Feature/deploy

.github/workflows/publish.yml

@@ -0,0 +1,35 @@
+name: Publish to PyPI
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  deploy:
+    name: Build & Publish
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Install build dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install build twine
+
+      - name: Build package
+        run: make build
+
+      - name: Check distribution
+        run: make test-dist
+
+      - name: Publish to PyPI
+        env:
+          TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
+          TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+        run: make upload

.github/workflows/test.yml

@@ -0,0 +1,46 @@
+name: Test
+
+on:
+  push:
+    branches:
+      - '**'
+  pull_request:
+    branches: [main]
+
+jobs:
+  test:
+    name: Test Python ${{ matrix.python-version }}
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
+    strategy:
+      matrix:
+        python-version: ['3.11', '3.12', '3.13']
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: astral-sh/setup-uv@v7
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Create environment
+        run: make env python-version=${{ matrix.python-version }}
+
+      - name: Run tests
+        run: source ./env/bin/activate && make test python=python
+
+      - name: Check format and types
+        run: source ./env/bin/activate && make format
+
+      - name: Build package
+        run: source ./env/bin/activate && make build
+
+      - name: Check distribution
+        run: source ./env/bin/activate && make test-dist
+
+      - name: Test installation from wheel
+        run: |
+          pip install dist/*.whl
+          python -c "import hpc_funcs; print(hpc_funcs.__version__)"

.pre-commit-config.yaml

@@ -1,17 +1,17 @@
 repos:
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v3.4.0
+    rev: v5.0.0
     hooks:
       - id: trailing-whitespace
         exclude: ^tests/resources/
       - id: end-of-file-fixer
         exclude: ^tests/resources/
       - id: check-yaml
         args: ["--unsafe"]
-      - id: check-added-large-files
       - id: check-ast
       - id: check-json
+        exclude: ^tests/resources/uge/qstat_jobinfo_(array|error)\.json$
       - id: debug-statements
       - id: detect-aws-credentials
         args: [--allow-missing-credentials]
@@ -20,79 +20,31 @@ repos:
       - id: check-added-large-files
         args: ['--maxkb=3000']
 
-  - repo: https://github.com/myint/autoflake
-    rev: v2.3.1
-    hooks:
-      - id: autoflake
-        name: Removes unused variables
-        args:
-          - --in-place
-          - --remove-all-unused-imports
-          - --expand-star-imports
-          - --ignore-init-module-imports
-
-  - repo: https://github.com/pre-commit/mirrors-isort
-    rev: v5.10.1
-    hooks:
-      - id: isort
-        name: Sorts imports
-        args: [
-          # Align isort with black formatting
-          "--multi-line=3",
-          "--trailing-comma",
-          "--force-grid-wrap=0",
-          "--use-parentheses",
-          "--line-width=99",
-        ]
-
-  - repo: https://github.com/psf/black
-    rev: 24.10.0
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.11.6
     hooks:
-      - id: black
-        name: Fixes formatting
-        language_version: python3
-        args: ["--line-length=99"]
-
-
-  - repo: https://github.com/pycqa/flake8
-    rev: 7.1.1
-    hooks:
-      - id: flake8
-        name: Checks pep8 style
-        args: [
-          "--max-line-length=99",
-          # Ignore imports in init files
-          "--per-file-ignores=*/__init__.py:F401,setup.py:E121",
-          # ignore long comments (E501), as long lines are formatted by black
-          # ignore Whitespace before ':' (E203)
-          # ignore Line break occurred before a binary operator (W503)
-          "--ignore=E501,E203,W503",
-        ]
-
-  # - repo: https://github.com/pre-commit/mirrors-mypy
-  #   rev: v0.782
-  #   hooks:
-  #   - id: mypy
-  #     args: [--ignore-missing-imports]
+      - id: ruff
+        args: [--fix]
+      - id: ruff-format
 
   - repo: local
     hooks:
 
-      - id: mypy
+      - id: ty
         name: Static type checking
-        entry: mypy
-        files: \.py$
-        language: python
+        entry: ty check
+        files: ^src/.*\.py$
+        language: system
 
       - id: jupyisort
         name: Sorts ipynb imports
-        entry: jupytext --pipe-fmt ".py" --pipe "isort - --multi-line=3 --trailing-comma --force-grid-wrap=0 --use-parentheses --line-width=99" --sync
+        entry: jupytext --pipe-fmt ".py" --pipe "ruff check --select I --fix -" --sync
         files: \.ipynb$
         language: python
 
-      - id: jupyblack
+      - id: jupyformat
         name: Fixes ipynb format
-        entry: jupytext --pipe-fmt ".py" --pipe "black - --line-length=99" --sync
+        entry: jupytext --pipe-fmt ".py" --pipe "ruff format -" --sync
         files: \.ipynb$
         language: python
 

Makefile

@@ -1,4 +1,4 @@
-.PHONY: update-format format test test-dist build types upload cov
+.PHONY: update-format format check test test-dist build types upload cov clean clean-env
 
 package=hpc_funcs
 version_file1=./src/hpc_funcs/version.py
@@ -21,16 +21,10 @@ env: ${env}_uv
 
 env_uv:
 	uv venv ${env}
-	uv pip install -r requirements.txt --python ${env}/bin/python
 	uv pip install -e . --python ${env}/bin/python
+	uv pip install -e .[dev] --python ${env}/bin/python
 	${python} -m pre_commit install
 
-env_conda:
-	conda env create -f ./environment.yml -p ${env} --quiet
-	${python} -m pre_commit install
-	${python} -m pip install -e .
-
-
 ## Development
 
 update-format:
@@ -39,6 +33,8 @@ update-format:
 format:
 	${python} -m pre_commit run --all-files
 
+check: format types
+
 test:
 	${python} -m pytest ./tests
 
@@ -107,3 +103,7 @@ clean:
 	rm -rf *.whl
 	rm -rf ./build/ ./__pycache__/
 	rm -rf ./dist/
+
+clean-env:
+	rm -rf ./${env}/
+	rm -f .git/hooks/pre-commit

pyproject.toml

@@ -1,18 +1,96 @@
 [build-system]
-requires = ["setuptools", "setuptools-scm"]
+requires = ["setuptools>=61.0"]
 build-backend = "setuptools.build_meta"
 
 [project]
-name = "hpce_utils"
+name = "hpc_funcs"
 dynamic = ["version"]
 authors = []
+description = "HPC utility functions"
+readme = "README.md"
+license = {text = "MIT"}
 requires-python = ">=3.11"
+classifiers = [
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: MIT License",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+]
+dependencies = [
+    "jinja2",
+    "tqdm",
+]
+
+[project.optional-dependencies]
+dev = [
+    "ruff",
+    "ty",
+    "pip",
+    "pre-commit",
+    "pytest",
+    "pytest-cov",
+    "pandas",
+    "twine",
+    "build",
+    "monkeytype",
+]
 
 [tool.setuptools.dynamic]
-version = {attr = "hpce_utils.version.VERSION"}
+version = {attr = "hpc_funcs.version.__version__"}
 
-[options.packages.find]
-where="src"
+[tool.setuptools.packages.find]
+where = ["src"]
 
 [tool.setuptools.package-data]
-"*" = ["*.jinja"]
+"*" = ["*.jinja", "py.typed"]
+
+[tool.ruff]
+line-length = 99
+target-version = "py311"
+exclude = [
+    ".git",
+    ".github",
+    "__pycache__",
+    "build",
+    "dist",
+    "*.egg-info",
+    "env",
+]
+
+[tool.ruff.lint]
+select = [
+    "E",      # pycodestyle errors
+    "F",      # pyflakes
+    "I",      # isort (import sorting)
+    "UP",     # pyupgrade (modern Python syntax)
+    "B",      # flake8-bugbear
+    "C4",     # flake8-comprehensions
+    "SIM",    # flake8-simplify
+]
+
+[tool.ruff.lint.isort]
+known-first-party = ["hpc_funcs"]
+
+[tool.ruff.lint.per-file-ignores]
+"tests/*" = ["B017", "B023", "E501"]
+"*/__init__.py" = ["F401"]
+
+[tool.ty]
+# Type checking with ty (Astral's extremely fast Python type checker)
+
+[tool.ty.environment]
+python-version = "3.11"
+
+[tool.ty.src]
+exclude = ["tests/"]
+
+[tool.ty.rules]
+# Ignore unresolved imports since pre-commit env doesn't have all packages
+unresolved-import = "ignore"
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+log_cli = true
+log_cli_level = "DEBUG"