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Change doxygen version from 1.10.0 to 1.9.7 #4371

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merged 1 commit into from
Apr 10, 2024
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Change doxygen version from 1.10.0 to 1.9.7 #4371

merged 1 commit into from
Apr 10, 2024

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byrnHDF
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@byrnHDF byrnHDF commented Apr 10, 2024

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@byrnHDF byrnHDF added Merge - To 1.14 Priority - 0. Blocker ⛔ This MUST be merged for the release to happen Type - Bug / Bugfix Please report security issues to [email protected] instead of creating an issue on GitHub Component - Misc Anything else (CODEOWNERS, etc.) labels Apr 10, 2024
@byrnHDF byrnHDF self-assigned this Apr 10, 2024
@ajelenak
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Why this downgrade? I've been building the docs with doxygen 1.10 for a few weeks now.

@byrnHDF
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byrnHDF commented Apr 10, 2024

Why this downgrade? I've been building the docs with doxygen 1.10 for a few weeks now.

Evidently. it has a problem with the NavTree - 1.10.0 doesn't display it 1.9.7 does. Proof was the generated docs in gh-pages.

@brtnfld
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brtnfld commented Apr 10, 2024

Is it an issue with Doxygen itself or our docs? Did something change for 1.10.0 that we need to fix?

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byrnHDF commented Apr 10, 2024

Is it an issue with Doxygen itself or our docs? Did something change for 1.10.0 that we need to fix?

I believe doxygen, but maybe there was a change that needs to be investigated to work with 1.10.0.

@byrnHDF byrnHDF closed this Apr 10, 2024
@byrnHDF byrnHDF reopened this Apr 10, 2024
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brtnfld commented Apr 10, 2024

I searched the GitHub issues and did not see any problems related to a missing navtree. I used the doxygen master, and I could not get the HDF5 develop or HDF5 1.14.x to show the navtree. Should we submit an issue with Doxgen?

FYI, unrelated:

/home/brtnfld/packages/hdf5.brtnfld/java/src/hdf/hdf5lib/H5.java:10063: warning: argument 'fapl_id' of command @param is not found in the argument list of H5::H5Pget_external(long plist, int idx, long name_size, String[] name, long[] size)
/home/brtnfld/packages/hdf5.brtnfld/java/src/hdf/hdf5lib/H5.java:10063: warning: argument 'fapl_id' of command @param is not found in the argument list of H5::H5Pget_external(long plist, int idx, long name_size, String[] name, long[] size)
/home/brtnfld/packages/hdf5.brtnfld/java/src/hdf/hdf5lib/H5.java:10063: warning: argument 'efc_size' of command @param is not found in the argument list of H5::H5Pget_external(long plist, int idx, long name_size, String[] name, long[] size)
/home/brtnfld/packages/hdf5.brtnfld/java/src/hdf/hdf5lib/H5.java:13922: warning: argument 'obj_id' of command @param is not found in the argument list of H5::H5Tenum_create(long base_id)

@ajelenak
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There is a custom .js file for our docs: hdf5_navtree_hacks.js. Probably good to first try without it before reporting to doxygen.

@byrnHDF
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byrnHDF commented Apr 10, 2024

I have found a number of issues with 1.10.0 and navtree problems - nothing with our exact problem. Note that we do have a custom css and a custom javascript file involved that could be causing the issue.

FYI here is an interesting possibility to use instead: https://github.com/jothepro/doxygen-awesome-css

@ajelenak
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FYI here is an interesting possibility to use instead: https://github.com/jothepro/doxygen-awesome-css

I've been testing it for two weeks now.

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byrnHDF commented Apr 10, 2024

FYI here is an interesting possibility to use instead: https://github.com/jothepro/doxygen-awesome-css

I've been testing it for two weeks now.

Then please put in a PR if it is a better replacement for our custom files!

@lrknox lrknox merged commit 823fdac into HDFGroup:develop Apr 10, 2024
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@byrnHDF byrnHDF deleted the develop-doxy-ver branch April 15, 2024 14:19
lrknox pushed a commit to lrknox/hdf5 that referenced this pull request Apr 22, 2024
@byrnHDF @lrknox
Change doxygen version from 1.10.0 to 1.9.7 (HDFGroup#4371)
e49f3db
lrknox added a commit that referenced this pull request Apr 25, 2024
@lrknox
Sync develop changes April 4 -April 22 to hdf5_1_14 (#4437)
5086959 
* Fixed dead links in docs (#4334)

* Revert "Fixed dead links in docs (#4334)" (#4335)

This reverts commit 408fc66.

* Fix grammar and content in HDF5Examples (#4333)

* Remove HD macros for C time functions (#4337)

* HDasctime
* HDclock
* HDctime
* HDdifftime
* HDgmtime
* HDlocaltime
* HDmktime
* HDtime
* HDtzset

HDgettimeofday will be done later

* Remove HD prefix from toupper/tolower (#4340)

* Add VDS and SWMR to documentation (#4336)

* Clean up random number generator code (#4338)

* Clean up random number generator code

Depending on the platform, we use a mix of random, rand, and rand_r
to generate pseudo-random numbers, along with a messy set of ifdefs
in H5private.h. We are not a cryptographic library, only use random
numbers in our test code, and have no need for anything more than the
C standard's (s)rand(). There's no point dithering about using rand()
vs random() when we're also doing bad things like using mod to
restrict the range, which introduces bias.

Also removes CMake/configure checks for rand_r and random

* Remove random/rand_r checks from build system

* Fix missed HDrandom after GitHub merge

* Remove the getting started guide (#4339)

This was moved to the wiki

* Remove noise comment from H5DO.c (#4342)

* Add note about H5Iregister_type hash_table param (#4345)

The hash_table parameter is unused in HDF5 1.8.13 and later, when we moved from using hash tables to skip lists for storing IDs. The current hash table implementation does not use this parameter.

* Remove `#undef ERR` from H5private.h (#4346)

This is an old work-around that is no longer necessary.

The only place where we defined ERR is in h5import, and that code
has been updated (in this PR) to rename ERR to INVALID_TOKEN.

* Add NAMECHECK_ONLY to macro list in .clang-format (#4343)

This caused H5TS.c functions to be mis-formatted

* Remove HD from last non-win32 C89 functions (#4348)

Removes the HD prefix from the last C89 functions with no special
Windows equilvalent:

* rename
* rewind
* setbuf
* signal
* tmpfile

* Fix dead links cont. (#4349)

Added img/images_to_copy.dox as a temporary solution because doxygen didn't copy
the images used in the examples/*.html files - will investigate more.  This was
necessary for the links to intro_SWMR.html and intro_VDS.html.

* Fix a typo (#4352)

* Fix use of possibly uninitialized memory in h5repack (#4354)

* Match content listing with content. (#4357)

* Remove obsolete c++ doxygen config files (#4358)

* Fix typo VERSIO (#4363)

* Removed duplicate entries in compile line for h5* compiler wrappers (#4360)

* h5fc remove duplicate args
* h5 wrappers remove duplicate args

* Added CVE info to RELEASE.txt (#4367)

* Change doxygen version from 1.10.0 to 1.9.7 (#4371)

* Fix all doxygen versions (#4377)

* Change date to data in INSTALL_parallel (#4384)

* Fix a broken link for zlib url (#4383)

* Fix broken links and references in INSTALL_Auto.txt (#4382)

* Remove  signature in comment (#4366)

* switched from \returns to commonly used \return (#4389)

* Add CXX flags (#4359)

* Remove TRACE macros (#4341)

* Set available CMake build types for non-multi-config generators (#4330)

* Correct the high-level library link (#4398)

* Correct the high-level library link

The link currently used points to 1.13 release.  Changed to use the md file instead.

* Update Doxyfile for md files

* Update to include md files

* Add additional terms to the glossary (#4401)

Fixes GH #4390

* added missing doxygen \since (#4410)

* Update Intel oneAPI version to 2024.1 (#4412)

* Update documentation (#4403)

- Added File Image Operations to Technical Notes

* Use a correct example location

* Use aliases for URLs (#4409)

* Fix CXX sanitizer by moving marco include to after CXX code. (#4414)

* Update and use more URL alias (#4413)

* Update documentation (#4415)

Added the replacement for https://docs.hdfgroup.org/archive/support/HDF5/doc/TechNotes/Version.html
Corrected some minor typos and another deadlink

* Remove obsolete file (#4416)

* Update oneAPI version to 2024.1 for Daily Build (#4418)

* Add training videos page (#4422)

* Updates for release_docs/NEWSLETTER.txt. (#4423)

* Add release process markdown file (#4312)

* Lowercase  in File Format Specification (#4424)

* Fixing string in RELEASE_PROCESS.md that is causing a doxygen error - (#4430)

Unsupported xml/html tag <n> found.

* Allow clang-format to format H5Cpkg.h (#4429)

Co-authored-by: Larry Knox <[email protected]>

* Fix broken links in md files needing full URLs.

* Add URL for Java examples that was accidentally dropped.
Change paths from develop to 1.14 directories for some doxygen generated
files.

* Correct typo.

* Fix 2 more dead URLs.

* Revert "Clean up random number generator code (#4338)"

This reverts commit 58e4d08.
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@jhendersonHDF jhendersonHDF jhendersonHDF approved these changes

@lrknox lrknox lrknox approved these changes

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