Merge pull request #441 from rsokl/ryan/upgrade

update python deps and ci and support numpy 2.0

.flake8

@@ -0,0 +1,3 @@
+[flake8]
+extend-ignore = F811,D1,D205,D209,D213,D400,D401,D999,D202,E203,E501,W503,E721,F403,F405,E701
+exclude = .git,__pycache__,docs,old,build,dis,tests/annotations/*, tests/test_py310.py,docs/*, src/mygrad/__init__.py, src/mygrad/numpy_compat/__init__.py,src/mygrad/nnet/__init__.py

.github/workflows/tox_run.yml

@@ -19,7 +19,7 @@ jobs:
     strategy:
       max-parallel: 3
       matrix:
-        python-version: [3.7, 3.8, 3.9]
+        python-version: [3.9, "3.10", 3.11]
       fail-fast: false
 
     steps:
@@ -40,7 +40,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.7"]
+        python-version: ["3.10"]
       fail-fast: false
 
     steps:
@@ -57,31 +57,11 @@ jobs:
       run: tox -e coverage
 
 
-  py310:
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        python-version: ["3.10"]
-      fail-fast: false
-
-    steps:
-    - uses: actions/checkout@v4
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v5
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install tox
-    - name: Test with tox
-      run: tox -e py310
-
-  py311:
+  py312:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.11"]
+        python-version: ["3.12"]
       fail-fast: false
 
     steps:
@@ -95,13 +75,13 @@ jobs:
         python -m pip install --upgrade pip
         pip install tox
     - name: Test with tox
-      run: tox -e py311
+      run: tox -e py312
 
   minimum_numpy:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.7"]
+        python-version: ["3.9"]
       fail-fast: false
 
     steps:
@@ -121,10 +101,10 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v4
-    - name: Set up Python 3.9
+    - name: Set up Python 3.11
       uses: actions/setup-python@v5
       with:
-        python-version: 3.9
+        python-version: 3.11
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip

.pre-commit-config.yaml

@@ -1,13 +1,13 @@
 repos:
 -   repo: https://github.com/psf/black
-    rev: 22.10.0
+    rev: 24.8.0
     hooks:
     - id: black
 -   repo: https://github.com/PyCQA/flake8
-    rev: 6.0.0
+    rev: 7.0.0
     hooks:
     - id: flake8
--   repo: https://github.com/pre-commit/mirrors-isort
-    rev: v5.10.1
+-   repo: https://github.com/pycqa/isort
+    rev: 5.13.2
     hooks:
     -   id: isort

MANIFEST.in

@@ -1,2 +1,3 @@
-include versioneer.py
-include mygrad/_version.py
+recursive-exclude tests *
+recursive-exclude project_tooling *
+global-exclude *.py[cod]

docs/source/changes.rst

@@ -6,6 +6,17 @@ This is a record of all past mygrad releases and what went into them,
 in reverse chronological order. All previous releases should still be available
 on pip.
 
+.. _v2.3.0:
+
+------------------
+2.3.0 - 2024-09-07
+------------------
+
+- Adds support for NumPy 2.0
+- Minimum supported NumPy version is now 1.24
+- Minimum supported Python version is now 3.9
+- Adds testing for Python 3.12
+
 .. _v2.2.0:
 
 ------------------

pyproject.toml

@@ -0,0 +1,183 @@
+[build-system]
+requires = [
+       "setuptools >= 35.0.2",
+       "wheel >= 0.29.0",
+       "setuptools_scm[toml]==7.0.5",
+]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "mygrad"
+dynamic = ["version"]
+description = "Drop-in automatic differentiation to NumPy"
+readme = "README.md"
+requires-python = ">=3.9"
+dependencies = ["numpy >= 1.24, !=1.25.0", "typing-extensions >= 4.1.0, !=4.6.0"]
+license = { text = "MIT" }
+
+authors = [
+       { name = "Ryan Soklaski", email = "[email protected]" },
+]
+maintainers = [{ name = "Ryan Soklaski", email = "[email protected]" }]
+
+classifiers = [
+    "Development Status :: 5 - Production/Stable",
+    "License :: OSI Approved :: MIT License",
+    "Operating System :: OS Independent",
+    "Intended Audience :: Science/Research",
+    "Intended Audience :: Education",
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Topic :: Scientific/Engineering",
+]
+
+
+[project.optional-dependencies]
+test = ["pytest >= 3.8", "hypothesis >= 6.17.1", "scipy"]
+rnn = ["numba>=0.34.0"]
+
+
+
+[project.urls]
+"Homepage" = "https://mygrad.readthedocs.io/en/latest/"
+"Bug Reports" = "https://github.com/rsokl/MyGrad/issues"
+"Source" = "https://github.com/rsokl/MyGrad"
+
+
+[tool.setuptools_scm]
+write_to = "src/mygrad/_version.py"
+version_scheme = "no-guess-dev"
+
+
+[tool.setuptools]
+package-dir = { "" = "src" }
+
+[tool.setuptools.packages.find]
+where = ["src"]
+exclude = ["tests*", "tests.*"]
+
+[tool.setuptools.package-data]
+mygrad = ["py.typed"]
+
+
+[tool.isort]
+known_third_party = ["graphviz", "hypothesis", "numpy", "numba", "pytest", "scipy"]
+known_first_party = ["mygrad", "tests"] 
+profile = "black"
+src_paths=["src/mygrad","tests"]
+
+[tool.coverage.run]
+omit = ["src/mygrad/_version.py", "src/mygrad/computational_graph.py"]
+
+[tool.coverage.report]
+omit = ["src/mygrad/_version.py"]
+
+[tool.codespell]
+skip = ["*.po","*.ts","**/_version.py","docs/source/generated/*"]
+ignore-words-list = ["ND","nd","nin","dout"]
+
+[tool.tox]
+legacy_tox_ini = """
+[tox]
+envlist = py39,py310,py311,py312,format,min_numpy
+
+[gh-actions]
+python =
+  3.9: py39
+  3.10: py310
+  3.11: py311
+  3.12: py312
+
+[testenv]
+deps =
+    pytest
+    hypothesis
+    scipy
+    pytest-xdist
+commands = pytest -n auto --hypothesis-profile ci \
+           {posargs}
+extras = rnn
+
+
+[testenv:min_numpy]
+deps = numpy==1.24
+       {[testenv]deps}
+basepython = python3.9
+commands = pytest -n auto --hypothesis-profile ci \
+           {posargs}
+extras =
+
+[testenv:py310]
+deps = {[testenv]deps}
+commands = pytest -n auto --hypothesis-profile ci \
+           {posargs}
+extras =
+
+[testenv:py311]
+deps = {[testenv]deps}
+commands = pytest -n auto --hypothesis-profile ci \
+           {posargs}
+extras =
+
+[testenv:py312]  # exclude numba dependency for now
+deps = pytest
+       pytest-xdist
+       hypothesis
+       scipy
+commands = pytest -n auto --hypothesis-profile ci \
+           {posargs}
+extras =
+
+
+[testenv:coverage]
+setenv = NUMBA_DISABLE_JIT=1
+         MYGRAD_COVERAGE_MODE=1
+usedevelop = true
+basepython = python3.10
+deps = {[testenv]deps}
+       coverage
+       pytest-cov
+commands = pytest -n auto --cov-report term-missing --cov-config=pyproject.toml --cov-fail-under=100 --cov=mygrad tests
+
+
+[testenv:format]
+deps =
+    autoflake
+    black
+    isort
+commands =
+    autoflake --recursive --in-place --remove-duplicate-keys --remove-unused-variables .
+    isort .
+    black .
+
+
+[testenv:pre-release]  # test against pre-releases of dependencies
+pip_pre = true
+deps = pytest
+       hypothesis
+       scipy
+       pytest-xdist
+basepython = python3.11
+commands = pytest -n auto --hypothesis-profile ci \
+           {posargs}
+extras =
+
+
+[testenv:enforce-format]
+skip_install=true
+basepython=python3.11
+deps=black
+     isort
+     flake8
+     pytest
+     codespell
+commands=
+    black src/ tests/ --diff --check
+    isort src/ tests/ --diff --check
+    flake8 src/ tests/
+    codespell src/ docs/
+"""