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* Documentation fixes right in time for the holidays (#1321)Gerd Heber2022-01-141-1/+2
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Sketch of the H5S life cycle. * Committing clang-format changes * Fix H5S_UNLIMITED snafu. * Updated RM template and RM page. * Added H5S life cycle. * Committing clang-format changes * Added H5T life cycle. * Committing clang-format changes * Cleaner layout (?) * Cleaned the H5F life cycle. Called out unfinished biz. * Committing clang-format changes * Remaining life cycle skeletons. * Committing clang-format changes * Committing clang-format changes * Added H5Z life cycle. * Committing clang-format changes * Added H5G life cycle. * Committing clang-format changes * H5 and H5I life cycle updates. * Committing clang-format changes * Added H5PL life cycle. * Committing clang-format changes * Added H5L life cycle. * Committing clang-format changes * Fix for Chris' comment. * Add a variable for Doxygen pre-processor definitions. * Forgot to add the H5M API. * Clarify the H5Z life cycle. * Committing clang-format changes * Add H5Zdevelop.h to Doxygen.in. Added H5I life cycle. * Committing clang-format changes * Clarified introduction and fixed missing label declaration. * Added H5O life cycle. * Committing clang-format changes * H5O cleanup, part 1. * Committing clang-format changes * Cleaned up some of the endless repetition in H5O. * Committing clang-format changes * Cookbook & RFC draft layouts. * Updated manifest. * Updated the manifest, the example paths, and sketched the 1st recipe. * Committing clang-format changes * Outlined two more recipes. * Committing clang-format changes * More recipes and RFCs. * Committing clang-format changes * Draft of templatized RFC references. * Another batch of RFC changes. * Another batch of RFCs. * Fixed reference. * RFCs in reverse chronological order. * First cut of RFCs. * Fixed reference. * Updated recipes. * Updated recipes. * More RFCs. * Updated D*PL comments. * Added H5P descriptions. * Committing clang-format changes * H5R life-cycle snapshot. * Committing clang-format changes * H5R life-cycle. Added line numbers to life-cycle examples. * Committing clang-format changes * Fixed formatting for H5Dchunk_iter(). * Added comment on collective mode requirement w/ compression. * Simplified API compat. macro dox. * More API vers. updates. * Hide the async macro entrails. * Latest VFD SWMR RFC. * Create a tag file for permalinks. * Added TODOs for metadoc. * Removed duplication. * Revised RM landing page. * Trimmed more duplication. * Committing clang-format changes * Revised H5D. * Committing clang-format changes * Updated survey link. * Added Doxygen RM entry template link. * Added the "Multi-Thread HDF5" RFC. * Added DOXYGEN_TAG_FILE. * Added selection I/O RFC. * Added the VFD Sub-filing RFC. * Updated meta-documentation and added two old presentations. * Added a few more RFCs (4). * Fixed MANIFEST. * Updated meta-documentation. * Added Filters technical note. * Fixed MANIFEST. * Restore the path stripper. * Experimental full-text search via Google. * Better full-text search integration. * Whoops. Forgot this one. * Oh boy. * Make CMake happy. * Added "Debugging HDF5 Applications" technical note. * Another batch of RFCs. * Fixes for #1221. * Updated overview. * Fixed image dependencies. * CMake updates. * Fixed SET. * Better? * Update doxygen/dox/Overview.dox * Fixed documentation errors. Added missing version info. * Callback documentation updates. * Fixed indexing errors in the outline. * Doxygen-ized the HDF5 glossary. * Fix a few minor typos . Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
* A batch of life-cycle examples for different modules (#654)Gerd Heber2021-09-011-24/+140
| | | | | | | | | * Create a tag file for permalinks. * Added DOXYGEN_TAG_FILE. * Added Doxygen life-cycle examples for different modules. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Merge doxygen2 into develop (#553)Gerd Heber2021-04-261-1/+4
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Fixed warnings and started H5Epublic.h. * Include H5FD* headers to correctly resolve references. * Doxygen2 (#330) * H5Eauto_is_v2. * Added a few more calls. * Added a few more H5E calls. * First cut of H5E v2. * Added the deprecated v1 calls. * Updated spacing. * Once more. * Taking some inspiration from Eigen3. * Add doxygen for the assigned functions: H5Pregister1,H5Pinsert1,H5Pen… (#352) * Add doxygen for the assigned functions: H5Pregister1,H5Pinsert1,H5Pencode1, H5Pget_filter_by_id1,H5Pget_version, H5Pset_file_space,H5Pget_file_space. Someone already adds H5Pget_filter1. Also fixs an extra parameter 'close' call back function for HPregister2. * doxygen work. fixs format by using clang-format. * doxgen work for H5Pregister1 etc. Addressed Barbara and Gerd's comments. For Quincey's comments, since we are not supposed to change the source code. I leave this to future improvements. * added documentation for H5P APIs (#350) * add documenation for H5Pget_buffer,H5Pget_data_transform,H5Pget_edc_check,H5Pget_hyper_vector_size,H5Pget_preserve,H5Pget_type_conv_cb,H5Pget_vlen_mem_manager,H5Pset_btree_ratios * format corrections * fixed grammer * fixed herr_t * Better name. * A fresh look. * add doxygen to H5Ppublic.h * use attention instead of warning * Add doxygen comments in H5Ppublic.h (#375) * Add doxygen comments in H5Ppublic.h * H5Pset_meta_block_size * H5Pset_metadata_read_attempts * H5Pset_multi_type * H5Pset_object_flush_cb * H5Pset_sieve_buf_size * H5Pset_small_data_block_size * H5Pset_all_coll_metadata_ops * H5Pget_all_coll_metadata_ops * Add DOXYGEN_EXAMPLES_DIR to src/CMakeLists.txt * Fix clang-format errors * Fix filenames in doxygen/examples * add doxygen to H5Ppublic.h (#378) * add doxygen to H5Ppublic.h * use attention instead of warning Co-authored-by: Kimmy Mu <kmu@hdfgroup.org> * Revert "add doxygen to H5Ppublic.h (#378)" This reverts commit 2ee1821b138a5c00b15ea57ce9e950367480f5f2. * Updated Doxygen variables. * I forgot to copy two images. * Enable desktop search by default. * Add my assigned Doxygen documentation. * Remove whitespace at EOL. Appease clang-format. * Addressed Chris' comments. * Added an alias for asynchronous functions. * One space is enough for all of us. * Slightly restructured RM page. * address some issues * reformatting * Style external links. * reformatting * reformatting * Added "Metadata Caching in HDF5" as a technical note example. * Revise this soon! * Added specification examples. * Fixed references. * Added H5AC cache image stuff and file format study. * Added older FMT versions. Where did 1.0 go? * Updated C/C++ note and replaced ambiguous labels. * Reformat source with clang v10.0.1. * Added the VFL technical note. * Added what I believe might be called version 1.0 of the format. * Added the remaining specs. * Added H5Z callback documentation and fixed a few mistakes. * Added dox for deprecated H5G calls and fixed a few snippet blockIDs. * clang-format happy? * Ok? * Bonus track: Deprecated H5D functions. * Carry over the more detailed group description. * Added documentation for the missing and deprecated H5R calls. * Life is easier and less repetitive w/ snippets. Use them! * Eliminate the snippet block ID artifacts in the HTML rendering. * Fixed snippet HTML artifacts and added a few missing calls. * Under 20 H5Ps to go! * Almost complete! * "This is a form of pedantry up with which I will not put." (Churchill) * Let's not waste as much space on bulleted lists! * First complete (?) draft of the Doxygen-based RM. * Completeness check and minor fixes along the way. * Pedantry. * Adding missing H5FD calls checkpoint. * Pedantry. * More pedantry. * Added H5Pset_fapl_log. * First draft of H5ES. * Fixed warnings. * Prep. for map module. * First cut of the map module. * Pedantry. * Possible H5F introduction. * Fix the indentation. * Pedantry. * Ditto. * Thanks to the reviewers for their comments. * Added missing images. * Line numbers are a distraction here. * More examples, references, and clean-up. Don't repeat yourself! * Clang pedantry. * Ditto. * More reviewer comments... * Templatized references and cleaned up \todos. * Committing clang-format changes * Fixed MANIFEST. * Addressed Quincey's comments. (OCPLs) * Fixed a few more \todo items. * Fixed more \todo items. * Added attribute life cycle. * Forgot the examples file. * Committing clang-format changes * Pedantry. * Live and learn! * Added a sample H5D life cycle. * Committing clang-format changes * Pedantry. Co-authored-by: kyang2014 <kyang2014@users.noreply.github.com> Co-authored-by: Scot Breitenfeld <brtnfld@hdfgroup.org> Co-authored-by: Kimmy Mu <kmu@hdfgroup.org> Co-authored-by: Christopher Hogan <ChristopherHogan@users.noreply.github.com> Co-authored-by: jya-kmu <53388330+jya-kmu@users.noreply.github.com> Co-authored-by: David Young <dyoung@hdfgroup.org> Co-authored-by: Larry Knox <lrknox@hdfgroup.org> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fixed many -Wreserved-id-macro warnings by fixing header guard spelling (#361)Sean McBride2021-02-231-3/+3
| | | | | | | | | | | | | | | | * Fixed many -Wreserved-id-macro warnings by fixing header guard spelling Removed leading underscore(s) from header guard spelling. Used 2 regexes: ` _H5(.*)_H` ` __H5(.*)_H` Applied case-insensitively to only .h files. * Modified scripts that generate header files to not use underscore prefix Interestingly, there was already no leading underscore in the trailing comment at the end of the file * Fixed remaining -Wreserved-id-macro warning not caught by regex
* Update license url (#332)Larry Knox2021-02-171-1/+1
| | | | | | * Modify temporary rpath for testing in java example scripts. * Update URL in source file Copyright headers for web copy of COPYING file - src and test directories.
* Doxygen - added (mostly) beginner functions (#112)bljhdf2020-11-231-0/+43
| | | | | * Doxygen - added (mostly) beginner functions * Removed duplicate H5Pset_szip function
* Clang-format of source filesAllen Byrne2020-09-301-4/+3
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* Clean up private / package / static namespace issues (function naming, whichQuincey Koziol2020-08-061-1/+1
| | | | | | header file, FUNC_ENTER / LEAVE, etc). Removed remaining personal email addresses from library source code (still needs cleaned from other directories). Misc. warning, style, and whitespace cleanup.
* Merge pull request #426 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:hdf5_1_10 to ↵Larry Knox2017-04-251-6/+4
| | | | | | | | | | hdf5_1_10 * commit '54957d37f5aa73912763dbb6e308555e863c43f4': Commit copyright header change for src/H5PLpkg.c which was added after running script to make changes. Add new files in release_docs to MANIFEST. Cimmit changes to Makefile.in(s) and H5PL.c that resulted from running autogen.sh. Merge pull request #407 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:hdf5_1_10_1 to hdf5_1_10_1 Change copyright headers to replace url referring to file to be removed and replace it with new url for COPYING file.
* [svn-r27768] Description:Quincey Koziol2015-09-141-0/+35
Complete revamp of package initialization/shutdown mechanism in the library. Each package now has a single init/term routine. This new way should avoid packages being re-initialized during library shutdown and is also be _much_ more proactive about giving feedback for resource leaks internal to the library. Introduces a new "module" header file for packages in the library (e.g src/H5Fmodule.h) which sets up some necessary package configuration macros for the FUNC_ENTER/LEAVE macros. (The VFL drivers have their own slightly modified version of this header, src/H5FDdrvr_module.h) Also cleaned up a bunch of resources leaks all across the library and tests, along with addressing many warnings, as I encountered them. Tested on: MacOSX/64 10.10.5 (amazon) w/serial & parallel Linux/64 3.10.x (kituo) w/serial & parallel Linux/64 2.6.x (ostrich) w/serial