labels
+        elif 'attributes' in result:
+            labels = result['attributes'].get('labels', {})
+
+        result['attributes']['labels'] = jsonp.loads(labels)
 
         if not quiet:
             print(jsonp.dumps(result, indent=4))

From ac0c33b784650f4e7d061099eb1dd1043c69d89c Mon Sep 17 00:00:00 2001
From: Vanessa Sochat <vsochat@stanford.edu>
Date: Sat, 2 Mar 2019 16:10:04 -0500
Subject: [PATCH 38/41] fixing labels

---
 spython/main/inspect.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/spython/main/inspect.py b/spython/main/inspect.py
index e5e77cc5..c31cc0ab 100644
--- a/spython/main/inspect.py
+++ b/spython/main/inspect.py
@@ -48,7 +48,7 @@ def inspect(self, image=None, json=True, app=None, quiet=True):
         cmd.append('--json')
 
     cmd.append(image)
-    result = run_command(cmd, quiet=True)
+    result = run_command(cmd, quiet=False)
 
     if result['return_code'] == 0:
         result = jsonp.loads(result['message'][0])

From e0590221cc151172e14c1ad9d7026e5cb30a839a Mon Sep 17 00:00:00 2001
From: Vanessa Sochat <vsochat@stanford.edu>
Date: Sat, 2 Mar 2019 16:15:18 -0500
Subject: [PATCH 39/41] fixing labels

---
 spython/main/inspect.py | 14 ++++++++++++--
 1 file changed, 12 insertions(+), 2 deletions(-)

diff --git a/spython/main/inspect.py b/spython/main/inspect.py
index c31cc0ab..6c430205 100644
--- a/spython/main/inspect.py
+++ b/spython/main/inspect.py
@@ -50,17 +50,27 @@ def inspect(self, image=None, json=True, app=None, quiet=True):
     cmd.append(image)
     result = run_command(cmd, quiet=False)
 
+    print('RESULT')
+    print(result['message'])
+    print(len(result['message']))
+
     if result['return_code'] == 0:
         result = jsonp.loads(result['message'][0])
 
-        # If labels included, try parsing to json
         if "data" in result:
             labels = result['data']['attributes'].get('labels', {})
 
         elif 'attributes' in result:
             labels = result['attributes'].get('labels', {})
 
-        result['attributes']['labels'] = jsonp.loads(labels)
+        # If labels included, try parsing to json
+
+        try:
+            labels = jsonp.loads(labels)
+        except:
+            pass
+
+        result['attributes']['labels'] = labels
 
         if not quiet:
             print(jsonp.dumps(result, indent=4))

From ceac6ffd2814ea17b1fd27b01f785428326c477c Mon Sep 17 00:00:00 2001
From: Vanessa Sochat <vsochat@stanford.edu>
Date: Sat, 2 Mar 2019 16:27:15 -0500
Subject: [PATCH 40/41] None should not return, do {} instead

---
 spython/main/inspect.py | 8 ++------
 1 file changed, 2 insertions(+), 6 deletions(-)

diff --git a/spython/main/inspect.py b/spython/main/inspect.py
index 6c430205..3838ddab 100644
--- a/spython/main/inspect.py
+++ b/spython/main/inspect.py
@@ -50,18 +50,14 @@ def inspect(self, image=None, json=True, app=None, quiet=True):
     cmd.append(image)
     result = run_command(cmd, quiet=False)
 
-    print('RESULT')
-    print(result['message'])
-    print(len(result['message']))
-
     if result['return_code'] == 0:
         result = jsonp.loads(result['message'][0])
 
         if "data" in result:
-            labels = result['data']['attributes'].get('labels', {})
+            labels = result['data']['attributes'].get('labels') or {}
 
         elif 'attributes' in result:
-            labels = result['attributes'].get('labels', {})
+            labels = result['attributes'].get('labels') or {}
 
         # If labels included, try parsing to json
 

From 5c4ac1de8b9f66b3302184819840d0a26e4024ab Mon Sep 17 00:00:00 2001
From: Vanessa Sochat <vsochat@stanford.edu>
Date: Sat, 2 Mar 2019 16:34:17 -0500
Subject: [PATCH 41/41] put into separate function

---
 spython/main/inspect.py | 42 +++++++++++++++++++++++++++++------------
 1 file changed, 30 insertions(+), 12 deletions(-)

diff --git a/spython/main/inspect.py b/spython/main/inspect.py
index 3838ddab..2a7c499b 100644
--- a/spython/main/inspect.py
+++ b/spython/main/inspect.py
@@ -53,22 +53,40 @@ def inspect(self, image=None, json=True, app=None, quiet=True):
     if result['return_code'] == 0:
         result = jsonp.loads(result['message'][0])
 
-        if "data" in result:
-            labels = result['data']['attributes'].get('labels') or {}
+        # Fix up labels
+        labels = parse_labels(result)
 
-        elif 'attributes' in result:
-            labels = result['attributes'].get('labels') or {}
+        if not quiet:
+            print(jsonp.dumps(result, indent=4))
 
-        # If labels included, try parsing to json
+    return result
 
-        try:
-            labels = jsonp.loads(labels)
-        except:
-            pass
 
-        result['attributes']['labels'] = labels
+def parse_labels(result):
+    '''fix up the labels, meaning parse to json if needed, and return
+       original updated object
 
-        if not quiet:
-            print(jsonp.dumps(result, indent=4))
+       Parameters
+       ==========
+       result: the json object to parse from inspect
+    '''
+
+    if "data" in result:
+        labels = result['data']['attributes'].get('labels') or {}
+
+    elif 'attributes' in result:
+        labels = result['attributes'].get('labels') or {}
+
+    # If labels included, try parsing to json
+
+    try:
+        labels = jsonp.loads(labels)
+    except:
+        pass
+
+    if "data" in result:
+        result['data']['attributes']['labels'] = labels
+    else:
+        result['attributes']['labels'] = labels
 
     return result