Finish pyproject.toml migration

.flake8

@@ -1,2 +1,14 @@
 [flake8]
 max-line-length = 100
+exclude =
+    .git,
+    .github,
+    .pytest_cache,
+    adhoc,
+    build,
+    c-blosc,
+    dist,
+    docs,
+    fixture,
+    notebooks,
+    numcodecs.egg-info,

.github/workflows/ci-linux.yaml

@@ -24,23 +24,16 @@ jobs:
 
       - name: Install numcodecs
         run: |
-          python -m pip install -U pip -r requirements_test.txt -r requirements.txt
-          python -m pip install -v -e .
+          python -m pip install -v -e .[test,msgpack,zfpy]
 
       - name: List installed packages
         run: python -m pip list
 
-      - name: Run tests
-        run: pytest -v --cov=numcodecs --cov-report xml --doctest-modules --doctest-glob=*.pyx numcodecs
-
       - name: Flake8
-        run: flake8 numcodecs
+        run: flake8
 
-      - name: Build Docs
-        run: |
-          pip install -r requirements_rtfd.txt
-          cd docs
-          sphinx-build -W -b html -d {envtmpdir}/doctrees . {envtmpdir}/html
+      - name: Run tests
+        run: pytest -v
 
       - uses: codecov/codecov-action@v3
         with:

.github/workflows/ci-osx.yaml

@@ -37,7 +37,6 @@ jobs:
           conda create -n env python=${{matrix.python-version}} wheel pip compilers 'clang>=12.0.1'
           conda activate env
           which pip
-          pip install -r requirements_test.txt -r requirements.txt
           conda env export
 
       - name: Show info about `env` environment
@@ -50,14 +49,13 @@ jobs:
         run: |
           conda activate env
           export CC=clang
-          python -m pip install -U pip -r requirements_test.txt -r requirements.txt
-          python -m pip install -v -e .
+          python -m pip install -v -e .[test,msgpack,zfpy]
 
       - name: Run tests
         shell: "bash -l {0}"
         run: |
           conda activate env
-          pytest -v --cov=numcodecs --cov-report xml numcodecs
+          pytest -v
 
       - uses: codecov/codecov-action@v3
         with:

.github/workflows/ci-windows.yaml

@@ -30,22 +30,20 @@ jobs:
           conda create -n env python=${{matrix.python-version}} wheel pip compilers
           conda activate env
           which pip
-          pip install -r requirements_test.txt -r requirements.txt
           conda env export
 
       - name: Install numcodecs
         shell: "bash -l {0}"
         run: |
           conda activate env
           export CC=clang
-          python -m pip install -U pip -r requirements_test.txt -r requirements.txt
-          python -m pip install -v -e .
+          python -m pip install -v -e .[test,msgpack,zfpy]
 
       - name: Run tests
         shell: "bash -l {0}"
         run: |
           conda activate env
-          pytest -v --cov=numcodecs --cov-report xml numcodecs
+          pytest -v
 
       - uses: codecov/codecov-action@v3
         with:

.pyup.yml

@@ -2,17 +2,3 @@
 # see https://pyup.io/docs/configuration/ for all available options
 
 schedule: every month
-
-requirements:
-  - requirements.txt:
-      pin: False
-      update: False
-  - requirements_test.txt:
-      pin: False
-      update: False
-  - requirements_rtfd.txt:
-      pin: False
-      update: False
-  - requirements_dev.txt:
-      pin: True
-      update: all

.readthedocs.yaml

@@ -13,6 +13,7 @@ sphinx:
 
 python:
   install:
-    - requirements: requirements_rtfd.txt
     - method: pip
       path: .
+      extra_requirements:
+        - docs

docs/contributing.rst

@@ -99,16 +99,11 @@ the repository, you can do something like the following::
     $ mkdir -p ~/pyenv/numcodecs-dev
     $ virtualenv --no-site-packages --python=/usr/bin/python3.9 ~/pyenv/numcodecs-dev
     $ source ~/pyenv/numcodecs-dev/bin/activate
-    $ pip install -r requirements_dev.txt
-    $ python setup.py build_ext --inplace
+    $ pip install -e .[docs,test,msgpack,zfpy]
 
 To verify that your development environment is working, you can run the unit tests::
 
-    $ pytest -v numcodecs
-
-To install numcodecs globally in editable mode run::
-
-    $ python -m pip install -e . 
+    $ pytest -v
 
 Creating a branch
 ~~~~~~~~~~~~~~~~~
@@ -147,11 +142,7 @@ Running the test suite
 NumCodecs includes a suite of unit tests, as well as doctests included in function and class
 docstrings. The simplest way to run the unit tests is to invoke::
 
-    $ pytest -v numcodecs
-
-To also run the doctests within docstrings, run::
-
-    $ pytest -v --doctest-modules numcodecs
+    $ pytest -v
 
 NumCodecs currently supports Python 6-3.9, so the above command must
 succeed before code can be accepted into the main code base.
@@ -167,14 +158,14 @@ All code must conform to the PEP8 standard. Regarding line length, lines up to 1
 characters are allowed, although please try to keep under 90 wherever possible.
 Conformance can be checked by running::
 
-    $ flake8 --max-line-length=100 numcodecs
+    $ flake8
 
 Test coverage
 ~~~~~~~~~~~~~
 
 NumCodecs maintains 100% test coverage under the latest Python stable release (currently
 Python 3.9). Both unit tests and docstring doctests are included when computing
-coverage. Running ``pytest -v --cov=numcodecs`` will automatically run the test suite with coverage
+coverage. Running ``pytest -v`` will automatically run the test suite with coverage
 and produce a coverage report. This should be 100% before code can be accepted into the
 main code base.
 

docs/release.rst

@@ -53,6 +53,9 @@ Maintenance
 * Add tests for all registry classes.
   By :user:`Josh Moore <joshmoore>`, :issue:`349`.
 
+* Finish ``pyproject.toml`` migration.
+  By :user:`John Kirkham <jakirkham>` :issue:`382`.
+
 * Drop tox.
   By :user:`John Kirkham <jakirkham>`, :issue:`384`.
 

numcodecs/astype.py

@@ -28,10 +28,10 @@ class AsType(Codec):
     >>> x = np.arange(100, 120, 2, dtype=np.int8)
     >>> x
     array([100, 102, 104, 106, 108, 110, 112, 114, 116, 118], dtype=int8)
-    >>> f = numcodecs.AsType(encode_dtype=x.dtype, decode_dtype=np.int64)
+    >>> f = numcodecs.AsType(encode_dtype=x.dtype, decode_dtype=np.int16)
     >>> y = f.decode(x)
     >>> y
-    array([100, 102, 104, 106, 108, 110, 112, 114, 116, 118])
+    array([100, 102, 104, 106, 108, 110, 112, 114, 116, 118], dtype=int16)
     >>> z = f.encode(y)
     >>> z
     array([100, 102, 104, 106, 108, 110, 112, 114, 116, 118], dtype=int8)

numcodecs/delta.py

@@ -28,14 +28,14 @@ class Delta(Codec):
     --------
     >>> import numcodecs
     >>> import numpy as np
-    >>> x = np.arange(100, 120, 2, dtype='i8')
-    >>> codec = numcodecs.Delta(dtype='i8', astype='i1')
+    >>> x = np.arange(100, 120, 2, dtype='i2')
+    >>> codec = numcodecs.Delta(dtype='i2', astype='i1')
     >>> y = codec.encode(x)
     >>> y
     array([100,   2,   2,   2,   2,   2,   2,   2,   2,   2], dtype=int8)
     >>> z = codec.decode(y)
     >>> z
-    array([100, 102, 104, 106, 108, 110, 112, 114, 116, 118])
+    array([100, 102, 104, 106, 108, 110, 112, 114, 116, 118], dtype=int16)
 
     """
 

numcodecs/vlen.pyx

@@ -310,11 +310,14 @@ class VLenArray(Codec):
     --------
     >>> import numcodecs
     >>> import numpy as np
-    >>> x = np.array([[1, 3, 5], [4], [7, 9]], dtype='object')
-    >>> codec = numcodecs.VLenArray('<i4')
+    >>> x1 = np.array([1, 3, 5], dtype=np.int16)
+    >>> x2 = np.array([4], dtype=np.int16)
+    >>> x3 = np.array([7, 9], dtype=np.int16)
+    >>> x = np.array([x1, x2, x3], dtype='object')
+    >>> codec = numcodecs.VLenArray('<i2')
     >>> codec.decode(codec.encode(x))
-    array([array([1, 3, 5], dtype=int32), array([4], dtype=int32),
-           array([7, 9], dtype=int32)], dtype=object)
+    array([array([1, 3, 5], dtype=int16), array([4], dtype=int16),
+           array([7, 9], dtype=int16)], dtype=object)
 
     See Also
     --------

pyproject.toml

@@ -1,7 +1,111 @@
 [build-system]
-requires = ["setuptools>=40.8.0", "setuptools_scm[toml]>=6.2", "Cython", "py-cpuinfo"]
-build-backend = "setuptools.build_meta:__legacy__"
+requires = [
+    "setuptools>=64",
+    "setuptools-scm[toml]>=6.2",
+    "Cython",
+    "py-cpuinfo"
+]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "numcodecs"
+description = """
+A Python package providing buffer compression and transformation codecs for use
+in data storage and communication applications.
+"""
+readme =  "README.rst"
+dependencies = [
+    "entrypoints",
+    "numpy>=1.7",
+    "typing-extensions>=3.7.4"
+]
+requires-python = ">=3.7"
+dynamic = [
+  "version",
+]
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Intended Audience :: Developers",
+    "Intended Audience :: Information Technology",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: MIT License",
+    "Programming Language :: Python",
+    "Topic :: Software Development :: Libraries :: Python Modules",
+    "Operating System :: Unix",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3 :: Only",
+]
+maintainers = [
+    { name = "Alistair Miles", email = "[email protected]" },
+]
+license = { text = "MIT" }
+
+[project.urls]
+"Bug Tracker" = "https://github.com/zarr-developers/numcodecs/issues"
+Changelog = "https://numcodecs.readthedocs.io/en/stable/release.html"
+Documentation = "https://numcodecs.readthedocs.io/"
+Homepage = "https://github.com/zarr-developers/numcodecs"
+
+[project.optional-dependencies]
+docs = [
+    "sphinx",
+    "sphinx-issues",
+    "numpydoc",
+    "mock",
+]
+test = [
+    "coverage",
+    "flake8",
+    "pytest",
+    "pytest-cov",
+]
+msgpack = [
+    "msgpack",
+]
+zfpy = [
+    "zfpy>=1.0.0",
+]
+
+[tool.setuptools]
+license-files = ["LICENSE.txt"]
+package-dir = {"" = "."}
+packages = ["numcodecs", "numcodecs.tests"]
+zip-safe = false
+
+[tool.setuptools_scm]
+version_scheme = "guess-next-dev"
+local_scheme = "dirty-tag"
+write_to = "numcodecs/version.py"
 
 [tool.codespell]
 skip = "./.git,fixture"
 ignore-words-list = "ba, compiletime, hist, nd, unparseable"
+
+[tool.coverage.report]
+exclude_lines = [
+    "pragma: no cover",
+    "pragma: ${PY_MAJOR_VERSION} no cover",
+]
+
+[tool.pytest.ini_options]
+addopts = "--cov=numcodecs --cov-report xml --doctest-modules --doctest-glob=*.pyx"
+doctest_optionflags = [
+    "NORMALIZE_WHITESPACE",
+    "ELLIPSIS",
+    "IGNORE_EXCEPTION_DETAIL",
+]
+testpaths = [
+    "numcodecs",
+]
+norecursedirs = [
+    ".git",
+    ".github",
+    ".pytest_cache",
+    "adhoc",
+    "build",
+    "c-blosc",
+    "docs",
+    "fixture",
+    "notebooks",
+    "numcodecs.egg-info",
+]