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flame graph CG #43

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5e173dc
wip: N-D `LinearOperator`
lucascolley Oct 16, 2025
8510ef5
WIP: batch `sparse.linalg.cg`
lucascolley Oct 21, 2025
99a6236
WIP: batch `sparse.linalg.cg`
lucascolley Oct 21, 2025
ed2646c
WIP: array API for `cg`
lucascolley Nov 14, 2025
6734fe4
flame
lucascolley Nov 28, 2025
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10,188 changes: 2,063 additions & 8,125 deletions pixi.lock
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245 changes: 142 additions & 103 deletions pixi.toml
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Expand Up @@ -26,115 +26,120 @@ solve-group = "default"

[environments.ipython]
# tasks: ipython
features = ["run-deps", "test-deps", "ipython"]
features = ["run-deps", "test-deps", "ipython-dep", "ipython-task"]
solve-group = "default"

[environments.build-debug]
# tasks: build-debug
features = ["build-deps", "build-debug"]
solve-group = "debug"

[environments.lldb]
# tasks: lldb
features = ["run-deps", "test-deps", "lldb"]
solve-group = "debug"

[environments.gdb]
# tasks: gdb
features = ["run-deps", "test-deps", "gdb"]
solve-group = "debug"

[environments.lint]
# tasks: lint, check-python-h
features = ["lint"]

# TODO(lucascolley): merge the `default` and `array-api-cpu` solve groups,
# and create a non-default solve group with minimal dependencies
# to more reliably test the very latest versions of core dependencies
[environments.build-cpu]
# tasks: build-cpu
features = ["build-deps", "build-cpu"]
solve-group = "array-api-cpu"

[environments.array-api-strict]
# tasks: test-strict
features = ["run-deps", "test-deps", "array_api_strict", "array_api_strict-tasks"]
solve-group = "array-api-cpu"

[environments.dask-cpu]
# tasks: test-dask
features = ["run-deps", "test-deps", "dask", "dask-tasks"]
solve-group = "array-api-cpu"

[environments.jax-cpu]
# tasks: test-jax
features = ["run-deps", "test-deps", "mkl", "jax-cpu", "jax-cpu-tasks"]
solve-group = "array-api-cpu"

[environments.torch-cpu]
# tasks: test-torch, test-torch-float32
features = ["run-deps", "test-deps", "mkl", "torch-cpu", "torch-cpu-tasks"]
solve-group = "array-api-cpu"

[environments.array-api-cpu]
# tasks: test-cpu
features = ["run-deps", "test-deps", "test-cpu", "mkl", "array_api_strict", "dask", "jax-cpu", "marray", "torch-cpu"]
solve-group = "array-api-cpu"

[environments.build-cuda]
# tasks: build-cuda
# note: py-cuda feature aims to ensure compatibility with both cuda12 and cuda13 solve groups
features = ["build-deps", "build-cuda", "py-cuda"]

[environments.cupy]
# tasks: test-cupy
features = ["run-deps", "test-deps", "cuda13", "py-cuda", "cupy"]
solve-group = "cuda13"

[environments.jax-cuda]
# tasks: test-jax-cuda
features = ["run-deps", "test-deps", "cuda12", "py-cuda", "mkl", "jax-cuda"]
solve-group = "cuda12"

[environments.torch-cuda]
# tasks: test-torch-cuda
features = ["run-deps", "test-deps", "cuda12", "py-cuda", "mkl", "torch-cuda"]
solve-group = "cuda12"

[environments.build-accelerate-lp64]
# tasks: build-accelerate-lp64
features = ["build-deps", "accelerate", "build-accelerate-lp64"]
solve-group = "accelerate-lp64"

[environments.accelerate-lp64]
# tasks: test-accelerate-lp64
features = ["run-deps", "test-deps", "accelerate", "accelerate-lp64"]
solve-group = "accelerate-lp64"

[environments.build-accelerate-ilp64]
# tasks: build-accelerate-ilp64
features = ["build-deps", "accelerate", "build-accelerate-ilp64"]
solve-group = "accelerate-ilp64"

[environments.accelerate-ilp64]
# tasks: test-accelerate-ilp64
features = ["run-deps", "test-deps", "accelerate", "accelerate-ilp64"]
solve-group = "accelerate-ilp64"

[environments.py311-system-libs-osx]
# tasks: build-system-libs, test-system-libs
features = ["build-deps", "run-deps", "test-deps", "py311", "umfpack", "scikit-sparse", "system-libs"]

[environments.scipy-openblas]
# tasks: build-scipy-openblas, test-scipy-openblas
features = ["build-deps", "run-deps", "test-deps", "scipy-openblas"]
[environments.profile]
# tasks: profile-shell
features = ["run-deps", "profile"]
solve-group = "default"

# [environments.build-debug]
# # tasks: build-debug
# features = ["build-deps", "build-debug"]
# solve-group = "debug"

# [environments.lldb]
# # tasks: lldb
# features = ["run-deps", "test-deps", "lldb"]
# solve-group = "debug"

# [environments.gdb]
# # tasks: gdb
# features = ["run-deps", "test-deps", "gdb"]
# solve-group = "debug"

# [environments.lint]
# # tasks: lint, check-python-h
# features = ["lint"]

# # TODO(lucascolley): merge the `default` and `array-api-cpu` solve groups,
# # and create a non-default solve group with minimal dependencies
# # to more reliably test the very latest versions of core dependencies
# [environments.build-cpu]
# # tasks: build-cpu
# features = ["build-deps", "build-cpu"]
# solve-group = "array-api-cpu"

# [environments.array-api-strict]
# # tasks: test-strict
# features = ["run-deps", "test-deps", "array_api_strict", "array_api_strict-tasks"]
# solve-group = "array-api-cpu"

# [environments.dask-cpu]
# # tasks: test-dask
# features = ["run-deps", "test-deps", "dask", "dask-tasks"]
# solve-group = "array-api-cpu"

# [environments.jax-cpu]
# # tasks: test-jax
# features = ["run-deps", "test-deps", "mkl", "jax-cpu", "jax-cpu-tasks"]
# solve-group = "array-api-cpu"

# [environments.torch-cpu]
# # tasks: test-torch, test-torch-float32
# features = ["run-deps", "test-deps", "mkl", "torch-cpu", "torch-cpu-tasks"]
# solve-group = "array-api-cpu"

# [environments.array-api-cpu]
# # tasks: test-cpu, ipython-cpu
# features = ["run-deps", "test-deps", "test-cpu", "mkl", "array_api_strict", "dask", "jax-cpu", "marray", "torch-cpu", "ipython-dep", "ipython-cpu-task"]
# solve-group = "array-api-cpu"

# [environments.build-cuda]
# # tasks: build-cuda
# # note: py-cuda feature aims to ensure compatibility with both cuda12 and cuda13 solve groups
# features = ["build-deps", "build-cuda", "py-cuda"]

# [environments.cupy]
# # tasks: test-cupy
# features = ["run-deps", "test-deps", "cuda13", "py-cuda", "cupy"]
# solve-group = "cuda13"

# [environments.jax-cuda]
# # tasks: test-jax-cuda
# features = ["run-deps", "test-deps", "cuda12", "py-cuda", "mkl", "jax-cuda"]
# solve-group = "cuda12"

# [environments.torch-cuda]
# # tasks: test-torch-cuda
# features = ["run-deps", "test-deps", "cuda12", "py-cuda", "mkl", "torch-cuda"]
# solve-group = "cuda12"

# [environments.build-accelerate-lp64]
# # tasks: build-accelerate-lp64
# features = ["build-deps", "accelerate", "build-accelerate-lp64"]
# solve-group = "accelerate-lp64"

# [environments.accelerate-lp64]
# # tasks: test-accelerate-lp64
# features = ["run-deps", "test-deps", "accelerate", "accelerate-lp64"]
# solve-group = "accelerate-lp64"

# [environments.build-accelerate-ilp64]
# # tasks: build-accelerate-ilp64
# features = ["build-deps", "accelerate", "build-accelerate-ilp64"]
# solve-group = "accelerate-ilp64"

# [environments.accelerate-ilp64]
# # tasks: test-accelerate-ilp64
# features = ["run-deps", "test-deps", "accelerate", "accelerate-ilp64"]
# solve-group = "accelerate-ilp64"

# [environments.py311-system-libs-osx]
# # tasks: build-system-libs, test-system-libs
# features = ["build-deps", "run-deps", "test-deps", "py311", "umfpack", "scikit-sparse", "system-libs"]

# [environments.scipy-openblas]
# # tasks: build-scipy-openblas, test-scipy-openblas
# features = ["build-deps", "run-deps", "test-deps", "scipy-openblas"]


### Default dependencies (included in all environments) ###

[dependencies]
spin = "*"
python = "*"
python = "3.13.*"


### Default run dependencies (for environments which run SciPy itself) ###
Expand Down Expand Up @@ -221,14 +226,20 @@ description = "Build the documentation"

### IPython ###

[feature.ipython.dependencies]
[feature.ipython-dep.dependencies]
ipython = "*"

[feature.ipython.tasks.ipython]
[feature.ipython-task.tasks.ipython]
cmd = "spin ipython --no-build"
depends-on = "build"
description = "Launch IPython"

[feature.ipython-cpu-task.tasks.ipython-cpu]
cmd = "spin ipython --build-dir=build-cpu --no-build"
depends-on = "build-cpu"
env.SCIPY_ARRAY_API = "1"
description = "Launch IPython"


### Debugging ###

Expand Down Expand Up @@ -265,6 +276,34 @@ depends-on = "build-debug"
description = "Debug with gdb"


### Profiling ###

[feature.profile.dependencies]
py-spy = "*"

[feature.profile.pypi-dependencies]
flamegraph.git = "https://github.com/nickodell/python-flamegraph.git"

[feature.profile.tasks._log_flamegraph]
cmd = "spin run 'cd tools && python -m flamegraph -o {{ log_name }}.log {{ script_name }}.py'"
args = ["script_name", "log_name"]
depends-on = "build"

[feature.profile.tasks.flamegraph]
cmd = "./flamegraph.pl {{ log_name }}.log > {{ log_name }}.svg"
args = ["script_name", "log_name"]
cwd = "tools"
depends-on = [{ task = "_log_flamegraph", args = ["{{ script_name }}", "{{ log_name }}"]}]
description = "Generate a flamegraph {{ log_name }}.svg from {{ script_name }}.py"

[feature.profile.tasks.py-spy]
cmd = "sudo py-spy record -o {{ log_name }}.svg -- python {{ script_name }}.py"
args = ["script_name", "log_name"]
cwd = "tools"
depends-on = "build"
description = "Generate a py-spy flamegraph {{ log_name }}.svg from {{ script_name }}.py"


### Linting ###

[feature.lint]
Expand Down
4 changes: 4 additions & 0 deletions scipy/_lib/_array_api.py
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Expand Up @@ -1028,3 +1028,7 @@ def xp_device_type(a: Array) -> Literal["cpu", "cuda", None]:
return xp_device_type(a._meta)
# array-api-strict is a stand-in for unknown libraries; don't special-case it
return None


def xp_isscalar(x):
return np.isscalar(x) or (is_array_api_obj(x) and x.ndim == 0)
4 changes: 2 additions & 2 deletions scipy/sparse/_sputils.py
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Expand Up @@ -369,14 +369,14 @@ def isintlike(x) -> bool:
return True


def isshape(x, nonneg=False, *, allow_nd=(2,)) -> bool:
def isshape(x, nonneg=False, *, allow_nd=(2,), check_nd=True) -> bool:
"""Is x a valid tuple of dimensions?

If nonneg, also checks that the dimensions are non-negative.
Shapes of length in the tuple allow_nd are allowed.
"""
ndim = len(x)
if ndim not in allow_nd:
if check_nd and ndim not in allow_nd:
return False

for d in x:
Expand Down
2 changes: 2 additions & 0 deletions scipy/sparse/linalg/_eigen/_svds.py
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Expand Up @@ -34,6 +34,8 @@ def _iv(A, k, ncv, tol, which, v0, maxiter,
if math.prod(A.shape) == 0:
message = "`A` must not be empty."
raise ValueError(message)
if len(A.shape) != 2:
raise ValueError("Only 2-D input is supported for `A` (a single matrix)")

# input validation/standardization for `k`
kmax = min(A.shape) if solver == 'propack' else min(A.shape) - 1
Expand Down
2 changes: 1 addition & 1 deletion scipy/sparse/linalg/_eigen/tests/test_svds.py
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Expand Up @@ -133,7 +133,7 @@ class SVDSCommonTests:
_A_empty_msg = "`A` must not be empty."
_A_dtype_msg = "`A` must be of numeric data type"
_A_type_msg = "type not understood"
_A_ndim_msg = "array must have ndim <= 2"
_A_ndim_msg = "Only 2-D input"
_A_validation_inputs = [
(np.asarray([[]]), ValueError, _A_empty_msg),
(np.array([['a', 'b'], ['c', 'd']], dtype='object'), ValueError, _A_dtype_msg),
Expand Down
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