New implementation of studentt function for ncm_stats_dist_kernel and reformulation of NcmStatsDist* objects.

INSTALL

@@ -1,8 +1,8 @@
 Installation Instructions
 *************************
 
-   Copyright (C) 1994-1996, 1999-2002, 2004-2016 Free Software
-Foundation, Inc.
+   Copyright (C) 1994-1996, 1999-2002, 2004-2017, 2020-2021 Free
+Software Foundation, Inc.
 
    Copying and distribution of this file, with or without modification,
 are permitted in any medium without royalty provided the copyright
@@ -225,7 +225,7 @@ order to use an ANSI C compiler:
 
 and if that doesn't work, install pre-built binaries of GCC for HP-UX.
 
-   HP-UX 'make' updates targets which have the same time stamps as their
+   HP-UX 'make' updates targets which have the same timestamps as their
 prerequisites, which makes it generally unusable when shipped generated
 files such as 'configure' are involved.  Use GNU 'make' instead.
 

aminclude_static.am

@@ -0,0 +1,126 @@
+
+# aminclude_static.am generated automatically by Autoconf
+# from AX_AM_MACROS_STATIC on Fri Aug 13 18:13:41 -03 2021
+
+
+# Code coverage
+#
+# Optional:
+#  - CODE_COVERAGE_DIRECTORY: Top-level directory for code coverage reporting.
+#    Multiple directories may be specified, separated by whitespace.
+#    (Default: $(top_builddir))
+#  - CODE_COVERAGE_OUTPUT_FILE: Filename and path for the .info file generated
+#    by lcov for code coverage. (Default:
+#    $(PACKAGE_NAME)-$(PACKAGE_VERSION)-coverage.info)
+#  - CODE_COVERAGE_OUTPUT_DIRECTORY: Directory for generated code coverage
+#    reports to be created. (Default:
+#    $(PACKAGE_NAME)-$(PACKAGE_VERSION)-coverage)
+#  - CODE_COVERAGE_BRANCH_COVERAGE: Set to 1 to enforce branch coverage,
+#    set to 0 to disable it and leave empty to stay with the default.
+#    (Default: empty)
+#  - CODE_COVERAGE_LCOV_SHOPTS_DEFAULT: Extra options shared between both lcov
+#    instances. (Default: based on )
+#  - CODE_COVERAGE_LCOV_SHOPTS: Extra options to shared between both lcov
+#    instances. (Default: )
+#  - CODE_COVERAGE_LCOV_OPTIONS_GCOVPATH: --gcov-tool pathtogcov
+#  - CODE_COVERAGE_LCOV_OPTIONS_DEFAULT: Extra options to pass to the
+#    collecting lcov instance. (Default: )
+#  - CODE_COVERAGE_LCOV_OPTIONS: Extra options to pass to the collecting lcov
+#    instance. (Default: )
+#  - CODE_COVERAGE_LCOV_RMOPTS_DEFAULT: Extra options to pass to the filtering
+#    lcov instance. (Default: empty)
+#  - CODE_COVERAGE_LCOV_RMOPTS: Extra options to pass to the filtering lcov
+#    instance. (Default: )
+#  - CODE_COVERAGE_GENHTML_OPTIONS_DEFAULT: Extra options to pass to the
+#    genhtml instance. (Default: based on )
+#  - CODE_COVERAGE_GENHTML_OPTIONS: Extra options to pass to the genhtml
+#    instance. (Default: )
+#  - CODE_COVERAGE_IGNORE_PATTERN: Extra glob pattern of files to ignore
+#
+# The generated report will be titled using the $(PACKAGE_NAME) and
+# $(PACKAGE_VERSION). In order to add the current git hash to the title,
+# use the git-version-gen script, available online.
+# Optional variables
+# run only on top dir
+if CODE_COVERAGE_ENABLED
+ ifeq ($(abs_builddir), $(abs_top_builddir))
+CODE_COVERAGE_DIRECTORY ?= $(top_builddir)
+CODE_COVERAGE_OUTPUT_FILE ?= $(PACKAGE_NAME)-$(PACKAGE_VERSION)-coverage.info
+CODE_COVERAGE_OUTPUT_DIRECTORY ?= $(PACKAGE_NAME)-$(PACKAGE_VERSION)-coverage
+
+CODE_COVERAGE_BRANCH_COVERAGE ?=
+CODE_COVERAGE_LCOV_SHOPTS_DEFAULT ?= $(if $(CODE_COVERAGE_BRANCH_COVERAGE),--rc lcov_branch_coverage=$(CODE_COVERAGE_BRANCH_COVERAGE))
+CODE_COVERAGE_LCOV_SHOPTS ?= $(CODE_COVERAGE_LCOV_SHOPTS_DEFAULT)
+CODE_COVERAGE_LCOV_OPTIONS_GCOVPATH ?= --gcov-tool "$(GCOV)"
+CODE_COVERAGE_LCOV_OPTIONS_DEFAULT ?= $(CODE_COVERAGE_LCOV_OPTIONS_GCOVPATH)
+CODE_COVERAGE_LCOV_OPTIONS ?= $(CODE_COVERAGE_LCOV_OPTIONS_DEFAULT)
+CODE_COVERAGE_LCOV_RMOPTS_DEFAULT ?=
+CODE_COVERAGE_LCOV_RMOPTS ?= $(CODE_COVERAGE_LCOV_RMOPTS_DEFAULT)
+CODE_COVERAGE_GENHTML_OPTIONS_DEFAULT ?=$(if $(CODE_COVERAGE_BRANCH_COVERAGE),--rc genhtml_branch_coverage=$(CODE_COVERAGE_BRANCH_COVERAGE))
+CODE_COVERAGE_GENHTML_OPTIONS ?= $(CODE_COVERAGE_GENHTML_OPTIONS_DEFAULT)
+CODE_COVERAGE_IGNORE_PATTERN ?=
+
+GITIGNOREFILES := $(GITIGNOREFILES) $(CODE_COVERAGE_OUTPUT_FILE) $(CODE_COVERAGE_OUTPUT_DIRECTORY)
+code_coverage_v_lcov_cap = $(code_coverage_v_lcov_cap_$(V))
+code_coverage_v_lcov_cap_ = $(code_coverage_v_lcov_cap_$(AM_DEFAULT_VERBOSITY))
+code_coverage_v_lcov_cap_0 = @echo "  LCOV   --capture" $(CODE_COVERAGE_OUTPUT_FILE);
+code_coverage_v_lcov_ign = $(code_coverage_v_lcov_ign_$(V))
+code_coverage_v_lcov_ign_ = $(code_coverage_v_lcov_ign_$(AM_DEFAULT_VERBOSITY))
+code_coverage_v_lcov_ign_0 = @echo "  LCOV   --remove /tmp/*" $(CODE_COVERAGE_IGNORE_PATTERN);
+code_coverage_v_genhtml = $(code_coverage_v_genhtml_$(V))
+code_coverage_v_genhtml_ = $(code_coverage_v_genhtml_$(AM_DEFAULT_VERBOSITY))
+code_coverage_v_genhtml_0 = @echo "  GEN   " "$(CODE_COVERAGE_OUTPUT_DIRECTORY)";
+code_coverage_quiet = $(code_coverage_quiet_$(V))
+code_coverage_quiet_ = $(code_coverage_quiet_$(AM_DEFAULT_VERBOSITY))
+code_coverage_quiet_0 = --quiet
+
+# sanitizes the test-name: replaces with underscores: dashes and dots
+code_coverage_sanitize = $(subst -,_,$(subst .,_,$(1)))
+
+# Use recursive makes in order to ignore errors during check
+check-code-coverage:
+	-$(AM_V_at)$(MAKE) $(AM_MAKEFLAGS) -k check
+	$(AM_V_at)$(MAKE) $(AM_MAKEFLAGS) code-coverage-capture
+
+# Capture code coverage data
+code-coverage-capture: code-coverage-capture-hook
+	$(code_coverage_v_lcov_cap)$(LCOV) $(code_coverage_quiet) $(addprefix --directory ,$(CODE_COVERAGE_DIRECTORY)) --capture --output-file "$(CODE_COVERAGE_OUTPUT_FILE).tmp" --test-name "$(call code_coverage_sanitize,$(PACKAGE_NAME)-$(PACKAGE_VERSION))" --no-checksum --compat-libtool $(CODE_COVERAGE_LCOV_SHOPTS) $(CODE_COVERAGE_LCOV_OPTIONS)
+	$(code_coverage_v_lcov_ign)$(LCOV) $(code_coverage_quiet) $(addprefix --directory ,$(CODE_COVERAGE_DIRECTORY)) --remove "$(CODE_COVERAGE_OUTPUT_FILE).tmp" "/tmp/*" $(CODE_COVERAGE_IGNORE_PATTERN) --output-file "$(CODE_COVERAGE_OUTPUT_FILE)" $(CODE_COVERAGE_LCOV_SHOPTS) $(CODE_COVERAGE_LCOV_RMOPTS)
+	-@rm -f "$(CODE_COVERAGE_OUTPUT_FILE).tmp"
+	$(code_coverage_v_genhtml)LANG=C $(GENHTML) $(code_coverage_quiet) $(addprefix --prefix ,$(CODE_COVERAGE_DIRECTORY)) --output-directory "$(CODE_COVERAGE_OUTPUT_DIRECTORY)" --title "$(PACKAGE_NAME)-$(PACKAGE_VERSION) Code Coverage" --legend --show-details "$(CODE_COVERAGE_OUTPUT_FILE)" $(CODE_COVERAGE_GENHTML_OPTIONS)
+	@echo "file://$(abs_builddir)/$(CODE_COVERAGE_OUTPUT_DIRECTORY)/index.html"
+
+code-coverage-clean:
+	-$(LCOV) --directory $(top_builddir) -z
+	-rm -rf "$(CODE_COVERAGE_OUTPUT_FILE)" "$(CODE_COVERAGE_OUTPUT_FILE).tmp" "$(CODE_COVERAGE_OUTPUT_DIRECTORY)"
+	-find . \( -name "*.gcda" -o -name "*.gcno" -o -name "*.gcov" \) -delete
+
+code-coverage-dist-clean:
+
+AM_DISTCHECK_CONFIGURE_FLAGS := $(AM_DISTCHECK_CONFIGURE_FLAGS) --disable-code-coverage
+ else # ifneq ($(abs_builddir), $(abs_top_builddir))
+check-code-coverage:
+
+code-coverage-capture: code-coverage-capture-hook
+
+code-coverage-clean:
+
+code-coverage-dist-clean:
+ endif # ifeq ($(abs_builddir), $(abs_top_builddir))
+else #! CODE_COVERAGE_ENABLED
+# Use recursive makes in order to ignore errors during check
+check-code-coverage:
+	@echo "Need to reconfigure with --enable-code-coverage"
+# Capture code coverage data
+code-coverage-capture: code-coverage-capture-hook
+	@echo "Need to reconfigure with --enable-code-coverage"
+
+code-coverage-clean:
+
+code-coverage-dist-clean:
+
+endif #CODE_COVERAGE_ENABLED
+# Hook rule executed before code-coverage-capture, overridable by the user
+code-coverage-capture-hook:
+
+.PHONY: check-code-coverage code-coverage-capture code-coverage-dist-clean code-coverage-clean code-coverage-capture-hook

configure.ac

@@ -820,7 +820,7 @@ if test "x$have_lapack" != "xno"; then
   LIBS="$LAPACK_LIBS $LIBS"
   AC_MSG_RESULT([$lapack_support])
 
-  AC_CHECK_FUNCS([dptsv_ dpotrf_ dpotri_ dpotrs_ dposv_ dsytrf_ dsytrs_ dsytri_ dsysvx_ dsysvxx_ dsyevr_ dsyevd_ dgeev_ dgeevx_ dggglm_ dgeqrf_ dgerqf_ dgeqlf_ dgelqf_ dtrsv_],[],[])
+  AC_CHECK_FUNCS([dptsv_ dpotrf_ dpotri_ dpotrs_ dposv_ dsytrf_ dsytrs_ dsytri_ dsysv_  dsysvx_ dsysvxx_ dsyevr_ dsyevd_ dgeev_ dgeevx_ dggglm_ dgeqrf_ dgerqf_ dgeqlf_ dgelqf_ dgels_ dtrsv_],[],[])
 
   if test "x$lapack_mkl" != "x"; then
     AC_CHECK_HEADERS([mkl_lapacke.h],
@@ -1115,6 +1115,7 @@ numcosmo/plc/Makefile
 numcosmo/class/Makefile
 numcosmo/sundials/Makefile
 numcosmo/toeplitz/Makefile
+numcosmo/misc/Makefile
 tools/Makefile
 tests/Makefile
 docs/Makefile

docs/Makefile.am

@@ -101,35 +101,48 @@ endif
 # Header files or dirs to ignore when scanning. Use base file/dir names
 # e.g. IGNORE_HFILES=gtkdebug.h gtkintl.h private_code
 IGNORE_HFILES= \
-              config.h                  \
-              config_extra.h            \
-              ncm_gsl_blas_types.h      \
-              ncm_fit_nlopt_enum_meta.h \
-              ncm_sphere_map_block.c    \
-              ncm_flapack.h             \
-              nc_hipert_private.h       \
-              gsl_rstat.h               \
-              gsl_cqp.h                 \
-              initial_point.h           \
-              rquantile.c               \
-              $(ignore_nlopt)           \
-              Faddeeva.h                \
-              levmar                    \
-              libcuba                   \
-              plc			\
-              class			\
-              class/source		\
-              class/hyrec		\
-              class/include             \
-              toeplitz                  \
-              sundials                  \
-              rcm.h                     \
-              rcm.c
+              config.h                        \
+              config_extra.h                  \
+              ncm_gsl_blas_types.h            \
+              ncm_fit_nlopt_enum_meta.h       \
+              ncm_sphere_map_block.c          \
+              ncm_flapack.h                   \
+              ncm_stats_dist_kernel_private.h \
+              ncm_stats_dist_private.h        \
+              ncm_stats_dist_kde_private.h    \
+              ncm_stats_dist_vkde_private.h   \
+              nc_hipert_private.h             \
+              gsl_rstat.h                     \
+              gsl_cqp.h                       \
+              initial_point.h                 \
+              rquantile.c                     \
+              $(ignore_nlopt)                 \
+              Faddeeva.h                      \
+              levmar                          \
+              libcuba                  	      \
+              plc                             \
+              class                           \
+              class/source      	      \
+              class/hyrec      	              \
+              class/include                   \
+              toeplitz                        \
+              sundials                        \
+              rcm.h                           \
+              rcm.c                           \
+              nnls.c                          \
+              libqp_gsmo.c                    \
+              libqp.h                         \
+              libqp_splx.c                    \
+              kdtree.h                        \
+              kdtree.c
+
 
 # Images to copy into HTML directory.
 # e.g. HTML_IMAGES=$(top_srcdir)/gtk/stock-icons/stock_about_24.png
 HTML_IMAGES= \
-	    $(srcdir)/images/spline_func_knots_evolution.png
+	    $(srcdir)/images/spline_func_knots_evolution.png \
+	    $(srcdir)/images/vkde.png 			     \
+	    $(srcdir)/images/kde.png
 
 # Extra SGML files that are included by $(DOC_MAIN_SGML_FILE).
 # e.g. content_files=running.sgml building.sgml changes-2.0.sgml

docs/numcosmo-docs.sgml

@@ -21,9 +21,11 @@
       <xi:include href="xml/ncm_c.xml"/>
       <xi:include href="xml/ncm_cfg.xml"/>
       <xi:include href="xml/ncm_util.xml"/>
+      <xi:include href="xml/ncm_iset.xml"/>
       <xi:include href="xml/ncm_diff.xml"/>
       <xi:include href="xml/ncm_vector.xml"/>
       <xi:include href="xml/ncm_matrix.xml"/>
+      <xi:include href="xml/ncm_nnls.xml"/>
       <xi:include href="xml/ncm_serialize.xml"/>
       <xi:include href="xml/ncm_obj_array.xml"/>
       <xi:include href="xml/ncm_integral1d.xml"/>
@@ -102,7 +104,6 @@
       <xi:include href="xml/ncm_vparam.xml"/>
       <xi:include href="xml/ncm_model_ctrl.xml"/>
       <xi:include href="xml/ncm_model_builder.xml"/>
-      <xi:include href="xml/ncm_model_mvnd.xml"/>
       <xi:include href="xml/ncm_mset.xml"/>
       <xi:include href="xml/ncm_mset_func.xml"/>
       <xi:include href="xml/ncm_mset_func1.xml"/>
@@ -124,7 +125,6 @@
       <xi:include href="xml/ncm_data_poisson.xml"/>    
       <xi:include href="xml/ncm_data_dist1d.xml"/>
       <xi:include href="xml/ncm_data_dist2d.xml"/>
-      <xi:include href="xml/ncm_data_gauss_cov_mvnd.xml"/>
     </section>
     <section>
     <title>Statistical Analysis</title>
@@ -134,8 +134,6 @@
       <xi:include href="xml/ncm_stats_dist1d_epdf.xml"/>
       <xi:include href="xml/ncm_stats_dist2d.xml"/>
       <xi:include href="xml/ncm_stats_dist2d_spline.xml"/>
-      <xi:include href="xml/ncm_stats_dist_nd.xml"/>
-      <xi:include href="xml/ncm_stats_dist_nd_kde_gauss.xml"/>
       <xi:include href="xml/ncm_bootstrap.xml"/>
       <xi:include href="xml/ncm_likelihood.xml"/>
       <xi:include href="xml/ncm_prior.xml"/>
@@ -160,16 +158,37 @@
       <xi:include href="xml/ncm_fit_levmar.xml"/>
       <xi:include href="xml/ncm_fit_mc.xml"/>
       <xi:include href="xml/ncm_fit_mcbs.xml"/>
+      <xi:include href="xml/ncm_lh_ratio1d.xml"/>
+      <xi:include href="xml/ncm_lh_ratio2d.xml"/>
+      <xi:include href="xml/ncm_abc.xml"/>
+    </section>
+    <section>
+      <title>Multivariate density estimation</title>
+      <xi:include href="xml/ncm_stats_dist.xml"/>
+      <xi:include href="xml/ncm_stats_dist_kde.xml"/>
+      <xi:include href="xml/ncm_stats_dist_vkde.xml"/>
+      <xi:include href="xml/ncm_stats_dist_kernel.xml"/>
+      <xi:include href="xml/ncm_stats_dist_kernel_gauss.xml"/>
+      <xi:include href="xml/ncm_stats_dist_kernel_st.xml"/>
+    </section>
+    <section>
+      <title>MCMC and ESMCMC</title>
       <xi:include href="xml/ncm_fit_mcmc.xml"/>
       <xi:include href="xml/ncm_fit_esmcmc.xml"/>
       <xi:include href="xml/ncm_fit_esmcmc_walker.xml"/>
       <xi:include href="xml/ncm_fit_esmcmc_walker_stretch.xml"/>
       <xi:include href="xml/ncm_fit_esmcmc_walker_walk.xml"/>
-      <xi:include href="xml/ncm_fit_esmcmc_walker_aps.xml"/>
-      <xi:include href="xml/ncm_lh_ratio1d.xml"/>
-      <xi:include href="xml/ncm_lh_ratio2d.xml"/>
-      <xi:include href="xml/ncm_abc.xml"/>
-    </section>
+      <xi:include href="xml/ncm_fit_esmcmc_walker_apes.xml"/>
+    </section>   
+    <section>
+      <title>MCMC Testing</title>
+      <xi:include href="xml/ncm_model_mvnd.xml"/>
+      <xi:include href="xml/ncm_data_gauss_cov_mvnd.xml"/>
+      <xi:include href="xml/ncm_model_rosenbrock.xml"/>
+      <xi:include href="xml/ncm_data_rosenbrock.xml"/>
+      <xi:include href="xml/ncm_model_funnel.xml"/>
+      <xi:include href="xml/ncm_data_funnel.xml"/>
+    </section>   
     <section>
       <title>Spherical maps and Healpix</title>
       <xi:include href="xml/ncm_sphere_map.xml"/>