Merge pull request #193 from admb-project/admb-12.3-docs

Merge admb-12.3 into master branch
admb-project · Feb 22, 2021 · 4a140f1 · 4a140f1
2 parents d3be66a + 07b6eec
commit 4a140f1
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diff --git a/CHANGES.md b/CHANGES.md
@@ -11,6 +11,95 @@ Describe new features, changes and improvements for each release.
 * Continually streamline installation and build process
 * Continually improve and update documentation
 
+ADMB-12.3
+---------
+*Released February 28, 2021*  
+
+#### New Features
+
+* Add **hess_step()** function for the capability to do single Newton steps using the inverse Hessian
+  (See [Issue #160](https://github.com/admb-project/admb/issues/160) and
+  [Pull #179](https://github.com/admb-project/admb/pull/179)).
+
+* Added function hessian_phase() which will return true if the hessian is being computed
+  ([See Issue #158](https://github.com/admb-project/admb/issues/158)).
+
+* Increased static allocation size of initial_params::max_num_initial_params to 4000 using -mip option.
+  If -mip is not used, the program will dynamically allocate memory for any amount of initial_params
+  ([See Issue #157](https://github.com/admb-project/admb/issues/157)).
+
+#### Changes and Improvements
+
+* Fixed compiler boolean warnings in hmc functions
+  ([See Pull #188](https://github.com/admb-project/admb/pull/186)).
+
+* Fix bug in labels and cleanup hess_step outputs in hmc functions
+  ([See Pull #185](https://github.com/admb-project/admb/pull/185)).
+
+* Use 'make verify' to run all unit and program testing.  All the testing outputs was streamlined
+  to be put into outputs.txt file
+  ([See Issue #188](https://github.com/admb-project/admb/issues/188)).
+
+  Also, added a output file option -o to the admb script with can rename and build to a specific directory.
+
+  For example, the admb script will build the executable for mymodel.tpl to ~/bin/myprogram. 
+
+  ```
+  $ admb -o ~/bin/myprogram mymodel.tpl
+  ```
+
+* Yukio Takeuchi updated the docs for teh natural cubic spline
+  ([See Issue #180](https://github.com/admb-project/admb/issues/180)).
+
+* C++14 is the default C++ compiler standard for ADMB. C++11 is still supported for older compilers
+  ([See Issue #166](https://github.com/admb-project/admb/issues/166)).
+
+* Able to use absolute path with ADMB program from any run directory with the data files
+  ([See Issue #165](https://github.com/admb-project/admb/issues/165)).
+
+  For example, run myprogram from the bin directory to be used to run in a differt directory at myrundirectory.
+
+  ```
+  myrundirectory$ ~/bin/myprogram
+  ```
+
+* If the hessian is not positive definite, the ADMB program will NOT exit.  It will instead stop
+  computing the hessian, then go to the FINAL_SECTION
+  ([See Issue #164](https://github.com/admb-project/admb/issues/164)).
+
+* Updated Git Ignore with more files to avoid displaying as unmodified list
+  ([See Issue #162](https://github.com/admb-project/admb/issues/162)).
+
+* Use CodeQL recommendations for setting size of input reads
+  ([See Issue #159](https://github.com/admb-project/admb/issues/159)).
+
+* Improved data file parser to work with different line ending including for older MacOS9 files
+  ([See Issue #155](https://github.com/admb-project/admb/issues/155)).
+
+* Added missing i5_array::initialize() function
+  ([See Issue #155](https://github.com/admb-project/admb/issues/155)).
+
+* Reverted to back to faster version of vector shape pooling code
+  ([See Issue #152](https://github.com/admb-project/admb/issues/152)).
+
+* Added a REPORT_SECTION section to the ADMB Manual
+  ([See Issue #97](https://github.com/admb-project/admb/issues/97)).
+
+* Fixed input stream for adstring to check if the buffer was exceeded
+  ([See Changes 7237a6a](https://github.com/admb-project/admb/commit/7237a6a1eb3e1ddee6195db4cf6bf080b0acc665)).
+
+* Fixed file input stream for dvector and dvar_vector to read in values from file
+  ([See Changes d3be66a](https://github.com/admb-project/admb/commit/d3be66a632b28c412cc84161cc5c3725c0ae06b4)).
+
+* Also restructed the build files and outputs scripts.
+
+#### Statistics
+
+* Total Code Coverage testing is ~ 48.54%
+  ([See ADMB Code Coverage](https://app.codecov.io/gh/admb-project/admb)).
+
+* Total Unit Tests is 914.
+
 ADMB-12.2
 ---------
 

diff --git a/INSTALL.md b/INSTALL.md
@@ -1,7 +1,7 @@
 ADMB Project  
 ============
-*ADMB-12.2*  
-*Released July 31, 2020*  
+*ADMB-12.3*  
+*Released February 28, 2021*  
 
 ADMB Installation procedures
 

diff --git a/LICENSE.txt b/LICENSE.txt
@@ -1,4 +1,4 @@
-Copyright (c) 2008-2020 ADMB Foundation and Regents of the
+Copyright (c) 2008-2021 ADMB Foundation and Regents of the
 University of California
 
 AD Model Builder and associated libraries and documentations are

diff --git a/README.md b/README.md
@@ -1,7 +1,7 @@
 ADMB Project
 ============
-*ADMB-12.2*  
-*Released July 31, 2020*  
+*ADMB-12.3*  
+*Released February 28, 2021*  
 
 ---
 

diff --git a/VERSION b/VERSION
@@ -1 +1 @@
-12.2-git
+12.3
diff --git a/docs/install/BuildingSourceUnix.md b/docs/install/BuildingSourceUnix.md
@@ -1,7 +1,7 @@
 # ADMB Building Source for Unix
 
-*ADMB-12.2*  
-*Released July 31, 2020*  
+*ADMB-12.3*  
+*Released February 28, 2021*  
 
 Describe building ADMB from source for Unix.
 
@@ -31,14 +31,14 @@ Building Source
 
 1. **Download**
 
-   Download ADMB source distribution [admb-12.2-src.zip](https://github.com/admb-project/admb/releases/download/admb-12.2/admb-12.2-src.zip)
+   Download ADMB source distribution [admb-12.3-src.zip](https://github.com/admb-project/admb/releases/download/admb-12.3/admb-12.3-src.zip)
 
    Open a **Terminal** window
 
    Use the command below to extract contents of zip file to _~/admb/_. 
 
    ```
-   [~]$ unzip admb-12.2-src.zip
+   [~]$ unzip admb-12.3-src.zip
    ```
 
    _**Alternative**_ &mdash; Use Git client (see command below) to get source from version control repository.

diff --git a/docs/install/BuildingSourceVisualStudio.md b/docs/install/BuildingSourceVisualStudio.md
@@ -1,7 +1,7 @@
 # ADMB Building Source with Visual Studio
 
-*ADMB-12.2*  
-*Released July 31, 2020*  
+*ADMB-12.3*  
+*Released February 28, 2021*  
 
 Describe building ADMB from source for Windows and Visual C++ compilers.
 
@@ -14,7 +14,7 @@ Building Source
 
 1. **Download**
 
-   Download source distribution [admb-12.2-src.zip](https://github.com/admb-project/admb/releases/download/admb-12.2/admb-12.2-src.zip).
+   Download source distribution [admb-12.3-src.zip](https://github.com/admb-project/admb/releases/download/admb-12.3/admb-12.3-src.zip).
 
    Double click downloaded zip file and extract admb directory to **C:\\admb\\>**.
 

diff --git a/docs/install/QuickStartMacOSZip.md b/docs/install/QuickStartMacOSZip.md
@@ -1,7 +1,7 @@
 # ADMB Quick Start MacOS
 
-*ADMB-12.2*  
-*Released July 31, 2020*  
+*ADMB-12.3*  
+*Released February 28, 2021*  
 
 Describe downloading, installing and using ADMB from binary release for MacOS.
 
@@ -14,14 +14,14 @@ Quick Start
 
 1. **Download**
 
-   Download zip file [admb-12.2-macos.zip](https://github.com/admb-project/admb/releases/download/admb-12.2/admb-12.2-macos.zip).
+   Download zip file [admb-12.3-macos.zip](https://github.com/admb-project/admb/releases/download/admb-12.3/admb-12.3-macos.zip).
 
 2. **Install**
 
    Open a Terminal, then use the command below to extract contents of zip file to **~/admb/**. 
 
    ```
-   [~]$ unzip admb-12.2-macos.zip
+   [~]$ unzip admb-12.3-macos.zip
    ```
 
 3. **Use** ADMB

diff --git a/docs/install/QuickStartUnix.md b/docs/install/QuickStartUnix.md
@@ -1,7 +1,7 @@
 # ADMB Quick Start Unix
 
-*ADMB-12.2*  
-*Released July 31, 2020*  
+*ADMB-12.3*  
+*Released February 28, 2021*  
 
 Describe downloading, installing and using ADMB from binary release for Linux.
 
@@ -20,14 +20,14 @@ Quick Start
 
 1. **Download**
 
-   Download linux ZIP file [admb-12.2-linux.zip](https://github.com/admb-project/admb/releases/download/admb-12.2/admb-12.2-linux.zip).
+   Download linux ZIP file [admb-12.3-linux.zip](https://github.com/admb-project/admb/releases/download/admb-12.3/admb-12.3-linux.zip).
 
 2. **Install**
 
    Open a **Terminal**, then use the command below to extract contents of downloaded zip file to _~/admb/_. 
 
    ```
-   [~]$ unzip admb-12.2-linux.zip
+   [~]$ unzip admb-12.3-linux.zip
    ```
 
 3. **Use** ADMB

diff --git a/docs/install/QuickStartWindows.md b/docs/install/QuickStartWindows.md
@@ -1,7 +1,7 @@
 # ADMB Quick Start Windows
 
-*ADMB-12.2*
-*Released July 31, 2020*
+*ADMB-12.3*  
+*Released February 28, 2021*  
 
 Describe downloading, installing and using ADMB from binary release for Windows.
 
@@ -12,7 +12,7 @@ Quick Start
 
 1. **Download**
 
-   Download installer [admb-12.2-windows.exe](https://github.com/admb-project/admb/releases/download/admb-12.2/admb-12.2-windows.exe).
+   Download installer [admb-12.3-windows.exe](https://github.com/admb-project/admb/releases/download/admb-12.3/admb-12.3-windows.exe).
 
    _**Note**_ &mdash; Installer includes MinGW-w64 C++ compiler.
 

diff --git a/docs/manuals/admb-re/admbre.tex b/docs/manuals/admb-re/admbre.tex
@@ -16,9 +16,9 @@
 \newcommand{\scGLM}{\textsc{glm}}
 \newcommand{\scGLMM}{\textsc{glmm}}
 \newcommand{\scLIDAR}{\textsc{lidar}}
-\newcommand\admbversion{12.2}
-\newcommand\admbyear{2020}
-\newcommand\admbdate{2020-07-07}
+\newcommand\admbversion{12.3}
+\newcommand\admbyear{2021}
+\newcommand\admbdate{2021-02-28}
 
 \makeindex
 

diff --git a/docs/manuals/admb/admb.tex b/docs/manuals/admb/admb.tex
@@ -26,9 +26,9 @@
 \newcommand\Pone{P_{t|t-1}}
 \newcommand\diag{\textrm{diag}}
 \newcommand\ep{\textrm{elem\_prod}}
-\newcommand\admbversion{12.2}
-\newcommand\admbyear{2020}
-\newcommand\admbdate{2020-07-07}
+\newcommand\admbversion{12.3}
+\newcommand\admbyear{2021}
+\newcommand\admbdate{2021-02-28}
 
 \makeindex
 

diff --git a/docs/manuals/autodif/autodif.tex b/docs/manuals/autodif/autodif.tex
@@ -7,9 +7,9 @@
 \hypersetup{urlcolor=black}
 
 % Some local definitions.
-\newcommand\admbversion{12.2}
-\newcommand\admbyear{2020}
-\newcommand\admbdate{2020-07-07}
+\newcommand\admbversion{12.3}
+\newcommand\admbyear{2021}
+\newcommand\admbdate{2021-02-28}
 
 % Do not use a blank line between the question and the answer.
 \newcommand{\question}[1]{\bigskip\noindent{\bf #1?}\par\medskip\noindent}

diff --git a/scripts/admb/admb b/scripts/admb/admb
@@ -8,7 +8,7 @@ shopt -s expand_aliases
 alias help='echo -e "
 Builds AD Model Builder executable or library.
 
-Release Version: 12.2
+Release Version: 12.3
 Location: $BASH_SOURCE
 
 Usage: admb [-c] [-d] [-f] [-g] [-p] [-r] model [src(s)]

diff --git a/scripts/admb/admb.bat b/scripts/admb/admb.bat
@@ -667,7 +667,7 @@ goto EOF
 :HELP
 echo Builds AD Model Builder executable or library.
 echo.
-echo Release Version: 12.2
+echo Release Version: 12.3
 echo Location: %~dp0
 echo.
 echo Usage: admb [-c] [-d] [-f] [-g] [-r] model [src(s)]

diff --git a/scripts/admb/admb.sh b/scripts/admb/admb.sh
@@ -8,7 +8,7 @@ shopt -s expand_aliases
 alias help='echo -e "
 Builds AD Model Builder executable or library.
 
-Release Version: 12.2
+Release Version: 12.3
 Location: $BASH_SOURCE
 
 Usage: admb [-c] [-d] [-f] [-g] [-p] [-r] model [src(s)]

diff --git a/scripts/installers/innosetup/admb.iss b/scripts/installers/innosetup/admb.iss
@@ -1,5 +1,5 @@
-#define ADMB_VERSION "ADMB-12.2"
-#define ADMB_VERSION2 "admb-12.2"
+#define ADMB_VERSION "ADMB-12.3"
+#define ADMB_VERSION2 "admb-12.3"
 
 [Setup]
 PrivilegesRequired=none

diff --git a/scripts/installers/packagemaker/QuickStartMacOS.md b/scripts/installers/packagemaker/QuickStartMacOS.md
@@ -1,7 +1,7 @@
 # ADMB Quick Start for MacOS
 
-*ADMB-12.2*  
-*Released July 31, 2020*  
+*ADMB-12.3*  
+*Released February 28, 2021*  
 
 Describe downloading, installing and using ADMBTerminal from binary release for MacOS.
 
@@ -20,7 +20,7 @@ Quick Start
 
 1. **Download**
 
-   Download [admb-12.2--macos.dmg](https://github.com/admb-project/admb/releases/download/admb-12.2/admb-12.2--macos.dmg).
+   Download [admb-12.3--macos.dmg](https://github.com/admb-project/admb/releases/download/admb-12.3/admb-12.3--macos.dmg).
 
 2. **Install**