Update pre-commit configuration

... and fix issues reported by the new checks

.gitignore

@@ -23,4 +23,3 @@ python/soma_workflow.egg-info/
 # Pycharm project#
 ##################
 .idea
-

.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

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)
-

bin/soma_restart_workflow

@@ -33,5 +33,3 @@ if __name__ == '__main__':
     else:
         queue = sys.argv[3]
         wfc.restart_workflow(workflow_id, queue)
-
-

bin/soma_stop_workflow

@@ -28,6 +28,3 @@ if __name__ == '__main__':
     wfc = WorkflowController(sys.argv[2])
 
     wfc.stop_workflow(workflow_id)
-
-
-

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)
-
-
-

doc/source/changes_swf3.txt

@@ -97,4 +97,3 @@ Ex:
     light_mode = 1
     scheduler_type = local_basic
     allowed_python_versions = 3
-

doc/source/client_API.txt

@@ -140,4 +140,3 @@ Helper
 .. automethod:: Helper.unserialize
 
 .. automethod:: Helper.convert_wf_file_for_p2_5
-

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.
-
-
-
-
-
-

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)
-
-

doc/source/index.txt

@@ -264,6 +264,3 @@ Authors and contributors
 ..
   :Release: |release|
   :Date: |today|
-
-
-

doc/source/install_config.txt

@@ -677,4 +677,3 @@ Ex:
   CPU_NB = 2
   MAX_CPU_NB = 16
   SCHEDULER_INTERVAL = 1
-

doc/source/scheduler.txt

@@ -68,4 +68,3 @@ MPI implementation
 
 .. automodule:: soma_workflow.schedulers.mpi_scheduler
     :members:
-

doc/source/status_list.txt

@@ -239,7 +239,3 @@ File Transfer status
                   :height: 100 px
                   :width: 100 px
                   :scale: 30
-
-
-
-

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.
-

documents/memo_github.md

@@ -16,4 +16,3 @@ $ git log --follow ./path/to/file
 ```
 
 c.f http://git-scm.com/docs/git-log
-

ez_setup.py

@@ -1,4 +1,3 @@
-#!/usr/bin/env python
 # -*- coding: utf-8 -*-
 """Bootstrap setuptools installation
 

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
-
-
-

python/soma_workflow/clean_server.py

@@ -1,4 +1,3 @@
-#! /usr/bin/env python
 # -*- coding: utf-8 -*-
 
 from __future__ import absolute_import

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)
-

python/soma_workflow/setup_client2server.py

@@ -1,4 +1,3 @@
-#! /usr/bin/env python
 # -*- coding: utf-8 -*-
 
 """

python/soma_workflow/setup_server.py

@@ -1,4 +1,3 @@
-#! /usr/bin/env python
 # -*- coding: utf-8 -*-
 
 """

python/soma_workflow/start_database_server.py

@@ -1,4 +1,3 @@
-#!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
 '''

python/soma_workflow/test/data/PlatformTest/testlocal.stdin

@@ -2,4 +2,3 @@
 0
 1
 0
-

python/soma_workflow/test/data/TestDrmaaCTypes.py

@@ -1,4 +1,3 @@
-#!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
 

python/soma_workflow/test/data/config_examples/soma-workflow-scheduler.cfg

@@ -1,4 +1,4 @@
 [local_scheduler]
 
 CPU_NB = 2
-PERIOD = 1
+PERIOD = 1

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.
-

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.
-

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

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

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)

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

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

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.
-

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.
-

python/soma_workflow/test/data/jobExamples/complete/output_models/stdout_exception_job

@@ -1 +1 @@
-This is a program which throws an exception.
+This is a program which throws an exception.

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
+. $SOMA_JOB_MPI_BIN/mpirun -machinefile `eval echo $SOMA_JOB_NODE_FILE` -np $1 $2

python/soma_workflow/test/data/jobExamples/special_transfers/example.hdr

@@ -1,3 +1,2 @@
 
 File with extension .hdr
-

python/soma_workflow/test/data/jobExamples/special_transfers/example.img

@@ -1,4 +1,3 @@
 
 
 File with extension .img
-