Add JAX array to registry (#20)

.github/workflows/main.yml

@@ -22,7 +22,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: ['ubuntu-latest', 'macos-latest', 'windows-latest']
+        os: ['ubuntu-latest', 'macos-latest']
         python-version: ['3.7', '3.8', '3.9', '3.10']
 
     steps:
@@ -46,6 +46,32 @@ jobs:
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
 
+  run-tests-windows:
+
+    name: Run tests for ${{ matrix.os }} on ${{ matrix.python-version }}
+    runs-on: ${{ matrix.os }}
+
+    strategy:
+      fail-fast: false
+      matrix:
+        os: ['windows-latest']
+        python-version: ['3.7', '3.8', '3.9', '3.10']
+
+    steps:
+      - uses: actions/checkout@v2
+      - uses: conda-incubator/setup-miniconda@v2
+        with:
+          auto-update-conda: true
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install core dependencies.
+        shell: bash -l {0}
+        run: conda install -c conda-forge tox-conda
+
+      - name: Run pytest.
+        shell: bash -l {0}
+        run: tox -e pytest-windows -- -m "not slow"
+
   docs:
 
     name: Run documentation.

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.2.0
+    rev: v4.3.0
     hooks:
     -   id: check-merge-conflict
     -   id: debug-statements
@@ -11,7 +11,7 @@ repos:
     -   id: reorder-python-imports
         types: [python]
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.2.0
+    rev: v4.3.0
     hooks:
     -   id: check-added-large-files
         args: ['--maxkb=100']
@@ -42,13 +42,13 @@ repos:
     rev: v1.12.1
     hooks:
     -   id: blacken-docs
-        additional_dependencies: [black]
+        additional_dependencies: [black==22.3.0]
         types: [rst]
 -   repo: https://github.com/psf/black
     rev: 22.3.0
     hooks:
     -   id: black
-        types: [python]
+        language_version: python3.9
 -   repo: https://github.com/PyCQA/flake8
     rev: 4.0.1
     hooks:
@@ -71,7 +71,7 @@ repos:
             Pygments,
         ]
 -   repo: https://github.com/PyCQA/doc8
-    rev: 0.11.1
+    rev: 0.11.2
     hooks:
         -   id: doc8
 -   repo: meta
@@ -84,7 +84,7 @@ repos:
     hooks:
     -   id: check-manifest
 -   repo: https://github.com/PyCQA/doc8
-    rev: 0.11.1
+    rev: 0.11.2
     hooks:
     -   id: doc8
 -   repo: https://github.com/asottile/setup-cfg-fmt
@@ -102,7 +102,7 @@ repos:
   hooks:
     -   id: codespell
 -   repo: https://github.com/asottile/pyupgrade
-    rev: v2.32.1
+    rev: v2.34.0
     hooks:
     -   id: pyupgrade
         args: [--py37-plus]

environment.yml

@@ -30,3 +30,5 @@ dependencies:
   - pdbpp
   - numpy
   - pandas
+  - jax
+  - jaxlib

src/pybaum/config.py

@@ -12,3 +12,12 @@
     IS_PANDAS_INSTALLED = False
 else:
     IS_PANDAS_INSTALLED = True
+
+
+try:
+    import jax  # noqa: F401
+    import jaxlib  # noqa: F401
+except ImportError:
+    IS_JAX_INSTALLED = False
+else:
+    IS_JAX_INSTALLED = True

src/pybaum/equality.py

@@ -1,4 +1,5 @@
 """Functions to check equality of pytree leaves."""
+from pybaum.config import IS_JAX_INSTALLED
 from pybaum.config import IS_NUMPY_INSTALLED
 from pybaum.config import IS_PANDAS_INSTALLED
 
@@ -10,6 +11,9 @@
 if IS_PANDAS_INSTALLED:
     import pandas as pd
 
+if IS_JAX_INSTALLED:
+    import jaxlib
+
 
 EQUALITY_CHECKERS = {}
 
@@ -21,3 +25,9 @@
 if IS_PANDAS_INSTALLED:
     EQUALITY_CHECKERS[pd.Series] = lambda a, b: a.equals(b)
     EQUALITY_CHECKERS[pd.DataFrame] = lambda a, b: a.equals(b)
+
+
+if IS_JAX_INSTALLED:
+    EQUALITY_CHECKERS[jaxlib.xla_extension.DeviceArray] = lambda a, b: bool(
+        (a == b).all()
+    )

src/pybaum/registry.py

@@ -15,6 +15,7 @@ def get_registry(types=None, include_defaults=True):
             - :obj:`None`
             - :class:`collections.OrderedDict`
             - "numpy.ndarray"
+            - "jax.numpy.ndarray"
             - "pandas.Series"
             - "pandas.DataFrame"
         include_defaults (bool): Whether the default pytree containers "tuple", "dict"

src/pybaum/registry_entries.py

@@ -3,6 +3,7 @@
 from collections import OrderedDict
 from itertools import product
 
+from pybaum.config import IS_JAX_INSTALLED
 from pybaum.config import IS_NUMPY_INSTALLED
 from pybaum.config import IS_PANDAS_INSTALLED
 
@@ -12,6 +13,10 @@
 if IS_PANDAS_INSTALLED:
     import pandas as pd
 
+if IS_JAX_INSTALLED:
+    import jax
+    import jaxlib
+
 
 def _none():
     """Create registry entry for NoneType."""
@@ -117,6 +122,22 @@ def _array_element_names(arr):
     return names
 
 
+def _jax_array():
+    if IS_JAX_INSTALLED:
+        entry = {
+            jaxlib.xla_extension.DeviceArray: {
+                "flatten": lambda arr: (arr.flatten().tolist(), arr.shape),
+                "unflatten": lambda aux_data, leaves: jax.numpy.array(leaves).reshape(
+                    aux_data
+                ),
+                "names": _array_element_names,
+            },
+        }
+    else:
+        entry = {}
+    return entry
+
+
 def _pandas_series():
     """Create registry entry for pandas.Series."""
     if IS_PANDAS_INSTALLED:
@@ -186,6 +207,7 @@ def _index_element_to_string(element):
     "tuple": _tuple,
     "dict": _dict,
     "numpy.ndarray": _numpy_array,
+    "jax.numpy.ndarray": _jax_array,
     "pandas.Series": _pandas_series,
     "pandas.DataFrame": _pandas_dataframe,
     "None": _none,

src/pybaum/tree_util.py

@@ -6,8 +6,6 @@
 - The treedef containing information to unflatten pytrees is implemented differently.
 
 """
-import itertools
-
 from pybaum.equality import EQUALITY_CHECKERS
 from pybaum.registry import get_registry
 from pybaum.typecheck import get_type
@@ -42,8 +40,8 @@ def tree_flatten(tree, is_leaf=None, registry=None):
     is_leaf = _process_is_leaf(is_leaf)
 
     flat = _tree_flatten(tree, is_leaf=is_leaf, registry=registry)
-    dummy_flat = ["*"] * len(flat)
-    treedef = tree_unflatten(tree, dummy_flat, is_leaf=is_leaf, registry=registry)
+    # unflatten the flat tree to make a copy
+    treedef = tree_unflatten(tree, flat, is_leaf=is_leaf, registry=registry)
     return flat, treedef
 
 
@@ -124,9 +122,7 @@ def tree_yield(tree, is_leaf=None, registry=None):
     is_leaf = _process_is_leaf(is_leaf)
 
     flat = _tree_yield(tree, is_leaf=is_leaf, registry=registry)
-    dummy_flat = itertools.repeat("*")
-    treedef = tree_unflatten(tree, dummy_flat, is_leaf=is_leaf, registry=registry)
-    return flat, treedef
+    return flat, tree
 
 
 def tree_just_yield(tree, is_leaf=None, registry=None):

tests/test_tree_util.py

@@ -31,20 +31,13 @@ def example_flat():
 
 
 @pytest.fixture
-def example_treedef():
-    return (["*", "*", {"a": "*", "b": "*"}], "*")
+def example_treedef(example_tree):
+    return example_tree
 
 
 @pytest.fixture
-def extended_treedef():
-    return (
-        [
-            "*",
-            np.array(["*", "*"]),
-            {"a": pd.Series(["*", "*"], index=["c", "d"]), "b": "*"},
-        ],
-        "*",
-    )
+def extended_treedef(example_tree):
+    return example_tree
 
 
 @pytest.fixture
@@ -195,7 +188,7 @@ def test_flatten_df_all_columns():
 def test_tree_yield(example_tree, example_treedef, example_flat):
     generator, treedef = tree_yield(example_tree)
 
-    assert treedef == example_treedef
+    assert tree_equal(treedef, example_treedef)
     assert inspect.isgenerator(generator)
     for a, b in zip(generator, example_flat):
         if isinstance(a, (np.ndarray, pd.Series)):

tests/test_with_jax.py

@@ -0,0 +1,45 @@
+import pytest
+from pybaum.config import IS_JAX_INSTALLED
+from pybaum.registry import get_registry
+from pybaum.tree_util import leaf_names
+from pybaum.tree_util import tree_equal
+from pybaum.tree_util import tree_flatten
+from pybaum.tree_util import tree_just_flatten
+
+if IS_JAX_INSTALLED:
+    import jax.numpy as jnp
+else:
+    # run the tests with normal numpy instead
+    import numpy as jnp
+
+
+@pytest.fixture
+def tree():
+    return {"a": {"b": jnp.arange(4).reshape(2, 2)}, "c": jnp.ones(2)}
+
+
+@pytest.fixture
+def flat():
+    return [0, 1, 2, 3, 1, 1]
+
+
+@pytest.fixture
+def registry():
+    return get_registry(types=["jax.numpy.ndarray", "numpy.ndarray"])
+
+
+def test_tree_just_flatten_with_jax(tree, registry, flat):
+    got = tree_just_flatten(tree, registry=registry)
+    assert got == flat
+
+
+def test_tree_flatten_with_jax(tree, registry, flat):
+    got_flat, got_treedef = tree_flatten(tree, registry=registry)
+    assert got_flat == flat
+    assert tree_equal(got_treedef, tree)
+
+
+def test_leaf_names_with_jax(tree, registry):
+    got = leaf_names(tree, registry=registry)
+    expected = ["a_b_0_0", "a_b_0_1", "a_b_1_0", "a_b_1_1", "c_0", "c_1"]
+    assert got == expected

tox.ini

@@ -7,6 +7,24 @@ skip_missing_interpreters = True
 basepython = python
 
 [testenv:pytest]
+setenv =
+    CONDA_DLL_SEARCH_MODIFICATION_ENABLE = 1
+conda_channels =
+    conda-forge
+    defaults
+conda_deps =
+    conda-build
+    numpy
+    pandas
+    pytest
+    pytest-cov
+    pytest-mock
+    pytest-xdist
+    jax
+    jaxlib
+commands = pytest {posargs}
+
+[testenv:pytest-windows]
 setenv =
     CONDA_DLL_SEARCH_MODIFICATION_ENABLE = 1
 conda_channels =