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Add `zfp` and `zfpy` (#5172) 

Co-authored-by: Gyeongjae Choi <def6488@gmail.com>
This commit is contained in:
Agriya Khetarpal 2024-11-09 22:30:01 +08:00 committed by GitHub
parent 870a67c9b1
commit 4c2878f01e
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GPG Key ID: B5690EEEBB952194
6 changed files with 216 additions and 1 deletions
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2
.pre-commit-config.yaml
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@ -82,7 +82,7 @@ repos:
name: mypy-tests
args: [--ignore-missing-imports]
files: ^(packages/|docs|/conftest.py|src/tests)
exclude: (^packages/.*/setup.py|/src|^packages/aiohttp/aiohttp_patch.py$)
exclude: (^packages/.*/setup.py|/src|^packages/aiohttp/aiohttp_patch.py$|^packages/zfpy/test_zfpy.py$)
additional_dependencies: *mypy-deps
- repo: https://github.com/pre-commit/mirrors-prettier

1
docs/project/changelog.md
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@ -105,6 +105,7 @@ myst:
- Added `tree-sitter-java` 0.23.2 {pr}`5102`
- Added `tree-sitter-python` 0.23.2 {pr}`5102`
- Added `Narwhals` 1.9.4 {pr}`5121`
- Added `libzfp` and `zfpy` 1.0.1 {pr}`5172`
## Version 0.26.3

34
packages/libzfp/meta.yaml Normal file
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@ -0,0 +1,34 @@
package:
name: libzfp
version: 1.0.1
tag:
- library
- static_library
source:
url: https://github.com/LLNL/zfp/archive/refs/tags/1.0.1.tar.gz
sha256: 4984db6a55bc919831966dd17ba5e47ca7ac58668f4fd278ebd98cd2200da66f
build:
type: static_library
exports: requested
script: |
mkdir -p build
cd build
emcmake cmake ${CMAKE_ARGS} \
-DBUILD_CFP=ON \
-DBUILD_UTILITIES=OFF \
-DBUILD_TESTING=OFF \
-DBUILD_SHARED_LIBS=OFF \
-DZFP_ENABLE_PIC=OFF \
-DCMAKE_BUILD_TYPE=Release \
-DCMAKE_C_FLAGS="-s WASM=1" \
-DZFP_WITH_OPENMP=OFF \
-DCMAKE_INSTALL_PREFIX=${WASM_LIBRARY_DIR} \
..
emmake make -j ${PYODIDE_JOBS:-3} install
about:
home: https://zfp.llnl.gov/
summary: Open-source software for compressed floating-point arrays
license: BSD-3-Clause

37
packages/zfpy/meta.yaml Normal file
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@ -0,0 +1,37 @@
package:
name: zfpy
version: 1.0.1
top-level:
- zfpy
source:
# There's no sdist for zfpy on PyPI, so we get the tarball from the GitHub release instead
url: https://github.com/LLNL/zfp/archive/refs/tags/1.0.1.tar.gz
sha256: 4984db6a55bc919831966dd17ba5e47ca7ac58668f4fd278ebd98cd2200da66f
patches:
- patches/Modernise-packaging.patch
build:
exports: requested
cflags: |
-I$(PYTHONINCLUDE)
-I$(WASM_LIBRARY_DIR)/include
ldflags: |
-L$(WASM_LIBRARY_DIR)/lib
requirements:
host:
- libzfp
- numpy
run:
- numpy
test:
imports:
- zfpy
about:
home: https://zfp.llnl.gov/
PyPI: https://pypi.org/project/zfpy/
summary: zfp compression in Python
license: BSD-3-Clause

69
packages/zfpy/patches/Modernise-packaging.patch Normal file
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@ -0,0 +1,69 @@
From f36ef86e67185b16b65445092c40a3d75d0be45c Mon Sep 17 00:00:00 2001
From: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>
Date: Fri, 8 Nov 2024 02:46:00 +0530
Subject: [PATCH] Modernise packaging
This patch introduces a PEP 517/518 compliant build system using setuptools and
declarative metadata in pyproject.toml, and fixes syntax errors in setup.py. The
sources for the extension module are correctly specified as Cython source files.
Some part of the credits go to the upstream
PR at https://github.com/LLNL/zfp/pull/234
Co-Authored-By: David M. Rogers <2243447+frobnitzem@users.noreply.github.com>
---
pyproject.toml | 13 +++++++++++++
setup.py | 18 +++++++++---------
2 files changed, 22 insertions(+), 9 deletions(-)
create mode 100644 pyproject.toml
diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 0000000..88adcc8
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,13 @@
+[build-system]
+requires = ["setuptools", "cython", "numpy"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "zfpy"
+version = "1.0.1"
+authors = [
+ { name = "Peter Lindstrom", email = "zfp@llnl.gov" },
+ { name = "Danielle Asher", email = "zfp@llnl.gov" },
+]
+description = "zfp compression in Python"
+requires-python = ">=3.0"
diff --git a/setup.py b/setup.py
index fa2da6e..919fa7c 100644
--- a/setup.py
+++ b/setup.py
@@ -2,14 +2,14 @@ from setuptools import setup, Extension
import numpy as np
setup(
- name="zfpy",
- version="1.0.1",
- author="Peter Lindstrom, Danielle Asher",
- author_email="zfp@llnl.gov",
url="https://zfp.llnl.gov",
- description="zfp compression in Python",
- long_description="zfp is a compressed format for representing multidimensional floating-point and integer arrays. zfp provides compressed-array classes that support high throughput read and write random access to individual array elements. zfp also supports serial and parallel compression of whole arrays using both lossless and lossy compression with error tolerances. zfp is primarily written in C and C++ but also includes Python and Fortran bindings.",
- ext_modules=[Extension("zfpy", ["build/python/zfpy.c"],
- include_dirs=["include", np.get_include()],
- libraries=["zfp"], library_dirs=["build/lib64", "build/lib/Release"]), language_level = "3"]
+ ext_modules=
+ [
+ Extension(
+ name="zfpy",
+ sources=["python/zfpy.pyx"],
+ include_dirs=["include", np.get_include()],
+ libraries=["zfp"],
+ library_dirs=["build/lib64", "build/lib"])
+ ],
)
--
2.39.3 (Apple Git-146)

74
packages/zfpy/test_zfpy.py Normal file
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@ -0,0 +1,74 @@
from pytest_pyodide import run_in_pyodide
@run_in_pyodide(packages=["zfpy", "numpy"])
def test_compression(selenium):
import numpy as np
import zfpy
my_array = np.arange(1, 20)
compressed_data = zfpy.compress_numpy(my_array)
decompressed_array = zfpy.decompress_numpy(compressed_data)
np.testing.assert_array_equal(my_array, decompressed_array)
@run_in_pyodide(packages=["zfpy", "numpy"])
def test_compression_with_tolerance(selenium):
import numpy as np
import zfpy
my_array = np.linspace(0, 1, 1000)
compressed_data = zfpy.compress_numpy(my_array, tolerance=1e-3)
decompressed_array = zfpy.decompress_numpy(compressed_data)
np.testing.assert_allclose(my_array, decompressed_array, atol=1e-3)
@run_in_pyodide(packages=["zfpy", "numpy"])
def test_different_dimensions(selenium) -> None:
import numpy as np
import zfpy
np.random.seed(42)
# Test arrays; from 1D to 4D
for dimensions in range(1, 5):
# 1. test with uniform dimensions
shape1 = tuple([5] * dimensions)
array = np.random.rand(*shape1).astype(np.float64)
compressed1 = zfpy.compress_numpy(array, write_header=True)
decompressed1 = zfpy.decompress_numpy(compressed1)
np.testing.assert_array_equal(decompressed1, array)
# 2. test with increasing dimensions
shape2 = tuple(range(2, 2 + dimensions))
array = np.random.rand(*shape2).astype(np.float64)
compressed2 = zfpy.compress_numpy(array, write_header=True)
decompressed2 = zfpy.decompress_numpy(compressed2)
np.testing.assert_array_equal(decompressed2, array)
@run_in_pyodide(packages=["zfpy", "numpy"])
def test_different_dtypes(selenium) -> None:
"""Test ZFP compression/decompression with different numeric dtypes."""
import numpy as np
import zfpy
np.random.seed(42)
shape = (5, 5)
num_elements = np.prod(shape)
# Test floating-point types
for dtype in [np.float32, np.float64]:
elements = np.random.random_sample(num_elements)
array = np.reshape(elements, shape).astype(dtype)
compressed1 = zfpy.compress_numpy(array, write_header=True)
decompressed1 = zfpy.decompress_numpy(compressed1)
np.testing.assert_array_equal(decompressed1, array)
# Test integer types
for dtype in [np.int32, np.int64]:
array = np.random.randint(low=-(2**30), high=2**30, size=shape, dtype=dtype)
compressed2 = zfpy.compress_numpy(array, write_header=True)
decompressed2 = zfpy.decompress_numpy(compressed2)
np.testing.assert_array_equal(decompressed2, array)