Merge pull request #1 from nishaq503/dev

Added github workflows and pre-commit hooks

.github/workflows/tool-release.yml

@@ -0,0 +1,22 @@
+name: Tool Release
+
+on:
+  push:
+    branches:
+      - master
+      - main
+      - dev
+
+permissions:
+  contents: write
+
+jobs:
+  tools-release:
+    name: Call workflow from image-tools
+    if: github.repository == 'polusai/tabular-tools'
+    uses: polusai/image-tools/.github/workflows/package-release.yml
+    with:
+      repo_name: "tabular-tools"
+    secrets:
+      DOCKER_USERNAME: ${{ secrets.DOCKER_USERNAME }}
+      DOCKER_PASSWORD: ${{ secrets.DOCKER_TOKEN }}

.github/workflows/tool-tests.yml

@@ -0,0 +1,27 @@
+name: Package tests
+
+on:
+  pull_request:
+    branches:
+      - main
+      - master
+      - dev
+  push:
+    branches-ignore:
+      - main
+      - master
+      - dev
+
+permissions:
+  contents: read
+
+jobs:
+  tools-tests:
+    name: Call workflow from image-tools
+    if: github.repository == 'polusai/tabular-tools'
+    uses: polusai/image-tools/.github/workflows/tests.yml
+    with:
+      repo_name: "tabular-tools"
+    secrets:
+      DOCKER_USERNAME: ${{ secrets.DOCKER_USERNAME }}
+      DOCKER_PASSWORD: ${{ secrets.DOCKER_TOKEN }}

.gitignore

@@ -99,7 +99,7 @@ ipython_config.py
 #   This is especially recommended for binary packages to ensure reproducibility, and is more
 #   commonly ignored for libraries.
 #   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
-#poetry.lock
+poetry.lock
 
 # pdm
 #   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
@@ -157,4 +157,4 @@ cython_debug/
 #  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
 #  and can be added to the global gitignore or merged into this file.  For a more nuclear
 #  option (not recommended) you can uncomment the following to ignore the entire idea folder.
-#.idea/
+.idea/

.pre-commit-config.yaml

@@ -0,0 +1,52 @@
+fail_fast: true
+
+repos:
+
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    hooks:
+      - id: check-added-large-files
+      - id: check-case-conflict
+      - id: check-json
+      - id: pretty-format-json
+        args:
+          - "--autofix"
+          - "--indent=2"
+          - "--no-sort-keys"
+      - id: check-toml
+      - id: check-xml
+      - id: check-yaml
+      - id: debug-statements
+      - id: detect-aws-credentials
+        args:
+          - "--allow-missing-credentials"
+      - id: detect-private-key
+      - id: end-of-file-fixer
+      - id: mixed-line-ending
+        args: ["--fix=lf"]
+        description: Forces to replace line ending by the UNIX 'lf' character.
+      - id: trailing-whitespace
+        exclude: '.bumpversion.cfg'
+      - id: check-merge-conflict
+
+  - repo: https://github.com/psf/black
+    rev: '23.3.0'
+    hooks:
+      - id: black
+        language_version: python3.9
+        exclude: ^src\/polus\/plugins\/_plugins\/models\/\w*Schema.py$
+
+  - repo: https://github.com/charliermarsh/ruff-pre-commit
+    # Ruff version.
+    rev: 'v0.0.274'
+    hooks:
+      - id: ruff
+        exclude: ^src\/polus\/plugins\/_plugins\/models\/\w*Schema.py$
+        args: [--fix]
+
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: 'v1.4.0'
+    hooks:
+      - id: mypy
+        exclude: ^src\/polus\/plugins\/_plugins\/models\/\w*Schema.py$
+        additional_dependencies: [types-requests==2.31.0.1]

ruff.toml

@@ -0,0 +1,51 @@
+select = [
+  "F",  # pyflakes
+  "E",  # pycodestyle errors
+  "W",  # pycodestyle warnings
+  "C90",  # mccabe
+  "I",  # isort
+  "N",  # pep8-naming
+  "D",  # pydocstyle
+  "UP",  # pyupgrade
+  "ANN",  # flake8-annotations
+  "S",  # flake8-bandit
+  "BLE",  # flake8-blind-except
+  "B",  # flake8-bugbear
+  "A",  # flake8-builtins
+  "COM",  # flake8-commas
+  "C4",  # flake8-comprehensions
+  "EM",  # flake8-errmsg
+  "INP",  # flake8-no-pep420
+  "T20",  # flake8-print
+  "PYI",  # flake8-pyi, type-hinting stub files
+  "PT",  # flake8-pytest-style
+  "RSE",  # flake8-raise
+  "RET",  # flake8-return
+  "SIM",  # flake8-simplify
+  "ARG",  # flake8-unused-arguments
+  "ERA", # flake8-eradicate
+  "PTH",  # flake8-use-pathlib
+  "PL",  # pylint
+  "FLY",  # flynt
+  "NPY",  # NumPy-specific rules
+  "RUF",  # Ruff-specific rules
+]
+ignore = ["ANN101", "ANN102"]
+unfixable = ["B"]  # Avoid trying to fix flake8-bugbear violations.
+target-version = "py39"  # Assume Python 3.9.
+
+[mccabe]
+# Unlike Flake8, default to a complexity level of 10.
+max-complexity = 12
+
+[pydocstyle]
+convention = "google"
+
+# Ignore `F401` (unused import violations) in all `__init__.py` files.
+[per-file-ignores]
+"__init__.py" = ["F401"]
+"__main__.py" = ["B008", "S101"]
+"./**/tests/*.py" = ["S101"]  # Use of assert detected.
+
+[isort]
+force-single-line = true