freealg 0.3.1__tar.gz → 0.3.3__tar.gz

{freealg-0.3.1 → freealg-0.3.3}/PKG-INFO

@@ -1,7 +1,12 @@
 Metadata-Version: 2.4
 Name: freealg
-Version: 0.3.1
+Version: 0.3.3
 Summary: Free probability for large matrices
+Home-page: https://github.com/ameli/freealg
+Download-URL: https://github.com/ameli/freealg/archive/main.zip
+Project-URL: Documentation, https://ameli.github.io/freealg
+Project-URL: Source, https://github.com/ameli/freealg
+Project-URL: Tracker, https://github.com/ameli/freealg/issues
 Keywords: linalg,free-probability
 Platform: Linux
 Platform: OSX
@@ -54,33 +59,42 @@ Requires-Dist: sphinx-gallery; extra == "docs"
 Requires-Dist: sphinxcontrib-youtube; extra == "docs"
 Requires-Dist: sphinxext-opengraph; extra == "docs"
 Requires-Dist: sphinx-argparse; extra == "docs"
+Requires-Dist: sphinx-sitemap; extra == "docs"
 Dynamic: classifier
 Dynamic: description
 Dynamic: description-content-type
+Dynamic: download-url
+Dynamic: home-page
 Dynamic: keywords
 Dynamic: license-file
 Dynamic: platform
+Dynamic: project-url
 Dynamic: provides-extra
 Dynamic: requires-dist
 Dynamic: requires-python
 Dynamic: summary
 
-.. image:: https://raw.githubusercontent.com/ameli/freealg/refs/heads/main/docs/source/_static/images/icons/logo-freealg-light.png
+.. .. image:: https://raw.githubusercontent.com/ameli/freealg/refs/heads/main/docs/source/_static/images/icons/logo-freealg-light.png
+..     :align: left
+..     :width: 240
+..     :class: custom-dark
+
+.. figure:: https://raw.githubusercontent.com/ameli/freealg/refs/heads/main/docs/source/_static/images/icons/logo-freealg-light.png
     :align: left
     :width: 240
-    :class: custom-dark
 
 `Paper <https://arxiv.org/abs/2506.11994>`__ |
 `Slides <https://www.dropbox.com/scl/fi/03gjuyz17k9yhsqy0isoz/free_decomporession_slides.pdf?rlkey=8f82mhciyl2ju02l7hv1md5li&st=26xmhjga&dl=0>`__ |
 `Docs <https://ameli.github.io/freealg>`__ |
-`Live Demo <https://ameli.github.io/freealg/jlite/lab/index.html?path=quick_start.ipynb>`__
+`Live Demo <https://colab.research.google.com/github/ameli/freealg/blob/main/notebooks/quick_start.ipynb>`__
 
 .. `Slides <https://ameli.github.io/freealg/_static/data/slides.pdf>`__ |
 
-*freealg* is a Python package that employs **free** probability to evaluate the spectral
-densities of large matrix **form**\ s. The fundamental algorithm employed by *freealg* is
-**free decompression**, which extrapolates from the empirical spectral densities of small 
-submatrices to infer the eigenspectrum of extremely large matrices. 
+*freealg* is a Python package that employs **free** probability to evaluate the
+spectral densities of large matrix **form**\ s. The fundamental algorithm
+employed by *freealg* is **free decompression**, which extrapolates from the
+empirical spectral densities of small  submatrices to infer the eigenspectrum
+of extremely large matrices. 
 
 Install
 =======
@@ -106,8 +120,8 @@ Documentation is available at `ameli.github.io/freealg <https://ameli.github.io/
 Quick Usage
 ===========
 
-The following code estimates the eigenvalues of a very large Wishart matrix using a much
-smaller Wishart matrix.
+The following code estimates the eigenvalues of a very large Wishart matrix
+using a much smaller Wishart matrix.
 
 .. code-block:: python
 
@@ -116,7 +130,8 @@ smaller Wishart matrix.
     >>> A = mp.matrix(1000)                         # Sample a 1000 x 1000 Wishart matrix
     >>> eigs = fa.eigfree(A, 100_000)               # Estimate the eigenvalues of 100000 x 100000
 
-For more details on how to interface with *freealg* check out the `Quick Start Guide <https://github.com/ameli/freealg/blob/main/notebooks/quick_start.ipynb>`__.
+For more details on how to interface with *freealg* check out the 
+`Quick Start Guide <https://github.com/ameli/freealg/blob/main/notebooks/quick_start.ipynb>`__.
 
 
 Test
@@ -140,14 +155,14 @@ How to Contribute
 =================
 
 We welcome contributions via GitHub's pull request. Developers should review
-our [Contributing Guidelines](CONTRIBUTING.rst) before submitting their code.
-If you do not feel comfortable modifying the code, we also welcome feature
-requests and bug reports.
+our [Contributing Guidelines](https://github.com/ameli/freealg/blob/main/CONTRIBUTING.rst)
+before submitting their code. If you do not feel comfortable modifying the
+code, we also welcome feature requests and bug reports.
 
 How to Cite
 ===========
 
-If you use this work, please cite the `arXiv paper <https://arxiv.org/abs/2506.11994>`__.
+If you use this work, please cite our `arXiv paper <https://arxiv.org/abs/2506.11994>`__.
 
   .. code::
 

{freealg-0.3.1 → freealg-0.3.3}/README.rst

@@ -1,19 +1,24 @@
-.. image:: https://raw.githubusercontent.com/ameli/freealg/refs/heads/main/docs/source/_static/images/icons/logo-freealg-light.png
+.. .. image:: https://raw.githubusercontent.com/ameli/freealg/refs/heads/main/docs/source/_static/images/icons/logo-freealg-light.png
+..     :align: left
+..     :width: 240
+..     :class: custom-dark
+
+.. figure:: https://raw.githubusercontent.com/ameli/freealg/refs/heads/main/docs/source/_static/images/icons/logo-freealg-light.png
     :align: left
     :width: 240
-    :class: custom-dark
 
 `Paper <https://arxiv.org/abs/2506.11994>`__ |
 `Slides <https://www.dropbox.com/scl/fi/03gjuyz17k9yhsqy0isoz/free_decomporession_slides.pdf?rlkey=8f82mhciyl2ju02l7hv1md5li&st=26xmhjga&dl=0>`__ |
 `Docs <https://ameli.github.io/freealg>`__ |
-`Live Demo <https://ameli.github.io/freealg/jlite/lab/index.html?path=quick_start.ipynb>`__
+`Live Demo <https://colab.research.google.com/github/ameli/freealg/blob/main/notebooks/quick_start.ipynb>`__
 
 .. `Slides <https://ameli.github.io/freealg/_static/data/slides.pdf>`__ |
 
-*freealg* is a Python package that employs **free** probability to evaluate the spectral
-densities of large matrix **form**\ s. The fundamental algorithm employed by *freealg* is
-**free decompression**, which extrapolates from the empirical spectral densities of small 
-submatrices to infer the eigenspectrum of extremely large matrices. 
+*freealg* is a Python package that employs **free** probability to evaluate the
+spectral densities of large matrix **form**\ s. The fundamental algorithm
+employed by *freealg* is **free decompression**, which extrapolates from the
+empirical spectral densities of small  submatrices to infer the eigenspectrum
+of extremely large matrices. 
 
 Install
 =======
@@ -39,8 +44,8 @@ Documentation is available at `ameli.github.io/freealg <https://ameli.github.io/
 Quick Usage
 ===========
 
-The following code estimates the eigenvalues of a very large Wishart matrix using a much
-smaller Wishart matrix.
+The following code estimates the eigenvalues of a very large Wishart matrix
+using a much smaller Wishart matrix.
 
 .. code-block:: python
 
@@ -49,7 +54,8 @@ smaller Wishart matrix.
     >>> A = mp.matrix(1000)                         # Sample a 1000 x 1000 Wishart matrix
     >>> eigs = fa.eigfree(A, 100_000)               # Estimate the eigenvalues of 100000 x 100000
 
-For more details on how to interface with *freealg* check out the `Quick Start Guide <https://github.com/ameli/freealg/blob/main/notebooks/quick_start.ipynb>`__.
+For more details on how to interface with *freealg* check out the 
+`Quick Start Guide <https://github.com/ameli/freealg/blob/main/notebooks/quick_start.ipynb>`__.
 
 
 Test
@@ -73,14 +79,14 @@ How to Contribute
 =================
 
 We welcome contributions via GitHub's pull request. Developers should review
-our [Contributing Guidelines](CONTRIBUTING.rst) before submitting their code.
-If you do not feel comfortable modifying the code, we also welcome feature
-requests and bug reports.
+our [Contributing Guidelines](https://github.com/ameli/freealg/blob/main/CONTRIBUTING.rst)
+before submitting their code. If you do not feel comfortable modifying the
+code, we also welcome feature requests and bug reports.
 
 How to Cite
 ===========
 
-If you use this work, please cite the `arXiv paper <https://arxiv.org/abs/2506.11994>`__.
+If you use this work, please cite our `arXiv paper <https://arxiv.org/abs/2506.11994>`__.
 
   .. code::
 

freealg-0.3.3/freealg/__version__.py

@@ -0,0 +1 @@
+__version__ = "0.3.3"

{freealg-0.3.1 → freealg-0.3.3}/freealg/_support.py

@@ -127,7 +127,7 @@ def detect_support(eigs, method='asymp', k=None, p=0.001, **kwargs):
         * ``'interior'``: estimates a support assuming the range overestimates;
             uses quantiles (p, 1-p).
         * ``'interior_smooth'``: same as ``'interior'`` but using kernel
-            density estimation, from [2].
+            density estimation, from [2]_.
 
     k : int, default = None
         Number of extreme order statistics to use for ``method='regression'``.

{freealg-0.3.1 → freealg-0.3.3}/freealg/eigh.py

@@ -17,6 +17,42 @@ from .freeform import FreeForm
 __all__ = ['eigh', 'cond', 'norm', 'trace', 'slogdet']
 
 
+# ===============
+# subsample apply
+# ===============
+
+def _subsample_apply(f, A, output_array=False):
+    """
+    Compute f(A_n) over subsamples A_n of A. If the output of
+    f is an array (e.g. eigvals), specify output_array to be True.
+    """
+
+    if A.ndim != 2 or A.shape[0] != A.shape[1]:
+        raise RuntimeError("Only square matrices are permitted.")
+
+    n = A.shape[0]
+
+    # Size of sample matrix
+    n_s = int(80*(1 + numpy.log(n)))
+    # If matrix is not large enough, return eigenvalues
+    if n < n_s:
+        return f(A), n, n
+
+    # Number of samples
+    num_samples = int(10 * (n / n_s)**0.5)
+
+    # Collect eigenvalue samples
+    samples = []
+    for _ in range(num_samples):
+        indices = numpy.random.choice(n, n_s, replace=False)
+        samples.append(f(A[numpy.ix_(indices, indices)]))
+
+    if output_array:
+        return numpy.concatenate(samples).ravel(), n, n_s
+
+    return numpy.array(samples), n, n_s
+
+
 # ====
 # eigh
 # ====
@@ -87,28 +123,11 @@ def eigh(A, N=None, psd=None, plots=False):
         >>> eigs = eigh(A)
     """
 
-    if A.ndim != 2 or A.shape[0] != A.shape[1]:
-        raise RuntimeError("Only square matrices are permitted.")
-    n = A.shape[0]
+    samples, n, n_s = _subsample_apply(compute_eig, A, output_array=True)
 
     if N is None:
         N = n
 
-    # Size of sample matrix
-    n_s = int(80*(1 + numpy.log(n)))
-    # If matrix is not large enough, return eigenvalues
-    if n < n_s:
-        return compute_eig(A)
-    # Number of samples
-    num_samples = int(10 * (n / n_s)**0.5)
-
-    # Collect eigenvalue samples
-    samples = []
-    for _ in range(num_samples):
-        indices = numpy.random.choice(n, n_s, replace=False)
-        samples.append(compute_eig(A[numpy.ix_(indices, indices)]))
-    samples = numpy.concatenate(samples).ravel()
-
     # If all eigenvalues are positive, set PSD flag
     if psd is None:
         psd = samples.min() > 0
@@ -224,7 +243,7 @@ def norm(A, N=None, order=None):
     order : {float, ``''inf``, ``'-inf'``, ``'fro'``, ``'nuc'``}, default=2
         Order of the norm.
 
-        * float :math:`p`: Schtten p-norm.
+        * float :math:`p`: Schatten p-norm.
         * ``'inf'``: Largest absolute eigenvalue
           :math:`\\max \\vert \\lambda_i \\vert)`
         * ``'-inf'``: Smallest absolute eigenvalue
@@ -300,19 +319,19 @@ def norm(A, N=None, order=None):
 # trace
 # =====
 
-def trace(A, N=None):
+def trace(A, N=None, p=1.0):
     """
-    Estimate the trace of a Hermitian matrix.
+    Estimate the trace of a power of a Hermitian matrix.
 
-    This function estimates the trace of the matrix :math:`\\mathbf{A}` or a
-    larger matrix containing :math:`\\mathbf{A}` using free decompression.
+    This function estimates the trace of the matrix power :math:`\\mathbf{A}^p`
+    or that of a larger matrix containing :math:`\\mathbf{A}`.
 
     Parameters
     ----------
 
     A : numpy.ndarray
-        The symmetric real-valued matrix :math:`\\mathbf{A}` whose condition
-        number (or that of a matrix containing :math:`\\mathbf{A}`) are to be
+        The symmetric real-valued matrix :math:`\\mathbf{A}` whose trace of
+        a power (or that of a matrix containing :math:`\\mathbf{A}`) is to be
         computed.
 
     N : int, default=None
@@ -320,6 +339,10 @@ def trace(A, N=None):
         eigenvalues of. If None, returns estimates of the eigenvalues of
         :math:`\\mathbf{A}` itself.
 
+    p : float, default=1.0
+        The exponent :math:`p` in :math:`\\mathbf{A}^p`.
+
+
     Returns
     -------
 
@@ -337,7 +360,9 @@ def trace(A, N=None):
     Notes
     -----
 
-    This is a convenience function using :func:`freealg.eigh`.
+    The trace is highly amenable to subsampling: under free decompression
+    the average eigenvalue is assumed constant, so the trace increases
+    linearly. Traces of powers fall back to :func:`freealg.eigh`.
 
     Examples
     --------
@@ -353,10 +378,14 @@ def trace(A, N=None):
         >>> trace(A, 100_000)
     """
 
-    eigs = eigh(A, N)
-    trace_ = numpy.sum(eigs)
+    if numpy.isclose(p, 1.0):
+        samples, n, n_s = _subsample_apply(numpy.trace, A, output_array=False)
+        if N is None:
+            N = n
+        return numpy.mean(samples) * (N / n_s)
 
-    return trace_
+    eig = eigh(A, N)
+    return numpy.sum(eig ** p)
 
 
 # =======

{freealg-0.3.1 → freealg-0.3.3}/freealg.egg-info/PKG-INFO

@@ -1,7 +1,12 @@
 Metadata-Version: 2.4
 Name: freealg
-Version: 0.3.1
+Version: 0.3.3
 Summary: Free probability for large matrices
+Home-page: https://github.com/ameli/freealg
+Download-URL: https://github.com/ameli/freealg/archive/main.zip
+Project-URL: Documentation, https://ameli.github.io/freealg
+Project-URL: Source, https://github.com/ameli/freealg
+Project-URL: Tracker, https://github.com/ameli/freealg/issues
 Keywords: linalg,free-probability
 Platform: Linux
 Platform: OSX
@@ -54,33 +59,42 @@ Requires-Dist: sphinx-gallery; extra == "docs"
 Requires-Dist: sphinxcontrib-youtube; extra == "docs"
 Requires-Dist: sphinxext-opengraph; extra == "docs"
 Requires-Dist: sphinx-argparse; extra == "docs"
+Requires-Dist: sphinx-sitemap; extra == "docs"
 Dynamic: classifier
 Dynamic: description
 Dynamic: description-content-type
+Dynamic: download-url
+Dynamic: home-page
 Dynamic: keywords
 Dynamic: license-file
 Dynamic: platform
+Dynamic: project-url
 Dynamic: provides-extra
 Dynamic: requires-dist
 Dynamic: requires-python
 Dynamic: summary
 
-.. image:: https://raw.githubusercontent.com/ameli/freealg/refs/heads/main/docs/source/_static/images/icons/logo-freealg-light.png
+.. .. image:: https://raw.githubusercontent.com/ameli/freealg/refs/heads/main/docs/source/_static/images/icons/logo-freealg-light.png
+..     :align: left
+..     :width: 240
+..     :class: custom-dark
+
+.. figure:: https://raw.githubusercontent.com/ameli/freealg/refs/heads/main/docs/source/_static/images/icons/logo-freealg-light.png
     :align: left
     :width: 240
-    :class: custom-dark
 
 `Paper <https://arxiv.org/abs/2506.11994>`__ |
 `Slides <https://www.dropbox.com/scl/fi/03gjuyz17k9yhsqy0isoz/free_decomporession_slides.pdf?rlkey=8f82mhciyl2ju02l7hv1md5li&st=26xmhjga&dl=0>`__ |
 `Docs <https://ameli.github.io/freealg>`__ |
-`Live Demo <https://ameli.github.io/freealg/jlite/lab/index.html?path=quick_start.ipynb>`__
+`Live Demo <https://colab.research.google.com/github/ameli/freealg/blob/main/notebooks/quick_start.ipynb>`__
 
 .. `Slides <https://ameli.github.io/freealg/_static/data/slides.pdf>`__ |
 
-*freealg* is a Python package that employs **free** probability to evaluate the spectral
-densities of large matrix **form**\ s. The fundamental algorithm employed by *freealg* is
-**free decompression**, which extrapolates from the empirical spectral densities of small 
-submatrices to infer the eigenspectrum of extremely large matrices. 
+*freealg* is a Python package that employs **free** probability to evaluate the
+spectral densities of large matrix **form**\ s. The fundamental algorithm
+employed by *freealg* is **free decompression**, which extrapolates from the
+empirical spectral densities of small  submatrices to infer the eigenspectrum
+of extremely large matrices. 
 
 Install
 =======
@@ -106,8 +120,8 @@ Documentation is available at `ameli.github.io/freealg <https://ameli.github.io/
 Quick Usage
 ===========
 
-The following code estimates the eigenvalues of a very large Wishart matrix using a much
-smaller Wishart matrix.
+The following code estimates the eigenvalues of a very large Wishart matrix
+using a much smaller Wishart matrix.
 
 .. code-block:: python
 
@@ -116,7 +130,8 @@ smaller Wishart matrix.
     >>> A = mp.matrix(1000)                         # Sample a 1000 x 1000 Wishart matrix
     >>> eigs = fa.eigfree(A, 100_000)               # Estimate the eigenvalues of 100000 x 100000
 
-For more details on how to interface with *freealg* check out the `Quick Start Guide <https://github.com/ameli/freealg/blob/main/notebooks/quick_start.ipynb>`__.
+For more details on how to interface with *freealg* check out the 
+`Quick Start Guide <https://github.com/ameli/freealg/blob/main/notebooks/quick_start.ipynb>`__.
 
 
 Test
@@ -140,14 +155,14 @@ How to Contribute
 =================
 
 We welcome contributions via GitHub's pull request. Developers should review
-our [Contributing Guidelines](CONTRIBUTING.rst) before submitting their code.
-If you do not feel comfortable modifying the code, we also welcome feature
-requests and bug reports.
+our [Contributing Guidelines](https://github.com/ameli/freealg/blob/main/CONTRIBUTING.rst)
+before submitting their code. If you do not feel comfortable modifying the
+code, we also welcome feature requests and bug reports.
 
 How to Cite
 ===========
 
-If you use this work, please cite the `arXiv paper <https://arxiv.org/abs/2506.11994>`__.
+If you use this work, please cite our `arXiv paper <https://arxiv.org/abs/2506.11994>`__.
 
   .. code::
 

{freealg-0.3.1 → freealg-0.3.3}/freealg.egg-info/requires.txt

@@ -24,6 +24,7 @@ sphinx-gallery
 sphinxcontrib-youtube
 sphinxext-opengraph
 sphinx-argparse
+sphinx-sitemap
 
 [test]
 tox

{freealg-0.3.1 → freealg-0.3.3}/setup.py

@@ -158,6 +158,12 @@ def main(argv):
     # Description
     description = 'Free probability for large matrices'
 
+    # URLs
+    url = 'https://github.com/ameli/freealg'
+    download_url = url + '/archive/main.zip'
+    documentation_url = 'https://ameli.github.io/freealg'
+    tracker_url = url + '/issues'
+
     # Inputs to setup
     metadata = dict(
         name=package_name,
@@ -166,6 +172,13 @@ def main(argv):
         long_description=long_description,
         long_description_content_type='text/x-rst',
         keywords="""linalg, free-probability""",
+        url=url,
+        download_url=download_url,
+        project_urls={
+            "Documentation": documentation_url,
+            "Source": url,
+            "Tracker": tracker_url,
+        },
         platforms=['Linux', 'OSX', 'Windows'],
         packages=setuptools.find_packages(exclude=[
             'tests.*',

freealg-0.3.1/freealg/__version__.py

@@ -1 +0,0 @@
-__version__ = "0.3.1"