Merge branch '_TMP_RELEASE_BRANCH_' into niak-cog

Author: poquirion

.circleci/config.yml

@@ -0,0 +1,22 @@
+version: 2
+jobs:
+  build:
+    working_directory: /niak
+    docker:
+      - image: docker:17.05.0-ce-git
+    steps:
+      - checkout
+      - setup_remote_docker
+      - run:
+          name: Niak test all
+          command: |
+            [ ! "$(docker ps -a | grep data_container)" ] && docker create -v /niak --name data_container alpine /bin/true
+            docker cp /niak data_container:/
+            docker run -it --volumes-from data_container simexp/niak_dependency:o4_cross_u16 /bin/bash -lic "cd /niak; octave --no-gui --eval \"addpath(genpath(pwd));[pipe,opt,status] = niak_test_all(struct(),struct('psom',struct('mode_pipeline_manager','session','mode','background','max_queued',6,'flag_pause',false))); exit(status)\""
+            docker cp data_container:/niak/result /niak/result
+      - store_artifacts:
+          path: /niak/result
+#      - deploy:
+#          name: Push application Docker image
+#          command: |
+#            docker build -t simexp/niak:${A_TAG} .

.gitignore

@@ -4,3 +4,4 @@ BCT/
 *.pyc
 *.asv
 psom_gb_vars_local.m
+TODO

README.md

@@ -1,4 +1,4 @@
-[![Build Status](https://circleci.com/gh/SIMEXP/niak.svg?style=shield&circle-token=:circle-token)](https://circleci.com/gh/SIMEXP/niak)
+[![Build Status](https://circleci.com/gh/SIMEXP/niak.svg?style=shield&circle-token=:circle-token)](https://circleci.com/gh/SIMEXP/niak) [![License: MIT](https://img.shields.io/badge/License-MIT-blue.svg)](https://opensource.org/licenses/MIT)
 
 The neuroimaging analysis kit (NIAK) is a library of functions for the preprocessing and connectivity analysis of large functional neuroimaging data, using GNU Octave, and distributed under a MIT license. Essential documentation can be found on the [NIAK website](http://niak.simexp-lab.org/). The NIAK is developed and maintained by members and collaborators of the [SIMEXP laboratory](simexp-lab.org), Department of Computer Science and Operations research ([DIRO](http://en.diro.umontreal.ca/home/)), Geriatric institute of Montreal ([CRIUGM](http://www.criugm.qc.ca/)), [University of Montreal](http://www.umontreal.ca/english/). Many of the functions of the kit are based on software developed over the years by members and collaborators of the [Brain Imaging Center](http://www.bic.mni.mcgill.ca/), [McGill University](http://www.mcgill.ca/). See the [contributors](https://github.com/SIMEXP/niak/wiki/NIAK-contributors) page for more details.
 

circle.yml

@@ -133,7 +133,7 @@
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
 %% NIAK version
-GB_NIAK.version = 'v1.1.3';
+GB_NIAK.version = 'v1.1.4';
 
 %% Target for tests
 GB_NIAK.target_test = 'aj';

commands/misc/niak_gb_vars.m

@@ -89,7 +89,13 @@ def main(args=None):
         raise IOError("Pipeline {} not supported".format(pipeline_name))
 
     if pipeline_name == "Niak_fmri_preprocess":
-        logging.basicConfig(level=logging.INFO, format=('%(lineno)s - %(name)s - %(levelname)s - %(message)s'))
+
+        try:
+            log_level = os.getenv("NIAK_LOG_LEVEL")
+            logging.basicConfig(level=log_level, format=('%(lineno)s - %(name)s - %(levelname)s - %(message)s'))
+        except ValueError:  # Unknown level
+            logging.basicConfig(level=logging.INFO, format=('%(lineno)s - %(name)s - %(levelname)s - %(message)s'))
+
         pipeline = pyniak.load_pipeline.FmriPreprocess(folder_in=parsed.file_in,
                                                        folder_out=parsed.folder_out,
                                                        subjects=parsed.subjects,

util/bin/niak_cmd.py

@@ -84,6 +84,8 @@ def run(self):
         self.psom_gb_vars_local_setup()
 
         try:
+            logging.info("{}".format(" ".join(self.octave_cmd)))
+            logging.info(("{0};\n{1}(files_in, opt);".format(";\n".join(self.octave_options), self.pipeline_name)))
             p = subprocess.Popen(self.octave_cmd)
             p.wait()
         except BaseException as e:
@@ -104,7 +106,7 @@ def octave_cmd(self):
         tmp_oct = tempfile.NamedTemporaryFile('w', prefix='niak_script_', suffix='.m', dir='/tmp', delete=False)
         tmp_oct.write(("{0};\n{1}(files_in, opt);".format(";\n".join(self.octave_options), self.pipeline_name)))
         tmp_oct.close()
-        return ["/usr/bin/env", "octave", "{}".format(tmp_oct.name)]
+        return ["/usr/bin/env", "octave", "--no-gui", "{}".format(tmp_oct.name)]
 
     @property
     def octave_options(self):
@@ -205,8 +207,8 @@ def grabber_construction(self):
                     logging.debug("func hint {}".format(self.func_hint))
                     opt_list += ["opt_gr.func_hint = '{0}'".format(self.func_hint)]
                 if self.anat_hint:
-                    logging.debug("anat hint {}".format(self.anat_hint))
-                    opt_list += ["opt_gr.anat_hint = '{0}'".format(self.func_hint)]
+                    logging.debug("anat_hint :{}".format(self.anat_hint))
+                    opt_list += ["opt_gr.anat_hint = '{0}'".format(self.anat_hint)]
 
                 opt_list += ["files_in=niak_grab_bids('{0}',opt_gr)".format(in_full_path)]