tpixel 0.1.1.dev0__tar.gz

tpixel-0.1.1.dev0/.github/workflows/ci.yml

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+name: CI
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+jobs:
+  test:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        python-version: ["3.9", "3.13"]
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install package with dev dependencies
+        run: pip install ".[dev]"
+
+      - name: Run tests
+        run: pytest -v

tpixel-0.1.1.dev0/.github/workflows/publish.yml

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+name: Publish to PyPI
+
+on:
+  push:
+    tags:
+      - 'v*'
+  release:
+    types: [published]
+  workflow_dispatch:
+
+permissions:
+  contents: read
+  id-token: write  # Required for trusted publishing
+
+jobs:
+  build:
+    name: Build distribution
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Install build dependencies
+        run: python -m pip install --upgrade pip build
+
+      - name: Build sdist and wheel
+        run: python -m build
+
+      - name: Upload artifacts
+        uses: actions/upload-artifact@v4
+        with:
+          name: dist
+          path: dist/
+
+  publish-to-pypi:
+    name: Publish to PyPI
+    needs: [build]
+    runs-on: ubuntu-latest
+    if: always() && needs.build.result == 'success'
+    environment:
+      name: pypi
+      url: https://pypi.org/p/tpixel
+    permissions:
+      id-token: write
+
+    steps:
+      - name: Download artifacts
+        uses: actions/download-artifact@v4
+        with:
+          name: dist
+          path: dist/
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

tpixel-0.1.1.dev0/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[codz]
+*$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
+
+# UV
+#   Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#uv.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+#poetry.toml
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#   pdm recommends including project-wide configuration in pdm.toml, but excluding .pdm-python.
+#   https://pdm-project.org/en/latest/usage/project/#working-with-version-control
+#pdm.lock
+#pdm.toml
+.pdm-python
+.pdm-build/
+
+# pixi
+#   Similar to Pipfile.lock, it is generally recommended to include pixi.lock in version control.
+#pixi.lock
+#   Pixi creates a virtual environment in the .pixi directory, just like venv module creates one
+#   in the .venv directory. It is recommended not to include this directory in version control.
+.pixi
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.envrc
+.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/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+# Abstra
+# Abstra is an AI-powered process automation framework.
+# Ignore directories containing user credentials, local state, and settings.
+# Learn more at https://abstra.io/docs
+.abstra/
+
+# Visual Studio Code
+#  Visual Studio Code specific template is maintained in a separate VisualStudioCode.gitignore 
+#  that can be found at https://github.com/github/gitignore/blob/main/Global/VisualStudioCode.gitignore
+#  and can be added to the global gitignore or merged into this file. However, if you prefer, 
+#  you could uncomment the following to ignore the entire vscode folder
+# .vscode/
+
+# Ruff stuff:
+.ruff_cache/
+
+# PyPI configuration file
+.pypirc
+
+# Cursor
+#  Cursor is an AI-powered code editor. `.cursorignore` specifies files/directories to
+#  exclude from AI features like autocomplete and code analysis. Recommended for sensitive data
+#  refer to https://docs.cursor.com/context/ignore-files
+.cursorignore
+.cursorindexingignore
+
+# Marimo
+marimo/_static/
+marimo/_lsp/
+__marimo__/

tpixel-0.1.1.dev0/LICENSE

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+MIT License
+
+Copyright (c) 2026 IAVI-DEV
+
+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.

tpixel-0.1.1.dev0/PKG-INFO

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+Metadata-Version: 2.4
+Name: tpixel
+Version: 0.1.1.dev0
+Summary: Pixel-block alignment viewer for hundreds of sequences (Roark-style PIXEL plots)
+Author-email: Troy Sincomb <troysincomb@gmail.com>
+License: MIT
+Keywords: bioinformatics,alignment,pixel,visualization,FASTA,mutation
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Scientific/Engineering :: Visualization
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: matplotlib>=3.5
+Requires-Dist: click>=8.0
+Provides-Extra: dev
+Requires-Dist: pytest>=7.0; extra == "dev"
+Dynamic: license-file
+
+# tpixel
+
+Pixel-block alignment viewer for hundreds of sequences. Renders Roark-style PIXEL plots: grey=match, red=substitution, black=gap.
+
+## Install
+
+```bash
+pip install -e .
+```
+
+## Usage
+
+```bash
+# Protein alignment (AA mode)
+tpixel --fasta examples/env_protein_aligned.fasta -o examples/test_hiv_pixel.png
+
+# Nucleotide alignment (NT mode — auto-detected)
+tpixel --fasta examples/env_codon_aligned.fasta -o examples/test_hiv_nt_pixel.png
+```
+
+HIV mode is auto-detected when the alignment contains HxB2 and a `*_ref` sequence. Force with `--hiv` or `--no-hiv`. Nucleotide vs amino-acid mode is auto-detected from sequence content. Force with `--nt` or `--aa`.
+
+## Examples
+
+Both alignments contain the same 33 sequences (HxB2, animal1_ref, and 31 sample sequences from 7 animals):
+
+| Sequence | Type |
+|----------|------|
+| HxB2 | Coordinate reference |
+| animal1_ref | Parental lineage reference |
+| animal1_s1 .. s7 | animal1 samples (7) |
+| animal2_s1 .. s5 | animal2 samples (5) |
+| animal3_s1 .. s8 | animal3 samples (8) |
+| animal4_s1 | animal4 sample (1) |
+| animal5_s1 .. s5 | animal5 samples (5) |
+| animal6_s1 .. s2 | animal6 samples (2) |
+| animal7_s1 .. s3 | animal7 samples (3) |
+
+### Protein alignment (AA)
+
+`env_protein_aligned.fasta` — 887 columns of HIV-1 Env protein. Each AA = 1 pixel.
+
+![PIXEL plot — protein](examples/test_hiv_pixel.png)
+
+### Nucleotide alignment (NT)
+
+`env_codon_aligned.fasta` — 2661 columns of codon-aligned HIV-1 Env DNA. Each NT = 1 pixel. PNGS markers are detected by translating internally and mapped back to NT columns.
+
+![PIXEL plot — nucleotide](examples/test_hiv_nt_pixel.png)

tpixel-0.1.1.dev0/README.md

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+# tpixel
+
+Pixel-block alignment viewer for hundreds of sequences. Renders Roark-style PIXEL plots: grey=match, red=substitution, black=gap.
+
+## Install
+
+```bash
+pip install -e .
+```
+
+## Usage
+
+```bash
+# Protein alignment (AA mode)
+tpixel --fasta examples/env_protein_aligned.fasta -o examples/test_hiv_pixel.png
+
+# Nucleotide alignment (NT mode — auto-detected)
+tpixel --fasta examples/env_codon_aligned.fasta -o examples/test_hiv_nt_pixel.png
+```
+
+HIV mode is auto-detected when the alignment contains HxB2 and a `*_ref` sequence. Force with `--hiv` or `--no-hiv`. Nucleotide vs amino-acid mode is auto-detected from sequence content. Force with `--nt` or `--aa`.
+
+## Examples
+
+Both alignments contain the same 33 sequences (HxB2, animal1_ref, and 31 sample sequences from 7 animals):
+
+| Sequence | Type |
+|----------|------|
+| HxB2 | Coordinate reference |
+| animal1_ref | Parental lineage reference |
+| animal1_s1 .. s7 | animal1 samples (7) |
+| animal2_s1 .. s5 | animal2 samples (5) |
+| animal3_s1 .. s8 | animal3 samples (8) |
+| animal4_s1 | animal4 sample (1) |
+| animal5_s1 .. s5 | animal5 samples (5) |
+| animal6_s1 .. s2 | animal6 samples (2) |
+| animal7_s1 .. s3 | animal7 samples (3) |
+
+### Protein alignment (AA)
+
+`env_protein_aligned.fasta` — 887 columns of HIV-1 Env protein. Each AA = 1 pixel.
+
+![PIXEL plot — protein](examples/test_hiv_pixel.png)
+
+### Nucleotide alignment (NT)
+
+`env_codon_aligned.fasta` — 2661 columns of codon-aligned HIV-1 Env DNA. Each NT = 1 pixel. PNGS markers are detected by translating internally and mapped back to NT columns.
+
+![PIXEL plot — nucleotide](examples/test_hiv_nt_pixel.png)