Merge pull request #1 from SilverLabUCL/initial-import

Initial import of code from old repository

.gitignore

@@ -1,3 +1,6 @@
+# Project-specific ignore patterns
+nwb_api_python/
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]
@@ -45,6 +48,7 @@ nosetests.xml
 coverage.xml
 *.cover
 .hypothesis/
+.pytest_cache/
 
 # Translations
 *.mo

LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2017-2018 University College London
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

MATLAB/README.md

@@ -0,0 +1,36 @@
+# Matlab API for NWB use in the Silver Lab
+
+Quick usage example:
+
+``` matlab
+nwb = NwbFile('Data/161215_15_34_21.nwb');
+gui = DisplayVideos(nwb);
+```
+
+For examples of using the API from Matlab analysis scripts, see
+https://github.com/SilverLabUCL/Data-Analysis-Hana/blob/hdf5-experiment/RunUsingNwb.m
+
+
+## Automated Matlab testing
+
+Tests are stored in the [tests](./tests) folder.
+New tests are written as classes named like `TestSomething` within this folder.
+It's probably easiest to start by copying the structure of an existing test.
+
+Tests may be run locally,
+and are also run automatically when pushing to the `master` branch or creating/updating pull requests.
+
+### Local test running
+
+Within Matlab, change to the `MATLAB/tests` folder (or add it to your path) then run
+```
+TestRunner()
+```
+
+### Automated tests
+
+Results are displayed at http://jenkins.rc.ucl.ac.uk/ - ask Jonathan Cooper to give your GitHub account permissions to see this.
+Tests of the master branch are at http://jenkins.rc.ucl.ac.uk/job/SilverLab-main/ and for pull requests under http://jenkins.rc.ucl.ac.uk/job/SilverLab-pull-request/.
+
+You can also see results of specific builds linked from the pull requests / [commits](https://github.com/SilverLabUCL/SilverLab_NWBv1/commits/master) themselves.
+Click on 'Console output' to see the actual test output (scrolling past a lot of test environment setup output!).

MATLAB/setup.py

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+# A little Python script to set the Matlab paths correctly for using NWB
+
+import argparse
+import os
+import re
+import sys
+
+
+def munge_path(path):
+    """Convert `path` to a native system path so Matlab understands it."""
+    if sys.platform.startswith('win32'):
+        if re.match(r'/\s/.*', path):
+            path = os.path.realpath('{}:{}'.format(path[1], path[2:]))
+    elif sys.platform.startswith('cygwin'):
+        if re.match(r'/cygdrive/\s/.*', path):
+            path = os.path.realpath('{}:{}'.format(path[10], path[11:]))
+    return path
+
+
+def setup_matlab(silverlab_path, nwb_api_path):
+    silverlab_path = munge_path(silverlab_path)
+    nwb_api_path = munge_path(os.path.join(nwb_api_path, 'matlab_bridge', 'matlab_bridge_api'))
+    print('Setting up Matlab with paths:')
+    print('  NWB API folder: {}'.format(nwb_api_path))
+    print('  Our Matlab folder: {}'.format(silverlab_path))
+    matlab_commands = [
+        "pyversion '{}';".format(sys.executable),
+        "addpath('{}');".format(nwb_api_path),
+        "addpath(genpath('{}'));".format(silverlab_path),
+        "success = savepath();",
+        "if success == 1; error('Failed to save Matlab path - set manually'); else quit; end;"
+    ]
+    os.system('matlab -nosplash -nodesktop -r "{}"'.format(' '.join(matlab_commands)))
+
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser(description='Setup Matlab for NWB use.')
+    parser.add_argument('nwb_api_path',
+                        help='path to the NWB API sources')
+    args = parser.parse_args()
+    our_matlab_path = os.path.join(os.path.dirname(__file__), 'source')
+    setup_matlab(our_matlab_path, args.nwb_api_path)