Initial commit: FlowDock pipeline configured for WES execution

.pre-commit-config.yaml

@@ -0,0 +1,150 @@
+default_language_version:
+  python: python3
+
+exclude: "^forks/"
+
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      # list of supported hooks: https://pre-commit.com/hooks.html
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-docstring-first
+      - id: check-yaml
+      - id: debug-statements
+      - id: detect-private-key
+      - id: check-executables-have-shebangs
+      - id: check-toml
+      - id: check-case-conflict
+      - id: check-added-large-files
+        args: ["--maxkb=20000"]
+
+  # python code formatting
+  - repo: https://github.com/psf/black
+    rev: 25.1.0
+    hooks:
+      - id: black
+        args: [--line-length, "99"]
+
+  # python import sorting
+  - repo: https://github.com/PyCQA/isort
+    rev: 6.0.1
+    hooks:
+      - id: isort
+        args: ["--profile", "black", "--filter-files"]
+
+  # python upgrading syntax to newer version
+  - repo: https://github.com/asottile/pyupgrade
+    rev: v3.19.1
+    hooks:
+      - id: pyupgrade
+        args: [--py38-plus]
+
+  # python docstring formatting
+  - repo: https://github.com/myint/docformatter
+    rev: eb1df347edd128b30cd3368dddc3aa65edcfac38 # Don't autoupdate until https://github.com/PyCQA/docformatter/issues/293 is fixed
+    hooks:
+      - id: docformatter
+        args:
+          [
+            --in-place,
+            --wrap-summaries=99,
+            --wrap-descriptions=99,
+            --style=sphinx,
+            --black,
+          ]
+
+  # python docstring coverage checking
+  - repo: https://github.com/econchick/interrogate
+    rev: 1.7.0 # or master if you're bold
+    hooks:
+      - id: interrogate
+        args:
+          [
+            --verbose,
+            --fail-under=80,
+            --ignore-init-module,
+            --ignore-init-method,
+            --ignore-module,
+            --ignore-nested-functions,
+            -vv,
+          ]
+
+  # python check (PEP8), programming errors and code complexity
+  - repo: https://github.com/PyCQA/flake8
+    rev: 7.1.2
+    hooks:
+      - id: flake8
+        args:
+          [
+            "--extend-ignore",
+            "E203,E402,E501,F401,F841,RST2,RST301",
+            "--exclude",
+            "logs/*,data/*",
+          ]
+        additional_dependencies: [flake8-rst-docstrings==0.3.0]
+
+  # python security linter
+  - repo: https://github.com/PyCQA/bandit
+    rev: "1.8.3"
+    hooks:
+      - id: bandit
+        args: ["-s", "B101"]
+
+  # yaml formatting
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: v4.0.0-alpha.8
+    hooks:
+      - id: prettier
+        types: [yaml]
+        exclude: "environment.yaml"
+
+  # shell scripts linter
+  - repo: https://github.com/shellcheck-py/shellcheck-py
+    rev: v0.10.0.1
+    hooks:
+      - id: shellcheck
+
+  # md formatting
+  - repo: https://github.com/executablebooks/mdformat
+    rev: 0.7.22
+    hooks:
+      - id: mdformat
+        args: ["--number"]
+        additional_dependencies:
+          - mdformat-gfm
+          - mdformat-tables
+          - mdformat_frontmatter
+          # - mdformat-toc
+          # - mdformat-black
+
+  # word spelling linter
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.4.1
+    hooks:
+      - id: codespell
+        args:
+          - --skip=logs/**,data/**,*.ipynb,flowdock/data/components/constants.py,flowdock/data/components/process_mols.py,flowdock/data/components/residue_constants.py,flowdock/data/components/uff_parameters.csv,flowdock/data/components/chemical/*,flowdock/utils/data_utils.py
+          # - --ignore-words-list=abc,def
+
+  # jupyter notebook cell output clearing
+  - repo: https://github.com/kynan/nbstripout
+    rev: 0.8.1
+    hooks:
+      - id: nbstripout
+
+  # jupyter notebook linting
+  - repo: https://github.com/nbQA-dev/nbQA
+    rev: 1.9.1
+    hooks:
+      - id: nbqa-black
+        args: ["--line-length=99"]
+      - id: nbqa-isort
+        args: ["--profile=black"]
+      - id: nbqa-flake8
+        args:
+          [
+            "--extend-ignore=E203,E402,E501,F401,F841",
+            "--exclude=logs/*,data/*",
+          ]