Large structure and pathing changes to move the notion of the lossless pipeline into derivatives.

.gitmodules

-[submodule "bids/code/lossless/dependencies/eeglab_asr_amica"]
-	path = bids/code/lossless/dependencies/eeglab_asr_amica
-	url = https://git.sharcnet.ca/bucanl_eeglab_versions/eeglab_lossless.git

eeglab_asr_amica @ 32e79550

-Subproject commit 32e79550469fbfdcf2a4c5aeed46586611d99fb7

bids/code/lossless/config/amica-sqsub.sesinit → bids/derivatives/lossless/code/config/amica-sqsub.sesinit

@@ -5,5 +5,5 @@ export OMPI_MCA_mpi_cuda_support
 module purge
 module load intel/17.0.1 ldwrapper torque/2.5.13 sq-tm/2.5
 # Uses module-force to force loading of incompatible packages
-eval `bids/code/lossless/tools/module-force load openmpi/intel/1.6.5`
+eval `bids/derivatives/lossless/code/tools/module-force load openmpi/intel/1.6.5`
 

bids/code/lossless/config/contextconfig.cfg → bids/derivatives/lossless/code/config/contextconfig.cfg

@@ -3,7 +3,7 @@ log
 local_project
 	
 local_dependency
-	bids/code/lossless/dependencies
+	bids/derivatives/lossless/code/dependencies
 remote_user_name
 	user_name
 remote_exec_host
@@ -11,17 +11,17 @@ remote_exec_host
 remote_project_archive
 	graham.computecanada.ca:/project/group_name/user_name/project_name/
 remote_project_work
-	graham.computecanada.ca:/scratch/group_name/user_name/project_name/
+	graham.computecanada.ca:/scratch/user_name/project_name/
 remote_dependency
-	graham.computecanada.ca:/scratch/group_name/user_name/project_name/bids/code/lossless/dependencies
+	graham.computecanada.ca:/scratch/user_name/project_name/bids/code/lossless/dependencies
 mount_archive
 	remote_archive
 mount_work
 	remote_work
 misc
-    [config_dir] bids/code/lossless/config
+    [config_dir] bids/derivatives/lossless/code/config
     [data_dir] bids/
-    [script_dir] bids/code/lossless/scripts
+    [script_dir] bids/derivatives/lossless/code/scripts
 system_cmds
 	sshfs [remote_user_name]@[remote_project_archive] [cd]/[mount_archive]
 	sshfs [remote_user_name]@[remote_project_work] [cd]/[mount_work]

bids/code/lossless/config/matlab.minit → bids/derivatives/lossless/code/config/matlab.minit

 warning off;
 
 addpath([pwd '/bids/code/lossless/dependencies/eeglab_asr_amica'], ...
-  [pwd '/bids/code/lossless/dependencies/matlog']);
+  [pwd '/bids/derivatives/lossless/code/dependencies/matlog']);
 
 % eeglab auto loads the path correctly instead of shotgun blasting with
 % addpath(genpath(<>)) as we were doing prior

bids/code/lossless/config/octave.minit → bids/derivatives/lossless/code/config/octave.minit

@@ -2,7 +2,7 @@ warning off;
 
 pkg load signal;
 addpath([pwd '/bids/code/lossless/dependencies/eeglab_asr_amica'], ...
-  [pwd '/bids/code/lossless/dependencies/matlog']);
+  [pwd '/bids/derivatives/lossless/code/dependencies/matlog']);
 cd '[:,1,remote_project_work]';
 
 % eeglab auto loads the path correctly instead of shotgun blasting with

bids/code/lossless/config/remote-sbatch/c01_scalpart_remote.cfg → bids/derivatives/lossless/code/config/remote-sbatch/c01_scalpart_remote.cfg

@@ -16,7 +16,7 @@ replace_string
 	[sd_ch_vals],[.15 .85]
 	[sd_ch_o],3
 	[sd_ch_p],.2
-	[ref_loc_file],bids/code/lossless/misc/standard_1020_bucanl19.elc
+	[ref_loc_file],bids/derivatives/lossless/code/misc/standard_1020_bucanl19.elc
 	[low_bound_hz],1
 	[high_bound_hz],30
 	[save_f_res],1
@@ -34,12 +34,12 @@ replace_string
 	[r_t_p],.2
 	[min_gap_ms],2000
 	[out_path],bids/derivatives/lossless
-	[amica_param_file],bids/code/lossless/misc/amica15_default.param
+	[amica_param_file],bids/derivatives/lossless/code/misc/amica15_default.param
 	[amica_threads_s02],8
 order
 	1
 session_init
-	bids/code/lossless/config/octave.sesinit
+	bids/derivatives/lossless/code/config/octave.sesinit
 job_name
 	[batch_hfn,.,1]_[/,-1,batch_dfn,.,-1]
 mfile_name
@@ -47,7 +47,7 @@ mfile_name
 job_init
 	 
 m_init
-	bids/code/lossless/config/octave.minit
+	bids/derivatives/lossless/code/config/octave.minit
 submit_options
 	--account=def-jdesjard
 memory

bids/code/lossless/config/remote-sbatch/c02_amica_init_remote.cfg → bids/derivatives/lossless/code/config/remote-sbatch/c02_amica_init_remote.cfg

@@ -3,19 +3,19 @@ file_name
 exec_func
 	ef_sbatch
 replace_string
-	[dep_path],bids/code/lossless/dependencies/eeglab_asr_amica/plugins/amica
+	[dep_path],bids/derivatives/lossless/code/dependencies/eeglab_asr_amica/plugins/amica
     [in_path],analysis/data/2_preproc
     [amica_ver],amica15
 order
 	[2 1]
 session_init
-	bids/code/lossless/config/amica.sesinit
+	bids/derivatives/lossless/code/config/amica.sesinit
 job_name
 	[batch_hfn,.,1]_[/,-1,batch_dfn,.,-1]
 mfile_name
 	[/,-1,batch_dfn,.,-1]
 job_init
-	 bids/code/lossless/config/amica.jobinit
+	 bids/derivatives/lossless/code/config/amica.jobinit
 m_init
 	
 submit_options

bids/code/lossless/config/remote-sbatch/c03_compart_data_remote.cfg → bids/derivatives/lossless/code/config/remote-sbatch/c03_compart_data_remote.cfg

@@ -12,12 +12,12 @@ replace_string
 	[sd_t_p],.2
 	[min_gap_ms],2000
 	[out_path],bids/derivatives/lossless
-	[amica_param_file],bids/code/lossless/misc/amica_default.param
+	[amica_param_file],bids/derivatives/lossless/code/misc/amica_default.param
 	[amica_threads_s07_08_09],8
 order
 	[3 2]
 session_init
-	bids/code/lossless/config/octave.sesinit
+	bids/derivatives/lossless/code/config/octave.sesinit
 job_name
 	[batch_hfn,.,1]_[/,-1,batch_dfn,.,-1]
 mfile_name
@@ -25,7 +25,7 @@ mfile_name
 job_init
 	 
 m_init
-	bids/code/lossless/config/octave.minit
+	bids/derivatives/lossless/code/config/octave.minit
 submit_options
 	--account=def-jdesjard
 memory