docs: rename ShapeOut to Shape-Out

.appveyor/hook-shapeout.py

@@ -7,7 +7,7 @@
 # The full license is in the file COPYING.txt, distributed with this software.
 #-----------------------------------------------------------------------------
 
-# Hook for ShapeOut: https://github.com/ZELLMECHANIK-DRESDEN/ShapeOut
+# Hook for Shape-Out: https://github.com/ZELLMECHANIK-DRESDEN/ShapeOut
 
 from PyInstaller.utils.hooks import collect_data_files
 

.appveyor/shapeout.iss_dummy

@@ -1,8 +1,8 @@
 ; Script generated by the Inno Setup Script Wizard.
 ; SEE THE DOCUMENTATION FOR DETAILS ON CREATING INNO SETUP SCRIPT FILES!
 
-#define MyAppName "ShapeOut"
-#define MyzmAppName "ShapeOut"
+#define MyAppName "Shape-Out"
+#define MyzmAppName "Shape-Out"
 #define MyAppVersion "0.1.0"
 #define MyAppPublisher "ZELLMECHANIK DRESDEN"
 #define MyAppURL "http://zellmechanik.com"
@@ -33,9 +33,9 @@ PrivilegesRequired=lowest
 
 [Registry]
 Root: HKCU; Subkey: ".zmso"; ValueType: string; ValueName: ""; ValueData: "{#MyAppName}"; Flags: uninsdeletevalue
-Root: HKCU; Subkey: "{#MyAppName}"; ValueType: string; ValueName: ""; ValueData: "ShapeOut Session"; Flags: uninsdeletekey
-Root: HKCU; Subkey: "{#MyAppName}\DefaultIcon"; ValueType: string; ValueName: ""; ValueData: "{app}\{#MyAppName}.EXE,0"
-Root: HKCU; Subkey: "{#MyAppName}\shell\open\command"; ValueType: string; ValueName: ""; ValueData: """{app}\{#MyAppName}.EXE"" ""%1""" 
+Root: HKCU; Subkey: "{#MyAppName}"; ValueType: string; ValueName: ""; ValueData: "Shape-Out Session"; Flags: uninsdeletekey
+Root: HKCU; Subkey: "{#MyAppName}\DefaultIcon"; ValueType: string; ValueName: ""; ValueData: "{app}\{#MyAppExeName},0"
+Root: HKCU; Subkey: "{#MyAppName}\shell\open\command"; ValueType: string; ValueName: ""; ValueData: """{app}\{#MyAppExeName}"" ""%1""" 
 
 
 [Languages]
@@ -46,7 +46,7 @@ Name: "german"; MessagesFile: "compiler:Languages\German.isl"
 Name: "desktopicon"; Description: "{cm:CreateDesktopIcon}"; GroupDescription: "{cm:AdditionalIcons}"; Flags: unchecked
 
 [Files]
-Source: "C:\projects\shapeout\dist\ShapeOut\ShapeOut.exe"; DestDir: "{app}"; Flags: ignoreversion
+Source: "C:\projects\shapeout\dist\ShapeOut\{#MyAppExeName}"; DestDir: "{app}"; Flags: ignoreversion
 Source: "C:\projects\shapeout\dist\ShapeOut\*"; DestDir: "{app}"; Flags: ignoreversion recursesubdirs createallsubdirs
 ; Include the entire R installation
 Source: "C:\Program Files\R\*"; DestDir: "{app}\R"; Flags: ignoreversion recursesubdirs createallsubdirs

CHANGELOG

@@ -105,7 +105,7 @@
  - Bugfixes:
    - Cannot open old session files with hierarchies when the measurement
      data location has changed (#174)
-   - Cannot open polygon filters exported with ShapeOut versions < 0.7.6 (#174)
+   - Cannot open polygon filters exported versions < 0.7.6 (#174)
  - Code cleanup:
    - Move program-relevant data to "shapeout" directory
    - Move computation of isoelastics to dclab (dclab 0.2.6.dev23)

README.rst

@@ -1,10 +1,10 @@
-|ShapeOut|
-==========
+|Shape-Out|
+===========
 
 |PyPI Version| |Build Status Win| |Coverage Status|
 
 
-ShapeOut is a graphical user interface for the analysis
+Shape-Out is a graphical user interface for the analysis
 and visualization of RT-DC data sets. For more informaion please visit
 http://zellmechanik.com/.
 
@@ -16,37 +16,37 @@ The manual and user guide can be found at http://www.zellmechanik.com/download.
 
 Installation
 ------------
-Installers for ShapeOut are available at the `release page <https://github.com/ZELLMECHANIK-DRESDEN/ShapeOut/releases>`__.
+Installers for Shape-Out are available at the `release page <https://github.com/ZELLMECHANIK-DRESDEN/ShapeOut/releases>`__.
 
 
-Citing ShapeOut
----------------
-Please cite ShapeOut either in-line
+Citing Shape-Out
+----------------
+Please cite Shape-Out either in-line
 
 ::
 
-  (...) using the analysis software ShapeOut version X.X.X (available at
+  (...) using the analysis software Shape-Out version X.X.X (available at
   https://github.com/ZELLMECHANIK-DRESDEN/ShapeOut).
 
 or in a bibliography
 
 ::
   
-  Paul Müller and others (2015), ShapeOut version X.X.X: Analysis software
+  Paul Müller and others (2015), Shape-Out version X.X.X: Analysis software
   for real-time deformability cytometry [Software]. Available at
   https://github.com/ZELLMECHANIK-DRESDEN/ShapeOut.
 
-and replace ``X.X.X`` with the version of ShapeOut that you used.
+and replace ``X.X.X`` with the version of Shape-Out that you used.
 
 
 Development
 -----------
-Details on running ShapeOut from source, contributing, testing, and releasing new versions
-of ShapeOut can be found at https://github.com/ZELLMECHANIK-DRESDEN/ShapeOut/tree/develop/dev.
+Details on running Shape-Out from source, contributing, testing, and releasing new versions
+of Shape-Out can be found at https://github.com/ZELLMECHANIK-DRESDEN/ShapeOut/tree/develop/dev.
 
 
 
-.. |ShapeOut| image:: https://raw.github.com/ZELLMECHANIK-DRESDEN/ShapeOut/master/shapeout/img/shapeout_logotype_h50.png
+.. |Shape-Out| image:: https://raw.github.com/ZELLMECHANIK-DRESDEN/ShapeOut/master/shapeout/img/shapeout_logotype_h50.png
 .. |PyPI Version| image:: http://img.shields.io/pypi/v/ShapeOut.svg
    :target: https://pypi.python.org/pypi/shapeout
 .. |Build Status Win| image:: https://img.shields.io/appveyor/ci/paulmueller/ShapeOut/master.svg?label=build_win

dev/Readme.rst

@@ -5,7 +5,7 @@ Information for developers
 
 Running from source
 ~~~~~~~~~~~~~~~~~~~
-The easiest way to run ShapeOut from source is to use
+The easiest way to run Shape-Out from source is to use
 `Anaconda <http://continuum.io/downloads>`__. 
 
 - **Windows**: Sketchy installation instructions can be found
@@ -14,7 +14,7 @@ The easiest way to run ShapeOut from source is to use
 - **Debian**: Run `this script <https://github.com/ZELLMECHANIK-DRESDEN/ShapeOut/blob/develop/dev/activate_linux.sh>`__
   which will create a Python virtual environment.
 
-- **MacOS**: ShapeOut should work with Anaconda (see Windows above).
+- **MacOS**: Shape-Out should work with Anaconda (see Windows above).
   It is also possible to install all dependencies with MacPorts:
 
   ::
@@ -41,7 +41,7 @@ The easiest way to run ShapeOut from source is to use
     #!/bin/bash
     export PYTHONPATH="${PYTHONPATH}:/path/to/dclab"
 
-  start ShapeOut with
+  start Shape-Out with
 
   ::
   
@@ -53,9 +53,9 @@ The easiest way to run ShapeOut from source is to use
 
 Contributing
 ~~~~~~~~~~~~
-The main branch for developing ShapeOut is ``develop``. Small changes that do not
+The main branch for developing Shape-Out is ``develop``. Small changes that do not
 break anything can be submitted to this branch.
-If you want to do big changes, please (fork ShapeOut and) create a separate branch,
+If you want to do big changes, please (fork Shape-Out and) create a separate branch,
 e.g. ``my_new_feature_dev``, and create a pull-request to ``develop`` once you are done making
 your changes.
 Please make sure to edit the 
@@ -77,7 +77,7 @@ to prevent confusions in the commit history.
 
 Tests
 ~~~~~
-ShapeOut is tested using pytest. If you have the time, please write test
+Shape-Out is tested using pytest. If you have the time, please write test
 methods for your code and put them in the ``tests`` directory. You may
 run the tests manually by issuing:
 
@@ -88,7 +88,7 @@ run the tests manually by issuing:
 
 Test binaries
 ~~~~~~~~~~~~~
-After each commit to the ShapeOut repository, a binary installer is created
+After each commit to the Shape-Out repository, a binary installer is created
 by `Appveyor <https://ci.appveyor.com/project/paulmueller/ShapeOut>`__. Click
 on a build and navigate to ``ARTIFACTS`` (upper right corner right under
 the running time of the build). From there you can download the executable
@@ -116,8 +116,8 @@ _________
        git push  
 	
 3. Create the release at https://github.com/ZELLMECHANIK-DRESDEN/ShapeOut/releases.  
-   Make sure that the tag of the release follows the version format of ShapeOut
-   (e.g. `0.5.3`) and also name the release correctly (e.g. `ShapeOut 0.5.3`).
+   Make sure that the tag of the release follows the version format of Shape-Out
+   (e.g. `0.5.3`) and also name the release correctly (e.g. `Shape-Out 0.5.3`).
    Also, copy and paste the changelog of the new version into the comments of the release.
    The first line of the release comments should contain the download counts shield like so:
 

docs/README.md

@@ -1,5 +1,5 @@
-ShapeOut documentation
-======================
+Shape-Out documentation
+=======================
 To install the requirements for building the documentation, run
 
     pip install -r requirements.txt

docs/conf.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python3
 # -*- coding: utf-8 -*-
 #
-# ShapeOut documentation build configuration file, created by
+# Shape-Out documentation build configuration file, created by
 # sphinx-quickstart on Tue Sep 26 17:55:31 2017.
 #
 # This file is execfile()d with the current directory set to its
@@ -101,7 +101,7 @@
 master_doc = 'index'
 
 # General information about the project.
-project = 'ShapeOut'
+project = 'Shape-Out'
 github_project = 'ZELLMECHANIK-DRESDEN/' + project
 copyright = '2015, Paul Müller'
 author = 'Paul Müller'
@@ -184,7 +184,7 @@
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-    (master_doc, 'shapeout.tex', 'ShapeOut Documentation',
+    (master_doc, 'shapeout.tex', 'Shape-Out Documentation',
      'Paul Müller', 'manual'),
 ]
 
@@ -194,7 +194,7 @@
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
 man_pages = [
-    (master_doc, 'shapeout', 'ShapeOut Documentation',
+    (master_doc, 'shapeout', 'Shape-Out Documentation',
      [author], 1)
 ]
 
@@ -205,7 +205,7 @@
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-    (master_doc, 'shapeout', 'ShapeOut Documentation',
+    (master_doc, 'shapeout', 'Shape-Out Documentation',
      author, 'shapeout', 'post-measurement analysis of RT-DC data sets',
      'Scientific'),
 ]

docs/index.rst

@@ -1,8 +1,8 @@
 .. _index:
 
-ShapeOut documentation
-======================
-This is the documentation of ShapeOut version |release|.
+Shape-Out documentation
+=======================
+This is the documentation of Shape-Out version |release|.
 
 .. warning:: This documentation is under construction and its existence
     thus not yet communicated publicly. Use it at your own risk.

docs/sec_changelog.rst

@@ -1,6 +1,6 @@
 =========
 Changelog
 =========
-List of changes in-between ShapeOut releases.
+List of changes in-between Shape-Out releases.
 
 .. include_changelog:: ../CHANGELOG

docs/sec_getting_started.rst

@@ -4,30 +4,30 @@ Getting started
 
 Installation
 ============
-ShapeOut can be installed via multiple channels.
+Shape-Out can be installed via multiple channels.
 
 1. **Windows installer:** Download the latest version for your architecture
    (e.g. ``ShapeOut_X.Y.Z_win_64bit_setup.exe`` for 64bit Windows) from the
    official
    `release page <https://github.com/ZELLMECHANIK-DRESDEN/ShapeOut/releases/latest>`__. 
 
-2. **Python 2.7 with pip:** ShapeOut can easily be installed with
+2. **Python 2.7 with pip:** Shape-Out can easily be installed with
    `pip <https://pip.pypa.io/en/stable/quickstart/>`__:
 
    .. code:: bash
 
        pip install shapeout
 
-   To start ShapeOut, simply run ``shapeout`` or ``python -m shapeout``
+   To start Shape-Out, simply run ``shapeout`` or ``python -m shapeout``
    in a command shell. 
 
 
 Update
 ======
-ShapeOut automatically searches for updates (you may opt-out via the
+Shape-Out automatically searches for updates (you may opt-out via the
 preferences menu) and notifies the user when a new version is available.
 
-1. **Windows installer:** The older version of ShapeOut will be
+1. **Windows installer:** The older version of Shape-Out will be
    automatically uninstalled when installing a new version.
 
 2. **Python 2.7 and pip:**

docs/sec_interface.rst

@@ -17,7 +17,7 @@ Menu bar
      not selected in the measurement browser.
    - Save session: saves the status of the analysis
    - Load session: loads a saved session
-   - Quit: quits the program ShapeOut
+   - Quit: quits the program
 
 - Export:
    - All event data (\*.tsv): tool to export datasets (filtered, unfiltered,

docs/sec_qg_youngs_modulus.rst

@@ -6,7 +6,7 @@ Young's Modulus
 ===============
 TODO: helpful screenshots when the new GUI is ready.
 
-With ShapeOut it is possible to convert deformation values to values
+With Shape-Out it is possible to convert deformation values to values
 of the Young's modulus based on the numerical simulation work for
 fully elastic spheres by Mokbel et al. :cite:`Mokbel2017`.
 

docs/sec_rtdc_basics.rst

@@ -34,7 +34,7 @@ A multitude of features can be extracted from the data recorded during an
 RT-DC measurement. These features are mostly computed live during data
 acquisition and stored alongside the raw data.
 Here, only the most important features are covered. A full list of the
-features available in ShapeOut is maintained by the
+features available in Shape-Out is maintained by the
 :ref:`dclab documentation <dclab:sec_features>`.
 Please note that some of the features are only available in expert mode
 (accessible via the preferences menu).
@@ -43,7 +43,7 @@ Please note that some of the features are only available in expert mode
 Area and porosity
 -----------------
 The area is the projected object area which is determined via the contour of the
-binarized event image. ShapeOut differentiates between two types of area,
+binarized event image. Shape-Out differentiates between two types of area,
 area of the measured contour ("Measured area [px]") and area of the convex
 contour ("Convex area [px]" and "Area [µm²]"). The convex contour is the
 `convex hull <https://en.wikipedia.org/wiki/Convex_hull>`__ of the measured
@@ -89,7 +89,7 @@ in a drop of blood :cite:`Toepfner2018`.
    Figure and caption adapted from Toepfner et al. [1]_.
 
 In addition to the average
-brightness values, ShapeOut also has access to the standard deviation of the
+brightness values, Shape-Out also has access to the standard deviation of the
 brightness in each image.
 
 
@@ -119,7 +119,7 @@ employed to visualize stiffness.
    trends in stiffness.
 
 Note that it is also possible to directly
-:ref:`access the Young's modulus in ShapeOut <sec_qg_youngs_modulus>`.
+:ref:`access the Young's modulus in Shape-Out <sec_qg_youngs_modulus>`.
 
 
 Fluorescence

shapeout/ShapeOut.py

@@ -1,8 +1,6 @@
 #!/usr/bin/python
 # -*- coding: utf-8 -*-
-""" 
-ShapeOut launcher with splash screen
-"""
+"""Shape-Out launcher with splash screen"""
 from __future__ import print_function
 
 import multiprocessing as mp
@@ -49,7 +47,7 @@ def splash_show():
     # alpha mask is only binary - don't use it, looks ugly.
     #img.ConvertAlphaToMask()
     bitmap = wx.BitmapFromImage(img)
-    frame = wx.Frame(None, -1, "ShapeOut Splash Screen")
+    frame = wx.Frame(None, -1, "Shape-Out Splash Screen")
     AS.AdvancedSplash(frame, bitmap=bitmap, 
                       agwStyle=AS.AS_NOTIMEOUT|AS.AS_CENTER_ON_SCREEN
                       )
@@ -61,6 +59,6 @@ def splash_show():
     mp.freeze_support()
     if 'unicode' not in wx.PlatformInfo:
         print("\nInstalled version: %s" % wx.version())
-        print("A unicode build of wxPython is required for ShapeOut.")
+        print("A unicode build of wxPython is required for Shape-Out.")
     else:
         main()

shapeout/__main__.py

@@ -19,7 +19,7 @@ def prepare_app():
     try:
         from ._version import version
     except:
-        warnings.warn("Could not determine ShapeOut version.")
+        warnings.warn("Could not determine Shape-Out version.")
         version = None
 
     app.frame = frontend.Frame(version)

shapeout/analysis.py

@@ -1,6 +1,6 @@
 #!/usr/bin/python
 # -*- coding: utf-8 -*-
-"""ShapeOut - Analysis class"""
+"""Shape-Out - Analysis class"""
 from __future__ import division, unicode_literals
 
 import gc
@@ -124,7 +124,7 @@ def _complete_config(self, measurements=None):
             measurements = self.measurements
 
         for mm in measurements:
-            # Update configuration with default values from ShapeOut,
+            # Update configuration with default values from Shape-Out,
             # but do not override anything.
             cfgold = mm.config.copy()
             mm.config.update(get_default_config())