Create pubs/FreemanEtAl23_PNAS

Python/requirements.txt

@@ -1,133 +1,150 @@
-anyio==3.6.1
-appnope==0.1.3
-argon2-cffi==21.3.0
-argon2-cffi-bindings==21.2.0
-astor==0.8.1
-asttokens==2.0.8
-attrs==22.1.0
-Babel==2.10.3
-backcall==0.2.0
-beautifulsoup4==4.11.1
-bleach==5.0.1
-certifi==2022.9.24
-cffi==1.15.1
-charset-normalizer==2.1.1
-contourpy==1.0.5
-coverage==6.5.0
-cryptography==38.0.3
-cycler==0.11.0
-debugpy==1.6.3
-decorator==5.1.1
-defusedxml==0.7.1
-dill==0.3.5.1
-entrypoints==0.4
-executing==1.1.1
-fastjsonschema==2.16.2
-flake8==5.0.4
-fonttools==4.37.4
-idna==3.4
-iniconfig==1.1.1
-ipykernel==6.16.0
-ipympl==0.9.2
-ipython==8.5.0
-ipython-genutils==0.2.0
-ipywidgets==8.0.2
-jedi==0.18.1
-Jinja2==3.1.2
-json5==0.9.10
-jsonschema==4.16.0
-jupyter-core==4.11.1
-jupyter-server==1.21.0
-jupyter_client==7.4.2
-jupyterlab==3.4.8
-jupyterlab-pygments==0.2.2
-jupyterlab-spellchecker==0.7.2
-jupyterlab-vim==0.15.1
-jupyterlab-widgets==3.0.3
-jupyterlab_server==2.16.0
-kiwisolver==1.4.4
-llvmlite==0.39.1
-lxml==4.9.1
-MarkupSafe==2.1.1
-matplotlib==3.6.1
-matplotlib-inline==0.1.6
-mccabe==0.7.0
-mistune==2.0.4
-more-itertools==8.14.0
-mpmath==1.2.1
-multiprocess==0.70.13
-mypy==0.982
-mypy-extensions==0.4.3
-nb-mypy==1.0.4
-nbclassic==0.4.5
-nbclient==0.7.0
-nbconvert==7.2.1
-nbformat==5.7.0
-nest-asyncio==1.5.6
--e git+https://github.com/dg227/NLSAdev@4a630361b10c287104afa4e914f78d5bab54c5da#egg=nlsa&subdirectory=Python
-nodeenv==1.7.0
-nodejs==0.1.1
-notebook==6.5.1
-notebook-shim==0.1.0
-nptyping==2.3.1
-ntlm-auth==1.5.0
-numba==0.56.3
-numpy==1.23.4
-optional-django==0.1.0
-packaging==21.3
-pandocfilters==1.5.0
-parso==0.8.3
-pbr==5.11.0
-pexpect==4.8.0
-pickleshare==0.7.5
-Pillow==9.2.0
-pluggy==1.0.0
-ply==3.11
-prometheus-client==0.15.0
-prompt-toolkit==3.0.31
-psutil==5.9.2
-ptyprocess==0.7.0
-pure-eval==0.2.2
-py==1.11.0
-pycodestyle==2.9.1
-pycparser==2.21
-pyflakes==2.5.0
-Pygments==2.13.0
-pylatexenc==2.10
-pyparsing==3.0.9
-pyrsistent==0.18.1
-pytest==7.1.3
-pytest-cov==4.0.0
-python-dateutil==2.8.2
-pytz==2022.4
-pyzmq==24.0.1
-qiskit==0.39.2
-qiskit-aer==0.11.1
-qiskit-ibmq-provider==0.19.2
-qiskit-terra==0.22.2
-requests==2.28.1
-requests-ntlm==1.1.0
-retworkx==0.12.0
-rustworkx==0.12.0
-scipy==1.9.2
-Send2Trash==1.8.0
-six==1.16.0
-sniffio==1.3.0
-soupsieve==2.3.2.post1
-stack-data==0.5.1
-stevedore==4.1.1
-symengine==0.9.2
-sympy==1.11.1
-terminado==0.16.0
-tinycss2==1.1.1
-tomli==2.0.1
-tornado==6.2
-traitlets==5.4.0
-tweedledum==1.1.1
-typing_extensions==4.4.0
-urllib3==1.26.12
-wcwidth==0.2.5
-webencodings==0.5.1
-websocket-client==1.4.1
-websockets==10.4
-widgetsnbextension==4.0.3
+anyio>=3.6.2
+appnope>=0.1.3
+argon2-cffi>=21.3.0
+argon2-cffi-bindings>=21.2.0
+arrow>=1.2.3
+astor>=0.8.1
+asttokens>=2.2.1
+attrs>=22.2.0
+Babel>=2.11.0
+backcall>=0.2.0
+beautifulsoup4>=4.11.1
+bleach>=5.0.1
+certifi>=2022.12.7
+cffi>=1.15.1
+charset-normalizer>=2.1.1
+comm>=0.1.2
+contourpy>=1.0.6
+coverage>=7.0.1
+cryptography>=38.0.4
+cycler>=0.11.0
+debugpy>=1.6.4
+decorator>=5.1.1
+defusedxml>=0.7.1
+dill>=0.3.6
+entrypoints>=0.4
+exceptiongroup>=1.1.0
+executing>=1.2.0
+fastjsonschema>=2.16.2
+flake8>=6.0.0
+fonttools>=4.38.0
+fqdn>=1.5.1
+h5py>=3.7.0
+idna>=3.4
+iniconfig>=1.1.1
+ipykernel>=6.19.4
+ipympl>=0.9.2
+ipython>=8.7.0
+ipython-genutils>=0.2.0
+ipywidgets>=8.0.4
+isoduration>=20.11.0
+jedi>=0.18.2
+Jinja2>=3.1.2
+json5>=0.9.10
+jsonpointer>=2.3
+jsonschema>=4.17.3
+jupyter-events>=0.5.0
+jupyter_client>=7.4.8
+jupyter_core>=5.1.1
+jupyter_server>=2.0.6
+jupyter_server_terminals>=0.4.3
+jupyterlab>=3.5.2
+jupyterlab-pygments>=0.2.2
+jupyterlab-spellchecker>=0.7.2
+jupyterlab-vim>=0.15.1
+jupyterlab-widgets>=3.0.5
+jupyterlab_server>=2.17.0
+kiwisolver>=1.4.4
+llvmlite>=0.39.1
+lxml>=4.9.2
+MarkupSafe>=2.1.1
+mat73>=0.59
+matplotlib>=3.6.2
+matplotlib-inline>=0.1.6
+mccabe>=0.7.0
+mistune>=2.0.4
+more-itertools>=9.0.0
+mpmath>=1.2.1
+multiprocess>=0.70.14
+mypy>=0.991
+mypy-extensions>=0.4.3
+nb-mypy>=1.0.4
+nbclassic>=0.4.8
+nbclient>=0.7.2
+nbconvert>=7.2.7
+nbformat>=5.7.1
+nest-asyncio>=1.5.6
+-e git+https://github.com/dg227/NLSAdev@db378330128c79f02b763e98319d05fb1f8416b9#egg=nlsa&subdirectory=Python
+nodeenv>=1.7.0
+nodejs>=0.1.1
+notebook>=6.5.2
+notebook_shim>=0.2.2
+nptyping>=2.4.1
+ntlm-auth>=1.5.0
+numba>=0.56.4
+numpy>=1.23.5
+optional-django>=0.1.0
+packaging>=22.0
+pandocfilters>=1.5.0
+parso>=0.8.3
+pbr>=5.11.0
+pexpect>=4.8.0
+pickleshare>=0.7.5
+Pillow>=9.3.0
+platformdirs>=2.6.2
+pluggy>=1.0.0
+ply>=3.11
+prometheus-client>=0.15.0
+prompt-toolkit>=3.0.36
+psutil>=5.9.4
+ptyprocess>=0.7.0
+pure-eval>=0.2.2
+py>=1.11.0
+pycodestyle>=2.10.0
+pycparser>=2.21
+pyflakes>=3.0.1
+Pygments>=2.13.0
+pylatexenc>=2.10
+pyparsing>=3.0.9
+pyrsistent>=0.19.3
+pytest>=7.2.0
+pytest-cov>=4.0.0
+python-dateutil>=2.8.2
+python-json-logger>=2.0.4
+pytz>=2022.7
+PyYAML>=6.0
+pyzmq>=24.0.1
+qiskit>=0.39.4
+qiskit-aer>=0.11.2
+qiskit-ibmq-provider>=0.19.2
+qiskit-terra>=0.22.3
+requests>=2.28.1
+requests-ntlm>=1.1.0
+retworkx>=0.12.1
+rfc3339-validator>=0.1.4
+rfc3986-validator>=0.1.1
+rustworkx>=0.12.1
+scipy>=1.9.3
+Send2Trash>=1.8.0
+six>=1.16.0
+sniffio>=1.3.0
+soupsieve>=2.3.2.post1
+stack-data>=0.6.2
+stevedore>=4.1.1
+symengine>=0.9.2
+sympy>=1.11.1
+terminado>=0.17.1
+tinycss2>=1.2.1
+tomli>=2.0.1
+tornado>=6.2
+traitlets>=5.8.0
+tweedledum>=1.1.1
+typing_extensions>=4.4.0
+uri-template>=1.2.0
+urllib3>=1.26.13
+wcwidth>=0.2.5
+webcolors>=1.12
+webencodings>=0.5.1
+websocket-client>=1.4.2
+websockets>=10.4
+widgetsnbextension>=4.0.5

Python/src/nlsa/abstract_algebra.py

@@ -3,7 +3,7 @@
 from functools import partial
 from itertools import accumulate, repeat
 from typing import Callable, Iterator, Optional, Protocol, TypeVar, \
-        runtime_checkable, Generic
+        runtime_checkable
 
 B = TypeVar('B')
 B_contra = TypeVar('B_contra', contravariant=True)
@@ -52,7 +52,7 @@ def __getitem__(self, key: int) -> T_co:
         ...
 
 
-class SupportsAdd(Protocol[T]):
+class SupportsAdd(Protocol):
     """Represents types supporting addition."""
     def __add__(a: T, b: T) -> T:
         ...
@@ -333,7 +333,7 @@ def make_l2_innerp(impl: ImplementsStarAlgebra[T], mu: Callable[[T], S])\
     return ip
 
 
-def riesz_dual(w: Callable[[U, T], S], u: U) -> Callable[[T], S]:
+def riesz_dual(w: Callable[[U, U], S], u: U) -> Callable[[U], S]:
     """Riesz dual vector associated with bilinear form.
 
     :w: Bilinear form

Python/src/nlsa/function_algebra.py

@@ -16,8 +16,7 @@
 X2 = TypeVar('X2')
 Y = TypeVar('Y')
 Z = TypeVar('Z')
-# A = TypeVar('A', bound=SupportsAdd)
-A = TypeVar('A')
+A = TypeVar('A', bound=SupportsAdd)
 S = TypeVar('S', bound=SupportsSub)
 K = TypeVar('K', bound=SupportsMul[object, object])
 M = TypeVar('M', bound=SupportsMatmul)
@@ -108,10 +107,9 @@ def incl(self, f: Callable[[X_co], T_contra]) -> V_co:
         ...
 
 
-def add(f: Callable[[X], SupportsAdd[A]], g: Callable[[X], SupportsAdd[A]])\
-        -> Callable[[X], SupportsAdd[A]]:
+def add(f: Callable[[X], A], g: Callable[[X], A]) -> Callable[[X], A]:
     """Implements function addition."""
-    def h(x: X) -> SupportsAdd[A]:
+    def h(x: X) -> A:
         y = f(x) + g(x)
         return y
     return h

Python/src/nlsa/matrix_algebra.py

@@ -97,15 +97,15 @@ def eig_sorted(a: A, n: Optional[int] = None,
 
     """
     wv = la.eig(a)
-    if which == 'LA' or 'SA' or 'LR' or 'SR':
+    if which in ('LA', 'SA', 'LR', 'SR'):
         idx = wv[0].real.argsort()
-    elif which == 'LI' or 'SI':
+    elif which in ('LI', 'SI'):
         idx = wv[0].imag.argsort()
-    elif which == 'LM' or 'SM':
+    elif which in ('LM', 'SM'):
         idx = wv[0].abs.argsort()
     if n is None:
         n = len(a)
-    if which == 'LA' or 'LM' or 'LR' or 'LI':
+    if which in ('LA', 'LM', 'LR', 'LI'):
         idx = idx[::-1]
     w: W = wv[0][idx[0:n]]
     v: A = wv[1][:, idx[0:n]]
@@ -135,7 +135,7 @@ def eigs_sorted(a: A, n: Optional[int] = None, which: WhichEigs = 'LR',
     else:
         wv = sla.eigs(a, n, which=which)
     idx = np.arange(0, n)
-    if which == 'LA' or 'LM' or 'LR' or 'LI':
+    if which in ('LA', 'LM', 'LR', 'LI'):
         idx = idx[::-1]
     w: W = wv[0][idx[0:n]]
     v: A = wv[1][:, idx[0:n]]