scirs 0.1.3__tar.gz

scirs-0.1.3/LICENSE.txt

@@ -0,0 +1,30 @@
+Copyright (c) 2026-2027 SciCore Developers.
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions
+are met:
+
+1. Redistributions of source code must retain the above copyright
+   notice, this list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above
+   copyright notice, this list of conditions and the following
+   disclaimer in the documentation and/or other materials provided
+   with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived
+   from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

scirs-0.1.3/PKG-INFO

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+Metadata-Version: 2.4
+Name: scirs
+Version: 0.1.3
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Intended Audience :: Science/Research
+Classifier: Intended Audience :: Developers
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Programming Language :: Rust
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Classifier: Programming Language :: Python :: 3.15
+Classifier: Topic :: Software Development :: Libraries
+Classifier: Topic :: Scientific/Engineering
+Classifier: Operating System :: Microsoft :: Windows
+Classifier: Operating System :: POSIX :: Linux
+Classifier: Operating System :: POSIX
+Classifier: Operating System :: Unix
+Classifier: Operating System :: MacOS
+Requires-Dist: rsnumpy>=1.2.5
+Requires-Dist: pooch ; extra == 'all'
+Requires-Dist: threadpoolctl ; extra == 'all'
+Requires-Dist: rsplotlib ; extra == 'all'
+Provides-Extra: all
+License-File: LICENSE.txt
+License-File: LICENSES_bundled.txt
+Summary: Fundamental algorithms for scientific computing in Python, built on rsnumpy
+Keywords: scientific,computing,linear-algebra,rsnumpy,rust
+Author: YJ-Niu
+Maintainer: SciCore Developers
+Requires-Python: >=3.12
+Description-Content-Type: text/x-rst; charset=UTF-8
+Project-URL: documentation, https://github.com/YJ-Niu/scicore#readme
+Project-URL: download, https://pypi.org/project/scirs/
+Project-URL: homepage, https://github.com/YJ-Niu/scicore
+Project-URL: source, https://github.com/YJ-Niu/scicore
+Project-URL: tracker, https://github.com/YJ-Niu/scicore/issues
+
+SciCore
+=======
+
+.. image:: https://img.shields.io/badge/powered%20by-rsnumpy-blue.svg
+  :target: https://github.com/YJ-Niu/rsnumpy
+
+**SciCore** is a port of `SciPy <https://github.com/scipy/scipy>`__ onto
+`rsnumpy <https://github.com/YJ-Niu/rsnumpy>`__ — a Rust-backed, NumPy-compatible
+array library.
+
+The import name stays ``scicore``, so it is a drop-in replacement::
+
+    pip install scirs
+    python -c "import scicore.linalg"
+
+Why
+---
+
+SciCore's compiled kernels are C, C++, Cython and Fortran. SciCore keeps the
+algorithms, migrates compiled kernels to Rust incrementally, and swaps the array
+backend from NumPy to rsnumpy. Until that migration is complete, some native
+extensions still use the upstream implementations. Two consequences worth
+knowing up front:
+
+- **No Python NumPy dependency at runtime.** Arrays are rsnumpy arrays. NumPy
+  remains a build-time dependency for the C/Cython extensions that have not yet
+  been ported.
+- **Native-kernel migration is ongoing.** Signal filtering kernels including
+  ``lfilter``, ``sosfilt``, ``upfirdn``, direct N-D ``correlate``,
+  ``convolve2d``/``correlate2d``, ``remez`` FIR design, spline filtering, and
+  2-D median filtering now run in Rust. FFTPACK's packed-spectrum convolution
+  kernels and convolution-kernel generation, as well as cluster VQ assignment
+  and cluster-mean updates, also run in Rust; other C, C++, Cython, and Fortran
+  production extensions are still being replaced. Regular-grid interpolation's
+  interval search and 2-D linear interpolation kernels, as well as reverse
+  Cuthill-McKee graph ordering and sparse-to-dense/distance-matrix graph
+  kernels, as well as least-squares Givens elimination, also run in Rust.
+  Sparse graph conversion adapters and sparse finite-difference column
+  grouping kernels are Rust-backed with Python adapters. Multidimensional
+  connected-component labeling and the one-dimensional rank-filter kernel
+  also run in Rust. The directed Hausdorff distance search kernel is Rust-backed
+  with its existing Python random-number and array API preserved. Boyett and
+  Patefield random contingency-table sampling and the Nolan stable-distribution
+  integration kernel also run in Rust.
+- **Recomputation over incremental update.** Where upstream keeps a factorisation
+  up to date with Givens rotations (``scicore.linalg.qr_update`` and friends), this
+  port recomputes the factorisation. The results match, but the complexity is
+  ``O(m n²)`` rather than ``O(m n)``. Each affected function says so in its
+  docstring.
+
+Status
+------
+
+This is a work in progress. Native kernels are still being migrated to Rust;
+until that is complete, some native extensions still use the upstream
+implementations. Treat the API as experimental and pin the version if you
+depend on it.
+
+Building from source
+--------------------
+
+The build is driven by **maturin**: it compiles the pyo3 crate in ``rust/``
+into the ``scicore._scicore_rs`` extension and packages the ``python/`` tree
+into a wheel.
+
+There is a helper that does the whole thing and installs the result into
+``.venv``::
+
+    ./build_wheel.sh
+
+Useful flags::
+
+    ./build_wheel.sh --debug        # debug build instead of release
+    ./build_wheel.sh --out-dir dist # where to put the wheel
+    ./build_wheel.sh --python /path/to/python
+
+To do it by hand::
+
+    pip install maturin
+    maturin build --release -i python -o dist
+    pip install dist/*.whl
+
+``build_wheel.sh`` also runs ``cargo fmt --check`` and ``cargo clippy`` before
+building, so a failing lint stops the build rather than shipping a wheel.
+
+Requirements: a Rust toolchain, Python >= 3.12.
+
+Development
+-----------
+
+Clone the repository::
+
+    git clone --recursive https://github.com/YJ-Niu/scicore.git
+
+The ``--recursive`` flag initializes the doc submodule (scipy-mathjax for
+formula rendering in the docs).
+
+Run the Rust unit tests from the workspace root::
+
+    cd rust
+    cargo test --workspace
+
+The repository's SciCore-owned Python tests live in ``test/`` and
+``tools/``. ``pytest.ini`` limits ``python -m pytest`` to those tests so the
+vendored upstream SciCore test corpus is not run as if it were a SciCore suite.
+The Python tests cover the rsnumpy migration and Rust-backed Python adapters;
+the Rust workspace tests cover each migrated kernel.
+
+Links
+-----
+
+- **Source code:** https://github.com/YJ-Niu/scicore
+- **Bug reports:** https://github.com/YJ-Niu/scicore/issues
+- **rsnumpy (array backend):** https://github.com/YJ-Niu/rsnumpy
+- **Upstream SciCore:** https://github.com/scicore-dev/scicore
+
+License
+-------
+
+BSD 3-Clause, matching upstream SciCore. See ``LICENSE.txt``.
+

scirs-0.1.3/README.rst

@@ -0,0 +1,120 @@
+SciCore
+=======
+
+.. image:: https://img.shields.io/badge/powered%20by-rsnumpy-blue.svg
+  :target: https://github.com/YJ-Niu/rsnumpy
+
+**SciCore** is a port of `SciPy <https://github.com/scipy/scipy>`__ onto
+`rsnumpy <https://github.com/YJ-Niu/rsnumpy>`__ — a Rust-backed, NumPy-compatible
+array library.
+
+The import name stays ``scicore``, so it is a drop-in replacement::
+
+    pip install scirs
+    python -c "import scicore.linalg"
+
+Why
+---
+
+SciCore's compiled kernels are C, C++, Cython and Fortran. SciCore keeps the
+algorithms, migrates compiled kernels to Rust incrementally, and swaps the array
+backend from NumPy to rsnumpy. Until that migration is complete, some native
+extensions still use the upstream implementations. Two consequences worth
+knowing up front:
+
+- **No Python NumPy dependency at runtime.** Arrays are rsnumpy arrays. NumPy
+  remains a build-time dependency for the C/Cython extensions that have not yet
+  been ported.
+- **Native-kernel migration is ongoing.** Signal filtering kernels including
+  ``lfilter``, ``sosfilt``, ``upfirdn``, direct N-D ``correlate``,
+  ``convolve2d``/``correlate2d``, ``remez`` FIR design, spline filtering, and
+  2-D median filtering now run in Rust. FFTPACK's packed-spectrum convolution
+  kernels and convolution-kernel generation, as well as cluster VQ assignment
+  and cluster-mean updates, also run in Rust; other C, C++, Cython, and Fortran
+  production extensions are still being replaced. Regular-grid interpolation's
+  interval search and 2-D linear interpolation kernels, as well as reverse
+  Cuthill-McKee graph ordering and sparse-to-dense/distance-matrix graph
+  kernels, as well as least-squares Givens elimination, also run in Rust.
+  Sparse graph conversion adapters and sparse finite-difference column
+  grouping kernels are Rust-backed with Python adapters. Multidimensional
+  connected-component labeling and the one-dimensional rank-filter kernel
+  also run in Rust. The directed Hausdorff distance search kernel is Rust-backed
+  with its existing Python random-number and array API preserved. Boyett and
+  Patefield random contingency-table sampling and the Nolan stable-distribution
+  integration kernel also run in Rust.
+- **Recomputation over incremental update.** Where upstream keeps a factorisation
+  up to date with Givens rotations (``scicore.linalg.qr_update`` and friends), this
+  port recomputes the factorisation. The results match, but the complexity is
+  ``O(m n²)`` rather than ``O(m n)``. Each affected function says so in its
+  docstring.
+
+Status
+------
+
+This is a work in progress. Native kernels are still being migrated to Rust;
+until that is complete, some native extensions still use the upstream
+implementations. Treat the API as experimental and pin the version if you
+depend on it.
+
+Building from source
+--------------------
+
+The build is driven by **maturin**: it compiles the pyo3 crate in ``rust/``
+into the ``scicore._scicore_rs`` extension and packages the ``python/`` tree
+into a wheel.
+
+There is a helper that does the whole thing and installs the result into
+``.venv``::
+
+    ./build_wheel.sh
+
+Useful flags::
+
+    ./build_wheel.sh --debug        # debug build instead of release
+    ./build_wheel.sh --out-dir dist # where to put the wheel
+    ./build_wheel.sh --python /path/to/python
+
+To do it by hand::
+
+    pip install maturin
+    maturin build --release -i python -o dist
+    pip install dist/*.whl
+
+``build_wheel.sh`` also runs ``cargo fmt --check`` and ``cargo clippy`` before
+building, so a failing lint stops the build rather than shipping a wheel.
+
+Requirements: a Rust toolchain, Python >= 3.12.
+
+Development
+-----------
+
+Clone the repository::
+
+    git clone --recursive https://github.com/YJ-Niu/scicore.git
+
+The ``--recursive`` flag initializes the doc submodule (scipy-mathjax for
+formula rendering in the docs).
+
+Run the Rust unit tests from the workspace root::
+
+    cd rust
+    cargo test --workspace
+
+The repository's SciCore-owned Python tests live in ``test/`` and
+``tools/``. ``pytest.ini`` limits ``python -m pytest`` to those tests so the
+vendored upstream SciCore test corpus is not run as if it were a SciCore suite.
+The Python tests cover the rsnumpy migration and Rust-backed Python adapters;
+the Rust workspace tests cover each migrated kernel.
+
+Links
+-----
+
+- **Source code:** https://github.com/YJ-Niu/scicore
+- **Bug reports:** https://github.com/YJ-Niu/scicore/issues
+- **rsnumpy (array backend):** https://github.com/YJ-Niu/rsnumpy
+- **Upstream SciCore:** https://github.com/scicore-dev/scicore
+
+License
+-------
+
+BSD 3-Clause, matching upstream SciCore. See ``LICENSE.txt``.

scirs-0.1.3/pyproject.toml

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+[build-system]
+# The build is driven by ``maturin``: it compiles the pyo3 crate
+# (``rust/scicore_rs``) into the ``scicore._scicore_rs`` extension and packages
+# the ``python/`` tree into a wheel. The only external tool required is
+# ``cargo``; maturin itself is provided by the build frontend.
+requires = ["maturin>=1.5,<2.0"]
+build-backend = "maturin"
+
+[tool.maturin]
+# pyo3 bindings; the Python package lives under `python/` and the pyo3 crate is
+# the `scicore_rs` workspace member. The extension is placed at
+# `scicore._scicore_rs` (i.e. `python/scicore/_scicore_rs`).
+bindings = "pyo3"
+python-source = "python"
+manifest-dir = "rust"
+module-name = "scicore._scicore_rs"
+
+[project]
+# The distribution is `scirs`; the *import* package stays `scicore` so this
+# remains a drop-in replacement -- `pip install scirs`, then `import scicore`.
+name = "scirs"
+version = "0.1.3"
+license = { file = "LICENSE.txt" }
+description = "Fundamental algorithms for scientific computing in Python, built on rsnumpy"
+authors = [
+    { name = "YJ-Niu" },
+]
+maintainers = [
+    { name = "SciCore Developers" },
+]
+keywords = [
+    "scientific",
+    "computing",
+    "linear-algebra",
+    "rsnumpy",
+    "rust",
+]
+requires-python = ">=3.12"
+dependencies = [
+    "rsnumpy>=1.2.5",
+]
+readme = "README.rst"
+classifiers = [
+    "Development Status :: 5 - Production/Stable",
+    "Intended Audience :: Science/Research",
+    "Intended Audience :: Developers",
+    "License :: OSI Approved :: BSD License",
+    "Programming Language :: Rust",
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+    "Programming Language :: Python :: 3.14",
+    "Programming Language :: Python :: 3.15",
+    "Topic :: Software Development :: Libraries",
+    "Topic :: Scientific/Engineering",
+    "Operating System :: Microsoft :: Windows",
+    "Operating System :: POSIX :: Linux",
+    "Operating System :: POSIX",
+    "Operating System :: Unix",
+    "Operating System :: MacOS",
+]
+
+[project.urls]
+homepage = "https://github.com/YJ-Niu/scicore"
+documentation = "https://github.com/YJ-Niu/scicore#readme"
+source = "https://github.com/YJ-Niu/scicore"
+download = "https://pypi.org/project/scirs/"
+tracker = "https://github.com/YJ-Niu/scicore/issues"
+
+# NOTE: when updating this table, also update `dependency-groups.optional-runtime-deps`
+[project.optional-dependencies]
+all = [
+    "pooch",  # datasets
+    "threadpoolctl",  # io.mm{...}
+    "rsplotlib",  # cluster.hierarchy.dendrogram, stats.probplot
+    # circular dependency issues, https://github.com/scipy/scipy/issues/19783
+    # "scikit-umfpack",  # optimize, sparse.linalg
+]
+
+[dependency-groups]
+optional-runtime-deps = [
+    "pooch",  # datasets
+    "threadpoolctl",  # io.mm{...}
+    "rsplotlib",  # cluster.hierarchy.dendrogram, stats.probplot
+    # circular dependency issues, https://github.com/scipy/scipy/issues/19783
+    # "scikit-umfpack",  # optimize, sparse.linalg
+]
+
+test-core = [
+    "pytest>=9.1.1",
+    "hypothesis>=6.30",
+    "pooch",
+    "pytest-xdist",  # not required, but used widely, belongs in -core
+    "pytest-timeout",  # not required, but used widely, belongs in -core
+]
+test-mp = [
+    "mpmath",
+    # for PyPI: 'gmpy2; sys_platform != "win32" or platform_machine != "ARM64"'
+    "gmpy2",
+]
+test-parallel = [
+    { include-group = "test-core" },
+    "pytest-run-parallel",
+]
+test-docs = [
+    { include-group = "test-core" },
+    "scipy-doctest>=2.0.0",
+    "rsplotlib",
+]
+test-array-types = [
+    { include-group = "test-core" },
+    "array-api-strict>=2.3.1",
+    "marray",
+    # for PyPI: 'sparse; sys_platform != "win32" or platform_machine != "ARM64"'
+    "sparse",
+]
+test = [
+    { include-group = "optional-runtime-deps" },
+    { include-group = "test-core" },
+    { include-group = "test-mp" },
+    { include-group = "test-parallel" },
+    { include-group = "test-docs" },
+    { include-group = "test-array-types" },
+    # useful but doesn't have its own group (rarely used, and has compiled wheels so can be hard to install)
+    "psutil",
+]
+test-fail-slow = [
+    { include-group = "test-core" },
+    "pytest-fail-slow",  # only one CI job; isolated so it doesn't cause failures for contributors randomly
+]
+coverage = [
+    { include-group = "test" },  # includes all optional test and runtime deps for maximum coverage
+    "pytest-cov",
+]
+dev = [
+    { include-group = "test" },
+    "scipy-stubs",
+]

scirs-0.1.3/python/scicore/__config__.py

@@ -0,0 +1,129 @@
+# This file is generated by scicore's build process (`maturin`).
+# It replaces the meson-generated `scipy/__config__.py`: the compiled layer is
+# now Rust, so the build reports the Rust toolchain instead of C/Cython/pythran.
+from enum import Enum
+
+import platform as _platform
+import sys as _sys
+
+__all__ = ["show"]
+
+_built_with_meson = False
+
+
+class DisplayModes(Enum):
+    stdout = "stdout"
+    dicts = "dicts"
+
+
+def _cleanup(d):
+    """Remove empty values in a `dict` recursively."""
+    if isinstance(d, dict):
+        return {k: _cleanup(v) for k, v in d.items() if v != '' and _cleanup(v) != ''}
+    return d
+
+
+def _rust_toolchain():
+    import json
+    import subprocess
+    try:
+        out = subprocess.run(
+            ["rustc", "--version", "--verbose"],
+            capture_output=True, text=True, timeout=30,
+        ).stdout
+        info = {}
+        for line in out.splitlines()[1:]:
+            if ":" in line:
+                k, _, v = line.partition(":")
+                info[k.strip()] = v.strip()
+        return {
+            "name": "rustc",
+            "version": info.get("release", ""),
+            "host": info.get("host", ""),
+        }
+    except Exception:
+        return {"name": "rustc", "version": "", "host": ""}
+
+
+def _backend_version(name):
+    try:
+        mod = __import__(name)
+        return getattr(mod, "__version__", "")
+    except Exception:
+        return ""
+
+
+CONFIG = _cleanup(
+    {
+        "Compilers": {
+            "rust": _rust_toolchain(),
+        },
+        "Machine Information": {
+            "host": {
+                "cpu": _platform.machine(),
+                "family": _platform.system(),
+            },
+        },
+        "Build Dependencies": {
+            "rsnumpy": {
+                "name": "rsnumpy",
+                "version": _backend_version("rsnumpy"),
+                "detection method": "pkgconfig",
+            },
+            "pyo3": {
+                "name": "pyo3",
+                "version": "0.29",
+                "detection method": "cargo",
+            },
+            # No BLAS/LAPACK backend is wired up yet: the Rust port of
+            # `scipy.linalg` will plug one in (see `rust/`).  Declaring the keys
+            # keeps `scipy.linalg.blas` importable in the meantime.
+            "blas": {
+                "name": "unknown",
+                "found": False,
+                "version": "",
+                "detection method": "",
+                "has ilp64": False,
+                "cython blas ilp64": False,
+            },
+            "lapack": {
+                "name": "unknown",
+                "found": False,
+                "version": "",
+                "detection method": "",
+                "has ilp64": False,
+            },
+        },
+        "Python Information": {
+            "path": _sys.executable,
+            "version": _sys.version.split()[0],
+        },
+    }
+)
+
+
+def _check_pyyaml():
+    import yaml
+
+    return yaml
+
+
+def show(mode=DisplayModes.stdout.value):
+    """Show the libraries and system information scicore was built with."""
+    if mode == DisplayModes.stdout.value:
+        try:  # Non-standard library, check import
+            yaml = _check_pyyaml()
+
+            print(yaml.dump(CONFIG))
+        except ModuleNotFoundError:
+            import json
+            import warnings
+
+            warnings.warn("Install `pyyaml` for better output", stacklevel=1)
+            print(json.dumps(CONFIG, indent=2))
+    elif mode == DisplayModes.dicts.value:
+        return CONFIG
+    else:
+        raise AttributeError(
+            f"Invalid `mode`, use one of: {', '.join([e.value for e in DisplayModes])}"
+        )