Merge pull request #6 from das-developers/3.0

3.0

Doxyfile

@@ -44,7 +44,7 @@ PROJECT_NUMBER         =
 # for a project that appears at the top of each page and should give viewer a
 # quick idea about the purpose of the project. Keep the description short.
 
-PROJECT_BRIEF          = "das2 core C utilities"
+PROJECT_BRIEF          = "das core C utilities (v3)"
 
 # With the PROJECT_LOGO tag one can specify a logo or an icon that is included
 # in the documentation. The maximum height of the logo should not exceed 55
@@ -914,7 +914,7 @@ EXAMPLE_RECURSIVE      = NO
 # that contain images that are to be included in the documentation (see the
 # \image command).
 
-IMAGE_PATH             =
+IMAGE_PATH             = notes
 
 # The INPUT_FILTER tag can be used to specify a program that doxygen should
 # invoke to filter for each input file. Doxygen will invoke the filter program

buildfiles/Linux.mak

@@ -48,19 +48,30 @@ BD=$(BUILD_DIR)
 LEX=flex
 YACC=bison
 
-DEFINES:=-DWISDOM_FILE=/etc/fftw/wisdom -D_XOPEN_SOURCE=600
-WARNINGS:=-Wall -Werror -Wno-format-truncation -Wno-deprecated-declarations
-#-Wno-format-security 
+# -Wno-deprecated needed for OpenSSL, removed when call to ERR_load_BIO_strings is fixed
+WARNINGS:=-Wall -Werror -Wno-deprecated-declarations 
+#-Wno-format-security
+
+# I use string trucation all the time intentianally and make sure it's null
+# terminated anyway, so this error doesn't apply
+
+DEFINES:=-DWISDOM_FILE=/etc/fftw/wisdom -D_XOPEN_SOURCE=600 -Wno-format-truncation 
+
+DBG_DEFINES=-ggdb 
+O2_DEFINES=-DNDEBUG -O2 -Wno-unused-result -Wno-stringop-truncation 
+
 
 # Conda build does NOT set the include and lib directories within the
 # compiler script itself, it merely exports ENV vars. This is unfortunate
 # because it means makefiles must be altered to work with anaconda.
 
 ifeq ($(CONDA_BUILD_STATE),)
 
-CC=gcc
-CFLAGS= $(WARNINGS) -fPIC -std=c99 -I. -ggdb $(DEFINES)
-#CFLAGS=-Wall -DNDEBUG -O2 -fPIC -std=c99 -Wno-format-security -I. $(DEFINES)
+CC=gcc 
+
+CFLAGS= $(WARNINGS) $(DBG_DEFINES) $(DEFINES) -fPIC -std=c99  -I.
+#CFLAGS=$(WARNINGS) $(O2_DEFINES) $(DEFINES) -fPIC -std=c99 -I.
+
 #-fstack-protector-strong 
 
 #CTESTFLAGS=-Wall -fPIC -std=c99 -ggdb -I. $(CFLAGS)
@@ -168,7 +179,7 @@ $(BD)/das2_psd:$(BD)/das2_psd.o $(BD)/send.o $(BD)/$(TARG).a
 
 cdf:$(BD)/das3_cdf
 
-$(BD)/das3_cdf:$(BD)/das3_cdf.o
+$(BD)/das3_cdf:$(BD)/das3_cdf.o $(BD)/$(TARG).a
 	@echo "An example CDF_INC value would be: /usr/local/include"
 	@echo "An example CDF_LIB value would be: /usr/local/lib/libcdf.a"
 	@if [ "$(CDF_INC)" = "" ] ; then echo "CDF_INC not set"; exit 3; fi
@@ -238,6 +249,9 @@ $(BD)/html:$(BD) $(BD)/$(TARG).a
 
 install_doc:$(INST_DOC)/libdas2
 
+clean_doc:
+	-rm -r $(BD)/html
+
 $(INST_DOC)/libdas2:$(BD)/html
 	-mkdir -p $(INST_DOC)
 	@if [ -e "$(INST_DOC)/libdas2" ]; then rm -r $(INST_DOC)/libdas2; fi

das2/array.h

@@ -39,10 +39,6 @@
 extern "C" {
 #endif
 
-/** @addtogroup datasets 
- * @{
- */
-
 /** The maximum number of array indices in das2 */
 #define DASIDX_MAX 8
 
@@ -133,6 +129,9 @@ char* das_idx_prn(int nRank, ptrdiff_t* pIdx, size_t uLen, char* sBuf);
 #define RNG_6(i,I,j,J,k,K,l,L,m,M,n,N) 6, (ptrdiff_t[6]){i,j,k,l,m,n}, (ptrdiff_t[6]){I,J,K,L,M,N}
 #define RNG_7(i,I,j,J,k,K,l,L,m,M,n,N,o,O) 7, (ptrdiff_t[7]){i,j,k,l,m,n,o}, (ptrdiff_t[7]){I,J,K,L,M,N,O}
 
+/** @addtogroup DM 
+ * @{
+ */
 
 /** Calculate a strided array shape from a min/max range.
  * 
@@ -197,6 +196,10 @@ typedef struct dyna_buf{
 
 } DynaBuf;
 
+/** @addtogroup DM 
+ * @{
+ */
+
 /** Dynamic recursive ragged arrays
  *
  * This class maps any number of indices, (i,j,k...) to elements stored into a
@@ -263,7 +266,6 @@ typedef struct dyna_buf{
  *    printf("\n");
  * }
  * @endcode
- * @ingroup datasets
  */
 typedef struct das_array {
 	char        sId[DAS_MAX_ID_BUFSZ];   /* A text identifier of this instance of the array */
@@ -312,6 +314,8 @@ typedef struct das_array {
 
 } DasAry;
 
+/** @} */
+
 
 /** Creates a new dynamic array buffer
  *

das2/buffer.h

@@ -30,11 +30,11 @@
 extern "C" {
 #endif
 
-/** @addtogroup utilities
+/** @addtogroup IO
  * @{
  */
 
-/** Little buffer class to handle accumulating string data.
+/** Buffer class to handle accumulating byte streams
  * 
  * DasBuf objects maintain a data buffer with a current write point, a current
  * read point and an end read point.  As data are written to the buffer the
@@ -43,8 +43,6 @@ extern "C" {
  * memory buffer, or when multiple functions need to read from a buffer without
  * memory re-allocations or placing null values to stop parsing.
  * 
- * It is hoped that the use of this class cuts down on alot of data copies and
- * sub-string allocations.
  */
 typedef struct das_buffer{
 	char* sBuf;

das2/codec.c

@@ -603,7 +603,10 @@ static int _var_text_read(
 		return -1 * das_error(DASERR_ENC, "Expected a text type for the external buffer");
 	}
 
+#ifndef NDEBUG
 	das_val_type vtAry = DasAry_valType( pThis->pAry );
+#endif
+
 	bool bParse = ((pThis->uProc & DASENC_PARSE) != 0);
 	int nRet;
 	char cSep = pThis->cSep;

das2/codec.h

@@ -32,6 +32,10 @@ extern "C" {
 /* Not public, only here because used in a macro */
 #define DASENC_VALID    0x0001 
 
+/** @addtogroup IO
+ * @{
+ */
+
 /** Reading and writing array data to buffers */
 typedef struct das_codec {
 
@@ -59,7 +63,11 @@ typedef struct das_codec {
 
 } DasCodec;
 
-/** Has the memory for this encoder been initialized? */
+
+/** Has the memory for this encoder been initialized? 
+ * 
+ * @memberof DasCodec 
+ */
 #define DasCodec_isValid(pCd) (((pCd)->uProc & DASENC_VALID)==(DASENC_VALID))
 
 /** Initialize a serial buffer decoder/encoder
@@ -106,6 +114,8 @@ typedef struct das_codec {
  *       Otherwise, no string larger then the last index will be written
  *       and zeros will be appended to fill out the last index when reading
  *       data.
+ * 
+ * @memberof DasCodec 
  */
 DAS_API DasErrCode DasCodec_init(
    DasCodec* pThis, DasAry* pAry, const char* sSemantic, const char* sEncType,
@@ -143,12 +153,16 @@ DAS_API DasErrCode DasCodec_init(
  * 
  * @returns the number of unread bytes or a negative ERR code if a data conversion
  *        error occured.
- * */
+ * @memberof DasCodec 
+ */
 DAS_API int DasCodec_decode(
    DasCodec* pThis, const ubyte* pBuf, int nBufLen, int nExpect, int* pValsRead
 );
 
-/** Release the reference count on the array given to this encoder/decoder */
+/** Release the reference count on the array given to this encoder/decoder 
+ * 
+ * @memberof DasCodec 
+ */
 DAS_API void DasCodec_deInit(DasCodec* pThis);
 
 #ifdef __cplusplus