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Merge pull request #2834 from WardF/fix_doxygen.wif

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Fix doxygen warnings
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Ward Fisher 2023-12-21 10:31:44 -07:00 committed by GitHub
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1
.gitignore vendored
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@ -35,6 +35,7 @@ test-driver
#####
### 'Normal' gitignore files.
docs/auth.html
.vscode
nug.tag
netcdf-c.tag

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docs/Doxyfile.in
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@ -1269,15 +1269,6 @@ HTML_COLORSTYLE_SAT = 100
HTML_COLORSTYLE_GAMMA = 80
# If the HTML_TIMESTAMP tag is set to YES then the footer of each generated HTML
# page will contain the date and time when the page was generated. Setting this
# to YES can help to show when doxygen was last run and thus if the
# documentation is up to date.
# The default value is: NO.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_TIMESTAMP = NO
# If the HTML_DYNAMIC_MENUS tag is set to YES then the generated HTML
# documentation will contain a main index with vertical navigation menus that
# are dynamically created via JavaScript. If disabled, the navigation index will
@ -1865,14 +1856,6 @@ LATEX_HIDE_INDICES = NO
LATEX_BIB_STYLE = plain
# If the LATEX_TIMESTAMP tag is set to YES then the footer of each generated
# page will contain the date and time when the page was generated. Setting this
# to NO can help when comparing the output of multiple runs.
# The default value is: NO.
# This tag requires that the tag GENERATE_LATEX is set to YES.
LATEX_TIMESTAMP = NO
# The LATEX_EMOJI_DIRECTORY tag is used to specify the (relative or absolute)
# path from which the emoji images will be read. If a relative path is entered,
# it will be relative to the LATEX_OUTPUT directory. If left blank the

6
docs/cloud.md
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@ -67,9 +67,9 @@ https://thredds-test.unidata.ucar.edu/thredds/fileServer/irma/metar/files/METAR_
# References {#nccloud_bib}
<a name="ref_aws">[1]</a> [Amazon Simple Storage Service Documentation](https://docs.aws.amazon.com/s3/index.html)<br>
<a name="ref_awssdk">[2]</a> [Amazon Simple Storage Service Library](https://github.com/aws/aws-sdk-cpp)<br>
<a name="ref_awssdk_conda">[11]</a> [Conda-forge / packages / aws-sdk-cpp](https://anaconda.org/conda-forge/aws-sdk-cpp)<br>
<a name="cloud_ref_aws">[1]</a> [Amazon Simple Storage Service Documentation](https://docs.aws.amazon.com/s3/index.html)<br>
<a name="cloud_ref_awssdk">[2]</a> [Amazon Simple Storage Service Library](https://github.com/aws/aws-sdk-cpp)<br>
<a name="cloud_ref_awssdk_conda">[11]</a> [Conda-forge / packages / aws-sdk-cpp](https://anaconda.org/conda-forge/aws-sdk-cpp)<br>
# Appendix A. S3 Build Support {#nccloud_s3build}

2
docs/dispatch.md
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@ -520,7 +520,7 @@ Modifying the dispatch version requires two steps:
The two should agree in value.
### NC_DISPATCH_VERSION Incompatibility
## NC_DISPATCH_VERSION Incompatibility
When dynamically adding a dispatch table
-- in nc_def_user_format (see libdispatch/dfile.c) --

24
docs/filters.md
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@ -65,6 +65,28 @@ The concept of a variable-sized type is defined as follows:
then that compound type is variable-sized.
4. All other types are fixed-size.
## A Warning on Backward Compatibility {#filters_compatibility}
The API defined in this document should accurately reflect the
current state of filters in the netCDF-c library. Be aware that
there was a short period in which the filter code was undergoing
some revision and extension. Those extensions have largely been
reverted. Unfortunately, some users may experience some
compilation problems for previously working code because of
these reversions. In that case, please revise your code to
adhere to this document. Apologies are extended for any
inconvenience.
A user may encounter an incompatibility if any of the following appears in user code.
* The function *\_nc\_inq\_var\_filter* was returning the error value NC\_ENOFILTER if a variable had no associated filters.
It has been reverted to the previous case where it returns NC\_NOERR and the returned filter id was set to zero if the variable had no filters.
* The function *nc\_inq\_var\_filterids* was renamed to *nc\_inq\_var\_filter\_ids*.
* Some auxilliary functions for parsing textual filter specifications have been moved to the file *netcdf\_aux.h*. See [Appendix A](#filters_appendixa).
* All of the "filterx" functions have been removed. This is unlikely to cause problems because they had limited visibility.
For additional information, see [Appendix B](#filters_appendixb).
## Enabling A HDF5 Compression Filter {#filters_enable}
HDF5 supports dynamic loading of compression filters using the
@ -717,7 +739,7 @@ This can be accomplished using this command.
Since ncdump is not being asked to access the data (the -h flag), it can obtain the filter information without failures.
Then it can print out the filter id and the parameters as well as the Codecs (via the -s flag).
### Test Cases {#filters_TestCase}
## Test Cases {#filters_TestCase}
Within the netcdf-c source tree, the directory two directories contain test cases for testing dynamic filter operation.

4
docs/internal.md
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@ -8,13 +8,13 @@ This document attempts to record important information about
the internal architecture and operation of the netcdf-c library.
It covers the following issues.
* [Including C++ Code in the netcdf-c Library](#intern_c++)
* [Including C++ Code in the netcdf-c Library](#intern_cpp)
* [Managing instances of variable-length data types](#intern_vlens)
* [Inferring File Types](#intern_infer)
* [Adding a Standard Filter](#intern_filters)
* [Test Interference](#intern_isolation)
# 1. Including C++ Code in the netcdf-c Library {#intern_c++}
# 1. Including C++ Code in the netcdf-c Library {#intern_cpp}
The state of C compiler technology has reached the point where
it is possible to include C++ code into the netcdf-c library

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docs/nczarr.md
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@ -417,7 +417,7 @@ In order to accomodate existing implementations, certain mode tags are provided
## XArray
The Xarray <a href="#ref_xarray">[7]</a> Zarr implementation uses its own mechanism for specifying shared dimensions.
The Xarray [XArray Zarr Encoding Specification](http://xarray.pydata.org/en/latest/internals.html#zarr-encoding-specification) Zarr implementation uses its own mechanism for specifying shared dimensions.
It uses a special attribute named ''_ARRAY_DIMENSIONS''.
The value of this attribute is a list of dimension names (strings).
An example might be ````["time", "lon", "lat"]````.
@ -449,16 +449,16 @@ Here are a couple of examples using the _ncgen_ and _ncdump_ utilities.
```
4. Create an nczarr file using S3 as storage and keeping to the pure zarr format.
```
ncgen -4 -lb -o "s3://s3.uswest-1.amazonaws.com/datasetbucket#mode=zarr" dataset.cdl
ncgen -4 -lb -o 's3://s3.uswest-1.amazonaws.com/datasetbucket\#mode=zarr dataset.cdl
```
5. Create an nczarr file using the s3 protocol with a specific profile
```
ncgen -4 -lb -o "s3://datasetbucket/rootkey#mode=nczarr,awsprofile=unidata" dataset.cdl
ncgen -4 -lb -o 's3://datasetbucket/rootkey\#mode=nczarr,awsprofile=unidata' dataset.cdl
```
Note that the URL is internally translated to this
````
https://s2.&lt;region&gt.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
```
# References {#nczarr_bib}
@ -473,7 +473,7 @@ collections — High-performance dataset datatypes](https://docs.python.org/2/li
<a name="dynamic_filter_loading">[8]</a> [Dynamic Filter Loading](https://support.hdfgroup.org/HDF5/doc/Advanced/DynamicallyLoadedFilters/HDF5DynamicallyLoadedFilters.pdf)<br>
<a name="official_hdf5_filters">[9]</a> [Officially Registered Custom HDF5 Filters](https://portal.hdfgroup.org/display/support/Registered+Filter+Plugins)<br>
<a name="blosc-c-impl">[10]</a> [C-Blosc Compressor Implementation](https://github.com/Blosc/c-blosc)<br>
<a name="ref_awssdk_conda">[11]</a> [Conda-forge / packages / aws-sdk-cpp](https://anaconda.org/conda-forge/aws-sdk-cpp)<br>
<a name="ref_awssdk_conda">[11]</a> [Conda-forge packages / aws-sdk-cpp](https://anaconda.org/conda-forge/aws-sdk-cpp)<br>
<a name="ref_gdal">[12]</a> [GDAL Zarr](https://gdal.org/drivers/raster/zarr.html)<br>
# Appendix A. Building NCZarr Support {#nczarr_build}
@ -539,7 +539,7 @@ PATH="$PATH:${AWSSDKBIN}"
Then the following options must be specified for cmake.
````
-DAWSSDK_ROOT_DIR=${AWSSDK_ROOT_DIR}
-DAWSSDK_DIR=${AWSSDK_ROOT_DIR}/lib/cmake/AWSSDK"
-DAWSSDK_DIR=${AWSSDK_ROOT_DIR}/lib/cmake/AWSSDK
````
# Appendix B. Amazon S3 Imposed Limits {#nczarr_s3limits}
@ -578,7 +578,7 @@ can in fact be any legal JSON expression.
This "convention" is currently used routinely to help support various
attributes created by other packages where the attribute is a
complex JSON expression. An example is the GDAL Driver
convention <a href="#ref_gdal">[12]</a>, where the value is a complex
convention <a href='#ref_gdal'>[12]</a>, where the value is a complex
JSON dictionary.
In order for NCZarr to be as consistent as possible with Zarr Version 2,