revseq 1.0.0__tar.gz → 1.3.1__tar.gz

{revseq-1.0.0 → revseq-1.3.1}/PKG-INFO

@@ -1,26 +1,26 @@
 Metadata-Version: 2.3
 Name: revseq
-Version: 1.0.0
+Version: 1.3.1
 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: Miles Smith
 Author-email: Miles Smith <mileschristiansmith@gmail.com>
-License-Expression: GPL-3.0
-License-File: LICENSE
+License: GPL-3.0-or-later
+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
+Requires-Dist: typer>=0.29.0
+Requires-Dist: icontract>=2.7.3
+Requires-Dist: rich>=15.0.0
+Requires-Dist: typeguard>=4.6.0
 Requires-Python: >=3.10
-Requires-Dist: icontract>=2.6.6
-Requires-Dist: rich>=13.7.1
-Requires-Dist: typeguard>=4.2.1
-Requires-Dist: typer>=0.11.0
+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
 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-1.3.1}/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-1.3.1/pyproject.toml

@@ -0,0 +1,75 @@
+[build-system]
+requires = ["uv_build>=0.7.0,<0.14.0"]
+build-backend = "uv_build"
+
+[project]
+name = "revseq"
+version = "1.3.1"
+description = "reverse and/or complement dna sequence"
+readme = "README.rst"
+requires-python = ">= 3.10"
+dependencies = [
+    "typer>=0.29.0",
+    "icontract>=2.7.3",
+    "rich>=15.0.0",
+    "typeguard>=4.6.0",
+]
+classifiers = [
+    "Programming Language :: Python :: Implementation :: CPython",
+    "Programming Language :: Python :: Implementation :: PyPy",
+    "Development Status :: 5 - Production/Stable",
+    "Environment :: Console",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+    "Typing :: Typed",
+]
+
+[[project.authors]]
+name = "Miles Smith"
+email = "mileschristiansmith@gmail.com"
+
+[project.license]
+text = "GPL-3.0-or-later"
+
+[project.urls]
+homepage = "https://github.com/milescsmith/revseq"
+repository = "https://github.com/milescsmith/revseq"
+changelog = "https://github.com/milescsmith/revseq/releases"
+
+[project.scripts]
+revseq = "revseq.__main__:app"
+
+[tool.coverage.paths]
+source = [
+    "src",
+    "*/site-packages",
+]
+
+[tool.coverage.run]
+branch = true
+source = ["revseq"]
+
+[tool.coverage.report]
+show_missing = true
+fail_under = 100
+
+[tool.mypy]
+strict = true
+warn_unreachable = true
+pretty = true
+show_column_numbers = true
+show_error_codes = true
+show_error_context = true
+
+[dependency-groups]
+dev = [
+    "codecov>=2.1.13",
+    "coverage>=7.16.2",
+    "hypothesis>=6.168.5",
+    "nox>=2026.10.20",
+    "pytest>=9.2.0",
+    "pytest-cov>=7.1.0",
+    "ruff>=0.17.4",
+    "ty>=0.0.100",
+]

revseq-1.0.0/pyproject.toml → revseq-1.3.1/pyproject.toml.orig

@@ -1,22 +1,22 @@
 [build-system]
-requires = ["hatchling"]
-build-backend = "hatchling.build"
+requires = ["uv_build>=0.7.0,<0.14.0"]
+build-backend = "uv_build"
 
 [project]
 name = "revseq"
-version = "1.0.0"
+version = "1.3.1"
 description = "reverse and/or complement dna sequence"
 authors = [
     { name = "Miles Smith", email = "mileschristiansmith@gmail.com" }
 ]
-license = "GPL-3.0"
 readme = "README.rst"
 requires-python = ">= 3.10"
+license = { text = "GPL-3.0-or-later" }
 dependencies = [
-    "typer>=0.11.0",
-    "icontract>=2.6.6",
-    "rich>=13.7.1",
-    "typeguard>=4.2.1",
+    "typer>=0.29.0",
+    "icontract>=2.7.3",
+    "rich>=15.0.0",
+    "typeguard>=4.6.0",
 ]
 classifiers = [
     "Programming Language :: Python :: Implementation :: CPython",
@@ -48,27 +48,6 @@ source = ["revseq"]
 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.hatch.metadata]
-allow-direct-references = true
-
 [tool.mypy]
 strict = true
 warn_unreachable = true
@@ -77,5 +56,15 @@ show_column_numbers = true
 show_error_codes = true
 show_error_context = true
 
-[tool.hatch.build.targets.wheel]
-packages = ["src/revseq"]
+[dependency-groups]
+dev = [
+    "codecov>=2.1.13",
+    "coverage>=7.16.2",
+    "hypothesis>=6.168.5",
+    "nox>=2026.10.20",
+    "pytest>=9.2.0",
+    "pytest-cov>=7.1.0",
+    "ruff>=0.17.4",
+    "ty>=0.0.100",
+]
+

revseq-1.3.1/src/revseq/__main__.py

@@ -0,0 +1,168 @@
+from collections import deque
+from importlib.metadata import version
+from typing import Annotated
+
+import typer
+from icontract import require
+from rich import print as rprint
+from typeguard import typechecked
+
+
+def version_callback(value: bool) -> None:
+    """Prints the version of the package."""
+    if value:
+        rprint(f"[red]'revseq'[/red] version: {version('revseq')}")
+        raise typer.Exit()
+
+
+app = typer.Typer(
+    name="revseq", help="Generate reversed, reverse complement, and complement sequences", no_args_is_help=True
+)
+
+
+@app.callback(invoke_without_command=True)
+@app.command(no_args_is_help=True)
+@require(
+    lambda seq: len(set(seq) - set("AGCTagctUuWwSsMmKkRrYyBbDdHhVvNn")) == 0,
+    error=lambda seq: ValueError(f"{seq} has non-standard DNA bases."),
+)
+def main(
+    seq: Annotated[str, typer.Argument()],
+    rev: Annotated[bool, typer.Option("-r", "--reverse", help="reverse sequence")] = False,
+    comp: Annotated[bool, typer.Option("-c", "--complement", help="complement sequence")] = False,
+    colorize: Annotated[bool, typer.Option("-l", "--colorize", help="add color to the sequence")] = False,
+    version: Annotated[
+        bool | None,
+        typer.Option(
+            "-v",
+            "--version",
+            callback=version_callback,
+            is_eager=True,
+            help="Prints the version.",
+        ),
+    ] = None,
+) -> None:
+
+    rprint(revseq(seq, rev, comp, colorize))
+
+
+@require(
+    lambda seq: len(seq) != 0,
+    error=lambda _: ValueError("Nothing to do with an empty sequence"),
+)
+@typechecked
+def revseq(
+    seq: str,
+    rev: bool = False,
+    comp: bool = False,
+    colorize: bool = False,
+) -> str:
+    """Generate a (reverse) (complement) of DNA sequence
+
+    Parameters
+    ----------
+    seq : str, required
+        sequence to manipulate
+    rev : bool, optional
+        return the reversed sequence
+    comp : bool, optional
+        return the complemented sequence
+    version : bool, optional
+        display version number
+
+    Returns
+    -------
+    str
+        the (reverse) (complement) sequence
+    """
+
+    seq_deque = deque(seq)
+
+    complement_dict = {
+        "A": "T",
+        "C": "G",
+        "G": "C",
+        "T": "A",
+        "a": "t",
+        "c": "g",
+        "g": "c",
+        "t": "a",
+        "U": "A",
+        "u": "a",
+        "W": "W",
+        "w": "w",
+        "S": "S",
+        "s": "s",
+        "M": "K",
+        "m": "k",
+        "K": "M",
+        "k": "m",
+        "R": "Y",
+        "r": "y",
+        "Y": "R",
+        "y": "r",
+        "B": "V",
+        "b": "v",
+        "D": "H",
+        "d": "h",
+        "H": "D",
+        "h": "d",
+        "V": "B",
+        "v": "b",
+        "N": "N",
+        "n": "n",
+    }
+
+    if rev:
+        seq_deque.reverse()
+
+    if comp:
+        seq_deque = deque([complement_dict[_] if _ in complement_dict else _ for _ in seq_deque])
+
+    if colorize:
+        seq_deque = add_color(seq_deque)
+
+    return "".join(seq_deque)
+
+
+def add_color(seq: deque[str]) -> deque[str]:
+    repl_dict = {
+        "A": r"[red]A[/]",
+        "a": r"[red]a[/]",
+        "C": r"[yellow1]C[/]",
+        "c": r"[yellow1]c[/]",
+        "G": r"[green3]G[/]",
+        "g": r"[green3]g[/]",
+        "T": r"[dodger_blue2]T[/]",
+        "t": r"[dodger_blue2]t[/]",
+        "U": r"[dark_khaki]U[/]",
+        "u": r"[dark_khaki]u[/]",
+        "W": r"[dark_cyan]W[/]",
+        "w": r"[dark_cyan]w[/]",
+        "S": r"[orange]S[/]",
+        "s": r"[orange]s[/]",
+        "M": r"[chartreuse1]M[/]",
+        "m": r"[chartreuse1]m[/]",
+        "K": r"[purple]K[/]",
+        "k": r"[purple]k[/]",
+        "R": r"[dark_red]R[/]",
+        "r": r"[dark_red]r[/]",
+        "Y": r"[dark_green]Y[/]",
+        "y": r"[dark_green]y[/]",
+        "B": r"[yellow4]B[/]",
+        "b": r"[yellow4]b[/]",
+        "D": r"[magenta]D[/]",
+        "d": r"[magenta]d[/]",
+        "H": r"[gold1]H[/]",
+        "h": r"[gold1]h[/]",
+        "V": r"[#b8860b]V[/]",
+        "v": r"[#b8860b]v[/]",
+        "N": r"[#2f4f4f]N[/]",
+        "n": r"[#2f4f4f]n[/]",
+    }
+
+    return deque([repl_dict[x] for x in seq])
+
+
+if __name__ == "__main__":
+    app()  # pragma: no cover

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'