Merge eccf514 into 8f6fd4c

NumCosmo · Mar 30, 2023 · a059001 · a059001
2 parents 8f6fd4c + eccf514
commit a059001
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Showing 43 changed files with 4,110 additions and 2,329 deletions.
diff --git a/.github/workflows/build_check.yml b/.github/workflows/build_check.yml
@@ -17,7 +17,10 @@ jobs:
     steps:
     - uses: actions/checkout@v2
     - name: Install prereq
-      run: sudo apt-get install gobject-introspection gir1.2-glib-2.0 libgirepository1.0-dev gcc gfortran pkg-config libglib2.0-dev libgmp3-dev libmpfr-dev libgsl0-dev libfftw3-dev libopenblas-dev libflint-arb-dev libcfitsio-dev libnlopt-dev libhdf5-dev gtk-doc-tools texlive texlive-bibtex-extra texlive-science texlive-publishers tex4ht perl libxml-libxml-perl
+      run: |
+        sudo apt-get update
+        sudo apt-get install gobject-introspection gir1.2-glib-2.0 libgirepository1.0-dev gcc gfortran pkg-config libglib2.0-dev libgmp3-dev libmpfr-dev libgsl0-dev libfftw3-dev libopenblas-dev libflint-arb-dev libcfitsio-dev libnlopt-dev libhdf5-dev gtk-doc-tools texlive texlive-bibtex-extra texlive-science texlive-publishers tex4ht perl libxml-libxml-perl
+        pip install pytest pytest-tap
     - name: Ensure clear Jupyter Notebooks
       uses: ResearchSoftwareActions/EnsureCleanNotebooksAction@1.1
     - name: Autogen
@@ -26,7 +29,15 @@ jobs:
       run: ./configure --enable-gtk-doc --enable-man --prefix=/usr --libdir=/usr/lib
     - name: make
       run: make -j8
-    - name: Test example compilation
+    - name: Test example compilation using non-installed library
+      run: |
+        source numcosmo_export.sh
+        cd examples
+        gcc -D_GNU_SOURCE -Wall example_simple.c -o example_simple -lnumcosmo -lgsl -lm $(pkg-config glib-2.0 gobject-2.0 --libs --cflags)
+        gcc -D_GNU_SOURCE -Wall example_ca.c -o example_ca -lnumcosmo -lgsl -lm $(pkg-config glib-2.0 gobject-2.0 --libs --cflags)
+        ./example_simple
+        ./example_ca
+    - name: Test example compilation using installed library
       run: |
         sudo make install
         cd examples
@@ -51,7 +62,10 @@ jobs:
     steps:
     - uses: actions/checkout@v2
     - name: Install prereq
-      run: sudo apt-get install gobject-introspection gir1.2-glib-2.0 libgirepository1.0-dev gcc gfortran lcov pkg-config libglib2.0-dev libgmp3-dev libmpfr-dev libgsl0-dev libfftw3-dev libopenblas-dev libflint-arb-dev libcfitsio-dev libnlopt-dev libhdf5-dev python3-setuptools gtk-doc-tools
+      run: |
+        sudo apt-get update
+        sudo apt-get install gobject-introspection gir1.2-glib-2.0 libgirepository1.0-dev gcc gfortran lcov pkg-config libglib2.0-dev libgmp3-dev libmpfr-dev libgsl0-dev libfftw3-dev libopenblas-dev libflint-arb-dev libcfitsio-dev libnlopt-dev libhdf5-dev python3-setuptools gtk-doc-tools
+        pip install pytest pytest-tap
     - name: Autogen
       run: NOCONFIGURE=yes ./autogen.sh
     - name: configure
@@ -85,7 +99,7 @@ jobs:
     - uses: actions/checkout@v2
     - name: Install prereq
       run: |
-        brew install autoconf automake libtool gobject-introspection gsl gmp mpfr fftw cfitsio nlopt gfortran gtk-doc glib-utils glib
+        brew install autoconf automake libtool gobject-introspection gsl gmp mpfr fftw cfitsio nlopt gfortran gtk-doc glib-utils glib pygobject3
         brew ls glib
         brew ls glib-utils
     - name: Ensure clear Jupyter Notebooks

diff --git a/Makefile.am b/Makefile.am
@@ -20,13 +20,15 @@ numcosmodoc_DATA = \
 	ChangeLog  \
 	NEWS
 
-#DISTCLEANFILES = intltool-extract intltool-merge intltool-update
+if HAVE_PYTHON
+include numcosmo_py.mk
+endif # HAVE_PYTHON
 
 EXTRA_DIST = \
-	INSTALL             \
-	$(numcosmodoc_DATA) \
-	numcosmo.pc.in      \
-        tap-driver.sh       \
+	INSTALL                \
+	$(numcosmodoc_DATA)    \
+	numcosmo-valgrind.supp \
+        tap-driver.sh          \
         tap-test
 
 AM_CFLAGS = 

diff --git a/configure.ac b/configure.ac
@@ -186,6 +186,14 @@ AC_C_CONST()
 AC_C_RESTRICT()
 AC_C_VOLATILE()
 
+dnl ***************************************************************************
+dnl C Sizes
+dnl ***************************************************************************
+AC_CHECK_SIZEOF(int)
+AC_CHECK_SIZEOF(long)
+AC_CHECK_SIZEOF(unsigned int)
+AC_CHECK_SIZEOF(unsigned long)
+
 dnl ***************************************************************************
 dnl Makefile.decl variable dependency (here glib_native_win32 is null)
 dnl ***************************************************************************
@@ -360,8 +368,10 @@ dnl ***************************************************************************
 AM_PATH_PYTHON([3.8], [
 AX_PYTHON_MODULE([gi])
 AX_PYTHON_MODULE([pytest])
+AX_PYTHON_MODULE([pytest_tap])
 ],[:])
 AM_CONDITIONAL([HAVE_PYTHON], [test "$PYTHON" != ":"])
+AM_CONDITIONAL([HAVE_PYTEST_TAP], [test "x$HAVE_PYMOD_PYTEST_TAP" = xyes])
 
 dnl ***************************************************************************
 dnl check for gtk-doc
@@ -372,23 +382,6 @@ GTK_DOC_CHECK([1.14],[--flavour no-tmpl])
 AM_CONDITIONAL([ENABLE_GTK_DOC], false)
 ])
 
-AC_ARG_ENABLE(man,
-              [AS_HELP_STRING([--enable-man],[regenerate man pages from Docbook [default=no]])],enable_man=yes,
-              enable_man=no)
-
-if test "${enable_man}" != no; then
-
-dnl ***************************************************************************
-dnl Check for xsltproc
-dnl ***************************************************************************
-AC_PATH_PROG([XSLTPROC], [xsltproc])
-  if test -z "$XSLTPROC"; then
-    enable_man=no
-  fi
-fi
-
-AM_CONDITIONAL(ENABLE_MAN, test x$enable_man != xno)
-
 dnl ***************************************************************************
 dnl Set PACKAGE_DATA_DIR in config.h.
 dnl ***************************************************************************
@@ -1052,6 +1045,20 @@ fi
 
 AC_SUBST(PLC_DEFINES)
 
+dnl ***************************************************************************
+dnl libfyaml
+dnl ***************************************************************************
+
+PKG_CHECK_MODULES(LIBFYAML, [ libfyaml ], HAVE_LIBFYAML=1, HAVE_LIBFYAML=0)
+
+AC_SUBST(HAVE_LIBFYAML)
+AC_SUBST(LIBFYAML_CFLAGS)
+AC_SUBST(LIBFYAML_LIBS)
+if test "x$HAVE_LIBFYAML" = "x1"; then
+  AC_DEFINE([HAVE_LIBFYAML], [], [Define if you have libfyaml available])
+fi
+AM_CONDITIONAL([HAVE_LIBFYAML], [ test x$HAVE_LIBFYAML = x1 ])
+
 dnl ***************************************************************************
 dnl Appending libs and setting up TEST_SHARED
 dnl ***************************************************************************
@@ -1147,6 +1154,11 @@ if [ test "x$HAVE_ARB" = xyes ]; then
 else
        echo "Building with ARB support: .......................................NO"
 fi
+if [ test "x$HAVE_LIBFYAML" = x1 ]; then
+       echo "Building with libfyaml support: .................................YES"
+else
+       echo "Building with libfyaml support: ..................................NO"
+fi
 if [ test "x$PYTHON_VERSION" != x ]; then
        echo "Building with Python support: ...................................$PYTHON"
        echo "Building with Python version: ...................................$PYTHON_VERSION"
@@ -1160,6 +1172,11 @@ if [ test "x$PYTHON_VERSION" != x ]; then
   else
        echo "Building with Python pytest support ..............................NO"
   fi
+  if [test "x$HAVE_PYMOD_PYTEST_TAP" = xyes]; then
+       echo "Building with Python pytest-tap support .........................YES"
+  else
+       echo "Building with Python pytest-tap support ..........................NO"
+  fi
 else
        echo "Building with Python support: ....................................NO"
 fi

diff --git a/docs/Makefile.am b/docs/Makefile.am
@@ -3,7 +3,6 @@
 # Local xml files
 XML_FILES= \
 	introduction.xml \
-	darkenergy.xml   \
 	refs.xml
 
 # Generated xml files
@@ -135,6 +134,8 @@ IGNORE_HFILES= \
               libqp_splx.c                    \
               kdtree.h                        \
               kdtree.c                        \
+              rb_knn_list.h                   \
+              rb_knn_list.c                   \
               clencurt.h                      \
               converged.h                     \
               vwrapper.h                      \
@@ -195,32 +196,9 @@ endif
 
 ########################################################################
 
-man_MANS := darkenergy.1
+MAINTAINERCLEANFILES = $(BUILT_SOURCES)
 
-EXTRA_DIST += $(man_MANS)
-
-if ENABLE_MAN
-
-%.1: %.xml
-	@@XSLTPROC@ -nonet http://docbook.sourceforge.net/release/xsl/current/manpages/docbook.xsl $<
-
-dist-local-check-mans-enabled:
-	if grep "Man generation disabled" $(man_MANS) >/dev/null; then $(RM) $(man_MANS); fi
-else
-
-$(man_MANS):
-	@echo Man generation disabled.  Creating dummy $@.  Configure with --enable-man to enable it.
-	@echo Man generation disabled.  Remove this file, configure with --enable-man, and rebuild > $@
-
-dist-local-check-mans-enabled:
-	@echo "*** --enable-man must be used in order to make dist"
-	false
-
-endif
-
-MAINTAINERCLEANFILES = $(man_MANS) $(BUILT_SOURCES)
-
-BUILT_EXTRA_DIST = $(man_MANS)
+BUILT_EXTRA_DIST = 
 
 CLEANFILES += \
 	addmathjax.stamp                                    \
@@ -238,7 +216,7 @@ CLEANFILES += \
 	$(addsuffix .xref, $(basename $(XML_GEN_FILES)))    \
 	$(addprefix $(top_srcdir)/docs/, $(XML_GEN_FILES))
 
-dist-hook-local: dist-local-check-mans-enabled all-local
+dist-hook-local: all-local
 
 numcosmo-docs-clean: clean
 	cd $(srcdir) && rm -rf xml html

diff --git a/docs/darkenergy.xml b/docs/darkenergy.xml
diff --git a/docs/numcosmo-docs.sgml b/docs/numcosmo-docs.sgml
@@ -407,6 +407,7 @@
       <xi:include href="xml/nc_galaxy_wl_dist.xml"/>
       <xi:include href="xml/nc_galaxy_wl_ellipticity_gauss.xml"/>
       <xi:include href="xml/nc_galaxy_wl_ellipticity_kde.xml"/>
+      <xi:include href="xml/nc_galaxy_wl_ellipticity_binned.xml"/>
       <xi:include href="xml/nc_galaxy_wl_proj.xml"/>
     </section>
     <section>

diff --git a/generate_py_makefile.py b/generate_py_makefile.py
@@ -0,0 +1,46 @@
+
+
+import os
+import os.path
+
+# Set the directory where the notebooks are located
+NOTEBOOK_DIR = 'numcosmo_py'
+
+# Get a list of all subdirectories in the notebook directory
+subdirs = []
+for root, dirs, files in os.walk(NOTEBOOK_DIR):
+    if "__pycache__" not in root:
+        normalized_path = os.path.normpath(root)
+        if normalized_path.startswith("./"):
+            normalized_path = normalized_path[2:]
+        subdirs.append(normalized_path)
+
+subdirs.sort()
+
+# Generate the Makefile.am contents
+makefile_contents = "## Generated automatically with generate_py_makefile.py\n\n\n"
+python_files = []
+
+for subdir in subdirs:
+    # Get a list of all notebook files in the subdirectory
+    for root, dirs, files in os.walk(subdir):
+        if subdir == root:
+            for file in files:
+                if file.endswith('.py'):
+                    file = os.path.join(root, file)
+                    python_files.append(file)
+
+
+max_length = max(len(extra_dist_file) for extra_dist_file in python_files)
+python_files = [extra_dist_file.ljust(max_length) for extra_dist_file in python_files]
+
+# Generate the EXTRA_DIST variable
+makefile_contents += "nobase_python_PYTHON = \\\n"
+for file in python_files[:-1]:
+    makefile_contents += f"\t{file} \\\n"
+makefile_contents += f"\t{python_files[-1]}\n"
+
+# Write the Makefile.am file
+with open('numcosmo_py.mk', 'w') as f:
+    f.write(makefile_contents)
+