Documentation and Travis fixes

5 files changed, 111 insertions, 49 deletions

diff --git a/.travis.yml b/.travis.yml
index 21df53e..ffd674f 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -41,8 +41,8 @@ script:
   - eval "${MATRIX_EVAL}"
   - $CXX --version
   # build and test debug version
-  - make      CXX=$CXX EIGEN_INCLUDE_PATH=$EIGEN_INCLUDE_PATH WITH_LAPACK=1 OPENBLAS_LEGACY=1 -j 4 -k
-  - time make CXX=$CXX EIGEN_INCLUDE_PATH=$EIGEN_INCLUDE_PATH WITH_LAPACK=1 OPENBLAS_LEGACY=1 check
+  - make      CXX=$CXX EIGEN_INCLUDE_PATH=$EIGEN_INCLUDE_PATH WITH_LAPACK=1 OPENBLAS_LEGACY=1 WITH_GSLCBLAS=1 -j 4 -k
+  - time make CXX=$CXX EIGEN_INCLUDE_PATH=$EIGEN_INCLUDE_PATH WITH_LAPACK=1 OPENBLAS_LEGACY=1 WITH_GSLCBLAS=1 check
   # - make clean
   # build and test release version (integration test mostly)
   # - make CXX=$CXX EIGEN_INCLUDE_PATH=$EIGEN_INCLUDE_PATH DEBUG= FORCE_DYNAMIC=1 WITH_OPENBLAS=1 OPENBLAS_LEGACY=1 -j 4
diff --git a/Makefile b/Makefile
index d7fb91b..f8bacbf 100644
--- a/Makefile
+++ b/Makefile
@@ -98,9 +98,11 @@ ifdef SHOW_COMPILER_WARNINGS
 endif
 
 ifndef FORCE_STATIC
-  LIBS = -lgsl -lopenblas -pthread -lz -lgfortran -lquadmath
+  LIBS = -lgsl -lopenblas -pthread -lz
   ifdef WITH_GSLCBLAS
     LIBS += -lgslcblas
+  else
+    LIBS += -lgfortran -lquadmath
   endif
 else
   ifndef TRAVIS_CI # Travis static compile we cheat a little
diff --git a/NEWS.md b/NEWS.md
deleted file mode 100644
index 19d81d9..0000000
--- a/NEWS.md
+++ /dev/null
@@ -1,45 +0,0 @@
-## GEMMA 0.96.0
-
-+ First stable release.
-
-## GEMMA 0.95.2
-
-+ Resolved Issue #36.
-
-## GEMMA 0.95.1
-
-+ Created first release of GEMMA 0.95a following request in Issue #33.
-
-## GEMMA 0.94.1
-
-+ Fixed a bug (the predict option for multiple phenotype imputation
-was not recoginzed with PLINK files).
-
-## GEMMA 0.94.0
-
-+ Implemented the multivariate linear mixed model.
-
-## GEMMA 0.93
-
-+ Implemented the Bayesian sparse linear mixed model.
-
-## GEMMA 0.92
-
-+ Fixed a few typos.
-
-+ Now allows for missing values in the covariates file.
-
-+ Included REMLE estimate for lambda in the output .log file.
-
-+ Added small GWAS example dataset
-
-+ Added detailed user manual.
-
-## GEMMA 0.91
-
-+ Fixed a bug (BIMBAM annotation file not recognized).
-
-## GEMMA 0.90
-
-+ Initial pre-release.
-
diff --git a/RELEASE-NOTES.md b/RELEASE-NOTES.md
new file mode 100644
index 0000000..de7f3b5
--- /dev/null
+++ b/RELEASE-NOTES.md
@@ -0,0 +1,101 @@
+## ChangeLog v0.97 (2017/12/19)
+
+This is a massive bug fix release with many improvements. For contributions
+see
+[contributors](https://github.com/genetics-statistics/GEMMA/graphs/contributors)
+and
+[commits](https://github.com/genetics-statistics/GEMMA/commits/master).
+
+### Speedup of GEMMA by using optimized OpenBlas
+
+* Providing a binary release with OpenBlas optimization for Intel Haswell
+* Dropped using standar lapack and gslcblas libs
+* Fixed NaN bug with GSL2 and made recent libraries the default
+* Minimized use of Eigenlib libraries (single threaded and slow compilation)
+* -legacy switch provides v0.96 behaviour (incl. eigenlib)
+
+### Added Leave One Chromosome Out (LOCO) support for Bimbam (K and LMM)
+
+* See 449d882a3b33ef81ef4f0127c3932b01fa796dbb
+* -snps [filename] option allow selecting a subset of SNPs for analysis
+* -loco [chr] option for K and LMM computations
+* added [gemma-wrapper](https://github.com/genetics-statistics/gemma-wrapper) to make using LOCO easy
+* LOCO examples in https://github.com/genetics-statistics/GEMMA/blob/master/test/dev_test_suite.sh
+
+### Added checks for matrices
+
+* #72 and #45 implements
+  1. Fail if K has negative eigen values
+  2. Fail if K is not symmetric
+  3. Fail if K is not positive definite
+  4. Warn in eigen values are very small
+  5. Warn if K is ill conditioned
+* Check for NaN values
+
+### Added test framework and unit tests
+
+* Added integration and unit tests, as well as
+  [Travis-CI](https://travis-ci.org/genenetwork/GEMMA) support
+* Improved debug information and testing of input files
+
+### Other
+
+* #81 printing out beta and se(beta) under -lmm 2 as well as logl_H1
+* Improved README and INSTALL docs
+* Added support info and code of conduct
+* Reformatted the full source tree with 3935ba39d30666dd7d4a831155631847c77b70c4
+* Merged LMM computation for Plink and Bimbam formats
+* Fixed progressbar issues
+* #46 removed support for Oxford format
+* Got rid of all compiler warnings
+* Updated copyright banner, info and license information for included software
+* Started a [discussion list](https://groups.google.com/forum/#!forum/gemma-discussion)
+
+See also [commits](https://github.com/genetics-statistics/GEMMA/commits/master).
+
+## GEMMA 0.96.0
+
++ First stable release.
+
+## GEMMA 0.95.2
+
++ Resolved Issue #36.
+
+## GEMMA 0.95.1
+
++ Created first release of GEMMA 0.95a following request in Issue #33.
+
+## GEMMA 0.94.1
+
++ Fixed a bug (the predict option for multiple phenotype imputation
+was not recoginzed with PLINK files).
+
+## GEMMA 0.94.0
+
++ Implemented the multivariate linear mixed model.
+
+## GEMMA 0.93
+
++ Implemented the Bayesian sparse linear mixed model.
+
+## GEMMA 0.92
+
++ Fixed a few typos.
+
++ Now allows for missing values in the covariates file.
+
++ Included REMLE estimate for lambda in the output .log file.
+
++ Added small GWAS example dataset
+
++ Added detailed user manual.
+
+## GEMMA 0.91
+
++ Fixed a bug (BIMBAM annotation file not recognized).
+
+## GEMMA 0.90
+
++ Initial pre-release.
+
+See also https://github.com/genetics-statistics/GEMMA/releases
diff --git a/src/gemma.cpp b/src/gemma.cpp
index e31eaed..edd79d7 100644
--- a/src/gemma.cpp
+++ b/src/gemma.cpp
@@ -543,9 +543,13 @@ void GEMMA::PrintHelp(size_t option) {
     cout << " -lmax     [num]          "
          << " specify maximum value for lambda (default 1e+5)" << endl;
     cout
-        << " -region   [num]          "
+        << " -region    [num]          "
         << " specify the number of regions used to evaluate lambda (default 10)"
         << endl;
+    cout << " -loco     [chr]          "
+         << " leave one chromosome out (LOCO) by name (requires -a annotation "
+            "file)"
+         << endl;
     cout << endl;
   }