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Three-way Merge between pele-python's old main branch and the current branch - #52
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* replaces numpy.distutils-reliant build system with meson build system * updates broken and deprecated API calls * changes the default Cython version and language level to 3 * replaces PyQT4 with PyQT5 * generates .py and resource files made with PyQT tools at build time * adds pyproject.toml and environment.yml to help pip and conda manage dependencies * ensures ALL (but one) unittests pass without warnings (but two)
- configured the installation of headers (including some .pxd files) - added pele.get_include() function together making building new cpp potentials against pele easier
- added meson build system for compiled potentials, gui source generation couldn't figure out how to build the fortran_iso_c_bindings example with meson
LAMMPSPotential is a pure python potential class that uses the LAMMPS python API to compute energies and gradients using the run command. Requires LAMMPS at runtime. LAMMPSPotentialCPP extends the LAMMPS library at the c++ level and subclasses the pele BasePotential c++ class. It is typically much faster than the pure python version. Requires LAMMPS at build and run time.
…ork) Brings in the pele-python history since the two repositories diverged in 2019 (7da72ba), including farrelljd's Python 3 / NumPy / SciPy / SQLAlchemy / NetworkX updates, the PyQt5 port of the GUI and the LAMMPS interface, with their original commits. Conflict resolution: - Build system and source layout: this repository's (top-level meson.build, C++ in source/). pele-python's per-directory meson.build files, its move of source/ into pele/include and pele/sources, its CI workflow and environment.yml are not taken. The LAMMPS sources stay where pele-python put them for now. - GUI (pele/gui, examples/gui): pele-python's PyQt5 port, without its meson.build files. - Everything else: this repository's version where both sides changed the same lines, pele-python's changes elsewhere. optim_compatibility.py keeps only the engine.execute -> session.execute fix; database.py and README.rst stay as they were here. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
The merge of pele-python took its PyQt5 port of pele/gui wholesale. This reapplies this fork's own changes to those files as a three-way merge (base: pele-python c3cfa05c; ours: this fork; theirs: farrelljd's port). Before merging, the base and his versions were normalized with the tools this fork applied to these files (pyupgrade --py3-plus, black 22.10 -l 80), so formatting-only differences do not conflict. Conflicts, resolved: - connect_all.py: time.process_time() (this fork; time.clock was removed in Python 3.8) - dlg_params.py: QtWidgets.QMenu and hasattr(..., "items") (his; "iteritems" is Python 2) - graph_viewer.py: iterate graph.degree() directly (his; networkx >= 2 DegreeView has no .items()) - normalmode_browser.py: formatting only (this fork) - pymolwidget/pymolwidget.py: this fork's explicit imports, from PyQt5 instead of PyQt4 __init__.py and pymol_viewer.py keep this fork's versions. pele/gui/nebdlg.py stays deleted, as in this fork (unused). savenlowest.py gets his binary-mode pickle fix, which the merge dropped in a conflicting hunk. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
farrelljd's port removed the generated pele/gui *_ui.py and resources_rc.py files. Generate them at build time with pyuic5/pyrcc5 (from PyQt5) and install them into the package, behind a new 'gui' feature option (auto: built when the tools are found). Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> (cherry picked from commit 5f42838)
np.random.random_integers(0, 1) was inclusive of 1; its replacement np.random.randint(0, 1) always returns 0, so every edge got phase 0. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
pele-python keeps its C++ in pele/include and pele/sources; this repository keeps it in source/. Files moved unchanged: lammps_pele.h becomes source/pele/lammps_pele.hpp (this repository's header suffix), and the vendored LAMMPS/nlohmann JSON headers go to source/lammps. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Adapt farrelljd's LAMMPS interface from pele-python to this repository: - LAMMPSPotential overrides this repository's BasePotential signatures (const Array<double>& coordinates, Array<double>& gradient). - meson.build builds pele.potentials.lammps_pele_cython against the liblammps shipped in the lammps Python package, behind a 'lammps' feature option (auto: built when lammps and mpi.h are found). - pele.potentials exports LAMMPSPotential and have_lammps, using the compiled version when it is built and the pure Python one otherwise; pele.systems exports AtomicClusterLAMMPS. - Export modifiedfire_cpp from pele.optimize, which AtomicClusterLAMMPS uses. - The LAMMPS energy tests compare with pele's LJ to 10 decimal places instead of exactly; they differed by one ulp after minimization. - pyproject: a 'lammps' extra; README: how to install it. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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Closed in favor of a three-way merge |
- The python jobs pip install lammps[mpi], so the compiled LAMMPS potential is built and the LAMMPS tests run instead of being skipped. - Run the LAMMPS potential tests against the pure Python fallback as well as the exported (compiled) class. - SaveN.load was a classmethod without cls, so it raised TypeError; fix it, close the pickle files, and test save/load. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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Copilot review overview
🟡 Changes recommended
Critical LAMMPS, GUI worker, and example-runner issues remain unresolved.
Review effort: Lite
Findings: 5
Open (5)
What changed in this PR
This PR merges divergent Pele branches, modernizes the GUI to PyQt5, adds optional LAMMPS support, and updates compatibility fixes and tests.
Changes:
- Adds compiled and Python LAMMPS potentials and systems.
- Migrates GUI components and generated forms to PyQt5.
- Expands regression tests, examples, and CI/build configuration.
| File | Description |
|---|---|
source/pele/lammps_pele.hpp |
Declares the compiled LAMMPS adapter. |
source/lammps/nlohmann/json_fwd.hpp |
Adds JSON forward declarations. |
source/lammps/json_fwd.h |
Exposes LAMMPS JSON types. |
source/lammps_pele.cpp |
Implements LAMMPS evaluation; sorting and MPI correctness issues remain. |
README.rst |
Documents GUI and LAMMPS installation. |
pyproject.toml |
Adds optional dependencies; isolated-build dependency handling needs correction. |
pele/utils/tests/test_disconnectivity_graph.py |
Configures headless plotting tests. |
pele/utils/optim_compatibility.py |
Updates SQLAlchemy compatibility. |
pele/thermodynamics/_utils.py |
Supports minima-only calculations. |
pele/thermodynamics/_normalmodes.py |
Removes debug output. |
pele/systems/tests/test_lammps_atomic_cluster.py |
Tests the LAMMPS cluster system. |
pele/systems/lammps_atomic_cluster.py |
Adds LAMMPS-backed atomic clusters. |
pele/systems/__init__.py |
Exports optional LAMMPS support. |
pele/storage/tests/test_savenlowest.py |
Tests SaveN persistence. |
pele/storage/savenlowest.py |
Fixes binary pickle persistence. |
pele/rates/tests/test_linalg.py |
Tests repeated rate calculations. |
pele/rates/_rates.py |
Tracks solver initialization. |
pele/potentials/xyspin.py |
Updates deprecated NumPy randomness. |
pele/potentials/tests/test_lammps_potential.py |
Tests LAMMPS potential implementations. |
pele/potentials/tests/test_hs_wca_cpp.py |
Updates Python 3 compatibility. |
pele/potentials/lammps_potential_python.py |
Adds the Python fallback; atom sorting can corrupt gradient ordering. |
pele/potentials/lammps_pele_cython.pyx |
Adds the compiled Python wrapper. |
pele/potentials/fortran/morse.f90 |
Initializes the Morse cutoff shift. |
pele/potentials/__init__.py |
Detects and exports LAMMPS support. |
pele/optimize/_quench.py |
Exports modified FIRE. |
pele/optimize/_modified_fire_cpp.pxd |
Removes an unused import. |
pele/mindist/backward_compatibility.py |
Updates Python 3 iteration syntax. |
pele/landscape/tests/test_connect_manager.py |
Tests connection-pair exhaustion. |
pele/landscape/connect_manager.py |
Adds deterministic pair fallback selection. |
pele/gui/ui/ui_takestep_explorer.ui |
Updates PyQt5 widget metadata. |
pele/gui/ui/ui_takestep_explorer.py |
Removes obsolete generated PyQt4 code. |
pele/gui/ui/ui_normalmode_explorer.ui |
Updates PyQt5 metadata. |
pele/gui/ui/ui_normalmode_explorer.py |
Removes obsolete generated PyQt4 code. |
pele/gui/ui/ui_neb_explorer.ui |
Updates resource metadata. |
pele/gui/ui/ui_neb_explorer.py |
Removes obsolete generated PyQt4 code. |
pele/gui/ui/show3d_with_slider_ui.ui |
Updates PyQt5 widget metadata. |
pele/gui/ui/show3d_with_slider_ui.py |
Removes obsolete generated PyQt4 code. |
pele/gui/ui/rate_gui.py |
Removes obsolete generated PyQt4 code. |
pele/gui/ui/nebbrowser.ui |
Updates PyQt5 metadata. |
pele/gui/ui/nebbrowser.py |
Removes obsolete generated PyQt4 code. |
pele/gui/ui/mplwidget.py |
Migrates Matplotlib Qt integration. |
pele/gui/ui/graph_view_ui.ui |
Updates PyQt5 metadata. |
pele/gui/ui/graph_view_ui.py |
Removes obsolete generated PyQt4 code. |
pele/gui/ui/dgraph_dlg.py |
Migrates disconnectivity graph dialogs. |
pele/gui/ui/dgraph_browser.ui |
Updates PyQt5 metadata. |
pele/gui/ui/dgraph_browser.py |
Removes obsolete generated PyQt4 code. |
pele/gui/ui/cv_viewer_ui.ui |
Updates layout and PyQt5 metadata. |
pele/gui/ui/cv_viewer_ui.py |
Removes obsolete generated PyQt4 code. |
pele/gui/ui/connect_run_ui.ui |
Updates PyQt5 widget metadata. |
pele/gui/ui/connect_run_ui.py |
Removes obsolete generated PyQt4 code. |
pele/gui/ui_params.py |
Removes obsolete generated PyQt4 code. |
pele/gui/tests/test_workers.py |
Adds worker lifecycle tests. |
pele/gui/tests/test_viewers.py |
Adds viewer regression tests. |
pele/gui/tests/test_main.py |
Adds main-window regression tests. |
pele/gui/tests/conftest.py |
Configures headless Qt tests. |
pele/gui/takestep_explorer.py |
Migrates the take-step explorer. |
pele/gui/show3d.py |
Migrates the OpenGL viewer. |
pele/gui/show3d_with_slider.py |
Improves animation handling. |
pele/gui/README |
Updates GUI build instructions. |
pele/gui/pymolwidget/pymolwidget.py |
Migrates the PyMOL widget. |
pele/gui/normalmode_browser.py |
Migrates the normal-mode browser. |
pele/gui/neb_explorer.py |
Migrates the NEB explorer. |
pele/gui/MainWindow.ui |
Updates custom-widget metadata. |
pele/gui/graph_viewer.py |
Migrates graph viewing APIs. |
pele/gui/double_ended_connect_runner.py |
Improves worker lifecycle handling. |
pele/gui/dlg_params.py |
Migrates parameter dialogs. |
pele/gui/connect_run_dlg.py |
Migrates connection-run dialogs. |
pele/gui/connect_explorer_ui.ui |
Updates PyQt5 metadata. |
pele/gui/connect_explorer_ui.py |
Removes obsolete generated PyQt4 code. |
pele/gui/connect_explorer_dlg.py |
Migrates the connection explorer. |
pele/gui/connect_all.py |
Improves connection lifecycle handling. |
pele/gui/bhrunner.py |
Improves basin-hopping worker handling. |
pele/gui/_rate_gui.py |
Adds rate validation and cancellation. |
pele/gui/_list_views.py |
Updates Qt models and selection handling. |
pele/gui/_cv_viewer.py |
Adds viewer worker handling; result-queue liveness logic can drop successful results. |
pele/angleaxis/rigidbody.py |
Escapes LaTeX backslashes. |
pele/angleaxis/aatopology.py |
Updates legacy Python syntax. |
meson.options |
Adds GUI and LAMMPS build options. |
meson.build |
Builds LAMMPS support and generated GUI forms. |
examples/new_potential/fortran_potential/mypotential.py |
Fixes relative extension imports. |
examples/new_potential/fortran_iso_c_bindings/mypotential.pyx |
Uses integer division for atom counts. |
examples/new_potential/fortran_iso_c_bindings/Makefile |
Updates compiler flags. |
examples/new_potential/cython_potential/mypotential.pyx |
Uses explicit double types. |
examples/new_potential/cpp_potential/mypotential.pyx |
Simplifies the Cython example. |
examples/new_potential/c_potential/mypotential.pyx |
Removes obsolete build documentation. |
examples/gui/ljsystem.py |
Migrates the GUI example to PyQt5. |
examples/gui/lammps_ljsystem.py |
Adds a LAMMPS GUI example; input path is not script-relative. |
examples/gui/lammps_ljsystem.in |
Adds LAMMPS LJ configuration. |
examples/gui/lammps_bljsystem.py |
Adds a binary LAMMPS GUI example; input path is not script-relative. |
examples/gui/lammps_bljsystem.in |
Adds binary LAMMPS configuration. |
examples/gui/bljsystem.py |
Migrates the BLJ example to PyQt5. |
examples/gui/_blj_dialog.py |
Regenerates the BLJ dialog. |
examples/_run_all_examples.sh |
Runs examples; including interactive GUI examples can block or fail headless execution. |
.gitignore |
Updates generated-file handling. |
.github/workflows/test.yml |
Installs LAMMPS in CI. |
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…xamples - LAMMPS potentials (compiled and Python) turn off LAMMPS's spatial atom sorting, which reordered atoms during run 0 so the returned gradient no longer matched the input coordinates, and reject multi-rank MPI runs, where each rank holds only its own atoms. Both go through prepare_lammps(). - GetThermodynamicInfoParallelQT.poll: a worker's last result can arrive between the empty() check and the liveness check; check the queue again before reporting a lost result. - _run_all_examples.sh no longer runs the interactive GUI examples. - The LAMMPS GUI examples read their .in file from the script's directory. - Tests: gradient vs numerical gradient with LAMMPS's default sorting, and the worker race. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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Goals
Editing this for clarity because this is a fairly involved merge. The goal of this merge is to merge the divergent branches of pele into a working version that passes all tests. and make sure everyone's commits are reflected on the final version. The fork happened between the 2 diverging branches happened in 2019, and the only new changes on pele-python came in 2025 that have now been merged into this
Description
The merge was done by
Forking the martiniani-lab branch, and merging it with pele-python's old branch, giving precedence to the martiniani-lab one in case of conflicts
Patching the GUI and lammps changes along with any extra issues that came along. I verified that the gui works
Submitting a PR back to the martininiani-lab branch
afaik all functionality has been preserved and all tests pass (both python and C++). I checked the GUI works properly with the PyQT5 update. Lammps tests pass and are covered (which is a very cool addition thanks to @farrelljd)