diff --git a/.gitignore b/.gitignore
index 02e56725..7a4f2ef3 100644
--- a/.gitignore
+++ b/.gitignore
@@ -23,4 +23,3 @@ python/soma_workflow.egg-info/
 # Pycharm project#
 ##################
 .idea
-
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 5b10eee2..0f2cf6f2 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -1,20 +1,24 @@
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v2.5.0
+    rev: v4.0.1
     hooks:
+    -   id: check-added-large-files
     -   id: check-case-conflict
     -   id: check-executables-have-shebangs
     -   id: check-json
     -   id: check-merge-conflict
+    -   id: check-shebang-scripts-are-executable
     -   id: check-symlinks
     -   id: check-xml
     -   id: check-yaml
     -   id: debug-statements
+    -   id: end-of-file-fixer
+    -   id: fix-byte-order-marker
     -   id: fix-encoding-pragma
-    -   id: check-added-large-files
+    #-   id: trailing-whitespace  # not ready yet
 
 -   repo: https://gitlab.com/pycqa/flake8
-    rev: 3.7.9
+    rev: 3.9.2
     hooks:
     -   id: flake8
         name: flake8 under python2
diff --git a/bin/soma_kill_servers b/bin/soma_kill_servers
index b0a79626..c61f60b5 100755
--- a/bin/soma_kill_servers
+++ b/bin/soma_kill_servers
@@ -24,4 +24,3 @@ clear_db = options.clear
 
 connection.RemoteConnection.kill_remote_servers(
     resource_id, login=login, passwd=passwd, clear_db=clear_db)
-
diff --git a/bin/soma_restart_workflow b/bin/soma_restart_workflow
index fde13d3b..5f608b48 100755
--- a/bin/soma_restart_workflow
+++ b/bin/soma_restart_workflow
@@ -33,5 +33,3 @@ if __name__ == '__main__':
     else:
         queue = sys.argv[3]
         wfc.restart_workflow(workflow_id, queue)
-
-
diff --git a/bin/soma_stop_workflow b/bin/soma_stop_workflow
index 3a1f5be4..b9175be3 100755
--- a/bin/soma_stop_workflow
+++ b/bin/soma_stop_workflow
@@ -28,6 +28,3 @@ if __name__ == '__main__':
     wfc = WorkflowController(sys.argv[2])
 
     wfc.stop_workflow(workflow_id)
-
-
-
diff --git a/bin/soma_submit_workflow b/bin/soma_submit_workflow
index ef1ef64e..02439017 100755
--- a/bin/soma_submit_workflow
+++ b/bin/soma_submit_workflow
@@ -41,6 +41,3 @@ if __name__ == '__main__':
     wfc = WorkflowController(args.resource)
 
     wfc.submit_workflow(workflow, name = args.name, queue = args.queue)
-
-
-
diff --git a/doc/source/changes_swf3.txt b/doc/source/changes_swf3.txt
index 90bbed9e..58e954ea 100644
--- a/doc/source/changes_swf3.txt
+++ b/doc/source/changes_swf3.txt
@@ -97,4 +97,3 @@ Ex:
     light_mode = 1
     scheduler_type = local_basic
     allowed_python_versions = 3
-
diff --git a/doc/source/client_API.txt b/doc/source/client_API.txt
index 72da4f5a..8567fcde 100644
--- a/doc/source/client_API.txt
+++ b/doc/source/client_API.txt
@@ -140,4 +140,3 @@ Helper
 .. automethod:: Helper.unserialize
 
 .. automethod:: Helper.convert_wf_file_for_p2_5
-
diff --git a/doc/source/examples.txt b/doc/source/examples.txt
index 89bc0f88..6884305c 100644
--- a/doc/source/examples.txt
+++ b/doc/source/examples.txt
@@ -439,9 +439,3 @@ the output files.
 
 The data directory "/tmp/soma_workflow_examples/" on your machine  should now 
 contains the file copy_of_myfile.
-
-
-
-
-
-
diff --git a/doc/source/gui.txt b/doc/source/gui.txt
index 8eb66816..622e1d33 100644
--- a/doc/source/gui.txt
+++ b/doc/source/gui.txt
@@ -181,5 +181,3 @@ Several plots can be displayed and refreshed at regular time interval:
 * the jobs function of the time, also showing the number or CPU cores used by each job (new in Soma-Workflow 3.0)
 * the number of jobs running function of the time.
 * the number of CPU cores running function of the time (new in Soma-Workflow 3.0)
-
-
diff --git a/doc/source/index.txt b/doc/source/index.txt
index 8288308d..645cce71 100644
--- a/doc/source/index.txt
+++ b/doc/source/index.txt
@@ -264,6 +264,3 @@ Authors and contributors
 ..
   :Release: |release|
   :Date: |today|
-
-
-
diff --git a/doc/source/install_config.txt b/doc/source/install_config.txt
index 8f30197a..2d94fe2f 100644
--- a/doc/source/install_config.txt
+++ b/doc/source/install_config.txt
@@ -677,4 +677,3 @@ Ex:
   CPU_NB = 2
   MAX_CPU_NB = 16
   SCHEDULER_INTERVAL = 1
-
diff --git a/doc/source/scheduler.txt b/doc/source/scheduler.txt
index a3ded141..698086d9 100644
--- a/doc/source/scheduler.txt
+++ b/doc/source/scheduler.txt
@@ -68,4 +68,3 @@ MPI implementation
 
 .. automodule:: soma_workflow.schedulers.mpi_scheduler
     :members:
-
diff --git a/doc/source/status_list.txt b/doc/source/status_list.txt
index f6755304..45749c4a 100644
--- a/doc/source/status_list.txt
+++ b/doc/source/status_list.txt
@@ -239,7 +239,3 @@ File Transfer status
                   :height: 100 px
                   :width: 100 px
                   :scale: 30
-
-
-
-
diff --git a/doc/source/workflow_creation.txt b/doc/source/workflow_creation.txt
index 77efc072..bb1d0814 100644
--- a/doc/source/workflow_creation.txt
+++ b/doc/source/workflow_creation.txt
@@ -477,4 +477,3 @@ A few engine execution jobs types have been defined and are available for workfl
 
 
 Such jobs are alternatives to :ref:`params_link_functions` described above.
-
diff --git a/doc/upload2github b/doc/upload2github
deleted file mode 100644
index 50d6a160..00000000
--- a/doc/upload2github
+++ /dev/null
@@ -1,29 +0,0 @@
-#!/bin/sh -e
-
-#
-# This script is not needed any longer, the github push automatically triggers
-# deploying docs on gh-pages (via travis-ci).
-#
-
-# clean build directory
-rm -rf ./build
-mkdir ./build
-
-# clone the repo into a dir called build/html
-git clone --branch gh-pages --no-checkout git@github.com:populse/soma-workflow.git ./build/html
-
-# create sphinx documentation in clear directory
-make html
-
-# add configaration file to enable _<dir>
-cd ./build/html/
-touch .nojekyll
-
-# commit changes
-git add .
-git commit -a -m "Automatic update of soma-workflow documentation"
-
-# send commit to github server
-git push origin gh-pages
-
-echo "You can now visit the soma-workflow page at http://neurospin.github.io/soma-workflow/" 
diff --git a/documents/memo_github.md b/documents/memo_github.md
index 52a2b255..8c8b8951 100644
--- a/documents/memo_github.md
+++ b/documents/memo_github.md
@@ -16,4 +16,3 @@ $ git log --follow ./path/to/file
 ```
 
 c.f http://git-scm.com/docs/git-log
-
diff --git a/ez_setup.py b/ez_setup.py
index 6af0b717..3f6ba601 100644
--- a/ez_setup.py
+++ b/ez_setup.py
@@ -1,4 +1,3 @@
-#!/usr/bin/env python
 # -*- coding: utf-8 -*-
 """Bootstrap setuptools installation
 
diff --git a/pack2pypi.sh b/pack2pypi.sh
index 22ed9ecf..051eaaa7 100755
--- a/pack2pypi.sh
+++ b/pack2pypi.sh
@@ -31,6 +31,3 @@ cat setup.py | sed -e "s/development version/$FULLVERSION/" > ./$PACKNAME/setup.
 VERSIONPATH=./$PACKNAME/python/soma_workflow
 echo fullVersion = \'$FULLVERSION\' > $VERSIONPATH/version.py
 echo shortVersion = \'$SHORTVERSION\' >> $VERSIONPATH/version.py
-
-
-
diff --git a/python/soma_workflow/clean_server.py b/python/soma_workflow/clean_server.py
index 0cb6495e..e08063bc 100644
--- a/python/soma_workflow/clean_server.py
+++ b/python/soma_workflow/clean_server.py
@@ -1,4 +1,3 @@
-#! /usr/bin/env python
 # -*- coding: utf-8 -*-
 
 from __future__ import absolute_import
diff --git a/python/soma_workflow/configuration.py b/python/soma_workflow/configuration.py
index b4d29dd3..735a1abc 100644
--- a/python/soma_workflow/configuration.py
+++ b/python/soma_workflow/configuration.py
@@ -1543,4 +1543,3 @@ def restore_soma_workflow_directory():
         else:
             Configuration.search_config_path \
                 = staticmethod(Configuration._old_search_config_path)
-
diff --git a/python/soma_workflow/setup_client2server.py b/python/soma_workflow/setup_client2server.py
index c95cc148..d581e66d 100644
--- a/python/soma_workflow/setup_client2server.py
+++ b/python/soma_workflow/setup_client2server.py
@@ -1,4 +1,3 @@
-#! /usr/bin/env python
 # -*- coding: utf-8 -*-
 
 """
diff --git a/python/soma_workflow/setup_server.py b/python/soma_workflow/setup_server.py
index 12b928de..54f2b016 100644
--- a/python/soma_workflow/setup_server.py
+++ b/python/soma_workflow/setup_server.py
@@ -1,4 +1,3 @@
-#! /usr/bin/env python
 # -*- coding: utf-8 -*-
 
 """
diff --git a/python/soma_workflow/start_database_server.py b/python/soma_workflow/start_database_server.py
index 53223b72..03609111 100644
--- a/python/soma_workflow/start_database_server.py
+++ b/python/soma_workflow/start_database_server.py
@@ -1,4 +1,3 @@
-#!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
 '''
diff --git a/python/soma_workflow/test/data/PlatformTest/testlocal.stdin b/python/soma_workflow/test/data/PlatformTest/testlocal.stdin
index 78ade449..3dbd4043 100644
--- a/python/soma_workflow/test/data/PlatformTest/testlocal.stdin
+++ b/python/soma_workflow/test/data/PlatformTest/testlocal.stdin
@@ -2,4 +2,3 @@
 0
 1
 0
-
diff --git a/python/soma_workflow/test/data/PlatformTest/ubuntu.sh b/python/soma_workflow/test/data/PlatformTest/ubuntu.sh
old mode 100644
new mode 100755
diff --git a/python/soma_workflow/test/data/TestDrmaaCTypes.py b/python/soma_workflow/test/data/TestDrmaaCTypes.py
index c88671d2..42f9f65a 100644
--- a/python/soma_workflow/test/data/TestDrmaaCTypes.py
+++ b/python/soma_workflow/test/data/TestDrmaaCTypes.py
@@ -1,4 +1,3 @@
-#!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
 
diff --git a/python/soma_workflow/test/data/config_examples/soma-workflow-scheduler.cfg b/python/soma_workflow/test/data/config_examples/soma-workflow-scheduler.cfg
index 2e9823ec..d74f4ac9 100644
--- a/python/soma_workflow/test/data/config_examples/soma-workflow-scheduler.cfg
+++ b/python/soma_workflow/test/data/config_examples/soma-workflow-scheduler.cfg
@@ -1,4 +1,4 @@
 [local_scheduler]
 
 CPU_NB = 2
-PERIOD = 1
\ No newline at end of file
+PERIOD = 1
diff --git a/python/soma_workflow/test/data/jobExamples/complete/file0 b/python/soma_workflow/test/data/jobExamples/complete/file0
old mode 100755
new mode 100644
index 580db7aa..0843220b
--- a/python/soma_workflow/test/data/jobExamples/complete/file0
+++ b/python/soma_workflow/test/data/jobExamples/complete/file0
@@ -13,4 +13,3 @@ Directions
 
    1. In a large bowl, sift together the flour, baking powder, salt and sugar. Make a well in the center and pour in the milk, egg and melted butter; mix until smooth.
    2. Heat a lightly oiled griddle or frying pan over medium high heat. Pour or scoop the batter onto the griddle, using approximately 1/4 cup for each pancake. Brown on both sides and serve hot.
-
diff --git a/python/soma_workflow/test/data/jobExamples/complete/file1 b/python/soma_workflow/test/data/jobExamples/complete/file1
index b5476077..cbe647f0 100644
--- a/python/soma_workflow/test/data/jobExamples/complete/file1
+++ b/python/soma_workflow/test/data/jobExamples/complete/file1
@@ -1,4 +1,3 @@
 
 
 This is a Soma-Workflow example file used as input to job and workflow tests.
-
diff --git a/python/soma_workflow/test/data/jobExamples/complete/job5.py b/python/soma_workflow/test/data/jobExamples/complete/job5.py
index 89aaa565..856154d2 100644
--- a/python/soma_workflow/test/data/jobExamples/complete/job5.py
+++ b/python/soma_workflow/test/data/jobExamples/complete/job5.py
@@ -1,4 +1,3 @@
-#!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
 # calls job1 using params IO as json
diff --git a/python/soma_workflow/test/data/jobExamples/complete/job6.py b/python/soma_workflow/test/data/jobExamples/complete/job6.py
index b501c06a..2efdab33 100644
--- a/python/soma_workflow/test/data/jobExamples/complete/job6.py
+++ b/python/soma_workflow/test/data/jobExamples/complete/job6.py
@@ -1,4 +1,3 @@
-#!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
 # calls job1 using params IO as json
diff --git a/python/soma_workflow/test/data/jobExamples/complete/job7.py b/python/soma_workflow/test/data/jobExamples/complete/job7.py
index 0ea2b98e..a907cae0 100644
--- a/python/soma_workflow/test/data/jobExamples/complete/job7.py
+++ b/python/soma_workflow/test/data/jobExamples/complete/job7.py
@@ -1,4 +1,3 @@
-#!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
 # inputs: as env var SOMAWF_INPUT_PARAMS
@@ -25,8 +24,8 @@
 if not os.path.exists(out_dir):
     os.mkdir(out_dir)
 
-filePathsOut = [os.path.join(out_dir, os.path.basename(f))
-                for f in filePathsIn]
+filePathsOut = [os.path.join(out_dir, os.path.basename(fp))
+                for fp in filePathsIn]
 
 for fin, fout in zip(filePathsIn, filePathsOut):
     shutil.copy2(fin, fout)
diff --git a/python/soma_workflow/test/data/jobExamples/complete/job8.py b/python/soma_workflow/test/data/jobExamples/complete/job8.py
index f5bcb820..a44a6c7d 100644
--- a/python/soma_workflow/test/data/jobExamples/complete/job8.py
+++ b/python/soma_workflow/test/data/jobExamples/complete/job8.py
@@ -1,4 +1,3 @@
-#!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
 # input: "input" param in json dict
diff --git a/python/soma_workflow/test/data/jobExamples/complete/job9.py b/python/soma_workflow/test/data/jobExamples/complete/job9.py
index 998642f6..08ab6be9 100644
--- a/python/soma_workflow/test/data/jobExamples/complete/job9.py
+++ b/python/soma_workflow/test/data/jobExamples/complete/job9.py
@@ -1,4 +1,3 @@
-#!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
 # input: "inputs" param in json dict, list of files
diff --git a/python/soma_workflow/test/data/jobExamples/complete/output_models/file13 b/python/soma_workflow/test/data/jobExamples/complete/output_models/file13
index 40d75144..d16c9eeb 100644
--- a/python/soma_workflow/test/data/jobExamples/complete/output_models/file13
+++ b/python/soma_workflow/test/data/jobExamples/complete/output_models/file13
@@ -21,4 +21,3 @@ job8 output:
 
 
 This is a Soma-Workflow example file used as input to job and workflow tests.
-
diff --git a/python/soma_workflow/test/data/jobExamples/complete/output_models/file17 b/python/soma_workflow/test/data/jobExamples/complete/output_models/file17
index b763448f..a39da92d 100644
--- a/python/soma_workflow/test/data/jobExamples/complete/output_models/file17
+++ b/python/soma_workflow/test/data/jobExamples/complete/output_models/file17
@@ -14,4 +14,3 @@ Directions
 
    1. In a large bowl, sift together the flour, baking powder, salt and sugar. Make a well in the center and pour in the milk, egg and melted butter; mix until smooth.
    2. Heat a lightly oiled griddle or frying pan over medium high heat. Pour or scoop the batter onto the griddle, using approximately 1/4 cup for each pancake. Brown on both sides and serve hot.
-
diff --git a/python/soma_workflow/test/data/jobExamples/complete/output_models/stdout_exception_job b/python/soma_workflow/test/data/jobExamples/complete/output_models/stdout_exception_job
index a3f3a814..31ddc763 100644
--- a/python/soma_workflow/test/data/jobExamples/complete/output_models/stdout_exception_job
+++ b/python/soma_workflow/test/data/jobExamples/complete/output_models/stdout_exception_job
@@ -1 +1 @@
-This is a program which throws an exception.
\ No newline at end of file
+This is a program which throws an exception.
diff --git a/python/soma_workflow/test/data/jobExamples/complete/stdin1 b/python/soma_workflow/test/data/jobExamples/complete/stdin1
old mode 100755
new mode 100644
diff --git a/python/soma_workflow/test/data/jobExamples/complete/stdin2 b/python/soma_workflow/test/data/jobExamples/complete/stdin2
old mode 100755
new mode 100644
diff --git a/python/soma_workflow/test/data/jobExamples/complete/stdin3 b/python/soma_workflow/test/data/jobExamples/complete/stdin3
old mode 100755
new mode 100644
diff --git a/python/soma_workflow/test/data/jobExamples/complete/stdin4 b/python/soma_workflow/test/data/jobExamples/complete/stdin4
old mode 100755
new mode 100644
diff --git a/python/soma_workflow/test/data/jobExamples/mpi/simple_mpi.sh b/python/soma_workflow/test/data/jobExamples/mpi/simple_mpi.sh
index 8ec3a779..3ee965d5 100755
--- a/python/soma_workflow/test/data/jobExamples/mpi/simple_mpi.sh
+++ b/python/soma_workflow/test/data/jobExamples/mpi/simple_mpi.sh
@@ -1,4 +1,4 @@
 #!/bin/bash
 echo "SOMA_JOB_MPI_BIN" $SOMA_JOB_MPI_BIN "SOMA_JOB_NODE_FILE" $SOMA_JOB_NODE_FILE
 
-. $SOMA_JOB_MPI_BIN/mpirun -machinefile `eval echo $SOMA_JOB_NODE_FILE` -np $1 $2
\ No newline at end of file
+. $SOMA_JOB_MPI_BIN/mpirun -machinefile `eval echo $SOMA_JOB_NODE_FILE` -np $1 $2
diff --git a/python/soma_workflow/test/data/jobExamples/special_transfers/example.hdr b/python/soma_workflow/test/data/jobExamples/special_transfers/example.hdr
index 0dda084f..f0369527 100644
--- a/python/soma_workflow/test/data/jobExamples/special_transfers/example.hdr
+++ b/python/soma_workflow/test/data/jobExamples/special_transfers/example.hdr
@@ -1,3 +1,2 @@
 
 File with extension .hdr
-
diff --git a/python/soma_workflow/test/data/jobExamples/special_transfers/example.img b/python/soma_workflow/test/data/jobExamples/special_transfers/example.img
index 9c09ed7c..14a80be7 100644
--- a/python/soma_workflow/test/data/jobExamples/special_transfers/example.img
+++ b/python/soma_workflow/test/data/jobExamples/special_transfers/example.img
@@ -1,4 +1,3 @@
  
 
 File with extension .img
-