pyranges1 0.1.0__tar.gz

pyranges1-0.1.0/.github/workflows/build-book.yml

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+name: Build and Deploy
+on: [workflow_dispatch]
+jobs:
+  build-and-deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2.3.1
+
+      - name: Add conda to system path
+        run: |
+          # $CONDA is an environment variable pointing to the root of the miniconda directory
+          echo $CONDA/bin >> $GITHUB_PATH
+
+      - name: Install pyranges
+        run: |
+          pip install cython
+          pip install sorted_nearest
+          python setup.py install
+          pip install bamread 
+          pip install fisher
+  
+      - name: Install dependencies
+        run: |
+          conda config --set always_yes yes --set changeps1 no
+          conda config --add channels bioconda
+          conda config --add channels r
+          conda install mamba -n base -c conda-forge
+          mamba install -c r r
+          mamba install -c conda-forge r-reticulate
+          # mamba install -c conda-forge r-bookdown
+          mamba install -y conda-forge::ncurses
+          mamba install -c conda-forge matplotlib
+          mamba install -c conda-forge pandoc
+          mamba install -c bioconda pybigwig
+          echo 'install.packages("bookdown")' > install.R
+          Rscript install.R
+
+      - name: Build book
+        run: |
+          cd book
+          Rscript compile.R
+
+      - name: Deploy
+        uses: JamesIves/github-pages-deploy-action@4.1.9
+        with:
+          branch: gh-pages # The branch the action should deploy to.
+          folder: book/build  # The folder the action should deploy.
+

pyranges1-0.1.0/.github/workflows/build_and_upload_wheels.yml

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+name: Build and upload to PyPI
+
+# Source: https://raw.githubusercontent.com/pypa/cibuildwheel/main/examples/github-deploy.yml
+
+env:
+  CIBW_SKIP: "cp36-*"
+
+# Build on every branch push, tag push, and pull request change:
+on:
+  workflow_dispatch:
+
+jobs:
+  build_and_upload_wheels:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+
+      - name: Build SDist and wheel
+        run: pipx run build
+
+      - uses: actions/upload-artifact@v3
+        with:
+          path: dist/*
+
+      - name: Check metadata
+        run: pipx run twine check dist/*
+
+      - uses: pypa/gh-action-pypi-publish@v1.5.0
+        with:
+          user: ${{ secrets.PYPI_USER }}
+          password: ${{ secrets.PYPI_PROD_PASSWORD }}
+          verbose: true
+          # To test: repository_url: https://test.pypi.org/legacy/

pyranges1-0.1.0/.github/workflows/check.yml

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+name: check
+on:
+  pull_request:
+  workflow_dispatch:
+  issue_comment:
+    types: [created]
+
+concurrency:
+  group: check-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  test:
+    name: test with ${{ matrix.py }} on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    if: >- 
+      github.event_name == 'pull_request' ||
+      github.event_name == 'workflow_dispatch' ||
+      (github.event_name == 'issue_comment' && github.event.issue.pull_request && contains(github.event.comment.body, '/rerun-precommit'))
+    strategy:
+      fail-fast: false
+      matrix:
+        py:
+          - "3.12"
+        os:
+          - ubuntu-latest
+          # - macos-latest
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+      - name: Setup python for test ${{ matrix.py }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.py }}
+      - name: Install tox
+        run: python -m pip install tox-gh>=1.2
+      - name: Setup test suite
+        run: tox -vv --notest
+      - name: Run test suite
+        run: tox --skip-pkg-install

pyranges1-0.1.0/.github/workflows/run_hypothesis_tests.yml

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+name: property-tests
+
+on:
+  workflow_run:
+    workflows: [linting-typechecking-doctests]
+    types: [completed]
+
+
+jobs:
+  on-success:
+    runs-on: ubuntu-latest
+    if: ${{ github.event.workflow_run.conclusion == 'success' }}
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        with:
+          python-version: "3.11.0"
+      - run: sudo apt-get install bedtools
+      - run: pip install hypothesis pytest pytest-xdist
+      - run: pip install .
+      - run: pytest -sv -n 2 tests/property_based
+        env:
+          GITHUB_ACTIONS: true
+  on-failure:
+    runs-on: ubuntu-latest
+    if: ${{ github.event.workflow_run.conclusion == 'failure' }}
+    steps:
+      - run: exit 1  # Fail the job

pyranges1-0.1.0/.gitignore

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+docs/chipseq.csv
+docs/chipseq.gtf
+docs/test.bed
+
+*.swp
+.snakemake/
+wheelhouse/
+.coverage
+htmlcov/
+*flycheck*
+*.pyc*
+*bk
+.hypothesis/
+*.RData
+*.Rhistory
+build/
+_build/
+workflow/data
+*#*
+*.pyc
+*.bk
+*cache/
+build/
+dist/
+
+
+*.txt
+*.so
+*.cpp
+*.lprof
+*.egg-*
+
+pyranges-*/
+*.bw

pyranges1-0.1.0/CHANGELOG.txt

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+# 0.1.0
+New pyranges version, redesigned from scratch.

pyranges1-0.1.0/LICENSE

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+Copyright (c) 2019 Endre Bakken Stovner
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

pyranges1-0.1.0/PKG-INFO

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+Metadata-Version: 2.1
+Name: pyranges1
+Version: 0.1.0
+Summary: GenomicRanges for Python.
+Author-email: Endre Bakken Stovner <endbak@pm.me>
+License: MIT
+Project-URL: Homepage, http://github.com/pyranges/pyranges_1.x
+Keywords: bioinformatics,genomicranges,genomics
+Classifier: Programming Language :: Python :: 3
+Classifier: Development Status :: 4 - Beta
+Classifier: Environment :: Other Environment
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: POSIX :: Linux
+Classifier: Operating System :: MacOS :: MacOS X
+Classifier: Topic :: Scientific/Engineering
+Requires-Python: >=3.11.0
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: pandas
+Requires-Dist: ncls>=0.0.63
+Requires-Dist: tabulate
+Requires-Dist: sorted_nearest>=0.0.33
+Requires-Dist: natsort
+Provides-Extra: add-ons
+Requires-Dist: pyrle>=0.0.39; extra == "add-ons"
+Requires-Dist: bamread; extra == "add-ons"
+Requires-Dist: bwread; extra == "add-ons"
+Requires-Dist: fisher; extra == "add-ons"
+Requires-Dist: pyfaidx; extra == "add-ons"
+Requires-Dist: joblib; extra == "add-ons"
+Provides-Extra: dev
+Requires-Dist: tox; extra == "dev"
+Requires-Dist: ruff==0.3.0; extra == "dev"
+Requires-Dist: pyright; extra == "dev"
+Requires-Dist: pandas-stubs; extra == "dev"
+Requires-Dist: types-tabulate; extra == "dev"
+Requires-Dist: pytest-watcher; extra == "dev"
+Requires-Dist: pytest-xdist; extra == "dev"
+Requires-Dist: hypothesis>=6.92.1; extra == "dev"
+Provides-Extra: docs
+Requires-Dist: sphinx; extra == "docs"
+Requires-Dist: sphinx_rtd_theme; extra == "docs"
+Requires-Dist: sphinx-autoapi; extra == "docs"
+Requires-Dist: sphinxcontrib-napoleon; extra == "docs"
+Provides-Extra: all
+Requires-Dist: pyranges[add-ons]; extra == "all"
+Requires-Dist: pyranges[dev]; extra == "all"
+Requires-Dist: pyranges[docs]; extra == "all"
+
+# pyranges
+
+[![Coverage Status](https://img.shields.io/coveralls/github/biocore-ntnu/pyranges.svg)](https://coveralls.io/github/biocore-ntnu/pyranges?branch=master) [![hypothesis tested](graphs/hypothesis-tested-brightgreen.svg)](http://hypothesis.readthedocs.io/) [![PyPI version](https://badge.fury.io/py/pyranges.svg)](https://badge.fury.io/py/pyranges) [![MIT](https://img.shields.io/pypi/l/pyranges.svg?color=green)](https://opensource.org/licenses/MIT) ![PyPI - Python Version](https://img.shields.io/pypi/pyversions/pyranges.svg) [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/pyranges/README.html)
+
+## Missing:
+
+- to_bigwig: needs a rewrite of the pyrle module
+
+## Introduction
+
+PyRanges is a Python library specifically designed for efficient and intuitive manipulation of genomics data,
+particularly genomic intervals (like genes, genomic features, or reads).
+The library is optimized for fast querying and manipulation of genomic annotations.
+
+*"Finally ... This was what Python badly needed for years."* - Heng Li
+
+## Documentation
+
+The pyranges documentation, including installation instructions, API, tutorial, and how-to-pages, will soon become available.
+
+## Features
+
+  - fast
+  - memory-efficient
+  - featureful
+  - pythonic/pandastic
+  - supports chaining with a terse syntax
+  - is a proper subclass of Pandas DataFrames
+
+## Paper/Cite
+
+Stovner EB, Sætrom P (2020) PyRanges: efficient comparison of genomic intervals in Python. *Bioinformatics 36(3):918-919*  http://dx.doi.org/10.1093/bioinformatics/btz615
+
+## Supporting pyranges
+
+  - most importantly, cite pyranges if you use it. It is the main metric funding sources care about.
+  - use pyranges in Stack Overflow/biostars questions and answers
+  - star the repo (possibly important for github visibility and as a proxy for project popularity)
+
+## Asking for help
+
+If you encounter bugs, or the documentation is not enough a cannot accomplish a specific task of interest, or if you'd like new features implemented, open an Issue at github: https://github.com/pyranges/pyranges/issues
+
+## Contributing to pyranges
+
+Pyranges accepts code contributions in form of pull request. For details, visit https://pyranges.readthedocs.io/developer_guide.html
+

pyranges1-0.1.0/README.md

@@ -0,0 +1,47 @@
+# pyranges
+
+[![Coverage Status](https://img.shields.io/coveralls/github/biocore-ntnu/pyranges.svg)](https://coveralls.io/github/biocore-ntnu/pyranges?branch=master) [![hypothesis tested](graphs/hypothesis-tested-brightgreen.svg)](http://hypothesis.readthedocs.io/) [![PyPI version](https://badge.fury.io/py/pyranges.svg)](https://badge.fury.io/py/pyranges) [![MIT](https://img.shields.io/pypi/l/pyranges.svg?color=green)](https://opensource.org/licenses/MIT) ![PyPI - Python Version](https://img.shields.io/pypi/pyversions/pyranges.svg) [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/pyranges/README.html)
+
+## Missing:
+
+- to_bigwig: needs a rewrite of the pyrle module
+
+## Introduction
+
+PyRanges is a Python library specifically designed for efficient and intuitive manipulation of genomics data,
+particularly genomic intervals (like genes, genomic features, or reads).
+The library is optimized for fast querying and manipulation of genomic annotations.
+
+*"Finally ... This was what Python badly needed for years."* - Heng Li
+
+## Documentation
+
+The pyranges documentation, including installation instructions, API, tutorial, and how-to-pages, will soon become available.
+
+## Features
+
+  - fast
+  - memory-efficient
+  - featureful
+  - pythonic/pandastic
+  - supports chaining with a terse syntax
+  - is a proper subclass of Pandas DataFrames
+
+## Paper/Cite
+
+Stovner EB, Sætrom P (2020) PyRanges: efficient comparison of genomic intervals in Python. *Bioinformatics 36(3):918-919*  http://dx.doi.org/10.1093/bioinformatics/btz615
+
+## Supporting pyranges
+
+  - most importantly, cite pyranges if you use it. It is the main metric funding sources care about.
+  - use pyranges in Stack Overflow/biostars questions and answers
+  - star the repo (possibly important for github visibility and as a proxy for project popularity)
+
+## Asking for help
+
+If you encounter bugs, or the documentation is not enough a cannot accomplish a specific task of interest, or if you'd like new features implemented, open an Issue at github: https://github.com/pyranges/pyranges/issues
+
+## Contributing to pyranges
+
+Pyranges accepts code contributions in form of pull request. For details, visit https://pyranges.readthedocs.io/developer_guide.html
+

pyranges1-0.1.0/check_typing_linting_and_formatting.py

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+#!/usr/bin/env python3
+
+import argparse
+import logging
+import shlex
+import subprocess
+import sys
+
+logging.basicConfig(level=logging.INFO)
+LOGGER = logging.getLogger(__name__)
+LOGGER.setLevel(logging.INFO)
+
+
+parser = argparse.ArgumentParser(description="This script runs various checks and tests.")
+parser.add_argument("-v", "--verbose", action="store_true", help="Show output from programs run.")
+parser.add_argument("-l", "--list", action="store_true", help="List all checks and tests and exits.")
+args = parser.parse_args()
+verbose: bool = args.verbose
+show_checks: bool = args.list
+
+
+def run_command(command, *, show_output: bool) -> int:
+    """Run a shell command and return its exit status."""
+    result = subprocess.run(command, capture_output=not show_output, text=True, check=False)  # noqa: S603
+    return result.returncode
+
+
+def main() -> int:
+    """Run all continuous integration checks."""
+    commands = {
+        "ruff format": ["ruff", "format", "--check", "--diff", "pyranges"],
+        "ruff check": ["ruff", "check", "pyranges"],
+        "pyright": ["pyright", "pyranges"],
+        "pytest": ["pytest", "--doctest-modules", "pyranges/", "tests/unit/"],
+        "more doctest": ["python", "tests/run_doctest_tutorial_howto.py"],
+    }
+    if show_checks:
+        LOGGER.info("Available checks and tests:")
+        for task, command in commands.items():
+            LOGGER.info("    %s: %s", task, shlex.join(command))
+        sys.exit(0)
+
+    failed_tasks = []
+
+    for task, command in commands.items():
+        LOGGER.debug("Running: %s", shlex.join(command))
+        retcode = run_command(command, show_output=verbose)
+        if retcode != 0:
+            LOGGER.debug("Task %s failed!", task)
+            failed_tasks.append(task)
+
+    if failed_tasks:
+        LOGGER.warning("The following tasks failed:")
+        for task in failed_tasks:
+            LOGGER.warning("%s:\n    %s", task, shlex.join(commands[task]))
+        return 1
+
+    LOGGER.debug("All tasks completed successfully.")
+    return 0
+
+
+if __name__ == "__main__":
+    sys.exit(main())

pyranges1-0.1.0/conftest.py

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+import pytest
+from hypothesis import settings
+
+
+@pytest.fixture(autouse=True)
+def set_max_console_width() -> None:
+    import pyranges
+
+    pyranges.options.set_option("console_width", 120)
+    # below: edit default dictionary so that reset_option() doesn't screw up testing
+    pyranges.options.options_default["console_width"] = (120, pyranges.options.options_in_use["console_width"][1])
+
+def pytest_addoption(parser):
+    parser.addoption("--derandomize", action="store_true", default=False, help="Derandomize Hypothesis tests")
+
+
+def pytest_configure(config):
+    if config.getoption("--derandomize"):
+        settings.register_profile("derandomize", derandomize=True)
+        settings.load_profile("derandomize")

pyranges1-0.1.0/docs/Makefile

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+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

pyranges1-0.1.0/docs/api_reference.rst

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+
+API reference
+~~~~~~~~~~~~~
+
+#. :doc:`PyRanges objects <./pyranges_objects>` are the main data structure in pyranges
+#. :doc:`The pyranges module <./pyranges_module>` offer file readers and other utilities
+#. :doc:`Extensions submodules <./pyranges_extensions>` provide additional domain-specific functionalities
+#. :doc:`RangeFrame <./range_frame>` is the parent class of PyRanges, supporting operations on simple intervals
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   pyranges_objects
+   pyranges_module
+   pyranges_extensions
+   range_frame

pyranges1-0.1.0/docs/conf.py

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+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+import os
+import sys
+# sys.path.insert(0, os.path.abspath('.'))
+
+# sys.path.insert(0, os.path.abspath('..'))  # Adjust this as necessary
+#
+# sys.path.insert(0, os.path.abspath('../pyranges'))  # Adjust this as necessary
+#
+# sys.path.insert(0, os.path.abspath('.'))  # Adjust this as necessary
+
+# -- Project information -----------------------------------------------------
+
+project = "pyranges"
+copyright = "2020, Endre Bakken Stovner"
+author = "Endre Bakken Stovner"
+
+
+# -- General configuration ---------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+
+
+extensions = [
+    "sphinx.ext.napoleon",
+    # "sphinxcontrib.napoleon",
+    #"autoapi.extension",
+    "sphinx.ext.autodoc",
+    # "autoapi.extension",
+    "sphinx.ext.autosummary",
+
+    # "sphinx.ext.doctest"
+]
+
+autosummary_generate = True  # Enable summary table generation
+
+
+autodoc_default_options = {
+    'members': True,
+    'imported-members': True,
+    # other options...
+}
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ["_templates"]
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = []
+
+master_doc = "index"
+
+# -- 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 = "alabaster"
+html_theme = 'sphinx_rtd_theme'
+
+
+# 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"]