Merge pull request #57 from adhusch/develop

Regular merge of develop

.artenolis.yml

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

.gitignore

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

README.rst

@@ -12,7 +12,7 @@ PaCER |br| Precise and Convenient Electrode Reconstruction for DBS
 
    <br>
    <a href="https://adhusch.github.io/PaCER/"><img src="https://img.shields.io/badge/PaCER-docs-blue.svg?maxAge=0"></a>
-   &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>
+   &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>
    <br><br>
 
 ..
@@ -31,7 +31,7 @@ PaCER |br| Precise and Convenient Electrode Reconstruction for DBS
 .. raw:: html
 
    <p align="center">
-     <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"/>
+     <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"/>
    </p>
 
 
@@ -207,4 +207,4 @@ for providing the `ARTENOLIS infrastructure <http://artenolis.lcsb.uni.lu>`__ an
 
 .. |br| raw:: html
 
-   <br>
+   <br>

SETUP_PACER.m

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

codecov.yml

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

docs/.documenter.enc

@@ -0,0 +1 @@
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

docs/requirements.txt

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

docs/source/conf.py

@@ -24,6 +24,8 @@
 sys.path.insert(0, os.path.abspath(os.path.join('..', '..', '..')))
 # sys.path.insert(0, os.path.abspath('.'))
 
+matlab_src_dir = os.path.abspath(os.path.join('..', '..'))
+
 # -- General configuration ------------------------------------------------
 
 # If your documentation needs a minimal Sphinx version, state it here.
@@ -34,6 +36,9 @@
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
+    'sphinx.ext.autodoc',
+    'sphinxcontrib.napoleon',
+    'sphinxcontrib.matlab',
     'sphinxcontrib.fulltoc']
 
 # remove path in function names

docs/source/contents.rst

@@ -6,6 +6,7 @@ PaCER
 
    Home <index>
    gettingStarted
+   modules/index
    literature
    help
    acknowledgments

docs/source/modules/functions/index.rst

@@ -0,0 +1,8 @@
+.. _functions:
+
+
+Functions
+---------
+
+.. automodule:: src.Functions
+   :members:

docs/source/modules/index.rst

@@ -0,0 +1,8 @@
+.. _modules_functions:
+
+Source code
+===========
+
+.. toctree::
+
+   functions/index

external/rdir/LICENSE.md

@@ -0,0 +1,25 @@
+Copyright (c) 2014, Thomas Vanaret
+Copyright (c) 2009, Gus Brown
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are
+met:
+
+    * Redistributions of source code must retain the above copyright
+      notice, this list of conditions and the following disclaimer.
+    * Redistributions in binary form must reproduce the above copyright
+      notice, this list of conditions and the following disclaimer in
+      the documentation and/or other materials provided with the distribution
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
+LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+POSSIBILITY OF SUCH DAMAGE.

external/rdir/README.md

@@ -0,0 +1,8 @@
+# Recursive directory listing
+
+Original version is
+[here](https://nl.mathworks.com/matlabcentral/fileexchange/19550-recursive-directory-listing?requestedDomain=true).
+
+The script has been adapted for `opencobra` repositories, such as [the COBRA
+Toolbox](https://github.com/opencobra/cobratoolbox) and [the
+MATLAB.devTools](https://github.com/opencobra/MATLAB.devTools).

external/rdir/enhanced_rdir.m

@@ -0,0 +1,65 @@
+%% RDIR Enhanced - Examples of use
+%
+% This script demonstrates how to use the different abilities of the
+% enhanced |rdir| function.
+%
+% Examples are based on |matlabroot| directory content. Results may vary
+% depending on your version of Matlab.
+%
+
+%% Standard use
+rdir([matlabroot, '\*.txt'])
+
+%% Using double wildcard **
+% List |".m"| files whose name contains |"tmpl"| in all subdirectories of
+% |matlabroot|
+rdir([matlabroot, '\**\*tmpl*.m'])
+
+%% RDIR output
+d = rdir([matlabroot, '\**\*tmpl*.m'])
+
+%%
+disp(d(1))
+
+
+%% Using 3rd argument to shorten output names
+% Remove |"C:\Program Files\"| in returned names
+rdir([matlabroot, '\*.txt'], '', 'C:\Program Files\')
+
+%%
+% Remove |matlabroot| in returned names
+rdir([matlabroot, '\*.txt'], '', true)
+
+%%
+% Optional 2nd |rdir| output indicates common path removed from each output
+% name
+[d, p] = rdir([matlabroot, '\*.txt'], '', true);
+
+fprintf('Common path : \n%s\n\n', p)
+
+disp( d(1) )
+
+%% Using a filter with "regexp"
+% List |".mat"| files, then select those whose name match regular expression
+% |'data\d'| (ie |"data"| followed by a numeric digit)
+rdir([matlabroot '\toolbox\**\*.mat'], 'regexp(name, ''data\d'')', true)
+
+%% Using a function handle as filter
+
+fun = @(d) ~isempty(regexp(d.name, 'data\d')) && (d.bytes < 10*1024)
+
+rdir([matlabroot '\toolbox\**\*.mat'], fun, true)
+
+%% Specific display - No item matching filter
+% When some items match input path, but none match filter, a specific
+% message is displayed.
+rdir(matlabroot, 'strcmp(name, ''unknowtoolbox'')', 1)
+
+
+%% Specific display - Wrong filter
+% A warning is displayed after the non-filtered result list if entered
+% filter is wrong.
+rdir(matlabroot, 'wrong filter', 1)
+
+
+% EOF