Restructure as Python package with Docker/CI support

[dpark01]

Summary

• Convert standalone scripts to installable Python package with src/ layout
• Create single CLI entry point qprimer with 7 subcommands (generate, pick-representatives, prepare-input, evaluate, filter, build-output, select-multiplex)
• Reduce environment.yml from 165 to ~15 packages (top-level dependencies only)
• Move ML models to package data (src/qprimer_designer/data/)
• Add external tool wrappers (ViennaRNA, bowtie2, MAFFT) using PATH-based discovery
• Fix hardcoded paths in training/ to use environment variables
• Move Snakefiles to workflows/ directory and update to use new CLI syntax
• Delete 37MB ViennaRNA tarball (use bioconda viennarna package instead)
• Add Dockerfile with mambaorg/micromamba base for multi-arch builds (linux/amd64, linux/arm64)
• Add GitHub Actions workflows:
  • Tests: pytest with CodeCov coverage reporting
  • Docker Build: multi-arch builds with GHCR push, merge queue support
  • Snakemake Validation: syntax validation using --list-rules
• Add README badges for Tests, Docker Build, and CodeCov
• Add placeholder tests for sequences and params modules
• Add CLAUDE.md development guide and update README.md

Test plan

• Verify pip install . works in conda environment (CI tests pass)
• Run qprimer --help and qprimer generate --help to verify CLI (Docker build verifies this)
• Run pytest tests/ -v to verify tests pass (CI tests pass)
• Run docker build -t qprimer:test . to verify Docker build (CI build passes)
• Run snakemake -s workflows/Snakefile.example --dry-run to validate Snakefile syntax (CI)
• Verify GitHub Actions workflows pass (all CI actions pass)
• Verify CodeCov receives coverage reports (codecov/patch and codecov/project pass)

🤖 Generated with Claude Code

[Copilot]

Pull request overview

This PR restructures the repository into an installable Python package with modern packaging, Docker support, and CI/CD workflows. The main goal is to improve maintainability and deployment by transitioning from standalone scripts to a unified CLI with subcommands, reducing dependency bloat, and adding automated testing infrastructure.

Changes:

• Converted standalone scripts to installable package with qprimer CLI entry point and 7 subcommands
• Streamlined dependencies from ~165 to ~15 top-level packages in environment.yml
• Added Docker support with multi-arch builds and GitHub Actions workflows for tests, Docker builds, and Snakemake validation

Reviewed changes

Copilot reviewed 40 out of 45 changed files in this pull request and generated no comments.

Show a summary per file

File	Description
workflows/params.txt.template	New parameter template file for workflow configuration
workflows/Snakefile.template	Updated to use new qprimer CLI commands instead of direct script calls
workflows/Snakefile.example	Updated to use new qprimer CLI commands instead of direct script calls
training/adapt_pcr_external_tools.py	Refactored to use environment variables and PATH-based tool discovery
training/__init__.py	Updated matplotlib configuration to use environment variables for font paths
tests/test_sequences.py	Added tests for sequence utility functions
tests/test_params.py	Added tests for parameter parsing
tests/conftest.py	Added pytest fixtures for testing
tests/__init__.py	Added test suite initialization
src/qprimer_designer/utils/sequences.py	New sequence manipulation utilities module
src/qprimer_designer/utils/params.py	New parameter parsing utilities module
src/qprimer_designer/utils/encoding.py	New sequence encoding utilities for ML models
src/qprimer_designer/utils/__init__.py	Utility module exports
src/qprimer_designer/models/inference.py	New model loading and inference utilities
src/qprimer_designer/models/architectures.py	ML model architectures for primer evaluation
src/qprimer_designer/models/__init__.py	Model module exports
src/qprimer_designer/external/vienna.py	ViennaRNA RNAduplex wrapper
src/qprimer_designer/external/mafft.py	MAFFT wrapper for sequence alignment
src/qprimer_designer/external/bowtie.py	Bowtie2 wrapper for sequence alignment
src/qprimer_designer/external/__init__.py	External tool wrapper exports
src/qprimer_designer/commands/select_multiplex.py	CLI command for selecting multiplex primer sets
src/qprimer_designer/commands/prepare_input.py	CLI command for preparing ML evaluation input
src/qprimer_designer/commands/pick_representatives.py	CLI command for selecting representative sequences
src/qprimer_designer/commands/generate.py	CLI command for generating primer candidates
src/qprimer_designer/commands/filter_primers.py	CLI command for filtering primers based on scores
src/qprimer_designer/commands/evaluate.py	CLI command for ML-based primer evaluation
src/qprimer_designer/commands/build_output.py	CLI command for building final primer design output
src/qprimer_designer/commands/__init__.py	CLI command module exports
src/qprimer_designer/cli.py	Main CLI entry point with subcommand registration
src/qprimer_designer/__init__.py	Package initialization with version
setup.sh	Removed legacy setup script
pyproject.toml	New Python package configuration
environment.yml	Streamlined conda environment with top-level dependencies only
README.md	Updated documentation for new package structure
Dockerfile	New Docker image configuration
CLAUDE.md	New development guide
.github/workflows/test.yml	New GitHub Actions workflow for testing
.github/workflows/snakemake.yml	New GitHub Actions workflow for Snakemake validation
.github/workflows/docker.yml	New GitHub Actions workflow for Docker builds
.dockerignore	Docker build exclusions

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