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Port read and write functions #70

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merged 4 commits into from
Jun 14, 2024
Merged

Port read and write functions #70

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097a117
Port `read` and `write` functions
mtsokol Jun 13, 2024
8724f7d
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mtsokol Jun 13, 2024
bbcb63c
Add remaining IO dependencies
mtsokol Jun 14, 2024
8813fd0
Add missing `resolve()`
mtsokol Jun 14, 2024
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6 changes: 6 additions & 0 deletions src/finch/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -130,6 +130,10 @@
iinfo,
can_cast,
)
from .io import (
read,
write,
)

__all__ = [
"Tensor",
Expand Down Expand Up @@ -252,6 +256,8 @@
"real",
"imag",
"conj",
"read",
"write",
]

__array_api_version__: str = "2023.12"
11 changes: 11 additions & 0 deletions src/finch/io.py
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@@ -0,0 +1,11 @@
from .julia import jl
from .tensor import Tensor


def read(filename: str) -> Tensor:
julia_obj = jl.fread(filename)
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return Tensor(julia_obj)


def write(filename: str, tns: Tensor) -> None:
jl.fwrite(filename, tns._obj)
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1 change: 1 addition & 0 deletions src/finch/julia.py
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Expand Up @@ -30,3 +30,4 @@

jl.seval("using Finch")
jl.seval("using Random")
jl.seval("using TensorMarket")
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Will this limit us to just this format?

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No, it's just a dependency. Here's a list of all supported formats: https://willowahrens.io/Finch.jl/stable/guides/fileio/#Finch.fread

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Do we need to pull in any other dependencies for other formats?

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@willow-ahrens Are there other IO related dependencies that we should install during the setup to fully support fread and fwrite?

In Finch.jl in Project.toml I found three more:

[weakdeps]
HDF5 = "f67ccb44-e63f-5c2f-98bd-6dc0ccc4ba2f"
NPZ = "15e1cf62-19b3-5cfa-8e77-841668bca605"
SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
TensorMarket = "8b7d4fe7-0b45-4d0d-9dd8-5cc9b23b4b77"

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HDF5, NPZ, and TensorMarket are required for binsparse and ttx files.

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These should be added with pkg.add when we add Finch, or loaded dynamically depending on whether we want to take a dependency on hdf5

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Thanks! I load them dynamically.

17 changes: 17 additions & 0 deletions tests/data/matrix_1.ttx
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%%MatrixMarket matrix coordinate integer general
3 5 15
1 1 0
2 1 1
3 1 0
1 2 0
2 2 0
3 2 5
1 3 3
2 3 0
3 3 0
1 4 2
2 4 1
3 4 0
1 5 0
2 5 0
3 5 0
25 changes: 25 additions & 0 deletions tests/test_io.py
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import os

from numpy.testing import assert_equal

import finch

base_path = "tests/data"


def test_read(arr2d):
tns = finch.read(f"{base_path}/matrix_1.ttx")

assert_equal(tns.todense(), arr2d)


def test_write(arr2d):
tns = finch.asarray(arr2d)
finch.write(f"{base_path}/tmp.ttx", tns)

expected = open(f"{base_path}/matrix_1.ttx").read()
actual = open(f"{base_path}/tmp.ttx").read()
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assert actual == expected

os.remove(f"{base_path}/tmp.ttx")
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