Merge pull request #25 from 23andMe/sync-minor-changes

Sync minor changes

Author: dpoznik

.pre-commit-config.yaml

@@ -2,11 +2,11 @@ default_stages: [commit, merge-commit]
 fail_fast: true
 repos:
   - repo: [email protected]:PyCQA/isort.git
-    rev: 5.12.0
+    rev: 5.13.2
     hooks:
       - id: isort
   - repo: [email protected]:psf/black.git
-    rev: 23.11.0
+    rev: 23.12.1
     hooks:
       - id: black
   - repo: [email protected]:pre-commit/pre-commit-hooks.git
@@ -18,7 +18,7 @@ repos:
       - id: trailing-whitespace
         exclude: tests/fixtures/output/haplogroups\..*\.txt|data/variants/isogg\.[0-9]{4}\.[0-9]{2}\.[0-9]{2}\.txt
   - repo: [email protected]:PyCQA/flake8.git
-    rev: 6.1.0
+    rev: 7.0.0
     hooks:
       - id: flake8
   - repo: [email protected]:PyCQA/pydocstyle.git
@@ -28,7 +28,7 @@ repos:
         additional_dependencies: [tomli]
         exclude: tests/
   - repo: [email protected]:pre-commit/mirrors-mypy.git
-    rev: v1.7.1
+    rev: v1.8.0
     hooks:
       - id: mypy
         additional_dependencies: [pandas-stubs,types-PyYAML,types-tabulate]

Makefile

@@ -27,10 +27,13 @@ dev-pyenv-virtualenv:  ## Set up pyenv-virtual-env-based development environment
 	pyenv local $(ENV_NAME)
 	pip install --upgrade pip setuptools wheel
 	$(MAKE) dev-install
+	$(MAKE) dev-jupyter
 	$(MAKE) init-hooks
 
 dev-install:  ## Install package as editable, with all optional dependencies
 	pip install --editable .[dev]
+
+dev-jupyter:  ## Add Jupyter kernel
 	python -m ipykernel install --user --name $(ENV_NAME) --display-name $(PACKAGE_NAME)
 
 

yhaplo/config.py

@@ -104,8 +104,8 @@ class Config:
 
     # 23andMe: Platform positions
     platform_pos_data_subdir = "platform"
-    platform_pos_data_filename_tp = "{platform}.b37.positions.txt"
-    platform_qc_exclude_data_filename_tp = "{platform}.b37.qc.exclude.txt"
+    platform_pos_fn_tp = "{platform}.b37.positions.txt"
+    platform_qc_exclude_fn_tp = "{platform}.b37.qc.exclude.txt"
 
     # Example input files
     # ----------------------------------------------------------------------

yhaplo/snp.py

@@ -272,15 +272,15 @@ def build_platform_to_pos_set() -> dict[str, set[int]]:
     for platform in Config.platforms:
         platform_pos_data_file = DataFile(
             Config.platform_pos_data_subdir,
-            Config.platform_pos_data_filename_tp.format(platform=platform),
+            Config.platform_pos_fn_tp.format(platform=platform),
             f"Platform {platform} SNP positions",
             ttam_only=True,
         )
         pos_set = load_position_set(platform_pos_data_file)
 
         platform_pos_exclude_data_file = DataFile(
             Config.platform_pos_data_subdir,
-            Config.platform_qc_exclude_data_filename_tp.format(platform=platform),
+            Config.platform_qc_exclude_fn_tp.format(platform=platform),
             f"Platform {platform} SNP QC exclusions table",
             ttam_only=True,
         )