Use /home/aljen.uitbeijerse in parameter xmls, and have a replace fun…

…ction for it in trigger_install

To prepare for adding windows test jobs that can use the same parameter xml

.github/workflows/aap_parameters_defaults_GitHub.xml

@@ -1,10 +1,10 @@
 <?xml version="1.0" encoding="utf-8"?>
 <aap xmlns:xi="http://www.w3.org/2001/XInclude">
-    <xi:include href="/home/runner/work/automaticanalysis/automaticanalysis/aa_parametersets/aap_parameters_defaults.xml" parse="xml"/>
+    <xi:include href="$HOME/work/automaticanalysis/automaticanalysis/aa_parametersets/aap_parameters_defaults.xml" parse="xml"/>
     <local>
         <directory_conventions>
-            <rawdatadir desc='Directories to find raw MRI data' ui='dir_list'>/home/runner/data/aa_demo</rawdatadir>
-            <rawmeegdatadir desc='Directory to find raw MEEG data' ui='dir'>/home/runner/data/aa_demo</rawmeegdatadir>
+            <rawdatadir desc='Directories to find raw MRI data' ui='dir_list'>$HOME/data/aa_demo</rawdatadir>
+            <rawmeegdatadir desc='Directory to find raw MEEG data' ui='dir'>$HOME/data/aa_demo</rawmeegdatadir>
             <rawdataafterconversionprefix desc='Prefix of raw data after conversion from DICOM to NIFTI' ui='text'>fMR</rawdataafterconversionprefix>
             <subject_directory_format desc='Format of subject directory' ui='optionlist' options='from subject_directory_names|from data|S#|manual'>3</subject_directory_format>
             <rawseries_usefileorder desc='In raw data, use number in file listing not filtering by series number' ui='yesno'>0</rawseries_usefileorder>
@@ -20,33 +20,33 @@
             <dicomfilter ui='text'>*.IMA</dicomfilter>
             <toolbox desc='Toolbox with implemented interface in extrafunctions/toolboxes' ui='custom'>
                 <name desc='Name corresponding to the name of the interface without the "Class" suffix' ui='text'>spm</name>
-                <dir ui='dir'>/home/runner/tools/spm12</dir>
-            </toolbox>                       
+                <dir ui='dir'>$HOME/tools/spm12</dir>
+            </toolbox>
             <toolbox desc='Toolbox with implemented interface in extrafunctions/toolboxes' ui='custom'>
                 <name desc='Name corresponding to the name of the interface without the "Class" suffix' ui='text'>wls</name>
-                <dir ui='dir'>/home/runner/tools/rwls</dir>
+                <dir ui='dir'>$HOME/tools/rwls</dir>
             </toolbox>
             <toolbox desc='Toolbox with implemented interface in extrafunctions/toolboxes' ui='custom'>
                 <name desc='Name corresponding to the name of the interface without the "Class" suffix' ui='text'>aroma</name>
-                <dir ui='dir'>/home/runner/tools/ICA-AROMA</dir>
+                <dir ui='dir'>$HOME/tools/ICA-AROMA</dir>
             </toolbox>
             <linuxshell desc='Linux shell used to run linux commands' ui='text'>bash</linuxshell>
-            <fsldir desc='Path to fsl' ui='dir'>/home/runner/tools/fsl</fsldir>
-            <fslsetup desc='Path to fsl setup script, executing before any fsl command' ui='text'>/home/runner/tools/config/fsl_bash.sh</fslsetup>
+            <fsldir desc='Path to fsl' ui='dir'>$HOME/tools/fsl</fsldir>
+            <fslsetup desc='Path to fsl setup script, executing before any fsl command' ui='text'>$HOME/tools/config/fsl_bash.sh</fslsetup>
             <fslshell desc='Shell used to run FSL' ui='text'>bash</fslshell>
             <fsloutputtype desc='Output type used by FSL' ui='text'>NIFTI</fsloutputtype>
-            <freesurferdir desc='Path to freesurfer' ui='dir'>/home/runner/tools/freesurfer</freesurferdir>        
+            <freesurferdir desc='Path to freesurfer' ui='dir'>$HOME/tools/freesurfer</freesurferdir>
             <freesurfershell desc='Shell used to run FreeSurfer' ui='text'>bash</freesurfershell>
             <freesurfersetup desc='Path to FreeSurfer setup script, executing before any FreeSurfer command' ui='text'></freesurfersetup>
-            <freesurferenvironment desc='Path to FreeSurfer environmental setup script, executing before any FreeSurfer command' ui='text'>/home/runner/tools/freesurfer/FreeSurferEnv.sh;</freesurferenvironment>
-            <templatedir desc='Path to folder with various templates (e.g. for aamod_freesurfer_deface)' ui='dir'>/home/runner/tools/templates</templatedir>
-            <FaceMaskingdir desc='Path to FaceMasking (WUSTL NRG)' ui='dir'>/home/runner/tools/mask_face/nrg-improc</FaceMaskingdir>
+            <freesurferenvironment desc='Path to FreeSurfer environmental setup script, executing before any FreeSurfer command' ui='text'>$HOME/tools/freesurfer/FreeSurferEnv.sh;</freesurferenvironment>
+            <templatedir desc='Path to folder with various templates (e.g. for aamod_freesurfer_deface)' ui='dir'>$HOME/tools/templates</templatedir>
+            <FaceMaskingdir desc='Path to FaceMasking (WUSTL NRG)' ui='dir'>$HOME/tools/mask_face/nrg-improc</FaceMaskingdir>
             <allowremotecache desc='Allow local caching of files from remote server' ui='optionlist'>1</allowremotecache>
             <poolprofile desc='Cluster Profile and (optional) initial submit argument (e.g. asking for specific queue or resource) separated with colon' ui='text'>local</poolprofile>
         </directory_conventions>
         <options>
-            <maximumretry desc='Maximum number of (re)tries to retrieve file' ui='double'>5</maximumretry>            
-            <NIFTI4D desc="Use NIFTI-4D instead of NIFTI-3D" ui="yesno">1</NIFTI4D> 
+            <maximumretry desc='Maximum number of (re)tries to retrieve file' ui='double'>5</maximumretry>
+            <NIFTI4D desc="Use NIFTI-4D instead of NIFTI-3D" ui="yesno">1</NIFTI4D>
             <hardlinks desc='Allow hardlinks during retrieving inputs' ui='yesno'>0</hardlinks>
             <wheretoprocess desc='where to do processing' options='localsingle|localparallel|aws|qsub' ui='optionlist'>localsingle</wheretoprocess>
             <garbagecollection desc='Perform garbage collection after the analysis' ui='yesno'>1</garbagecollection>
@@ -55,11 +55,11 @@
             <restorepath desc='Restore linux and MATLAB path upon closing' ui='yesno'>1</restorepath>
             <diagnostic_videos desc='Enable diagnostic videos (matlab not stable on some platforms)' ui='yesno'>0</diagnostic_videos>
             <autoidentifyfieldmaps desc='Automatically identify field maps?' ui='yesno'>0</autoidentifyfieldmaps>
-            <autoidentifyt2 desc='Automatically identify T2?' ui='yesno'>0</autoidentifyt2>		
+            <autoidentifyt2 desc='Automatically identify T2?' ui='yesno'>0</autoidentifyt2>
             <autoidentifytmaps desc='Automatically identify t maps?' ui='yesno'>0</autoidentifytmaps>
         </options>
         <acq_details>
-            <root desc='Root on local machine for processed data' ui='dir'>/home/runner/projects</root>
+            <root desc='Root on local machine for processed data' ui='dir'>$HOME/projects</root>
         </acq_details>
     </local>
 </aap>

.github/workflows/aap_parameters_defaults_GitHub_minimal.xml

@@ -1,16 +1,16 @@
 <?xml version="1.0" encoding="utf-8"?>
 <aap xmlns:xi="http://www.w3.org/2001/XInclude">
-    <xi:include href="/home/runner/work/automaticanalysis/automaticanalysis/aa_parametersets/aap_parameters_defaults.xml" parse="xml"/>
+    <xi:include href="$HOME/work/automaticanalysis/automaticanalysis/aa_parametersets/aap_parameters_defaults.xml" parse="xml"/>
     <local>
         <directory_conventions>
-            <rawdatadir desc='Directories to find raw MRI data' ui='dir_list'>/home/runner/data/aa_demo</rawdatadir>
+            <rawdatadir desc='Directories to find raw MRI data' ui='dir_list'>$HOME/data/aa_demo</rawdatadir>
             <toolbox desc='Toolbox with implemented interface in extrafunctions/toolboxes' ui='custom'>
                 <name desc='Name corresponding to the name of the interface without the "Class" suffix' ui='text'>spm</name>
-                <dir ui='dir'>/home/runner/tools/spm12</dir>
+                <dir ui='dir'>$HOME/tools/spm12</dir>
             </toolbox>
         </directory_conventions>
         <acq_details>
-            <root desc='Root on local machine for processed data' ui='dir'>/home/runner/projects</root>
+            <root desc='Root on local machine for processed data' ui='dir'>$HOME/projects</root>
         </acq_details>
     </local>
 </aap>

.github/workflows/trigger_install.py

@@ -3,14 +3,47 @@
 # 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 os
 import sys
 import subprocess
 import platform
 
 def main():
+    # Replace before any install, because various install steps use the parameter xml
+    parameter_xml_env_var_replace()
     do_install()
 
+
+def parameter_xml_env_var_replace():
+    """Platform-indepent replacement of environment variables in the source parameter xml
+
+    Path specifications in the parameter xml use environment variable references because
+    paths are different on the different runner platforms. However, environment variable
+    references themselves are also platform-dependent.
+
+    Replace specific unix-style environment variable references in the parameter xml file
+    with the value of the environment variable on the current runner platform, to produce
+    a parameter xml file without env var references."""
+
+    var_workspace = os.environ['GITHUB_WORKSPACE']
+    var_par_xml = os.environ['PARAMETER_XML']
+    # TODO: check that home is also ok on windows.
+    var_home = os.environ['HOME']
+
+    # Read in the file
+    fname = os.path.join(var_workspace, '.github', 'workflows', var_par_xml)
+    with open(fname, 'r') as file :
+        filedata = file.read()
+
+    # Replace $HOME with its value
+    filedata = filedata.replace('$HOME', var_home)
+
+    # Write the file out again
+    with open(fname, 'w') as file:
+        file.write(filedata)
+
 def do_install():
+    """Install tools and parameter xml """
     plt = platform.system()
     if plt == "Windows":
         print("Your system is Windows")