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pymepack binding for gem #2166

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pymepack binding for gem #2166

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cc8eb37
pymepack binding: cont lyap dense
AlexMaleyko May 31, 2023
e58af6c
added binding for iterative refinement solvers, added default options…
AlexMaleyko Jun 6, 2023
fb47cc5
added documentation for pymor/bindings/pymepack.py
AlexMaleyko Jun 8, 2023
7e377d9
updated options resolution in case of iterative refinement
AlexMaleyko Jun 24, 2023
4dfa433
added support for Schur vectors and (generalized) Hessenberg form in …
AlexMaleyko Aug 22, 2023
96c740b
restricted pymepack binding to support only general matrices
AlexMaleyko Aug 28, 2023
520e95e
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Aug 28, 2023
005083c
reverted copyright information in lyapunov.py
almalejko Sep 8, 2023
5232b81
modified inplace parameter default value
AlexMaleyko Nov 20, 2023
27d663f
[bindings.pymepack] fix ruff issues
pmli Nov 28, 2023
aafe4c2
[pyproject.toml] add pymepack
pmli Nov 28, 2023
1e63830
[Makefile] add pymepack
pmli Nov 28, 2023
3ca48f6
upgrade minimum SciPy
pmli Nov 28, 2023
59a7585
Up pymepack version to 1.1.1
almalejko Jul 2, 2024
d0c518d
updates pymepack version to 1.1.1 and makes update to ci requirements
almalejko Jul 3, 2024
75a2793
fixes style-check warnings
almalejko Jul 4, 2024
b668054
[.mailmap] update
pmli Jul 4, 2024
bcbb942
updates pymepack version to 1.1.1.post2, updates ci_requirements
almalejko Jul 7, 2024
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3 changes: 3 additions & 0 deletions .mailmap
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Original file line number Diff line number Diff line change
@@ -1,4 +1,7 @@
# Prevent git from showing duplicate names with commands like "git shortlog" (see docs/RELEASE_CHECKLIST.md)
Aleksey Maleyko <maleyko@mpi-magdeburg.mpg.de>
Aleksey Maleyko <maleyko@mpi-magdeburg.mpg.de> <alexeymaleyko@gmail.com>
Aleksey Maleyko <maleyko@mpi-magdeburg.mpg.de> almalejko <133660027+almalejko@users.noreply.github.com>
Alexandre Pasco <103425970+alexandre-pasco@users.noreply.github.com>
Art Pelling <a.pelling@tu-berlin.de> <account@artpelling.de>
Art Pelling <a.pelling@tu-berlin.de> Art J. R. Pelling <a.pelling@tu-berlin.de>
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3 changes: 2 additions & 1 deletion Makefile
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Expand Up @@ -43,6 +43,7 @@ CI_EXTRAS= \
--extra tests \
--extra ann \
--extra slycot \
--extra pymepack \
--extra ipyparallel \
--extra mpi \
--extra gui \
Expand Down Expand Up @@ -100,7 +101,7 @@ CONDA_EXTRAS = \
--extras gui \
--extras jupyter \
--extras vtk
# dune, ngsolve, scikit-fem (no recent version) not available as conda-forge packages
# pymepack, dune, ngsolve, scikit-fem (no recent version) not available as conda-forge packages
# pytorch not available for win64
# docs-additional not needed
# gmsh is incompatible with pyside6>=6.4.3 needed for windows ci not to hang
Expand Down
10 changes: 7 additions & 3 deletions pyproject.toml
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Expand Up @@ -33,7 +33,7 @@ dependencies = [
"pillow",
"pygments",
"qtpy>=2.3.1",
"scipy>=1.5.4",
"scipy>=1.6.0",
"typer",
]

Expand Down Expand Up @@ -76,11 +76,15 @@ dev = [
ann = [
"torch>=1.11.0",
]
# dense matrix equation solver for system-theoretic methods and H-infinity norm calculation
# dense matrix equation solvers for system-theoretic methods and H-infinity norm calculation
# requires OpenBLAS headers and a Fortran compiler
slycot = [
"slycot>=0.5.4",
]
# dense matrix equation solvers
pymepack = [
"pymepack>=1.1.1.post2",
]
# parallelization of some MOR algorithms (e.g. greedy search) using ipyparallel
ipyparallel = [
"ipyparallel>=6.2.5",
Expand Down Expand Up @@ -130,7 +134,7 @@ scikit-fem = [
# # Meta dependencies
# install all optional dependencies, except those requiring a compiler toolchain to build
full = [
"pymor[docs_additional,tests,dev,ann,ipyparallel,gui,jupyter,vtk,gmsh,dune,ngsolve,scikit-fem]",
"pymor[docs_additional,tests,dev,ann,pymepack,ipyparallel,gui,jupyter,vtk,gmsh,dune,ngsolve,scikit-fem]",
]
# install all optional dependencies, including those requiring a compiler toolchain to build
full-compiled = [
Expand Down
8 changes: 7 additions & 1 deletion requirements-ci-current.txt
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Expand Up @@ -2,7 +2,7 @@
# This file is autogenerated by pip-compile with Python 3.12
# by the following command:
#
# pip-compile --extra-index-url=https://download.pytorch.org/whl/cpu --extra=ann --extra=docs-additional --extra=gmsh --extra=gui --extra=ipyparallel --extra=jupyter --extra=mpi --extra=ngsolve --extra=scikit-fem --extra=slycot --extra=tests --extra=vtk --output-file=requirements-ci-current.txt --resolver=backtracking
# pip-compile --extra-index-url=https://download.pytorch.org/whl/cpu --extra=ann --extra=docs-additional --extra=gmsh --extra=gui --extra=ipyparallel --extra=jupyter --extra=mpi --extra=ngsolve --extra=pymepack --extra=scikit-fem --extra=slycot --extra=tests --extra=vtk --output-file=requirements-ci-current.txt --resolver=backtracking
#
--extra-index-url https://download.pytorch.org/whl/cpu

Expand Down Expand Up @@ -329,6 +329,7 @@ numpy==1.26.4
# matplotlib
# meshio
# pyevtk
# pymepack
# pymor (pyproject.toml)
# scikit-fem
# scipy
Expand All @@ -349,6 +350,8 @@ packaging==23.2
# sphinx
pandocfilters==1.5.1
# via nbconvert
parameterized==0.9.0
# via pymepack
parso==0.8.3
# via jedi
pexpect==4.9.0
Expand Down Expand Up @@ -400,6 +403,8 @@ pygments==2.17.2
# pymor (pyproject.toml)
# rich
# sphinx
pymepack==1.1.1.post2
# via pymor (pyproject.toml)
pyopengl==3.1.7
# via pymor (pyproject.toml)
pyparsing==3.1.1
Expand Down Expand Up @@ -481,6 +486,7 @@ scikit-fem==9.0.1
# via pymor (pyproject.toml)
scipy==1.12.0
# via
# pymepack
# pymor (pyproject.toml)
# scikit-fem
send2trash==1.8.2
Expand Down
8 changes: 7 additions & 1 deletion requirements-ci-oldest.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@
# This file is autogenerated by pip-compile with Python 3.8
# by the following command:
#
# pip-compile --extra-index-url=https://download.pytorch.org/whl/cpu --extra=ann --extra=docs-additional --extra=dune --extra=gmsh --extra=gui --extra=ipyparallel --extra=jupyter --extra=mpi --extra=ngsolve --extra=scikit-fem --extra=slycot --extra=tests --extra=vtk --output-file=requirements-ci-oldest.txt --resolver=backtracking pyproject.toml requirements-ci-oldest-pins.in
# pip-compile --extra-index-url=https://download.pytorch.org/whl/cpu --extra=ann --extra=docs-additional --extra=dune --extra=gmsh --extra=gui --extra=ipyparallel --extra=jupyter --extra=mpi --extra=ngsolve --extra=pymepack --extra=scikit-fem --extra=slycot --extra=tests --extra=vtk --output-file=requirements-ci-oldest.txt --resolver=backtracking pyproject.toml requirements-ci-oldest-pins.in
#
--extra-index-url https://download.pytorch.org/whl/cpu

Expand Down Expand Up @@ -354,6 +354,7 @@ numpy==1.20.3
# matplotlib
# meshio
# pyevtk
# pymepack
# pymor (pyproject.toml)
# scikit-fem
# scipy
Expand All @@ -374,6 +375,8 @@ packaging==23.2
# sphinx
pandocfilters==1.5.1
# via nbconvert
parameterized==0.9.0
# via pymepack
parso==0.8.3
# via jedi
pexpect==4.9.0
Expand Down Expand Up @@ -429,6 +432,8 @@ pygments==2.17.2
# pymor (pyproject.toml)
# rich
# sphinx
pymepack==1.1.1.post2
# via pymor (pyproject.toml)
pyopengl==3.1.7
# via pymor (pyproject.toml)
pyparsing==3.1.1
Expand Down Expand Up @@ -516,6 +521,7 @@ scipy==1.6.0
# via
# -r requirements-ci-oldest-pins.in
# dune-xt
# pymepack
# pymor (pyproject.toml)
# scikit-fem
send2trash==1.8.2
Expand Down
35 changes: 25 additions & 10 deletions src/pymor/algorithms/lyapunov.py
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Expand Up @@ -15,7 +15,7 @@
'cont': FrozenDict(
{
'sparse': 'lradi',
'dense': 'slycot' if config.HAVE_SLYCOT else 'scipy',
'dense': 'slycot' if config.HAVE_SLYCOT else 'pymepack' if config.HAVE_PYMEPACK else 'scipy',
}
),
'disc': FrozenDict({'dense': 'slycot' if config.HAVE_SLYCOT else 'scipy'}),
Expand Down Expand Up @@ -74,6 +74,7 @@ def solve_cont_lyap_lrcf(A, E, B, trans=False, options=None,

1. `slycot` (see :func:`pymor.bindings.slycot.solve_lyap_lrcf`),
2. `scipy` (see :func:`pymor.bindings.scipy.solve_lyap_lrcf`).
3. `pymepack` (see :func:`pymor.bindings.pymepack.solve_lyap_lrcf`),

Parameters
----------
Expand All @@ -92,11 +93,12 @@ def solve_cont_lyap_lrcf(A, E, B, trans=False, options=None,
- :func:`pymor.algorithms.lradi.lyap_lrcf_solver_options`,
- :func:`pymor.bindings.scipy.lyap_lrcf_solver_options`,
- :func:`pymor.bindings.slycot.lyap_lrcf_solver_options`,
- :func:`pymor.bindings.pymepack.lyap_lrcf_solver_options`.

default_sparse_solver_backend
Default sparse solver backend to use (lradi).
default_dense_solver_backend
Default dense solver backend to use (slycot, scipy).
Default dense solver backend to use (slycot, scipy, pymepack).

Returns
-------
Expand All @@ -118,6 +120,8 @@ def solve_cont_lyap_lrcf(A, E, B, trans=False, options=None,
from pymor.bindings.slycot import solve_lyap_lrcf as solve_lyap_impl
elif backend == 'lradi':
from pymor.algorithms.lradi import solve_lyap_lrcf as solve_lyap_impl
elif backend == 'pymepack':
from pymor.bindings.pymepack import solve_lyap_lrcf as solve_lyap_impl
else:
raise ValueError(f'Unknown solver backend ({backend}).')
return solve_lyap_impl(A, E, B, trans=trans, cont_time=True, options=options)
Expand Down Expand Up @@ -159,7 +163,8 @@ def solve_disc_lyap_lrcf(A, E, B, trans=False, options=None,
availability in the following order:

1. `slycot` (see :func:`pymor.bindings.slycot.solve_lyap_lrcf`),
2. `scipy` (see :func:`pymor.bindings.scipy.solve_lyap_lrcf`).
2. `pymepack` (see :func:`pymor.bindings.pymepack.solve_lyap_lrcf`),
3. `scipy` (see :func:`pymor.bindings.scipy.solve_lyap_lrcf`).

Parameters
----------
Expand All @@ -176,10 +181,11 @@ def solve_disc_lyap_lrcf(A, E, B, trans=False, options=None,
See:

- :func:`pymor.bindings.scipy.lyap_lrcf_solver_options`,
- :func:`pymor.bindings.slycot.lyap_lrcf_solver_options`.
- :func:`pymor.bindings.slycot.lyap_lrcf_solver_options`,
- :func:`pymor.bindings.pymepack.lyap_lrcf_solver_options`.

default_dense_solver_backend
Default dense solver backend to use (slycot, scipy).
Default dense solver backend to use (slycot, pymepack, scipy).

Returns
-------
Expand All @@ -196,6 +202,8 @@ def solve_disc_lyap_lrcf(A, E, B, trans=False, options=None,
from pymor.bindings.scipy import solve_lyap_lrcf as solve_lyap_impl
elif backend == 'slycot':
from pymor.bindings.slycot import solve_lyap_lrcf as solve_lyap_impl
elif backend == 'pymepack':
from pymor.bindings.pymepack import solve_lyap_lrcf as solve_lyap_impl
else:
raise ValueError(f'Unknown solver backend ({backend}).')
return solve_lyap_impl(A, E, B, trans=trans, cont_time=False, options=options)
Expand Down Expand Up @@ -250,6 +258,7 @@ def solve_cont_lyap_dense(A, E, B, trans=False, options=None,

1. `slycot` (see :func:`pymor.bindings.slycot.solve_lyap_dense`)
2. `scipy` (see :func:`pymor.bindings.scipy.solve_lyap_dense`)
3. `pymepack` (see :func:`pymor.bindings.pymepack.solve_lyap_dense`)

Parameters
----------
Expand All @@ -267,9 +276,10 @@ def solve_cont_lyap_dense(A, E, B, trans=False, options=None,

- :func:`pymor.bindings.scipy.lyap_dense_solver_options`,
- :func:`pymor.bindings.slycot.lyap_dense_solver_options`,
- :func:`pymor.bindings.pymepack.lyap_dense_solver_options`.

default_solver_backend
Default solver backend to use (slycot, scipy).
Default solver backend to use (slycot, scipy, pymepack).

Returns
-------
Expand All @@ -286,6 +296,8 @@ def solve_cont_lyap_dense(A, E, B, trans=False, options=None,
from pymor.bindings.scipy import solve_lyap_dense as solve_lyap_impl
elif backend == 'slycot':
from pymor.bindings.slycot import solve_lyap_dense as solve_lyap_impl
elif backend == 'pymepack':
from pymor.bindings.pymepack import solve_lyap_dense as solve_lyap_impl
else:
raise ValueError(f'Unknown solver backend ({backend}).')
return solve_lyap_impl(A, E, B, trans=trans, cont_time=True, options=options)
Expand Down Expand Up @@ -325,7 +337,8 @@ def solve_disc_lyap_dense(A, E, B, trans=False, options=None,
availability in the following order:

1. `slycot` (see :func:`pymor.bindings.slycot.solve_lyap_dense`)
2. `scipy` (see :func:`pymor.bindings.scipy.solve_lyap_dense`)
2. `pymepack` (see :func:`pymor.bindings.pymepack.solve_lyap_dense`)
3. `scipy` (see :func:`pymor.bindings.scipy.solve_lyap_dense`)

Parameters
----------
Expand All @@ -343,10 +356,11 @@ def solve_disc_lyap_dense(A, E, B, trans=False, options=None,
See:

- :func:`pymor.bindings.scipy.lyap_dense_solver_options`,
- :func:`pymor.bindings.slycot.lyap_dense_solver_options`.
- :func:`pymor.bindings.slycot.lyap_dense_solver_options`,
- :func:`pymor.bindings.pymepack.lyap_dense_solver_options`.

default_solver_backend
Default solver backend to use (slycot, scipy).
Default solver backend to use (slycot, pymepack, scipy).

Returns
-------
Expand All @@ -363,6 +377,8 @@ def solve_disc_lyap_dense(A, E, B, trans=False, options=None,
from pymor.bindings.scipy import solve_lyap_dense as solve_lyap_impl
elif backend == 'slycot':
from pymor.bindings.slycot import solve_lyap_dense as solve_lyap_impl
elif backend == 'pymepack':
from pymor.bindings.pymepack import solve_lyap_dense as solve_lyap_impl
else:
raise ValueError(f'Unknown solver backend ({backend}).')
return solve_lyap_impl(A, E, B, trans=trans, cont_time=False, options=options)
Expand All @@ -381,7 +397,6 @@ def _solve_lyap_dense_check_args(A, E, B, trans):
assert A.ndim == 2
assert not trans and B.shape[0] == A.shape[0] or trans and B.shape[1] == A.shape[0]


def _chol(A):
"""Cholesky decomposition.

Expand Down
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