Merge branch 'main' into md-docs

maxrjones · maxrjones · commit a26bbbe7f5ad · 2026-03-18T20:36:16.000-04:00
diff --git a/.github/codecov.yml b/.github/codecov.yml
@@ -8,7 +8,7 @@ coverage:
       default:
         target: 100
   ignore:
-    - "numcodecs/tests/**"
+    - "tests/**"
 comment:
   layout: "diff, files"
   behavior: default
diff --git a/MANIFEST.in b/MANIFEST.in
@@ -1,4 +1,3 @@
 recursive-include c-blosc *
 recursive-include numcodecs *.pyx
 recursive-include numcodecs *.pxd
-include numcodecs/tests/package_with_entrypoint-0.1.dist-info/entry_points.txt
diff --git a/README.md b/README.md
@@ -0,0 +1,9 @@
+# Numcodecs
+
+Numcodecs is a Python package providing buffer compression and transformation
+codecs for use in data storage and communication applications.
+
+[![Docs](https://readthedocs.org/projects/numcodecs/badge/?version=latest)](https://numcodecs.readthedocs.io/en/latest/?badge=latest)
+[![Tests](https://github.com/zarr-developers/numcodecs/actions/workflows/ci.yaml/badge.svg?branch=main)](https://github.com/zarr-developers/numcodecs/actions/workflows/ci.yaml)
+[![Wheels](https://github.com/zarr-developers/numcodecs/actions/workflows/wheel.yaml/badge.svg?branch=main)](https://github.com/zarr-developers/numcodecs/actions/workflows/wheel.yaml)
+[![Codecov](https://codecov.io/gh/zarr-developers/numcodecs/branch/main/graph/badge.svg)](https://codecov.io/gh/zarr-developers/numcodecs)
diff --git a/docs/release.md b/docs/release.md
@@ -17,7 +17,10 @@
 ### Maintenance
 
 * Convert documentation from reStructuredText to Markdown using MyST.
-  By {user}`Max Jones <maxrjones>`
+  By {user}`Max Jones <maxrjones>`, :issue:`830`
+
+* Move tests out of installable package into top-level ``tests/`` directory.
+  By :user:`Max Jones <maxrjones>`, :issue:`829`
 
 (release_0.16.5)=
 
diff --git a/notebooks/benchmark_vlen.ipynb b/notebooks/benchmark_vlen.ipynb
@@ -63,18 +63,10 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
-   "source": [
-    "from numcodecs.tests.common import greetings\n",
-    "\n",
-    "msgpack_codec = numcodecs.MsgPack()\n",
-    "json_codec = numcodecs.JSON()\n",
-    "pickle_codec = numcodecs.Pickle()\n",
-    "cat_codec = numcodecs.Categorize(greetings, dtype=object, astype='u1')\n",
-    "vlen_codec = numcodecs.VLenUTF8()"
-   ]
+   "source": "from tests.common import greetings\n\nmsgpack_codec = numcodecs.MsgPack()\njson_codec = numcodecs.JSON()\npickle_codec = numcodecs.Pickle()\ncat_codec = numcodecs.Categorize(greetings, dtype=object, astype='u1')\nvlen_codec = numcodecs.VLenUTF8()"
   },
   {
    "cell_type": "markdown",
@@ -677,4 +669,4 @@
  },
  "nbformat": 4,
  "nbformat_minor": 2
-}
+}
diff --git a/numcodecs/tests/__init__.py b/numcodecs/tests/__init__.py
diff --git a/pyproject.toml b/pyproject.toml
@@ -13,7 +13,7 @@ name = "numcodecs"
 description = """
 A Python package providing buffer compression and transformation codecs \
 for use in data storage and communication applications."""
-readme = "README.rst"
+readme = "README.md"
 dependencies = ["numpy>=1.24", "typing_extensions"]
 requires-python = ">=3.11"
 dynamic = [
@@ -102,14 +102,11 @@ test-zarr-main = [
 
 [tool.setuptools]
 package-dir = {"" = "."}
-packages = ["numcodecs", "numcodecs.tests"]
+packages = ["numcodecs"]
 zip-safe = false
 
 [tool.setuptools.package-data]
-numcodecs = [
-    "tests/package_with_entrypoint/__init__.py",
-    "tests/package_with_entrypoint-0.1.dist-info/entry_points.txt"
-]
+numcodecs = []
 
 [tool.setuptools_scm]
 version_scheme = "guess-next-dev"
@@ -121,7 +118,7 @@ skip = "./.git,fixture"
 ignore-words-list = "ba, compiletime, hist, nd, unparseable"
 
 [tool.coverage.run]
-omit = ["numcodecs/tests/*"]
+omit = ["tests/*"]
 
 [tool.coverage.report]
 exclude_lines = [
@@ -140,7 +137,7 @@ doctest_optionflags = [
     "IGNORE_EXCEPTION_DETAIL",
 ]
 testpaths = [
-    "numcodecs/tests",
+    "tests",
 ]
 norecursedirs = [
     ".git",
@@ -231,7 +228,7 @@ ignore = [
 ]
 
 [tool.ruff.lint.extend-per-file-ignores]
-"numcodecs/tests/**" = ["SIM201", "SIM202", "SIM300", "TRY002"]
+"tests/**" = ["SIM201", "SIM202", "SIM300", "TRY002"]
 "notebooks/**" = ["W391"]  # https://github.com/astral-sh/ruff/issues/13763
 
 [tool.ruff.format]
@@ -288,9 +285,9 @@ test-google-crc32c = ["test", "test-google-crc32c"]
 ls-deps-312 = "uv run --group test-zarr-312 uv pip freeze"
 ls-deps-313 = "uv run --group test-zarr-313 uv pip freeze"
 ls-deps-main = "uv run --group test-zarr-main uv pip freeze"
-test-zarr-312 = "uv run --group test-zarr-312 pytest --cov=numcodecs --cov-report=xml --cov-report=term numcodecs/tests/test_zarr3.py numcodecs/tests/test_zarr3_import.py"
-test-zarr-313 = "uv run --group test-zarr-313 pytest --cov=numcodecs --cov-report=xml --cov-report=term numcodecs/tests/test_zarr3.py numcodecs/tests/test_zarr3_import.py"
-test-zarr-main = "uv run --group test-zarr-main pytest --cov=numcodecs --cov-report=xml --cov-report=term numcodecs/tests/test_zarr3.py numcodecs/tests/test_zarr3_import.py"
+test-zarr-312 = "uv run --group test-zarr-312 pytest --cov=numcodecs --cov-report=xml --cov-report=term tests/test_zarr3.py tests/test_zarr3_import.py"
+test-zarr-313 = "uv run --group test-zarr-313 pytest --cov=numcodecs --cov-report=xml --cov-report=term tests/test_zarr3.py tests/test_zarr3_import.py"
+test-zarr-main = "uv run --group test-zarr-main pytest --cov=numcodecs --cov-report=xml --cov-report=term tests/test_zarr3.py tests/test_zarr3_import.py"
 
 [tool.pixi.feature.test.tasks]
 run-tests = "pytest -v"
diff --git a/tests/__init__.py b/tests/__init__.py
@@ -0,0 +1,3 @@
+import pytest
+
+pytest.register_assert_rewrite('tests.common')
diff --git a/tests/common.py b/tests/common.py
@@ -6,11 +6,10 @@
 
 import numpy as np
 import pytest
-from numpy.testing import assert_array_almost_equal, assert_array_equal
-
 from numcodecs import *  # noqa: F403  # for eval to find names in repr tests
 from numcodecs.compat import ensure_bytes, ensure_ndarray
 from numcodecs.registry import get_codec
+from numpy.testing import assert_array_almost_equal, assert_array_equal
 
 greetings = [
     '¡Hola mundo!',
diff --git a/tests/package_with_entrypoint-0.1.dist-info/entry_points.txt b/tests/package_with_entrypoint-0.1.dist-info/entry_points.txt
diff --git a/tests/package_with_entrypoint/__init__.py b/tests/package_with_entrypoint/__init__.py
diff --git a/tests/test_astype.py b/tests/test_astype.py
@@ -1,8 +1,8 @@
 import numpy as np
+from numcodecs.astype import AsType
 from numpy.testing import assert_array_equal
 
-from numcodecs.astype import AsType
-from numcodecs.tests.common import (
+from tests.common import (
     check_backwards_compatibility,
     check_config,
     check_encode_decode,
diff --git a/tests/test_base64.py b/tests/test_base64.py
@@ -2,9 +2,9 @@
 
 import numpy as np
 import pytest
-
 from numcodecs.base64 import Base64
-from numcodecs.tests.common import (
+
+from tests.common import (
     check_backwards_compatibility,
     check_encode_decode,
     check_err_decode_object_buffer,
diff --git a/tests/test_bitround.py b/tests/test_bitround.py
@@ -1,6 +1,5 @@
 import numpy as np
 import pytest
-
 from numcodecs.bitround import BitRound, max_bits
 
 # adapted from https://github.com/milankl/BitInformation.jl/blob/main/test/round_nearest.jl
diff --git a/tests/test_blosc.py b/tests/test_blosc.py
@@ -11,7 +11,7 @@
     pytest.skip("numcodecs.blosc not available", allow_module_level=True)
 
 
-from numcodecs.tests.common import (
+from tests.common import (
     check_backwards_compatibility,
     check_config,
     check_encode_decode,
diff --git a/tests/test_bz2.py b/tests/test_bz2.py
@@ -1,9 +1,9 @@
 import itertools
 
 import numpy as np
-
 from numcodecs.bz2 import BZ2
-from numcodecs.tests.common import (
+
+from tests.common import (
     check_backwards_compatibility,
     check_config,
     check_encode_decode,
diff --git a/tests/test_categorize.py b/tests/test_categorize.py
@@ -1,9 +1,9 @@
 import numpy as np
 import pytest
+from numcodecs.categorize import Categorize
 from numpy.testing import assert_array_equal
 
-from numcodecs.categorize import Categorize
-from numcodecs.tests.common import (
+from tests.common import (
     check_backwards_compatibility,
     check_config,
     check_encode_decode,
diff --git a/tests/test_checksum32.py b/tests/test_checksum32.py
@@ -4,9 +4,9 @@
 
 import numpy as np
 import pytest
-
 from numcodecs.checksum32 import CRC32, Adler32
-from numcodecs.tests.common import (
+
+from tests.common import (
     check_backwards_compatibility,
     check_config,
     check_encode_decode,
diff --git a/tests/test_compat.py b/tests/test_compat.py
@@ -3,7 +3,6 @@
 
 import numpy as np
 import pytest
-
 from numcodecs.compat import ensure_bytes, ensure_contiguous_ndarray, ensure_text
 
 
diff --git a/tests/test_delta.py b/tests/test_delta.py
@@ -1,9 +1,9 @@
 import numpy as np
 import pytest
+from numcodecs.delta import Delta
 from numpy.testing import assert_array_equal
 
-from numcodecs.delta import Delta
-from numcodecs.tests.common import (
+from tests.common import (
     check_backwards_compatibility,
     check_config,
     check_encode_decode,
diff --git a/tests/test_entrypoints.py b/tests/test_entrypoints.py
@@ -1,9 +1,8 @@
 import os.path
 import sys
 
-import pytest
-
 import numcodecs.registry
+import pytest
 
 here = os.path.abspath(os.path.dirname(__file__))
 
diff --git a/tests/test_entrypoints_backport.py b/tests/test_entrypoints_backport.py
@@ -3,9 +3,8 @@
 import sys
 from multiprocessing import Process
 
-import pytest
-
 import numcodecs.registry
+import pytest
 
 importlib_spec = importlib.util.find_spec("importlib_metadata")
 if importlib_spec is None or importlib_spec.loader is None:  # pragma: no cover
diff --git a/tests/test_fixedscaleoffset.py b/tests/test_fixedscaleoffset.py
@@ -2,10 +2,10 @@
 
 import numpy as np
 import pytest
+from numcodecs.fixedscaleoffset import FixedScaleOffset
 from numpy.testing import assert_array_equal
 
-from numcodecs.fixedscaleoffset import FixedScaleOffset
-from numcodecs.tests.common import (
+from tests.common import (
     check_backwards_compatibility,
     check_config,
     check_encode_decode,
diff --git a/tests/test_fletcher32.py b/tests/test_fletcher32.py
@@ -1,6 +1,5 @@
 import numpy as np
 import pytest
-
 from numcodecs.fletcher32 import Fletcher32
 
 
diff --git a/tests/test_gzip.py b/tests/test_gzip.py
@@ -2,9 +2,9 @@
 
 import numpy as np
 import pytest
-
 from numcodecs.gzip import GZip
-from numcodecs.tests.common import (
+
+from tests.common import (
     check_backwards_compatibility,
     check_config,
     check_encode_decode,
diff --git a/tests/test_jenkins.py b/tests/test_jenkins.py
@@ -1,6 +1,5 @@
 import numpy as np
 import pytest
-
 from numcodecs.checksum32 import JenkinsLookup3
 from numcodecs.jenkins import jenkins_lookup3
 
diff --git a/tests/test_json.py b/tests/test_json.py
@@ -2,9 +2,9 @@
 
 import numpy as np
 import pytest
-
 from numcodecs.json import JSON
-from numcodecs.tests.common import (
+
+from tests.common import (
     check_backwards_compatibility,
     check_config,
     check_encode_decode_array,
diff --git a/tests/test_lz4.py b/tests/test_lz4.py
@@ -9,7 +9,7 @@
     pytest.skip("numcodecs.lz4 not available", allow_module_level=True)
 
 
-from numcodecs.tests.common import (
+from tests.common import (
     check_backwards_compatibility,
     check_config,
     check_encode_decode,
diff --git a/tests/test_lzma.py b/tests/test_lzma.py
@@ -13,7 +13,7 @@
     raise unittest.SkipTest("LZMA not available") from e
 
 
-from numcodecs.tests.common import (
+from tests.common import (
     check_backwards_compatibility,
     check_config,
     check_encode_decode,
diff --git a/tests/test_msgpacks.py b/tests/test_msgpacks.py
@@ -9,7 +9,7 @@
     raise unittest.SkipTest("msgpack not available") from e
 
 
-from numcodecs.tests.common import (
+from tests.common import (
     check_backwards_compatibility,
     check_config,
     check_encode_decode_array,
diff --git a/tests/test_ndarray_like.py b/tests/test_ndarray_like.py
@@ -1,5 +1,4 @@
 import pytest
-
 from numcodecs.ndarray_like import DType, FlagsObj, NDArrayLike
 
 
diff --git a/tests/test_packbits.py b/tests/test_packbits.py
@@ -1,7 +1,7 @@
 import numpy as np
-
 from numcodecs.packbits import PackBits
-from numcodecs.tests.common import (
+
+from tests.common import (
     check_backwards_compatibility,
     check_config,
     check_encode_decode,
diff --git a/tests/test_pcodec.py b/tests/test_pcodec.py
@@ -6,7 +6,7 @@
 except ImportError:  # pragma: no cover
     pytest.skip("pcodec not available", allow_module_level=True)
 
-from numcodecs.tests.common import (
+from tests.common import (
     check_backwards_compatibility,
     check_config,
     check_encode_decode_array,
diff --git a/tests/test_pickles.py b/tests/test_pickles.py
@@ -3,9 +3,9 @@
 
 import numpy as np
 import pytest
-
 from numcodecs.pickles import Pickle
-from numcodecs.tests.common import (
+
+from tests.common import (
     check_backwards_compatibility,
     check_config,
     check_encode_decode_array,
diff --git a/tests/test_pyzstd.py b/tests/test_pyzstd.py
@@ -3,7 +3,6 @@
 import numpy as np
 import pytest
 import pyzstd
-
 from numcodecs.zstd import Zstd
 
 test_data = [
diff --git a/tests/test_quantize.py b/tests/test_quantize.py
diff --git a/tests/test_registry.py b/tests/test_registry.py
diff --git a/tests/test_shuffle.py b/tests/test_shuffle.py
diff --git a/tests/test_vlen_array.py b/tests/test_vlen_array.py
diff --git a/tests/test_vlen_bytes.py b/tests/test_vlen_bytes.py
diff --git a/tests/test_vlen_utf8.py b/tests/test_vlen_utf8.py
diff --git a/tests/test_zarr3.py b/tests/test_zarr3.py
diff --git a/tests/test_zarr3_import.py b/tests/test_zarr3_import.py
diff --git a/tests/test_zfpy.py b/tests/test_zfpy.py
diff --git a/tests/test_zlib.py b/tests/test_zlib.py
diff --git a/tests/test_zstd.py b/tests/test_zstd.py

Original file line number	Diff line number	Diff line change
`@@ -0,0 +1,3 @@`
	`1`	`+import pytest`
	`2`	`+`
	`3`	`+pytest.register_assert_rewrite('tests.common')`