Release WASP2 v1.3.0: PyPI publication + docs

.claude/settings.json

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+{
+  "permissions": {
+    "allow": [
+      "Read",
+      "Edit",
+      "Write",
+      "Grep",
+      "Glob",
+      "Bash(git diff *)",
+      "Bash(git log *)",
+      "Bash(git status)",
+      "Bash(git show *)",
+      "Bash(pytest *)",
+      "Bash(python *)",
+      "Bash(maturin *)",
+      "Bash(cargo *)",
+      "Bash(ruff *)",
+      "Bash(ls *)"
+    ],
+    "deny": [
+      "Bash(curl *)",
+      "Bash(wget *)",
+      "Bash(ssh *)",
+      "Bash(scp *)",
+      "Bash(rm -rf *)",
+      "Bash(rm -r *)",
+      "Bash(chmod 777 *)",
+      "Bash(sudo *)",
+      "WebFetch",
+      "Read(.env*)",
+      "Read(~/.ssh/*)",
+      "Read(~/.aws/*)",
+      "Read(~/.gnupg/*)"
+    ]
+  }
+}

.dockerignore

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+# Git
+.git
+.gitignore
+.gitattributes
+
+# GitHub
+.github
+
+# Documentation (keep README for build)
+docs
+doc
+*.md
+!README.md
+
+# Tests
+tests
+.pytest_cache
+.nf-test
+.coverage
+htmlcov
+coverage.xml
+
+# Python cache and environments
+__pycache__
+*.pyc
+*.pyo
+*.pyd
+*.egg-info
+.eggs
+dist
+build
+.venv
+venv
+.tox
+.nox
+
+# Rust build artifacts (handled by multi-stage)
+rust/target
+
+# IDE and editors
+.vscode
+.idea
+*.swp
+*.swo
+*~
+.project
+.pydevproject
+.settings
+
+# Nextflow
+.nextflow*
+work
+results
+pipelines/test_output
+
+# Other build/runtime artifacts
+*.log
+.DS_Store
+Thumbs.db
+*.tmp
+*.bak
+
+# Security - never include in build context
+.env
+.env.*
+*.pem
+*.key
+credentials*
+secrets*
+
+# CI/CD configs (not needed in image)
+.pre-commit-config.yaml
+.readthedocs.yml
+.travis.yml
+Jenkinsfile
+Makefile
+
+# Container definitions (prevent recursion)
+Dockerfile*
+docker-compose*
+Singularity*
+
+# Benchmarks and profiling
+*.prof
+*.benchmark
+
+# Galaxy and Bioconda (distribution only)
+galaxy
+bioconda-recipe
+
+# Large data files
+*.bam
+*.bai
+*.vcf
+*.vcf.gz
+*.bed
+*.fastq
+*.fastq.gz
+*.fasta
+*.fa

.github/CODEOWNERS

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+# CODEOWNERS - Require review for security-sensitive files
+# See: https://docs.github.com/en/repositories/managing-your-repositorys-settings-and-features/customizing-your-repository/about-code-owners
+#
+# RELEASE AUDIT TEAM ROLES:
+# - PI (@Jaureguy760): Admin - strategic oversight, release approval
+# - Software Engineer (@SOFTWARE_ENGINEER_USERNAME): Maintain - CI/CD, Rust, build systems
+# - Bioinformatician (@BIOINFORMATICIAN_USERNAME): Write - statistical analysis, benchmarks
+# - Staff Research Scientist (@SCIENTIST_USERNAME): Write - test data, scientific validation
+#
+# NOTE: Replace placeholder usernames with actual GitHub usernames
+
+# =============================================================================
+# SECURITY-SENSITIVE FILES (require owner/admin review)
+# =============================================================================
+
+# CI/CD workflows - require owner review for any workflow changes
+.github/workflows/ @Jaureguy760
+
+# Dependabot configuration
+.github/dependabot.yml @Jaureguy760
+
+# Security configuration
+.gitleaks.toml @Jaureguy760
+
+# Dockerfile and container configs
+Dockerfile @Jaureguy760
+Dockerfile.optimized @Jaureguy760
+Singularity.def @Jaureguy760
+
+# =============================================================================
+# STATISTICAL ANALYSIS (require bioinformatician review)
+# =============================================================================
+
+# Core analysis module - statistical models
+/src/analysis/ @BIOINFORMATICIAN_USERNAME @Jaureguy760
+
+# Counting logic - allele counting accuracy
+/src/counting/ @BIOINFORMATICIAN_USERNAME
+
+# Benchmarking - validation against gold standards
+/benchmarking/ @BIOINFORMATICIAN_USERNAME
+
+# =============================================================================
+# RUST CODE (require software engineer review)
+# =============================================================================
+
+# Rust implementation - performance-critical code
+/rust/ @SOFTWARE_ENGINEER_USERNAME @Jaureguy760
+
+# Build configuration
+pyproject.toml @SOFTWARE_ENGINEER_USERNAME @Jaureguy760
+Makefile @SOFTWARE_ENGINEER_USERNAME
+
+# =============================================================================
+# SCIENTIFIC DOCUMENTATION (require PI approval)
+# =============================================================================
+
+# Main documentation
+/docs/*.md @Jaureguy760
+README.md @Jaureguy760
+CHANGELOG.md @Jaureguy760
+CITATION.cff @Jaureguy760
+
+# Security documentation
+SECURITY.md @Jaureguy760
+SECURITY_AUDIT.md @Jaureguy760
+
+# =============================================================================
+# TEST DATA VALIDATION (require wet lab scientist review)
+# =============================================================================
+
+# Test data and sanity checks
+/tests/data/ @SCIENTIST_USERNAME @BIOINFORMATICIAN_USERNAME
+/tests/sanity/ @SCIENTIST_USERNAME @BIOINFORMATICIAN_USERNAME
+
+# Tutorials - user-facing documentation
+/tutorials/ @SCIENTIST_USERNAME @Jaureguy760
+
+# =============================================================================
+# AUDIT INFRASTRUCTURE (any team member can review)
+# =============================================================================
+
+# Audit documentation
+/docs/AUDITOR_GUIDE.md @Jaureguy760 @SOFTWARE_ENGINEER_USERNAME @BIOINFORMATICIAN_USERNAME @SCIENTIST_USERNAME
+/docs/AUDIT_CHECKLIST.md @Jaureguy760 @SOFTWARE_ENGINEER_USERNAME @BIOINFORMATICIAN_USERNAME @SCIENTIST_USERNAME
+/.github/ISSUE_TEMPLATE/ @Jaureguy760

.github/ISSUE_TEMPLATE/audit-finding.yml

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+name: "Audit Finding"
+description: "Report an issue found during human review of AI-generated code"
+title: "[AUDIT] "
+labels: ["audit", "human-review", "needs-triage"]
+body:
+  - type: markdown
+    attributes:
+      value: |
+        ## AI Code Audit Finding
+        Use this template to report issues discovered during human review of AI-generated code.
+        Please be as specific as possible about the location and nature of the concern.
+
+  - type: dropdown
+    id: severity
+    attributes:
+      label: Severity
+      description: "How critical is this finding?"
+      options:
+        - Critical (blocks release)
+        - High (must fix before release)
+        - Medium (should fix)
+        - Low (nice to have)
+    validations:
+      required: true
+
+  - type: dropdown
+    id: category
+    attributes:
+      label: Category
+      description: "What type of issue is this?"
+      options:
+        - Scientific Accuracy
+        - Code Quality
+        - Security Concern
+        - Documentation
+        - Test Coverage Gap
+        - Performance Issue
+        - User Experience
+    validations:
+      required: true
+
+  - type: dropdown
+    id: reviewer-role
+    attributes:
+      label: Reviewer Role
+      description: "Your role on the audit team"
+      options:
+        - PI
+        - Software Engineer
+        - Bioinformatician
+        - Staff Research Scientist
+        - Other
+    validations:
+      required: true
+
+  - type: textarea
+    id: location
+    attributes:
+      label: Location
+      description: "File path and line numbers where the issue was found"
+      placeholder: "src/analysis/as_analysis.py:150-175"
+    validations:
+      required: true
+
+  - type: textarea
+    id: description
+    attributes:
+      label: Description
+      description: "What did you find? Be specific about the problem."
+      placeholder: "Describe the issue in detail..."
+    validations:
+      required: true
+
+  - type: textarea
+    id: expected
+    attributes:
+      label: Expected Behavior
+      description: "What should happen instead?"
+      placeholder: "Describe the correct behavior..."
+    validations:
+      required: true
+
+  - type: textarea
+    id: evidence
+    attributes:
+      label: Evidence/References
+      description: "Literature citations, benchmark comparisons, test results, or other supporting evidence"
+      placeholder: |
+        - Paper: Author et al., 2024, DOI: ...
+        - Benchmark: GATK ASEReadCounter shows r² = 0.95 vs expected 0.99
+        - Test output: ...
+
+  - type: textarea
+    id: suggested-fix
+    attributes:
+      label: Suggested Fix
+      description: "If you have ideas on how to resolve this, please share them"
+      placeholder: "Optional: Describe potential solutions..."
+
+  - type: checkboxes
+    id: verification
+    attributes:
+      label: Verification
+      description: "Confirm you've done the following"
+      options:
+        - label: I have read the relevant code section
+          required: true
+        - label: I have checked if this issue already exists
+          required: true
+        - label: I have provided enough detail for someone else to understand and fix this
+          required: true

.github/ISSUE_TEMPLATE/config.yml

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+blank_issues_enabled: false
+contact_links:
+  - name: Security Vulnerability
+    url: https://github.com/Jaureguy760/wasp2-final/security/advisories/new
+    about: Report security issues privately via GitHub Security Advisories
+
+  - name: General Question
+    url: https://github.com/Jaureguy760/wasp2-final/discussions
+    about: Ask questions or discuss WASP2 usage in Discussions
+
+  - name: Feature Request
+    url: https://github.com/Jaureguy760/wasp2-final/discussions/categories/ideas
+    about: Suggest new features or improvements in Discussions
+
+  - name: Bug Report (Non-Audit)
+    url: https://github.com/Jaureguy760/wasp2-final/issues/new
+    about: For general bug reports outside of release audits, create a blank issue