Merge pull request #17 from LEB-EPFL/PRERELEASE_v0.3.0

v0.3.0 prerelease.
LEB-EPFL · Sep 10, 2017 · 19f35f3 · 19f35f3
2 parents 27a2a42 + 97d9ed0
commit 19f35f3
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diff --git a/.travis.yml b/.travis.yml
@@ -13,5 +13,4 @@ script:
   # The line below is needed for the Travis build specifically
   - cp -r src/lib/*.jar dist/lib
   - ant -f build-travis.xml
-  - java -jar ./store/SASS*.jar
   - ./scripts/tests/test_scripts.sh scripts ./store/SASS*.jar
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,7 +1,9 @@
 # Change Log
 All notable changes to this project will be documented in this file.
 
-## Unreleased
+## [v0.3.0]
+Contains [ALICA v0.2.1]
+
 ### Added
 - `StateLogger` object for recording each fluorophore state transition
    and the time at which it occurs.
@@ -29,8 +31,7 @@ All notable changes to this project will be documented in this file.
   (by setting the EM gain to a non-zero value) and sCMOS (by setting
   the EM gain to zero.)
 - A problem preventing the creation of new dStormProperties
-  fluorophore models.
-
+  fluorophore models.	
 
 ## [v0.2.0]
 Contains [ALICA v0.2.1]
@@ -87,12 +88,13 @@ Contains [ALICA v0.0.2]
 - default.nix was added to more easily port the development
   environment across machines.
 
-[ALICA v0.2.1]: https://github.com/MStefko/ALICA/releases/tag/v0.2.1
-[ALICA v0.0.2]: https://github.com/MStefko/ALICA/releases/tag/v0.0.2
-[ALICA v0.1.0]: https://github.com/MStefko/ALICA/releases/tag/v0.1.0
-[v0.0.2]: https://github.com/MStefko/SASS/releases/tag/v0.0.2
-[v0.1.0]: https://github.com/MStefko/SASS/releases/tag/v0.1.0
-[v0.1.1]: https://github.com/MStefko/SASS/releases/tag/v0.1.1
-[v0.1.2]: https://github.com/MStefko/SASS/releases/tag/v0.1.2
-[v0.2.0]: https://github.com/MStefko/SASS/releases/tag/v0.2.0
-[v0.2.1]: https://github.com/MStefko/SASS/releases/tag/v0.2.1
+[ALICA v0.2.1]: https://github.com/LEB-EPFL/ALICA/releases/tag/v0.2.1
+[ALICA v0.0.2]: https://github.com/LEB-EPFL/ALICA/releases/tag/v0.0.2
+[ALICA v0.1.0]: https://github.com/LEB-EPFL/ALICA/releases/tag/v0.1.0
+[v0.0.2]: https://github.com/LEB-EPFL/SASS/releases/tag/v0.0.2
+[v0.1.0]: https://github.com/LEB-EPFL/SASS/releases/tag/v0.1.0
+[v0.1.1]: https://github.com/LEB-EPFL/SASS/releases/tag/v0.1.1
+[v0.1.2]: https://github.com/LEB-EPFL/SASS/releases/tag/v0.1.2
+[v0.2.0]: https://github.com/LEB-EPFL/SASS/releases/tag/v0.2.0
+[v0.2.1]: https://github.com/LEB-EPFL/SASS/releases/tag/v0.2.1
+[v0.3.0]: https://github.com/LEB-EPFL/SASS/releases/tag/v0.3.0
diff --git a/MATLAB/evaluate.m b/MATLAB/evaluate.m
diff --git a/MATLAB/normalizeColumnsByMean.m b/MATLAB/normalizeColumnsByMean.m
diff --git a/build-travis.xml b/build-travis.xml
@@ -3,7 +3,7 @@
 <project name="SASS" default="default" basedir=".">
     <description>Builds, tests, and runs the project SASS.</description>
     <import file="nbproject/build-impl.xml"/>
-    <property name="store.jar.name" value="SASS_v0.2.1.jar"/>
+    <property name="store.jar.name" value="SASS_v0.3.0.jar"/>
     <property name="store.dir" value="store"/>
     <property name="store.jar" value="${store.dir}/${store.jar.name}"/>
     <target name="-post-jar">

diff --git a/build.xml b/build.xml
@@ -4,7 +4,7 @@
     <description>Builds, tests, and runs the project SASS.</description>
     <import file="nbproject/build-impl.xml"/>
     <property name="pluginsDir"  location="/home/douglass/apps/Fiji.app/plugins" />
-    <property name="store.jar.name" value="SASS_v0.2.1.jar"/>
+    <property name="store.jar.name" value="SASS_v0.3.0.jar"/>
     <property name="store.dir" value="store"/>
     <property name="store.jar" value="${store.dir}/${store.jar.name}"/>
     <target name="-post-jar">

diff --git a/default.nix b/default.nix
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -61,9 +61,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = '0.2.1'
+version = '0.3.0'
 # The full version, including alpha/beta/rc tags.
-release = '0.2.1'
+release = '0.3.0'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

diff --git a/scripts/example_run_generator_3D.bsh b/scripts/example_run_generator_3D.bsh
@@ -58,7 +58,7 @@ STORMsim generator = new STORMsim(device);
 generator.setControlSignal(0.03);
 
 // simulate frames
-for (i=0;i<5000;i++) {
+for (i=0;i<2500;i++) {
     if (i%1000==0) {
 		System.out.println(i);
 	}

diff --git a/shell.nix b/shell.nix
@@ -36,7 +36,8 @@ with import <nixpkgs> {};
                       pkgs.python35Packages.beautifulsoup4
 	       	      pkgs.python35Packages.future
 		      pkgs.python35Packages.docutils
-		      pkgs.python35Packages.sphinx];
+		      pkgs.python35Packages.sphinx
+		    ];
 
       meta = {
         homepage = "https://github.com/bronto/javasphinx";
@@ -50,6 +51,7 @@ with import <nixpkgs> {};
       pkgs.netbeans
       javalang
       javasphinx
+      pkgs.jdk
     ]
   )
 ).env