Update Makefile to build expected files

doc/Doxyfile

@@ -1817,7 +1817,7 @@ COMPACT_LATEX          = YES
 # The default value is: a4.
 # This tag requires that the tag GENERATE_LATEX is set to YES.
 
-PAPER_TYPE             = a4
+PAPER_TYPE             = letter
 
 # The EXTRA_PACKAGES tag can be used to specify one or more LaTeX package names
 # that should be included in the LaTeX output. The package can be specified just
@@ -2206,15 +2206,17 @@ SEARCH_INCLUDES        = YES
 # preprocessor.
 # This tag requires that the tag SEARCH_INCLUDES is set to YES.
 
-INCLUDE_PATH           =
+INCLUDE_PATH           = ../common-diffusion/ \
+                         ../common-spinodal/  
 
 # You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard
 # patterns (like *.h and *.hpp) to filter out the header-files in the
 # directories. If left blank, the patterns specified with FILE_PATTERNS will be
 # used.
 # This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
 
-INCLUDE_FILE_PATTERNS  =
+INCLUDE_FILE_PATTERNS  = *.h \
+                         *.cuh
 
 # The PREDEFINED tag can be used to specify one or more macro names that are
 # defined before the preprocessor is started (similar to the -D option of e.g.

doc/Makefile

@@ -13,16 +13,19 @@ dox:
 
 .PHONY: tex
 tex: dox
-	$(MAKE) -C latex && cd latex && $(LATEX) refman.tex
+	$(MAKE) -C latex && \
+	cd latex && \
+	cp refman.tex hiperc.tex && \
+	$(LATEX) hiperc.tex
 
 .PHONY: pdf
 pdf: tex
-	cp latex/refman.pdf hiperc_guide.pdf
+	cp latex/hiperc.pdf hiperc_guide.pdf
 
 .PHONY: html
 html: dox
 	$(SPHINX) -b html . _build
 
 .PHONY: clean
 clean:
-	rm -rf _build/* _static/* latex xml rst/*
+	rm -rf _build/* _static/* html latex xml rst/*

doc/requirements.txt

@@ -1,3 +1,4 @@
 Sphinx>2.2
 breathe>4.13
 recommonmark
+sphinxcontrib-doxylink