Feature/349 linux

CHANGELOG.md

@@ -2,6 +2,7 @@ This is an overview of major changes. Refer to the git repository for a full log
 
 Version 0.1.34
 -------------
+- #349 Linux instructions
 - #347 Explicitly reference python2 in scripts
 - #342 Conda environment files
 - #333 Ugly error message when opening or saving a file

DevelopingOnLinux.md

@@ -0,0 +1,93 @@
+# Inselect on Linux
+
+These instructions use the system's Python and many system python packages.
+Tested on Ubuntu 14.04 and 16.04, both with 2GB RAM.
+For an approach using `miniconda` see `.travis.yml`.
+
+# Setup Python virtual environment
+
+```
+sudo apt-get install python-pip python-dev build-essential
+sudo pip2 install --upgrade pip
+sudo pip2 install virtualenv virtualenvwrapper
+```
+
+Append to ``~/.bash_profile`
+
+
+```
+
+## Setup virtualenvwrapper
+export WORKON_HOME=~/Envs/
+source /usr/local/bin/virtualenvwrapper.sh
+```
+
+
+# Install system dependencies
+```
+sudo apt-get install python-pyside pyside-tools python-numpy python-scipy python-sklearn python-opencv python-pil libdmtx-dev libzbar-dev
+```
+
+# Create virtual environment for Inselect and install dependencies from pip
+
+```
+mkvirtualenv --system-site-packages inselect
+pip2 install -r requirements.pip
+```
+
+## LibDMTX barcode reading library
+
+* Get source for the wrappers
+
+    ```
+    cd ~/projects
+    git clone git://libdmtx.git.sourceforge.net/gitroot/libdmtx/dmtx-wrappers
+    ```
+
+* Install Python library
+
+    ```
+    cd dmtx-wrappers/python
+    python2 setup.py install
+    cd ~/projects/inselect
+    ```
+
+## Test barcode reading libraries
+
+Inselect has optional barcode reading capabilities. The dependent libraries
+should have been installed.
+
+```
+python -c "from gouda.engines import ZbarEngine; print(ZbarEngine.available())"
+python -c "from gouda.engines import LibDMTXEngine; print(LibDMTXEngine.available())"
+```
+
+# Developing
+
+Icons are stored as individual files in `icons`. They are frozen into
+a python file `inselect/gui/icons.py` by running
+
+```
+python2 -m bin.freeze_icons
+```
+
+# Test and run
+
+```
+nosetests --verbose --with-coverage --cover-inclusive --cover-tests --cover-package=inselect inselect
+```
+
+Ubuntu 16.04 appears to come with `nose` already installed so the
+`pip2 install -r requirements.pip` step above will not install `nose` within
+the virtual env. `nosetests` will not find the packages within the
+virtualenv and you will see lots of `ImportErrors`. If this is the case, run
+
+```
+python -m nose --verbose --with-coverage --cover-inclusive --cover-tests --cover-package=inselect inselect
+```
+
+Run inselect
+
+```
+./inselect.py
+```

inselect/lib/sort_document_items.py

@@ -27,7 +27,7 @@ def _do_kde(values):
     bins = np.append(samples[minima], RESCALE)
 
     # Cut data
-    return (v[0] for v in np.digitize(values, bins, right=True).tolist())
+    return np.digitize(values.reshape(len(values)), bins, right=True)
 
 
 def sort_document_items(items, by_columns):
@@ -36,6 +36,9 @@ def sort_document_items(items, by_columns):
     if not items:
         # Algorithm is not tolerant of empty values
         return []
+    elif 1 == len(items):
+        # Breaks algorithm when using older numpy (< 10.1)
+        return items
     else:
         rects = [i['rect'] for i in items]
         x_bins = _do_kde(r.x_centre for r in rects)