From bc26d5dc407c793b1998de613817d838aaf1592c Mon Sep 17 00:00:00 2001
From: Aljen Uitbeijerse <aljen.uitbeijerse@vortech.nl>
Date: Thu, 25 Nov 2021 12:14:33 +0100
Subject: [PATCH] Final?

---
 .github/workflows/configure_aa.sh    |  5 ----
 .github/workflows/tools_install.sh   | 18 ++++++++++++++
 .github/workflows/tools_install_b.sh | 16 -------------
 .github/workflows/trigger_install.m  | 36 ----------------------------
 .github/workflows/trigger_install.py | 26 ++------------------
 5 files changed, 20 insertions(+), 81 deletions(-)
 delete mode 100644 .github/workflows/configure_aa.sh
 delete mode 100644 .github/workflows/tools_install_b.sh
 delete mode 100644 .github/workflows/trigger_install.m

diff --git a/.github/workflows/configure_aa.sh b/.github/workflows/configure_aa.sh
deleted file mode 100644
index 964dd3b30..000000000
--- a/.github/workflows/configure_aa.sh
+++ /dev/null
@@ -1,5 +0,0 @@
-echo "Free space:"
-df -h
-mkdir $HOME/.aa
-cp $GITHUB_WORKSPACE/.github/workflows/$PARAMETER_XML $HOME/.aa/aap_parameters_user.xml
-mkdir $HOME/projects
\ No newline at end of file
diff --git a/.github/workflows/tools_install.sh b/.github/workflows/tools_install.sh
index 2c36a5274..71d51ec5e 100644
--- a/.github/workflows/tools_install.sh
+++ b/.github/workflows/tools_install.sh
@@ -11,3 +11,21 @@ python $TOOLDIR/get-pip.py --force-reinstall
 # All MATLAB tools MUST be installed referred by the parameterset
 source $GITHUB_WORKSPACE/.github/workflows/tools_urls.sh
 source $GITHUB_WORKSPACE/aa_tools/toolboxes/installation_scripts/install_tools.sh $GITHUB_WORKSPACE/.github/workflows/$PARAMETER_XML $TOOLDIR
+
+echo "FSL: ${LOAD_FSL}; FREESURFER: ${LOAD_FREESURFER}"
+
+if [[ "x${LOAD_FSL}x" == "x1x" ]]; then
+    source $GITHUB_WORKSPACE/aa_tools/toolboxes/installation_scripts/install_fsl.sh $TOOLDIR 6.0.5 centos7 0 $TOOLDIR/config/fsl_bash.sh
+else # FSL standards are needed for some modules
+    source $GITHUB_WORKSPACE/aa_tools/toolboxes/installation_scripts/install_fsl.sh $TOOLDIR 6.0.5 centos7 1
+fi
+
+if [[ "x${LOAD_FREESURFER}x" == "x1x" ]]; then
+    source $GITHUB_WORKSPACE/aa_tools/toolboxes/installation_scripts/install_freesurfer.sh $TOOLDIR 7.2.0 centos7 "tibor.auer@gmail.com\n7061\n *Ccpi6x7PAIeQ\n FS96pPK5vW.0g" $TEMPLATEDIR
+fi
+
+echo "Free space:"
+df -h
+mkdir $HOME/.aa
+cp $GITHUB_WORKSPACE/.github/workflows/$PARAMETER_XML $HOME/.aa/aap_parameters_user.xml
+mkdir $HOME/projects
\ No newline at end of file
diff --git a/.github/workflows/tools_install_b.sh b/.github/workflows/tools_install_b.sh
deleted file mode 100644
index d86cad0de..000000000
--- a/.github/workflows/tools_install_b.sh
+++ /dev/null
@@ -1,16 +0,0 @@
-TOOLDIR=$HOME/tools
-TEMPLATEDIR=$TOOLDIR/templates
-
-echo "FSL: ${LOAD_FSL}; FREESURFER: ${LOAD_FREESURFER}"
-
-if [[ "x${LOAD_FSL}x" == "x1x" ]]; then
-    source $GITHUB_WORKSPACE/aa_tools/toolboxes/installation_scripts/install_fsl.sh $TOOLDIR 6.0.5 centos7 0 $TOOLDIR/config/fsl_bash.sh
-else # FSL standards are needed for some modules
-    source $GITHUB_WORKSPACE/aa_tools/toolboxes/installation_scripts/install_fsl.sh $TOOLDIR 6.0.5 centos7 1
-fi
-
-if [[ "x${LOAD_FREESURFER}x" == "x1x" ]]; then
-    source $GITHUB_WORKSPACE/aa_tools/toolboxes/installation_scripts/install_freesurfer.sh $TOOLDIR 7.2.0 centos7 "tibor.auer@gmail.com\n7061\n *Ccpi6x7PAIeQ\n FS96pPK5vW.0g" $TEMPLATEDIR
-fi
-
-whatwhat
\ No newline at end of file
diff --git a/.github/workflows/trigger_install.m b/.github/workflows/trigger_install.m
deleted file mode 100644
index 97234df54..000000000
--- a/.github/workflows/trigger_install.m
+++ /dev/null
@@ -1,36 +0,0 @@
-% Script to trigger tools etc. installation
-% Make sure to throw an error on failure.
-
-if ismac()
-    % Code to run on Mac platform
-    % Before isunix, because Mac is also unix
-    throw(MException('trigger_install:platform_support', 'Mac not supported yet'))
-elseif isunix()
-    % Code to run on Linux platform
-    [status, cmdout] = system('source $GITHUB_WORKSPACE/.github/workflows/tools_install.sh');
-    cmdout
-    if ~status
-        % 0 if ok, non-zero if problem
-        throw(MException('trigger_install:install_status', 'Problem while running tools_install'))
-    end
-
-    [status, cmdout] = system('source $GITHUB_WORKSPACE/.github/workflows/tools_install_b.sh');
-    cmdout
-    if ~status
-        % 0 if ok, non-zero if problem
-        throw(MException('trigger_install:install_status', 'Problem while running tools_install_b'))
-    end
-
-    % Configure aa
-    [status, cmdout] = system('source $GITHUB_WORKSPACE/.github/workflows/configure_aa.sh');
-    cmdout
-    if ~status
-        % 0 if ok, non-zero if problem
-        throw(MException('trigger_install:install_status', 'Problem while running configure_aa'))
-    end
-elseif ispc()
-    % Code to run on Windows platform
-    throw(MException('trigger_install:platform_support', 'Windows not supported yet'))
-else
-    throw(MException('trigger_install:platform_support', 'Platform not supported'))
-end
diff --git a/.github/workflows/trigger_install.py b/.github/workflows/trigger_install.py
index d2abcc3e3..e8ae28e80 100644
--- a/.github/workflows/trigger_install.py
+++ b/.github/workflows/trigger_install.py
@@ -1,6 +1,7 @@
 # Note: Assume Python 2.7, since that will have been installed for facemasking requirements.
 #
-# Using python (instead of matlab) because using system() in matlab gives enormous amount of command window output.
+# Using python (instead of matlab) because using system() in matlab gives enormous amount of
+# command window output, and there is some problem with the status code from system()
 
 import sys
 import subprocess
@@ -16,29 +17,6 @@
     print("Your system is Linux")
     sys.stdout.flush()
     subprocess.check_call('source $GITHUB_WORKSPACE/.github/workflows/tools_install.sh', shell=True, executable="/bin/bash")
-    #if status<0:
-    #    # 0 if ok, non-zero if problem
-    #    raise Exception('Problem while running tools_install')
-    #else:
-    #    print(status)
-    #    sys.stdout.flush()
-
-    subprocess.check_call('source $GITHUB_WORKSPACE/.github/workflows/tools_install_b.sh', shell=True, executable="/bin/bash")
-    #if status!=0:
-    #    # 0 if ok, non-zero if problem
-    #    raise Exception('Problem while running tools_install_b')
-    #else:
-    #    print(status)
-    #    sys.stdout.flush()
-
-    # Configure aa
-    subprocess.check_call('source $GITHUB_WORKSPACE/.github/workflows/configure_aa.sh', shell=True, executable="/bin/bash")
-    #if status!=0:
-    #    # 0 if ok, non-zero if problem
-    #    raise Exception('Problem while running configure_aa')
-    #else:
-    #    print(status)
-    #    sys.stdout.flush()
 
 elif plt == "Darwin":
     print("Your system is MacOS")