pytensor-ml 0.0.3__tar.gz → 0.0.5__tar.gz

pytensor_ml-0.0.5/.gitattributes

@@ -0,0 +1 @@
+pytensor_ml/_version.py export-subst

pytensor_ml-0.0.5/.github/workflows/mypy.yml

@@ -0,0 +1,57 @@
+name: mypy
+
+on:
+  pull_request:
+  push:
+    branches: [main]
+    paths:
+      - ".github/workflows/mypy.yml"
+      - "pytensor_ml/**"
+      - "scripts/run_mypy.py"
+      - "pyproject.toml"
+      - "conda_envs/**"
+
+# Cancels all previous workflow runs for pull requests that have not completed.
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event_name == 'pull_request' && github.head_ref || github.sha }}
+  cancel-in-progress: true
+
+jobs:
+  mypy:
+    runs-on: ubuntu-latest
+
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    steps:
+    - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
+    - uses: actions/cache@27d5ce7f107fe9357f9df03efb73ab90386fccae # v5.0.5
+      env:
+        CACHE_NUMBER: 0
+      with:
+        path: ~/conda_pkgs_dir
+        key: ${{ runner.os }}-py312-conda-${{ env.CACHE_NUMBER }}-${{
+          hashFiles('conda_envs/pytensor_ml.yml') }}
+    - uses: conda-incubator/setup-miniconda@8ee1f361103df19b6f8c8655fd3967a8ecb162d5 # v4.0.1
+      with:
+        miniforge-variant: Miniforge3
+        miniforge-version: latest
+        mamba-version: "*"
+        activate-environment: pytensor_ml
+        channel-priority: strict
+        environment-file: conda_envs/pytensor_ml.yml
+        python-version: 3.12
+        use-mamba: true
+        use-only-tar-bz2: false
+
+    - name: Install current branch
+      run: |
+        conda activate pytensor_ml
+        pip install -e .
+        python --version
+
+    - name: Run mypy
+      run: |
+        conda activate pytensor_ml
+        python ./scripts/run_mypy.py

pytensor_ml-0.0.5/.github/workflows/pre-commit.yml

@@ -0,0 +1,16 @@
+name: pre-commit
+
+on:
+  pull_request:
+  push:
+    branches: [main]
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+    env:
+      SKIP: no-commit-to-branch
+    steps:
+    - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
+    - uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0
+    - uses: pre-commit/action@2c7b3805fd2a0fd8c1884dcaebf91fc102a13ecd # v3.0.1

pytensor_ml-0.0.5/.github/workflows/release.yml

@@ -0,0 +1,50 @@
+name: release-pipeline
+
+permissions: {}
+
+on:
+  push:
+    branches:
+      - main
+  release:
+    types:
+      - published
+
+jobs:
+  build-package:
+    runs-on: ubuntu-latest
+    permissions:
+      # write attestations and id-token are necessary for attest-build-provenance-github
+      attestations: write
+      id-token: write
+    steps:
+      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
+        with:
+          # hatch-vcs derives the version from git tags, so the full history is required.
+          fetch-depth: 0
+          persist-credentials: false
+      - uses: hynek/build-and-inspect-python-package@d44ca7d91762de7a7d5436ddae667c6da6d1c3df # v2.18.0
+        with:
+          # Prove that the packages were built in the context of this workflow.
+          attest-build-provenance-github: true
+
+  publish-package:
+    # Don't publish from forks
+    if: github.repository_owner == 'pymc-devs' && github.event_name == 'release' && github.event.action == 'published'
+    # Use the `release` GitHub environment to protect the Trusted Publishing (OIDC)
+    # workflow by requiring signoff from a maintainer.
+    environment: release
+    needs: build-package
+    runs-on: ubuntu-latest
+    permissions:
+      # write id-token is necessary for trusted publishing (OIDC)
+      id-token: write
+    steps:
+      - name: Download Distribution Artifacts
+        uses: actions/download-artifact@3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c # v8.0.1
+        with:
+          # The build-and-inspect-python-package action invokes upload-artifact.
+          name: Packages
+          path: dist
+      - name: Publish Package to PyPI
+        uses: pypa/gh-action-pypi-publish@cef221092ed1bacb1cc03d23a2d87d1d172e277b # v1.14.0

pytensor_ml-0.0.5/.github/workflows/run_tests.yml

@@ -0,0 +1,86 @@
+name: run_tests
+
+on:
+  pull_request:
+  push:
+    branches: [main]
+
+# Cancels all previous workflow runs for pull requests that have not completed.
+concurrency:
+  # The concurrency group contains the workflow name and the branch name for pull requests
+  # or the commit hash for any other events.
+  group: ${{ github.workflow }}-${{ github.event_name == 'pull_request' && github.head_ref || github.sha }}
+  cancel-in-progress: true
+
+jobs:
+  unittest:
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, windows-latest]
+        python-version: ["3.12"]
+        test-subset:
+          - |
+            tests/
+
+    runs-on: ${{ matrix.os }}
+
+    env:
+      TEST_SUBSET: ${{ matrix.test-subset }}
+
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    steps:
+    - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
+    - uses: actions/cache@27d5ce7f107fe9357f9df03efb73ab90386fccae # v5.0.5
+      env:
+        CACHE_NUMBER: 0
+      with:
+        path: ~/conda_pkgs_dir
+        key: ${{ runner.os }}-py${{matrix.python-version}}-conda-${{ env.CACHE_NUMBER }}-${{
+          hashFiles('conda_envs/pytensor_ml.yml') }}
+    - name: Cache multiple paths
+      uses: actions/cache@27d5ce7f107fe9357f9df03efb73ab90386fccae # v5.0.5
+      env:
+        # Increase this value to reset cache if pyproject.toml has not changed
+        CACHE_NUMBER: 0
+      with:
+        path: |
+          ~/.cache/pip
+          $RUNNER_TOOL_CACHE/Python/*
+          ~\AppData\Local\pip\Cache
+        key: ${{ runner.os }}-build-${{ matrix.python-version }}-${{ env.CACHE_NUMBER }}-${{
+          hashFiles('pyproject.toml') }}
+    - uses: conda-incubator/setup-miniconda@8ee1f361103df19b6f8c8655fd3967a8ecb162d5 # v4.0.1
+      with:
+        miniforge-variant: Miniforge3
+        miniforge-version: latest
+        mamba-version: "*"
+        activate-environment: pytensor_ml
+        channel-priority: strict
+        environment-file: conda_envs/pytensor_ml.yml
+        python-version: 3.12
+        use-mamba: true
+
+        # IMPORTANT: This may break caching of conda packages! See https://github.com/conda-incubator/setup-miniconda/issues/267
+        use-only-tar-bz2: false
+
+    - name: Install current branch
+      run: |
+        conda activate pytensor_ml
+        pip install -e .
+        python --version
+
+    - name: Run tests
+      run: |
+        python -m pytest -vv --cov=pytensor_ml --cov-report=xml --no-cov-on-fail --cov-report term $TEST_SUBSET
+    - name: Upload coverage to Codecov
+      uses: codecov/codecov-action@e79a6962e0d4c0c17b229090214935d2e33f8354 # v6.0.1
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }} # use token for more robust uploads
+        env_vars: TEST_SUBSET
+        name: ${{ matrix.os }}
+        fail_ci_if_error: false
+        verbose: true

pytensor_ml-0.0.5/.gitignore

@@ -0,0 +1,59 @@
+*.pkl
+_build
+__pycache__
+.coverage
+*.linkinfo
+*.o
+*.c
+*.orig
+*.pyc
+*.pyo
+*.so
+*.sw?
+*~
+*.aux
+*.log
+*.nav
+*.out
+*.snm
+*.toc
+*.vrb
+*.nbc
+*.nbi
+.noseids
+*.DS_Store
+*.bak
+*.egg-info/
+\#*\#
+build
+compiled/*.cpp
+core.*
+cutils_ext.cpp
+dist
+doc/.build/
+doc/indexes/oplist.txt
+doc/indexes/typelist.txt
+html
+pdf
+setuptools-*.egg
+pytensor/generated_version.py
+pytensor/generated_version.py.out
+distribute-*.egg
+distribute-*.tar.gz
+PyTensor.suo
+.ipynb_checkpoints
+.pydevproject
+.ropeproject
+core
+.idea
+.vs
+.mypy_cache/
+/htmlcov/
+pytensor_ml/_version.py
+
+pytensor-venv/
+/notebooks/Sandbox*
+.vscode/
+testing-report.html
+coverage.xml
+.coverage.*

pytensor_ml-0.0.5/.pre-commit-config.yaml

@@ -0,0 +1,65 @@
+repos:
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v6.0.0
+  hooks:
+    -   id: check-merge-conflict
+    -   id: check-toml
+    -   id: check-yaml
+    -   id: debug-statements
+    -   id: end-of-file-fixer
+    -   id: no-commit-to-branch
+        args: [--branch, main]
+    -   id: trailing-whitespace
+
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.15.17
+  hooks:
+    - id: ruff
+      args: [ --fix, --exit-non-zero-on-fix ]
+    - id: ruff-format
+      types_or: [ python, pyi, jupyter ]
+
+- repo: https://github.com/MarcoGorelli/madforhooks
+  rev: 0.4.1
+  hooks:
+    - id: no-print-statements
+      types: [python]
+      exclude: |
+        (?x)^
+        |pytensor_ml/_version.py
+    - id: check-execution-order
+      args: [--strict]
+
+- repo: local
+  hooks:
+    - id: notebook_name
+      entry: '\(notebook_name\)='
+      language: pygrep
+      minimum_pre_commit_version: 2.8.0
+      name: Check notebooks do not use literally notebook_name as target
+      types: [jupyter]
+
+    - id: no-references-as-links
+      name: Check no references that should be sphinx cross-references are urls
+      description: >-
+        'A quick check to prevent urls pointing to pymc docs or other sphinx built docs like arviz, numpy, scipy...'
+      files: ^examples/.+\.ipynb$
+      exclude: >
+          (?x)(index.md|
+               404.md|
+               conf.py)
+      entry: >
+          (?x)(arviz-devs.github.io|
+               pymc-extras.readthedocs.io|
+               docs.pymc.io|
+               numpy.org/doc|
+               pymc-examples.readthedocs.io|
+               docs.python.org|
+               xarray.pydata.org|
+               python.arviz.org|
+               pytensor.readthedocs.io|
+               docs.xarray.dev|
+               www.pymc.io|
+               docs.scipy.org/doc)
+      language: pygrep
+      types_or: [markdown, rst, jupyter]

{pytensor_ml-0.0.3 → pytensor_ml-0.0.5}/PKG-INFO

@@ -1,7 +1,10 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: pytensor_ml
-Version: 0.0.3
+Version: 0.0.5
 Summary: A(nother) deep learning library, built on top of Pytensor
+Project-URL: Homepage, https://github.com/pymc-devs/pytensor_ml
+Project-URL: Source, https://github.com/pymc-devs/pytensor_ml
+Project-URL: Tracker, https://github.com/pymc-devs/pytensor_ml/issues
 Author: Ricardo Vieira
 Author-email: Jesse Grabowski <jessegrabowski@gmail.com>
 License:                                  Apache License
@@ -205,19 +208,32 @@ License:                                  Apache License
            WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
            See the License for the specific language governing permissions and
            limitations under the License.
-        
-Keywords: neural network,deep learning,autograd,gradient descent,pymc
+License-File: LICENSE
+Keywords: autograd,deep learning,gradient descent,neural network,pymc
 Classifier: Development Status :: 2 - Pre-Alpha
 Classifier: Intended Audience :: Science/Research
-Classifier: Programming Language :: Python
-Classifier: Topic :: Scientific/Engineering
+Classifier: Operating System :: MacOS
 Classifier: Operating System :: Microsoft :: Windows
 Classifier: Operating System :: POSIX
 Classifier: Operating System :: Unix
-Classifier: Operating System :: MacOS
+Classifier: Programming Language :: Python
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.10
-Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Classifier: Topic :: Scientific/Engineering
+Requires-Python: >=3.12
+Requires-Dist: numpy
+Requires-Dist: pytensor<4.0.0,>=3.2.3
+Requires-Dist: safetensors
 Provides-Extra: dev
-License-File: LICENSE
+Requires-Dist: jax; extra == 'dev'
+Requires-Dist: mypy; extra == 'dev'
+Requires-Dist: pre-commit; extra == 'dev'
+Requires-Dist: pytest; extra == 'dev'
+Requires-Dist: pytest-cov; extra == 'dev'
+Requires-Dist: scikit-learn; extra == 'dev'
+Description-Content-Type: text/markdown
+
+# pytensor_ml
+Neural network package built on Pytensor

pytensor_ml-0.0.5/conda_envs/pytensor_ml-gpu_jax.yml

@@ -0,0 +1,42 @@
+name: pytensor_ml
+channels:
+  - conda-forge
+  - nvidia
+  - nodefaults
+
+dependencies:
+  - python>=3.12
+  - pytensor>=3.2.3,<4.0.0
+  - numpy
+  - scikit-learn
+
+  # GPU Stuff
+  - jax
+  - numpyro
+  - blackjax
+  - jaxlib=*=*cuda*
+  - cuda-nvcc
+
+  # For testing
+  - coveralls
+  - diff-cover
+  - pytest
+  - pytest-cov
+  - pytest-xdist
+  - pytest-benchmark
+  - pytest-mock
+
+  # For building docs
+  - sphinx
+  - sphinx_rtd_theme
+  - pygments
+  - pydot
+  - ipython
+
+  # code style
+  - ruff
+
+  # developer tools
+  - pre-commit
+  - packaging
+  - typing_extensions

pytensor_ml-0.0.5/conda_envs/pytensor_ml.yml

@@ -0,0 +1,36 @@
+name: pytensor_ml
+channels:
+  - conda-forge
+  - nodefaults
+
+dependencies:
+  - python>=3.12
+  - pytensor>=3.2.3,<4.0.0
+  - numpy
+  - safetensors
+  - scikit-learn
+
+  # For testing
+  - coveralls
+  - diff-cover
+  - pytest
+  - pytest-cov
+  - pytest-xdist
+  - pytest-benchmark
+  - pytest-mock
+
+  # For building docs
+  - sphinx
+  - sphinx_rtd_theme
+  - pygments
+  - pydot
+  - ipython
+
+  # developer tools
+  - pre-commit
+  - mypy
+
+  # JAX backend for dispatch tests; via pip so Windows pulls CPU wheels instead of conda jaxlib
+  - pip
+  - pip:
+      - jax

pytensor_ml-0.0.5/examples/mnist_feed_forward.ipynb

@@ -0,0 +1,198 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "15279e7f",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "%load_ext autoreload\n",
+    "%autoreload 2"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "00915a61",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import pytensor\n",
+    "\n",
+    "floatX = \"float32\"\n",
+    "pytensor.config.floatX = floatX"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "fae24c05",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import numpy as np\n",
+    "\n",
+    "from sklearn.datasets import load_digits\n",
+    "from sklearn.preprocessing import MinMaxScaler, OneHotEncoder\n",
+    "\n",
+    "from pytensor_ml.activations import LeakyReLU\n",
+    "from pytensor_ml.layers import BatchNorm2D, Dropout, Linear, Sequential\n",
+    "from pytensor_ml.loss import CrossEntropy\n",
+    "from pytensor_ml.model import Model\n",
+    "from pytensor_ml.optim import adagrad\n",
+    "from pytensor_ml.util import DataLoader"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "65882b64",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "X, y = load_digits(return_X_y=True)\n",
+    "y_onehot = OneHotEncoder().fit_transform(y[:, None]).toarray().astype(floatX)\n",
+    "X_normed = MinMaxScaler().fit_transform(X).astype(floatX)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "f81f9076",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# X_in = Input('X_in', shape=(64, ))\n",
+    "X_in = pytensor.tensor.tensor(\"X_in\", shape=(None, 64))"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "41840fac",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "prediction_network = Sequential(\n",
+    "    Linear(\"Linear_1\", n_in=64, n_out=256),\n",
+    "    BatchNorm2D(\"BatchNorm_1\"),\n",
+    "    Dropout(\"Dropout_1\", p=0.5),\n",
+    "    LeakyReLU(),\n",
+    "    Linear(\"Linear_2\", n_in=256, n_out=128),\n",
+    "    BatchNorm2D(\"BatchNorm_2\"),\n",
+    "    Dropout(\"Dropout_2\", p=0.5),\n",
+    "    LeakyReLU(),\n",
+    "    Linear(\"Logits\", n_in=128, n_out=10),\n",
+    ")\n",
+    "\n",
+    "y_hat = prediction_network(X_in)\n",
+    "model = Model(X_in, y_hat, compile_kwargs={\"mode\": \"NUMBA\"})\n",
+    "model"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "3bfa0ddc",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "loss_fn = CrossEntropy(expect_onehot_labels=True, expect_logits=True, reduction=\"mean\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "290d3191",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# `model.compile_train` is the training companion to `model.predict`: it builds the loss against a target,\n",
+    "# differentiates it, folds in the BatchNorm running-statistic updates, and compiles a one-step training\n",
+    "# function (reusing the model's NUMBA compile settings).\n",
+    "step = model.compile_train(adagrad(learning_rate=1e-3), loss_fn, ndim_out=2)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "e77b697f",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "model.initialize()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "dd6dede5",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from tqdm.notebook import tqdm\n",
+    "\n",
+    "loader = DataLoader(X_normed, y_onehot)\n",
+    "loss_history = []\n",
+    "n_epochs = 10_000\n",
+    "\n",
+    "for _ in tqdm(range(n_epochs)):\n",
+    "    X_batch, y_batch = loader()\n",
+    "    loss_value = step(X_batch, y_batch)\n",
+    "    loss_history.append(loss_value)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "ab1ad6ef",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import matplotlib.pyplot as plt\n",
+    "\n",
+    "plt.plot(loss_history)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "fb38dd99",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from scipy.special import softmax\n",
+    "\n",
+    "# `model.predict` compiles a forward pass specialized for inference: Dropout is dropped and BatchNorm uses its\n",
+    "# running statistics.\n",
+    "y_hat_logits = model.predict(X_normed)\n",
+    "y_hat_probs = softmax(y_hat_logits, axis=-1)\n",
+    "y_pred = np.argmax(y_hat_probs, axis=-1)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "4393b9c3",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import seaborn as sns\n",
+    "\n",
+    "from sklearn.metrics import confusion_matrix\n",
+    "\n",
+    "sns.heatmap(confusion_matrix(y, y_pred), annot=True, fmt=\"0.0f\")"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}