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ExternalProject SUNDIALS 3.2.1 #1960

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ExternalProject SUNDIALS 3.2.1 #1960

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Commits on Aug 20, 2022

  1. ExternalProject SUNDIALS 3.2.1 

    * include work from cvode3 branch
    @alexsavulescu
    alexsavulescu committed Aug 20, 2022
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  2. ninja needs BUILD_BYPRODUCTS in ExternalProject_Add

    @alexsavulescu
    alexsavulescu committed Aug 20, 2022
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Commits on Dec 11, 2022

  1. Merge branch 'master' into slds

    @alkino
    alkino authored Dec 11, 2022
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  2. Format

    @alkino
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Commits on May 1, 2023

  1. Merge remote-tracking branch 'origin/master'

    @alkino
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  2. Format

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  3. Fix name of SUNR functions

    @alkino
    alkino committed May 1, 2023
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Commits on May 4, 2023

  1. Fix segfault (missing IDASetUserData) and N_VSpace_... prototypes.

    @nrnhines
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  2. Build sundials with the same type than nrn

    @alkino
    alkino committed May 4, 2023
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  3. Fully remove sundials

    @alkino
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  4. Merge remote-tracking branch 'origin/master'

    @alkino
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  5. IDASetStopTime should not be called for interpolation.

    @nrnhines
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Commits on May 5, 2023

  1. ctest -R netpar passes. MPI_Comm not available from cvodeobj.cpp

    @nrnhines
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  2. Revert "ctest -R netpar passes. MPI_Comm not available from cvodeobj.… 

    …cpp"

This reverts commit e0b3ef1.
    @nrnhines
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  3. ctest -R netpar passes. Works with NRNMPI_DYNAMICLOAD.

    @nrnhines
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  4. Problem translating long long foo for NRNMPI_DYNAMICLOAD

    @nrnhines
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Commits on May 6, 2023

  1. update nrntest (cvode version 3 and no hhtable)

    @nrnhines
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Commits on May 11, 2023

  1. Merge branch 'master' into slds

    @alkino
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Commits on May 15, 2023

  1. Selected messages from old digest-debug branch 

    Print digest of cvode f(y,t) and solvex(b,...)
  cmake -DNRN_DIGEST=ON
  nrn_digest() starts the accumulation of cvode digest info.
  nrn_digest("filename") prints accumulated cvode digest info.
  filename format is:
    message threadid t t(in exact hex format) digest
    where digest is the first 16 hex characters of the SHA1 hash
    of the double* array indicated by the message.

-DNRN_ENABLE_ARCH_INDEP_EXP_POW=ON (default OFF)
  Provides h.use_exp_pow_precision(style)
  style = 0 means use normal machine IEEE precision for exp(x) and pow(x,y)
  style = 1 means use 53 bit mpfr
  style = 2 means use IEEE but truncate to 32 bit precision.

   sundials uses hoc_pow.

   digest format has a f(y,t) call count.

Use 32bit mantissa round for hoc_Exp (as well as hoc_pow).

See if pow is the culprit (round mantissa to 32 bit accuracy).

print y and ydot for first t>0

%a format different between linux and windows
    @nrnhines
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  2. libcrypt for mac

    @nrnhines
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Commits on May 17, 2023

  1. Merge branch 'master' into slds

    @nrnhines
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  2. No need link libsundials_nvecparallel.a

    @nrnhines
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  3. Merge branch 'master' into slds

    @nrnhines
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  4. format

    @nrnhines
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  5. Left out }

    @nrnhines
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  6. Revert "No need link libsundials_nvecparallel.a" 

    This reverts commit 824732b.
    @nrnhines
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Commits on May 25, 2023

  1. Merge branch 'master' into slds

    @nrnhines
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Commits on May 26, 2023

  1. "major.minor.patch" = h.CVode().version()

    @nrnhines
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  2. eliminate pytest warning

    @nrnhines
    nrnhines committed May 26, 2023
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Commits on May 28, 2023

  1. CVode 3.2.1 json data for test_nrntest_fast.py

    @nrnhines
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Commits on Jun 1, 2023

  1. Merge branch 'master' into slds

    @alkino
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  2. Merge remote-tracking branch 'origin/master'

    @alkino
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  3. sundials nvecparallel needs MPI

    @alkino
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  4. Merge remote-tracking branch 'origin/slds'

    @alkino
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  5. Fix FindSUNDIALS.cmake

    @alkino
    alkino committed Jun 1, 2023
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  6. fix linkage

    @alkino
    alkino committed Jun 1, 2023
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  7. Try to clean linkage with sundials

    @alkino
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  8. Format

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  9. Don't use corenrn if corenrn not set

    @alkino
    alkino committed Jun 1, 2023
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  10. Fix fix and fix

    @alkino
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  11. Format

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  12. trick depends

    @alkino
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  13. try to help sundials to find MPI

    @alkino
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Commits on Jun 2, 2023

  1. set LIBDIR

    @alkino
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  2. -tp=haswell is not accepted by sundials

    @alkino
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  3. Merge branch 'master' into slds

    @alkino
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Commits on Jun 12, 2023

  1. Merge remote-tracking branch 'origin/master'

    @alkino
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  2. Remove too more spaces

    @alkino
    alkino committed Jun 12, 2023
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  3. Merge remote-tracking branch 'origin/master'

    @alkino
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  4. CVodeSetFdata => CVodeSetUserData

    @alkino
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Commits on Nov 4, 2023

  1. Merge branch 'master' into slds

    @nrnhines
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Commits on Nov 5, 2023

  1. eliminate some compiler warnings

    @nrnhines
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  2. update nrntest to master merged hines/update-t12

    @nrnhines
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Commits on Dec 30, 2023

  1. Merge branch 'master' into slds

    @nrnhines
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  2. on previous master merge, resolve conflict incorrectly

    @nrnhines
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Commits on Mar 9, 2024

  1. Merge branch 'master' into slds

    @nrnhines
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Commits on May 7, 2024

  1. Merge remote-tracking branch 'origin/master'

    @alkino
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Commits on Oct 1, 2024

  1. Merge branch 'master' into slds

    @nrnhines
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Commits on Oct 3, 2024

  1. some files missing in NRN_PARALLEL_SRC_FILES

    @nrnhines
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  2. ninja format

    @nrnhines
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  3. Merge branch 'master' into slds (master for test_nlayer.py conflict)

    @nrnhines
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  4. cvode.version() got lost in a merge

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Commits on Oct 4, 2024

  1. test_kschan data for cvode 3.2.1

    @nrnhines
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  2. test_nrntest_fast.py tolerance adjustment for t14

    @nrnhines
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  3. missing json file for ctest -R parallel::nrntest_fast

    @nrnhines
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  4. cv3 version of json file for test_netcvode.py

    @nrnhines
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  5. Merge branch 'master' into slds

    @nrnhines
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  6. temporarily turn off CI tests of rxd

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Commits on Oct 6, 2024

  1. temporarily turn off (most) wheel builds and gitlab CI

    @nrnhines
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  2. adust a few tolerance values to see if more CI pass

    @nrnhines
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Commits on Oct 7, 2024

  1. Merge branch 'digest-debug-2' into digest-debug-3

    @nrnhines
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Commits on Oct 8, 2024

  1. nrn_digest(i) will print the details of the i'th digest item.

    @nrnhines
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Commits on Oct 9, 2024

  1. missing include

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Commits on Oct 15, 2024

  1. Allow digest when multiple threads.

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  2. digest print solvex enter y

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Commits on Oct 17, 2024

  1. sundial RPowerR uses hoc_pow. nrn_digest(i, "abort") calls abort() on 

    reaching index i
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Commits on Oct 18, 2024

  1. Documentation for nrn_digest and use_exp_pow_precision

    @nrnhines
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  2. nrn_digest signature consistent with documentation

    @nrnhines
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  3. occvode.cpp -Wall free

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  4. Merge branch 'master' into hines/digest-debug-3

    @nrnhines
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  5. Merge branch 'master' into hines/digest-debug-3

    @nrnhines
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  6. The configure option is NRN_ENABLE_ARCH_INDEP_EXP_POW

    @nrnhines
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  7. format

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  8. Revert "adust a few tolerance values to see if more CI pass" 

    This reverts commit 21c7826.
    @nrnhines
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  9. Revert "temporarily turn off (most) wheel builds and gitlab CI" 

    This reverts commit 0d4cc21.
    @nrnhines
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  10. Revert "temporarily turn off CI tests of rxd" 

    This reverts commit eb5e85a.
    @nrnhines
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  11. Merge branch 'master' into slds

    @nrnhines
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  12. Merge branch 'hines/digest-debug-3' into hines/cv3-digest

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Commits on Oct 19, 2024

  1. Use the neuronsimulator fork of sundials

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  2. passes ctest -j 8 (with "-ffp-model=strict")

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Commits on Oct 21, 2024

  1. Merge branch 'master' into hines/cv3-digest

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Commits on Oct 22, 2024

  1. Merge branch 'master' into hines/cv3-digest

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  2. Update test/rxd/testdata for cvode3

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  3. document how to update rxd test data

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Commits on Oct 23, 2024

  1. Revert "Update test/rxd/testdata for cvode3" 

    This reverts commit 7c670b7.
    @nrnhines
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  2. fix typo

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  3. update rxdtest repository (e0a6bc2) 2024-10-22

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Commits on Oct 24, 2024

  1. Merge branch 'master' into hines/cv3

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  2. cd share/lib/python/neuron/tests; python test_rxd.py --save test_rxd.… 

    …json
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  3. extend the rxd test data instructions

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Commits on Oct 25, 2024

  1. propagate compiler from nrn to sundials. SUNDIALS MPI_ENABLE=OFF

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  2. Merge branch 'master' into hines/cv3

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  3. Since sundials MPI_ENABLE=OFF have our own nvector_parallel.h

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    nrnhines committed Oct 25, 2024
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Commits on Oct 26, 2024

  1. nvector_parallel.cpp agnostic with respect to MPI_Comm

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    nrnhines committed Oct 26, 2024
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Commits on Oct 28, 2024

  1. cast between sunindextype and long

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    nrnhines committed Oct 28, 2024
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  2. update a cv3.json file.

    @nrnhines
    nrnhines committed Oct 28, 2024
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  3. nrnparallel_ld follows nvector_parallel style for MPI_Comm

    @nrnhines
    nrnhines committed Oct 28, 2024
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  4. relax resolution requirements so macosx will pass CI without needing 

    -DNRN_ENABLE_ARCH_INDEP_EXP_POW=ON
-DCMAKE_C_FLAGS="-ffp-model=strict" -DCMAKE_CXX_FLAGS="-ffp-model=strict"
    @nrnhines
    nrnhines committed Oct 28, 2024
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  5. adjust tol of test_nrntest_fast.py::test_t14[cvode_long_double-3-t] 

      needed for 4 ubuntu CI. Not sure about the underlying cause.
    @nrnhines
    nrnhines committed Oct 28, 2024
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  6. black format for test/.../*.py

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    nrnhines committed Oct 28, 2024
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Commits on Oct 31, 2024

  1. Changes after ctest coverage analysis.

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    nrnhines committed Oct 31, 2024
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  2. Merge branch 'master' into slds

    @nrnhines
    nrnhines authored Oct 31, 2024
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Commits on Nov 1, 2024

  1. Replace cvode.extra_scatter_gather with h.beforestep_callback

    @nrnhines
    nrnhines committed Nov 1, 2024
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  2. rxd tests use rxdtestdata hines/data-fix af269297

    @nrnhines
    nrnhines committed Nov 1, 2024
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  3. rxd/testdata when test/rxd/3d/test_multi_gridding_mix.py not skipped

    @nrnhines
    nrnhines committed Nov 1, 2024
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  4. Merge branch 'master' into hines/cv3

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    nrnhines committed Nov 1, 2024
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  5. Replace cvode.extra_scatter_gather with h.beforestep_callback

    @nrnhines
    nrnhines committed Nov 1, 2024
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  6. use rxdtestdata hines/cvode3 721ac55a

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    nrnhines committed Nov 1, 2024
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Commits on Nov 2, 2024

  1. Don't use cvode version specific filenames or keys for json data.

    @nrnhines
    nrnhines committed Nov 2, 2024
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Commits on Nov 6, 2024

  1. ecs_diffusion needs section to gather data.

    @nrnhines
    nrnhines committed Nov 6, 2024
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  2. Merge branch 'master' into hines/rxd-data-fix

    @nrnhines
    nrnhines authored Nov 6, 2024
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  3. Merge branch 'hines/rxd-data-fix' into hines/cv3 and update testdata

    @nrnhines
    nrnhines committed Nov 6, 2024
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