Bump version number to 7.9.0 and merge recent bug fixes from `main` [WIP]#140

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The9Cat wants to merge 235 commits intomainfrom

Commits on Jul 18, 2025

Add inner/outer boundary restrictions for SL solution to prevent underflow while computing basis elements with large harmonic orders
Martin D. Weinberg
committed

Commits on Jul 21, 2025

Update test codes to handle high-order Ylm evaluation using prenormalized Legendre evaluation
Martin D. Weinberg
committed
Add surface output to checkcoefs2; fix constexpr problem
Martin D. Weinberg
committed

Commits on Jul 22, 2025

Remove debug lines; only print mismatch info to root process
Martin D. Weinberg
committed
Remove unused variables; tweak DiskEval parameters
Martin D. Weinberg
committed

Commits on Jul 23, 2025

Update utils/ICs/DiskEval.H

michael-petersen
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Copilot
authored
Update utils/ICs/DiskEval.H

michael-petersen
and
Copilot
authored
Update exputil/SLGridMP2.cc

michael-petersen
and
Copilot
authored
Update utils/ICs/check_coefs2.cc

The9Cat
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Copilot
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tid not needed for verbose progress report header
Martin D. Weinberg
committed
For testing Doxygen integration into EXP-docs
Martin D. Weinberg
committed

Commits on Jul 25, 2025

Test YAMl documentation in class header
Martin D. Weinberg
committed
Check \param rather than @param
Martin D. Weinberg
committed
Return to @ rather than \ notation since it doesn't seem to matter
Martin D. Weinberg
committed
Updated YAML parameter documentaion for AxisymmetricBasis, Cube, Cylindr, FlatDisk, Sphere, and SphericalBasis
Martin D. Weinberg
committed

Commits on Jul 28, 2025

Merge branch 'devel' into SLboundaries
The9Cat
authored

Commits on Jul 29, 2025

Comment change only
Martin D. Weinberg
committed
Merge branch 'SLboundaries' of github.com:EXP-code/EXP into SLboundaries
Martin D. Weinberg
committed
Merge branch 'devel' of github.com:EXP-code/EXP into devel
Martin D. Weinberg
committed
Preliminary implementation of rotation matrix enhancement
Martin D. Weinberg
committed
Update utils/PhaseSpace/KDE2d.cc

The9Cat
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Copilot
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Updated from std::vector<double> to Eigen::Vector3d for center parameter
Martin D. Weinberg
committed
Merge branch 'RotationMatrix' of github.com:EXP-code/EXP into RotationMatrix
Martin D. Weinberg
committed
Exploit scalar*vector algebra in Eigen
Martin D. Weinberg
committed

Commits on Jul 30, 2025

Work around for HighFive std::vector and Eigen::Vector dimensionality in attribute reading/writing
Martin D. Weinberg
committed
Added a comment on the Center autodeduction workaround for HighFive
Martin D. Weinberg
committed

Commits on Jul 31, 2025

Ignore dimensionality when reading center vector
Martin D. Weinberg
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Use different variable names for total variance/power and normalization values
Martin D. Weinberg
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Update exputil/SLGridMP2.cc

The9Cat
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Copilot
authored
Update expui/expMSSA.cc

The9Cat
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Copilot
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Update expui/expMSSA.cc

The9Cat
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Copilot
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Commits on Aug 1, 2025

Remove debug output to stdout
Martin D. Weinberg
committed

Commits on Aug 6, 2025

Wrong type in HighFive attribute creation
Martin D. Weinberg
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initialize() must come before non-root nodes return for correct parameter tag parsing
Martin D. Weinberg
committed
Update exputil/SLGridMP2.cc

The9Cat
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Copilot
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Update exputil/SLGridMP2.cc

The9Cat
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Copilot
authored

Commits on Aug 7, 2025

Enable parallel reading from a Tipsy file
Martin D. Weinberg
committed
Update exputil/SLGridMP2.cc

The9Cat
and
Copilot
authored
Update exputil/SLGridMP2.cc

The9Cat
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Copilot
authored
Need to reposition file pointer after reading each particle type
Martin D. Weinberg
committed
Merge branch 'parallelTipsy' of github.com:EXP-code/EXP into parallelTipsy
Martin D. Weinberg
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Promote stream arithmetic to unsigned long
Martin D. Weinberg
committed
Add losts more comments [no CI]
Martin D. Weinberg
committed

Commits on Aug 8, 2025

Added more explanation for setMPI()
Martin D. Weinberg
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Commits on Aug 10, 2025

Save native Tipsy particle offsets per node for creating unique sequential indices
Martin D. Weinberg
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Assign EXP index from native Tipsy beginning with 1
Martin D. Weinberg
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Typo in Centering routine; missing count variable update
Martin D. Weinberg
committed

Commits on Aug 13, 2025

Updated Bonsai reader variant to v2
Martin D. Weinberg
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Change Tipsy tag from ChaNGa to Bonsai1; since I can't figure out what ChaNGa is doing for particle ID.
Martin D. Weinberg
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Commits on Aug 14, 2025

Add factory member to BiorthBasis
Martin D. Weinberg
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Update expui/BiorthBasis.cc

The9Cat
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Copilot
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Update exputil/SLGridMP2.cc

The9Cat
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Copilot
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Add expui and exputils to Doxygen build
Martin D. Weinberg
committed

Commits on Aug 17, 2025

Update include/tipsy.H

The9Cat
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Copilot
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Update expui/Centering.cc

The9Cat
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Copilot
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Remove debug cruft
Martin D. Weinberg
committed
Fix a missing registration of the rotation matrix; interface with numpy in row-major space
Martin D. Weinberg
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Remove some debug output
Martin D. Weinberg
committed

Commits on Aug 18, 2025

Make rotation matrices row-major everywhere
Martin D. Weinberg
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Commits on Aug 19, 2025

Add a OpenMP aware acceleration vector computation
Martin D. Weinberg
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Commits on Aug 20, 2025

Use local storage for acceleration rather than dynamic temporaries
Martin D. Weinberg
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Merge branch 'getAccelArray' into biorthFactory
Martin D. Weinberg
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Move from std::vector to Eigen::Vector returns for getAccel
Martin D. Weinberg
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Commits on Aug 25, 2025

Two minor fixes necessary for successful compilation with g++15
Martin D. Weinberg
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Set explicit C-language standard for Clang
Martin D. Weinberg
committed

Commits on Sep 29, 2025

Commits on Oct 1, 2025

Merge pull request #163 from EXP-code/DebugFlagFix
michael-petersen
authored

Commits on Oct 14, 2025

Added Sturm to AxiSymBio class for biorth->ortho test routines; added 'makeFromFunction' to BiorthBasis:Spherical and BiorthBasis::Cylindrical
Martin D. Weinberg
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Wrong header file for progress bar fixed
Martin D. Weinberg
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Wrong header file for progress bar fixed (again, this time in Biorth2Ortho.H)
Martin D. Weinberg
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Wrong namespace for progress bar
Martin D. Weinberg
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Reduce the number of python function calls
Martin D. Weinberg
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Add GIL release to the makeFromFunction call
Martin D. Weinberg
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Fixed Jacobian in makeFromFunction, ooops
Martin D. Weinberg
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add a conditional disable of passing openmp flags on mac with clang
adrn
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fix mac math
michael-petersen
committed
Remove unneeded radial restriction
Martin D. Weinberg
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Merge branch 'Projection' of github.com:EXP-code/EXP into Projection
Martin D. Weinberg
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More fixes to Jacobian in makeFromFunction
Martin D. Weinberg
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Added quadrature drivers to BiorthBasis
Martin D. Weinberg
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Added defaults to params in makeFromFunction and computeQuadrature from BiorthBasis
Martin D. Weinberg
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Fixed range checking typo in BiorthBasis::makeFromFunction that was throwing an inappropriate runtime exception
Martin D. Weinberg
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Commits on Oct 15, 2025

Move fixes into Spherical::computeQuadrature for completeness
Martin D. Weinberg
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Fix one more dang Jacobian bug and simplify/speed up OpenMP loop
Martin D. Weinberg
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Commits on Oct 16, 2025

Added a boolean toggle allow makeFromFunction() to be a potential rather than a density field (the default)
Martin D. Weinberg
committed

Commits on Oct 17, 2025

Make sure that lambda closures do not throw exceptions inside the makeFromFunction and computeQuadrature member functions
Martin D. Weinberg
committed
Fix accidentally swapped potential/density toggle for Spherical
Martin D. Weinberg
committed
Add a derived class of EmpCylSL::AxiDisk that implements an axisymmetric pyDens by evaluating pyDens for phi=0
Martin D. Weinberg
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Appropriately scope variables so that static libraries can be built
Lee Newberg
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Fix scaling pythong functor
Martin D. Weinberg
committed

Commits on Oct 18, 2025

Update include/DiskModels.H

The9Cat
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Copilot
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Use const std::string& pyname to avoid unnecessary copies.
Martin D. Weinberg
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Merge branch 'PythonDeproject' of github.com:EXP-code/EXP into PythonDeproject
Martin D. Weinberg
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Implement two minimal build flavors
Martin D. Weinberg
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Update CMakeLists.txt

The9Cat
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Copilot
authored
A preliminary implementation of partition covariance
Martin D. Weinberg
committed

Commits on Oct 19, 2025

Cleanup up bindings for new variance members
Martin D. Weinberg
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Implementation of HDF5 writing
Martin D. Weinberg
committed
Fix storage assignment mistake in covariance arrays
Martin D. Weinberg
committed
Update expui/BiorthBasis.cc

The9Cat
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Copilot
authored
Update pyEXP/BasisWrappers.cc

The9Cat
and
Copilot
authored
Update pyEXP/BasisWrappers.cc

The9Cat
and
Copilot
authored
Minor updates following Copilot review
Martin D. Weinberg
committed
Merge branch 'covariance' of github.com:EXP-code/EXP into covariance
Martin D. Weinberg
committed
Implemented overload
Martin D. Weinberg
committed
Update pyEXP/BasisWrappers.cc

The9Cat
and
Copilot
authored
Update expui/BiorthBasis.cc

The9Cat
and
Copilot
authored
Change square to triangular allocation for storage efficiency
Martin D. Weinberg
committed
Merge branch 'covariance' of github.com:EXP-code/EXP into covariance
Martin D. Weinberg
committed
More dimensioning consistency fixes
Martin D. Weinberg
committed
Implementation of the CovarianceReader
Martin D. Weinberg
committed
Update pyEXP/BasisWrappers.cc

The9Cat
and
Copilot
authored
Update expui/BiorthBasis.cc

The9Cat
and
Copilot
authored
Some docstring corrections
Martin D. Weinberg
committed
Merge branch 'covariance' of github.com:EXP-code/EXP into covariance
Martin D. Weinberg
committed
Update pyEXP/BasisWrappers.cc

The9Cat
and
Copilot
authored
Update expui/BiorthBasis.cc

The9Cat
and
Copilot
authored
More minor fixes
Martin D. Weinberg
committed
Merge branch 'covariance' of github.com:EXP-code/EXP into covariance
Martin D. Weinberg
committed
Data was not copied to CovarianceReader internal array
Martin D. Weinberg
committed
Update expui/BiorthBasis.cc

The9Cat
and
Copilot
authored
Update expui/BiorthBasis.cc

The9Cat
and
Copilot
authored
Generalize type detection for covariance geometry
Martin D. Weinberg
committed
Merge branch 'covariance' of github.com:EXP-code/EXP into covariance
Martin D. Weinberg
committed
More minor fixes based on a Copilot review
Martin D. Weinberg
committed
Update expui/BiorthBasis.cc

The9Cat
and
Copilot
authored
Update expui/BiorthBasis.cc

The9Cat
and
Copilot
authored
Update expui/BiorthBasis.cc

The9Cat
and
Copilot
authored
Update expui/BiorthBasis.cc

The9Cat
and
Copilot
authored
Update expui/BiorthBasis.cc

The9Cat
and
Copilot
authored
Update pyEXP/BasisWrappers.cc

The9Cat
and
Copilot
authored
Update exputil/EmpCylSL.cc

The9Cat
and
Copilot
authored
Update expui/BiorthBasis.cc

The9Cat
and
Copilot
authored
Update pyEXP/BasisWrappers.cc

The9Cat
and
Copilot
authored
Update pyEXP/BasisWrappers.cc

The9Cat
and
Copilot
authored
More minor fixes based on a Copilot review
Martin D. Weinberg
committed
Update pyEXP/BasisWrappers.cc

The9Cat
and
Copilot
authored
Update pyEXP/BasisWrappers.cc

The9Cat
and
Copilot
authored

Commits on Oct 20, 2025

Update pyEXP/BasisWrappers.cc

The9Cat
and
Copilot
authored
Update include/EmpCylSL.H

The9Cat
and
Copilot
authored
Update expui/BiorthBasis.H

The9Cat
and
Copilot
authored
Simplify pcavar computation by separating the computation from expcoef
Martin D. Weinberg
committed
Merge branch 'covariance' of github.com:EXP-code/EXP into covariance
Martin D. Weinberg
committed
Use Eigen reduction for totalCounts accumulation
Martin D. Weinberg
committed
Remove default value for pybind11 overloads for covariance access
Martin D. Weinberg
committed
Update expui/BiorthBasis.cc

The9Cat
and
Copilot
authored
Remove getAccelArray in favor of a C++ overload of getAccel. Updates the pybind11 interface accordingly.
Martin D. Weinberg
committed
Clean up
Martin D. Weinberg
committed
Merge pull request #168 from EXP-code/minimalBuild
michael-petersen
authored
Added particle index to accumulate() members. Fixed Cylindrical calls with pcavar
Martin D. Weinberg
committed
Update pyEXP/BasisWrappers.cc

The9Cat
and
Copilot
authored
Minor formatting changes
Martin D. Weinberg
committed

Commits on Oct 21, 2025

Adds support for installing public include libraries
Martin D. Weinberg
committed
Merge branch 'covariance' of github.com:EXP-code/EXP into covariance
Martin D. Weinberg
committed
Merge pull request #167 from EXP-code/PythonDeproject
michael-petersen
authored
Merge branch 'devel' into conditional-openmp-mac
michael-petersen
authored

Commits on Oct 23, 2025

Use double quotes rather than angle brackets for including headers in EXP source
Martin D. Weinberg
committed
cmake: add more headers used from public interface
lgarrison
committed
Merge pull request #171 from Leengit/static_library
The9Cat
authored
Merge pull request #172 from lgarrison/more-install-headers
The9Cat
authored
Merge branch 'devel' into getAccelVector
Martin D. Weinberg
committed
More separation of interface and translation units; added matrix input to getAccel(); both vector and matrix input interace is checked against scalar version
Martin D. Weinberg
committed
Merge branch 'getAccelVector' of github.com:EXP-code/EXP into getAccelVector
Martin D. Weinberg
committed
Merge branch 'devel' into getAccelVector
The9Cat
authored
Newly added implementions, separated from definition headers
Martin D. Weinberg
committed
Merge branch 'getAccelVector' of github.com:EXP-code/EXP into getAccelVector
Martin D. Weinberg
committed
Comment out Hankel.cc
Martin D. Weinberg
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Merge pull request #170 from EXP-code/getAccelVector
The9Cat
authored
Added some terse documentation for the new minimal build options
Martin D. Weinberg
committed

Commits on Oct 24, 2025

Implemented complex covariance with the option of setting float4 complex values
Martin D. Weinberg
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Some minor logic fixes for EmpCylSL
Martin D. Weinberg
committed

Commits on Oct 25, 2025

Remove an overlooked debug line
Martin D. Weinberg
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Commits on Oct 26, 2025

Implemente HDF5 compression
Martin D. Weinberg
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Remove debug lines
Martin D. Weinberg
committed
Decreased granularity of HDF5 stanzas to allow the compressor to be efficient
Martin D. Weinberg
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Removed some debugging output; checked against original version
Martin D. Weinberg
committed
Restore 1MB as the default chunk size
Martin D. Weinberg
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Added Python doc strings
Martin D. Weinberg
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Commits on Oct 27, 2025

Fixed loop misorder in complex covariance accumulation
Martin D. Weinberg
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Commits on Oct 28, 2025

Remove a noisy DEBUG line
Martin D. Weinberg
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Commits on Oct 29, 2025

More debug output removal
Martin D. Weinberg
committed

Commits on Oct 30, 2025

Remove some unused Cylindrical parameters and update the attribute output
Martin D. Weinberg
committed

Commits on Nov 1, 2025

BiorthBasis: use Eigen::Ref for getAccel inputs
lgarrison
committed

Commits on Nov 2, 2025

Add KD density estimation utility
Martin D. Weinberg
committed
Fixed a few errors in the PSPhdf5 version of the ParticleReader
Martin D. Weinberg
committed
Merge pull request #173 from lgarrison/getAccel-api
The9Cat
authored

Commits on Nov 3, 2025

Added defaults for 'verbose'
Martin D. Weinberg
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Fix override binding for KDdensity::getDensityAtPoint()
Martin D. Weinberg
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Fix up restarts of ParticleReader to restore initial file
Martin D. Weinberg
committed
Compute KDE density in real units; allow verbose flag to toggle restart message
Martin D. Weinberg
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Commits on Nov 4, 2025

Add sech2 toggle for gendisk
Martin D. Weinberg
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Change to keep gcc 15.x happy
Martin D. Weinberg
committed

Commits on Nov 5, 2025

Fix sampT default for Cylindrical
Martin D. Weinberg
committed
Merge branch 'covariance' of github.com:EXP-code/EXP into covariance
Martin D. Weinberg
committed
Added enableCoefCovariance() member function to override the 'pcavar' and 'subsamp' config tags. Also, double checked 'subsamp' logic to enforce nonzero-sized samples.
Martin D. Weinberg
committed

Commits on Nov 6, 2025

Fix typo in enableCoefCovariance for Spherical
Martin D. Weinberg
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Restore the original default of TRUE for ENABLE_UTILS to allow the EXP unit tests to run more fully
Martin D. Weinberg
committed

Commits on Nov 7, 2025

Check for existence of model file if file type 0 is selected
Martin D. Weinberg
committed

Commits on Nov 10, 2025

Remove some cruft
Martin D. Weinberg
committed

Commits on Nov 11, 2025

Fixed halo covariance MPI type mistake
Martin D. Weinberg
committed

Commits on Nov 12, 2025

pyEXP: add get_shared_ptr_capsule() to BiorthBasis and Coefs
lgarrison
committed

Commits on Nov 13, 2025

Added covariance computation for the Cube
Martin D. Weinberg
committed
Missing stanza for deducing Cube coefficients
Martin D. Weinberg
committed
More Cube updates for BiorthBasis
Martin D. Weinberg
committed
Comment in typo only [no CI]
Martin D. Weinberg
committed

Commits on Nov 14, 2025

Commits on Nov 16, 2025

Typo in index bounds fixed
Martin D. Weinberg
committed
Remove unused loop variable
Martin D. Weinberg
committed
Added covariance toggle to Cube
Martin D. Weinberg
committed

Commits on Nov 18, 2025

Commits on Nov 19, 2025

Fix minor initialization bug for Cube covariance
Martin D. Weinberg
committed