Create v0.3.0

fraenkel-lab · Sep 3, 2016 · 99309ee · 99309ee
1 parent 823aecc
commit 99309ee
Show file tree

Hide file tree

Showing 8 changed files with 21 additions and 7 deletions.
diff --git a/.gitignore b/.gitignore
@@ -8,7 +8,6 @@
 *.egg
 *.eggs
 *.egg-info
-dist
 build
 eggs
 .eggs

diff --git a/HISTORY.rst b/HISTORY.rst
@@ -3,6 +3,18 @@
 History
 -------
 
+0.3.0 (2016-09-03)
+---------------------
+* Remove conflicts between Forest edge noise and garnetBeta parameters
+* Correctly query for whether prize nodes are in a directed network
+* Use correct p-value or q-value to filter Garnet output
+* Switch to msgsteiner-1.3 to fix bugs with directed edges and suboptimal forests
+* BSD license
+* Forest unit tests to assess the effects of w, beta, mu, and D
+* Continuous integration testing with Travis CI
+* Option to save plots from Garnet motif regression
+* Write Forest objective function value of optimal forest to info file
+
 0.2.0 (2016-04-13)
 ---------------------
 * Add a Forest integration test

diff --git a/Makefile b/Makefile
@@ -53,7 +53,7 @@ release: clean
 	python setup.py bdist_wheel upload
 
 dist: clean
-	python setup.py sdist
+	python setup.py sdist --formats=gztar
 	tar cvzf OmicsIntegratorExamples.tar.gz example/*
 	mv OmicsIntegratorExamples.tar.gz dist/
 	ls -l dist

diff --git a/README.md b/README.md
@@ -64,8 +64,8 @@ To use the [Homebrew](http://brew.sh/) package manager for Mac simply type `brew
 4. Enter the `msgsteiner-1.3` subdirectory and run `make`
   * See [this advice](./patches) on compiling the C++ code if you encounter problems. 
   * Make a note of the path to the compiled msgsteiner file that was created, which you will use when running Forest.
-5. Download the Omics Integrator package: [OmicsIntegrator-0.2.0.tar.gz](./dist/OmicsIntegrator-0.2.0.tar.gz)
-6. Unpack files from the archive: `tar -xvzf OmicsIntegrator-0.2.0.tar.gz`
+5. Download the Omics Integrator package: [OmicsIntegrator-0.3.0.tar.gz](./dist/OmicsIntegrator-0.3.0.tar.gz)
+6. Unpack files from the archive: `tar -xvzf OmicsIntegrator-0.3.0.tar.gz`
 7. Make sure you have all the requirements using the pip tool by entering the
 directory and typing: `pip install -r requirements.txt`
 

diff --git a/dist/OmicsIntegrator-0.2.0.tar.gz b/dist/OmicsIntegrator-0.2.0.tar.gz
diff --git a/dist/OmicsIntegrator-0.3.0.tar.gz b/dist/OmicsIntegrator-0.3.0.tar.gz
diff --git a/dist/OmicsIntegratorExamples.tar.gz b/dist/OmicsIntegratorExamples.tar.gz
diff --git a/setup.py b/setup.py
@@ -45,7 +45,7 @@ def run_tests(self):
 
 setup(
     name='OmicsIntegrator',
-    version='0.2.0',
+    version='0.3.0',
     description="Python tool for high throughput data integration",
     long_description=readme + '\n\n' + history,
     author="Sara Gosline",