From 2b1f1e69efbaa45732c108f80ad7db4d6b64d12f Mon Sep 17 00:00:00 2001 From: Paul Hobson Date: Sat, 24 Oct 2026 01:02:49 -0700 Subject: [PATCH 1/3] first pass at a basic refresh --- .github/dependabot.yml | 10 + .github/workflows/black.yml | 19 - .github/workflows/check-test-coverage.yml | 30 - .github/workflows/docs.yml | 40 + .github/workflows/lint.yml | 22 + .github/workflows/publish.yml | 81 + .github/workflows/python-publish-pypi.yml | 95 - .github/workflows/python-publish-testpypi.yml | 57 - .github/workflows/python-runtests-basic.yml | 33 - .../workflows/python-runtests-img-comp.yml | 30 - .github/workflows/tests.yml | 31 + .pre-commit-config.yaml | 28 +- readme.rst => README.md | 75 +- docs/api.md | 9 + docs/api.rst | 9 - docs/api/activity.md | 7 + docs/api/activity.rst | 7 - docs/api/{paramnormal.rst => paramnormal.md} | 8 +- docs/api/utils.md | 7 + docs/api/utils.rst | 7 - docs/conf.py | 299 +- docs/examples/index.rst | 85 - docs/includeme.rst | 1 - docs/index.md | 26 + docs/index.rst | 29 - .../sphinxext/ipython_console_highlighting.py | 109 - docs/sphinxext/ipython_directive.py | 1105 ---- docs/sphinxext/plot_directive.py | 845 --- docs/sphinxext/plot_generator.py | 364 -- docs/sphinxext/requirements.txt | 2 - docs/tutorial/tools/nb_to_doc.py | 4 +- paramnormal/dist.py | 15 + paramnormal/tests/__init__.py | 4 +- pyproject.toml | 55 + requirements.txt | 3 - requirements_dev.txt | 13 - ruff.toml | 37 +- setup.cfg | 21 - setup.py | 54 - uv.lock | 4636 +++++++++++++++++ 40 files changed, 5025 insertions(+), 3287 deletions(-) create mode 100644 .github/dependabot.yml delete mode 100644 .github/workflows/black.yml delete mode 100644 .github/workflows/check-test-coverage.yml create mode 100644 .github/workflows/docs.yml create mode 100644 .github/workflows/lint.yml create mode 100644 .github/workflows/publish.yml delete mode 100644 .github/workflows/python-publish-pypi.yml delete mode 100644 .github/workflows/python-publish-testpypi.yml delete mode 100644 .github/workflows/python-runtests-basic.yml delete mode 100644 .github/workflows/python-runtests-img-comp.yml create mode 100644 .github/workflows/tests.yml rename readme.rst => README.md (55%) create mode 100644 docs/api.md delete mode 100644 docs/api.rst create mode 100644 docs/api/activity.md delete mode 100644 docs/api/activity.rst rename docs/api/{paramnormal.rst => paramnormal.md} (53%) create mode 100644 docs/api/utils.md delete mode 100644 docs/api/utils.rst delete mode 100644 docs/examples/index.rst delete mode 100644 docs/includeme.rst create mode 100644 docs/index.md delete mode 100644 docs/index.rst delete mode 100644 docs/sphinxext/ipython_console_highlighting.py delete mode 100644 docs/sphinxext/ipython_directive.py delete mode 100644 docs/sphinxext/plot_directive.py delete mode 100644 docs/sphinxext/plot_generator.py delete mode 100644 docs/sphinxext/requirements.txt create mode 100644 pyproject.toml delete mode 100644 requirements.txt delete mode 100644 requirements_dev.txt delete mode 100644 setup.cfg delete mode 100644 setup.py create mode 100644 uv.lock diff --git a/.github/dependabot.yml b/.github/dependabot.yml new file mode 100644 index 0000000..27f2246 --- /dev/null +++ b/.github/dependabot.yml @@ -0,0 +1,10 @@ +version: 2 +updates: + - package-ecosystem: github-actions + directory: / + schedule: + interval: weekly + - package-ecosystem: uv + directory: / + schedule: + interval: weekly diff --git a/.github/workflows/black.yml b/.github/workflows/black.yml deleted file mode 100644 index 055acb4..0000000 --- a/.github/workflows/black.yml +++ /dev/null @@ -1,19 +0,0 @@ -name: ruff 'n' stuff -on: [pull_request] - -jobs: - build: - runs-on: ubuntu-latest - steps: - - uses: actions/checkout@v3 - - name: Install Python - uses: actions/setup-python@v4 - with: - python-version: "3.12" - - name: Install dependencies - run: | - python -m pip install --upgrade pip - pip install ruff - # Update output format to enable automatic inline annotations. - - name: Run Ruff - run: ruff check --output-format=github . diff --git a/.github/workflows/check-test-coverage.yml b/.github/workflows/check-test-coverage.yml deleted file mode 100644 index 4379d60..0000000 --- a/.github/workflows/check-test-coverage.yml +++ /dev/null @@ -1,30 +0,0 @@ -name: Run coverage via codecov -on: - push: - branches: [ main ] - pull_request: - branches: [ main ] - -jobs: - run: - runs-on: ubuntu-latest - steps: - - uses: actions/checkout@v2 - - name: Setup Python - uses: actions/setup-python@v2 - with: - python-version: 3.11 - - name: Generate coverage report - run: | - python -m pip install --upgrade pip - pip install flake8 pytest - if [ -f requirements_dev.txt ]; then pip install -r requirements_dev.txt; fi - coverage run --source paramnormal check_paramnormal.py --doctest-modules --cov-report=xml - - name: Upload coverage to Codecov - uses: codecov/codecov-action@v1 - with: - # directory: ./coverage/reports/ - flags: unittests - name: codecov-umbrella - fail_ci_if_error: true - path_to_write_report: ./codecov_report.gz diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml new file mode 100644 index 0000000..23435c5 --- /dev/null +++ b/.github/workflows/docs.yml @@ -0,0 +1,40 @@ +name: Docs + +on: + push: + branches: [main] + pull_request: + workflow_dispatch: + +permissions: + contents: read + +jobs: + build: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v5 + - uses: astral-sh/setup-uv@v7 + with: + enable-cache: true + - name: Build docs + run: uv run --group docs sphinx-build -b html docs docs/_build/html + env: + MPLBACKEND: agg + - uses: actions/upload-pages-artifact@v4 + with: + path: docs/_build/html + + deploy: + if: github.event_name != 'pull_request' && github.ref == 'refs/heads/main' + needs: build + runs-on: ubuntu-latest + permissions: + pages: write + id-token: write + environment: + name: github-pages + url: ${{ steps.deployment.outputs.page_url }} + steps: + - id: deployment + uses: actions/deploy-pages@v4 diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml new file mode 100644 index 0000000..bf459ae --- /dev/null +++ b/.github/workflows/lint.yml @@ -0,0 +1,22 @@ +name: Lint + +on: + push: + branches: [main] + pull_request: + +permissions: + contents: read + +jobs: + ruff: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v5 + - uses: astral-sh/setup-uv@v7 + with: + enable-cache: true + - name: Ruff lint + run: uv run --only-group dev ruff check --output-format=github . + - name: Ruff format + run: uv run --only-group dev ruff format --check . diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml new file mode 100644 index 0000000..a361cd7 --- /dev/null +++ b/.github/workflows/publish.yml @@ -0,0 +1,81 @@ +name: Publish + +on: + push: + tags: + - "v*/release" # PyPI + - "v**test*" # TestPyPI + +permissions: + contents: read + +jobs: + build: + name: Build distributions + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v5 + - uses: astral-sh/setup-uv@v7 + - run: uv build + - uses: actions/upload-artifact@v5 + with: + name: python-package-distributions + path: dist/ + + publish-testpypi: + name: Publish to TestPyPI + if: contains(github.ref_name, 'test') + needs: build + runs-on: ubuntu-latest + environment: + name: test + url: https://test.pypi.org/p/paramnormal + permissions: + id-token: write + steps: + - uses: astral-sh/setup-uv@v7 + - uses: actions/download-artifact@v5 + with: + name: python-package-distributions + path: dist/ + - run: uv publish --trusted-publishing always --publish-url https://test.pypi.org/legacy/ + + publish-pypi: + name: Publish to PyPI + if: endsWith(github.ref_name, '/release') + needs: build + runs-on: ubuntu-latest + environment: + name: release + url: https://pypi.org/p/paramnormal + permissions: + id-token: write + steps: + - uses: astral-sh/setup-uv@v7 + - uses: actions/download-artifact@v5 + with: + name: python-package-distributions + path: dist/ + - run: uv publish --trusted-publishing always + + github-release: + name: Create GitHub release + needs: publish-pypi + runs-on: ubuntu-latest + permissions: + contents: write + id-token: write + steps: + - uses: actions/download-artifact@v5 + with: + name: python-package-distributions + path: dist/ + - uses: sigstore/gh-action-sigstore-python@v3.0.1 + with: + inputs: ./dist/*.tar.gz ./dist/*.whl + - name: Create release and upload artifacts + env: + GITHUB_TOKEN: ${{ github.token }} + run: >- + gh release create '${{ github.ref_name }}' dist/** + --repo '${{ github.repository }}' --generate-notes diff --git a/.github/workflows/python-publish-pypi.yml b/.github/workflows/python-publish-pypi.yml deleted file mode 100644 index 9808e39..0000000 --- a/.github/workflows/python-publish-pypi.yml +++ /dev/null @@ -1,95 +0,0 @@ -name: Publish Python 🐍 distribution 📦 to PyPI -on: - push: - # Pattern matched against refs/tags - tags: - - 'v*/release' # Push events to every that ends in /release (only 1 /-level) -jobs: - build: - name: Build distribution 📦 - runs-on: ubuntu-latest - - steps: - - uses: actions/checkout@v4 - - name: Set up Python - uses: actions/setup-python@v4 - with: - python-version: "3.x" - - name: Install pypa/build - run: >- - python3 -m - pip install - build - --user - - name: Build a binary wheel and a source tarball - run: python3 -m build - - name: Store the distribution packages - uses: actions/upload-artifact@v3 - with: - name: python-package-distributions - path: dist/ - - publish-to-pypi: - name: >- - Publish Python 🐍 distribution 📦 to PyPI - if: startsWith(github.ref, 'refs/tags/') # only publish to PyPI on tag pushes - needs: - - build - runs-on: ubuntu-latest - environment: - name: release - url: https://pypi.org/p/paramnormal # Replace with your PyPI project name - permissions: - id-token: write # IMPORTANT: mandatory for trusted publishing - - steps: - - name: Download all the dists - uses: actions/download-artifact@v4.1.7 - with: - name: python-package-distributions - path: dist/ - - name: Publish distribution 📦 to PyPI - uses: pypa/gh-action-pypi-publish@release/v1 - - github-release: - name: >- - Sign the Python 🐍 distribution 📦 with Sigstore - and upload them to GitHub Release - needs: - - publish-to-pypi - runs-on: ubuntu-latest - - permissions: - contents: write # IMPORTANT: mandatory for making GitHub Releases - id-token: write # IMPORTANT: mandatory for sigstore - - steps: - - name: Download all the dists - uses: actions/download-artifact@v4.1.7 - with: - name: python-package-distributions - path: dist/ - - name: Sign the dists with Sigstore - uses: sigstore/gh-action-sigstore-python@v1.2.3 - with: - inputs: >- - ./dist/*.tar.gz - ./dist/*.whl - - name: Create GitHub Release - env: - GITHUB_TOKEN: ${{ github.token }} - run: >- - gh release create - '${{ github.ref_name }}' - --repo '${{ github.repository }}' - --notes "" - - name: Upload artifact signatures to GitHub Release - env: - GITHUB_TOKEN: ${{ github.token }} - # Upload to GitHub Release using the `gh` CLI. - # `dist/` contains the built packages, and the - # sigstore-produced signatures and certificates. - run: >- - gh release upload - '${{ github.ref_name }}' dist/** - --repo '${{ github.repository }}' diff --git a/.github/workflows/python-publish-testpypi.yml b/.github/workflows/python-publish-testpypi.yml deleted file mode 100644 index 08d6a7e..0000000 --- a/.github/workflows/python-publish-testpypi.yml +++ /dev/null @@ -1,57 +0,0 @@ -name: Publish Python 🐍 distribution 📦 to TestPyPI - -on: - push: - # Pattern matched against refs/tags - tags: - - 'v**test*' # Push events to every that ends in "test[something]" (can have many /-levels) - -jobs: - build: - name: Build distribution 📦 - runs-on: ubuntu-latest - - steps: - - uses: actions/checkout@v4 - - name: Set up Python - uses: actions/setup-python@v4 - with: - python-version: "3.x" - - name: Install pypa/build - run: >- - python3 -m - pip install - build - --user - - name: Build a binary wheel and a source tarball - run: python3 -m build - - name: Store the distribution packages - uses: actions/upload-artifact@v3 - with: - name: python-package-distributions - path: dist/ - - - publish-to-testpypi: - name: Publish Python 🐍 distribution 📦 to TestPyPI - needs: - - build - runs-on: ubuntu-latest - - environment: - name: test - url: https://test.pypi.org/p/paramnormal - - permissions: - id-token: write # IMPORTANT: mandatory for trusted publishing - - steps: - - name: Download all the dists - uses: actions/download-artifact@v4.1.7 - with: - name: python-package-distributions - path: dist/ - - name: Publish distribution 📦 to TestPyPI - uses: pypa/gh-action-pypi-publish@release/v1 - with: - repository-url: https://test.pypi.org/legacy/ diff --git a/.github/workflows/python-runtests-basic.yml b/.github/workflows/python-runtests-basic.yml deleted file mode 100644 index 77c4393..0000000 --- a/.github/workflows/python-runtests-basic.yml +++ /dev/null @@ -1,33 +0,0 @@ -# This workflow will install Python dependencies, run tests and lint with a variety of Python versions -# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions - -name: Run basic unit tests - -on: - push: - branches: [ main ] - pull_request: - branches: [ main ] - -jobs: - build: - - runs-on: ubuntu-latest - strategy: - matrix: - python-version: ["3.9", "3.10", "3.11", "3.12"] - - steps: - - uses: actions/checkout@v2 - - 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 pytest - if [ -f requirements_dev.txt ]; then pip install -r requirements_dev.txt; fi - - name: Test with pytest - run: | - python check_paramnormal.py --doctest-modules diff --git a/.github/workflows/python-runtests-img-comp.yml b/.github/workflows/python-runtests-img-comp.yml deleted file mode 100644 index a904005..0000000 --- a/.github/workflows/python-runtests-img-comp.yml +++ /dev/null @@ -1,30 +0,0 @@ -# This workflow will install Python dependencies, run tests and lint with a variety of Python versions -# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions - -name: Run image comparison tests - -on: - push: - branches: [ master ] - pull_request: - branches: [ master ] - -jobs: - build: - - runs-on: ubuntu-latest - steps: - - uses: actions/checkout@v2 - - name: Set up Python 3.12 - uses: actions/setup-python@v2 - with: - python-version: 3.12 - - name: Install dependencies - run: | - python -m pip install --upgrade pip - pip install flake8 pytest - if [ -f requirements_dev.txt ]; then pip install -r requirements_dev.txt; fi - - name: Test with pytest - run: | - export MPL_IMGCOMP_TOLERANCE=20 - python check_paramnormal.py --strict --verbose diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml new file mode 100644 index 0000000..7cd8640 --- /dev/null +++ b/.github/workflows/tests.yml @@ -0,0 +1,31 @@ +name: Tests + +on: + push: + branches: [main] + pull_request: + +permissions: + contents: read + +jobs: + test: + runs-on: ubuntu-latest + strategy: + fail-fast: false + matrix: + python-version: ["3.11", "3.12", "3.13", "3.14"] + steps: + - uses: actions/checkout@v5 + - uses: astral-sh/setup-uv@v7 + with: + python-version: ${{ matrix.python-version }} + enable-cache: true + - name: Run tests + run: >- + uv run --group dev pytest paramnormal + --cov=paramnormal --cov-report=xml + env: + MPLBACKEND: agg + MPL_IMGCOMP_TOLERANCE: "20" + diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 4a2462b..ea73e31 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,29 +1,7 @@ repos: - repo: https://github.com/astral-sh/ruff-pre-commit - # Ruff version. - rev: v0.2.0 + rev: v0.15.0 hooks: - # Run the linter. - - id: ruff - args: [ --fix ] - # Run the formatter. + - id: ruff-check + args: [--fix] - id: ruff-format - - - repo: https://github.com/pycqa/isort - rev: 5.13.2 - hooks: - - id: isort - language_version: python3 - - - repo: https://github.com/asottile/pyupgrade - rev: v3.15.0 - hooks: - - id: pyupgrade - args: - - --py310-plus - - - repo: https://github.com/MarcoGorelli/absolufy-imports - rev: v0.3.1 - hooks: - - id: absolufy-imports - name: absolufy-imports diff --git a/readme.rst b/README.md similarity index 55% rename from readme.rst rename to README.md index 4c444c5..f444223 100644 --- a/readme.rst +++ b/README.md @@ -1,23 +1,16 @@ -paramnormal: Conventionally parameterized probability distributions -=================================================================== - -.. image:: https://coveralls.io/repos/phobson/paramnormal/badge.svg?branch=master&service=github - :target: https://coveralls.io/github/phobson/paramnormal?branch=master - +# paramnormal: Conventionally parameterized probability distributions Scipy distributions are weird. Maybe these will be less weird. - -The problem this is solving ---------------------------- +## The problem this is solving Let's look at the lognormal distribution. -The `wikipedia article `__ states that they are parameterized by μ and σ, the mean and standard deviation of the underlying normal distribution. +The [wikipedia article](https://en.wikipedia.org/wiki/Log-normal_distribution) states that they are parameterized by μ and σ, the mean and standard deviation of the underlying normal distribution. In this case, μ and σ can also be known as the location and scale parameters, respectively. However, to create a lognormal distribution in scipy, you need three parameters: location, scale, and shape. -The tricky part is, however, is that "location" in scipy refers to an offset from zero, "shape" refers to σ, and the "scale" refers to :math:`e^\mu`. +The tricky part is, however, is that "location" in scipy refers to an offset from zero, "shape" refers to σ, and the "scale" refers to $e^\mu$. This is all explained the scipy documentation, but it took me a couple of readings and bad mistakes to figure it out. It's also never really explicitly stated that scipy's location parameter should be zero 99.999% of the time. That's a very import point to understand when you're fitting lognormal parameters to a sample and you end with three crazy numbers that don't make any sense and distribution with values less than zero despite the fact that you thought lognormal distribution couldn't have values less than zero. @@ -26,48 +19,60 @@ Point of all of this is that *paramnormal* is trying to make easy what scipy som So where as in scipy, you would do this: -.. code:: python +```python +import numpy +from scipy import stats - import numpy - from scipy import stats - mu = 0.75 - sigma = 1.25 - dist = stats.lognorm(sigma, loc=0, scale=numpy.exp(mu)) +mu = 0.75 +sigma = 1.25 +dist = stats.lognorm(sigma, loc=0, scale=numpy.exp(mu)) +``` In paramnormal, you can do this: -.. code:: python +```python +import paramnormal - import paramnormal - dist = paramnormal.lognormal(mu=0.75, sigma=1.25) +dist = paramnormal.lognormal(mu=0.75, sigma=1.25) +``` You can even use Greek letters -.. code:: python +```python +dist = paramnormal.lognormal(μ=0.75, σ=1.25) +``` - dist = paramnormal.lognormal(μ=0.75, σ=1.25) - -All three snippets return the same scipy distribution objects and have the same numerical methods (e.g., ``cdf``, ``pdf``, ``rvs``, ``ppf``). +All three snippets return the same scipy distribution objects and have the same numerical methods (e.g., `cdf`, `pdf`, `rvs`, `ppf`). Paramnormal just provides a short cut that let's you only specify the traditional distribution parameters you read about in your text book. -Documentation -------------- -We have `HTML docs built with sphinx `_. +## Documentation + +We have [HTML docs built with sphinx](http://phobson.github.io/paramnormal/). + +## Installation -Installation ------------- Binaries are available through my conda channel -``conda install --channel=phobson paramnormal`` +`conda install --channel=phobson paramnormal` This is a pure python package, so installation from source should be as easy as running -``pip install .`` from the source directory if you've cloned the repo. +`pip install .` (or `uv pip install .`) from the source directory if you've cloned the repo. + +Otherwise, `pip install paramnormal` or `pip install git+https://github.com/phobson/paramnormal.git` will work. + +## Development + +This project is managed with [uv](https://docs.astral.sh/uv/): + +```shell +uv sync # create .venv with dev dependencies +uv run pytest # run the tests +uv run ruff check . && uv run ruff format --check . +uv run --group docs sphinx-build -b html docs docs/_build/html +``` -Otherwise, I think ``pip install git+https://github.com/phobson/paramnormal.git`` will work. -(I'll upload to pip after this has sat around for a while. +## Development status -Development status ------------------- From my perspective this is now feature complete, meaning it has all of the distribution that I use somewhat regularly. If you want to add a new distribution, get in touch. Otherwise, I'll just be fixing bugs and typos/ommisions in the documentaion. diff --git a/docs/api.md b/docs/api.md new file mode 100644 index 0000000..e190273 --- /dev/null +++ b/docs/api.md @@ -0,0 +1,9 @@ +# API Reference + +```{toctree} +:maxdepth: 2 + +api/activity +api/paramnormal +api/utils +``` diff --git a/docs/api.rst b/docs/api.rst deleted file mode 100644 index a10efa2..0000000 --- a/docs/api.rst +++ /dev/null @@ -1,9 +0,0 @@ -API Reference -------------- - -.. toctree:: - :maxdepth: 2 - - api/activity.rst - api/paramnormal.rst - api/utils.rst diff --git a/docs/api/activity.md b/docs/api/activity.md new file mode 100644 index 0000000..87cc8cc --- /dev/null +++ b/docs/api/activity.md @@ -0,0 +1,7 @@ +(act_auto)= +# Paramnormal Activity + +```{eval-rst} +.. automodule:: paramnormal.activity + :members: +``` diff --git a/docs/api/activity.rst b/docs/api/activity.rst deleted file mode 100644 index db947ed..0000000 --- a/docs/api/activity.rst +++ /dev/null @@ -1,7 +0,0 @@ -.. _act_auto: - -Paramnormal Activity -==================== - -.. automodule:: paramnormal.activity - :members: diff --git a/docs/api/paramnormal.rst b/docs/api/paramnormal.md similarity index 53% rename from docs/api/paramnormal.rst rename to docs/api/paramnormal.md index f079091..ea373c6 100644 --- a/docs/api/paramnormal.rst +++ b/docs/api/paramnormal.md @@ -1,9 +1,9 @@ -.. _paramnormal_auto: - -Probability Distributions -========================= +(paramnormal_auto)= +# Probability Distributions +```{eval-rst} .. automodule:: paramnormal.dist :members: :undoc-members: :show-inheritance: +``` diff --git a/docs/api/utils.md b/docs/api/utils.md new file mode 100644 index 0000000..d991358 --- /dev/null +++ b/docs/api/utils.md @@ -0,0 +1,7 @@ +(utils_auto)= +# Miscellaneous Utilities + +```{eval-rst} +.. automodule:: paramnormal.utils + :members: +``` diff --git a/docs/api/utils.rst b/docs/api/utils.rst deleted file mode 100644 index f2bd0aa..0000000 --- a/docs/api/utils.rst +++ /dev/null @@ -1,7 +0,0 @@ -.. _utils_auto: - -Miscellaneous Utilities -======================= - -.. automodule:: paramnormal.utils - :members: diff --git a/docs/conf.py b/docs/conf.py index d200ea9..617b42e 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -1,35 +1,13 @@ -#!/usr/bin/env python3 -# -# paramnormal documentation build configuration file, created by -# sphinx-quickstart on Wed Dec 2 17:36:54 2015. -# -# This file is execfile()d with the current directory set to its -# containing dir. -# -# Note that not all possible configuration values are present in this -# autogenerated file. -# -# All configuration values have a default; values that are commented out -# serve to show the default. - -import os -import sys - import seaborn clean_bkgd = {"axes.facecolor": "none", "figure.facecolor": "none"} -seaborn.set(style="ticks", rc=clean_bkgd) - -source_suffix = [".rst"] +seaborn.set_theme(style="ticks", rc=clean_bkgd) -numpydoc_show_class_members = False -autodoc_member_order = "bysource" -html_theme = "sphinx_rtd_theme" +project = "paramnormal" +copyright = "2015 - 2024, Paul Hobson" +author = "Paul Hobson" +version = release = "0.4.4" -# Add any Sphinx extension module names here, as strings. They can be -# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom -# ones. -sys.path.insert(0, os.path.abspath("sphinxext")) extensions = [ "sphinx.ext.autodoc", "sphinx.ext.doctest", @@ -37,270 +15,23 @@ "sphinx.ext.todo", "sphinx.ext.mathjax", "sphinx.ext.viewcode", - "plot_generator", - "plot_directive", "numpydoc", - "ipython_directive", - "ipython_console_highlighting", + "myst_nb", ] -# Add any paths that contain templates here, relative to this directory. -templates_path = ["_templates"] - -# The suffix(es) of source filenames. -# You can specify multiple suffix as a list of string: -# source_suffix = ['.rst', '.md'] -source_suffix = ".rst" - -# The encoding of source files. -# source_encoding = 'utf-8-sig' - -# Include the example source for plots in API docs -plot_include_source = True -plot_formats = [("png", 90)] -plot_html_show_formats = False -plot_html_show_source_link = False - -# The master toctree document. +source_suffix = {".md": "myst-nb", ".ipynb": "myst-nb"} master_doc = "index" +exclude_patterns = ["_build", "**.ipynb_checkpoints"] +myst_enable_extensions = ["dollarmath", "amsmath"] +nb_execution_mode = "off" +suppress_warnings = ["myst.header"] -# General information about the project. -project = "paramnormal" -copyright = "2015 - 2016, Paul Hobson" -author = "Paul Hobson" - -# The version info for the project you're documenting, acts as replacement for -# |version| and |release|, also used in various other places throughout the -# built documents. -# -# The short X.Y version. -version = "0.4.4" -# The full version, including alpha/beta/rc tags. -release = "0.4.4" - -# The language for content autogenerated by Sphinx. Refer to documentation -# for a list of supported languages. -# -# This is also used if you do content translation via gettext catalogs. -# Usually you set "language" from the command line for these cases. -language = None - -# There are two options for replacing |today|: either, you set today to some -# non-false value, then it is used: -# today = '' -# Else, today_fmt is used as the format for a strftime call. -# today_fmt = '%B %d, %Y' - -# List of patterns, relative to source directory, that match files and -# directories to ignore when looking for source files. -exclude_patterns = ["_build"] - -# The reST default role (used for this markup: `text`) to use for all -# documents. -# default_role = None - -# If true, '()' will be appended to :func: etc. cross-reference text. -# add_function_parentheses = True - -# If true, the current module name will be prepended to all description -# unit titles (such as .. function::). -# add_module_names = True - -# If true, sectionauthor and moduleauthor directives will be shown in the -# output. They are ignored by default. -# show_authors = False - -# The name of the Pygments (syntax highlighting) style to use. -pygments_style = "sphinx" - -# A list of ignored prefixes for module index sorting. -# modindex_common_prefix = [] - -# If true, keep warnings as "system message" paragraphs in the built documents. -# keep_warnings = False - -# If true, `todo` and `todoList` produce output, else they produce nothing. +numpydoc_show_class_members = False +autodoc_member_order = "bysource" todo_include_todos = True +pygments_style = "sphinx" - -# -- Options for HTML output ---------------------------------------------- - -# The theme to use for HTML and HTML Help pages. See the documentation for -# a list of builtin themes. html_theme = "sphinx_rtd_theme" - -# Theme options are theme-specific and customize the look and feel of a theme -# further. For a list of options available for each theme, see the -# documentation. -# html_theme_options = {} - -# Add any paths that contain custom themes here, relative to this directory. -# html_theme_path = [] - -# The name for this set of Sphinx documents. If None, it defaults to -# " v documentation". -# html_title = None - -# A shorter title for the navigation bar. Default is the same as html_title. -# html_short_title = None - -# The name of an image file (relative to this directory) to place at the top -# of the sidebar. -# html_logo = None - -# The name of an image file (within the static path) to use as favicon of the -# docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32 -# pixels large. -# html_favicon = None - -# Add any paths that contain custom static files (such as style sheets) here, -# relative to this directory. They are copied after the builtin static files, -# so a file named "default.css" will overwrite the builtin "default.css". -html_static_path = ["_static"] - -# Add any extra paths that contain custom files (such as robots.txt or -# .htaccess) here, relative to this directory. These files are copied -# directly to the root of the documentation. -# html_extra_path = [] - -# If not '', a 'Last updated on:' timestamp is inserted at every page bottom, -# using the given strftime format. -# html_last_updated_fmt = '%b %d, %Y' - -# If true, SmartyPants will be used to convert quotes and dashes to -# typographically correct entities. -# html_use_smartypants = True - -# Custom sidebar templates, maps document names to template names. -# html_sidebars = {} - -# Additional templates that should be rendered to pages, maps page names to -# template names. -# html_additional_pages = {} - -# If false, no module index is generated. -# html_domain_indices = True - -# If false, no index is generated. -# html_use_index = True - -# If true, the index is split into individual pages for each letter. -# html_split_index = False - -# If true, links to the reST sources are added to the pages. -# html_show_sourcelink = True - -# If true, "Created using Sphinx" is shown in the HTML footer. Default is True. -# html_show_sphinx = True - -# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True. -# html_show_copyright = True - -# If true, an OpenSearch description file will be output, and all pages will -# contain a tag referring to it. The value of this option must be the -# base URL from which the finished HTML is served. -# html_use_opensearch = '' - -# This is the file name suffix for HTML files (e.g. ".xhtml"). -# html_file_suffix = None - -# Language to be used for generating the HTML full-text search index. -# Sphinx supports the following languages: -# 'da', 'de', 'en', 'es', 'fi', 'fr', 'h', 'it', 'ja' -# 'nl', 'no', 'pt', 'ro', 'r', 'sv', 'tr' -# html_search_language = 'en' - -# A dictionary with options for the search language support, empty by default. -# Now only 'ja' uses this config value -# html_search_options = {'type': 'default'} - -# The name of a javascript file (relative to the configuration directory) that -# implements a search results scorer. If empty, the default will be used. -# html_search_scorer = 'scorer.js' - -# Output file base name for HTML help builder. htmlhelp_basename = "paramnormaldoc" -# -- Options for LaTeX output --------------------------------------------- - -latex_elements = { - # The paper size ('letterpaper' or 'a4paper'). - #'papersize': 'letterpaper', - # The font size ('10pt', '11pt' or '12pt'). - #'pointsize': '10pt', - # Additional stuff for the LaTeX preamble. - #'preamble': '', - # Latex figure (float) alignment - #'figure_align': 'htbp', -} - -# Grouping the document tree into LaTeX files. List of tuples -# (source start file, target name, title, -# author, documentclass [howto, manual, or own class]). -latex_documents = [ - (master_doc, "paramnormal.tex", "paramnormal Documentation", "Paul Hobson", "manual"), -] - -# The name of an image file (relative to this directory) to place at the top of -# the title page. -# latex_logo = None - -# For "manual" documents, if this is true, then toplevel headings are parts, -# not chapters. -# latex_use_parts = False - -# If true, show page references after internal links. -# latex_show_pagerefs = False - -# If true, show URL addresses after external links. -# latex_show_urls = False - -# Documents to append as an appendix to all manuals. -# latex_appendices = [] - -# If false, no module index is generated. -# latex_domain_indices = True - - -# -- Options for manual page output --------------------------------------- - -# One entry per manual page. List of tuples -# (source start file, name, description, authors, manual section). -man_pages = [(master_doc, "paramnormal", "paramnormal Documentation", [author], 1)] - -# If true, show URL addresses after external links. -# man_show_urls = False - - -# -- Options for Texinfo output ------------------------------------------- - -# Grouping the document tree into Texinfo files. List of tuples -# (source start file, target name, title, author, -# dir menu entry, description, category) -texinfo_documents = [ - ( - master_doc, - "paramnormal", - "paramnormal Documentation", - author, - "paramnormal", - "One line description of project.", - "Miscellaneous", - ), -] - -# Documents to append as an appendix to all manuals. -# texinfo_appendices = [] - -# If false, no module index is generated. -# texinfo_domain_indices = True - -# How to display URL addresses: 'footnote', 'no', or 'inline'. -# texinfo_show_urls = 'footnote' - -# If true, do not generate a @detailmenu in the "Top" node's menu. -# texinfo_no_detailmenu = False - - -# Example configuration for intersphinx: refer to the Python standard library. -intersphinx_mapping = {"https://docs.python.org/": None} +intersphinx_mapping = {"python": ("https://docs.python.org/3", None)} diff --git a/docs/examples/index.rst b/docs/examples/index.rst deleted file mode 100644 index 144aedc..0000000 --- a/docs/examples/index.rst +++ /dev/null @@ -1,85 +0,0 @@ - - -.. raw:: html - - - -.. _example_gallery: - -Example gallery -=============== - - - -.. toctree:: - :hidden: - - - - - - - -.. raw:: html - -
diff --git a/docs/includeme.rst b/docs/includeme.rst deleted file mode 100644 index 482827f..0000000 --- a/docs/includeme.rst +++ /dev/null @@ -1 +0,0 @@ -.. include:: ../readme.rst diff --git a/docs/index.md b/docs/index.md new file mode 100644 index 0000000..d07db63 --- /dev/null +++ b/docs/index.md @@ -0,0 +1,26 @@ +```{include} ../README.md +``` + +# Tutorials + +```{toctree} +:maxdepth: 2 + +tutorial/overview +tutorial/fitting +tutorial/activities +``` + +# API Reference + +```{toctree} +:maxdepth: 2 + +api +``` + +# Indices and tables + +* {ref}`genindex` +* {ref}`modindex` +* {ref}`search` diff --git a/docs/index.rst b/docs/index.rst deleted file mode 100644 index 40a7ce9..0000000 --- a/docs/index.rst +++ /dev/null @@ -1,29 +0,0 @@ -.. include:: ../readme.rst - - -Tutorials -========= - -.. toctree:: - :maxdepth: 2 - - tutorial/overview - tutorial/fitting - tutorial/activities - -API Reference -============= - -.. toctree:: - :maxdepth: 2 - - api.rst - - -Indices and tables -================== - -* :ref:`genindex` -* :ref:`modindex` -* :ref:`search` - diff --git a/docs/sphinxext/ipython_console_highlighting.py b/docs/sphinxext/ipython_console_highlighting.py deleted file mode 100644 index b07bf18..0000000 --- a/docs/sphinxext/ipython_console_highlighting.py +++ /dev/null @@ -1,109 +0,0 @@ -"""reST directive for syntax-highlighting ipython interactive sessions. - -XXX - See what improvements can be made based on the new (as of Sept 2009) -'pycon' lexer for the python console. At the very least it will give better -highlighted tracebacks. -""" - -# ----------------------------------------------------------------------------- -# Needed modules - -# Standard library -import re - -# Third party -from pygments.lexer import Lexer, do_insertions -from pygments.lexers.agile import PythonLexer, PythonTracebackLexer -from pygments.token import Comment, Generic -from sphinx import highlighting - -# ----------------------------------------------------------------------------- -# Global constants -line_re = re.compile(".*?\n") - -# ----------------------------------------------------------------------------- -# Code begins - classes and functions - - -class IPythonConsoleLexer(Lexer): - - """ - For IPython console output or doctests, such as: - - .. sourcecode:: ipython - - In [1]: a = 'foo' - - In [2]: a - Out[2]: 'foo' - - In [3]: print(a) - foo - - In [4]: 1 / 0 - - Notes: - - - Tracebacks are not currently supported. - - - It assumes the default IPython prompts, not customized ones. - """ - - name = "IPython console session" - aliases = ["ipython"] - mimetypes = ["text/x-ipython-console"] - input_prompt = re.compile(r"(In \[[0-9]+\]: )|( \.\.\.+:)") - output_prompt = re.compile(r"(Out\[[0-9]+\]: )|( \.\.\.+:)") - continue_prompt = re.compile(r" \.\.\.+:") - tb_start = re.compile(r"\-+") - - def get_tokens_unprocessed(self, text): - pylexer = PythonLexer(**self.options) - PythonTracebackLexer(**self.options) - - curcode = "" - insertions = [] - for match in line_re.finditer(text): - line = match.group() - input_prompt = self.input_prompt.match(line) - continue_prompt = self.continue_prompt.match(line.rstrip()) - output_prompt = self.output_prompt.match(line) - if line.startswith("#"): - insertions.append((len(curcode), [(0, Comment, line)])) - elif input_prompt is not None: - insertions.append((len(curcode), [(0, Generic.Prompt, input_prompt.group())])) - curcode += line[input_prompt.end() :] - elif continue_prompt is not None: - insertions.append((len(curcode), [(0, Generic.Prompt, continue_prompt.group())])) - curcode += line[continue_prompt.end() :] - elif output_prompt is not None: - # Use the 'error' token for output. We should probably make - # our own token, but error is typicaly in a bright color like - # red, so it works fine for our output prompts. - insertions.append((len(curcode), [(0, Generic.Error, output_prompt.group())])) - curcode += line[output_prompt.end() :] - else: - if curcode: - for item in do_insertions(insertions, pylexer.get_tokens_unprocessed(curcode)): - yield item - curcode = "" - insertions = [] - yield match.start(), Generic.Output, line - if curcode: - for item in do_insertions(insertions, pylexer.get_tokens_unprocessed(curcode)): - yield item - - -def setup(app): - """Setup as a sphinx extension.""" - - # This is only a lexer, so adding it below to pygments appears sufficient. - # But if somebody knows that the right API usage should be to do that via - # sphinx, by all means fix it here. At least having this setup.py - # suppresses the sphinx warning we'd get without it. - pass - - -# ----------------------------------------------------------------------------- -# Register the extension as a valid pygments lexer -highlighting.lexers["ipython"] = IPythonConsoleLexer() diff --git a/docs/sphinxext/ipython_directive.py b/docs/sphinxext/ipython_directive.py deleted file mode 100644 index 1e19e3c..0000000 --- a/docs/sphinxext/ipython_directive.py +++ /dev/null @@ -1,1105 +0,0 @@ -r""" -Sphinx directive to support embedded IPython code. - -This directive allows pasting of entire interactive IPython sessions, prompts -and all, and their code will actually get re-executed at doc build time, with -all prompts renumbered sequentially. It also allows you to input code as a pure -python input by giving the argument python to the directive. The output looks -like an interactive ipython section. - -To enable this directive, simply list it in your Sphinx ``conf.py`` file -(making sure the directory where you placed it is visible to sphinx, as is -needed for all Sphinx directives). For example, to enable syntax highlighting -and the IPython directive:: - - extensions = ['IPython.sphinxext.ipython_console_highlighting', - 'IPython.sphinxext.ipython_directive'] - -The IPython directive outputs code-blocks with the language 'ipython'. So -if you do not have the syntax highlighting extension enabled as well, then -all rendered code-blocks will be uncolored. By default this directive assumes -that your prompts are unchanged IPython ones, but this can be customized. -The configurable options that can be placed in conf.py are: - -ipython_savefig_dir: - The directory in which to save the figures. This is relative to the - Sphinx source directory. The default is `html_static_path`. -ipython_rgxin: - The compiled regular expression to denote the start of IPython input - lines. The default is re.compile('In \[(\d+)\]:\s?(.*)\s*'). You - shouldn't need to change this. -ipython_rgxout: - The compiled regular expression to denote the start of IPython output - lines. The default is re.compile('Out\[(\d+)\]:\s?(.*)\s*'). You - shouldn't need to change this. -ipython_promptin: - The string to represent the IPython input prompt in the generated ReST. - The default is 'In [%d]:'. This expects that the line numbers are used - in the prompt. -ipython_promptout: - The string to represent the IPython prompt in the generated ReST. The - default is 'Out [%d]:'. This expects that the line numbers are used - in the prompt. -ipython_mplbackend: - The string which specifies if the embedded Sphinx shell should import - Matplotlib and set the backend. The value specifies a backend that is - passed to `matplotlib.use()` before any lines in `ipython_execlines` are - executed. If not specified in conf.py, then the default value of 'agg' is - used. To use the IPython directive without matplotlib as a dependency, set - the value to `None`. It may end up that matplotlib is still imported - if the user specifies so in `ipython_execlines` or makes use of the - @savefig pseudo decorator. -ipython_execlines: - A list of strings to be exec'd in the embedded Sphinx shell. Typical - usage is to make certain packages always available. Set this to an empty - list if you wish to have no imports always available. If specified in - conf.py as `None`, then it has the effect of making no imports available. - If omitted from conf.py altogether, then the default value of - ['import numpy as np', 'import matplotlib.pyplot as plt'] is used. -ipython_holdcount - When the @suppress pseudo-decorator is used, the execution count can be - incremented or not. The default behavior is to hold the execution count, - corresponding to a value of `True`. Set this to `False` to increment - the execution count after each suppressed command. - -As an example, to use the IPython directive when `matplotlib` is not available, -one sets the backend to `None`:: - - ipython_mplbackend = None - -An example usage of the directive is: - -.. code-block:: rst - - .. ipython:: - - In [1]: x = 1 - - In [2]: y = x**2 - - In [3]: print(y) - -See http://matplotlib.org/sampledoc/ipython_directive.html for additional -documentation. - -ToDo ----- - -- Turn the ad-hoc test() function into a real test suite. -- Break up ipython-specific functionality from matplotlib stuff into better - separated code. - -Authors -------- - -- John D Hunter: orignal author. -- Fernando Perez: refactoring, documentation, cleanups, port to 0.11. -- VáclavŠmilauer : Prompt generalizations. -- Skipper Seabold, refactoring, cleanups, pure python addition -""" - -# ----------------------------------------------------------------------------- -# Imports -# ----------------------------------------------------------------------------- - -import ast -import contextlib - -# Stdlib -import os -import re -import sys -import tempfile -import warnings - -from pandas.compat import cStringIO as StringIO -from pandas.compat import range - -# To keep compatibility with various python versions -with contextlib.suppress(ImportError): - pass - -# Third-party -from docutils.parsers.rst import directives -from IPython import InteractiveShell -from IPython.core.profiledir import ProfileDir -from IPython.utils import io -from IPython.utils.py3compat import PY3 -from sphinx.util.compat import Directive - -# Our own -from traitlets.config import Config - -if PY3: - from io import StringIO - - text_type = str -else: - from StringIO import StringIO - -# ----------------------------------------------------------------------------- -# Globals -# ----------------------------------------------------------------------------- -# for tokenizing blocks -COMMENT, INPUT, OUTPUT = range(3) - -# ----------------------------------------------------------------------------- -# Functions and class declarations -# ----------------------------------------------------------------------------- - - -def block_parser(part, rgxin, rgxout, fmtin, fmtout): - """ - part is a string of ipython text, comprised of at most one - input, one ouput, comments, and blank lines. The block parser - parses the text into a list of:: - - blocks = [ (TOKEN0, data0), (TOKEN1, data1), ...] - - where TOKEN is one of [COMMENT | INPUT | OUTPUT ] and - data is, depending on the type of token:: - - COMMENT : the comment string - - INPUT: the (DECORATOR, INPUT_LINE, REST) where - DECORATOR: the input decorator (or None) - INPUT_LINE: the input as string (possibly multi-line) - REST : any stdout generated by the input line (not OUTPUT) - - OUTPUT: the output string, possibly multi-line - - """ - block = [] - lines = part.split("\n") - N = len(lines) - i = 0 - decorator = None - while 1: - if i == N: - # nothing left to parse -- the last line - break - - line = lines[i] - i += 1 - line_stripped = line.strip() - if line_stripped.startswith("#"): - block.append((COMMENT, line)) - continue - - if line_stripped.startswith("@"): - # we're assuming at most one decorator -- may need to - # rethink - decorator = line_stripped - continue - - # does this look like an input line? - matchin = rgxin.match(line) - if matchin: - lineno, inputline = int(matchin.group(1)), matchin.group(2) - - # the ....: continuation string - continuation = " %s:" % "".join(["."] * (len(str(lineno)) + 2)) - Nc = len(continuation) - # input lines can continue on for more than one line, if - # we have a '\' line continuation char or a function call - # echo line 'print'. The input line can only be - # terminated by the end of the block or an output line, so - # we parse out the rest of the input line if it is - # multiline as well as any echo text - - rest = [] - while i < N: - # look ahead; if the next line is blank, or a comment, or - # an output line, we're done - - nextline = lines[i] - matchout = rgxout.match(nextline) - - if matchout or nextline.startswith("#"): - break - elif nextline.startswith(continuation): - nextline = nextline[Nc:] - if nextline and nextline[0] == " ": - nextline = nextline[1:] - - inputline += "\n" + nextline - - else: - rest.append(nextline) - i += 1 - - block.append((INPUT, (decorator, inputline, "\n".join(rest)))) - continue - - # if it looks like an output line grab all the text to the end - # of the block - matchout = rgxout.match(line) - if matchout: - lineno, output = int(matchout.group(1)), matchout.group(2) - if i < N - 1: - output = "\n".join([output] + lines[i:]) - - block.append((OUTPUT, output)) - break - - return block - - -class DecodingStringIO(StringIO): - def __init__(self, buf="", encodings=("utf8",), *args, **kwds): - super().__init__(buf, *args, **kwds) - self.set_encodings(encodings) - - def set_encodings(self, encodings): - self.encodings = encodings - - def write(self, data): - if isinstance(data, text_type): - return super().write(data) - else: - for enc in self.encodings: - try: - data = data.decode(enc) - return super().write(data) - except Exception: - pass - # default to brute utf8 if no encoding succeded - return super().write(data.decode("utf8", "replace")) - - -class EmbeddedSphinxShell: - """An embedded IPython instance to run inside Sphinx""" - - def __init__(self, exec_lines=None, state=None): - self.cout = DecodingStringIO("") - - if exec_lines is None: - exec_lines = [] - - self.state = state - - # Create config object for IPython - config = Config() - config.InteractiveShell.autocall = False - config.InteractiveShell.autoindent = False - config.InteractiveShell.colors = "NoColor" - - # create a profile so instance history isn't saved - tmp_profile_dir = tempfile.mkdtemp(prefix="profile_") - profname = "auto_profile_sphinx_build" - pdir = os.path.join(tmp_profile_dir, profname) - profile = ProfileDir.create_profile_dir(pdir) - - # Create and initialize global ipython, but don't start its mainloop. - # This will persist across different EmbededSphinxShell instances. - IP = InteractiveShell.instance(config=config, profile_dir=profile) - - # io.stdout redirect must be done after instantiating InteractiveShell - io.stdout = self.cout - io.stderr = self.cout - - # For debugging, so we can see normal output, use this: - # from IPython.utils.io import Tee - # io.stdout = Tee(self.cout, channel='stdout') # dbg - # io.stderr = Tee(self.cout, channel='stderr') # dbg - - # Store a few parts of IPython we'll need. - self.IP = IP - self.user_ns = self.IP.user_ns - self.user_global_ns = self.IP.user_global_ns - - self.input = "" - self.output = "" - - self.is_verbatim = False - self.is_doctest = False - self.is_suppress = False - - # Optionally, provide more detailed information to shell. - self.directive = None - - # on the first call to the savefig decorator, we'll import - # pyplot as plt so we can make a call to the plt.gcf().savefig - self._pyplot_imported = False - - # Prepopulate the namespace. - for line in exec_lines: - self.process_input_line(line, store_history=False) - - def clear_cout(self): - self.cout.seek(0) - self.cout.truncate(0) - - def process_input_line(self, line, store_history=True): - """process the input, capturing stdout""" - - stdout = sys.stdout - splitter = self.IP.input_splitter - try: - sys.stdout = self.cout - splitter.push(line) - more = splitter.push_accepts_more() - if not more: - try: - source_raw = splitter.source_raw_reset()[1] - except Exception: - # recent ipython #4504 - source_raw = splitter.raw_reset() - self.IP.run_cell(source_raw, store_history=store_history) - finally: - sys.stdout = stdout - - def process_image(self, decorator): - """ - # build out an image directive like - # .. image:: somefile.png - # :width 4in - # - # from an input like - # savefig somefile.png width=4in - """ - savefig_dir = self.savefig_dir - source_dir = self.source_dir - saveargs = decorator.split(" ") - filename = saveargs[1] - # insert relative path to image file in source - outfile = os.path.relpath(os.path.join(savefig_dir, filename), source_dir) - - imagerows = [".. image:: %s" % outfile] - - for kwarg in saveargs[2:]: - arg, val = kwarg.split("=") - arg = arg.strip() - val = val.strip() - imagerows.append(f" :{arg}: {val}") - - image_file = os.path.basename(outfile) # only return file name - image_directive = "\n".join(imagerows) - return image_file, image_directive - - # Callbacks for each type of token - def process_input(self, data, input_prompt, lineno): - """ - Process data block for INPUT token. - - """ - decorator, input, rest = data - image_file = None - image_directive = None - - is_verbatim = decorator == "@verbatim" or self.is_verbatim - is_doctest = (decorator is not None and decorator.startswith("@doctest")) or self.is_doctest - is_suppress = decorator == "@suppress" or self.is_suppress - is_okexcept = decorator == "@okexcept" or self.is_okexcept - is_okwarning = decorator == "@okwarning" or self.is_okwarning - is_savefig = decorator is not None and decorator.startswith("@savefig") - - # set the encodings to be used by DecodingStringIO - # to convert the execution output into unicode if - # needed. this attrib is set by IpythonDirective.run() - # based on the specified block options, defaulting to ['ut - self.cout.set_encodings(self.output_encoding) - - input_lines = input.split("\n") - - if len(input_lines) > 1 and input_lines[-1] != "": - input_lines.append("") # make sure there's a blank line - # so splitter buffer gets reset - - continuation = " %s:" % "".join(["."] * (len(str(lineno)) + 2)) - - if is_savefig: - image_file, image_directive = self.process_image(decorator) - - ret = [] - is_semicolon = False - - # Hold the execution count, if requested to do so. - store_history = not (is_suppress and self.hold_count) - - # Note: catch_warnings is not thread safe - with warnings.catch_warnings(record=True) as ws: - for i, line in enumerate(input_lines): - if line.endswith(";"): - is_semicolon = True - - if i == 0: - # process the first input line - if is_verbatim: - self.process_input_line("") - self.IP.execution_count += 1 # increment it anyway - else: - # only submit the line in non-verbatim mode - self.process_input_line(line, store_history=store_history) - formatted_line = f"{input_prompt} {line}" - else: - # process a continuation line - if not is_verbatim: - self.process_input_line(line, store_history=store_history) - - formatted_line = f"{continuation} {line}" - - if not is_suppress: - ret.append(formatted_line) - - if not is_suppress and len(rest.strip()) and is_verbatim: - # the "rest" is the standard output of the - # input, which needs to be added in - # verbatim mode - ret.append(rest) - - self.cout.seek(0) - output = self.cout.read() - if not is_suppress and not is_semicolon: - ret.append(output) - elif is_semicolon: # get spacing right - ret.append("") - - # context information - filename = self.state.document.current_source - lineno = self.state.document.current_line - - # output any exceptions raised during execution to stdout - # unless :okexcept: has been specified. - if not is_okexcept and "Traceback" in output: - s = f"\nException in {filename} at block ending on line {lineno}\n" - s += "Specify :okexcept: as an option in the ipython:: block to suppress this message\n" - sys.stdout.write("\n\n>>>" + ("-" * 73)) - sys.stdout.write(s) - sys.stdout.write(output) - sys.stdout.write("<<<" + ("-" * 73) + "\n\n") - - # output any warning raised during execution to stdout - # unless :okwarning: has been specified. - if not is_okwarning: - for w in ws: - s = f"\nWarning in {filename} at block ending on line {lineno}\n" - s += ( - "Specify :okwarning: as an option in " - "the ipython:: block to suppress this message\n" - ) - sys.stdout.write("\n\n>>>" + ("-" * 73)) - sys.stdout.write(s) - sys.stdout.write("-" * 76 + "\n") - s = warnings.formatwarning(w.message, w.category, w.filename, w.lineno, w.line) - sys.stdout.write(s) - sys.stdout.write("<<<" + ("-" * 73) + "\n") - - self.cout.truncate(0) - return (ret, input_lines, output, is_doctest, decorator, image_file, image_directive) - - def process_output( - self, data, output_prompt, input_lines, output, is_doctest, decorator, image_file - ): - """ - Process data block for OUTPUT token. - - """ - TAB = " " * 4 - - if is_doctest and output is not None: - found = output - found = found.strip() - submitted = data.strip() - - if self.directive is None: - source = "Unavailable" - content = "Unavailable" - else: - source = self.directive.state.document.current_source - content = self.directive.content - # Add tabs and join into a single string. - content = "\n".join([TAB + line for line in content]) - - # Make sure the output contains the output prompt. - ind = found.find(output_prompt) - if ind < 0: - e = ( - "output does not contain output prompt\n\n" - "Document source: {0}\n\n" - "Raw content: \n{1}\n\n" - "Input line(s):\n{TAB}{2}\n\n" - "Output line(s):\n{TAB}{3}\n\n" - ) - e = e.format(source, content, "\n".join(input_lines), repr(found), TAB=TAB) - raise RuntimeError(e) - found = found[len(output_prompt) :].strip() - - # Handle the actual doctest comparison. - if decorator.strip() == "@doctest": - # Standard doctest - if found != submitted: - e = ( - "doctest failure\n\n" - "Document source: {0}\n\n" - "Raw content: \n{1}\n\n" - "On input line(s):\n{TAB}{2}\n\n" - "we found output:\n{TAB}{3}\n\n" - "instead of the expected:\n{TAB}{4}\n\n" - ) - e = e.format( - source, - content, - "\n".join(input_lines), - repr(found), - repr(submitted), - TAB=TAB, - ) - raise RuntimeError(e) - else: - self.custom_doctest(decorator, input_lines, found, submitted) - - def process_comment(self, data): - """Process data fPblock for COMMENT token.""" - if not self.is_suppress: - return [data] - - def save_image(self, image_file): - """ - Saves the image file to disk. - """ - self.ensure_pyplot() - command = 'plt.gcf().savefig("%s", bbox_inches="tight", ' "dpi=100)" % image_file - - # print 'SAVEFIG', command # dbg - self.process_input_line("bookmark ipy_thisdir", store_history=False) - self.process_input_line("cd -b ipy_savedir", store_history=False) - self.process_input_line(command, store_history=False) - self.process_input_line("cd -b ipy_thisdir", store_history=False) - self.process_input_line("bookmark -d ipy_thisdir", store_history=False) - self.clear_cout() - - def process_block(self, block): - """ - process block from the block_parser and return a list of processed lines - """ - ret = [] - output = None - input_lines = None - lineno = self.IP.execution_count - - input_prompt = self.promptin % lineno - output_prompt = self.promptout % lineno - image_file = None - image_directive = None - - for token, data in block: - if token == COMMENT: - out_data = self.process_comment(data) - elif token == INPUT: - ( - out_data, - input_lines, - output, - is_doctest, - decorator, - image_file, - image_directive, - ) = self.process_input(data, input_prompt, lineno) - elif token == OUTPUT: - out_data = self.process_output( - data, output_prompt, input_lines, output, is_doctest, decorator, image_file - ) - if out_data: - ret.extend(out_data) - - # save the image files - if image_file is not None: - self.save_image(image_file) - - return ret, image_directive - - def ensure_pyplot(self): - """ - Ensures that pyplot has been imported into the embedded IPython shell. - - Also, makes sure to set the backend appropriately if not set already. - - """ - # We are here if the @figure pseudo decorator was used. Thus, it's - # possible that we could be here even if python_mplbackend were set to - # `None`. That's also strange and perhaps worthy of raising an - # exception, but for now, we just set the backend to 'agg'. - - if not self._pyplot_imported: - if "matplotlib.backends" not in sys.modules: - # Then ipython_matplotlib was set to None but there was a - # call to the @figure decorator (and ipython_execlines did - # not set a backend). - # raise Exception("No backend was set, but @figure was used!") - import matplotlib - - matplotlib.use("agg") - - # Always import pyplot into embedded shell. - self.process_input_line("import matplotlib.pyplot as plt", store_history=False) - self._pyplot_imported = True - - def process_pure_python(self, content): - """ - content is a list of strings. it is unedited directive content - - This runs it line by line in the InteractiveShell, prepends - prompts as needed capturing stderr and stdout, then returns - the content as a list as if it were ipython code - """ - output = [] - savefig = False # keep up with this to clear figure - multiline = False # to handle line continuation - multiline_start = None - fmtin = self.promptin - - ct = 0 - - for lineno, line in enumerate(content): - line_stripped = line.strip() - if not len(line): - output.append(line) - continue - - # handle decorators - if line_stripped.startswith("@"): - output.extend([line]) - if "savefig" in line: - savefig = True # and need to clear figure - continue - - # handle comments - if line_stripped.startswith("#"): - output.extend([line]) - continue - - # deal with lines checking for multiline - continuation = " %s:" % "".join(["."] * (len(str(ct)) + 2)) - if not multiline: - modified = f"{fmtin % ct} {line_stripped}" - output.append(modified) - ct += 1 - try: - ast.parse(line_stripped) - output.append("") - except Exception: # on a multiline - multiline = True - multiline_start = lineno - else: # still on a multiline - modified = f"{continuation} {line}" - output.append(modified) - - # if the next line is indented, it should be part of multiline - if len(content) > lineno + 1: - nextline = content[lineno + 1] - if len(nextline) - len(nextline.lstrip()) > 3: - continue - try: - mod = ast.parse("\n".join(content[multiline_start : lineno + 1])) - if isinstance(mod.body[0], ast.FunctionDef): - # check to see if we have the whole function - for element in mod.body[0].body: - if isinstance(element, ast.Return): - multiline = False - else: - output.append("") - multiline = False - except Exception: - pass - - if savefig: # clear figure if plotted - self.ensure_pyplot() - self.process_input_line("plt.clf()", store_history=False) - self.clear_cout() - savefig = False - - return output - - def custom_doctest(self, decorator, input_lines, found, submitted): - """ - Perform a specialized doctest. - - """ - from docs.sphinxext.custom_doctests import doctests - - args = decorator.split() - doctest_type = args[1] - if doctest_type in doctests: - doctests[doctest_type](self, args, input_lines, found, submitted) - else: - e = f"Invalid option to @doctest: {doctest_type}" - raise Exception(e) - - -class IPythonDirective(Directive): - has_content = True - required_arguments = 0 - optional_arguments = 4 # python, suppress, verbatim, doctest - final_argumuent_whitespace = True - option_spec = { - "python": directives.unchanged, - "suppress": directives.flag, - "verbatim": directives.flag, - "doctest": directives.flag, - "okexcept": directives.flag, - "okwarning": directives.flag, - "output_encoding": directives.unchanged_required, - } - - shell = None - - seen_docs = set() - - def get_config_options(self): - # contains sphinx configuration variables - config = self.state.document.settings.env.config - - # get config variables to set figure output directory - confdir = self.state.document.settings.env.app.confdir - savefig_dir = config.ipython_savefig_dir - source_dir = os.path.dirname(self.state.document.current_source) - if savefig_dir is None: - savefig_dir = config.html_static_path - if isinstance(savefig_dir, list): - savefig_dir = savefig_dir[0] # safe to assume only one path? - savefig_dir = os.path.join(confdir, savefig_dir) - - # get regex and prompt stuff - rgxin = config.ipython_rgxin - rgxout = config.ipython_rgxout - promptin = config.ipython_promptin - promptout = config.ipython_promptout - mplbackend = config.ipython_mplbackend - exec_lines = config.ipython_execlines - hold_count = config.ipython_holdcount - - return ( - savefig_dir, - source_dir, - rgxin, - rgxout, - promptin, - promptout, - mplbackend, - exec_lines, - hold_count, - ) - - def setup(self): - # Get configuration values. - ( - savefig_dir, - source_dir, - rgxin, - rgxout, - promptin, - promptout, - mplbackend, - exec_lines, - hold_count, - ) = self.get_config_options() - - if self.shell is None: - # We will be here many times. However, when the - # EmbeddedSphinxShell is created, its interactive shell member - # is the same for each instance. - - if mplbackend: - import matplotlib - - # Repeated calls to use() will not hurt us since `mplbackend` - # is the same each time. - matplotlib.use(mplbackend) - - # Must be called after (potentially) importing matplotlib and - # setting its backend since exec_lines might import pylab. - self.shell = EmbeddedSphinxShell(exec_lines, self.state) - - # Store IPython directive to enable better error messages - self.shell.directive = self - - # reset the execution count if we haven't processed this doc - # NOTE: this may be borked if there are multiple seen_doc tmp files - # check time stamp? - if self.state.document.current_source not in self.seen_docs: - self.shell.IP.history_manager.reset() - self.shell.IP.execution_count = 1 - self.shell.IP.prompt_manager.width = 0 - self.seen_docs.add(self.state.document.current_source) - - # and attach to shell so we don't have to pass them around - self.shell.rgxin = rgxin - self.shell.rgxout = rgxout - self.shell.promptin = promptin - self.shell.promptout = promptout - self.shell.savefig_dir = savefig_dir - self.shell.source_dir = source_dir - self.shell.hold_count = hold_count - - # setup bookmark for saving figures directory - self.shell.process_input_line("bookmark ipy_savedir %s" % savefig_dir, store_history=False) - self.shell.clear_cout() - - return rgxin, rgxout, promptin, promptout - - def teardown(self): - # delete last bookmark - self.shell.process_input_line("bookmark -d ipy_savedir", store_history=False) - self.shell.clear_cout() - - def run(self): - debug = False - - # TODO, any reason block_parser can't be a method of embeddable shell - # then we wouldn't have to carry these around - rgxin, rgxout, promptin, promptout = self.setup() - - options = self.options - self.shell.is_suppress = "suppress" in options - self.shell.is_doctest = "doctest" in options - self.shell.is_verbatim = "verbatim" in options - self.shell.is_okexcept = "okexcept" in options - self.shell.is_okwarning = "okwarning" in options - - self.shell.output_encoding = [options.get("output_encoding", "utf8")] - - # handle pure python code - if "python" in self.arguments: - content = self.content - self.content = self.shell.process_pure_python(content) - - parts = "\n".join(self.content).split("\n\n") - - lines = [".. code-block:: ipython", ""] - figures = [] - - for part in parts: - block = block_parser(part, rgxin, rgxout, promptin, promptout) - if len(block): - rows, figure = self.shell.process_block(block) - for row in rows: - lines.extend([" %s" % line for line in row.split("\n")]) - - if figure is not None: - figures.append(figure) - - for figure in figures: - lines.append("") - lines.extend(figure.split("\n")) - lines.append("") - - if len(lines) > 2: - if debug: - print("\n".join(lines)) - else: - # This has to do with input, not output. But if we comment - # these lines out, then no IPython code will appear in the - # final output. - self.state_machine.insert_input(lines, self.state_machine.input_lines.source(0)) - - # cleanup - self.teardown() - - return [] - - -# Enable as a proper Sphinx directive -def setup(app): - setup.app = app - - app.add_directive("ipython", IPythonDirective) - app.add_config_value("ipython_savefig_dir", None, "env") - app.add_config_value("ipython_rgxin", re.compile(r"In \[(\d+)\]:\s?(.*)\s*"), "env") - app.add_config_value("ipython_rgxout", re.compile(r"Out\[(\d+)\]:\s?(.*)\s*"), "env") - app.add_config_value("ipython_promptin", "In [%d]:", "env") - app.add_config_value("ipython_promptout", "Out[%d]:", "env") - - # We could just let matplotlib pick whatever is specified as the default - # backend in the matplotlibrc file, but this would cause issues if the - # backend didn't work in headless environments. For this reason, 'agg' - # is a good default backend choice. - app.add_config_value("ipython_mplbackend", "agg", "env") - - # If the user sets this config value to `None`, then EmbeddedSphinxShell's - # __init__ method will treat it as []. - execlines = ["import numpy as np", "import matplotlib.pyplot as plt"] - app.add_config_value("ipython_execlines", execlines, "env") - - app.add_config_value("ipython_holdcount", True, "env") - - -# Simple smoke test, needs to be converted to a proper automatic test. -def test(): - examples = [ - r""" -In [9]: pwd -Out[9]: '/home/jdhunter/py4science/book' - -In [10]: cd bookdata/ -/home/jdhunter/py4science/book/bookdata - -In [2]: from pylab import * - -In [2]: ion() - -In [3]: im = imread('stinkbug.png') - -@savefig mystinkbug.png width=4in -In [4]: imshow(im) -Out[4]: - -""", - r""" - -In [1]: x = 'hello world' - -# string methods can be -# used to alter the string -@doctest -In [2]: x.upper() -Out[2]: 'HELLO WORLD' - -@verbatim -In [3]: x.st -x.startswith x.strip -""", - r""" - -In [130]: url = 'http://ichart.finance.yahoo.com/table.csv?s=CROX\ - .....: &d=9&e=22&f=2009&g=d&a=1&br=8&c=2006&ignore=.csv' - -In [131]: print url.split('&') -['http://ichart.finance.yahoo.com/table.csv?s=CROX', 'd=9', 'e=22', 'f=2009', -'g=d', 'a=1', 'b=8', 'c=2006', 'ignore=.csv'] - -In [60]: import urllib - -""", - r"""\ - -In [133]: import numpy.random - -@suppress -In [134]: numpy.random.seed(2358) - -@doctest -In [135]: numpy.random.rand(10,2) -Out[135]: -array([[ 0.64524308, 0.59943846], - [ 0.47102322, 0.8715456 ], - [ 0.29370834, 0.74776844], - [ 0.99539577, 0.1313423 ], - [ 0.16250302, 0.21103583], - [ 0.81626524, 0.1312433 ], - [ 0.67338089, 0.72302393], - [ 0.7566368 , 0.07033696], - [ 0.22591016, 0.77731835], - [ 0.0072729 , 0.34273127]]) - -""", - r""" -In [106]: print x -jdh - -In [109]: for i in range(10): - .....: print i - .....: - .....: -0 -1 -2 -3 -4 -5 -6 -7 -8 -9 -""", - r""" - -In [144]: from pylab import * - -In [145]: ion() - -# use a semicolon to suppress the output -@savefig test_hist.png width=4in -In [151]: hist(np.random.randn(10000), 100); - - -@savefig test_plot.png width=4in -In [151]: plot(np.random.randn(10000), 'o'); - """, - r""" -# use a semicolon to suppress the output -In [151]: plt.clf() - -@savefig plot_simple.png width=4in -In [151]: plot([1,2,3]) - -@savefig hist_simple.png width=4in -In [151]: hist(np.random.randn(10000), 100); - -""", - r""" -# update the current fig -In [151]: ylabel('number') - -In [152]: title('normal distribution') - - -@savefig hist_with_text.png -In [153]: grid(True) - -@doctest float -In [154]: 0.1 + 0.2 -Out[154]: 0.3 - -@doctest float -In [155]: np.arange(16).reshape(4,4) -Out[155]: -array([[ 0, 1, 2, 3], - [ 4, 5, 6, 7], - [ 8, 9, 10, 11], - [12, 13, 14, 15]]) - -In [1]: x = np.arange(16, dtype=float).reshape(4,4) - -In [2]: x[0,0] = np.inf - -In [3]: x[0,1] = np.nan - -@doctest float -In [4]: x -Out[4]: -array([[ inf, nan, 2., 3.], - [ 4., 5., 6., 7.], - [ 8., 9., 10., 11.], - [ 12., 13., 14., 15.]]) - - - """, - ] - # skip local-file depending first example: - examples = examples[1:] - - # ipython_directive.DEBUG = True # dbg - # options = dict(suppress=True) # dbg - options = dict() - for example in examples: - content = example.split("\n") - IPythonDirective( - "debug", - arguments=None, - options=options, - content=content, - lineno=0, - content_offset=None, - block_text=None, - state=None, - state_machine=None, - ) - - -# Run test suite as a script -if __name__ == "__main__": - if not os.path.isdir("_static"): - os.mkdir("_static") - test() - print("All OK? Check figures in _static/") diff --git a/docs/sphinxext/plot_directive.py b/docs/sphinxext/plot_directive.py deleted file mode 100644 index 717620e..0000000 --- a/docs/sphinxext/plot_directive.py +++ /dev/null @@ -1,845 +0,0 @@ -# noqa -""" -A directive for including a matplotlib plot in a Sphinx document. - -By default, in HTML output, `plot` will include a .png file with a -link to a high-res .png and .pdf. In LaTeX output, it will include a -.pdf. - -The source code for the plot may be included in one of three ways: - - 1. **A path to a source file** as the argument to the directive:: - - .. plot:: path/to/plot.py - - When a path to a source file is given, the content of the - directive may optionally contain a caption for the plot:: - - .. plot:: path/to/plot.py - - This is the caption for the plot - - Additionally, one my specify the name of a function to call (with - no arguments) immediately after importing the module:: - - .. plot:: path/to/plot.py plot_function1 - - 2. Included as **inline content** to the directive:: - - .. plot:: - - import matplotlib.pyplot as plt - import matplotlib.image as mpimg - import numpy as np - img = mpimg.imread('_static/stinkbug.png') - imgplot = plt.imshow(img) - - 3. Using **doctest** syntax:: - - .. plot:: - A plotting example: - >>> import matplotlib.pyplot as plt - >>> plt.plot([1,2,3], [4,5,6]) - -Options -------- - -The ``plot`` directive supports the following options: - - format : {'python', 'doctest'} - Specify the format of the input - - include-source : bool - Whether to display the source code. The default can be changed - using the `plot_include_source` variable in conf.py - - encoding : str - If this source file is in a non-UTF8 or non-ASCII encoding, - the encoding must be specified using the `:encoding:` option. - The encoding will not be inferred using the ``-*- coding -*-`` - metacomment. - - context : bool or str - If provided, the code will be run in the context of all - previous plot directives for which the `:context:` option was - specified. This only applies to inline code plot directives, - not those run from files. If the ``:context: reset`` option is - specified, the context is reset for this and future plots, and - previous figures are closed prior to running the code. - ``:context:close-figs`` keeps the context but closes previous figures - before running the code. - - nofigs : bool - If specified, the code block will be run, but no figures will - be inserted. This is usually useful with the ``:context:`` - option. - -Additionally, this directive supports all of the options of the -`image` directive, except for `target` (since plot will add its own -target). These include `alt`, `height`, `width`, `scale`, `align` and -`class`. - -Configuration options ---------------------- - -The plot directive has the following configuration options: - - plot_include_source - Default value for the include-source option - - plot_html_show_source_link - Whether to show a link to the source in HTML. - - plot_pre_code - Code that should be executed before each plot. - - plot_basedir - Base directory, to which ``plot::`` file names are relative - to. (If None or empty, file names are relative to the - directory where the file containing the directive is.) - - plot_formats - File formats to generate. List of tuples or strings:: - - [(suffix, dpi), suffix, ...] - - that determine the file format and the DPI. For entries whose - DPI was omitted, sensible defaults are chosen. - - plot_html_show_formats - Whether to show links to the files in HTML. - - plot_rcparams - A dictionary containing any non-standard rcParams that should - be applied before each plot. - - plot_apply_rcparams - By default, rcParams are applied when `context` option is not used in - a plot directive. This configuration option overrides this behavior - and applies rcParams before each plot. - - plot_working_directory - By default, the working directory will be changed to the directory of - the example, so the code can get at its data files, if any. Also its - path will be added to `sys.path` so it can import any helper modules - sitting beside it. This configuration option can be used to specify - a central directory (also added to `sys.path`) where data files and - helper modules for all code are located. - - plot_template - Provide a customized template for preparing restructured text. -""" - -import io -import os -import re -import shutil -import sys -import textwrap -import traceback -from os.path import relpath - -import sphinx -from docutils.parsers.rst import directives -from docutils.parsers.rst.directives.images import Image - -align = Image.align - -sphinx_version = sphinx.__version__.split(".") -# The split is necessary for sphinx beta versions where the string is -# '6b1' -sphinx_version = tuple([int(re.split("[^0-9]", x)[0]) for x in sphinx_version[:2]]) - -try: - # Sphinx depends on either Jinja or Jinja2 - import jinja2 - - def format_template(template, **kw): - return jinja2.Template(template).render(**kw) -except ImportError: - import jinja - - def format_template(template, **kw): - return jinja.from_string(template, **kw) - - -import matplotlib # noqa -import matplotlib.cbook as cbook # noqa - -matplotlib.use("Agg") -import matplotlib.pyplot as plt # noqa -from matplotlib import _pylab_helpers # noqa - -__version__ = 2 - -# ------------------------------------------------------------------------------ -# Registration hook -# ------------------------------------------------------------------------------ - - -def plot_directive( - name, arguments, options, content, lineno, content_offset, block_text, state, state_machine -): - return run(arguments, content, options, state_machine, state, lineno) - - -plot_directive.__doc__ = __doc__ - - -def _option_boolean(arg): - if not arg or not arg.strip(): - # no argument given, assume used as a flag - return True - elif arg.strip().lower() in ("no", "0", "false"): - return False - elif arg.strip().lower() in ("yes", "1", "true"): - return True - else: - raise ValueError('"%s" unknown boolean' % arg) - - -def _option_context(arg): - if arg in [None, "reset", "close-figs"]: - return arg - raise ValueError("argument should be None or 'reset' or 'close-figs'") - - -def _option_format(arg): - return directives.choice(arg, ("python", "doctest")) - - -def _option_align(arg): - return directives.choice(arg, ("top", "middle", "bottom", "left", "center", "right")) - - -def mark_plot_labels(app, document): - """ - To make plots referenceable, we need to move the reference from - the "htmlonly" (or "latexonly") node to the actual figure node - itself. - """ - for name, explicit in document.nametypes.items(): - if not explicit: - continue - labelid = document.nameids[name] - if labelid is None: - continue - node = document.ids[labelid] - if node.tagname in ("html_only", "latex_only"): - for n in node: - if n.tagname == "figure": - sectname = name - for c in n: - if c.tagname == "caption": - sectname = c.astext() - break - - node["ids"].remove(labelid) - node["names"].remove(name) - n["ids"].append(labelid) - n["names"].append(name) - document.settings.env.labels[name] = ( - document.settings.env.docname, - labelid, - sectname, - ) - break - - -def setup(app): - setup.app = app - setup.config = app.config - setup.confdir = app.confdir - - options = { - "alt": directives.unchanged, - "height": directives.length_or_unitless, - "width": directives.length_or_percentage_or_unitless, - "scale": directives.nonnegative_int, - "align": _option_align, - "class": directives.class_option, - "include-source": _option_boolean, - "format": _option_format, - "context": _option_context, - "nofigs": directives.flag, - "encoding": directives.encoding, - } - - app.add_directive("plot", plot_directive, True, (0, 2, False), **options) - app.add_config_value("plot_pre_code", None, True) - app.add_config_value("plot_include_source", False, True) - app.add_config_value("plot_html_show_source_link", True, True) - app.add_config_value("plot_formats", ["png", "hires.png", "pdf"], True) - app.add_config_value("plot_basedir", None, True) - app.add_config_value("plot_html_show_formats", True, True) - app.add_config_value("plot_rcparams", {}, True) - app.add_config_value("plot_apply_rcparams", False, True) - app.add_config_value("plot_working_directory", None, True) - app.add_config_value("plot_template", None, True) - - app.connect("doctree-read", mark_plot_labels) - - -# ------------------------------------------------------------------------------ -# Doctest handling -# ------------------------------------------------------------------------------ - - -def contains_doctest(text): - try: - # check if it's valid Python as-is - compile(text, "", "exec") - return False - except SyntaxError: - pass - r = re.compile(r"^\s*>>>", re.M) - m = r.search(text) - return bool(m) - - -def unescape_doctest(text): - """ - Extract code from a piece of text, which contains either Python code - or doctests. - - """ - if not contains_doctest(text): - return text - - code = "" - for line in text.split("\n"): - m = re.match(r"^\s*(>>>|\.\.\.) (.*)$", line) - if m: - code += m.group(2) + "\n" - elif line.strip(): - code += "# " + line.strip() + "\n" - else: - code += "\n" - return code - - -def split_code_at_show(text): - """ - Split code at plt.show() - - """ - - parts = [] - is_doctest = contains_doctest(text) - - part = [] - for line in text.split("\n"): - if (not is_doctest and line.strip() == "plt.show()") or ( - is_doctest and line.strip() == ">>> plt.show()" - ): - part.append(line) - parts.append("\n".join(part)) - part = [] - else: - part.append(line) - if "\n".join(part).strip(): - parts.append("\n".join(part)) - return parts - - -def remove_coding(text): - """ - Remove the coding comment, which six.exec_ doesn't like. - """ - sub_re = re.compile(r"^#\s*-\*-\s*coding:\s*.*-\*-$", flags=re.MULTILINE) - return sub_re.sub("", text) - - -# ------------------------------------------------------------------------------ -# Template -# ------------------------------------------------------------------------------ - - -TEMPLATE = """ -{{ source_code }} - -{{ only_html }} - - {% if source_link or (html_show_formats and not multi_image) %} - ( - {%- if source_link -%} - `Source code <{{ source_link }}>`__ - {%- endif -%} - {%- if html_show_formats and not multi_image -%} - {%- for img in images -%} - {%- for fmt in img.formats -%} - {%- if source_link or not loop.first -%}, {% endif -%} - `{{ fmt }} <{{ dest_dir }}/{{ img.basename }}.{{ fmt }}>`__ - {%- endfor -%} - {%- endfor -%} - {%- endif -%} - ) - {% endif %} - - {% for img in images %} - .. figure:: {{ build_dir }}/{{ img.basename }}.png - {% for option in options -%} - {{ option }} - {% endfor %} - - {% if html_show_formats and multi_image -%} - ( - {%- for fmt in img.formats -%} - {%- if not loop.first -%}, {% endif -%} - `{{ fmt }} <{{ dest_dir }}/{{ img.basename }}.{{ fmt }}>`__ - {%- endfor -%} - ) - {%- endif -%} - - {{ caption }} - {% endfor %} - -{{ only_latex }} - - {% for img in images %} - {% if 'pdf' in img.formats -%} - .. image:: {{ build_dir }}/{{ img.basename }}.pdf - {% endif -%} - {% endfor %} - -{{ only_texinfo }} - - {% for img in images %} - .. image:: {{ build_dir }}/{{ img.basename }}.png - {% for option in options -%} - {{ option }} - {% endfor %} - - {% endfor %} - -""" - -exception_template = """ -.. htmlonly:: - - [`source code <%(linkdir)s/%(basename)s.py>`__] - -Exception occurred rendering plot. - -""" - -# the context of the plot for all directives specified with the -# :context: option -plot_context = dict() - - -class ImageFile: - def __init__(self, basename, dirname): - self.basename = basename - self.dirname = dirname - self.formats = [] - - def filename(self, format): - return os.path.join(self.dirname, f"{self.basename}.{format}") - - def filenames(self): - return [self.filename(fmt) for fmt in self.formats] - - -def out_of_date(original, derived): - """ - Returns True if derivative is out-of-date wrt original, - both of which are full file paths. - """ - return not os.path.exists(derived) or ( - os.path.exists(original) and os.stat(derived).st_mtime < os.stat(original).st_mtime - ) - - -class PlotError(RuntimeError): - pass - - -def run_code(code, code_path, ns=None, function_name=None): - """ - Import a Python module from a path, and run the function given by - name, if function_name is not None. - """ - - # Change the working directory to the directory of the example, so - # it can get at its data files, if any. Add its path to sys.path - # so it can import any helper modules sitting beside it. - pwd = os.getcwd() - old_sys_path = list(sys.path) - if setup.config.plot_working_directory is not None: - try: - os.chdir(setup.config.plot_working_directory) - except OSError as err: - raise OSError( - str(err) + "\n`plot_working_directory` option in" - "Sphinx configuration file must be a valid " - "directory path" - ) - except TypeError as err: - raise TypeError( - str(err) + "\n`plot_working_directory` option in " - "Sphinx configuration file must be a string or " - "None" - ) - sys.path.insert(0, setup.config.plot_working_directory) - elif code_path is not None: - dirname = os.path.abspath(os.path.dirname(code_path)) - os.chdir(dirname) - sys.path.insert(0, dirname) - - # Reset sys.argv - old_sys_argv = sys.argv - sys.argv = [code_path] - - # Redirect stdout - stdout = sys.stdout - sys.stdout = io.StringIO() - - # Assign a do-nothing print function to the namespace. There - # doesn't seem to be any other way to provide a way to (not) print - # that works correctly across Python 2 and 3. - def _dummy_print(*arg, **kwarg): - pass - - try: - try: - code = unescape_doctest(code) - if ns is None: - ns = {} - if not ns: - if setup.config.plot_pre_code is None: - exec( - str("import numpy as np\n" + "from matplotlib import pyplot as plt\n"), - ns, - ) - else: - exec(str(setup.config.plot_pre_code), ns) - ns["print"] = _dummy_print - if "__main__" in code: - exec("__name__ = '__main__'", ns) - code = remove_coding(code) - exec(code, ns) - if function_name is not None: - exec(function_name + "()", ns) - except (Exception, SystemExit): - raise PlotError(traceback.format_exc()) - finally: - os.chdir(pwd) - sys.argv = old_sys_argv - sys.path[:] = old_sys_path - sys.stdout = stdout - return ns - - -def clear_state(plot_rcparams, close=True): - if close: - plt.close("all") - matplotlib.rc_file_defaults() - matplotlib.rcParams.update(plot_rcparams) - - -def render_figures( - code, - code_path, - output_dir, - output_base, - context, - function_name, - config, - context_reset=False, - close_figs=False, -): - """ - Run a pyplot script and save the low and high res PNGs and a PDF - in *output_dir*. - - Save the images under *output_dir* with file names derived from - *output_base* - """ - # -- Parse format list - default_dpi = {"png": 80, "hires.png": 200, "pdf": 200} - formats = [] - plot_formats = config.plot_formats - if isinstance(plot_formats, str): - plot_formats = eval(plot_formats) - for fmt in plot_formats: - if isinstance(fmt, str): - formats.append((fmt, default_dpi.get(fmt, 80))) - elif type(fmt) in (tuple, list) and len(fmt) == 2: - formats.append((str(fmt[0]), int(fmt[1]))) - else: - raise PlotError('invalid image format "%r" in plot_formats' % fmt) - - # -- Try to determine if all images already exist - - code_pieces = split_code_at_show(code) - - # Look for single-figure output files first - all_exists = True - img = ImageFile(output_base, output_dir) - for format, dpi in formats: - if out_of_date(code_path, img.filename(format)): - all_exists = False - break - img.formats.append(format) - - if all_exists: - return [(code, [img])] - - # Then look for multi-figure output files - results = [] - all_exists = True - for i, code_piece in enumerate(code_pieces): - images = [] - for j in range(1000): - if len(code_pieces) > 1: - img = ImageFile("%s_%02d_%02d" % (output_base, i, j), output_dir) - else: - img = ImageFile("%s_%02d" % (output_base, j), output_dir) - for format, dpi in formats: - if out_of_date(code_path, img.filename(format)): - all_exists = False - break - img.formats.append(format) - - # assume that if we have one, we have them all - if not all_exists: - all_exists = j > 0 - break - images.append(img) - if not all_exists: - break - results.append((code_piece, images)) - - if all_exists: - return results - - # We didn't find the files, so build them - - results = [] - ns = plot_context if context else {} - - if context_reset: - clear_state(config.plot_rcparams) - plot_context.clear() - - close_figs = not context or close_figs - - for i, code_piece in enumerate(code_pieces): - if not context or config.plot_apply_rcparams: - clear_state(config.plot_rcparams, close_figs) - elif close_figs: - plt.close("all") - - run_code(code_piece, code_path, ns, function_name) - - images = [] - fig_managers = _pylab_helpers.Gcf.get_all_fig_managers() - for j, figman in enumerate(fig_managers): - if len(fig_managers) == 1 and len(code_pieces) == 1: - img = ImageFile(output_base, output_dir) - elif len(code_pieces) == 1: - img = ImageFile("%s_%02d" % (output_base, j), output_dir) - else: - img = ImageFile("%s_%02d_%02d" % (output_base, i, j), output_dir) - images.append(img) - for format, dpi in formats: - try: - figman.canvas.figure.savefig(img.filename(format), dpi=dpi, bbox_inches="tight") - except Exception: - raise PlotError(traceback.format_exc()) - img.formats.append(format) - - results.append((code_piece, images)) - - if not context or config.plot_apply_rcparams: - clear_state(config.plot_rcparams, close=not context) - - return results - - -def run(arguments, content, options, state_machine, state, lineno): - # The user may provide a filename *or* Python code content, but not both - if arguments and content: - raise RuntimeError("plot:: directive can't have both args and content") - - document = state_machine.document - config = document.settings.env.config - nofigs = "nofigs" in options - - options.setdefault("include-source", config.plot_include_source) - keep_context = "context" in options - context_opt = None if not keep_context else options["context"] - - rst_file = document.attributes["source"] - rst_dir = os.path.dirname(rst_file) - - if len(arguments): - if not config.plot_basedir: - source_file_name = os.path.join(setup.app.builder.srcdir, directives.uri(arguments[0])) - else: - source_file_name = os.path.join( - setup.confdir, config.plot_basedir, directives.uri(arguments[0]) - ) - - # If there is content, it will be passed as a caption. - caption = "\n".join(content) - - # If the optional function name is provided, use it - function_name = arguments[1] if len(arguments) == 2 else None - - with open(source_file_name, encoding="utf-8") as fd: - code = fd.read() - output_base = os.path.basename(source_file_name) - else: - source_file_name = rst_file - code = textwrap.dedent("\n".join(map(str, content))) - counter = document.attributes.get("_plot_counter", 0) + 1 - document.attributes["_plot_counter"] = counter - base, ext = os.path.splitext(os.path.basename(source_file_name)) - output_base = "%s-%d.py" % (base, counter) - function_name = None - caption = "" - - base, source_ext = os.path.splitext(output_base) - if source_ext in (".py", ".rst", ".txt"): - output_base = base - else: - source_ext = "" - - # ensure that LaTeX includegraphics doesn't choke in foo.bar.pdf filenames - output_base = output_base.replace(".", "-") - - # is it in doctest format? - is_doctest = contains_doctest(code) - if "format" in options: - is_doctest = options["format"] != "python" - - # determine output directory name fragment - source_rel_name = relpath(source_file_name, setup.confdir) - source_rel_dir = os.path.dirname(source_rel_name) - while source_rel_dir.startswith(os.path.sep): - source_rel_dir = source_rel_dir[1:] - - # build_dir: where to place output files (temporarily) - build_dir = os.path.join( - os.path.dirname(setup.app.doctreedir), "plot_directive", source_rel_dir - ) - # get rid of .. in paths, also changes pathsep - # see note in Python docs for warning about symbolic links on Windows. - # need to compare source and dest paths at end - build_dir = os.path.normpath(build_dir) - - if not os.path.exists(build_dir): - os.makedirs(build_dir) - - # output_dir: final location in the builder's directory - dest_dir = os.path.abspath(os.path.join(setup.app.builder.outdir, source_rel_dir)) - if not os.path.exists(dest_dir): - os.makedirs(dest_dir) # no problem here for me, but just use built-ins - - # how to link to files from the RST file - dest_dir_link = os.path.join(relpath(setup.confdir, rst_dir), source_rel_dir).replace( - os.path.sep, "/" - ) - build_dir_link = relpath(build_dir, rst_dir).replace(os.path.sep, "/") - source_link = dest_dir_link + "/" + output_base + source_ext - - # make figures - try: - results = render_figures( - code, - source_file_name, - build_dir, - output_base, - keep_context, - function_name, - config, - context_reset=context_opt == "reset", - close_figs=context_opt == "close-figs", - ) - errors = [] - except PlotError as err: - reporter = state.memo.reporter - sm = reporter.system_message( - 2, - f"Exception occurred in plotting {output_base}\n from {source_file_name}:\n{err}", - line=lineno, - ) - results = [(code, [])] - errors = [sm] - - # Properly indent the caption - caption = "\n".join(" " + line.strip() for line in caption.split("\n")) - - # generate output restructuredtext - total_lines = [] - for j, (code_piece, images) in enumerate(results): - if options["include-source"]: - if is_doctest: - lines = [""] - lines += [row.rstrip() for row in code_piece.split("\n")] - else: - lines = [".. code-block:: python", ""] - lines += [" %s" % row.rstrip() for row in code_piece.split("\n")] - source_code = "\n".join(lines) - else: - source_code = "" - - if nofigs: - images = [] - - opts = [ - f":{key}: {val}" - for key, val in options.items() - if key in ("alt", "height", "width", "scale", "align", "class") - ] - - only_html = ".. only:: html" - only_latex = ".. only:: latex" - only_texinfo = ".. only:: texinfo" - - # Not-None src_link signals the need for a source link in the generated - # html - src_link = source_link if j == 0 and config.plot_html_show_source_link else None - - result = format_template( - config.plot_template or TEMPLATE, - dest_dir=dest_dir_link, - build_dir=build_dir_link, - source_link=src_link, - multi_image=len(images) > 1, - only_html=only_html, - only_latex=only_latex, - only_texinfo=only_texinfo, - options=opts, - images=images, - source_code=source_code, - html_show_formats=config.plot_html_show_formats and not nofigs, - caption=caption, - ) - - total_lines.extend(result.split("\n")) - total_lines.extend("\n") - - if total_lines: - state_machine.insert_input(total_lines, source=source_file_name) - - # copy image files to builder's output directory, if necessary - if not os.path.exists(dest_dir): - cbook.mkdirs(dest_dir) - - for code_piece, images in results: - for img in images: - for fn in img.filenames(): - destimg = os.path.join(dest_dir, os.path.basename(fn)) - if fn != destimg: - shutil.copyfile(fn, destimg) - - # copy script (if necessary) - target_name = os.path.join(dest_dir, output_base + source_ext) - with open(target_name, "w", encoding="utf-8") as f: - code_escaped = unescape_doctest(code) if source_file_name == rst_file else code - f.write(code_escaped) - - return errors diff --git a/docs/sphinxext/plot_generator.py b/docs/sphinxext/plot_generator.py deleted file mode 100644 index a3c0579..0000000 --- a/docs/sphinxext/plot_generator.py +++ /dev/null @@ -1,364 +0,0 @@ -""" -Sphinx plugin to run example scripts and create a gallery page. - -Lightly modified from the mpld3 project. - -""" -import glob -import os -import os.path as op -import re -import shutil -import token -import tokenize - -import matplotlib - -matplotlib.use("Agg") -import matplotlib.pyplot as plt -from matplotlib import image - -RST_TEMPLATE = """ -.. _{sphinx_tag}: - -{docstring} - -.. image:: {img_file} - -**Python source code:** :download:`[download source: {fname}]<{fname}>` - -.. literalinclude:: {fname} - :lines: {end_line}- -""" - - -INDEX_TEMPLATE = """ - -.. raw:: html - - - -.. _{sphinx_tag}: - -Example gallery -=============== - -{toctree} - -{contents} - -.. raw:: html - -
-""" - - -def create_thumbnail(infile, thumbfile, width=300, height=300, cx=0.5, cy=0.5, border=4): - baseout, extout = op.splitext(thumbfile) - - im = image.imread(infile) - rows, cols = im.shape[:2] - x0 = int(cx * cols - 0.5 * width) - y0 = int(cy * rows - 0.5 * height) - xslice = slice(x0, x0 + width) - yslice = slice(y0, y0 + height) - thumb = im[yslice, xslice] - thumb[:border, :, :3] = thumb[-border:, :, :3] = 0 - thumb[:, :border, :3] = thumb[:, -border:, :3] = 0 - - dpi = 100 - fig = plt.figure(figsize=(width / dpi, height / dpi), dpi=dpi) - - ax = fig.add_axes([0, 0, 1, 1], aspect="auto", frameon=False, xticks=[], yticks=[]) - ax.imshow(thumb, aspect="auto", resample=True, interpolation="bilinear") - fig.savefig(thumbfile, dpi=dpi) - return fig - - -def indent(s, N=4): - """indent a string""" - return s.replace("\n", "\n" + N * " ") - - -class ExampleGenerator: - """Tools for generating an example page from a file""" - - def __init__(self, filename, target_dir): - self.filename = filename - self.target_dir = target_dir - self.thumbloc = 0.5, 0.5 - self.extract_docstring() - with open(filename) as fid: - self.filetext = fid.read() - - outfilename = op.join(target_dir, self.rstfilename) - - # Only actually run it if the output RST file doesn't - # exist or it was modified less recently than the example - if not op.exists(outfilename) or (op.getmtime(outfilename) < op.getmtime(filename)): - self.exec_file() - else: - print(f"skipping {self.filename}") - - @property - def dirname(self): - return op.split(self.filename)[0] - - @property - def fname(self): - return op.split(self.filename)[1] - - @property - def modulename(self): - return op.splitext(self.fname)[0] - - @property - def pyfilename(self): - return self.modulename + ".py" - - @property - def rstfilename(self): - return self.modulename + ".rst" - - @property - def htmlfilename(self): - return self.modulename + ".html" - - @property - def pngfilename(self): - pngfile = self.modulename + ".png" - return "_images/" + pngfile - - @property - def thumbfilename(self): - pngfile = self.modulename + "_thumb.png" - return pngfile - - @property - def sphinxtag(self): - return self.modulename - - @property - def pagetitle(self): - return self.docstring.strip().split("\n")[0].strip() - - @property - def plotfunc(self): - match = re.search(r"sns\.(.+plot)\(", self.filetext) - if match: - return match.group(1) - match = re.search(r"sns\.(.+map)\(", self.filetext) - if match: - return match.group(1) - match = re.search(r"sns\.(.+Grid)\(", self.filetext) - if match: - return match.group(1) - return "" - - def extract_docstring(self): - """Extract a module-level docstring""" - with open(self.filename) as f: - lines = f.readlines() - start_row = 0 - if lines[0].startswith("#!"): - lines.pop(0) - start_row = 1 - - docstring = "" - first_par = "" - tokens = tokenize.generate_tokens(lines.__iter__().next) - for tok_type, tok_content, _, (erow, _), _ in tokens: - tok_type = token.tok_name[tok_type] - if tok_type in ("NEWLINE", "COMMENT", "NL", "INDENT", "DEDENT"): - continue - elif tok_type == "STRING": - docstring = eval(tok_content) - # If the docstring is formatted with several paragraphs, - # extract the first one: - paragraphs = "\n".join(line.rstrip() for line in docstring.split("\n")).split( - "\n\n" - ) - if len(paragraphs) > 0: - first_par = paragraphs[0] - break - - thumbloc = None - for i, line in enumerate(docstring.split("\n")): - m = re.match(r"^_thumb: (\.\d+),\s*(\.\d+)", line) - if m: - thumbloc = float(m.group(1)), float(m.group(2)) - break - if thumbloc is not None: - self.thumbloc = thumbloc - docstring = "\n".join( - [ # noqa - word - for word in docstring.split("\n") - if not word.startswith("_thumb") # noqa - ] - ) # noqa - - self.docstring = docstring - self.short_desc = first_par - self.end_line = erow + 1 + start_row - - def exec_file(self): - print(f"running {self.filename}") - - plt.close("all") - my_globals = {"pl": plt, "plt": plt} # noqa - # execfile(self.filename, my_globals) # noqa - - fig = plt.gcf() - fig.canvas.draw() - pngfile = op.join(self.target_dir, self.pngfilename) - thumbfile = op.join("example_thumbs", self.thumbfilename) - self.html = "" % self.pngfilename - fig.savefig(pngfile, dpi=75, bbox_inches="tight") - - cx, cy = self.thumbloc - create_thumbnail(pngfile, thumbfile, cx=cx, cy=cy) - - def toctree_entry(self): - return " ./%s\n\n" % op.splitext(self.htmlfilename)[0] - - def contents_entry(self): - return ( - ".. raw:: html\n\n" - "
\n" - f" \n" - f" \n" - " \n" - f"

{self.plotfunc}

\n" - " \n" - " \n" - "
\n\n" - "\n\n" - "" - ) - - -def main(app): - static_dir = op.join(app.builder.srcdir, "_static") - target_dir = op.join(app.builder.srcdir, "examples") - image_dir = op.join(app.builder.srcdir, "examples/_images") - thumb_dir = op.join(app.builder.srcdir, "example_thumbs") - source_dir = op.abspath(op.join(app.builder.srcdir, "..", "examples")) - if not op.exists(static_dir): - os.makedirs(static_dir) - - if not op.exists(target_dir): - os.makedirs(target_dir) - - if not op.exists(image_dir): - os.makedirs(image_dir) - - if not op.exists(thumb_dir): - os.makedirs(thumb_dir) - - if not op.exists(source_dir): - os.makedirs(source_dir) - - banner_data = [] - - toctree = "\n\n" ".. toctree::\n" " :hidden:\n\n" - contents = "\n\n" - - # Write individual example files - for filename in glob.glob(op.join(source_dir, "*.py")): - ex = ExampleGenerator(filename, target_dir) - - banner_data.append( - { - "title": ex.pagetitle, - "url": op.join("examples", ex.htmlfilename), - "thumb": op.join(ex.thumbfilename), - } - ) - shutil.copyfile(filename, op.join(target_dir, ex.pyfilename)) - output = RST_TEMPLATE.format( - sphinx_tag=ex.sphinxtag, - docstring=ex.docstring, - end_line=ex.end_line, - fname=ex.pyfilename, - img_file=ex.pngfilename, - ) - with open(op.join(target_dir, ex.rstfilename), "w") as f: - f.write(output) - - toctree += ex.toctree_entry() - contents += ex.contents_entry() - - if len(banner_data) < 10: - banner_data = (4 * banner_data)[:10] - - # write index file - index_file = op.join(target_dir, "index.rst") - with open(index_file, "w") as index: - index.write( - INDEX_TEMPLATE.format(sphinx_tag="example_gallery", toctree=toctree, contents=contents) - ) - - -def setup(app): - app.connect("builder-inited", main) diff --git a/docs/sphinxext/requirements.txt b/docs/sphinxext/requirements.txt deleted file mode 100644 index ddad227..0000000 --- a/docs/sphinxext/requirements.txt +++ /dev/null @@ -1,2 +0,0 @@ -numpy>=1.8 -numpydoc diff --git a/docs/tutorial/tools/nb_to_doc.py b/docs/tutorial/tools/nb_to_doc.py index 84d3c82..5da22dc 100755 --- a/docs/tutorial/tools/nb_to_doc.py +++ b/docs/tutorial/tools/nb_to_doc.py @@ -13,8 +13,8 @@ def convert_nb(nbname): sh(["jupyter", "nbconvert", "--to", "notebook", "--execute", "--inplace", nbname + ".ipynb"]) - # Convert to .rst for Sphinx - sh(["jupyter", "nbconvert", "--to", "rst", nbname + ".ipynb"]) + # Convert to .md for Sphinx + sh(["jupyter", "nbconvert", "--to", "markdown", nbname + ".ipynb"]) # Clear notebook output sh(["jupyter", "nbconvert", "--to", "notebook", "--inplace", diff --git a/paramnormal/dist.py b/paramnormal/dist.py index bb16a5b..1daa818 100644 --- a/paramnormal/dist.py +++ b/paramnormal/dist.py @@ -1,4 +1,5 @@ from collections import namedtuple +from typing import Literal import numpy from scipy import stats @@ -897,3 +898,17 @@ def fit(cls, data, **guesses): "exponential", "rice", ] + + +DistNames = Literal[ + "normal", + "lognormal", + "weibull", + "alpha", + "beta", + "gamma", + "chi_squared", + "pareto", + "exponential", + "rice", +] diff --git a/paramnormal/tests/__init__.py b/paramnormal/tests/__init__.py index 0fb216d..9c0e30c 100644 --- a/paramnormal/tests/__init__.py +++ b/paramnormal/tests/__init__.py @@ -1,4 +1,4 @@ -from pkg_resources import resource_filename +from pathlib import Path def test(*args): @@ -7,6 +7,6 @@ def test(*args): except ImportError: raise ImportError("`pytest` is required to run the test suite") - options = [resource_filename("paramnormal", "tests")] + options = [str(Path(__file__).parent)] options.extend(list(args)) return pytest.main(options) diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 0000000..ee1a6e8 --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,55 @@ +[build-system] +requires = ["setuptools>=77"] +build-backend = "setuptools.build_meta" + +[project] +name = "paramnormal" +version = "0.4.4" +description = "paramnormal: Conventionally parameterized probability distributions" +readme = "README.md" +requires-python = ">=3.10" +license = "BSD-3-Clause" +license-files = ["LICENSE"] +authors = [{ name = "Paul Hobson", email = "pmhobson@gmail.com" }] +classifiers = [ + "Programming Language :: Python", + "Operating System :: OS Independent", + "Development Status :: 5 - Production/Stable", + "Intended Audience :: Science/Research", + "Topic :: Scientific/Engineering :: Mathematics", + "Programming Language :: Python :: 3.11", + "Programming Language :: Python :: 3.12", + "Programming Language :: Python :: 3.13", + "Programming Language :: Python :: 3.14", +] +dependencies = ["numpy", "scipy", "matplotlib"] + +[project.urls] +Homepage = "http://phobson.github.io/paramnormal/" +Source = "https://github.com/phobson/paramnormal" + +[dependency-groups] +dev = [ + "pytest", + "pytest-cov", + "pytest-mpl", + "pre-commit", + "ruff", +] +docs = [ + "sphinx", + "sphinx-rtd-theme", + "myst-nb", + "numpydoc", + "seaborn", + "ipython", +] + +[tool.setuptools.packages.find] +include = ["paramnormal*"] + +[tool.setuptools.package-data] +"paramnormal.tests.baseline_images.test_activity" = ["*.png"] + +[tool.pytest.ini_options] +markers = ["mpl_image_compare"] diff --git a/requirements.txt b/requirements.txt deleted file mode 100644 index 19ba798..0000000 --- a/requirements.txt +++ /dev/null @@ -1,3 +0,0 @@ -numpy>=1.6 -scipy>=0.14 -matplotlib>=1.5 \ No newline at end of file diff --git a/requirements_dev.txt b/requirements_dev.txt deleted file mode 100644 index bdc7ed0..0000000 --- a/requirements_dev.txt +++ /dev/null @@ -1,13 +0,0 @@ -numpy>=1.6 -scipy>=0.14 -matplotlib>=1.5 -pytest -pytest-cov -pytest-mpl -coverage -docopt -requests -pyyaml -ruff -pre-commit -isort \ No newline at end of file diff --git a/ruff.toml b/ruff.toml index 54d5afd..f930b6a 100644 --- a/ruff.toml +++ b/ruff.toml @@ -1,22 +1,5 @@ line-length = 100 -[lint] -select = [ - # pycodestyle - "E", - # Pyflakes - "F", - # pyupgrade - "UP", - ## flake8-bugbear - # "B", - # flake8-simplify - "SIM", -] - -[format] -indent-style = "space" - exclude = [ ".bzr", ".direnv", @@ -47,3 +30,23 @@ exclude = [ "docs", "docs/sphinxext", ] + +[lint] +isort.known-first-party = ["paramnormal"] +select = [ + # pycodestyle + "E", + # Pyflakes + "F", + # isort + "I", + # pyupgrade + "UP", + ## flake8-bugbear + # "B", + # flake8-simplify + "SIM", +] + +[format] +indent-style = "space" diff --git a/setup.cfg b/setup.cfg deleted file mode 100644 index 972961b..0000000 --- a/setup.cfg +++ /dev/null @@ -1,21 +0,0 @@ -[metadata] -description-file = readme.rst - -markers = - mpl_image_compare - -[tool:pytest] -pep8ignore = - E501 - E131 - check_paramnormal.py ALL - paramnormal/examples/* ALL - paramnormal/tests/* E501 E241 - docs/* ALL - -[pep8] -max-line-length = 100 - -[isort] -profile=black -src_paths=paramnormal \ No newline at end of file diff --git a/setup.py b/setup.py deleted file mode 100644 index 18385d5..0000000 --- a/setup.py +++ /dev/null @@ -1,54 +0,0 @@ -# Setup script for the paramnormal package -# -# Usage: python setup.py install - -from setuptools import find_packages, setup - -DESCRIPTION = "paramnormal: Conventionally parameterized probability distributions" -LONG_DESCRIPTION = DESCRIPTION -NAME = "paramnormal" -VERSION = "v0.4.4" -AUTHOR = "Paul Hobson" -AUTHOR_EMAIL = "pmhobson@gmail.com" -URL = "http://phobson.github.io/paramnormal/" -DOWNLOAD_URL = "https://github.com/phobson/paramnormal/archive/master.zip" -LICENSE = "BSD 3-clause" -PACKAGES = find_packages() -PLATFORMS = "Python 3.10 and later." -CLASSIFIERS = [ - "Programming Language :: Python", - "Operating System :: OS Independent", - "License :: OSI Approved :: BSD License", - "Development Status :: 5 - Production/Stable", - "Intended Audience :: Science/Research", - "Topic :: Scientific/Engineering :: Mathematics", - "Programming Language :: Python :: 3.10", - "Programming Language :: Python :: 3.11", - "Programming Language :: Python :: 3.12", -] 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a/.github/workflows/lint.yml +++ b/.github/workflows/lint.yml @@ -20,3 +20,5 @@ jobs: run: uv run --only-group dev ruff check --output-format=github . - name: Ruff format run: uv run --only-group dev ruff format --check . + - name: ty + run: uv run --group dev ty check diff --git a/paramnormal/activity.py b/paramnormal/activity.py index a961cf5..8e0ee2e 100644 --- a/paramnormal/activity.py +++ b/paramnormal/activity.py @@ -1,30 +1,37 @@ +from __future__ import annotations + +from typing import Literal, TypeAlias, overload + import numpy from matplotlib import pyplot +from matplotlib.axes import Axes +from matplotlib.figure import Figure, SubFigure +from scipy.stats.distributions import rv_frozen from paramnormal import dist, utils +from paramnormal.types import FloatArray, NDArrayLike, ParamsLike + +Distro: TypeAlias = str | type[dist.BaseDist_Mixin] | rv_frozen -def _check_distro(distro, **params): - # check if we're returning the class definition or an instance - as_class = params.pop("as_class", False) - if hasattr(distro, "pdf"): +def _get_class(distro: Distro) -> type[dist.BaseDist_Mixin]: + if isinstance(distro, type) and issubclass(distro, dist.BaseDist_Mixin): return distro - elif hasattr(distro, "from_params"): - return _check_distro(distro.name, as_class=as_class, **params) - else: - try: - distro = getattr(dist, distro) - except (AttributeError, TypeError): - raise ValueError(f"{distro} is not a valid paramnormal distribution") + if isinstance(distro, str): + cls = getattr(dist, distro, None) + if isinstance(cls, type) and issubclass(cls, dist.BaseDist_Mixin): + return cls + raise ValueError(f"{distro} is not a valid paramnormal distribution") + - _params = utils._remove_nones(**params) - if as_class: +def _check_distro(distro: Distro, **params: float | None) -> rv_frozen: + # frozen scipy distributions pass straight through + if isinstance(distro, rv_frozen): return distro - else: - return distro(**_params) + return _get_class(distro)(**utils._remove_nones(**params)) -def _check_ax(ax): +def _check_ax(ax: Axes | None) -> tuple[Figure | SubFigure, Axes]: if ax is None: ax = pyplot.gca() fig = ax.figure @@ -34,7 +41,9 @@ def _check_ax(ax): return fig, ax -def random(distro, **params): +def random( + distro: Distro, *, shape: int | tuple[int, ...] | None = None, **params: float | None +) -> float | FloatArray: """ Generate random data from a probability distribution. @@ -73,12 +82,21 @@ def random(distro, **params): """ - shape = params.pop("shape", None) distro = _check_distro(distro, **params) return distro.rvs(size=shape) -def fit(distro, data, as_params=True, **guesses): +@overload +def fit( + distro: Distro, data: NDArrayLike, as_params: Literal[True] = True, **guesses: float | None +) -> ParamsLike: ... +@overload +def fit( + distro: Distro, data: NDArrayLike, as_params: Literal[False], **guesses: float | None +) -> rv_frozen: ... +def fit( + distro: Distro, data: NDArrayLike, as_params: bool = True, **guesses: float | None +) -> ParamsLike | rv_frozen: """ Estimate the distribution parameters of sample data. @@ -112,25 +130,25 @@ def fit(distro, data, as_params=True, **guesses): params(mu=6.4790576880446782, sigma=2) """ - distro = _check_distro(distro, as_class=True) - params = distro.fit(data, **guesses) + cls = _get_class(distro) + params = cls.fit(data, **guesses) if as_params: return params else: - return distro.from_params(params) + return cls.from_params(params) def plot( - distro, - which="PDF", - data=None, - fit_dist=True, - ax=None, - pad=0.05, - xscale="linear", - line_opts=None, - **guesses, -): + distro: Distro, + which: str = "PDF", + data: NDArrayLike | None = None, + fit_dist: bool = True, + ax: Axes | None = None, + pad: float = 0.05, + xscale: Literal["linear", "log"] = "linear", + line_opts: dict[str, str | float] | None = None, + **guesses: float | None, +) -> Axes: """ Plot the PDF of a dataset and other representations of the distribution (histogram, kernel density estimate, and rug plot). @@ -250,20 +268,20 @@ def plot( # validate the axes and distribution function (`which`) fig, ax = _check_ax(ax) if data is not None: - distro = fit(distro, data, as_params=False, **guesses) + frozen = fit(distro, data, as_params=False, **guesses) else: - distro = _check_distro(distro, **guesses) - fxn = getattr(distro, which.lower()) + frozen = _check_distro(distro, **guesses) + fxn = getattr(frozen, which.lower()) # determine and set the xlimits of the plot - xlimits = distro.ppf([pad / 100, 1 - pad / 100]) + xlimits = frozen.ppf([pad / 100, 1 - pad / 100]) # determine the x-values + lo, hi = (float(v) for v in xlimits) if xscale == "log": - # xlimits = numpy.log10(xlimits) - x_hat = numpy.logspace(*numpy.log10(xlimits), num=100) + x_hat = numpy.logspace(numpy.log10(lo), numpy.log10(hi), num=100) else: - x_hat = numpy.linspace(*xlimits, num=100) + x_hat = numpy.linspace(lo, hi, num=100) # compute y-values y_hat = fxn(x_hat) @@ -271,7 +289,7 @@ def plot( line_opts = dict() if line_opts is None else line_opts line_opts["label"] = line_opts.pop("label", which) - (line,) = ax.plot(x_hat, y_hat, **line_opts) + (line,) = ax.plot(x_hat, y_hat, **line_opts) # ty: ignore[invalid-argument-type] ax.set_xscale(xscale) return ax diff --git a/paramnormal/dist.py b/paramnormal/dist.py index 1daa818..f141a41 100644 --- a/paramnormal/dist.py +++ b/paramnormal/dist.py @@ -1,25 +1,39 @@ from collections import namedtuple -from typing import Literal +from collections.abc import Callable +from typing import ClassVar, Literal, Never, cast import numpy from scipy import stats +from scipy.stats import rv_continuous +from scipy.stats.distributions import rv_frozen from paramnormal import utils +from paramnormal.types import NDArrayLike, ParamsLike class BaseDist_Mixin: - def __new__(cls, **params): - dist_params = cls._process_args(fit=False, **params) + dist: ClassVar[rv_continuous] + param_template: ClassVar[Callable[..., ParamsLike]] + name: ClassVar[str] + + @staticmethod + def _process_args(*args: Never, **kwargs: Never) -> dict[str, float | None]: + raise NotImplementedError + + def __new__(cls, **params: float | None) -> rv_frozen: + process_args = cast(Callable[..., dict[str, float | None]], cls._process_args) + dist_params = process_args(fit=False, **params) return cls.dist(**dist_params) @classmethod - def _fit(cls, data, **guesses): - args = utils._remove_nones(**cls._process_args(fit=True, **guesses)) - _sp_params = cls.dist.fit(data, **args) + def _fit(cls, data: NDArrayLike, **guesses: float | None) -> tuple[float, ...]: + process_args = cast(Callable[..., dict[str, float | None]], cls._process_args) + args = utils._remove_nones(**process_args(fit=True, **guesses)) + _sp_params = cls.dist.fit(numpy.asarray(data, dtype=float), **args) # ty: ignore[invalid-argument-type] return _sp_params @classmethod - def fit(cls, data, **guesses): + def fit(cls, data: NDArrayLike, **guesses: float | None) -> ParamsLike: """Fit a distribution to sample using scipy's maximum likelihood estimation methods. @@ -43,7 +57,7 @@ def fit(cls, data, **guesses): return cls.param_template(*cls._fit(data, **guesses)) @classmethod - def from_params(cls, params): + def from_params(cls, params: ParamsLike) -> rv_frozen: """Create a distribution from the ``namedtuple`` result of the :meth:`~fit` method. @@ -59,7 +73,7 @@ def from_params(cls, params): """ kwargs = dict(zip(params._fields, params)) - return cls(**kwargs) + return cls.__new__(cls, **kwargs) class normal(BaseDist_Mixin): @@ -126,7 +140,9 @@ class normal(BaseDist_Mixin): @staticmethod @utils.greco_deco - def _process_args(mu=None, sigma=None, fit=False): + def _process_args( + mu: float | None = None, sigma: float | None = None, fit: bool = False + ) -> dict[str, float | None]: loc_key, scale_key = utils._get_loc_scale_keys(fit=fit) return {loc_key: mu, scale_key: sigma} @@ -212,7 +228,12 @@ class lognormal(BaseDist_Mixin): @staticmethod @utils.greco_deco - def _process_args(mu=None, sigma=None, offset=0, fit=False): + def _process_args( + mu: float | None = None, + sigma: float | None = None, + offset: float | None = 0, + fit: bool = False, + ) -> dict[str, float | None]: loc_key, scale_key = utils._get_loc_scale_keys(fit=fit) key = "f0" if fit else "s" if offset is None and not fit: @@ -220,7 +241,7 @@ def _process_args(mu=None, sigma=None, offset=0, fit=False): return {key: sigma, scale_key: numpy.exp(mu) if mu is not None else mu, loc_key: offset} @classmethod - def fit(cls, data, **guesses): + def fit(cls, data: NDArrayLike, **guesses: float | None) -> ParamsLike: params = cls._fit(data, **guesses) return cls.param_template(mu=numpy.log(params[2]), sigma=params[0], offset=params[1]) @@ -301,7 +322,9 @@ class weibull(BaseDist_Mixin): @staticmethod @utils.greco_deco - def _process_args(k=None, loc=0, scale=1, fit=False): + def _process_args( + k: float | None = None, loc: float | None = 0, scale: float | None = 1, fit: bool = False + ) -> dict[str, float | None]: loc_key, scale_key = utils._get_loc_scale_keys(fit=fit) key = "f0" if fit else "c" return {key: k, loc_key: loc, scale_key: scale} @@ -380,7 +403,12 @@ class alpha(BaseDist_Mixin): @staticmethod @utils.greco_deco - def _process_args(alpha=None, loc=0, scale=1, fit=False): + def _process_args( + alpha: float | None = None, + loc: float | None = 0, + scale: float | None = 1, + fit: bool = False, + ) -> dict[str, float | None]: loc_key, scale_key = utils._get_loc_scale_keys(fit=fit) alpha_key = "f0" if fit else "a" return {alpha_key: alpha, loc_key: loc, scale_key: scale} @@ -468,7 +496,13 @@ class beta(BaseDist_Mixin): @staticmethod @utils.greco_deco - def _process_args(alpha=None, beta=None, loc=0, scale=1, fit=False): + def _process_args( + alpha: float | None = None, + beta: float | None = None, + loc: float | None = 0, + scale: float | None = 1, + fit: bool = False, + ) -> dict[str, float | None]: loc_key, scale_key = utils._get_loc_scale_keys(fit=fit) alpha_key = "f0" if fit else "a" beta_key = "f1" if fit else "b" @@ -552,7 +586,9 @@ class gamma(BaseDist_Mixin): @staticmethod @utils.greco_deco - def _process_args(k=None, theta=None, loc=0, fit=False): + def _process_args( + k: float | None = None, theta: float | None = None, loc: float | None = 0, fit: bool = False + ) -> dict[str, float | None]: loc_key, scale_key = utils._get_loc_scale_keys(fit=fit) key = "f0" if fit else "a" return {key: k, loc_key: loc, scale_key: theta} @@ -627,7 +663,9 @@ class chi_squared(BaseDist_Mixin): @staticmethod @utils.greco_deco - def _process_args(k=None, loc=0, scale=1, fit=False): + def _process_args( + k: float | None = None, loc: float | None = 0, scale: float | None = 1, fit: bool = False + ) -> dict[str, float | None]: loc_key, scale_key = utils._get_loc_scale_keys(fit=fit) key = "f0" if fit else "df" return {key: k, loc_key: loc, scale_key: 1} @@ -706,7 +744,12 @@ class pareto(BaseDist_Mixin): @staticmethod @utils.greco_deco - def _process_args(alpha=None, loc=0, scale=1, fit=False): + def _process_args( + alpha: float | None = None, + loc: float | None = 0, + scale: float | None = 1, + fit: bool = False, + ) -> dict[str, float | None]: loc_key, scale_key = utils._get_loc_scale_keys(fit=fit) key = "f0" if fit else "b" return {key: alpha, loc_key: loc, scale_key: scale} @@ -788,12 +831,14 @@ class exponential(BaseDist_Mixin): @staticmethod @utils.greco_deco - def _process_args(lamda=None, loc=0, fit=False): + def _process_args( + lamda: float | None = None, loc: float | None = 0, fit: bool = False + ) -> dict[str, float | None]: loc_key, scale_key = utils._get_loc_scale_keys(fit=fit) return {loc_key: loc, scale_key: lamda**-1 if lamda is not None else lamda} @classmethod - def fit(cls, data, **guesses): + def fit(cls, data: NDArrayLike, **guesses: float | None) -> ParamsLike: params = cls._fit(data, **guesses) return cls.param_template(loc=params[0], lamda=params[1] ** -1) @@ -871,7 +916,9 @@ class rice(BaseDist_Mixin): @staticmethod @utils.greco_deco - def _process_args(R=None, loc=0, sigma=None, fit=False): + def _process_args( + R: float | None = None, loc: float | None = 0, sigma: float | None = None, fit: bool = False + ) -> dict[str, float | None]: loc_key, scale_key = utils._get_loc_scale_keys(fit=fit) bkey = "fb" if fit else "b" @@ -881,7 +928,7 @@ def _process_args(R=None, loc=0, sigma=None, fit=False): return {loc_key: loc, scale_key: sigma, bkey: b} @classmethod - def fit(cls, data, **guesses): + def fit(cls, data: NDArrayLike, **guesses: float | None) -> ParamsLike: b, loc, sigma = cls._fit(data, **guesses) return cls.param_template(R=b * sigma, loc=loc, sigma=sigma) diff --git a/paramnormal/py.typed b/paramnormal/py.typed new file mode 100644 index 0000000..e69de29 diff --git a/paramnormal/tests/test_activity.py b/paramnormal/tests/test_activity.py index ce45b3d..2db9d13 100644 --- a/paramnormal/tests/test_activity.py +++ b/paramnormal/tests/test_activity.py @@ -36,11 +36,11 @@ def test_number(): def test_pndist_as_class(): - assert activity._check_distro(dist.normal, as_class=True) == dist.normal + assert activity._get_class(dist.normal) == dist.normal def test_string_good_as_class(): - assert activity._check_distro("normal", as_class=True) == dist.normal + assert activity._get_class("normal") == dist.normal def test_pndist(): diff --git a/paramnormal/types.py b/paramnormal/types.py new file mode 100644 index 0000000..e3f5ade --- /dev/null +++ b/paramnormal/types.py @@ -0,0 +1,34 @@ +"""Type aliases shared across paramnormal.""" + +from __future__ import annotations + +from collections.abc import Iterator, Sequence +from typing import Protocol, TypeAlias + +import numpy +from numpy.typing import NDArray + +FloatArray: TypeAlias = NDArray[numpy.float64] + +# Anything numpy can coerce into an ndarray: scalars, (nested) sequences, +# and ndarrays (including masked arrays and other ndarray subclasses). +NDArrayLike: TypeAlias = ( + float + | int + | numpy.number + | NDArray[numpy.generic] + | Sequence[float | int | numpy.number] + | Sequence["NDArrayLike"] +) + + +class ParamsLike(Protocol): + """The namedtuples returned by the ``fit`` methods.""" + + @property + def _fields(self) -> tuple[str, ...]: ... + + def __iter__(self) -> Iterator[float]: ... + + +__all__ = ["FloatArray", "NDArrayLike", "ParamsLike"] diff --git a/paramnormal/utils.py b/paramnormal/utils.py index e42fecd..d59eff1 100644 --- a/paramnormal/utils.py +++ b/paramnormal/utils.py @@ -1,8 +1,16 @@ +from __future__ import annotations + +from collections.abc import Callable from functools import wraps from inspect import signature +from typing import ParamSpec, TypeVar import numpy +P = ParamSpec("P") +R = TypeVar("R") +T = TypeVar("T") + SYMBOLS = { "μ": "mu", "σ": "sigma", @@ -14,38 +22,38 @@ } -def greco_deco(func): +def greco_deco(func: Callable[P, R]) -> Callable[P, R]: """Decorator to let you use greek characters for fxn kwargs.""" @wraps(func) - def wrapper(*args, **kwargs): + def wrapper(*args: P.args, **kwargs: P.kwargs) -> R: sig = signature(func) - kwargs = {SYMBOLS.get(k, k): v for k, v in kwargs.items()} - bound = sig.bind(*args, **kwargs) - return func(**bound.arguments) + renamed = {SYMBOLS.get(k, k): v for k, v in kwargs.items()} + bound = sig.bind(*args, **renamed) + return func(*bound.args, **bound.kwargs) return wrapper -def seed(func): +def seed(func: Callable[P, R]) -> Callable[P, R]: """Decorator to seed the RNG before any function.""" @wraps(func) - def wrapper(*args, **kwargs): + def wrapper(*args: P.args, **kwargs: P.kwargs) -> R: numpy.random.seed(0) return func(*args, **kwargs) return wrapper -def _get_loc_scale_keys(fit=False): +def _get_loc_scale_keys(fit: bool = False) -> tuple[str, str]: if fit: return "floc", "fscale" else: return "loc", "scale" -def _remove_nones(**kwargs): +def _remove_nones(**kwargs: T) -> dict[str, T]: """ Removes any kwargs whose values are `None`. """ diff --git a/pyproject.toml b/pyproject.toml index ee1a6e8..5fad5d4 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -4,14 +4,15 @@ build-backend = "setuptools.build_meta" [project] name = "paramnormal" -version = "0.4.4" +version = "0.5.0" description = "paramnormal: Conventionally parameterized probability distributions" readme = "README.md" -requires-python = ">=3.10" +requires-python = ">=3.11" license = "BSD-3-Clause" license-files = ["LICENSE"] authors = [{ name = "Paul Hobson", email = "pmhobson@gmail.com" }] classifiers = [ + "Typing :: Typed", "Programming Language :: Python", "Operating System :: OS Independent", "Development Status :: 5 - Production/Stable", @@ -35,6 +36,8 @@ dev = [ "pytest-mpl", "pre-commit", "ruff", + "scipy-stubs>=1.15.3.0", + "ty>=0.0.91", ] docs = [ "sphinx", @@ -49,7 +52,16 @@ docs = [ include = ["paramnormal*"] [tool.setuptools.package-data] +"paramnormal" = ["py.typed"] "paramnormal.tests.baseline_images.test_activity" = ["*.png"] [tool.pytest.ini_options] markers = ["mpl_image_compare"] + +[tool.ty.src] +include = ["paramnormal"] +exclude = ["paramnormal/tests"] + +[tool.ty.rules] +# the distributions deliberately name their namedtuples "params" +mismatched-type-name = "ignore" diff --git a/uv.lock b/uv.lock index 3725d5f..6251a34 100644 --- a/uv.lock +++ b/uv.lock @@ -1,6 +1,6 @@ version = 1 revision = 5 -requires-python = ">=3.10" +requires-python = ">=3.11" resolution-markers = [ "python_full_version >= '3.14' and sys_platform == 'win32'", "python_full_version >= '3.14' and sys_platform == 'emscripten'", @@ -11,10 +11,9 @@ resolution-markers = [ "python_full_version == '3.12.*' and sys_platform == 'win32'", "python_full_version == '3.12.*' and sys_platform == 'emscripten'", "python_full_version == '3.12.*' and sys_platform != 'emscripten' and sys_platform != 'win32'", - "python_full_version == '3.11.*' and sys_platform == 'win32'", - "python_full_version == '3.11.*' and sys_platform == 'emscripten'", - 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pyproject.toml | 5 +++ uv.lock | 11 +++++ 9 files changed, 174 insertions(+), 19 deletions(-) diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index 23435c5..9136ca6 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -18,7 +18,7 @@ jobs: with: enable-cache: true - name: Build docs - run: uv run --group docs sphinx-build -b html docs docs/_build/html + run: uv run --group docs sphinx-build -W --keep-going -b html docs docs/_build/html env: MPLBACKEND: agg - uses: actions/upload-pages-artifact@v4 diff --git a/README.md b/README.md index f444223..6020ba9 100644 --- a/README.md +++ b/README.md @@ -71,6 +71,12 @@ uv run ruff check . && uv run ruff format --check . uv run --group docs sphinx-build -b html docs docs/_build/html ``` +Then view the docs with: + +```shell +uv run python -m http.server 8001 --directory docs/_build/html +``` + ## Development status From my perspective this is now feature complete, meaning it has all of the distribution that I use somewhat regularly. diff --git a/docs/conf.py b/docs/conf.py index 617b42e..61b0d09 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -13,25 +13,60 @@ "sphinx.ext.doctest", "sphinx.ext.intersphinx", "sphinx.ext.todo", - "sphinx.ext.mathjax", "sphinx.ext.viewcode", + # Renders the `.. plot::` blocks embedded in the API docstrings. + "matplotlib.sphinxext.plot_directive", + # numpydoc renders the docstrings (all numpydoc-style after the 2025 + # clean-up) into the API reference pages. + "matplotlib.sphinxext.plot_directive", "numpydoc", + # myst-nb executes the tutorial notebooks during the build. "myst_nb", + # sphinx-gallery turns examples/*.py into an image gallery. + # "sphinx_gallery.gen_gallery", ] source_suffix = {".md": "myst-nb", ".ipynb": "myst-nb"} master_doc = "index" exclude_patterns = ["_build", "**.ipynb_checkpoints"] myst_enable_extensions = ["dollarmath", "amsmath"] -nb_execution_mode = "off" +nb_execution_mode = "force" +nb_execution_raise_on_error = True +nb_execution_timeout = 300 suppress_warnings = ["myst.header"] numpydoc_show_class_members = False +numpydoc_class_members_toctree = False autodoc_member_order = "bysource" todo_include_todos = True pygments_style = "sphinx" + + +# Options for the matplotlib .. plot:: directive (used in API docstrings) +plot_include_source = True +plot_html_show_formats = False +plot_html_show_source_link = False + +intersphinx_mapping = { + "python": ("https://docs.python.org/3/", None), + "matplotlib": ("https://matplotlib.org/stable/", None), + "numpy": ("https://numpy.org/doc/stable/", None), + "scipy": ("https://docs.scipy.org/doc/scipy/", None), + "seaborn": ("https://seaborn.pydata.org/", None), +} + +myst_enable_extensions = ["colon_fence", "deflist", "dollarmath"] +myst_heading_anchors = 3 + +# # -- myst-nb (tutorial notebooks) -------------------------------------------- + +# -- Options for HTML output ------------------------------------------------- html_theme = "sphinx_rtd_theme" htmlhelp_basename = "paramnormaldoc" - -intersphinx_mapping = {"python": ("https://docs.python.org/3", None)} +# html_theme = "pydata_sphinx_theme" +# html_theme_options = { +# "github_url": "https://github.com/phobson/paramnormal", +# "logo": {"text": "paramnormal"}, +# } +# htmlhelp_basename = "paramnormaldoc" diff --git a/docs/tutorial/fitting.ipynb b/docs/tutorial/fitting.ipynb index b785caf..a217d36 100644 --- a/docs/tutorial/fitting.ipynb +++ b/docs/tutorial/fitting.ipynb @@ -83,7 +83,7 @@ "source": [ "bins = np.logspace(-0.5, 1.75, num=25)\n", "fig, ax = plt.subplots()\n", - "_ = ax.hist(x, bins=bins, normed=True)\n", + "_ = ax.hist(x, bins=bins, density=True)\n", "ax.set_xscale('log')\n", "ax.set_xlabel('$X$')\n", "ax.set_ylabel('Probability')\n", @@ -158,7 +158,7 @@ "\n", "bins = np.logspace(-0.5, 1.75, num=25)\n", "fig, ax = plt.subplots()\n", - "_ = ax.hist(x, bins=bins, normed=True, alpha=0.375)\n", + "_ = ax.hist(x, bins=bins, density=True, alpha=0.375)\n", "ax.plot(x_hat, y_hat, zorder=2, color='g')\n", "ax.set_xscale('log')\n", "ax.set_xlabel('$X$')\n", diff --git a/paramnormal/__init__.py b/paramnormal/__init__.py index a51f7d9..942eb29 100644 --- a/paramnormal/__init__.py +++ b/paramnormal/__init__.py @@ -1,2 +1,3 @@ +from paramnormal import activity, utils # noqa from paramnormal.dist import * # noqa from paramnormal.tests import test # noqa diff --git a/paramnormal/activity.py b/paramnormal/activity.py index 8e0ee2e..e525612 100644 --- a/paramnormal/activity.py +++ b/paramnormal/activity.py @@ -1,6 +1,6 @@ from __future__ import annotations -from typing import Literal, TypeAlias, overload +from typing import Any, Literal, TypeAlias, overload import numpy from matplotlib import pyplot @@ -138,6 +138,46 @@ def fit( return cls.from_params(params) +def _draw_distplot(sample: FloatArray, ax: Axes, opts: dict[str, Any] | None) -> None: + """Histogram, KDE and rug plot of ``sample``. + + Replaces the deprecated ``seaborn.distplot``, accepting its common options: + ``hist``, ``kde``, ``rug``, ``norm_hist``, ``bins``, ``color``, and the + ``hist_kws``, ``kde_kws`` and ``rug_kws`` dictionaries. + """ + try: + import seaborn + except ImportError as err: + raise ImportError( + "`seaborn` is required for `distplot=True`; install `paramnormal[plot]`" + ) from err + + o = dict(opts or {}) + hist = o.pop("hist", True) + kde = o.pop("kde", True) + rug = o.pop("rug", False) + norm_hist = o.pop("norm_hist", False) + bins = o.pop("bins", "auto") + color = o.pop("color", None) + hist_kws = dict(o.pop("hist_kws", None) or {}) + kde_kws = dict(o.pop("kde_kws", None) or {}) + rug_kws = dict(o.pop("rug_kws", None) or {}) + if o: + raise TypeError(f"unsupported `distplot_opts`: {sorted(o)}") + + if color is not None: + for kws in (hist_kws, kde_kws, rug_kws): + kws.setdefault("color", color) + + if hist: + stat = "density" if (norm_hist or kde) else "count" + seaborn.histplot(x=sample, bins=bins, stat=stat, ax=ax, **hist_kws) + if kde: + seaborn.kdeplot(x=sample, ax=ax, **kde_kws) + if rug: + seaborn.rugplot(x=sample, ax=ax, **rug_kws) + + def plot( distro: Distro, which: str = "PDF", @@ -147,6 +187,8 @@ def plot( pad: float = 0.05, xscale: Literal["linear", "log"] = "linear", line_opts: dict[str, str | float] | None = None, + distplot: bool = False, + distplot_opts: dict[str, Any] | None = None, **guesses: float | None, ) -> Axes: """ @@ -265,31 +307,33 @@ def plot( """ - # validate the axes and distribution function (`which`) fig, ax = _check_ax(ax) - if data is not None: - frozen = fit(distro, data, as_params=False, **guesses) + sample = None if data is None else numpy.asarray(data, dtype=float) + if sample is not None and fit_dist: + frozen = fit(distro, sample, as_params=False, **guesses) else: frozen = _check_distro(distro, **guesses) + if any(v is None for v in (*frozen.args, *frozen.kwds.values())): + raise ValueError("`distro` must be fully specified when it is not being fit to `data`") fxn = getattr(frozen, which.lower()) - # determine and set the xlimits of the plot - xlimits = frozen.ppf([pad / 100, 1 - pad / 100]) + if distplot and sample is not None: + _draw_distplot(sample, ax, distplot_opts) - # determine the x-values - lo, hi = (float(v) for v in xlimits) + # determine the x-values from the distribution's quantiles + lo, hi = (float(v) for v in frozen.ppf([pad / 100, 1 - pad / 100])) if xscale == "log": x_hat = numpy.logspace(numpy.log10(lo), numpy.log10(hi), num=100) else: x_hat = numpy.linspace(lo, hi, num=100) - # compute y-values y_hat = fxn(x_hat) - line_opts = dict() if line_opts is None else line_opts - line_opts["label"] = line_opts.pop("label", which) + # copy so the caller's dict is never modified + opts = dict(line_opts or {}) + opts.setdefault("label", which) - (line,) = ax.plot(x_hat, y_hat, **line_opts) # ty: ignore[invalid-argument-type] + ax.plot(x_hat, y_hat, **opts) # ty: ignore[invalid-argument-type] ax.set_xscale(xscale) return ax diff --git a/paramnormal/tests/test_activity.py b/paramnormal/tests/test_activity.py index 2db9d13..ee9930e 100644 --- a/paramnormal/tests/test_activity.py +++ b/paramnormal/tests/test_activity.py @@ -208,3 +208,56 @@ def test_plot_bad_attribute(): with pytest.raises(AttributeError): loc_dist = dist.lognormal(μ=1.25, σ=0.75) activity.plot(loc_dist, xscale="log", which="JUNK") + + +def test_plot_line_opts_not_mutated(): + opts = dict(color="red") + activity.plot("normal", mu=0, sigma=1, line_opts=opts) + assert opts == dict(color="red") + + +def test_plot_fit_dist_false_requires_full_spec(): + data = numpy.random.normal(size=20) + with pytest.raises(ValueError): + activity.plot("normal", data=data, fit_dist=False, mu=0) + ax = activity.plot("normal", data=data, fit_dist=False, mu=0, sigma=1) + assert isinstance(ax, pyplot.Axes) + + +def test_plot_fit_dist_false_does_not_fit(): + data = numpy.random.normal(loc=50, size=20) + pyplot.close("all") + fig, ax = pyplot.subplots() + activity.plot("normal", data=data, fit_dist=False, mu=0, sigma=1, ax=ax) + assert ax.lines[0].get_xdata().max() < 10 + + +@pytest.mark.parametrize( + "opts", + [ + None, + dict(rug=True, kde=False, norm_hist=True), + dict(hist=False, rug=True, color="green"), + dict(bins=numpy.logspace(-1, 1, 10), kde=False), + ], +) +def test_plot_distplot(opts): + pytest.importorskip("seaborn") + data = numpy.random.lognormal(size=50) + fig, ax = pyplot.subplots() + out = activity.plot("lognormal", data=data, distplot=True, distplot_opts=opts, ax=ax) + assert out is ax + assert len(ax.lines) >= 1 + assert len(ax.patches) > 0 or (opts and opts.get("hist") is False) + + +def test_plot_distplot_bad_option(): + pytest.importorskip("seaborn") + with pytest.raises(TypeError): + activity.plot("normal", data=numpy.arange(10.0), distplot=True, distplot_opts=dict(foo=1)) + + +def test_plot_distplot_without_data_is_noop(): + fig, ax = pyplot.subplots() + activity.plot("normal", mu=0, sigma=1, distplot=True, ax=ax) + assert len(ax.patches) == 0 diff --git a/pyproject.toml b/pyproject.toml index 5fad5d4..b59097f 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -29,9 +29,13 @@ dependencies = ["numpy", "scipy", "matplotlib"] Homepage = "http://phobson.github.io/paramnormal/" Source = "https://github.com/phobson/paramnormal" +[project.optional-dependencies] +plot = ["seaborn"] + [dependency-groups] dev = [ "pytest", + "seaborn", "pytest-cov", "pytest-mpl", "pre-commit", @@ -46,6 +50,7 @@ docs = [ "numpydoc", "seaborn", "ipython", + "ipykernel>=7.4.0", ] [tool.setuptools.packages.find] diff --git a/uv.lock b/uv.lock index 6251a34..73f1842 100644 --- a/uv.lock +++ b/uv.lock @@ -1840,6 +1840,11 @@ dependencies = [ { name = "scipy", version = "1.18.1", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.12'" }, ] +[package.optional-dependencies] +plot = [ + { name = "seaborn" }, +] + [package.dev-dependencies] dev = [ { name = "pre-commit" }, @@ -1849,9 +1854,11 @@ dev = [ { name = "ruff" }, { name = "scipy-stubs", version = "1.17.1.5", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.12'" }, { name = "scipy-stubs", version = "1.18.1.1", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.12'" }, + { name = "seaborn" }, { name = "ty" }, ] docs = [ + { name = "ipykernel" }, { name = "ipython" }, { name = "myst-nb" }, { name = "numpydoc" }, @@ -1867,7 +1874,9 @@ requires-dist = [ { name = "matplotlib" }, { name = "numpy" }, { name = "scipy" }, + { name = "seaborn", marker = "extra == 'plot'" }, ] +provides-extras = ["plot"] [package.metadata.requires-dev] dev = [ @@ -1877,9 +1886,11 @@ dev = [ { name = "pytest-mpl" }, { name = "ruff" }, { name = "scipy-stubs", specifier = ">=1.15.3.0" }, + { name = "seaborn" }, { name = "ty", specifier = ">=0.0.91" }, ] docs = [ + { name = "ipykernel", specifier = ">=7.4.0" }, { name = "ipython" }, { name = "myst-nb" }, { name = "numpydoc" },