Add support for (transparently) reading binary sparseX files - #686

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bernstei wants to merge 114 commits into

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binary_sparseX

Commits on May 13, 2025

Add support for (transparently) reading binary sparseX files. Also extend default line length in xyz.c
bernstei
committed
c3f3348

Commits on Jan 29, 2026

Fix memory leak when initializing GAP by finalising parse_cur_data after xml parsing (also vdW)

bernstei
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albapa
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81cd1e0
updated module versions for archer2 makefile

James Darby
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albapa
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b362d33
Update README.md

computerscienceiscool
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4381ad4
Update System.f95

gabor1
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75c4989
Update Dictionary.f95

gabor1
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albapa
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1147a94
Update Dictionary.f95

gabor1
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albapa
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f368b8c
Update Makefile.archer2

gabor1
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albapa
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dd4438c
Update python and cibuildwheel versions

ATM-Jahid
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albapa
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a4b0d62
Revert the dockerfile

ATM-Jahid
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albapa
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4264fc2
add upper version bound for f90wrap

jameskermode
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albapa
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3def35b
TST: update for recent ASE release I/O beahviour change

jameskermode
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albapa
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ad724c4
Lower f90wrap version upper bound

ATM-Jahid
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albapa
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30e4fc7
Do not use numpy 2

ATM-Jahid
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albapa
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1e3a472
force -> forces property name

jameskermode
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albapa
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3c3f6e6
Omit manylinux2010 (EOL) from build-wheels

ATM-Jahid
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albapa
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49b198d
Make manylinux2014 the default in openblas_support

ATM-Jahid
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albapa
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2008409
Update Dockerfile

ATM-Jahid
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albapa
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6205420
Change rdkit-pypi to rdkit in Dockerfile

ATM-Jahid
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albapa
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256b89d
updating the version of GAP

sujona
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albapa
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7e45157
MAINT: Fix return type errors from macros

HaoZeke
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albapa
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45b8f5d
updating the version of GAP (#659)
albapa
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efcad30
Arch file for ARM MacOS with OpenMPI

stenczelt
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albapa
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e2e46f0
Added SphericalIterative() and GradSphericalIterative() to angular_functions.f95 (#619)

lraybould
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albapa
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6c20bba
update version bound on f90wrap.

jameskermode
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albapa
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eb6122a
removed test program
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7dda7fb
remove references of F95
albapa
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b057d7b
changed references of F95 to F90
albapa
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c260a21
changed references of F95 to F90
albapa
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0cfb1cf
changed references of F95 to F90
albapa
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401a2eb
renamed source files to have F90 extension
albapa
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0b22764
renamed source files to have F90 extension
albapa
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5c83c03
renamed source files to have F90 extension
albapa
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9852203
renamed source files to have F90 extension
albapa
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4cb187d
renamed source files to have F90 extension
albapa
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8405c09
renamed source files to have F90 extension
albapa
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870cac4
renamed source files to have F90 extension
albapa
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a19733b
renamed source files to have F90 extension
albapa
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dd52014
renamed source files to have F90 extension
albapa
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dacd6f6
renamed source files to have F90 extension
albapa
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f9a5a7a
renamed source files to have F90 extension
albapa
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57bc236
renamed source files to have F90 extension
albapa
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df04550
changed references of F95 to F90
albapa
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ecc9cfb
remove references of F95
albapa
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ccf5e9d
changed references of F95 to F90
albapa
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812f0bf
changed references of F95 to F90
albapa
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080d4bf
changed preprocessor directive to conventional __APPLE__
albapa
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14f7ac3
remove references of F95
albapa
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d31a222
added meson files
albapa
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ea68453
added missing error files
albapa
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35f1a38
temporarily change file (MacOS is NOT case sensitive)
albapa
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a606d35
change files to F90 (MacOS is NOT case sensitive)
albapa
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d2e3073
removed tmp file
albapa
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9acda23
sorted tmp files
albapa
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395fa64
sorted tmp files
albapa
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d2fbcde
updating the version of GAP and fox
albapa
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6f9605d
Update cutil.c (#683)

green-br
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albapa
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46ef45a
Complete meson-python build system migration with test fixes

authored and
albapa
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3195d40
Modernize GitHub CI workflows for meson build system

authored and
albapa
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e960f83
Update GAP submodule and relax gap_fit test tolerances

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albapa
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4519bdf
Add f90wrap_stub.F90 to libAtoms build for standalone compilation

authored and
albapa
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908b0dd
Fix Python version requirement to match CI test matrix

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albapa
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eec6720
Add comment about f90wrap dependency in pyproject.toml

authored and
albapa
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3e0e1f0
Update f90wrap dependency comment with latest fixes

authored and
albapa
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dc8deea
Fix wheel build dependencies: openblas and gfortran

authored and
albapa
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061f78a
Add debug output and fix paths for wheel build dependencies

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albapa
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b568087
Fix openblas and gfortran detection for wheel builds

authored and
albapa
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224e4de
Build QUIP libraries before building quippy wheel

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albapa
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36caab3
Fix CIBW_BEFORE_BUILD to build QUIP from correct directory

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albapa
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c822919
Install f90wrap and build QUIP in CIBW_BEFORE_ALL

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albapa
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564e776
CI working locally

jameskermode
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albapa
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c219407
Attempt to fix macosx CI builds

jameskermode
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albapa
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75bf869
Link gfortran

jameskermode
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albapa
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2cff2b2
Fix CI workflows: update f90wrap repo and remove editable installs

authored and
albapa
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1358741
Fix macOS gfortran detection for f90wrap installation

jameskermode
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albapa
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0f745a0
Skip Python 3.7 and 3.8 in wheel builds

jameskermode
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albapa
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6c0c422
CI: WIP on wheel building

jameskermode
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albapa
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6048b7d
do not include f90wap_stub in libAtoms build, since it shadows quippy abort calls

jameskermode
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albapa
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f470fd3
Revert "do not include f90wap_stub in libAtoms build, since it shadows quippy abort calls"

jameskermode
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albapa
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a46492f
Fix f90wrap_abort symbol conflict causing GAP/SOAP test failures

authored and
albapa
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a215fc0
Fix f90wrap_abort symbol conflict causing test failures

authored and
albapa
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763872f
Fix NumPy 1.25+ deprecation warning in potential.py

authored and
albapa
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582c9de
Fix CI: Allow undefined f90wrap_abort in executables

authored and
albapa
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c2c8b93
Fix symbol resolution issue by loading _quippy with RTLD_GLOBAL

authored and
albapa
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1832289
Workaround for f90wrap overload resolution bug in convert.py

authored and
albapa
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6a34def
Fix f90wrap overload resolution by using fixed branch

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albapa
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9244b52
Update f90wrap to use fix-overload-resolution-order branch

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albapa
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c5e0f5c
Fix build-wheels CI failures on Linux and macOS

authored and
albapa
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215a21a
Fix build-wheels path issue for QUIP root directory

authored and
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65bcf29
Fix build-wheels CI failures on Linux and macOS

authored and
albapa
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e7f79a6
Fix build-wheels: Build QUIP natively before cibuildwheel

authored and
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16f5660
Fix build-wheels: Build QUIP in containers with simple cd ..

authored and
albapa
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f2fa1ca
Fix build-wheels workflow by using CIBW_BEFORE_BUILD with script

authored and
albapa
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9113859
Fix CIBW_BEFORE_BUILD to use inline script instead of external file

authored and
albapa
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6183ea6
Build QUIP libraries before cibuildwheel and copy to quippy/

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albapa
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348b294
Fix openblas detection on macOS by setting PKG_CONFIG_PATH

authored and
albapa
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9daf0f4
skip enable_timing() because of name clash issue

jameskermode
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albapa
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469d89f
Revert "skip enable_timing() because of name clash issue"

jameskermode
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albapa
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5efbd57
Fix wheel building workflow to build QUIP in isolated environments

authored and
albapa
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e5d6d57
Fix meson/ninja installation in cibuildwheel environments

authored and
albapa
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4c321ae
Fix openblas libdir detection for system library fallback

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14115cf
Add fallback to skip wheel repair on macOS if delocate fails

authored and
albapa
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de61814
Update .gitignore and README.md for meson build system

jameskermode
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albapa
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8423436
prepare for GHA macos-13 deprecation

jameskermode
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albapa
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a2ba453
Fix f90wrap finalizer bug: _initialise -> _finalise

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albapa
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74d3fa5
Remove finalizer patch now fixed upstream in f90wrap

authored and
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dfc6e5e
Reduce duplication and simplify meson build files

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albapa
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ef62c1f
Fix f90wrap install instruction in CLAUDE.md

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febd02b
Fix PyPI version override for tagged releases

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2e039fa
Temporarily disable docs and docker builds

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albapa
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b56e6fd
Fix macOS wheel bundling by setting DYLD_LIBRARY_PATH for delocate (#698)

authored and
albapa
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5ed244c
Add NumPy 2.x support with conditional dependencies (#701)

authored and
albapa
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160eec1
Fix missing CLI executables in quippy-ase wheel (#703) (#704)

authored and
albapa
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962d981
Get rid of libAtoms/lbfgs.f, now that it's supposed to be lbfgs.F (#708)

bernstei
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albapa
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1537995

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Commits

Commits on May 13, 2025

Commits on Jan 29, 2026