Merge pull request #2363 from edwardhartnett/ejh_doc_2

fixed some doxygen warnings

Author: WardF

docs/dispatch.md

@@ -499,7 +499,7 @@ The code in *hdf4var.c* does an *nc_get_vara()* on the HDF4 SD
 dataset. This is all that is needed for all the nc_get_* functions to
 work.
 
-# Point of Contact {#filters_poc}
+# Point of Contact {#dispatch_poc}
 
 *Author*: Dennis Heimbigner<br>
 *Email*: dmh at ucar dot edu<br>

docs/internal.md

@@ -59,8 +59,8 @@ term "deep" is also used to mean recursive.
 
 Two deep walking operations are provided by the netcdf-c library
 to aid in managing instances of complex structures.
-* free'ing an instance of the complex type
-* copying an instance of the complex type.
+- free'ing an instance of the complex type
+- copying an instance of the complex type.
 
 Previously The netcdf-c library only did shallow free and shallow copy of
 complex types. This meant that only the top level was properly
@@ -72,7 +72,7 @@ internally and the user's data.
 Note that the term "vector" is used to mean a contiguous (in
 memory) sequence of instances of some type. Given an array with,
 say, dimensions 2 X 3 X 4, this will be stored in memory as a
-vector of length 2*3*4=24 instances.
+vector of length 2\*3\*4=24 instances.
 
 The use cases are primarily these.
 
@@ -328,7 +328,7 @@ The model output is actually a struct containing two fields:
 ## The Inference Algorithm
 
 The construction of the model is primarily carried out by the function
-*NC\_infermodel()* (in *libdispatch/dinfermodel.c).
+*NC\_infermodel()* (in *libdispatch/dinfermodel.c*).
 It is given the following parameters:
 1. path -- (IN) absolute file path or URL
 2. modep -- (IN/OUT) the set of mode flags given to *NC\_open* or *NC\_create*.
@@ -493,7 +493,7 @@ int nc_inq_var_zstandard(int ncid, int varid, int* has_filterp, int* levelp);
 ````
 So generally the API has the ncid and the varid as fixed, and then
 a list of parameters specific to the filter -- level in this case.
-For the inquire function, there is an additional argument -- has_filterp --
+For the inquire function, there is an additional argument -- has\_filterp --
 that is set to 1 if the filter is defined for the given variable
 and is 0 if not.
 The remainder of the inquiry parameters are pointers to memory
@@ -506,10 +506,10 @@ requires three supporting objects:
    libzstd must be installed in order to use the zstandard
    API.
 2. A HDF5 wrapper for the filter must be installed in the
-   directory pointed to by the HDF5_PLUGIN_PATH environment
+   directory pointed to by the HDF5\_PLUGIN\_PATH environment
    variable.
 3. (Optional) An NCZarr Codec implementation must be installed
-   in the the HDF5_PLUGIN_PATH directory.
+   in the the HDF5\_PLUGIN\_PATH directory.
 
 ## Adding a New Standard Filter
 
@@ -521,7 +521,7 @@ of several locations.
 3. or it can be loaded as part of an external library such as libccr.
 
 However, the three objects listed above need to be 
-stored in the HDF5_PLUGIN_DIR directory, so adding a standard
+stored in the HDF5\_PLUGIN\_PATH directory, so adding a standard
 filter still requires modification to the netcdf build system.
 This limitation may be lifted in the future.
 
@@ -543,7 +543,7 @@ fi
 AC_MSG_CHECKING([whether libzstd library is available])
 AC_MSG_RESULT([${have_zstd}])
 ````
-Note the the entry point (*ZSTD_compress*) is library dependent
+Note the the entry point (*ZSTD\_compress*) is library dependent
 and is used to see if the library is available.
 
 #### Makefile.am
@@ -558,22 +558,23 @@ libh5szip_la_SOURCES = H5Zzstd.c H5Zzstd.h
 endif
 ````
 
+````
 # Need our version of szip if libsz available and we are not using HDF5
 if HAVE_SZ
 noinst_LTLIBRARIES += libh5szip.la
 libh5szip_la_SOURCES = H5Zszip.c H5Zszip.h
 endif
-
+````
 #### CMakeLists.txt
 In an analog to *configure.ac*, a block like
 this needs to be in *netcdf-c/CMakeLists.txt*.
 ````
 FIND_PACKAGE(Zstd)
 set_std_filter(Zstd)
 ````
-The FIND_PACKAGE requires a CMake module for the filter
+The FIND\_PACKAGE requires a CMake module for the filter
 in the cmake/modules directory.
-The *set_std_filter* function is a macro.
+The *set\_std\_filter* function is a macro.
 
 An entry in the file config.h.cmake.in will also be needed.
 ````

docs/nczarr.md

@@ -331,12 +331,12 @@ Amazon S3 accepts two forms for specifying the endpoint for accessing the data.
 1. Virtual -- the virtual addressing style places the bucket in the host part of a URL.
 For example:
 ```
-https://<bucketname>.s2.<region>.amazonaws.com/
+https://<bucketname>.s2.&lt;region&gt.amazonaws.com/
 ```
 2. Path -- the path addressing style places the bucket in at the front of the path part of a URL.
 For example:
 ```
-https://s2.<region>.amazonaws.com/<bucketname>/
+https://s2.&lt;region&gt.amazonaws.com/<bucketname>/
 ```
 
 The NCZarr code will accept either form, although internally, it is standardized on path style.
@@ -470,7 +470,7 @@ Here are a couple of examples using the _ncgen_ and _ncdump_ utilities.
     ```
     Note that the URLis internally translated to this
     ````
-    https://s2.<region>.amazonaws.com/datasetbucket/rootkey#mode=nczarr,awsprofile=unidata" dataset.cdl
+    https://s2.&lt;region&gt.amazonaws.com/datasetbucket/rootkey#mode=nczarr,awsprofile=unidata" dataset.cdl
     ````
     The region is from the algorithm described in Appendix E1.
 
@@ -752,7 +752,7 @@ s3://<bucket>/key
 ````
 Then this is rebuilt to this form:
 ````
-s3://s2.<region>.amazonaws.com>/key
+s3://s2.&lt;region&gt.amazonaws.com>/key
 ````
 However this requires figuring out the region to use.
 The algorithm for picking an region is as follows.
@@ -783,7 +783,7 @@ The content of these objects is the same as the contents of the corresponding ke
 * ''.nczarray <=> ''_NCZARR_ARRAY_''
 * ''.nczattr <=> ''_NCZARR_ATTR_''
 
-# Appendix G. JSON Attribute Convention. {#nczarr_version1}
+# Appendix G. JSON Attribute Convention. {#nczarr_json}
 
 An attribute may be encountered on read whose value when parsed
 by JSON is a dictionary. As a special conventions, the value

docs/notes.md

@@ -4,8 +4,6 @@
 
 <H2>See Also:</H2>
 
-* \subpage nc-error-codes
-
 # Ignored if NULL {#ignored_if_null}
 
 Many of the argurments of netCDF functions are pointers. For example,