revseq 1.0.0__tar.gz → 1.2.0__tar.gz

{revseq-1.0.0 → revseq-1.2.0}/PKG-INFO

@@ -1,26 +1,26 @@
-Metadata-Version: 2.3
+Metadata-Version: 2.1
 Name: revseq
-Version: 1.0.0
+Version: 1.2.0
 Summary: reverse and/or complement dna sequence
-Project-URL: homepage, https://github.com/milescsmith/revseq
-Project-URL: repository, https://github.com/milescsmith/revseq
-Project-URL: changelog, https://github.com/milescsmith/revseq/releases
-Author-email: Miles Smith <mileschristiansmith@gmail.com>
-License-Expression: GPL-3.0
-License-File: LICENSE
+Home-page: https://github.com/milescsmith/revseq
+Author-Email: Miles Smith <mileschristiansmith@gmail.com>
+License: GPL-3.0
+Classifier: Programming Language :: Python :: Implementation :: CPython
+Classifier: Programming Language :: Python :: Implementation :: PyPy
 Classifier: Development Status :: 5 - Production/Stable
 Classifier: Environment :: Console
 Classifier: Intended Audience :: Science/Research
 Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
-Classifier: Programming Language :: Python :: Implementation :: CPython
-Classifier: Programming Language :: Python :: Implementation :: PyPy
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
 Classifier: Typing :: Typed
+Project-URL: Homepage, https://github.com/milescsmith/revseq
+Project-URL: Repository, https://github.com/milescsmith/revseq
+Project-URL: Changelog, https://github.com/milescsmith/revseq/releases
 Requires-Python: >=3.10
+Requires-Dist: typer>=0.11.0
 Requires-Dist: icontract>=2.6.6
 Requires-Dist: rich>=13.7.1
 Requires-Dist: typeguard>=4.2.1
-Requires-Dist: typer>=0.11.0
 Description-Content-Type: text/x-rst
 
 revseq
@@ -45,8 +45,8 @@ A simple script to generate the (reverse) (complement) of a sequence
 .. |License| image:: https://img.shields.io/pypi/l/revseq
    :target: https://opensource.org/licenses/GPL-3.0
    :alt: License
-.. |Tests| image:: https://github.com/milescsmith/revseq/workflows/Tests/badge.svg
-   :target: https://github.com/milescsmith/revseq/actions?workflow=Tests
+.. |Tests| image:: https://github.com/milescsmith/revseq/actions/workflows/python-package.yml/badge.svg
+   :target: https://github.com/milescsmith/revseq/actions?workflow=python-package
    :alt: Tests
 .. |Codecov| image:: https://codecov.io/gh/milescsmith/revseq/branch/main/graph/badge.svg
    :target: https://codecov.io/gh/milescsmith/revseq
@@ -136,4 +136,4 @@ Credits
 .. _file an issue: https://github.com/milescsmith/revseq/issues
 .. _pip: https://pip.pypa.io/
 .. github-only
-.. _Contributor Guide: CONTRIBUTING.rst
+.. _Contributor Guide: CONTRIBUTING.rst

{revseq-1.0.0 → revseq-1.2.0}/README.rst

@@ -20,8 +20,8 @@ A simple script to generate the (reverse) (complement) of a sequence
 .. |License| image:: https://img.shields.io/pypi/l/revseq
    :target: https://opensource.org/licenses/GPL-3.0
    :alt: License
-.. |Tests| image:: https://github.com/milescsmith/revseq/workflows/Tests/badge.svg
-   :target: https://github.com/milescsmith/revseq/actions?workflow=Tests
+.. |Tests| image:: https://github.com/milescsmith/revseq/actions/workflows/python-package.yml/badge.svg
+   :target: https://github.com/milescsmith/revseq/actions?workflow=python-package
    :alt: Tests
 .. |Codecov| image:: https://codecov.io/gh/milescsmith/revseq/branch/main/graph/badge.svg
    :target: https://codecov.io/gh/milescsmith/revseq
@@ -111,4 +111,4 @@ Credits
 .. _file an issue: https://github.com/milescsmith/revseq/issues
 .. _pip: https://pip.pypa.io/
 .. github-only
-.. _Contributor Guide: CONTRIBUTING.rst
+.. _Contributor Guide: CONTRIBUTING.rst

{revseq-1.0.0 → revseq-1.2.0}/pyproject.toml

@@ -1,17 +1,18 @@
 [build-system]
-requires = ["hatchling"]
-build-backend = "hatchling.build"
+requires = [
+    "pdm-backend",
+]
+build-backend = "pdm.backend"
 
 [project]
 name = "revseq"
-version = "1.0.0"
+version = "1.2.0"
 description = "reverse and/or complement dna sequence"
 authors = [
-    { name = "Miles Smith", email = "mileschristiansmith@gmail.com" }
+    { name = "Miles Smith", email = "mileschristiansmith@gmail.com" },
 ]
-license = "GPL-3.0"
-readme = "README.rst"
 requires-python = ">= 3.10"
+readme = "README.rst"
 dependencies = [
     "typer>=0.11.0",
     "icontract>=2.6.6",
@@ -29,6 +30,9 @@ classifiers = [
     "Typing :: Typed",
 ]
 
+[project.license]
+text = "GPL-3.0"
+
 [project.urls]
 homepage = "https://github.com/milescsmith/revseq"
 repository = "https://github.com/milescsmith/revseq"
@@ -38,44 +42,52 @@ changelog = "https://github.com/milescsmith/revseq/releases"
 revseq = "revseq.__main__:app"
 
 [tool.coverage.paths]
-source = ["src", "*/site-packages"]
+source = [
+    "src",
+    "*/site-packages",
+]
 
 [tool.coverage.run]
 branch = true
-source = ["revseq"]
+source = [
+    "revseq",
+]
 
 [tool.coverage.report]
 show_missing = true
 fail_under = 100
 
-[tool.rye]
-managed = true
-dev-dependencies = [
-    "codecov>=2.1.13",
-    "hypothesis>=6.99.13",
-    "nox>=2024.3.2",
-    "pytest>=8.1.1",
-    "mypy>=1.9.0",
-    "coverage>=7.4.4",
-    "pytest-cov>=4.1.0",
-    "ruff>=0.3.4",
-]
-
-[tool.rye.scripts]
-lint = { chain = ["lint:ruff", "lint:black"] }
-"lint:black" = "black --check src"
-"lint:ruff" = "ruff --fix src"
+[tool.pdm.scripts]
+format = "ruff format src/"
+lint = "ruff check --fix src/"
+test = "nox"
 
-[tool.hatch.metadata]
-allow-direct-references = true
+[tool.pdm.scripts.all]
+composite = [
+    "format",
+    "lint",
+    "test",
+]
 
-[tool.mypy]
-strict = true
-warn_unreachable = true
-pretty = true
-show_column_numbers = true
-show_error_codes = true
-show_error_context = true
+[tool.pdm.dev-dependencies]
+dev = [
+    "nox>=2024.4.15",
+    "pytest>=8.3.2",
+    "mypy>=1.11.0",
+    "ruff>=0.5.5",
+    "pytest-cov>=5.0.0",
+    "coverage>=7.6.0",
+    "hypothesis>=6.108.4",
+    "codecov>=2.1.13",
+    "pre-commit>=3.7.1",
+    "safety>=3.2.4",
+    "pytest-random-order>=1.1.1",
+    "pytest-xdist[psutil]>=3.6.1",
+]
 
-[tool.hatch.build.targets.wheel]
-packages = ["src/revseq"]
+[tool.pytest.ini_options]
+pythonpath = "."
+addopts = [
+    "--import-mode=importlib",
+]
+typeguard-packages = "revseq"

{revseq-1.0.0 → revseq-1.2.0}/src/revseq/__main__.py

@@ -25,21 +25,12 @@ app = typer.Typer(
 @app.command(no_args_is_help=True)
 @require(
     lambda seq: len(set(seq) - set("AGCTagct")) == 0,
-    error=lambda seq: ValueError("{} has non-standard DNA bases."),
+    error=lambda seq: ValueError("{} has non-standard DNA bases."),  # noqa: ARG005
 )
 def main(
-    seq: Annotated[
-        str,
-        typer.Argument()
-    ],
-    rev: Annotated[
-        bool,
-        typer.Option("-r", "--reverse", help="reverse sequence")
-    ] = True,
-    comp: Annotated[
-        bool,
-        typer.Option("-c", "--complement", help="complement sequence")
-    ] = True,
+    seq: Annotated[str, typer.Argument()],
+    rev: Annotated[bool, typer.Option("-r", "--reverse", help="reverse sequence")] = True,
+    comp: Annotated[bool, typer.Option("-c", "--complement", help="complement sequence")] = True,
     version: Annotated[
         Optional[bool],
         typer.Option(
@@ -48,16 +39,15 @@ def main(
             callback=version_callback,
             is_eager=True,
             help="Prints the version.",
-        )
+        ),
     ] = None,
 ) -> None:
-
     print(revseq(seq, rev, comp))
 
 
 @require(
     lambda seq: len(seq) != 0,
-    error=lambda seq: ValueError("Nothing to do with an empty sequence"),
+    error=lambda seq: ValueError("Nothing to do with an empty sequence"),  # noqa: ARG005
 )
 @typechecked
 def revseq(

{revseq-1.0.0 → revseq-1.2.0}/tests/test_revseq.py

@@ -1,7 +1,6 @@
 import hypothesis.strategies as st
 import pytest
 from hypothesis import example, given, settings
-
 from revseq import revseq
 
 

revseq-1.0.0/.gitattributes

@@ -1 +0,0 @@
-* text=auto eol=lf

revseq-1.0.0/.github/workflows/python-package.yml

@@ -1,47 +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
-# modeled after https://github.com/python-poetry/poetry/blob/master/.github/workflows/release.yml
-name: Python package
-
-on:
-  push:
-    branches: [ "main" ]
-  pull_request:
-    branches: [ "main" ]
-
-jobs:
-  build:
-    runs-on: ubuntu-latest
-    strategy:
-      fail-fast: false
-      matrix:
-        python-version: ["3.8", "3.9", "3.10"]
-    steps:
-    - name: checkout code
-      uses: actions/checkout@v3
-    
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v3
-      with:
-        python-version: ${{ matrix.python-version }}
-    
-    - name: Install Poetry
-      uses: abatilo/actions-poetry@v2.1.6
-    
-    - name: Install dependencies
-      run: |
-       poetry config virtualenvs.create false
-       poetry install
-    
-    - name: Run tests and collect coverage
-      run: pytest --cov --cov-report=xml --cov-fail-under=50
-    
-    - name: Upload coverage reports to Codecov with GitHub Action
-      uses: codecov/codecov-action@v3
-      with:
-        token: ${{ secrets.CODECOV_TOKEN }} # not required for public repos
-        files: ./coverage.xml
-        flags: unittests # optional
-        name: codecov-umbrella # optional
-        fail_ci_if_error: true # optional (default = false)
-        verbose: true # optional (default = false)

revseq-1.0.0/.gitignore

@@ -1,139 +0,0 @@
-# Byte-compiled / optimized / DLL files
-__pycache__/
-*.py[cod]
-*$py.class
-
-# C extensions*.so
-
-# Distribution / packaging
-.Python
-build/
-develop-eggs/
-dist/
-downloads/
-eggs/
-.eggs/
-lib/
-lib64/
-parts/
-sdist/
-var/
-wheels/
-share/python-wheels/
-*.egg-info/
-.installed.cfg
-*.egg
-MANIFEST
-
-# PyInstaller
-#  Usually these files are written by a python script from a template
-#  before PyInstaller builds the exe, so as to inject date/other infos into it.
-*.manifest
-*.spec
-
-# Installer logs
-pip-log.txt
-pip-delete-this-directory.txt
-
-# Unit test / coverage reports
-htmlcov/
-.tox/
-.nox/
-.coverage
-.coverage.*
-.cache
-nosetests.xml
-coverage.xml
-*.cover
-*.py,cover
-.hypothesis/
-.pytest_cache/
-cover/
-
-# Translations
-*.mo
-*.pot
-
-# Django stuff:
-*.log
-local_settings.py
-db.sqlite3
-db.sqlite3-journal
-
-# Flask stuff:
-instance/
-.webassets-cache
-
-# Scrapy stuff:
-.scrapy
-
-# Sphinx documentation
-docs/_build/
-
-# PyBuilder
-.pybuilder/
-target/
-
-# Jupyter Notebook
-.ipynb_checkpoints
-
-# IPython
-profile_default/
-ipython_config.py
-
-# pyenv
-#   For a library or package, you might want to ignore these files since the code is
-#   intended to run in multiple environments; otherwise, check them in:
-# .python-version
-
-# pipenv
-#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
-#   However, in case of collaboration, if having platform-specific dependencies or dependencies
-#   having no cross-platform support, pipenv may install dependencies that don't work, or not
-#   install all needed dependencies.
-#Pipfile.lock
-
-# PEP 582; used by e.g. github.com/David-OConnor/pyflow
-__pypackages__/
-
-# Celery stuff
-celerybeat-schedule
-celerybeat.pid
-
-# SageMath parsed files
-*.sage.py
-
-# Environments
-.env
-.venv
-env/
-venv/
-ENV/
-env.bak/
-venv.bak/
-
-# Spyder project settings
-.spyderproject
-.spyproject
-
-# Rope project settings
-.ropeproject
-
-# mkdocs documentation
-/site
-
-# mypy
-.mypy_cache/
-.dmypy.json
-dmypy.json
-
-# Pyre type checker
-.pyre/
-
-# pytype static type analyzer
-.pytype/
-
-# Cython debug symbols
-cython_debug/
-
-debug.py

revseq-1.0.0/.pre-commit-config.yml

@@ -1,51 +0,0 @@
-repos:
-  - repo: local
-    hooks:
-      # - id: black
-      #   name: black
-      #   entry: black
-      #   language: system
-      #   types: [python]
-      #   require_serial: true
-      - id: check-added-large-files
-        name: Check for added large files
-        entry: check-added-large-files
-        language: system
-      - id: check-toml
-        name: Check Toml
-        entry: check-toml
-        language: system
-        types: [toml]
-      - id: check-yaml
-        name: Check Yaml
-        entry: check-yaml
-        language: system
-        types: [yaml]
-      # - id: end-of-file-fixer
-      #   name: Fix End of Files
-      #   entry: end-of-file-fixer
-      #   language: system
-      #   types: [text]
-      #   stages: [commit, push, manual]
-      - id: flake8
-        name: flake8
-        entry: flake8
-        language: system
-        types: [python]
-        require_serial: true
-      # - id: reorder-python-imports
-      #   name: Reorder python imports
-      #   entry: reorder-python-imports
-      #   language: system
-      #   types: [python]
-      #   args: [--application-directories=src]
-      - id: trailing-whitespace
-        name: Trim Trailing Whitespace
-        entry: trailing-whitespace-fixer
-        language: system
-        types: [text]
-        stages: [commit, push, manual]
-  # - repo: https://github.com/pre-commit/mirrors-prettier
-  #   rev: v2.4.1
-  #   hooks:
-  #     - id: prettier

revseq-1.0.0/.vscode/launch.json

@@ -1,20 +0,0 @@
-{
-    // Use IntelliSense to learn about possible attributes.
-    // Hover to view descriptions of existing attributes.
-    // For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
-    "version": "0.2.0",
-    "configurations": [
-      {
-        "name": "this file",
-        "type": "python",
-        "request": "launch",
-        "module": "pyplier.${fileBasenameNoExtension}",
-        // "cwd": "${workspaceFolder}",
-        // "console": "integratedTerminal",
-        "justMyCode": true,
-        "envFile": "${workspaceFolder}/.env",
-        "env": {"PYDEVD_WARN_SLOW_RESOLVE_TIMEOUT": "2"}
-      }
-    ]
-  }
-  

revseq-1.0.0/.vscode/settings.json

@@ -1,3 +0,0 @@
-{
-    "esbonio.sphinx.confDir": ""
-}

revseq-1.0.0/.zprofile

@@ -1 +0,0 @@
-source '/home/milo/.rye/env'

revseq-1.0.0/CODE_OF_CONDUCT.rst

@@ -1,105 +0,0 @@
-Contributor Covenant Code of Conduct
-====================================
-
-Our Pledge
-----------
-
-We as members, contributors, and leaders pledge to make participation in our community a harassment-free experience for everyone, regardless of age, body size, visible or invisible disability, ethnicity, sex characteristics, gender identity and expression, level of experience, education, socio-economic status, nationality, personal appearance, race, religion, or sexual identity and orientation.
-
-We pledge to act and interact in ways that contribute to an open, welcoming, diverse, inclusive, and healthy community.
-
-
-Our Standards
--------------
-
-Examples of behavior that contributes to a positive environment for our community include:
-
-- Demonstrating empathy and kindness toward other people
-- Being respectful of differing opinions, viewpoints, and experiences
-- Giving and gracefully accepting constructive feedback
-- Accepting responsibility and apologizing to those affected by our mistakes, and learning from the experience
-- Focusing on what is best not just for us as individuals, but for the overall community
-
-Examples of unacceptable behavior include:
-
-- The use of sexualized language or imagery, and sexual attention or
-  advances of any kind
-- Trolling, insulting or derogatory comments, and personal or political attacks
-- Public or private harassment
-- Publishing others' private information, such as a physical or email
-  address, without their explicit permission
-- Other conduct which could reasonably be considered inappropriate in a
-  professional setting
-
-Enforcement Responsibilities
-----------------------------
-
-Community leaders are responsible for clarifying and enforcing our standards of acceptable behavior and will take appropriate and fair corrective action in response to any behavior that they deem inappropriate, threatening, offensive, or harmful.
-
-Community leaders have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct, and will communicate reasons for moderation decisions when appropriate.
-
-
-Scope
------
-
-This Code of Conduct applies within all community spaces, and also applies when an individual is officially representing the community in public spaces. Examples of representing our community include using an official e-mail address, posting via an official social media account, or acting as an appointed representative at an online or offline event.
-
-
-Enforcement
------------
-
-Instances of abusive, harassing, or otherwise unacceptable behavior may be reported to the community leaders responsible for enforcement at mileschristiansmith@gmail.com. All complaints will be reviewed and investigated promptly and fairly.
-
-All community leaders are obligated to respect the privacy and security of the reporter of any incident.
-
-
-Enforcement Guidelines
-----------------------
-
-Community leaders will follow these Community Impact Guidelines in determining the consequences for any action they deem in violation of this Code of Conduct:
-
-
-1. Correction
-~~~~~~~~~~~~~
-
-**Community Impact**: Use of inappropriate language or other behavior deemed unprofessional or unwelcome in the community.
-
-**Consequence**: A private, written warning from community leaders, providing clarity around the nature of the violation and an explanation of why the behavior was inappropriate. A public apology may be requested.
-
-
-2. Warning
-~~~~~~~~~~
-
-**Community Impact**: A violation through a single incident or series of actions.
-
-**Consequence**: A warning with consequences for continued behavior. No interaction with the people involved, including unsolicited interaction with those enforcing the Code of Conduct, for a specified period of time. This includes avoiding interactions in community spaces as well as external channels like social media. Violating these terms may lead to a temporary or permanent ban.
-
-
-3. Temporary Ban
-~~~~~~~~~~~~~~~~
-
-**Community Impact**: A serious violation of community standards, including sustained inappropriate behavior.
-
-**Consequence**: A temporary ban from any sort of interaction or public communication with the community for a specified period of time. No public or private interaction with the people involved, including unsolicited interaction with those enforcing the Code of Conduct, is allowed during this period. Violating these terms may lead to a permanent ban.
-
-
-4. Permanent Ban
-~~~~~~~~~~~~~~~~
-
-**Community Impact**: Demonstrating a pattern of violation of community standards, including sustained inappropriate behavior, harassment of an individual, or aggression toward or disparagement of classes of individuals.
-
-**Consequence**: A permanent ban from any sort of public interaction within the community.
-
-
-Attribution
------------
-
-This Code of Conduct is adapted from the `Contributor Covenant <homepage_>`__, version 2.0,
-available at https://www.contributor-covenant.org/version/2/0/code_of_conduct.html.
-
-Community Impact Guidelines were inspired by `Mozilla’s code of conduct enforcement ladder <https://github.com/mozilla/diversity>`__.
-
-.. _homepage: https://www.contributor-covenant.org
-
-For answers to common questions about this code of conduct, see the FAQ at
-https://www.contributor-covenant.org/faq. Translations are available at https://www.contributor-covenant.org/translations.

revseq-1.0.0/CONTRIBUTING.rst

@@ -1,123 +0,0 @@
-Contributor Guide
-=================
-
-Thank you for your interest in improving this project.
-This project is open-source under the `GPL 3.0 license`_ and
-welcomes contributions in the form of bug reports, feature requests, and pull requests.
-
-Here is a list of important resources for contributors:
-
-- `Source Code`_
-- `Documentation`_
-- `Issue Tracker`_
-- `Code of Conduct`_
-
-.. _GPL 3.0 license: https://opensource.org/licenses/GPL-3.0
-.. _Source Code: https://github.com/mcsmith/revseq
-.. _Documentation: https://revseq.readthedocs.io/
-.. _Issue Tracker: https://github.com/mcsmith/revseq/issues
-
-How to report a bug
--------------------
-
-Report bugs on the `Issue Tracker`_.
-
-When filing an issue, make sure to answer these questions:
-
-- Which operating system and Python version are you using?
-- Which version of this project are you using?
-- What did you do?
-- What did you expect to see?
-- What did you see instead?
-
-The best way to get your bug fixed is to provide a test case,
-and/or steps to reproduce the issue.
-
-
-How to request a feature
-------------------------
-
-Request features on the `Issue Tracker`_.
-
-
-How to set up your development environment
-------------------------------------------
-
-You need Python 3.7+ and the following tools:
-
-- Poetry_
-- Nox_
-- nox-poetry_
-
-Install the package with development requirements:
-
-.. code:: console
-
-   $ poetry install
-
-You can now run an interactive Python session,
-or the command-line interface:
-
-.. code:: console
-
-   $ poetry run python
-   $ poetry run revseq
-
-.. _Poetry: https://python-poetry.org/
-.. _Nox: https://nox.thea.codes/
-.. _nox-poetry: https://nox-poetry.readthedocs.io/
-
-
-How to test the project
------------------------
-
-Run the full test suite:
-
-.. code:: console
-
-   $ nox
-
-List the available Nox sessions:
-
-.. code:: console
-
-   $ nox --list-sessions
-
-You can also run a specific Nox session.
-For example, invoke the unit test suite like this:
-
-.. code:: console
-
-   $ nox --session=tests
-
-Unit tests are located in the ``tests`` directory,
-and are written using the pytest_ testing framework.
-
-.. _pytest: https://pytest.readthedocs.io/
-
-
-How to submit changes
----------------------
-
-Open a `pull request`_ to submit changes to this project.
-
-Your pull request needs to meet the following guidelines for acceptance:
-
-- The Nox test suite must pass without errors and warnings.
-- Include unit tests. This project maintains 100% code coverage.
-- If your changes add functionality, update the documentation accordingly.
-
-Feel free to submit early, though—we can always iterate on this.
-
-To run linting and code formatting checks before committing your change, you can install pre-commit as a Git hook by running the following command:
-
-.. code:: console
-
-   $ nox --session=pre-commit -- install
-
-It is recommended to open an issue before starting work on anything.
-This will allow a chance to talk it over with the owners and validate your approach.
-
-.. _pull request: https://github.com/mcsmith/revseq/pulls
-.. github-only
-.. _Code of Conduct: CODE_OF_CONDUCT.rst

revseq-1.0.0/codecov.yml

@@ -1,9 +0,0 @@
-comment: false
-coverage:
-  status:
-    project:
-      default:
-        target: "80"
-    patch:
-      default:
-        target: "80"

revseq-1.0.0/noxfile.py

@@ -1,221 +0,0 @@
-"""Nox sessions."""
-import shutil
-import sys
-from pathlib import Path
-from textwrap import dedent
-
-import nox
-
-try:
-    from nox_poetry import Session, session
-except ImportError:
-    message = f"""\
-    Nox failed to import the 'nox-poetry' package.
-
-    Please install it using the following command:
-
-    {sys.executable} -m pip install nox-poetry"""
-    raise SystemExit(dedent(message)) from None
-
-
-package = "revseq"
-python_versions = ["3.10", "3.9", "3.8"]
-nox.needs_version = ">= 2021.6.6"
-nox.options.sessions = (
-    "pre-commit",
-    "safety",
-    "mypy",
-    "tests",
-    "typeguard",
-    "xdoctest",
-    "docs-build",
-)
-
-locations = (
-    "src",
-    "tests",
-)
-
-
-@session(python=["3.10"])
-def isort(session: Session) -> None:
-    """Run black code formatter."""
-    args = session.posargs or locations
-    session.install("isort")
-    session.run("isort", *args)
-
-
-@session(python=["3.10"])
-def black(session: Session) -> None:
-    """Run black code formatter."""
-    args = session.posargs or locations
-    session.install("black[jupyter]")
-    session.run("black", *args)
-
-
-def activate_virtualenv_in_precommit_hooks(session: Session) -> None:
-    """Activate virtualenv in hooks installed by pre-commit.
-
-    This function patches git hooks installed by pre-commit to activate the
-    session's virtual environment. This allows pre-commit to locate hooks in
-    that environment when invoked from git.
-
-    Args:
-        session: The Session object.
-    """
-    assert session.bin is not None  # noqa: S101
-
-    virtualenv = session.env.get("VIRTUAL_ENV")
-    if virtualenv is None:
-        return
-
-    hookdir = Path(".git") / "hooks"
-    if not hookdir.is_dir():
-        return
-
-    for hook in hookdir.iterdir():
-        if hook.name.endswith(".sample") or not hook.is_file():
-            continue
-
-        text = hook.read_text()
-        bindir = repr(session.bin)[1:-1]  # strip quotes
-        if not (
-            Path("A") == Path("a") and bindir.lower() in text.lower() or bindir in text
-        ):
-            continue
-
-        lines = text.splitlines()
-        if not (lines[0].startswith("#!") and "python" in lines[0].lower()):
-            continue
-
-        header = dedent(
-            f"""\
-            import os
-            os.environ["VIRTUAL_ENV"] = {virtualenv!r}
-            os.environ["PATH"] = os.pathsep.join((
-                {session.bin!r},
-                os.environ.get("PATH", ""),
-            ))
-            """
-        )
-
-        lines.insert(1, header)
-        hook.write_text("\n".join(lines))
-
-
-@session(name="pre-commit", python="3.10")
-def precommit(session: Session) -> None:
-    """Lint using pre-commit."""
-    args = session.posargs or ["run", "--all-files", "--show-diff-on-failure"]
-    session.install(
-        "darglint",
-        "flake8",
-        "flake8-bandit",
-        "flake8-bugbear",
-        "flake8-docstrings",
-        "flake8-rst-docstrings",
-        "pep8-naming",
-        "pre-commit",
-        "pre-commit-hooks",
-        "reorder-python-imports",
-    )
-    session.run("pre-commit", *args)
-    if args and args[0] == "install":
-        activate_virtualenv_in_precommit_hooks(session)
-
-
-@session(python="3.9")
-def safety(session: Session) -> None:
-    """Scan dependencies for insecure packages."""
-    requirements = session.poetry.export_requirements()
-    session.install("safety")
-    session.run("safety", "check", "--full-report", f"--file={requirements}")
-
-
-@session(python=python_versions)
-def mypy(session: Session) -> None:
-    """Type-check using mypy."""
-    args = session.posargs or locations
-    session.install(".")
-    session.install("mypy", "pytest")
-    session.run("mypy", "--install-types", "--non-interactive", "out", *args)
-    if not session.posargs:
-        session.run(
-            "mypy",
-            "--install-types",
-            "--non-interactive",
-            f"--python-executable={sys.executable}",
-            "noxfile.py",
-        )
-
-
-@session(python=python_versions)
-def tests(session: Session) -> None:
-    """Run the test suite."""
-    session.install(".")
-    session.install("coverage[toml]", "pytest", "pygments", "hypothesis")
-    try:
-        session.run("coverage", "run", "--parallel", "-m", "pytest", *session.posargs)
-    finally:
-        if session.interactive:
-            session.notify("coverage", posargs=[])
-
-
-@session
-def coverage(session: Session) -> None:
-    """Produce the coverage report."""
-    # args = session.posargs or ["report"]
-
-    session.install("coverage[toml]", "codecov")
-
-    if not session.posargs and any(Path().glob(".coverage.*")):
-        session.run("coverage", "combine")
-
-    session.run("coverage", "xml", "--fail-under=0")
-    session.run("codecov", *session.posargs)
-    # session.run("coverage", *args)
-
-
-@session(python=python_versions)
-def typeguard(session: Session) -> None:
-    """Runtime type checking using Typeguard."""
-    session.install(".")
-    session.install("pytest", "typeguard", "pygments", "hypothesis")
-    session.run("pytest", f"--typeguard-packages={package}", *session.posargs)
-
-
-# @session(python=python_versions)
-# def xdoctest(session: Session) -> None:
-#     """Run examples with xdoctest."""
-#     args = session.posargs or ["all"]
-#     session.install(".")
-#     session.install("xdoctest[colors]")
-#     session.run("python", "-m", "xdoctest", package, *args)
-
-
-# @session(name="docs-build", python="3.10")
-# def docs_build(session: Session) -> None:
-#     """Build the documentation."""
-#     args = session.posargs or ["docs", "docs/_build"]
-#     session.install(".")
-#     session.install("sphinx", "sphinx-click", "sphinx-rtd-theme")
-
-#     build_dir = Path("docs", "_build")
-#     if build_dir.exists():
-#         shutil.rmtree(build_dir)
-
-#     session.run("sphinx-build", *args)
-
-
-# @session(python="3.10")
-# def docs(session: Session) -> None:
-#     """Build and serve the documentation with live reloading on file changes."""
-#     args = session.posargs or ["--open-browser", "docs", "docs/_build"]
-#     session.install(".")
-#     session.install("sphinx", "sphinx-autobuild", "sphinx-click", "sphinx-rtd-theme")
-
-#     build_dir = Path("docs", "_build")
-#     if build_dir.exists():
-#         shutil.rmtree(build_dir)
-
-#     session.run("sphinx-autobuild", *args)

revseq-1.0.0/requirements-dev.lock

@@ -1,88 +0,0 @@
-# generated by rye
-# use `rye lock` or `rye sync` to update this lockfile
-#
-# last locked with the following flags:
-#   pre: false
-#   features: []
-#   all-features: false
-#   with-sources: false
-
--e file:.
-argcomplete==3.1.1
-    # via nox
-asttokens==2.2.1
-    # via icontract
-attrs==23.1.0
-    # via hypothesis
-certifi==2023.5.7
-    # via requests
-charset-normalizer==3.2.0
-    # via requests
-click==8.1.6
-    # via typer
-codecov==2.1.13
-colorlog==6.7.0
-    # via nox
-coverage==7.4.4
-    # via codecov
-    # via pytest-cov
-distlib==0.3.7
-    # via virtualenv
-exceptiongroup==1.2.0
-    # via hypothesis
-    # via pytest
-filelock==3.12.2
-    # via virtualenv
-hypothesis==6.99.13
-icontract==2.6.6
-    # via revseq
-idna==3.4
-    # via requests
-iniconfig==2.0.0
-    # via pytest
-markdown-it-py==3.0.0
-    # via rich
-mdurl==0.1.2
-    # via markdown-it-py
-mypy==1.9.0
-mypy-extensions==1.0.0
-    # via mypy
-nox==2024.3.2
-packaging==23.1
-    # via nox
-    # via pytest
-platformdirs==3.9.1
-    # via virtualenv
-pluggy==1.4.0
-    # via pytest
-pygments==2.15.1
-    # via rich
-pytest==8.1.1
-    # via pytest-cov
-pytest-cov==4.1.0
-requests==2.31.0
-    # via codecov
-rich==13.7.1
-    # via revseq
-ruff==0.3.4
-six==1.16.0
-    # via asttokens
-sortedcontainers==2.4.0
-    # via hypothesis
-tomli==2.0.1
-    # via coverage
-    # via mypy
-    # via pytest
-typeguard==4.2.1
-    # via revseq
-typer==0.11.0
-    # via revseq
-typing-extensions==4.10.0
-    # via icontract
-    # via mypy
-    # via typeguard
-    # via typer
-urllib3==2.0.4
-    # via requests
-virtualenv==20.24.0
-    # via nox

revseq-1.0.0/requirements.lock

@@ -1,34 +0,0 @@
-# generated by rye
-# use `rye lock` or `rye sync` to update this lockfile
-#
-# last locked with the following flags:
-#   pre: false
-#   features: []
-#   all-features: false
-#   with-sources: false
-
--e file:.
-asttokens==2.2.1
-    # via icontract
-click==8.1.6
-    # via typer
-icontract==2.6.6
-    # via revseq
-markdown-it-py==3.0.0
-    # via rich
-mdurl==0.1.2
-    # via markdown-it-py
-pygments==2.15.1
-    # via rich
-rich==13.7.1
-    # via revseq
-six==1.16.0
-    # via asttokens
-typeguard==4.2.1
-    # via revseq
-typer==0.11.0
-    # via revseq
-typing-extensions==4.10.0
-    # via icontract
-    # via typeguard
-    # via typer

revseq-1.0.0/ruff.toml

@@ -1,92 +0,0 @@
-line-length = 120
-target-version = "py310"
-
-[lint]
-select = [
-    "A",
-    "ARG",
-    "B",
-    "C",
-    "DTZ",
-    "E",
-    "EM",
-    "F",
-    "FBT",
-    "I",
-    "I001",
-    "ICN",
-    "ISC",
-    "N",
-    "PLC",
-    "PLE",
-    "PLR",
-    "PLW",
-    "Q",
-    "RUF",
-    "S",
-    "T",
-    "TID",
-    "UP",
-    "W",
-    "YTT",
-]
-ignore = [
-    "B027",
-    "C901",
-    "D100",
-    "D103",
-    "D205",
-    "D212",
-    "D415",
-    "E203",
-    "E501",
-    "FBT001",
-    "FBT002",
-    "FBT003",
-    "N802",
-    "N803",
-    "PLR0911",
-    "PLR0912",
-    "PLR0913",
-    "PLR0915",
-    "S105",
-    "S106",
-    "S107",
-    "ARG001",
-    "UP007",
-]
-unfixable = [
-    "F401",
-    "UP007",
-]
-exclude = [
-    ".git",
-    ".hg",
-    "__pycache__",
-    "_bin/*",
-    "_build/*",
-    "_ig_fbcode_wheel/*",
-    "buck-out/*",
-    "third-party-buck/*",
-    "third-party2/*",
-    "dist",
-    ".venv",
-    ".nox",
-    ".mypy_cache",
-    ".pytype",
-    ".svn",
-    "__pypackages__",
-]
-
-[format]
-# Like Black, use double quotes for strings.
-quote-style = "double"
-
-# Like Black, indent with spaces, rather than tabs.
-indent-style = "space"
-
-# Like Black, respect magic trailing commas.
-skip-magic-trailing-comma = false
-
-# Like Black, automatically detect the appropriate line ending.
-line-ending = "auto"