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Merge branch 'master' of https://github.com/adhusch/PaCER 
2 parents 9a5b053 + ff6fe43 commit 93b0cce

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‎.artenolis.yml

+17-3
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@@ -7,6 +7,11 @@ script:
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# set the environment variable CURRENT_DIR
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- CURRENT_DIR=`pwd`
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# update the data repository
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- cd $PACER_DATA_PATH
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- git checkout develop
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- git pull origin develop
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# change to the current directory
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- cd $CURRENT_DIR
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@@ -16,6 +21,15 @@ script:
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after_success:
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# submit coverage report
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#- if [[ "$MATLAB_VER" == "R2018b" && "$ARCH" == "Linux" ]]; then
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# bash <(curl -s https://codecov.io/bash) -f "!*.lst";
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# fi
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- if [[ "$MATLAB_VER" == "R2018b" && "$ARCH" == "Linux" ]]; then
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bash <(curl -s https://codecov.io/bash) -f "!*.lst";
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fi
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# deploy documentation
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- if [[ "$MATLAB_VER" == "R2018b" && "$ARCH" == "Linux" && "$JENKINS_PULL_REQUEST" != "True" ]]; then
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export PATH="/home/jenkins/.local/bin":$PATH;
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pip install --upgrade --user -r docs/requirements.txt;
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export GIT_LOCAL_BRANCH=${GIT_BRANCH##origin/};
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echo $GIT_LOCAL_BRANCH;
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python -c "from documenter.deploy import Documentation; doc = Documentation('github.com/adhusch/PaCER', local_upstream='$(pwd)', ci='jenkins'); doc.deploy()";
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fi

‎.gitignore

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@@ -1,3 +1,5 @@
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coverage.json
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coverage_html/
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*.asv
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*.m~
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*.mex*
@@ -6,3 +8,4 @@ pacer_sample_dataset/
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exampledata/
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.DS_Store
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docs/build
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*.log

‎README.rst

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@@ -12,7 +12,7 @@ PaCER |br| Precise and Convenient Electrode Reconstruction for DBS
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<br>
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<a href="https://adhusch.github.io/PaCER/"><img src="https://img.shields.io/badge/PaCER-docs-blue.svg?maxAge=0"></a>
15-
&nbsp;&nbsp;&nbsp;<a href="https://prince.lcsb.uni.lu/jenkins/job/PaCER-branches-auto-linux/"><img src="https://prince.lcsb.uni.lu/jenkins/job/PaCER-branches-auto-linux/badge/icon"></a>
15+
&nbsp;&nbsp;&nbsp;<a href="https://prince.lcsb.uni.lu/jenkins/job/PaCER-branches-auto-linux/"><img src="https://prince.lcsb.uni.lu/jenkins/buildStatus/icon?job=PaCER-pr-auto-linux"></a>
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<br><br>
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..
@@ -31,7 +31,7 @@ PaCER |br| Precise and Convenient Electrode Reconstruction for DBS
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.. raw:: html
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<p align="center">
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<img alt="Image of a PaCER electrode reconstruction at two different time points of resolving brain shift." class="readme_main" src="https://prince.lcsb.uni.lu/userContent/mainPacer.png" height="400px"/>
34+
<img alt="Image of a PaCER electrode reconstruction at two different time points of resolving brain shift." class="readme_main" src="https://prince.lcsb.uni.lu/PaCER/img/mainPacer.png" height="400px"/>
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</p>
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@@ -207,4 +207,4 @@ for providing the `ARTENOLIS infrastructure <http://artenolis.lcsb.uni.lu>`__ an
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.. |br| raw:: html
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<br>
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<br>

‎SETUP_PACER.m

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@@ -9,4 +9,4 @@
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%% RUN this file once (F5) to automatically make sure all PaCER files (including subdirectories) are in your MATLAB path!
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pacerDir = fileparts(mfilename('fullpath'));
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addpath(genpath(pacerDir));
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savepath();
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savepath();

‎codecov.yml

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@@ -0,0 +1,6 @@
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coverage:
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status:
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project:
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default:
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threshold: 15
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patch: off

‎docs/.documenter.enc

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@@ -0,0 +1 @@
1+
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

‎docs/requirements.txt

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@@ -1,4 +1,7 @@
1-
git+https://github.com/uni-lu/sphinx.git@develop#egg=sphinx
1+
git+https://github.com/LCSB-BioCore/sphinx.git@develop#egg=sphinx
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sphinx_rtd_theme
3-
git+https://github.com/uni-lu/sphinx_julia_theme.git@develop#egg=sphinx_julia_theme
3+
git+https://github.com/LCSB-BioCore/sphinx_julia_theme.git@develop#egg=sphinx_julia_theme
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git+https://github.com/syarra/Documenter.py@develop#egg=documenter
5+
git+https://github.com/LCSB-BioCore/sphinxcontrib-napoleon.git@develop#egg=sphinxcontrib_napoleon
6+
git+https://github.com/syarra/sphinxcontrib-matlabdomain#egg=sphinxcontrib-matlabdomain
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sphinxcontrib-fulltoc

‎docs/source/conf.py

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sys.path.insert(0, os.path.abspath(os.path.join('..', '..', '..')))
2525
# sys.path.insert(0, os.path.abspath('.'))
2626

27+
matlab_src_dir = os.path.abspath(os.path.join('..', '..'))
28+
2729
# -- General configuration ------------------------------------------------
2830

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# If your documentation needs a minimal Sphinx version, state it here.
@@ -34,6 +36,9 @@
3436
# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
3537
# ones.
3638
extensions = [
39+
'sphinx.ext.autodoc',
40+
'sphinxcontrib.napoleon',
41+
'sphinxcontrib.matlab',
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'sphinxcontrib.fulltoc']
3843

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# remove path in function names

‎docs/source/contents.rst

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66

77
Home <index>
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gettingStarted
9+
modules/index
910
literature
1011
help
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acknowledgments

‎docs/source/modules/functions/index.rst

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.. _functions:
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3+
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Functions
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---------
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7+
.. automodule:: src.Functions
8+
:members:

‎docs/source/modules/index.rst

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.. _modules_functions:
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Source code
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===========
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6+
.. toctree::
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functions/index

‎external/rdir/LICENSE.md

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Copyright (c) 2014, Thomas Vanaret
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Copyright (c) 2009, Gus Brown
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All rights reserved.
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Redistribution and use in source and binary forms, with or without
6+
modification, are permitted provided that the following conditions are
7+
met:
8+
9+
* Redistributions of source code must retain the above copyright
10+
notice, this list of conditions and the following disclaimer.
11+
* Redistributions in binary form must reproduce the above copyright
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notice, this list of conditions and the following disclaimer in
13+
the documentation and/or other materials provided with the distribution
14+
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THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
16+
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
17+
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
18+
ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
19+
LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
20+
CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
21+
SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
22+
INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
23+
CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
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ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
25+
POSSIBILITY OF SUCH DAMAGE.

‎external/rdir/README.md

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# Recursive directory listing
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Original version is
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[here](https://nl.mathworks.com/matlabcentral/fileexchange/19550-recursive-directory-listing?requestedDomain=true).
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The script has been adapted for `opencobra` repositories, such as [the COBRA
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Toolbox](https://github.com/opencobra/cobratoolbox) and [the
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MATLAB.devTools](https://github.com/opencobra/MATLAB.devTools).

‎external/rdir/enhanced_rdir.m

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%% RDIR Enhanced - Examples of use
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%
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% This script demonstrates how to use the different abilities of the
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% enhanced |rdir| function.
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%
6+
% Examples are based on |matlabroot| directory content. Results may vary
7+
% depending on your version of Matlab.
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%
9+
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%% Standard use
11+
rdir([matlabroot, '\*.txt'])
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13+
%% Using double wildcard **
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% List |".m"| files whose name contains |"tmpl"| in all subdirectories of
15+
% |matlabroot|
16+
rdir([matlabroot, '\**\*tmpl*.m'])
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18+
%% RDIR output
19+
d = rdir([matlabroot, '\**\*tmpl*.m'])
20+
21+
%%
22+
disp(d(1))
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24+
25+
%% Using 3rd argument to shorten output names
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% Remove |"C:\Program Files\"| in returned names
27+
rdir([matlabroot, '\*.txt'], '', 'C:\Program Files\')
28+
29+
%%
30+
% Remove |matlabroot| in returned names
31+
rdir([matlabroot, '\*.txt'], '', true)
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33+
%%
34+
% Optional 2nd |rdir| output indicates common path removed from each output
35+
% name
36+
[d, p] = rdir([matlabroot, '\*.txt'], '', true);
37+
38+
fprintf('Common path : \n%s\n\n', p)
39+
40+
disp( d(1) )
41+
42+
%% Using a filter with "regexp"
43+
% List |".mat"| files, then select those whose name match regular expression
44+
% |'data\d'| (ie |"data"| followed by a numeric digit)
45+
rdir([matlabroot '\toolbox\**\*.mat'], 'regexp(name, ''data\d'')', true)
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47+
%% Using a function handle as filter
48+
49+
fun = @(d) ~isempty(regexp(d.name, 'data\d')) && (d.bytes < 10*1024)
50+
51+
rdir([matlabroot '\toolbox\**\*.mat'], fun, true)
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%% Specific display - No item matching filter
54+
% When some items match input path, but none match filter, a specific
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% message is displayed.
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rdir(matlabroot, 'strcmp(name, ''unknowtoolbox'')', 1)
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%% Specific display - Wrong filter
60+
% A warning is displayed after the non-filtered result list if entered
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% filter is wrong.
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rdir(matlabroot, 'wrong filter', 1)
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% EOF

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