Merge pull request #22 from 23andMe/port-2.0.2

Add BCF support and refactor

.github/CODEOWNERS

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+*    @dpoznik

.gitignore

@@ -1,8 +1,59 @@
-__pycache__
-*.egg-info
-*.pyc
+# Binaries, byte compilations, etc.
+#----------------------------------
+__pycache__/
+*.py[cod]
+*.so
+
+# Caches
+#----------------------------------
+.cache
+.ipynb_checkpoints
+.metaflow
+.minio.sys
+.mypy_cache
+.pytest_cache
+.tox
+
+# Distribution & packaging
+#----------------------------------
+build/
+dist/
+eggs/
+sdist/
+wheels/
+.eggs/
+*.egg
+*.egg-info/
+_version.py
+
+# Editors & IDEs
+#----------------------------------
+*~
+\#*
+.#*
 .project
 .pydevproject
 .settings
-.venv
-output/
+.vscode
+
+# Environments
+#----------------------------------
+.python-version
+
+# macOS
+#----------------------------------
+.DS_Store
+._*
+.Trash*
+
+# Project-specific
+#----------------------------------
+logs/
+output*/
+tests/fixtures/input/1000Y.all.bcf
+tests/fixtures/input/1000Y.all.bcf.csi
+tests/fixtures/input/1000Y.subset.bcf
+tests/fixtures/input/1000Y.subset.bcf.csi
+tests/fixtures/input/ALL.chrY_10Mbp_mask.glia_freebayes_maxLikGT_siteQC.20130502.60555_biallelic_snps.vcf.gz
+tests/fixtures/input/ALL.chrY_10Mbp_mask.glia_freebayes_maxLikGT_siteQC.20130502.60555_biallelic_snps.vcf.gz.tbi
+!tests/fixtures/output/

.pre-commit-config.yaml

@@ -1,17 +1,34 @@
 default_stages: [commit, merge-commit]
+fail_fast: true
 repos:
-  - repo: https://gitlab.com/pycqa/flake8
-    rev: 3.9.0
-    hooks:
-      - id: flake8
-        types: [file, python]
-        args: [--select, "F401,F841"]  # Check for unused imports and variables
-  - repo: https://github.com/pycqa/isort
-    rev: 5.8.0
+  - repo: [email protected]:PyCQA/isort.git
+    rev: 5.12.0
     hooks:
       - id: isort
-  - repo: https://github.com/psf/black
-    rev: 20.8b1
+  - repo: git@github.com:psf/black.git
+    rev: 23.7.0
     hooks:
       - id: black
-        language_version: python3
+  - repo: [email protected]:pre-commit/pre-commit-hooks.git
+    rev: v4.4.0
+    hooks:
+      - id: check-yaml
+        args: [--allow-multiple-documents]
+      - id: pretty-format-json
+      - id: trailing-whitespace
+        exclude: haplogroups.*.txt|isogg_tree/|isogg.[0-9.]*.txt
+  - repo: [email protected]:PyCQA/flake8.git
+    rev: 6.1.0
+    hooks:
+      - id: flake8
+  - repo: [email protected]:PyCQA/pydocstyle.git
+    rev: 6.3.0
+    hooks:
+      - id: pydocstyle
+        additional_dependencies: [tomli]
+        exclude: tests/
+  - repo: [email protected]:pre-commit/mirrors-mypy.git
+    rev: v1.5.1
+    hooks:
+      - id: mypy
+        additional_dependencies: [types-PyYAML]

CHANGELOG.md

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+# Changelog for `yhaplo`
+
+Format based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
+
+
+## Planned
+
+- Correct ISOGG polarization errors for a few dozen SNPs.
+
+
+## [Unreleased]
+
+No unreleased changes
+
+[Unreleased]: https://github.com/23andMe/yhaplo/compare/2.0.2...HEAD
+
+
+## [2.0.2] - 2023-09-15
+
+This is a major clean-up and refactoring release.
+Core logic has not changed, and output should be equivalent to prior versions.
+The key changes from an end-user perspective are BCF support, a cleaner API,
+and faster processing of most input types.
+
+### Added
+- BCF support
+- Automated tests
+- Optional dependencies
+- `Sample` subclasses: `TextSample`, `VCFSample`, `AblockSample`
+- API for processing ablocks (23andMe internal)
+- `Dockerfile` defining image for Batch computes (23andMe internal)
+- Compute flow (23andMe internal)
+- Script for copying and altering files for open sourcing (23andMe internal)
+- `CHANGELOG.md`
+
+### Changed
+- Lint and update pre-commit hooks
+- Set up Drone CI (23andMe internal)
+- Set up `tox` testing (23andMe internal)
+- Update `Makefile` and configuration files
+- Refactor for PEP-8 compliance (snake case, etc.)
+- Update directory structure
+- Modernize packaging and infer version dynamically
+- Namespace command-line entry points: `yhaplo`, `yhaplo_convert_to_genos`, `yhaplo_plot_tree`
+- Replace static methods
+- Clean up logging and use file handlers
+- Use f-strings
+- Reformat docstrings
+- Add type annotations
+- Use `importlib.resources` to load metadata files
+- Move example input from package to `tests/fixtures/`
+- Update `README.md`, `README.23andMe.md`, and `yhaplo_manual.pdf`
+- Speed up sample-major file processing
+- Speed up ablock processing (23andMe internal)
+- Use Pysam to process VCF/BCF input
+- Map physical coordinates to block indexes (23andMe internal)
+- Handle platform SNPs natively (23andMe internal)
+
+### Removed
+- Support for Python 2 and Python 3.8
+- Use of research-environment utilities (23andMe internal)
+
+[2.0.2]: https://github.com/23andMe/yhaplo/compare/1.1.2..2.0.2
+