Merge pull request #411 from rsokl/fix-nightly

Improve test suite and CI

.github/dependabot.yml

@@ -0,0 +1,11 @@
+version: 2
+updates:
+  - package-ecosystem: "github-actions" # See documentation for possible values
+    directory: "/" # Location of package manifests
+    schedule:
+      interval: "daily"
+  - package-ecosystem: "pip"
+    directory: "/docs/"
+    schedule:
+      interval: "weekly"
+    target-branch: "docs"

.github/workflows/tox_run.yml

@@ -74,9 +74,29 @@ jobs:
       run: |
         python -m pip install --upgrade pip
         pip install tox
-    - name: Python 3.10
+    - name: Test with tox
       run: tox -e py310
 
+  py311:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.11"]
+      fail-fast: false
+
+    steps:
+    - uses: actions/checkout@v1
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      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 py311
+
   minimum_numpy:
     runs-on: ubuntu-latest
     strategy:
@@ -96,3 +116,18 @@ jobs:
         pip install tox
     - name: Test vs Minimum Python/Numpy
       run: tox -e min_numpy
+
+  check-repo-format:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python 3.9
+      uses: actions/setup-python@v4
+      with:
+        python-version: 3.9
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install tox tox-gh-actions
+    - name: Test with tox
+      run: tox -e enforce-format

.pre-commit-config.yaml

@@ -0,0 +1,13 @@
+repos:
+-   repo: https://github.com/psf/black
+    rev: 22.10.0
+    hooks:
+    - id: black
+-   repo: https://github.com/PyCQA/flake8
+    rev: 6.0.0
+    hooks:
+    - id: flake8
+-   repo: https://github.com/pre-commit/mirrors-isort
+    rev: v5.10.1
+    hooks:
+    -   id: isort

README.md

@@ -3,7 +3,7 @@
 [![Documentation Status](https://readthedocs.org/projects/mygrad/badge/?version=latest)](https://mygrad.readthedocs.io/en/latest/?badge=latest)
 [![Automated tests status](https://github.com/rsokl/MyGrad/workflows/Tests/badge.svg)](https://github.com/rsokl/MyGrad/actions?query=workflow%3ATests+branch%3Amaster)
 [![PyPi version](https://img.shields.io/pypi/v/mygrad.svg)](https://pypi.python.org/pypi/mygrad)
-![Python version support](https://img.shields.io/badge/python-3.7%20‐%203.10-blue.svg)
+![Python version support](https://img.shields.io/badge/python-3.7%20‐%203.11-blue.svg)
 
 # [MyGrad's Documentation](https://mygrad.readthedocs.io/en/latest/)
 

docs/source/changes.rst

@@ -6,6 +6,18 @@ 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.
 
+.. _v2.2.0:
+
+--------------------
+2.2.0rc - 2022-XX-XX
+--------------------
+
+- MyGrad is now tested against Python 3.11. (:pull:`411`)
+- `mygrad.bool8` has been removed. Use `mygrad.bool_` instead. (:pull:`411`)
+- Adds ufunc support for `resolve_dtypes`. (:pull:`411`) 
+- Modifies automatic differentiation framework to be simpler and more memory efficient. In the future, MyGrad will be able to expose an API akin to `torch.autograd.grad <https://pytorch.org/docs/stable/generated/torch.autograd.grad.html>_`. (:pull:`407`)
+- MyGrad's CI now enforces formatting and spell check requirements on all pull requests. (:pull:`411`)
+
 .. _v2.1.0:
 
 ------------------

docs/source/conf.py

@@ -78,6 +78,16 @@
 # The name of the Pygments (syntax highlighting) style to use.
 pygments_style = None
 
+_repo = "https://github.com/rsokl/MyGrad/"
+extlinks = {
+    "commit": (_repo + "commit/%s", "commit %s"),
+    "gh-file": (_repo + "blob/master/%s", "%s"),
+    "gh-link": (_repo + "%s", "%s"),
+    "issue": (_repo + "issues/%s", "issue #%s"),
+    "pull": (_repo + "pull/%s", "pull request #%s"),
+    "plymi": ("https://www.pythonlikeyoumeanit.com/%s", "%s"),
+    "hydra": ("https://hydra.cc/docs/%s", "%s"),
+}
 
 # -- Options for HTML output -------------------------------------------------
 

setup.cfg

@@ -9,8 +9,8 @@ line_length = 88
 src_paths=src/mygrad,tests
 
 [flake8]
-exclude = docs/*, src/mygrad/__init__.py, src/mygrad/numpy_compat/__init__.py
-
+extend-ignore = F811,D1,D205,D209,D213,D400,D401,D999,D202,E203,E501,W503,E721,F403,F405
+exclude = .git,__pycache__,docs,old,build,dis,tests/annotations/*, tests/test_py310.py,versioneer.py,docs/*, src/mygrad/__init__.py, src/mygrad/numpy_compat/__init__.py,src/mygrad/nnet/__init__.py
 
 [versioneer]
 VCS = git
@@ -26,22 +26,28 @@ omit = src/mygrad/_version.py
        src/mygrad/computational_graph.py
 
 
+[codespell]
+skip = *.po,*.ts,**/_version.py, 
+ignore-words-list = ND,nd,nin,dout
+
 [tox:tox]
-envlist = py37,py38,py39,format,min_numpy
+envlist = py37,py38,py39,,format,min_numpy
 
 [gh-actions]
 python =
   3.7: py37
   3.8: py38
   3.9: py39
   3.10: py310
+  3.11: py311
 
 [testenv]
 deps =
     pytest
     hypothesis
     scipy
-commands = pytest --hypothesis-profile ci \
+    pytest-xdist
+commands = pytest -n auto --hypothesis-profile ci \
            {posargs}
 extras = rnn
 
@@ -50,15 +56,22 @@ extras = rnn
 deps = numpy==1.20
        {[testenv]deps}
 basepython = python3.7
-commands = pytest --hypothesis-profile ci \
+commands = pytest -n auto --hypothesis-profile ci \
            {posargs}
 extras =
 
 [testenv:py310]  # exclude numba dependency for now
 deps = pytest
+       pytest-xdist
        hypothesis
        scipy
-commands = pytest --hypothesis-profile ci \
+commands = pytest -n auto --hypothesis-profile ci \
+           {posargs}
+extras =
+
+[testenv:py311]  # exclude numba dependency for now
+deps = {[testenv:py310]deps}
+commands = pytest -n auto --hypothesis-profile ci \
            {posargs}
 extras =
 
@@ -70,7 +83,7 @@ basepython = python3.7
 deps = {[testenv]deps}
        coverage
        pytest-cov
-commands = pytest --cov-report term-missing --cov-config=setup.cfg --cov-fail-under=100 --cov=mygrad tests
+commands = pytest -n auto --cov-report term-missing --cov-config=setup.cfg --cov-fail-under=100 --cov=mygrad tests
 
 
 [testenv:format]
@@ -89,7 +102,23 @@ pip_pre = true
 deps = pytest
        hypothesis
        scipy
+       pytest-xdist
 basepython = python3.8
-commands = pytest --hypothesis-profile ci \
+commands = pytest -n auto --hypothesis-profile ci \
            {posargs}
 extras =
+
+
+[testenv:enforce-format]
+skip_install=true
+basepython=python3.9
+deps=black
+     isort
+     flake8
+     pytest
+     codespell
+commands=
+    black src/ tests/ --diff --check
+    isort src/ tests/ --diff --check
+    flake8 src/ tests/
+    codespell src/ docs/

src/mygrad/__init__.py

@@ -32,9 +32,9 @@
 from mygrad.tensor_manip.tiling.funcs import *
 from mygrad.tensor_manip.transpose_like.funcs import *
 from mygrad.ufuncs._ufunc_creators import ufunc
-from ._io import load, save
 
 from . import random
+from ._io import load, save
 from ._version import get_versions
 
 __version__ = get_versions()["version"]

src/mygrad/_dtype_mirrors.py

@@ -1,7 +1,7 @@
 import numpy
 
 __all__ = [
-    "bool8",
+    "bool_",
     "int8",
     "int16",
     "int32",
@@ -21,7 +21,8 @@
     "longdouble",
 ]
 
-bool8 = numpy.bool8
+
+bool_ = numpy.bool_
 int8 = numpy.int8
 int16 = numpy.int16
 int32 = numpy.int32

src/mygrad/_utils/__init__.py

@@ -18,7 +18,7 @@
 
 if TYPE_CHECKING:  # pragma: no cover
     from mygrad import Tensor
-    from mygrad.operation_base import Operation
+    from mygrad.operation_base import Operation  # noqa: F401
 
 __all__ = [
     "collect_all_operations_and_clear_grads",

src/mygrad/_utils/duplicating_graph.py

@@ -191,7 +191,7 @@ def __iter__(self) -> Iterator[Node]:
         yield from self._yield_children(self.base.placeholder)
 
     def get_path_to_base(self, tensor: "Tensor") -> List[Node]:
-        """ Returns [leaf, (parent), ..., base]"""
+        """Returns [leaf, (parent), ..., base]"""
         path = []
         node = self[tensor]
         while node.parent is not None:
@@ -201,7 +201,7 @@ def get_path_to_base(self, tensor: "Tensor") -> List[Node]:
         return path
 
     def restore_old_graph(self):
-        """ Reroute graph back to original tensors."""
+        """Reroute graph back to original tensors."""
         # call tuple to ensure iteration is completed
         # before information gets deleted / mutated
         for node in tuple(self):

src/mygrad/_utils/graph_tracking.py

@@ -2,7 +2,7 @@
 Provides user interface for suspending computational graph tracking and back-propagation
 """
 from functools import wraps
-from typing import Callable, TypeVar, Any, cast, Optional
+from typing import Any, Callable, TypeVar, cast
 
 import numpy as np
 

src/mygrad/computational_graph.py

@@ -97,7 +97,7 @@ def build_graph(
 
 
 def _add_node(node, graph, op_id=None, **kwargs):
-    """ Recursively traces computational graph and adds nodes to Digraph. """
+    """Recursively traces computational graph and adds nodes to Digraph."""
     node_id = str(id(node))
     node_lab = repr(node)
     if kwargs["names"] is not None:

src/mygrad/linalg/__init__.py

@@ -1 +1 @@
-from .funcs import norm
+from .funcs import norm  # noqa: F401

src/mygrad/linalg/funcs.py

@@ -4,7 +4,6 @@
 import numpy as np
 from numpy.core.einsumfunc import _parse_einsum_input
 
-import mygrad as mg
 from mygrad.math.misc.funcs import absolute
 from mygrad.math.sequential.funcs import max as mg_max, min as mg_min
 from mygrad.tensor_base import Tensor, implements_numpy_override
@@ -105,7 +104,7 @@ def norm(
 
     References
     ----------
-    .. [1] Retrived from: https://numpy.org/doc/stable/reference/generated/numpy.linalg.norm.html
+    .. [1] Retrieved from: https://numpy.org/doc/stable/reference/generated/numpy.linalg.norm.html
     .. [2] G. H. Golub and C. F. Van Loan, *Matrix Computations*,
            Baltimore, MD, Johns Hopkins University Press, 1985, pg. 15
 
@@ -118,7 +117,7 @@ def norm(
     >>> l2_norms
     Tensor([3.74165739, 1.        ])
 
-    The presence of the elementwise absolute values in the norm operation means that zero-valued entries in any of 
+    The presence of the elementwise absolute values in the norm operation means that zero-valued entries in any of
     input vectors have an undefined derivative. When `nan_to_num=False` is specified these derivatives will be reported
     as `nan`, otherwise they will be made to be 0.0.
 

src/mygrad/linalg/ops.py

@@ -329,7 +329,7 @@ def backward_var(self, grad: np.ndarray, index: int, **kwargs) -> np.ndarray:
             if out.size:
                 # if out.size is 0, then this produces div-by-zero
                 _norm = self._norm / np.sum(
-                    out ** self.ord, axis=self.axis, keepdims=True
+                    out**self.ord, axis=self.axis, keepdims=True
                 )
             else:
                 _norm = +self._norm

src/mygrad/math/arithmetic/ops.py

@@ -61,7 +61,7 @@ def backward_var(self, grad, index, **kwargs):
         if index == 0:  # backprop through a
             return grad / b.data
         else:  # broadcast through b
-            return -grad * a.data / (b.data ** 2)
+            return -grad * a.data / (b.data**2)
 
 
 class Power(BinaryUfunc):
@@ -73,7 +73,7 @@ def backward_var(self, grad, index, **kwargs):
         if index == 0:
             return grad * y * (x ** np.where(y, (y - 1), 1))
         else:
-            return grad * (x ** y) * np.log(np.where(x, x, 1))
+            return grad * (x**y) * np.log(np.where(x, x, 1))
 
 
 # Unary Ops
@@ -84,7 +84,7 @@ class Reciprocal(UnaryUfunc):
 
     def backward_var(self, grad, index, **kwargs):
         (a,) = self.variables
-        return -grad * np.reciprocal(a.data ** 2)
+        return -grad * np.reciprocal(a.data**2)
 
 
 class Square(UnaryUfunc):
@@ -124,7 +124,7 @@ def backward_var(self, grad, index, **kwargs):
 
 
 class MultiplySequence(Operation):
-    """ Performs f(a, b, ..., z) = a * b * ... * z"""
+    """Performs f(a, b, ..., z) = a * b * ... * z"""
 
     def __call__(self, *input_vars: "Tensor") -> np.ndarray:
         self.variables = input_vars