Merge branch 'dev/1.2.4' into 'release/1.2'

Merge dev/1.2.4 into release/1.2

See merge request !38

Author: emarinier

CHANGELOG.md

@@ -2,6 +2,24 @@
 
 All notable changes to Neptune will be documented in this file.
 
+## [1.2.4] - 2017-02-27
+
+This release makes several small improvements, including: reducing the standard
+output clutter, adding timings to stages, and updating the documentation.
+
+### Added
+- Links in the README to the manual.
+- Walkthrough to the manual.
+- Example data to test the software.
+- Timings for stages.
+
+### Changed:
+- Improved clarity in manual.
+- Codeblocks in the manual.
+
+### Removed
+- Considerable clutter has been removed from standard output.
+
 ## [1.2.3] - 2016-07-11
 
 This release simplifies the installation process.

INSTALL.sh

@@ -15,17 +15,7 @@ BIN=$PREFIX/bin
 LIB=$PREFIX/lib
 
 # Create directories if needed:
-if [ ! -d "$PREFIX" ]; then
-    mkdir $PREFIX
-fi
-
-if [ ! -d "$BIN" ]; then
-    mkdir $BIN
-fi
-
-if [ ! -d "$LIB" ]; then
-    mkdir $LIB
-fi
+mkdir -p "$PREFIX"/{bin,lib}
 
 # Create Python virtual environment:
 VENV=$LIB/neptune

NOTICE.txt

@@ -1,6 +1,6 @@
 Neptune
 
-Copyright Government of Canada 2015-2016
+Copyright Government of Canada 2015-2017
 
 Written by: Eric Marinier, Public Health Agency of Canada,
     National Microbiology Laboratory

README.md

@@ -6,7 +6,7 @@
 
 Neptune
 
-Copyright Government of Canada 2015-2016
+Copyright Government of Canada 2015-2017
 
 Written by: Eric Marinier, Public Health Agency of Canada,
     National Microbiology Laboratory
@@ -38,11 +38,10 @@ probabilistic models instead of heuristic strategies.
 ## Release ##
 -------------
 
-**Neptune 1.2.3**
+**Neptune 1.2.4**
 
-2016 July 11
-
-This release simplifies the installation process.
+This release makes several small improvements, including: reducing the standard
+output clutter, adding timings to stages, and updating the documentation.
 
 ## Requirements ##
 ------------------
@@ -68,8 +67,9 @@ Otherwise, the following dependencies must be installed manually:
 ## Installation ##
 ------------------
 
-It is strongly recommended you refer to the manual for full installation
-instructions. Neptune may be installed using the following command:
+It is strongly recommended you refer to the
+[manual](documentation/manual/Manual.pdf) for full installation instructions.
+Neptune may be installed using the following command:
 
         $ INSTALL.sh
 
@@ -89,7 +89,7 @@ A simple example of running Neptune:
 	$ neptune --inclusion /path/to/inclusion/ --exclusion /path/to/exclusion/
 		--output /path/to/output/
 
-Please refer to the documentation for more details.
+Please refer to the [manual](documentation/manual/Manual.pdf) for more details.
 
 ## Contact ##
 -------------