.pre-commit-config.yaml

repos:
  - repo: local
    hooks:
      - id: condalock
        name: condalock
        entry: ./scripts/condalock.sh
        language: script
        exclude: '.*'
        always_run: true
        fail_fast: true
  - repo: https://github.com/pre-commit/pre-commit-hooks
    rev: v4.5.0
    hooks:
      - id: check-merge-conflict
      - id: debug-statements
      - id: mixed-line-ending
      - id: detect-private-key
      - id: check-case-conflict
      - id: check-yaml
      - id: trailing-whitespace
  - repo: https://github.com/asottile/reorder_python_imports
    rev: v3.12.0
    hooks:
      - id: reorder-python-imports
        args:
          [
            --application-directories=python,
            --unclassifiable-application-module=_tskit,
          ]
  - repo: https://github.com/charliermarsh/ruff-pre-commit
    rev: "v0.1.2"
    hooks:
      - id: ruff
        args:
          [
            "--per-file-ignores=tests/test_utils.py:E501,manticore/tests/wm/snakemake.py:E501",
          ]
  - repo: https://github.com/psf/black
    rev: 23.10.1
    hooks:
      - id: black
        language_version: python3
  - repo: https://github.com/asottile/blacken-docs
    rev: 1.16.0
    hooks:
      - id: blacken-docs
        args: [--skip-errors]
        additional_dependencies: [black==22.3.0]
        language_version: python3
  - repo: https://github.com/DavidAnson/markdownlint-cli2
    rev: v0.10.0
    hooks:
      - id: markdownlint-cli2
        files: \.(md|qmd)$
        types: [file]
        exclude: LICENSE.md
      - id: markdownlint-cli2-fix
        files: \.(md|qmd)$
        types: [file]
        exclude: LICENSE.md
  - repo: https://github.com/editorconfig-checker/editorconfig-checker.python
    rev: '2.7.3'
    hooks:
      - id: editorconfig-checker
        alias: ec
        pass_filenames: true
        exclude: |
          (?x)^(
          docs/slides/population_structure/data/DavidReich/AADR\.ind|
          docs/slides/population_structure/data/DavidReich/AADR\.snp|
          docs/slides/population_structure/data/DavidReich/AADR\.geno|
          docs/archive/.footer.html|
          docs/archive/.header.html|
          )
  - repo: https://github.com/lorenzwalthert/precommit
    rev: v0.3.2.9023
    hooks:
      - id: style-files
        name: style-files
        description: style files with {styler}
        entry: Rscript inst/hooks/exported/style-files.R
        language: r
        files: '(\.[rR]profile|\.[rR]|\.[rR]md|\.[rR]nw|\.[qQ]md)$'
        exclude: |
          (?x)^(
          renv/activate\.R|
          docs/slides/pgip/index\.qmd|
          docs/slides/datageneration/index\.qmd|
          docs/slides/foundations/index\.qmd|
          docs/slides/variant_filtering/index\.qmd|
          docs/slides/variant_calling/index\.qmd|
          docs/exercises/variant_filtering/index\.qmd|
          docs/slides/simulation/index\.qmd
          )$
        minimum_pre_commit_version: "2.13.0"
      - id: parsable-R
        name: parsable-R
        description: check if a .R file is parsable
        entry: Rscript inst/hooks/exported/parsable-R.R
        language: r
        files: '\.[rR](md)?$'
        minimum_pre_commit_version: "2.13.0"
      - id: lintr
        name: lintr
        description: check if a `.R` file is lint free (using {lintr})
        entry: Rscript inst/hooks/exported/lintr.R
        language: r
        files: '(\.[rR]profile|\.R|\.Rmd|\.Rnw|\.r|\.rmd|\.rnw)$'
        exclude: 'renv/activate\.R'
        minimum_pre_commit_version: "2.13.0"