From 9d9177dbca52c717931d284fd94a5b74d4c0ab47 Mon Sep 17 00:00:00 2001
From: Kevin Bui <kvb2univpitt@gmail.com>
Date: Wed, 17 May 2017 12:24:05 -0400
Subject: [PATCH 1/2] Updated project version to 0.1.2-SNAPSHOT. Updated
 tetrad-lib dependency to version 6.2.0.

---
 pom.xml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pom.xml b/pom.xml
index 1c7811d..98a1555 100644
--- a/pom.xml
+++ b/pom.xml
@@ -3,7 +3,7 @@
     <modelVersion>4.0.0</modelVersion>
     <groupId>edu.pitt.dbmi</groupId>
     <artifactId>causal-cmd</artifactId>
-    <version>0.1.1-SNAPSHOT</version>
+    <version>0.1.2-SNAPSHOT</version>
     <packaging>jar</packaging>
     <properties>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
@@ -125,7 +125,7 @@
         <dependency>
             <groupId>edu.cmu</groupId>
             <artifactId>tetrad-lib</artifactId>
-            <version>6.0.1-SNAPSHOT</version>
+            <version>6.2.0</version>
         </dependency>
         <dependency>
             <groupId>junit</groupId>

From b92994fe298c1e669b70d2d98469b39b4f2f595a Mon Sep 17 00:00:00 2001
From: Kevin Bui <kvb2univpitt@gmail.com>
Date: Wed, 17 May 2017 12:34:09 -0400
Subject: [PATCH 2/2] Updated project version in the readme file.

---
 README.md | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/README.md b/README.md
index a995826..290acf3 100644
--- a/README.md
+++ b/README.md
@@ -1,4 +1,4 @@
-# causal-cmd v0.1.1
+# causal-cmd v0.1.2
 
 ## Introduction
 
@@ -28,7 +28,7 @@ java -jar causal-cmd-0.1.1-jar-with-dependencies.jar
 And you'll see the following instructions:
 
 ```
-usage: java -jar causal-cmd-0.1.1.jar --algorithm <arg> | --simulate-data <arg>  [--version]
+usage: java -jar causal-cmd-0.1.2.jar --algorithm <arg> | --simulate-data <arg>  [--version]
     --algorithm <arg>       FGESc, FGESd, GFCIc, GFCId
     --simulate-data <arg>   sem-rand-fwd, bayes-net-rand-fwd
     --version               Show software version.
@@ -125,7 +125,7 @@ The GFCI algorithm has additional edge types:
 ## Complete Usage Guide
 
 ```
-usage: java -jar causal-cmd-0.1.1.jar --algorithm <arg> | --simulate-data <arg>  [--version]
+usage: java -jar causal-cmd-0.1.2.jar --algorithm <arg> | --simulate-data <arg>  [--version]
     --algorithm <arg>       FGESc, FGESd, GFCIc, GFCId
     --simulate-data <arg>   sem-rand-fwd, bayes-net-rand-fwd
     --version               Show software version.
@@ -136,7 +136,7 @@ You can use the `--algorithm <arg>` parameter to see specific algorithm usage in
 ### FGESc
 
 ```
-usage: java -jar causal-cmd-0.1.1.jar --algorithm FGESc [-d <arg>] [--exclude-variables <arg>] -f <arg> [--faithfulness-assumed] [--help] [--json] [--knowledge <arg>] [--max-degree <arg>] [--no-validation-output] [-o <arg>] [--output-prefix <arg>] [--penalty-discount <arg>] [--skip-latest] [--skip-nonzero-variance] [--skip-unique-var-name] [--tetrad-graph-json] [--thread <arg>] [--verbose]
+usage: java -jar causal-cmd-0.1.2.jar --algorithm FGESc [-d <arg>] [--exclude-variables <arg>] -f <arg> [--faithfulness-assumed] [--help] [--json] [--knowledge <arg>] [--max-degree <arg>] [--no-validation-output] [-o <arg>] [--output-prefix <arg>] [--penalty-discount <arg>] [--skip-latest] [--skip-nonzero-variance] [--skip-unique-var-name] [--tetrad-graph-json] [--thread <arg>] [--verbose]
  -d,--delimiter <arg>           Data delimiter either comma, semicolon, space, colon, or tab. Default: comma for *.csv, else tab.
     --exclude-variables <arg>   A file containing variables to exclude.
  -f,--data <arg>                Data file.
@@ -160,7 +160,7 @@ usage: java -jar causal-cmd-0.1.1.jar --algorithm FGESc [-d <arg>] [--exclude-va
 ### FGESd
 
 ```
-usage: java -jar causal-cmd-0.1.1.jar --algorithm FGESd [-d <arg>] [--exclude-variables <arg>] -f <arg> [--faithfulness-assumed] [--help] [--json] [--knowledge <arg>] [--max-degree <arg>] [--no-validation-output] [-o <arg>] [--output-prefix <arg>] [--sample-prior <arg>] [--skip-category-limit] [--skip-latest] [--skip-unique-var-name] [--structure-prior <arg>] [--tetrad-graph-json] [--thread <arg>] [--verbose]
+usage: java -jar causal-cmd-0.1.2.jar --algorithm FGESd [-d <arg>] [--exclude-variables <arg>] -f <arg> [--faithfulness-assumed] [--help] [--json] [--knowledge <arg>] [--max-degree <arg>] [--no-validation-output] [-o <arg>] [--output-prefix <arg>] [--sample-prior <arg>] [--skip-category-limit] [--skip-latest] [--skip-unique-var-name] [--structure-prior <arg>] [--tetrad-graph-json] [--thread <arg>] [--verbose]
  -d,--delimiter <arg>           Data delimiter either comma, semicolon, space, colon, or tab. Default: comma for *.csv, else tab.
     --exclude-variables <arg>   A file containing variables to exclude.
  -f,--data <arg>                Data file.
@@ -185,7 +185,7 @@ usage: java -jar causal-cmd-0.1.1.jar --algorithm FGESd [-d <arg>] [--exclude-va
 ### GFCIc
 
 ```
-usage: java -jar causal-cmd-0.1.1.jar --algorithm GFCIc [--alpha <arg>] [-d <arg>] [--exclude-variables <arg>] -f <arg> [--faithfulness-assumed] [--help] [--json] [--knowledge <arg>] [--max-degree <arg>] [--no-validation-output] [-o <arg>] [--output-prefix <arg>] [--penalty-discount <arg>] [--skip-latest] [--skip-nonzero-variance] [--skip-unique-var-name] [--tetrad-graph-json] [--thread <arg>] [--verbose]
+usage: java -jar causal-cmd-0.1.2.jar --algorithm GFCIc [--alpha <arg>] [-d <arg>] [--exclude-variables <arg>] -f <arg> [--faithfulness-assumed] [--help] [--json] [--knowledge <arg>] [--max-degree <arg>] [--no-validation-output] [-o <arg>] [--output-prefix <arg>] [--penalty-discount <arg>] [--skip-latest] [--skip-nonzero-variance] [--skip-unique-var-name] [--tetrad-graph-json] [--thread <arg>] [--verbose]
     --alpha <arg>               Cutoff for p values (alpha). Default is 0.01.
  -d,--delimiter <arg>           Data delimiter either comma, semicolon, space, colon, or tab. Default: comma for *.csv, else tab.
     --exclude-variables <arg>   A file containing variables to exclude.
@@ -210,7 +210,7 @@ usage: java -jar causal-cmd-0.1.1.jar --algorithm GFCIc [--alpha <arg>] [-d <arg
 ### GFCId
 
 ```
-usage: java -jar causal-cmd-0.1.1.jar --algorithm GFCId [--alpha <arg>] [-d <arg>] [--exclude-variables <arg>] -f <arg> [--faithfulness-assumed] [--help] [--json] [--knowledge <arg>] [--max-degree <arg>] [--no-validation-output] [-o <arg>] [--output-prefix <arg>] [--sample-prior <arg>] [--skip-category-limit] [--skip-latest] [--skip-unique-var-name] [--structure-prior <arg>] [--tetrad-graph-json] [--thread <arg>] [--verbose]
+usage: java -jar causal-cmd-0.1.2.jar --algorithm GFCId [--alpha <arg>] [-d <arg>] [--exclude-variables <arg>] -f <arg> [--faithfulness-assumed] [--help] [--json] [--knowledge <arg>] [--max-degree <arg>] [--no-validation-output] [-o <arg>] [--output-prefix <arg>] [--sample-prior <arg>] [--skip-category-limit] [--skip-latest] [--skip-unique-var-name] [--structure-prior <arg>] [--tetrad-graph-json] [--thread <arg>] [--verbose]
     --alpha <arg>               Cutoff for p values (alpha). Default is 0.01.
  -d,--delimiter <arg>           Data delimiter either comma, semicolon, space, colon, or tab. Default: comma for *.csv, else tab.
     --exclude-variables <arg>   A file containing variables to exclude.