From a40537bbfdf746f0f4dac179846f30b8acb07aa6 Mon Sep 17 00:00:00 2001 From: Binh-Minh Date: Fri, 22 Mar 2024 14:35:05 -0400 Subject: [PATCH 01/10] Fix broken URLs in documentation Fixes GH-3881 partially. There are pages that need to be recreated. --- doxygen/aliases | 10 +++++----- doxygen/dox/GettingStarted.dox | 4 ++-- doxygen/dox/IntroHDF5.dox | 2 +- doxygen/dox/LearnHDFView.dox | 2 +- doxygen/dox/UsersGuide.dox | 8 ++++---- doxygen/dox/VOLConnGuide.dox | 4 ++-- doxygen/dox/ViewTools.dox | 2 +- src/H5Fmodule.h | 8 ++++---- src/H5VLmodule.h | 2 +- 9 files changed, 21 insertions(+), 21 deletions(-) diff --git a/doxygen/aliases b/doxygen/aliases index ad868432bee..71d0d67709a 100644 --- a/doxygen/aliases +++ b/doxygen/aliases @@ -234,14 +234,14 @@ ALIASES += sa_metadata_ops="\sa \li H5Pget_all_coll_metadata_ops() \li H5Pget_co # References ################################################################################ -ALIASES += ref_cons_semantics="Enabling a Strict Consistency Semantics Model in Parallel HDF5" -ALIASES += ref_file_image_ops="HDF5 File Image Operations" +ALIASES += ref_cons_semantics="Enabling a Strict Consistency Semantics Model in Parallel HDF5" +ALIASES += ref_file_image_ops="HDF5 File Image Operations" ALIASES += ref_filter_pipe="Data Flow Pipeline for H5Dread()" -ALIASES += ref_group_impls="Group implementations in HDF5" -ALIASES += ref_h5lib_relver="HDF5 Library Release Version Numbers" +ALIASES += ref_group_impls="Group implementations in HDF5" +ALIASES += ref_h5lib_relver="HDF5 Library Release Version Numbers" ALIASES += ref_mdc_in_hdf5="Metadata Caching in HDF5" ALIASES += ref_mdc_logging="Metadata Cache Logging" -ALIASES += ref_news_112="New Features in HDF5 Release 1.12" +ALIASES += ref_news_112="New Features in HDF5 Release 1.12" ALIASES += ref_h5ocopy="Copying Committed Datatypes with H5Ocopy()" ALIASES += ref_sencode_fmt_change="RFC H5Secnode() / H5Sdecode() Format Change" ALIASES += ref_vlen_strings="\Emph{Creating variable-length string datatypes}" diff --git a/doxygen/dox/GettingStarted.dox b/doxygen/dox/GettingStarted.dox index 87f3566361e..58f71f82a4e 100644 --- a/doxygen/dox/GettingStarted.dox +++ b/doxygen/dox/GettingStarted.dox @@ -42,7 +42,7 @@ Parallel HDF5, and the HDF5-1.10 VDS and SWMR new features: diff --git a/doxygen/dox/IntroHDF5.dox b/doxygen/dox/IntroHDF5.dox index afe534be614..33cf4a91ca8 100644 --- a/doxygen/dox/IntroHDF5.dox +++ b/doxygen/dox/IntroHDF5.dox @@ -608,7 +608,7 @@ on the HDF-EOS Tools and Information Center pag \section secHDF5Examples Examples \li \ref LBExamples \li \ref ExAPI -\li Examples in the Source Code +\li Examples in the Source Code \li Other Examples \section secHDF5ExamplesCompile How To Compile diff --git a/doxygen/dox/LearnHDFView.dox b/doxygen/dox/LearnHDFView.dox index 8c617f21477..2916db841e6 100644 --- a/doxygen/dox/LearnHDFView.dox +++ b/doxygen/dox/LearnHDFView.dox @@ -7,7 +7,7 @@ This tutorial enables you to get a feel for HDF5 by using the HDFView browser. I any programming experience. \section sec_learn_hv_install HDFView Installation -\li Download and install HDFView. It can be downloaded from the Download HDFView page. +\li Download and install HDFView. It can be downloaded from the Download HDFView page. \li Obtain the storm1.txt text file, used in the tutorial. \section sec_learn_hv_begin Begin Tutorial diff --git a/doxygen/dox/UsersGuide.dox b/doxygen/dox/UsersGuide.dox index b6113ad15bd..3dd26f1a40a 100644 --- a/doxygen/dox/UsersGuide.dox +++ b/doxygen/dox/UsersGuide.dox @@ -374,7 +374,7 @@ These documents provide additional information for the use and tuning of specifi
-Using the High Level APIs +Using the High Level APIs \ref H5LT \ref H5IM \ref H5TB \ref H5PT \ref H5DS @@ -72,7 +72,7 @@ HDF5-1.10 New Features \li Introduction to the Virtual Dataset - VDS -\li Introduction to Single-Writer/Multiple-Reader (SWMR) +\li Introduction to Single-Writer/Multiple-Reader (SWMR)
-

HDF5 Dynamically Loaded Filters

+

HDF5 Dynamically Loaded Filters

Describes how an HDF5 application can apply a filter that is not registered with the HDF5 Library.

@@ -382,7 +382,7 @@ These documents provide additional information for the use and tuning of specifi
-

HDF5 File Image Operations

+

HDF5 File Image Operations

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.

@@ -390,7 +390,7 @@ These documents provide additional information for the use and tuning of specifi
-

Modified Region Writes

+

Modified Region Writes

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.

@@ -438,4 +438,4 @@ Previous Chapter \ref sec_plist HDF5 repo, make changes, and create a pull request !\n -*/ \ No newline at end of file +*/ diff --git a/doxygen/dox/VOLConnGuide.dox b/doxygen/dox/VOLConnGuide.dox index fb662a0ef5a..7a03ab1590d 100644 --- a/doxygen/dox/VOLConnGuide.dox +++ b/doxygen/dox/VOLConnGuide.dox @@ -92,7 +92,7 @@ Public header Files you will need to be familiar with include:
Many VOL connectors are listed on The HDF Group's VOL plugin registration page, located at: -Registered VOL Connectors. +Registered VOL Connectors. Not all of these VOL connectors are supported by The HDF Group and the level of completeness varies, but the connectors found there can serve as examples of working implementations @@ -195,7 +195,7 @@ contact help@hdfgroup.org for help with this. We name you've chosen will appear on the registered VOL connectors page. As noted above, registered VOL connectors will be listed at: -Registered VOL Connectors +Registered VOL Connectors A new \b conn_version field has been added to the class struct for 1.13. This field is currently not used by the library so its use is determined by the connector author. Best practices for this field will be determined diff --git a/doxygen/dox/ViewTools.dox b/doxygen/dox/ViewTools.dox index 951605674be..f4c31c83663 100644 --- a/doxygen/dox/ViewTools.dox +++ b/doxygen/dox/ViewTools.dox @@ -48,7 +48,7 @@ Navigate back: \ref index "Main" / \ref GettingStarted \section secViewToolsCommandObtain Obtain Tools and Files (Optional) Pre-built binaries for Linux and Windows are distributed within the respective HDF5 binary release -packages, which can be obtained from the Download HDF5 page. +packages, which can be obtained from the Download HDF5 page. HDF5 files can be obtained from various places such as \ref HDF5Examples and HDF-EOS and Tools and Information Center. Specifically, the following examples are used in this tutorial topic: diff --git a/src/H5Fmodule.h b/src/H5Fmodule.h index 098e703eac9..726f81f756e 100644 --- a/src/H5Fmodule.h +++ b/src/H5Fmodule.h @@ -235,10 +235,10 @@ * Note that the root group, indicated above by /, was automatically created when the file was created. * * h5dump is described on the - * Tools + * Tools * page under - * - * Libraries and Tools Reference. + * + * Command-line Tools. * The HDF5 DDL grammar is described in the document \ref DDLBNF114. * * \subsection subsec_file_summary File Function Summaries @@ -888,7 +888,7 @@ * * Additional parameters may be added to these functions in the future. * - * @see + * @see * HDF5 File Image Operations * section for information on more advanced usage of the Memory file driver, and * @see diff --git a/src/H5VLmodule.h b/src/H5VLmodule.h index 19baf344d57..0cca38cf1db 100644 --- a/src/H5VLmodule.h +++ b/src/H5VLmodule.h @@ -83,7 +83,7 @@ * to be much more common than internal implementations. * * A list of VOL connectors can be found here: - * + * * Registered VOL Connectors * * This list is incomplete and only includes the VOL connectors that have been registered with From 6ec0fe43d64d2e9240a3a39fdfe42b80f702e98c Mon Sep 17 00:00:00 2001 From: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Date: Fri, 22 Mar 2024 18:38:55 +0000 Subject: [PATCH 02/10] Committing clang-format changes --- src/H5Fmodule.h | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/H5Fmodule.h b/src/H5Fmodule.h index 726f81f756e..3ae8b38247a 100644 --- a/src/H5Fmodule.h +++ b/src/H5Fmodule.h @@ -235,7 +235,8 @@ * Note that the root group, indicated above by /, was automatically created when the file was created. * * h5dump is described on the - * Tools + * Tools * page under * * Command-line Tools. From 5171db8bb6bd1248f0c1a8531e0fa742d53c1270 Mon Sep 17 00:00:00 2001 From: Binh-Minh Date: Fri, 22 Mar 2024 15:29:18 -0400 Subject: [PATCH 03/10] Fix typos --- doxygen/aliases | 2 +- doxygen/dox/GettingStarted.dox | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/doxygen/aliases b/doxygen/aliases index 71d0d67709a..0f5a4a4ed8f 100644 --- a/doxygen/aliases +++ b/doxygen/aliases @@ -237,7 +237,7 @@ ALIASES += sa_metadata_ops="\sa \li H5Pget_all_coll_metadata_ops() \li H5Pget_co ALIASES += ref_cons_semantics="Enabling a Strict Consistency Semantics Model in Parallel HDF5" ALIASES += ref_file_image_ops="HDF5 File Image Operations" ALIASES += ref_filter_pipe="Data Flow Pipeline for H5Dread()" -ALIASES += ref_group_impls="Group implementations in HDF5" +ALIASES += ref_group_impls="Group implementations in HDF5" ALIASES += ref_h5lib_relver="HDF5 Library Release Version Numbers" ALIASES += ref_mdc_in_hdf5="Metadata Caching in HDF5" ALIASES += ref_mdc_logging="Metadata Cache Logging" diff --git a/doxygen/dox/GettingStarted.dox b/doxygen/dox/GettingStarted.dox index 58f71f82a4e..feb5f919f9a 100644 --- a/doxygen/dox/GettingStarted.dox +++ b/doxygen/dox/GettingStarted.dox @@ -72,7 +72,7 @@ HDF5-1.10 New Features \li Introduction to the Virtual Dataset - VDS -\li Introduction to Single-Writer/Multiple-Reader (SWMR) +\li Introduction to Single-Writer/Multiple-Reader (SWMR) From 792ea467d211ddd5736daa91f4257dcac36adae4 Mon Sep 17 00:00:00 2001 From: Binh-Minh Date: Fri, 22 Mar 2024 15:49:54 -0400 Subject: [PATCH 04/10] Fix typos --- src/H5Fmodule.h | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/src/H5Fmodule.h b/src/H5Fmodule.h index 3ae8b38247a..fd457570e75 100644 --- a/src/H5Fmodule.h +++ b/src/H5Fmodule.h @@ -235,11 +235,9 @@ * Note that the root group, indicated above by /, was automatically created when the file was created. * * h5dump is described on the - * Tools + * Tools * page under - * - * Command-line Tools. + * Command-line Tools. * The HDF5 DDL grammar is described in the document \ref DDLBNF114. * * \subsection subsec_file_summary File Function Summaries From ba645075a7dfd18bd8fd6a57e0e9f6689a88256e Mon Sep 17 00:00:00 2001 From: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Date: Fri, 22 Mar 2024 19:51:21 +0000 Subject: [PATCH 05/10] Committing clang-format changes --- src/H5Fmodule.h | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/H5Fmodule.h b/src/H5Fmodule.h index fd457570e75..d0212dd9925 100644 --- a/src/H5Fmodule.h +++ b/src/H5Fmodule.h @@ -235,7 +235,8 @@ * Note that the root group, indicated above by /, was automatically created when the file was created. * * h5dump is described on the - * Tools + * Tools * page under * Command-line Tools. * The HDF5 DDL grammar is described in the document \ref DDLBNF114. From 3401c555b82298e8c603eb9ff29945a5c080c565 Mon Sep 17 00:00:00 2001 From: Binh-Minh Date: Fri, 22 Mar 2024 16:11:30 -0400 Subject: [PATCH 06/10] Adjust long line --- src/H5Fmodule.h | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/H5Fmodule.h b/src/H5Fmodule.h index d0212dd9925..47af4f81197 100644 --- a/src/H5Fmodule.h +++ b/src/H5Fmodule.h @@ -235,8 +235,8 @@ * Note that the root group, indicated above by /, was automatically created when the file was created. * * h5dump is described on the - * Tools + * + * Tools * page under * Command-line Tools. * The HDF5 DDL grammar is described in the document \ref DDLBNF114. From 9edd088b6af327d87d6b9b986d79447c903c7396 Mon Sep 17 00:00:00 2001 From: Binh-Minh Date: Sat, 23 Mar 2024 22:37:59 -0400 Subject: [PATCH 07/10] Fix more broken links --- doc/parallel-compression.md | 4 ++-- src/H5Fmodule.h | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/doc/parallel-compression.md b/doc/parallel-compression.md index 040c8aa702c..20f6df7bde2 100644 --- a/doc/parallel-compression.md +++ b/doc/parallel-compression.md @@ -154,7 +154,7 @@ optimal performance out of the parallel compression feature. ### Begin with a good chunking strategy -[Starting with a good chunking strategy](https://portal.hdfgroup.org/display/HDF5/Chunking+in+HDF5) +[Starting with a good chunking strategy](https://portal.hdfgroup.org/documentation/hdf5-docs/chunking_in_hdf5.html) will generally have the largest impact on overall application performance. The different chunking parameters can be difficult to fine-tune, but it is essential to start with a well-performing @@ -166,7 +166,7 @@ chosen chunk size becomes a very important factor when compression is involved, as data chunks have to be completely read and re-written to perform partial writes to the chunk. -[Improving I/O performance with HDF5 compressed datasets](https://portal.hdfgroup.org/display/HDF5/Improving+IO+Performance+When+Working+with+HDF5+Compressed+Datasets) +[Improving I/O performance with HDF5 compressed datasets](https://support.hdfgroup.org/HDF5/doc/TechNotes/TechNote-HDF5-ImprovingIOPerformanceCompressedDatasets.pdf) is a useful reference for more information on getting good performance when using a chunked dataset layout. diff --git a/src/H5Fmodule.h b/src/H5Fmodule.h index 47af4f81197..f72d4463707 100644 --- a/src/H5Fmodule.h +++ b/src/H5Fmodule.h @@ -888,7 +888,7 @@ * * Additional parameters may be added to these functions in the future. * - * @see + * @see * HDF5 File Image Operations * section for information on more advanced usage of the Memory file driver, and * @see From 863d316bf4389bbe4b031e73b72a351404b093b7 Mon Sep 17 00:00:00 2001 From: Binh-Minh Date: Sat, 23 Mar 2024 23:43:43 -0400 Subject: [PATCH 08/10] Fix broken links --- HDF5Examples/README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/HDF5Examples/README.md b/HDF5Examples/README.md index 9a658365245..8ccec6a8b23 100644 --- a/HDF5Examples/README.md +++ b/HDF5Examples/README.md @@ -19,7 +19,7 @@ HELP AND SUPPORT ---------------- Information regarding Help Desk and Support services is available at - https://portal.hdfgroup.org/display/support/The+HDF+Help+Desk + https://hdfgroup.atlassian.net/servicedesk/customer/portals @@ -56,7 +56,7 @@ Periodically development code snapshots are provided at the following URL: Source packages for current and previous releases are located at: - https://portal.hdfgroup.org/display/support/Downloads + https://portal.hdfgroup.org/downloads/ Development code is available at our Github location: From dc01e803d23abc7758372cc167b02afca23ea9a5 Mon Sep 17 00:00:00 2001 From: Binh-Minh Date: Mon, 25 Mar 2024 10:42:28 -0400 Subject: [PATCH 09/10] Fix broken links --- CONTRIBUTING.md | 2 +- HDF5Examples/README.md | 2 +- test/API/README.md | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index de81b1c8e05..00c884b692c 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -122,7 +122,7 @@ Please make sure that you check the items applicable to your pull request: * [ ] If changes were done to Autotools build, were they added to CMake and vice versa? * [ ] Is the pull request applicable to any other branches? If yes, which ones? Please document it in the GitHub issue. * [ ] Is the new code sufficiently documented for future maintenance? - * [ ] Does the new feature require a change to an existing API? See "API Compatibility Macros" document (https://portal.hdfgroup.org/display/HDF5/API+Compatibility+Macros) + * [ ] Does the new feature require a change to an existing API? See "API Compatibility Macros" document (https://docs.hdfgroup.org/hdf5/develop/api-compat-macros.html) * Documentation * [ ] Was the change described in the release_docs/RELEASE.txt file? * [ ] Was the new function documented in the corresponding public header file using [Doxygen](https://hdfgroup.github.io/hdf5/develop/_r_m_t.html)? diff --git a/HDF5Examples/README.md b/HDF5Examples/README.md index 8ccec6a8b23..2f0090ba02c 100644 --- a/HDF5Examples/README.md +++ b/HDF5Examples/README.md @@ -48,7 +48,7 @@ HDF5 SNAPSHOTS, PREVIOUS RELEASES AND SOURCE CODE -------------------------------------------- Full Documentation and Programming Resources for this HDF5 can be found at - https://portal.hdfgroup.org/display/HDF5 + https://portal.hdfgroup.org/documentation/index.html Periodically development code snapshots are provided at the following URL: diff --git a/test/API/README.md b/test/API/README.md index 2f5a0650412..aa5884995e1 100644 --- a/test/API/README.md +++ b/test/API/README.md @@ -1,7 +1,7 @@ # HDF5 API Tests This directory contains several test applications that exercise HDF5's -public API and serve as regression tests for HDF5 [VOL Connectors](https://portal.hdfgroup.org/display/HDF5/Virtual+Object+Layer). +public API and serve as regression tests for HDF5 [VOL Connectors](https://docs.hdfgroup.org/hdf5/develop/_h5_v_l__u_g.html). ## Build Process and options From a2274c25afb64521f3747fc744728effc6a8f063 Mon Sep 17 00:00:00 2001 From: Binh-Minh Date: Mon, 25 Mar 2024 11:21:57 -0400 Subject: [PATCH 10/10] Fix conflict --- doc/parallel-compression.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/parallel-compression.md b/doc/parallel-compression.md index 20f6df7bde2..a0567bfa546 100644 --- a/doc/parallel-compression.md +++ b/doc/parallel-compression.md @@ -166,7 +166,7 @@ chosen chunk size becomes a very important factor when compression is involved, as data chunks have to be completely read and re-written to perform partial writes to the chunk. -[Improving I/O performance with HDF5 compressed datasets](https://support.hdfgroup.org/HDF5/doc/TechNotes/TechNote-HDF5-ImprovingIOPerformanceCompressedDatasets.pdf) +[Improving I/O performance with HDF5 compressed datasets](https://docs.hdfgroup.org/archive/support/HDF5/doc/TechNotes/TechNote-HDF5-ImprovingIOPerformanceCompressedDatasets.pdf) is a useful reference for more information on getting good performance when using a chunked dataset layout.