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* Sync with develop (#1863)feature/onion_vfdDana Robinson2022-07-09158-1678/+6142
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* Enable the Onion VFD to support H5Pset_driver_by_name (#1813)raylu-hdf2022-06-292-12/+403
| | | | | | | | | | | | | | | * Enable the Onion VFD to support H5Pset_driver_by_name and added a test case for it. * Committing clang-format changes * Revised a private function to return an error if it fails. * Committing clang-format changes * Refactored some code in the previous commit. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Enabling h5repack to support onion VFD (#1788)raylu-hdf2022-06-295-0/+145
| | | | | | | * Enable h5repack to support onion VFD. The input file can take options for onion VFD. But output file doesn't. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Onion VFD: Refactoring (#1765)Dana Robinson2022-05-1212-669/+751
| | | | | | | | | | | | | | | | | | | | | * Struct cleanup * More renaming * Minor cleanup * Removed aspirational code from the feature * Revert "Removed aspirational code from the feature" This reverts commit 0b162d16a175a08565089f829014d0d93e171a23. * Split header code into new files, history_header --> header * In-memory things are size_t now * Minor renaming * More encode/decode functions use size_t instead of uint64_t
* Onion VFD: Refactoring (#1756)Dana Robinson2022-05-089-2035/+2122
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* Onion VFD: Sync with develop (#1753)Dana Robinson2022-05-0811-120/+77
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* Added a test case for object and region references (#1752)raylu-hdf2022-05-081-1/+383
| | | | | | | * Added a test case for object and region references. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Onion VFD: sync with develop (#1747)Dana Robinson2022-05-0612-153/+126
| | | Sync with develop
* Onion VFD: Removes the user info from the revision entries (#1737)Dana Robinson2022-05-0615-177/+91
| | | | | | | * Removes the user info from the onion VFD revision entries * Formatted source * Fixed codespell issue
* Cleaned up new public call to get the number of onion revisions (#1735)Dana Robinson2022-05-061-17/+33
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* Added the standard output file ↵raylu-hdf2022-05-062-2/+3
| | | | (tools/testfiles/tst_onion_revision_count.ddl) which was left out in the previous checkin. (#1736)
* Adds the onion VFD to Github workflows (#1734)Dana Robinson2022-05-062-2/+2
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* Onion VFD: Cleans up warnings related to onion VFD stuff in tools code (#1733)Dana Robinson2022-05-065-42/+50
| | | | | | | | | * Cleans up warnings related to onion VFD stuff in tools code Also disables an h5dump test that has a missing file * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Onion VFD: Sync with develop. (#1732)Dana Robinson2022-05-06130-30491/+29650
| | | | | | | * Sync with develop. h5dump is broken, so I can't test the tools. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Added the support to get the revision count for the onion file into the ↵raylu-hdf2022-05-055-19/+36
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | h5dump. (#1726) * Removes unused definitions from module headers (#1624) * Fix these Doxygen warnings #1581 (#1589) * Fixes a typo in H5.c (#1639) * free MPI_Group/MPI_Comm/MPI_Datatype objects (#1638) * free MPI_Group/MPI_Comm/MPI_Datatype objects * fix clang-format style * Adds build and license shields to README.md (#1641) * First stab at a Github status bar * Adds a .tokeignore file for counting lines of code accurately * Yanks lines of code calculation since it wildly overcounts * not depend on doIO to free an MPI_Comm object (#1642) * free MPI datatypes previously created (#1637) * Retrieve MPI-IO hints used by MPI library after file open (#1636) H5Pget_fapl_mpio() should return an MPI info object containing all the MPI-IO hints used by the MPI library underneath, after the file is opened. Some hints, such as cb_nodes (number of I/O aggregators), are useful for HDF5 applications and I/O libraries built on top of HDF5. * OESS-168: Remove clang warnings. (#1309) * OESS-168: Remove clang warnings. * OESS-168: Address @lrknox review. * OESS-168: Remove clang warnings. (#1376) * Added the support to get the revision count for the onion file into the h5dump. * Committing clang-format changes * Changed the function from H5FDget_onion_revision_count to H5FDonion_get_revision_count for better name. * Fixed compiler warnings. Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com> Co-authored-by: Allen Byrne <50328838+byrnHDF@users.noreply.github.com> Co-authored-by: Wei-keng Liao <wkliao@users.noreply.github.com> Co-authored-by: H. Joe Lee <hyoklee@hdfgroup.org> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Adding a new API function to get the number of revisions for an onion file ↵raylu-hdf2022-05-034-25/+122
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | (#1692) * Removes unused definitions from module headers (#1624) * Fix these Doxygen warnings #1581 (#1589) * Fixes a typo in H5.c (#1639) * free MPI_Group/MPI_Comm/MPI_Datatype objects (#1638) * free MPI_Group/MPI_Comm/MPI_Datatype objects * fix clang-format style * Adds build and license shields to README.md (#1641) * First stab at a Github status bar * Adds a .tokeignore file for counting lines of code accurately * Yanks lines of code calculation since it wildly overcounts * not depend on doIO to free an MPI_Comm object (#1642) * free MPI datatypes previously created (#1637) * Retrieve MPI-IO hints used by MPI library after file open (#1636) H5Pget_fapl_mpio() should return an MPI info object containing all the MPI-IO hints used by the MPI library underneath, after the file is opened. Some hints, such as cb_nodes (number of I/O aggregators), are useful for HDF5 applications and I/O libraries built on top of HDF5. * OESS-168: Remove clang warnings. (#1309) * OESS-168: Remove clang warnings. * OESS-168: Address @lrknox review. * OESS-168: Remove clang warnings. (#1376) * Adding a new API function to get the number of revisions for an onion file. This function uses H5FD_ctl(). * Committing clang-format changes * Removed a few unused variables. * Modified the way that the API function H5FDget_onion_revision_count is organized and added Doxygen comments for the three API functions. * Committing clang-format changes * Minor changes: modified some Doxygen comments. Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com> Co-authored-by: Allen Byrne <50328838+byrnHDF@users.noreply.github.com> Co-authored-by: Wei-keng Liao <wkliao@users.noreply.github.com> Co-authored-by: H. Joe Lee <hyoklee@hdfgroup.org> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Onion VFD: Misc cleanup (#1693)Dana Robinson2022-04-2623-641/+652
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Removes unused definitions from module headers (#1624) * Fix these Doxygen warnings #1581 (#1589) * Fixes a typo in H5.c (#1639) * free MPI_Group/MPI_Comm/MPI_Datatype objects (#1638) * free MPI_Group/MPI_Comm/MPI_Datatype objects * fix clang-format style * Adds build and license shields to README.md (#1641) * First stab at a Github status bar * Adds a .tokeignore file for counting lines of code accurately * Yanks lines of code calculation since it wildly overcounts * not depend on doIO to free an MPI_Comm object (#1642) * free MPI datatypes previously created (#1637) * Retrieve MPI-IO hints used by MPI library after file open (#1636) H5Pget_fapl_mpio() should return an MPI info object containing all the MPI-IO hints used by the MPI library underneath, after the file is opened. Some hints, such as cb_nodes (number of I/O aggregators), are useful for HDF5 applications and I/O libraries built on top of HDF5. * OESS-168: Remove clang warnings. (#1309) * OESS-168: Remove clang warnings. * OESS-168: Address @lrknox review. * OESS-168: Remove clang warnings. (#1376) * Remove H5_NO_ALIGNMENT_RESTRICTIONS (#1426) * Do not conditionally compile code that uses a pointer dereference and assignment to copy a potentially unaligned variable to aligned automatic storage, or vice versa. Instead, always use naked `memcpy(3)`s. Disassembling the generated code reveals that the `memcpy(3)`s optimize (`-O3`) to a single `mov` instruction for x86_64, which is not strict about alignment. This change reduces the size of code and scripts by 143 lines, eases our way to cross-compilation, and avoids invoking undefined behavior. * Committing clang-format changes * Per discussion, use HD and add comments. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Cleans up some HL library code that inappropriately returns htri_t values cast to herr_t (#1651) * Cleans up some HL library code that inappropriately returns htri_t values cast to herr_t * Committing clang-format changes * Formatted source Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Mirror vfd test fixes (#1629) * Use the FAPL that was created earlier in the test (and delete an unused variable). This allows 'make check-vfd' to pass with --enable-mirror-vfd. * Check for testing directory before creating, to avoid warning from bash. Clean out .libs directory before re-using it (after a failed test), to remove any files generated by libtool. * Committing clang-format changes * Increment error count on failed file open and skip tests for VFDs that need modified filenames. * Skip the mirror VFD for 'make check-vfd' - the mirror VFD requires networking configuration parameters and can't be provided for an automated test that is configured with an environment variable. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Removes HDF Group paths, adds shellcheck fixes (#1656) For more information: https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ... https://www.shellcheck.net/wiki/SC2230 -- which is non-standard. Use builti... https://www.shellcheck.net/wiki/SC2006 -- Use $(...) notation instead of le... * HDFFV-11306 Fixed (#1657) * HDFFV-11306, * Fixed it so both h5open_f and h5close_f can be called multiple times. * Fixed an issue with open objects remaining after h5close_f was called. * Added additional tests. * comments clean-up * Develop clang format java (#1653) * added HDFFV-11306 entry (#1662) * Adds the -q flag to all swmr test programs, quieting noisy output (#1665) * Adds paths-ignore to the Github pull request workflow (#1663) * Changes Github action `hdf5 dev CI` to `PR hdf5 dev CI` (#1666) So the PR action name is not the same as the one in main.yml * Replace H5detect's build-time detection of C99 integer properties with a (#1400) * Replace H5detect's build-time detection of C99 integer properties with a table-driven routine, `H5T__init_native_int()`, that is run at library initialization time. * Improve handling of copying of dynamic libraries and clean them up after (#1681) test finishes. * Warnings fixes (#1680) * Clean stack size warnings in sio_engine (#1687) * Fixes stack size warnings in tcoords.c (#1688) * Minor things noticed while bringing VFD SWMR in line with develop (#1691) * Removed dead code, weird formatting, and other badness * Fixed remaining stack size warnings in onion VFD * Committing clang-format changes Co-authored-by: Allen Byrne <50328838+byrnHDF@users.noreply.github.com> Co-authored-by: Wei-keng Liao <wkliao@users.noreply.github.com> Co-authored-by: H. Joe Lee <hyoklee@hdfgroup.org> Co-authored-by: David Young <dyoung@hdfgroup.org> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Quincey Koziol <koziol@lbl.gov> Co-authored-by: Scot Breitenfeld <brtnfld@hdfgroup.org> Co-authored-by: jhendersonHDF <jhenderson@hdfgroup.org>
* Onion VFD: Cleaned up code and warnings in onion VFD tools code (#1686)Dana Robinson2022-04-252-213/+142
| | | | | | | * Cleaned up code and warnings in onion VFD tools code * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Onion VFD: Sync with develop (#1685)Dana Robinson2022-04-25247-11494/+14414
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Removes unused definitions from module headers (#1624) * Fix these Doxygen warnings #1581 (#1589) * Fixes a typo in H5.c (#1639) * free MPI_Group/MPI_Comm/MPI_Datatype objects (#1638) * free MPI_Group/MPI_Comm/MPI_Datatype objects * fix clang-format style * Adds build and license shields to README.md (#1641) * First stab at a Github status bar * Adds a .tokeignore file for counting lines of code accurately * Yanks lines of code calculation since it wildly overcounts * not depend on doIO to free an MPI_Comm object (#1642) * free MPI datatypes previously created (#1637) * Retrieve MPI-IO hints used by MPI library after file open (#1636) H5Pget_fapl_mpio() should return an MPI info object containing all the MPI-IO hints used by the MPI library underneath, after the file is opened. Some hints, such as cb_nodes (number of I/O aggregators), are useful for HDF5 applications and I/O libraries built on top of HDF5. * OESS-168: Remove clang warnings. (#1309) * OESS-168: Remove clang warnings. * OESS-168: Address @lrknox review. * OESS-168: Remove clang warnings. (#1376) * Remove H5_NO_ALIGNMENT_RESTRICTIONS (#1426) * Do not conditionally compile code that uses a pointer dereference and assignment to copy a potentially unaligned variable to aligned automatic storage, or vice versa. Instead, always use naked `memcpy(3)`s. Disassembling the generated code reveals that the `memcpy(3)`s optimize (`-O3`) to a single `mov` instruction for x86_64, which is not strict about alignment. This change reduces the size of code and scripts by 143 lines, eases our way to cross-compilation, and avoids invoking undefined behavior. * Committing clang-format changes * Per discussion, use HD and add comments. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Cleans up some HL library code that inappropriately returns htri_t values cast to herr_t (#1651) * Cleans up some HL library code that inappropriately returns htri_t values cast to herr_t * Committing clang-format changes * Formatted source Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Mirror vfd test fixes (#1629) * Use the FAPL that was created earlier in the test (and delete an unused variable). This allows 'make check-vfd' to pass with --enable-mirror-vfd. * Check for testing directory before creating, to avoid warning from bash. Clean out .libs directory before re-using it (after a failed test), to remove any files generated by libtool. * Committing clang-format changes * Increment error count on failed file open and skip tests for VFDs that need modified filenames. * Skip the mirror VFD for 'make check-vfd' - the mirror VFD requires networking configuration parameters and can't be provided for an automated test that is configured with an environment variable. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Removes HDF Group paths, adds shellcheck fixes (#1656) For more information: https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ... https://www.shellcheck.net/wiki/SC2230 -- which is non-standard. Use builti... https://www.shellcheck.net/wiki/SC2006 -- Use $(...) notation instead of le... * HDFFV-11306 Fixed (#1657) * HDFFV-11306, * Fixed it so both h5open_f and h5close_f can be called multiple times. * Fixed an issue with open objects remaining after h5close_f was called. * Added additional tests. * comments clean-up * Develop clang format java (#1653) * added HDFFV-11306 entry (#1662) * Adds the -q flag to all swmr test programs, quieting noisy output (#1665) * Adds paths-ignore to the Github pull request workflow (#1663) * Changes Github action `hdf5 dev CI` to `PR hdf5 dev CI` (#1666) So the PR action name is not the same as the one in main.yml * Replace H5detect's build-time detection of C99 integer properties with a (#1400) * Replace H5detect's build-time detection of C99 integer properties with a table-driven routine, `H5T__init_native_int()`, that is run at library initialization time. * Improve handling of copying of dynamic libraries and clean them up after (#1681) test finishes. Co-authored-by: Allen Byrne <50328838+byrnHDF@users.noreply.github.com> Co-authored-by: Wei-keng Liao <wkliao@users.noreply.github.com> Co-authored-by: H. Joe Lee <hyoklee@hdfgroup.org> Co-authored-by: David Young <dyoung@hdfgroup.org> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Quincey Koziol <koziol@lbl.gov> Co-authored-by: Scot Breitenfeld <brtnfld@hdfgroup.org>
* Onion VFD: Cleanup and refactoring in the onion VFD (#1679)Dana Robinson2022-04-244-1280/+954
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Trivial comment change * Misc refactoring in the onion test * Committing clang-format changes * Fix unused parameter warning * Removed printf debugging statements * checkposix fixes * Cleaned up some function headers * Remove useless casts * Fixes most warnings in the onion VFD test code (exception: stack size warnings) * Make TEST_ERROR semicolons consistent * Much tidying in the onion VFD tests * Formatted source Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Adding the support of H5FDctl for the Onion VFD and the test case. (#1677)raylu-hdf2022-04-223-1/+267
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* Onion VFD: Misc refactoring in the tests (#1654)Dana Robinson2022-04-181-142/+84
| | | | | | | | | * Trivial comment change * Misc refactoring in the onion test * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Changed the field name 'revision_id' of H5FD_onion_fapl_info_t to ↵raylu-hdf2022-04-166-102/+102
| | | | | | | | | 'revision_num' for better description (#1650) * Changed the field name 'revision_id' of H5FD_onion_fapl_info_t to 'revision_num' for better description. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Trivial comment change (#1646)Dana Robinson2022-04-151-2/+1
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* Changed the options for the Onion VFD to use the generic VFD options in ↵raylu-hdf2022-04-156-23/+99
| | | | | | | | | h5diff and h5dump (#1643) * Changed the options for the Onion VFD to use the generic VFD options in h5diff and h5dump. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Merge pull request #1626 from HDFGroup/raylu_onion_vfd_7raylu-hdf2022-04-08238-2250/+2225
|\ | | | | Syncing with the Develop Branch
| * Changed FUNC_ENTER_STATIC_NOERR to FUNC_ENTER_PACKAGE_NOERR and ↵Ray Lu2022-04-081-22/+22
| | | | | | | | FUNC_ENTER_STATIC to FUNC_ENTER_PACKAGE to follow the changes in the develop branch.
| * Merge branch 'develop' of https://github.com/HDFGroup/hdf5 into ↵Ray Lu2022-04-08237-2228/+2203
| |\ |/ / | | | | raylu_onion_vfd_7
| * Removes the STATIC flavor of FUNC_ENTER macros (#1622)Dana Robinson2022-04-08221-2213/+2188
| | | | | | | | | | * Removes the STATIC flavor of FUNC_ENTER macros
| * Minor things discovered while preparing 1.12.2 (#1620)Dana Robinson2022-04-086-7/+7
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| * Updates bin/restore.sh to clean up src/H5config.h.in (#1605)Dana Robinson2022-04-071-0/+3
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| * Minor C++ changes noticed while normalizing with 1.12 (#1606)Dana Robinson2022-04-078-6/+5
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| * Removes bin/README (#1602)Dana Robinson2022-04-071-2/+0
| | | | | | | | This README file refers to scripts that were removed when the MANIFEST went away.
| * Adds additional files/paths to ignore for github actions (#1585)Dana Robinson2022-04-051-0/+3
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| * Adds release timeline to README.md (#1584)Dana Robinson2022-04-053-0/+65
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* | Merge pull request #1601 from HDFGroup/raylu_onion_vfd_4raylu-hdf2022-04-07867-27918/+47227
|\ \ | | | | | | Sync with the develop branch
| * | Corrected some spelling errors.Ray Lu2022-04-071-9/+9
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| * | Committing clang-format changesgithub-actions2022-04-061-1/+0
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| * | Merge remote-tracking branch 'canonical/develop' into feature/onion_vfdDana Robinson2022-04-06867-27909/+47219
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| * Add missing release note for h5repack timing (#1572)Allen Byrne2022-04-051-0/+8
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| * Move error-stack text to top of usage display (#1564)Allen Byrne2022-04-0128-68/+122
| | | | | | | | | | | | | | | | | | * Move error-stack text to top of usage display * Add optional tag ti list * format changes * Revert incorrect change
| * Fix for unexported global variable on Windows (#1568)Dana Robinson2022-04-011-2/+5
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| * spelling fixes (#1561)Scot Breitenfeld2022-03-3121-25/+25
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| * Update command format, avoid policy warning (#1550)Allen Byrne2022-03-301-3/+3
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| * Add H5_CHECK_MPI_VERSION macro to check for at least MPI version of ↵jhendersonHDF2022-03-306-18/+27
| | | | | | | | | | | | | | | | | | (version, subversion) (#1556) * Fix MPI version check for MPI_Aint_diff usage * Add H5_CHECK_MPI_VERSION macro Adds new H5_CHECK_MPI_VERSION macro to check for MPI library version/subversion pair of at least the specified pair
| * Update MacOS configure, bringing it closer to Linux configure (#1554)Quincey Koziol2022-03-301-27/+40
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| * Add missing H5FL_TRACK debug parameters to free list array routines (#1555)jhendersonHDF2022-03-301-6/+12
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| * Minor comment corrections (#1544)Allen Byrne2022-03-303-15/+13
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| * Removes unused H5HP (private heap) package (#1548)Dana Robinson2022-03-3010-2076/+2
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| * Removes unused memory pool (H5MP) package (#1547)Dana Robinson2022-03-3010-1657/+2
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