restructured repository by JensWehner · Pull Request #127 · microsoft/skala

Jens (JensWehner) · 2026-08-24T11:14:58Z

Restructure the repository around four clearly owned components while limiting published artifacts to the Skala runtime package:

skala: publishable ASE, PySCF, and GPU4PySCF runtime
model: trainable model definition and compiled-model examples
gauxc: GauXC integration, exporters, native examples, and documentation
benchmark for the creation of benchmarks
docs: documentation for the website.

also a few typing fixes, dispersion handling and usage of small gpu runners as enabled in #125

Copilot

Pull request overview

Restructures the repository into separately owned runtime, model, GauXC, and documentation components while limiting published artifacts to the Skala runtime.

Changes:

Separates development tooling into skala_model, skala_gauxc, and skala_benchmark.
Updates packaging, release validation, CI, native examples, and documentation paths.
Adds runtime, model, integration, and benchmark tests and utilities.

Reviewed changes

Copilot reviewed 83 out of 333 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
`tools/check_release_artifacts.py`	Validates release contents.
`tools/build_release.py`	Builds component-aware releases.
`src/skala/gauxc/__init__.py`	Removes old GauXC namespace.
`skala/tests/test_xc_integrator.py`	Tests XC integration.
`skala/tests/test_traditional.py`	Tests traditional functionals.
`skala/tests/test_scf_retry.py`	Tests SCF retries.
`skala/tests/test_model_chunking.py`	Tests model chunking.
`skala/tests/test_memory_estimators.py`	Tests memory estimates.
`skala/tests/test_hash_pinning.py`	Tests checkpoint hashes.
`skala/tests/test_evaluation.py`	Tests evaluation policy.
`skala/tests/test_enhancement_factor.py`	Tests spin symmetry.
`skala/tests/test_download_model.py`	Updates example path.
`skala/tests/test_backend.py`	Tests NumPy conversion.
`skala/tests/test_ase.py`	Tests ASE integration.
`skala/tests/ridders.py`	Adds finite-difference helpers.
`skala/tests/__init__.py`	Defines test package.
`skala/src/skala/utils/torch_allocator.py`	Integrates PyTorch/CuPy allocation.
`skala/src/skala/utils/__init__.py`	Defines utility package.
`skala/src/skala/typing.py`	Adds shared type aliases.
`skala/src/skala/pyscf/utils.py`	Adds PySCF version check.
`skala/src/skala/pyscf/grids.py`	Adds cached Skala grids.
`skala/src/skala/pyscf/features.py`	Adds runtime feature generation.
`skala/src/skala/pyscf/evaluation.py`	Defines evaluation requirements.
`skala/src/skala/pyscf/backend.py`	Normalizes CPU/GPU backends.
`skala/src/skala/py.typed`	Marks typed runtime package.
`skala/src/skala/gpu4pyscf/grids.py`	Adds GPU grid caching.
`skala/src/skala/functional/base.py`	Defines runtime functional base.
`skala/src/skala/functional/_hashes.py`	Pins checkpoint hashes.
`skala/src/skala/functional/__init__.py`	Removes trainable-model export.
`skala/src/skala/features.py`	Defines runtime features.
`skala/src/skala/dispersion.py`	Normalizes D3 backends.
`skala/src/skala/ase/__init__.py`	Exposes ASE calculator.
`skala/src/skala/__init__.py`	Defines runtime package metadata.
`skala/pyproject.toml`	Configures runtime distribution.
`skala/pixi.toml`	Configures runtime Pixi package.
`skala/LICENSE.txt`	Adds runtime license.
`skala/conftest.py`	Updates collection paths.
`README.md`	Documents four components.
`pyproject.toml`	Centralizes lint/type configuration.
`model/tests/test_utils.py`	Updates model utility imports.
`model/tests/test_traced_model_comparison.py`	Uses model namespace.
`model/tests/test_model.py`	Uses model namespace.
`model/src/skala_model/utils/symmetric_contraction.py`	Updates utility import.
`model/src/skala_model/utils/pad_ragged.py`	Adds ragged tensor utilities.
`model/src/skala_model/utils/irreps.py`	Updates namespace documentation.
`model/src/skala_model/utils/cg.py`	Adds coefficient utilities.
`model/src/skala_model/utils/__init__.py`	Defines utility package.
`model/src/skala_model/model.py`	Moves trainable model.
`model/src/skala_model/layers.py`	Moves neural layers.
`model/src/skala_model/__init__.py`	Exposes trainable model.
`model/examples/fortran/ftorch_integration/CMakeLists.txt`	Adds FTorch build.
`model/examples/fortran/ftorch_integration/cmake/skala-ftorch.cmake`	Fetches FTorch.
`model/examples/fortran/ftorch_integration/cmake/skala-dep-versions.cmake`	Pins FTorch.
`model/examples/fortran/ftorch_integration/.gitignore`	Ignores generated assets.
`model/examples/cpp/cpp_integration/README.md`	Updates build path.
`model/examples/cpp/cpp_integration/prepare_inputs.py`	Uses model namespace.
`model/examples/cpp/cpp_integration/download_model.py`	Downloads example models.
`model/examples/cpp/cpp_integration/CMakeLists.txt`	Adds C++ build.
`model/examples/cpp/cpp_integration/.gitignore`	Ignores generated assets.
`model/conftest.py`	Adds model fixtures.
`gauxc/UPSTREAM.md`	Documents upstream location.
`gauxc/tests/test_gauxc_export.py`	Uses GauXC namespace.
`gauxc/src/skala_gauxc/__init__.py`	Exposes exporter API.
`gauxc/examples/fortran/gauxc_integration/CMakeLists.txt`	Adds Fortran example build.
`gauxc/examples/fortran/gauxc_integration/cmake/skala-hdf5.cmake`	Finds Fortran HDF5.
`gauxc/examples/fortran/gauxc_integration/cmake/skala-gauxc.cmake`	Configures GauXC.
`gauxc/examples/fortran/gauxc_integration/cmake/skala-flap.cmake`	Configures FLAP.
`gauxc/examples/fortran/gauxc_integration/cmake/skala-dep-versions.cmake`	Pins native dependencies.
`gauxc/examples/fortran/gauxc_integration/.gitignore`	Ignores build outputs.
`gauxc/examples/cpp/gauxc_integration/CMakeLists.txt`	Adds C++ GauXC build.
`gauxc/examples/cpp/gauxc_integration/cmake/skala-sdftd3.cmake`	Configures s-dftd3.
`gauxc/examples/cpp/gauxc_integration/cmake/skala-hdf5.cmake`	Configures HDF5.
`gauxc/examples/cpp/gauxc_integration/cmake/skala-gauxc.cmake`	Configures GauXC.
`gauxc/examples/cpp/gauxc_integration/cmake/skala-eigen3.cmake`	Configures Eigen.
`gauxc/examples/cpp/gauxc_integration/cmake/skala-dep-versions.cmake`	Pins C++ dependencies.
`gauxc/examples/cpp/gauxc_integration/cmake/skala-cli11.cmake`	Configures CLI11.
`gauxc/examples/cpp/gauxc_integration/.gitignore`	Ignores build outputs.
`gauxc/examples/c/gauxc_integration/CMakeLists.txt`	Adds C GauXC build.
`gauxc/examples/c/gauxc_integration/cmake/skala-hdf5.cmake`	Configures C HDF5.
`gauxc/examples/c/gauxc_integration/cmake/skala-gauxc.cmake`	Configures GauXC.
`gauxc/examples/c/gauxc_integration/cmake/skala-dep-versions.cmake`	Pins C dependencies.
`gauxc/examples/c/gauxc_integration/cmake/skala-argtable3.cmake`	Configures Argtable3.
`gauxc/examples/c/gauxc_integration/.gitignore`	Ignores build outputs.
`gauxc/docs/scripts/export-h5.py`	Uses exporter namespace.
`gauxc/docs/index.rst`	Adds GauXC documentation index.
`gauxc/docs/gauxc.bib`	Adds GauXC references.
`gauxc/docs/conf.py`	Configures GauXC Sphinx site.
`gauxc/docs/api/macros.rst`	Documents GauXC macros.
`gauxc/docs/api/index.rst`	Adds API index.
`gauxc/docs/api/exceptions.rst`	Documents error APIs.
`gauxc/docs/api/cmake.rst`	Updates example includes.
`gauxc/conftest.py`	Adds GauXC test fixture.
`docs/site/pyscf/singlepoint.ipynb`	Adds PySCF tutorial.
`docs/site/pyscf/scf_settings.ipynb`	Adds SCF settings tutorial.
`docs/site/pyscf/gpu4pyscf.rst`	Documents GPU usage.
`docs/site/model-card/skala-1.1.rst`	Updates license path.
`docs/site/model-card/skala-1.0.rst`	Updates license path.
`docs/site/model-card/index.rst`	Adds older-model index.
`docs/site/installation.rst`	Adds installation guide.
`docs/site/index.rst`	Links GauXC site.
`docs/site/conf.py`	Updates documentation paths.
`docs/site/benchmarks.rst`	Updates benchmark commands.
`docs/site/_ext/benchmark_report.py`	Uses benchmark namespace.
`docs/benchmark/tests/utils.py`	Adds benchmark test helpers.
`docs/benchmark/tests/test_workflow.py`	Updates workflow imports.
`docs/benchmark/tests/test_runner.py`	Updates runner imports.
`docs/benchmark/tests/test_report.py`	Updates report paths.
`docs/benchmark/tests/test_orchestrator.py`	Updates orchestrator imports.
`docs/benchmark/tests/test_metrics.py`	Updates metric imports.
`docs/benchmark/tests/test_docs.py`	Updates extension path.
`docs/benchmark/tests/test_dataset.py`	Updates dataset namespace.
`docs/benchmark/tests/test_cli.py`	Updates CLI namespace.
`docs/benchmark/tests/test_ao_screening_benchmark.py`	Uses local helpers.
`docs/benchmark/tests/__init__.py`	Defines benchmark tests.
`docs/benchmark/src/skala_benchmark/timing.py`	Updates references.
`docs/benchmark/src/skala_benchmark/schema/measurements.py`	Updates schema references.
`docs/benchmark/src/skala_benchmark/schema/environment.py`	Defines environment schema.
`docs/benchmark/src/skala_benchmark/schema/__init__.py`	Defines schema package.
`docs/benchmark/src/skala_benchmark/runner.py`	Moves benchmark runner.
`docs/benchmark/src/skala_benchmark/report/prose.py`	Adds report prose rendering.
`docs/benchmark/src/skala_benchmark/report/data.py`	Updates report imports.
`docs/benchmark/src/skala_benchmark/report/_normalize.py`	Adds report normalization.
`docs/benchmark/src/skala_benchmark/report/__init__.py`	Exposes report generation.
`docs/benchmark/src/skala_benchmark/README.md`	Updates documentation link.
`docs/benchmark/src/skala_benchmark/protocol.py`	Defines benchmark protocol.
`docs/benchmark/src/skala_benchmark/orchestrator.py`	Moves benchmark orchestration.
`docs/benchmark/src/skala_benchmark/node_info.py`	Updates schema import.
`docs/benchmark/src/skala_benchmark/models.py`	Defines benchmark records.
`docs/benchmark/src/skala_benchmark/metrics.py`	Updates metric references.
`docs/benchmark/src/skala_benchmark/fetch.py`	Updates dataset references.
`docs/benchmark/src/skala_benchmark/dataset.py`	Updates dataset namespace.
`docs/benchmark/src/skala_benchmark/collect_results.py`	Updates collection imports.
`docs/benchmark/src/skala_benchmark/__main__.py`	Updates benchmark CLI.
`docs/benchmark/src/skala_benchmark/__init__.py`	Defines benchmark package.
`docs/benchmark/run_pyscf_vxc_precision_benchmark.py`	Adds precision benchmark.
`docs/benchmark/results/rotation_comparison/tables/validation-failures.csv`	Adds validation results.
`docs/benchmark/results/rotation_comparison/tables/status-summary.csv`	Adds status results.
`docs/benchmark/results/rotation_comparison/tables/runtime-statistics.csv`	Adds runtime results.
`docs/benchmark/results/rotation_comparison/tables/route-summary.csv`	Adds route results.
`docs/benchmark/results/rotation_comparison/tables/orientation-sensitivity-fits.csv`	Adds orientation fits.
`docs/benchmark/results/rotation_comparison/tables/memory-statistics.csv`	Adds memory results.
`docs/benchmark/results/rotation_comparison/tables/gradient-diagnostics.csv`	Adds gradient results.
`docs/benchmark/results/rotation_comparison/tables/environment-and-source-metadata.csv`	Adds benchmark metadata.
`docs/benchmark/reference/README.md`	Documents reference data.
`docs/benchmark/reference/prose.yaml`	Adds report prose.
`docs/benchmark/reference/measurements.json`	Adds LFS measurements.
`docs/benchmark/reference/environments.json`	Adds environment metadata.
`docs/benchmark/pyproject.toml`	Packages benchmark tooling.
`docs/benchmark/conftest.py`	Adds benchmark fixtures.
`CONTRIBUTING.md`	Updates contributor commands.
`AGENTS.md`	Documents new architecture.
`.pre-commit-config.yaml`	Updates mypy source paths.
`.gitignore`	Updates generated-file exclusions.
`.github/workflows/test.yml`	Adds component tests.
`.github/workflows/model-examples.yml`	Updates model example paths.
`.github/workflows/model-benchmark.yml`	Updates benchmark paths.
`.github/workflows/examples.yml`	Updates GauXC paths.
`.github/workflows/docs.yml`	Updates documentation artifact path.

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Stephanie Lanius (steph409) · 2026-08-26T10:02:26Z

+h5py = "*"
+
+[feature.component-sources.activation.env]
+PYTHONPATH = "$PIXI_PROJECT_ROOT/model/src:$PIXI_PROJECT_ROOT/gauxc/src:$PIXI_PROJECT_ROOT/docs/benchmark/src"


this looks.. hacky

made those folders packages, it is nearly not hacky anymore, only gauxc left, which will be removed soon #129

Stephanie Lanius (steph409)

a little bit hard to review because many things happen at once, the moving of files + the fixing to make the typechecker happy instead of ignoring the changes. tried to review, looks good!

…ntation

Jan Hermann (jhrmnn)

Looks good. Two questions:

Thinking about a small CI test ensuring the versions are the same across all packages?
Thinking about docs/site -> site?

Jens (JensWehner) · 2026-08-26T19:53:27Z

Looks good. Two questions:

Thinking about a small CI test ensuring the versions are the same across all packages?

Thinking about docs/site -> site?

added
moved docs/site -> website

Jens (JensWehner) requested a balanced review from Copilot August 24, 2026 11:15

Copilot started reviewing on behalf of Jens (JensWehner) August 24, 2026 11:15 View session

Copilot AI reviewed Aug 24, 2026

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Comment thread tools/check_release_artifacts.py

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