masster 0.3.0__tar.gz → 0.3.2__tar.gz

{masster-0.3.0 → masster-0.3.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: masster
-Version: 0.3.0
+Version: 0.3.2
 Summary: Mass spectrometry data analysis package
 Project-URL: homepage, https://github.com/zamboni-lab/masster
 Project-URL: repository, https://github.com/zamboni-lab/masster

{masster-0.3.0 → masster-0.3.2}/pyproject.toml

@@ -1,141 +1,141 @@
-
-[project]
-name = "masster"
-version = "0.3.0"
-description = "Mass spectrometry data analysis package"
-authors = [
-    { name = "Zamboni Lab" }
-]
-license = { file = "LICENSE" }
-readme = "README.md"
-requires-python = ">=3.11"
-keywords = ["mass spectrometry", "metabolomics", "lc-ms", "chromatography"]
-classifiers = [
-    "Development Status :: 3 - Alpha",
-    "Intended Audience :: Science/Research",
-    "License :: OSI Approved :: GNU Affero General Public License v3",
-    "Operating System :: OS Independent",
-    "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.11",
-    "Programming Language :: Python :: 3.12",
-    "Programming Language :: Python :: 3.13",
-    "Topic :: Scientific/Engineering :: Bio-Informatics",
-    "Topic :: Scientific/Engineering :: Chemistry"
-]
-urls.homepage = "https://github.com/zamboni-lab/masster"
-urls.repository = "https://github.com/zamboni-lab/masster"
-urls.documentation = "https://github.com/zamboni-lab/masster#readme"
-dependencies = [
-    "alphabase>=1.0.0",
-    "alpharaw>=0.4.8",
-    "altair>=5.5.0",
-    "bokeh>=3.7.3",
-    "datashader>=0.18.1",
-    "python-dotenv>=1.0.0",
-    "holoviews>=1.21.0",
-    "h5py>=3.14.0",
-    "hvplot>=0.11.3",
-    "loguru>=0.7.3",
-    "numpy>=2.0.0",
-    "marimo>=0.14.16",
-    "matchms>=0.30.2",
-    "matplotlib>=3.8.0",
-    "pandas>=2.2.0",
-    "panel>=1.7.0",
-    "plotly>=5.15.0",
-    "polars>=1.0.0",
-    "pyopenms>=3.3.0",
-    "pyteomics>=4.7.0",
-    "pythonnet>=3.0.0",
-    "scipy>=1.12.0",
-    "simple-parsing>=0.1.7",
-    "tqdm>=4.65.0",
-    "ipykernel>=6.30.0",
-    "openpyxl>=3.1.5",
-]
-
-[project.optional-dependencies]
-dev = [
-    "pytest>=7.0.0",
-    "pytest-cov>=4.0.0",
-    "pytest-mock>=3.10.0",
-    "black>=23.0.0",
-    "flake8>=5.0.0",
-    "mypy>=1.0.0",
-    "pre-commit>=3.0.0",
-    "twine>=4.0.0",
-    "build>=0.10.0",
-    "safety>=2.0.0",
-    "bandit>=1.7.0"
-]
-docs = [
-    "sphinx>=5.0.0",
-    "sphinx-rtd-theme>=1.2.0",
-    "sphinxcontrib-napoleon>=0.7"
-]
-test = [
-    "pytest>=7.0.0",
-    "pytest-cov>=4.0.0",
-    "pytest-mock>=3.10.0",
-    "coverage>=7.0.0"
-]
-
-[project.scripts]
-masster-version = "masster._version:main"
-
-[build-system]
-requires = ["hatchling>=1.18.0"]
-build-backend = "hatchling.build"
-
-# Testing configuration
-[tool.pytest.ini_options]
-testpaths = ["tests"]
-python_files = ["test_*.py"]
-python_classes = ["Test*"]
-python_functions = ["test_*"]
-addopts = [
-    "--strict-markers",
-    "--strict-config",
-    "--verbose",
-    "--cov=masster",
-    "--cov-report=term-missing",
-    "--cov-report=html",
-    "--cov-report=xml",
-]
-markers = [
-    "slow: marks tests as slow (deselect with '-m \"not slow\"')",
-    "integration: marks tests as integration tests",
-]
-filterwarnings = [
-    "error",
-    "ignore::UserWarning",
-    "ignore::DeprecationWarning",
-]
-
-# Coverage configuration
-[tool.coverage.run]
-source = ["masster"]
-omit = [
-    "*/tests/*",
-    "*/test_*.py",
-    "masster/_version.py",
-]
-
-[tool.coverage.report]
-exclude_lines = [
-    "pragma: no cover",
-    "def __repr__",
-    "raise AssertionError",
-    "raise NotImplementedError",
-    "if __name__ == .__main__.:",
-    "if TYPE_CHECKING:",
-]
-
-# Black configuration
-[tool.black]
-line-length = 88
-target-version = ['py311']
-include = '\.pyi?$'
+
+[project]
+name = "masster"
+version = "0.3.2"
+description = "Mass spectrometry data analysis package"
+authors = [
+    { name = "Zamboni Lab" }
+]
+license = { file = "LICENSE" }
+readme = "README.md"
+requires-python = ">=3.11"
+keywords = ["mass spectrometry", "metabolomics", "lc-ms", "chromatography"]
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: GNU Affero General Public License v3",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+    "Topic :: Scientific/Engineering :: Chemistry"
+]
+urls.homepage = "https://github.com/zamboni-lab/masster"
+urls.repository = "https://github.com/zamboni-lab/masster"
+urls.documentation = "https://github.com/zamboni-lab/masster#readme"
+dependencies = [
+    "alphabase>=1.0.0",
+    "alpharaw>=0.4.8",
+    "altair>=5.5.0",
+    "bokeh>=3.7.3",
+    "datashader>=0.18.1",
+    "python-dotenv>=1.0.0",
+    "holoviews>=1.21.0",
+    "h5py>=3.14.0",
+    "hvplot>=0.11.3",
+    "loguru>=0.7.3",
+    "numpy>=2.0.0",
+    "marimo>=0.14.16",
+    "matchms>=0.30.2",
+    "matplotlib>=3.8.0",
+    "pandas>=2.2.0",
+    "panel>=1.7.0",
+    "plotly>=5.15.0",
+    "polars>=1.0.0",
+    "pyopenms>=3.3.0",
+    "pyteomics>=4.7.0",
+    "pythonnet>=3.0.0",
+    "scipy>=1.12.0",
+    "simple-parsing>=0.1.7",
+    "tqdm>=4.65.0",
+    "ipykernel>=6.30.0",
+    "openpyxl>=3.1.5",
+]
+
+[project.optional-dependencies]
+dev = [
+    "pytest>=7.0.0",
+    "pytest-cov>=4.0.0",
+    "pytest-mock>=3.10.0",
+    "black>=23.0.0",
+    "flake8>=5.0.0",
+    "mypy>=1.0.0",
+    "pre-commit>=3.0.0",
+    "twine>=4.0.0",
+    "build>=0.10.0",
+    "safety>=2.0.0",
+    "bandit>=1.7.0"
+]
+docs = [
+    "sphinx>=5.0.0",
+    "sphinx-rtd-theme>=1.2.0",
+    "sphinxcontrib-napoleon>=0.7"
+]
+test = [
+    "pytest>=7.0.0",
+    "pytest-cov>=4.0.0",
+    "pytest-mock>=3.10.0",
+    "coverage>=7.0.0"
+]
+
+[project.scripts]
+masster-version = "masster._version:main"
+
+[build-system]
+requires = ["hatchling>=1.18.0"]
+build-backend = "hatchling.build"
+
+# Testing configuration
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+python_files = ["test_*.py"]
+python_classes = ["Test*"]
+python_functions = ["test_*"]
+addopts = [
+    "--strict-markers",
+    "--strict-config",
+    "--verbose",
+    "--cov=masster",
+    "--cov-report=term-missing",
+    "--cov-report=html",
+    "--cov-report=xml",
+]
+markers = [
+    "slow: marks tests as slow (deselect with '-m \"not slow\"')",
+    "integration: marks tests as integration tests",
+]
+filterwarnings = [
+    "error",
+    "ignore::UserWarning",
+    "ignore::DeprecationWarning",
+]
+
+# Coverage configuration
+[tool.coverage.run]
+source = ["masster"]
+omit = [
+    "*/tests/*",
+    "*/test_*.py",
+    "masster/_version.py",
+]
+
+[tool.coverage.report]
+exclude_lines = [
+    "pragma: no cover",
+    "def __repr__",
+    "raise AssertionError",
+    "raise NotImplementedError",
+    "if __name__ == .__main__.:",
+    "if TYPE_CHECKING:",
+]
+
+# Black configuration
+[tool.black]
+line-length = 88
+target-version = ['py311']
+include = '\.pyi?$'
 extend-exclude = '''
 /(
   # directories
@@ -148,42 +148,42 @@ extend-exclude = '''
   | build
   | dist
 )/
-'''
-
-# MyPy configuration
-[tool.mypy]
-python_version = "3.11"
-warn_return_any = true
-warn_unused_configs = true
-disallow_untyped_defs = false
-disallow_incomplete_defs = false
-check_untyped_defs = true
-disallow_untyped_decorators = false
-no_implicit_optional = true
-warn_redundant_casts = true
-warn_unused_ignores = true
-warn_no_return = true
-warn_unreachable = true
-strict_equality = true
-ignore_missing_imports = true
-
-# Flake8 configuration
-[tool.flake8]
-max-line-length = 88
-extend-ignore = ["E203", "W503"]
-exclude = [
-    ".git",
-    "__pycache__",
-    "docs",
-    "build",
-    "dist",
-    ".eggs",
-    "*.egg-info",
-    ".venv",
-    "venv",
-]
-
-# Bandit configuration
-[tool.bandit]
-exclude_dirs = ["tests"]
-skips = ["B101", "B601"]
+'''
+
+# MyPy configuration
+[tool.mypy]
+python_version = "3.11"
+warn_return_any = true
+warn_unused_configs = true
+disallow_untyped_defs = false
+disallow_incomplete_defs = false
+check_untyped_defs = true
+disallow_untyped_decorators = false
+no_implicit_optional = true
+warn_redundant_casts = true
+warn_unused_ignores = true
+warn_no_return = true
+warn_unreachable = true
+strict_equality = true
+ignore_missing_imports = true
+
+# Flake8 configuration
+[tool.flake8]
+max-line-length = 88
+extend-ignore = ["E203", "W503"]
+exclude = [
+    ".git",
+    "__pycache__",
+    "docs",
+    "build",
+    "dist",
+    ".eggs",
+    "*.egg-info",
+    ".venv",
+    "venv",
+]
+
+# Bandit configuration
+[tool.bandit]
+exclude_dirs = ["tests"]
+skips = ["B101", "B601"]