Merge pull request #300 from lkurz/master

Several corrections.  Mostly .md to .html

Author: gheber

_layouts/default.html

@@ -35,7 +35,7 @@ <h1><a href="{{ "/" | absolute_url }}">{{ site.title | default: site.github.repo
         <li><a href="https://help.hdfgroup.org">Help Desk</a></li>
         <li><a href="https://www.hdfgroup.org/solutions/priority-support/">HDF Software Priority Support</a>
         <li><a href="https://www.hdfgroup.org/solutions/consulting/">HDF Consulting</a></li>
-        <li><a href="/archive/support/index.html">Archive</a></li>
+        <li><a href="{{site.url_docs}}/archive/support/index.html">Archive</a></li>
       </ul>
         <br>
   <!-- 

documentation/hdf5-docs/advanced_topics/chunking_in_hdf5.md

@@ -224,7 +224,7 @@ The slide set [HDF5 Advanced Topics: Chunking in HDF5 (PDF)](Chunking_Tutorial_E
 
 The page [HDF5 Examples](https://hdfgroup.github.io/hdf5/develop/_h_d_f5_examples.html) lists many code examples that are regularly tested with the HDF5 library. Several illustrate the use of chunking in HDF5, particularly [Read/Write Chunked Dataset](https://hdfgroup.github.io/hdf5/develop/_ex_a_p_i.html) and any examples demonstrating filters.
 
-[Dataset Chunking Issues](DSChunkingIssues.md) provides additional information regarding chunking that has not yet been incorporated into this document.
+[Dataset Chunking Issues](DSChunkingIssues.html) provides additional information regarding chunking that has not yet been incorporated into this document.
 
 ## Directions for Future Development
 As seen above, the HDF5 chunk cache currently requires careful control of the parameters in order to achieve optimal performance. In the future, we plan to improve the chunk cache to be more foolproof in many ways, and deliver acceptable performance in most cases even when no thought is given to the chunking parameters.

documentation/hdf5-docs/advanced_topics_list.md

@@ -9,18 +9,18 @@ redirect_from:
 
 | Topic                         | Description                                                  |
 | ----------------------------- | ------------------------------------------------------------ |
-| [Chunking in HDF5](advanced_topics/chunking_in_hdf5.md) | Provides detailed information regarding chunking in HDF5 |
+| [Chunking in HDF5](advanced_topics/chunking_in_hdf5.html) | Provides detailed information regarding chunking in HDF5 |
 | [HDF5 File Image Operations (PDF)](https://docs.hdfgroup.org/hdf5/rfc/HDF5FileImageOperations.pdf) | Describes how to work with HDF5 files in memory. Disk I/O is not required when file images are opened, created, read from, or written to |
 | [Copying Committed Datatypes with H5Ocopy (PDF)](advanced_topics/CopyingCommittedDatatypesWithH5Ocopy.pdf) | Describes how to copy to another file a dataset that uses a committed datatype or an object with an attribute that uses a committed datatype so that the committed datatype in the destination file can be used by multiple objects|
-| [Collective Metadata I/O](advanced_topics/CollectiveMetadataIO.md) | Describes optimizing HDF5 by collecting metadata I/O |
+| [Collective Metadata I/O](advanced_topics/CollectiveMetadataIO.html) | Describes optimizing HDF5 by collecting metadata I/O |
 | [Enabling a Strict Consistency Semantics Model in Parallel HDF5 (PDF)](https://docs.hdfgroup.org/hdf5/rfc/RFC%20PHDF5%20Consistency%20Semantics%20MC%20120328.docx.pdf) | Describes how to improve file access consistency semantics with the Parallel HDF5 library |
-| [File Space Management](advanced_topics/FileSpaceManagement.md) | Describes mechanisms to manage space in an HDF5 file |
-| [Fine-tuning the Metadata Cache](advanced_topics/FineTuningMetadataCache.md) | Describes how to provide better control of the metadata cache |
+| [File Space Management](advanced_topics/FileSpaceManagement.html) | Describes mechanisms to manage space in an HDF5 file |
+| [Fine-tuning the Metadata Cache](advanced_topics/FineTuningMetadataCache.html) | Describes how to provide better control of the metadata cache |
 | [Freeing Memory Allocated by the HDF5 Library (PDF)](https://docs.hdfgroup.org/hdf5/rfc/RFC%20H5free_memory%20v2.pdf) | Describes how inconsistent memory management can cause heap corruption or resource leaks and possible solutions |
-| [HDF5 Data Flow Pipeline for H5Dread](advanced_topics/data_flow_pline_H5Dread.md) | Describes data flow when reading raw data from an HDF5 dataset |
+| [HDF5 Data Flow Pipeline for H5Dread](advanced_topics/data_flow_pline_H5Dread.html) | Describes data flow when reading raw data from an HDF5 dataset |
 | [HDF5 Metadata](advanced_topics/) | Provides a comprehensive overview of the types of metadata used in HDF5 |
-| [Introduction to Single-Writer_Multiple-Reader (SWMR)](advanced_topics/intro_SWMR.md) | Enables writing to a file while multiple readers are accessing it |
-| [Introduction to the Virtual Dataset - VDS](advanced_topics/intro_VDS.md) | Describes how to present data stored in several HDF5 datasets and files as a single dataset and access the data using HDF5 APIs |
+| [Introduction to Single-Writer_Multiple-Reader (SWMR)](advanced_topics/intro_SWMR.html) | Enables writing to a file while multiple readers are accessing it |
+| [Introduction to the Virtual Dataset - VDS](advanced_topics/intro_VDS.html) | Describes how to present data stored in several HDF5 datasets and files as a single dataset and access the data using HDF5 APIs |
 | [Modified Region Writes (PDF)](advanced_topics/ModifiedRegionWrites.pdf) | Describes how to set write operations for in-memory files so that only modified regions are written to storage. Available when the Core (Memory) VFD is used |
 | [Page Buffering (PDF)](https://docs.hdfgroup.org/hdf5/rfc/RFC-Page_Buffering.pdf) | Describes how to reduce the number of small accesses in HDF5 by buffering metadata and raw data accesses |
 | [Partial Edge Chunks]() | Describes how to control the filtering of partial edge chunks to improve performance when extending datasets |

documentation/hdf5-docs/release_specific_info.md

@@ -6,24 +6,24 @@ redirect_from:
 
 # Release Specific Information
 
-### [HDF5 1.14](release_specifics/hdf5_1_14.md)
-* [New Features](release_specifics/new_features_1_14.md)
-* [Software Changes from Release to Release](release_specifics/sw_changes_1.14.md)
-* [Migrating to HDF5 1.14 from previous releases](release_specifics/Migrating_from_HDF5_1.12_to_HDF5_1.14.md)
+### [HDF5 1.14](release_specifics/hdf5_1_14.html)
+* [New Features](release_specifics/new_features_1_14.html)
+* [Software Changes from Release to Release](release_specifics/sw_changes_1.14.html)
+* [Migrating to HDF5 1.14 from previous releases](release_specifics/Migrating_from_HDF5_1.12_to_HDF5_1.14.html)
 
-### [HDF5 1.12](release_specifics/hdf5_1_12.md)
-* [New Features](release_specifics/new_features_1_12.md)
-* [Software Changes from Release to Release](release_specifics/sw_changes_1.12.md)
-* [Migrating from HDF5 1.10 to HDF5 1.12](release_specifics/Migrating_from_HDF5_1.10_to_HDF5_1.12.md)
+### [HDF5 1.12](release_specifics/hdf5_1_12.html)
+* [New Features](release_specifics/new_features_1_12.html)
+* [Software Changes from Release to Release](release_specifics/sw_changes_1.12.html)
+* [Migrating from HDF5 1.10 to HDF5 1.12](release_specifics/Migrating_from_HDF5_1.10_to_HDF5_1.12.html)
 
-### [HDF5 1.10](release_specifics/hdf5_1_10.md)
-* [New Features](release_specifics/new_features_1_10.md)
+### [HDF5 1.10](release_specifics/hdf5_1_10.html)
+* [New Features](release_specifics/new_features_1_10.html)
 * [Why should I care about the HDF5-1.10.2 release? (blog)]()
-* [Software Changes from Release to Release](release_specifics/sw_changes_1.10.md)
-* [Migrating from HDF5 1.8 to HDF5 1.10](release_specifics/Migrating_from_HDF5_1.8_to_HDF5_1.10.md)
+* [Software Changes from Release to Release](release_specifics/sw_changes_1.10.html)
+* [Migrating from HDF5 1.8 to HDF5 1.10](release_specifics/Migrating_from_HDF5_1.8_to_HDF5_1.10.html)
 
-### [HDF5 1.8](release_specifics/hdf5_1_8.md)
+### [HDF5 1.8](release_specifics/hdf5_1_8.html)
 * New Features
-* [Software Changes from Release to Release](release_specifics/sw_changes_1.8.md)
+* [Software Changes from Release to Release](release_specifics/sw_changes_1.8.html)
 
 ### [API Compatibility Macros in HDF5](https://docs.hdfgroup.org/hdf5/develop/api-compat-macros.html)

documentation/hdf5-docs/release_specifics/new_features_1_14.md

@@ -16,7 +16,7 @@ need the precision of larger floating-point datatypes. It can also allow
 for improved performance when converting between 16-bit floating-point
 data and data of another HDF5 datatype.
 
-* [Asynchronous I/O operations](asyn_ops_wHDF5_VOL_connectors.md)
+* [Asynchronous I/O operations](asyn_ops_wHDF5_VOL_connectors.html)
 HDF5 provides asynchronous APIs for the HDF5 VOL connectors that
 support asynchronous HDF5 operations using the HDF5 Event Set (H5ES)
 API. This allows I/O to proceed in the background while the application

documentation/index.md

@@ -7,22 +7,20 @@ redirect_from:
 # HDF Software Documentation
 
 ## HDF5 Library, Tools, and Extensions
-* [Documentation (lastest)](https://docs.hdfgroup.org/releases/hdf5/latest-docs.html) - User Guide, Reference Manual, and other documentation
+* [Documentation (latest)](https://docs.hdfgroup.org/releases/hdf5/latest-docs.html) - User Guide, Reference Manual, and other documentation
 * [Release Specific Information](hdf5-docs/release_specific_info.html) - Information specific to each release series
-* [HDF5 Application Topics](hdf5-docs/hdf5_topics_list.md) - General and advanced topics in HDF5 for application developers
+* [HDF5 Application Topics](hdf5-docs/hdf5_topics_list.html) - General and advanced topics in HDF5 for application developers
 * [Registered Filter Plugins](https://github.com/HDFGroup/hdf5_plugins/blob/master/docs/RegisteredFilterPlugins.md) - List of registered filter plugins
 * [Registered Virtual File Drivers (VFDs)](/documentation/hdf5-docs/registered_virtual_file_drivers_vfds.html) - List of registered VFDs
 * [Registered Virtual Object Layer (VOL) Connectors](/documentation/hdf5-docs/registered_vol_connectors.html) - List of registered VOL connectors
 
 ## HDFView 
 
-* [User Guide (old)](https://docs.hdfgroup.org/releases/hdfview/v3_3/v3_3_2/documentation/UsersGuide/index.html)
 * [User Guide (lastest)](https://docs.hdfgroup.org/releases/hdfview/latest-docs.html)
 
 ## HDF5/JSON
 
-* [User Guide (latest)](https://docs.hdfgroup.org/releases/hdf5-json/latest-docs.html) 
-* [User Guide (full path)](https://docs.hdfgroup.org/releases/hdf5-json/v1_1/v1_1_3/documentation/hdf5-json/index.html) 
+* [User Guide (latest)](https://docs.hdfgroup.org/releases/hdf5-json/latest-docs.html)  
 
 
 ## Highly Scalable Data Service (HSDS)

downloads/hdf5/hdf5_1_14_4.md

@@ -11,10 +11,10 @@ title: HDF5 Library and Tools 1.14.4
 | Version | HDF5 1.14.4.3 |
 | Release Date | 05/22/24 |
 | Additional Release Information | [Release Notes](https://github.com/HDFGroup/hdf5/blob/hdf5_1_14_4/release_docs/RELEASE.txt) |
-|| [Software Changes from Release to Release](../../documentation/hdf5-docs/release_specifics/sw_changes_1.14.md) |
+|| [Software Changes from Release to Release](../../documentation/hdf5-docs/release_specifics/sw_changes_1.14.html) |
 || [New Features in HDF5 Release 1.14](../../documentation/hdf5-docs/release_specifics/new_features_1_14.html) |
 || [Newsletter Announcement](https://www.hdfgroup.org/2024/04/release-of-hdf5-1-14-4-newsletter-202/) |
-|| [Doxygen generated Reference Manual](https://docs.hdfgroup.org/hdf5/v1_14/index.html) |
+|| [Doxygen generated Reference Manual](https://docs.hdfgroup.org/releases/hdf5/latest-docs.html) |
 || [API Compatibility Report between 1.14.3 and 1.14.4](https://github.com/HDFGroup/hdf5/releases/download/hdf5_1.14.4.2/hdf5-1.14.4-2.html.abi.reports.tar.gz) | 
 
 
@@ -37,7 +37,7 @@ Please refer to [Build instructions](https://github.com/HDFGroup/hdf5/blob/hdf5_
 
 ## Doxygen Generated Reference Manual         
 
-The new HDF5 documentation based on [Doxygen](https://www.doxygen.nl/index.html) is available [here](https://portal.hdfgroup.org/hdf5/v1_14_4/index.html)
+The new HDF5 documentation based on [Doxygen](https://www.doxygen.nl/index.html) is available [here]({{site.url_docs}}/releases/hdf5/latest-docs.html)
 
 This documentation is WORK-IN-PROGRESS. 
 

downloads/index.md

@@ -11,23 +11,23 @@ redirect_from:
 
 | Version | Usage | 
 | ---- | ----| 
-| [HDF5 1.14.4](/hdf5/hdf5_1_14_4.md) | Most recent HDF5 library version. | 
+| [HDF5 1.14.4](hdf5/hdf5_1_14_4.html) | Most recent HDF5 library version. | 
 
 ## HDFView
 
 | Version | Usage | 
 | ---- | ----| 
-| [HDFView 3.3.2](/hdfview/hdfview3_3_2.md) | Most recent version; built and tested with HDF5-1.14.4, HDF 4.3.0, and openjdk 21.  |
+| [HDFView 3.3.2](hdfview/hdfview3_3_2.html) | Most recent version; built and tested with HDF5-1.14.4, HDF 4.3.0, and openjdk 21.  |
 
 ## HDF4 Library
 
 | Version | Usage | 
 | ---- | ----| 
-| [HDF 4.3.0](hdf4/hdf4_3_0.md) | New 4.3.x series with significant changes in public/private components | 
-| [HDF 4.2.16-2](hdf4/hdf4_2_16-2.md) (Patch Release) | Last release of the 4.2.x series | 
+| [HDF 4.3.0](hdf4/hdf4_3_0.html) | New 4.3.x series with significant changes in public/private components | 
+| [HDF 4.2.16-2](hdf4/hdf4_2_16-2.html) (Patch Release) | Last release of the 4.2.x series | 
 
 ## h4h5tools
 
 | Version | Usage | 
 | ---- | ----| 
-| [h4h5tools 2.2.5](h4h5tools/h4h5tools_2_2_5.md) | Convert HDF4 files to HDF5 files | 
+| [h4h5tools 2.2.5](h4h5tools/h4h5tools_2_2_5.html) | Convert HDF4 files to HDF5 files |