jax-sklearn 0.1.0__tar.gz

jax_sklearn-0.1.0/.binder/postBuild

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+#!/bin/bash
+
+set -e
+
+# This script is called in a binder context. When this script is called, we are
+# inside a git checkout of the jax-sklearn/jax-sklearn repo. This script is
+# generating notebooks from the jax-sklearn python examples.
+
+if [[ -z "${REPO_DIR}" ]]; then
+    echo "This script was written for repo2docker and the REPO_DIR environment variable is supposed to be set."
+    echo "Exiting because this script can delete data if run outside of a repo2docker context."
+    exit 1
+fi
+
+# Back up content we need from the jax-sklearn repo
+TMP_CONTENT_DIR=/tmp/jax-sklearn
+mkdir -p $TMP_CONTENT_DIR
+cp -r examples .binder $TMP_CONTENT_DIR
+# delete everything in current directory including dot files and dot folders
+find . -delete
+
+# Generate notebooks and remove other files from examples folder
+GENERATED_NOTEBOOKS_DIR=.generated-notebooks
+cp -r $TMP_CONTENT_DIR/examples $GENERATED_NOTEBOOKS_DIR
+
+find $GENERATED_NOTEBOOKS_DIR -name '*.py' -exec sphinx_gallery_py2jupyter '{}' +
+NON_NOTEBOOKS=$(find $GENERATED_NOTEBOOKS_DIR -type f | grep -v '\.ipynb')
+rm -f $NON_NOTEBOOKS
+
+# Put the .binder folder back (may be useful for debugging purposes)
+mv $TMP_CONTENT_DIR/.binder .
+# Final clean up
+rm -rf $TMP_CONTENT_DIR
+
+# This is for compatibility with binder sphinx-gallery integration: this makes
+# sure that the binder links generated by sphinx-gallery are correct even tough
+# the repo we use for binder (jax-sklearn/jax-sklearn) is not the repo of the
+# generated doc (jax-sklearn/jax-sklearn.github.io)
+mkdir notebooks
+ln -s ../$GENERATED_NOTEBOOKS_DIR notebooks/auto_examples

jax_sklearn-0.1.0/.binder/requirements.txt

@@ -0,0 +1,10 @@
+--find-links https://pypi.anaconda.org/scientific-python-nightly-wheels/simple/jax-sklearn
+--pre
+matplotlib
+scikit-image
+pandas
+seaborn
+Pillow
+sphinx-gallery
+jax-sklearn
+polars

jax_sklearn-0.1.0/.binder/runtime.txt

@@ -0,0 +1 @@
+python-3.9

jax_sklearn-0.1.0/.circleci/config.yml

@@ -0,0 +1,129 @@
+version: 2.1
+
+jobs:
+  lint:
+    docker:
+      - image: cimg/python:3.10.16
+    steps:
+      - checkout
+      - run:
+          name: dependencies
+          command: |
+            source build_tools/shared.sh
+            # Include pytest compatibility with mypy
+            pip install pytest $(get_dep ruff min) $(get_dep mypy min) cython-lint
+      - run:
+          name: linting
+          command: ./build_tools/linting.sh
+
+  doc-min-dependencies:
+    docker:
+      - image: cimg/base:current-22.04
+    environment:
+      - MKL_NUM_THREADS: 2
+      - OPENBLAS_NUM_THREADS: 2
+      - CONDA_ENV_NAME: testenv
+      - LOCK_FILE: build_tools/circle/doc_min_dependencies_linux-64_conda.lock
+      # Do not fail if the documentation build generates warnings with minimum
+      # dependencies as long as we can avoid raising warnings with more recent
+      # versions of the same dependencies.
+      - XLEARN_WARNINGS_AS_ERRORS: '0'
+    steps:
+      - checkout
+      - run: ./build_tools/circle/checkout_merge_commit.sh
+      - restore_cache:
+          key: v1-doc-min-deps-datasets-{{ .Branch }}
+      - restore_cache:
+          keys:
+            - doc-min-deps-ccache-{{ .Branch }}
+            - doc-min-deps-ccache
+      - run: ./build_tools/circle/build_doc.sh
+      - save_cache:
+          key: doc-min-deps-ccache-{{ .Branch }}-{{ .BuildNum }}
+          paths:
+            - ~/.ccache
+            - ~/.cache/pip
+      - save_cache:
+          key: v1-doc-min-deps-datasets-{{ .Branch }}
+          paths:
+            - ~/scikit_learn_data
+      - store_artifacts:
+          path: doc/_build/html/stable
+          destination: doc
+      - store_artifacts:
+          path: ~/log.txt
+          destination: log.txt
+
+  doc:
+    docker:
+      - image: cimg/base:current-22.04
+    environment:
+      - MKL_NUM_THREADS: 2
+      - OPENBLAS_NUM_THREADS: 2
+      - CONDA_ENV_NAME: testenv
+      - LOCK_FILE: build_tools/circle/doc_linux-64_conda.lock
+      # Make sure that we fail if the documentation build generates warnings with
+      # recent versions of the dependencies.
+      - XLEARN_WARNINGS_AS_ERRORS: '1'
+    steps:
+      - checkout
+      - run: ./build_tools/circle/checkout_merge_commit.sh
+      - restore_cache:
+          key: v1-doc-datasets-{{ .Branch }}
+      - restore_cache:
+          keys:
+            - doc-ccache-{{ .Branch }}
+            - doc-ccache
+      - run: ./build_tools/circle/build_doc.sh
+      - save_cache:
+          key: doc-ccache-{{ .Branch }}-{{ .BuildNum }}
+          paths:
+            - ~/.ccache
+            - ~/.cache/pip
+      - save_cache:
+          key: v1-doc-datasets-{{ .Branch }}
+          paths:
+            - ~/scikit_learn_data
+      - store_artifacts:
+          path: doc/_build/html/stable
+          destination: doc
+      - store_artifacts:
+          path: ~/log.txt
+          destination: log.txt
+      # Persists generated documentation so that it can be attached and deployed
+      # in the 'deploy' step.
+      - persist_to_workspace:
+          root: doc/_build/html
+          paths: .
+
+  deploy:
+    docker:
+      - image: cimg/base:current-22.04
+    steps:
+      - checkout
+      - run: ./build_tools/circle/checkout_merge_commit.sh
+      # Attach documentation generated in the 'doc' step so that it can be
+      # deployed.
+      - attach_workspace:
+          at: doc/_build/html
+      - run: ls -ltrh doc/_build/html/stable
+      - run:
+          command: |
+            if [[ "${CIRCLE_BRANCH}" =~ ^main$|^[0-9]+\.[0-9]+\.X$ ]]; then
+              bash build_tools/circle/push_doc.sh doc/_build/html/stable
+            fi
+
+workflows:
+  version: 2
+  build-doc-and-deploy:
+    jobs:
+      - lint
+      - doc:
+          requires:
+            - lint
+      - doc-min-dependencies:
+          requires:
+            - lint
+      - deploy:
+          requires:
+            - doc

jax_sklearn-0.1.0/.codecov.yml

@@ -0,0 +1,33 @@
+comment: false
+
+coverage:
+  status:
+    project:
+      default:
+        # Commits pushed to main should not make the overall
+        # project coverage decrease by more than 1%:
+        target: auto
+        threshold: 1%
+    patch:
+      default:
+        # Be tolerant on slight code coverage diff on PRs to limit
+        # noisy red coverage status on github PRs.
+        # Note: The coverage stats are still uploaded
+        # to codecov so that PR reviewers can see uncovered lines
+        target: auto
+        threshold: 1%
+
+codecov:
+  notify:
+    # Prevent coverage status to upload multiple times for parallel and long
+    # running CI pipelines. This configuration is particularly useful on PRs
+    # to avoid confusion. Note that this value is set to the number of Azure
+    # Pipeline jobs uploading coverage reports.
+    after_n_builds: 6
+
+ignore:
+- "xlearn/externals"
+- "xlearn/_build_utils"
+- "xlearn/__check_build"
+- "xlearn/_min_dependencies.py"
+- "**/conftest.py"

jax_sklearn-0.1.0/.coveragerc

@@ -0,0 +1,11 @@
+[run]
+# Use statement coverage rather than branch coverage because
+# COVERAGE_CORE=sysmon can make branch coverage slower rather than faster. See
+# https://github.com/nedbat/coveragepy/issues/1812 for more details.
+branch = False
+source = xlearn
+parallel = True
+omit =
+    */xlearn/externals/*
+    */xlearn/_build_utils/*
+    */benchmarks/*

jax_sklearn-0.1.0/.github/FUNDING.yml

@@ -0,0 +1,12 @@
+# These are supported funding model platforms
+
+github: # Replace with up to 4 GitHub Sponsors-enabled usernames e.g., [user1, user2]
+patreon: # Replace with a single Patreon username
+open_collective: # Replace with a single Open Collective username
+ko_fi: # Replace with a single Ko-fi username
+tidelift: # Replace with a single Tidelift platform-name/package-name e.g., npm/babel
+community_bridge: # Replace with a single Community Bridge project-name e.g., cloud-foundry
+liberapay: # Replace with a single Liberapay username
+issuehunt: # Replace with a single IssueHunt username
+otechie: # Replace with a single Otechie username
+custom: ['https://numfocus.org/donate-to-jax-sklearn']

jax_sklearn-0.1.0/.github/ISSUE_TEMPLATE/bug_report.yml

@@ -0,0 +1,95 @@
+name: Bug Report
+description: Create a report to help us reproduce and correct the bug
+labels: ['Bug', 'Needs Triage']
+
+body:
+- type: markdown
+  attributes:
+    value: >
+      #### Before submitting a bug, please make sure the issue hasn't been already
+      addressed by searching through [the past issues](https://github.com/chenxingqiang/jax-sklearn/issues).
+- type: textarea
+  attributes:
+    label: Describe the bug
+    description: >
+      A clear and concise description of what the bug is.
+  validations:
+    required: true
+- type: textarea
+  attributes:
+    label: Steps/Code to Reproduce
+    description: |
+      Please add a [minimal code example](https://jax-sklearn.org/dev/developers/minimal_reproducer.html) that can reproduce the error when running it. Be as succinct as possible, **do not depend on external data files**: instead you can generate synthetic data using `numpy.random`, [xlearn.datasets.make_regression](https://jax-sklearn.org/stable/modules/generated/xlearn.datasets.make_regression.html), [xlearn.datasets.make_classification](https://jax-sklearn.org/stable/modules/generated/xlearn.datasets.make_classification.html) or a few lines of Python code. Example:
+
+      ```python
+      from xlearn.feature_extraction.text import CountVectorizer
+      from xlearn.decomposition import LatentDirichletAllocation
+      docs = ["Help I have a bug" for i in range(1000)]
+      vectorizer = CountVectorizer(input=docs, analyzer='word')
+      lda_features = vectorizer.fit_transform(docs)
+      lda_model = LatentDirichletAllocation(
+          n_topics=10,
+          learning_method='online',
+          evaluate_every=10,
+          n_jobs=4,
+      )
+      model = lda_model.fit(lda_features)
+      ```
+
+      If the code is too long, feel free to put it in a public gist and link it in the issue: https://gist.github.com.
+
+      In short, **we are going to copy-paste your code** to run it and we expect to get the same result as you.
+
+      We acknowledge that crafting a [minimal reproducible code example](https://jax-sklearn.org/dev/developers/minimal_reproducer.html) requires some effort on your side but it really helps the maintainers quickly reproduce the problem and analyze its cause without any ambiguity. Ambiguous bug reports tend to be slower to fix because they will require more effort and back and forth discussion between the maintainers and the reporter to pin-point the precise conditions necessary to reproduce the problem.
+    placeholder: |
+      ```
+      Sample code to reproduce the problem
+      ```
+  validations:
+    required: true
+- type: textarea
+  attributes:
+    label: Expected Results
+    description: >
+      Please paste or describe the expected results.
+    placeholder: >
+      Example: No error is thrown.
+  validations:
+    required: true
+- type: textarea
+  attributes:
+    label: Actual Results
+    description: |
+      Please paste or describe the results you observe instead of the expected results. If you observe an error, please paste the error message including the **full traceback** of the exception. For instance the code above raises the following exception:
+
+      ```python-traceback
+      ---------------------------------------------------------------------------
+      TypeError                                 Traceback (most recent call last)
+      <ipython-input-1-a674e682c281> in <module>
+            4 vectorizer = CountVectorizer(input=docs, analyzer='word')
+            5 lda_features = vectorizer.fit_transform(docs)
+      ----> 6 lda_model = LatentDirichletAllocation(
+            7     n_topics=10,
+            8     learning_method='online',
+
+      TypeError: __init__() got an unexpected keyword argument 'n_topics'
+      ```
+    placeholder: >
+      Please paste or specifically describe the actual output or traceback.
+  validations:
+    required: true
+- type: textarea
+  attributes:
+    label: Versions
+    render: shell
+    description: |
+      Please run the following and paste the output below.
+      ```python
+      import xlearn; xlearn.show_versions()
+      ```
+  validations:
+    required: true
+- type: markdown
+  attributes:
+    value: >
+      Thanks for contributing 🎉!

jax_sklearn-0.1.0/.github/ISSUE_TEMPLATE/config.yml

@@ -0,0 +1,17 @@
+blank_issues_enabled: false
+contact_links:
+  - name: Discussions
+    url: https://github.com/chenxingqiang/jax-sklearn/discussions/new
+    about: Ask questions and discuss with other jax-sklearn community members
+  - name: Stack Overflow
+    url: https://stackoverflow.com/questions/tagged/jax-sklearn
+    about: Please ask and answer usage questions on Stack Overflow
+  - name: Mailing list
+    url: https://mail.python.org/mailman/listinfo/jax-sklearn
+    about: General discussions and announcements on the mailing list
+  - name: Discord server
+    url: https://discord.gg/h9qyrK8Jc8
+    about: Developers and users can be found on the Discord server
+  - name: Blank issue
+    url: https://github.com/chenxingqiang/jax-sklearn/issues/new?template=BLANK_ISSUE
+    about: Please note that GitHub Discussions should be used in most cases instead

jax_sklearn-0.1.0/.github/ISSUE_TEMPLATE/doc_improvement.yml

@@ -0,0 +1,17 @@
+name: Documentation improvement
+description: Create a report to help us improve the documentation. Alternatively you can just open a pull request with the suggested change.
+labels: [Documentation, 'Needs Triage']
+
+body:
+- type: textarea
+  attributes:
+    label: Describe the issue linked to the documentation
+    description: >
+      Tell us about the confusion introduced in the documentation.
+  validations:
+    required: true
+- type: textarea
+  attributes:
+    label: Suggest a potential alternative/fix
+    description: >
+      Tell us how we could improve the documentation in this regard.

jax_sklearn-0.1.0/.github/ISSUE_TEMPLATE/feature_request.yml

@@ -0,0 +1,25 @@
+name: Feature request
+description: Suggest a new algorithm, enhancement to an existing algorithm, etc.
+labels: ['New Feature', 'Needs Triage']
+
+body:
+- type: markdown
+  attributes:
+    value: >
+      #### If you want to propose a new algorithm, please refer first to the [jax-sklearn inclusion criterion](https://jax-sklearn.org/stable/faq.html#what-are-the-inclusion-criteria-for-new-algorithms).
+- type: textarea
+  attributes:
+    label: Describe the workflow you want to enable
+  validations:
+    required: true
+- type: textarea
+  attributes:
+    label: Describe your proposed solution
+  validations:
+    required: true
+- type: textarea
+  attributes:
+    label: Describe alternatives you've considered, if relevant
+- type: textarea
+  attributes:
+    label: Additional context

jax_sklearn-0.1.0/.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,32 @@
+<!--
+Thanks for contributing a pull request! Please ensure you have taken a look at
+the contribution guidelines: https://github.com/chenxingqiang/jax-sklearn/blob/main/CONTRIBUTING.md
+-->
+
+#### Reference Issues/PRs
+<!--
+Example: Fixes #1234. See also #3456.
+Please use keywords (e.g., Fixes) to create link to the issues or pull requests
+you resolved, so that they will automatically be closed when your pull request
+is merged. See https://github.com/blog/1506-closing-issues-via-pull-requests
+-->
+
+
+#### What does this implement/fix? Explain your changes.
+
+
+#### Any other comments?
+
+
+<!--
+Please be aware that we are a loose team of volunteers so patience is
+necessary; assistance handling other issues is very welcome. We value
+all user contributions, no matter how minor they are. If we are slow to
+review, either the pull request needs some benchmarking, tinkering,
+convincing, etc. or more likely the reviewers are simply busy. In either
+case, we ask for your understanding during the review process.
+For more information, see our FAQ on this topic:
+https://jax-sklearn.org/dev/faq.html#why-is-my-pull-request-not-getting-any-attention.
+
+Thanks for contributing!
+-->

jax_sklearn-0.1.0/.github/dependabot.yml

@@ -0,0 +1,21 @@
+version: 2
+updates:
+  # Maintain dependencies for GitHub Actions as recommended in SPEC8:
+  # https://github.com/scientific-python/specs/pull/325
+  # At the time of writing, release critical workflows such as
+  # pypa/gh-action-pypi-publish should use hash-based versioning for security
+  # reasons. This strategy may be generalized to all other github actions
+  # in the future.
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "monthly"
+    groups:
+      actions:
+        patterns:
+          - "*"
+    labels:
+      - "Build / CI"
+      - "dependencies"
+    reviewers:
+      - "jax-sklearn/core-devs"

jax_sklearn-0.1.0/.github/labeler-file-extensions.yml

@@ -0,0 +1,8 @@
+cython:
+- xlearn/**/*.pyx
+- xlearn/**/*.pxd
+- xlearn/**/*.pxi
+# Tempita templates
+- xlearn/**/*.pyx.tp
+- xlearn/**/*.pxd.tp
+- xlearn/**/*.pxi.tp

jax_sklearn-0.1.0/.github/labeler-module.yml

@@ -0,0 +1,80 @@
+module:cluster:
+- xlearn/cluster/**/*
+
+module:common:
+- xlearn/common/**/*
+
+module:compose:
+- xlearn/compose/**/*
+
+module:covariance:
+- xlearn/covariance/**/*
+
+module:cross_decomposition:
+- xlearn/cross_decomposition/**/*
+
+module:datasets:
+- xlearn/datasets/**/*
+
+module:decomposition:
+- xlearn/decomposition/**/*
+
+module:ensemble:
+- xlearn/ensemble/**/*
+
+module:feature_extraction:
+- xlearn/feature_extraction/**/*
+
+module:feature_selection:
+- xlearn/feature_selection/**/*
+
+module:gaussian_process:
+- xlearn/gaussian_process/**/*
+
+module:impute:
+- xlearn/impute/**/*
+
+module:inspection:
+- xlearn/inspection/**/*
+
+module:linear_model:
+- xlearn/linear_model/**/*
+
+module:manifold:
+- xlearn/manifold/**/*
+
+module:metrics:
+- xlearn/metrics/**/*
+
+module:mixture:
+- xlearn/mixture/**/*
+
+module:model_selection:
+- xlearn/model_selection/**/*
+
+module:naive_bayes:
+- xlearn/naive_bayes.py
+
+module:neighbors:
+- xlearn/neighbors/**/*
+
+module:neural_network:
+- xlearn/neural_network/**/*
+
+module:pipeline:
+- xlearn/pipeline.py
+
+module:preprocessing:
+- xlearn/preprocessing/**/*
+
+module:semi_supervised:
+- xlearn/semi_supervised/**/*
+
+module:svm:
+- xlearn/svm/**/*
+
+module:tree:
+- xlearn/tree/**/*
+
+module:utils:
+- xlearn/utils/**/*

jax_sklearn-0.1.0/.github/scripts/label_title_regex.py

@@ -0,0 +1,25 @@
+"""Labels PRs based on title. Must be run in a github action with the
+pull_request_target event."""
+
+import json
+import os
+import re
+
+from github import Github
+
+context_dict = json.loads(os.getenv("CONTEXT_GITHUB"))
+
+repo = context_dict["repository"]
+g = Github(context_dict["token"])
+repo = g.get_repo(repo)
+pr_number = context_dict["event"]["number"]
+issue = repo.get_issue(number=pr_number)
+title = issue.title
+
+
+regex_to_labels = [(r"\bDOC\b", "Documentation"), (r"\bCI\b", "Build / CI")]
+
+labels_to_add = [label for regex, label in regex_to_labels if re.search(regex, title)]
+
+if labels_to_add:
+    issue.add_to_labels(*labels_to_add)

jax_sklearn-0.1.0/.github/workflows/arm-unit-tests.yml

@@ -0,0 +1,54 @@
+name: Unit test for ARM
+permissions:
+  contents: read
+
+on:
+  push:
+  pull_request:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.head_ref || github.run_id }}
+  cancel-in-progress: true
+
+jobs:
+  lint:
+    name: Lint
+    runs-on: ubuntu-latest
+    if: github.repository == 'jax-sklearn/jax-sklearn'
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.12'
+          cache: 'pip'
+      - name: Install linters
+        run: |
+          source build_tools/shared.sh
+          # Include pytest compatibility with mypy
+          pip install pytest $(get_dep ruff min) $(get_dep mypy min) cython-lint
+      - name: Run linters
+        run: ./build_tools/linting.sh
+      - name: Run Meson OpenMP checks
+        run: |
+          pip install ninja meson scipy
+          python build_tools/check-meson-openmp-dependencies.py
+
+  run-unit-tests:
+    name: Run unit tests
+    runs-on: ubuntu-24.04-arm
+    if: github.repository == 'jax-sklearn/jax-sklearn'
+    needs: [lint]
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - uses: mamba-org/setup-micromamba@v2
+        with:
+          environment-file: build_tools/github/pymin_conda_forge_arm_linux-aarch64_conda.lock
+          environment-name: ci
+          cache-environment: true
+
+      - name: Build and run tests
+        shell: bash -el {0}
+        run: bash build_tools/github/build_test_arm.sh

jax_sklearn-0.1.0/.github/workflows/artifact-redirector.yml

@@ -0,0 +1,24 @@
+name: CircleCI artifacts redirector
+on: [status]
+
+# Restrict the permissions granted to the use of secrets.GITHUB_TOKEN in this
+# github actions workflow:
+# https://docs.github.com/en/actions/security-guides/automatic-token-authentication
+permissions:
+  statuses: write
+
+jobs:
+  circleci_artifacts_redirector_job:
+    runs-on: ubuntu-latest
+    # For testing this action on a fork, remove the "github.repository =="" condition.
+    if: "github.repository == 'jax-sklearn/jax-sklearn' && github.event.context == 'ci/circleci: doc'"
+    name: Run CircleCI artifacts redirector
+    steps:
+      - name: GitHub Action step
+        uses: scientific-python/circleci-artifacts-redirector-action@v1
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+          api-token: ${{ secrets.CIRCLECI_TOKEN }}
+          artifact-path: 0/doc/_changed.html
+          circleci-jobs: doc
+          job-title: Check the rendered docs here!