Merge pull request #14 from dnv-opensource/13-solve-errors-that-lead-…

…to-nightly-build-failing

13 solve errors that lead to nightly build failing

.github/workflows/_build_and_publish_documentation.yml

@@ -17,7 +17,7 @@ jobs:
         with:
           lfs: true
       - name: Install uv
-        uses: astral-sh/setup-uv@v2
+        uses: astral-sh/setup-uv@v5
         with:
           enable-cache: true
           cache-dependency-glob: "uv.lock"

.github/workflows/_build_package.yml

@@ -11,7 +11,7 @@ jobs:
         with:
           lfs: true
       - name: Install uv
-        uses: astral-sh/setup-uv@v2
+        uses: astral-sh/setup-uv@v5
         with:
           enable-cache: true
           cache-dependency-glob: "uv.lock"

.github/workflows/_code_quality.yml

@@ -9,7 +9,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - name: Install uv
-        uses: astral-sh/setup-uv@v2
+        uses: astral-sh/setup-uv@v5
         with:
           enable-cache: true
           cache-dependency-glob: "uv.lock"
@@ -28,7 +28,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - name: Install uv
-        uses: astral-sh/setup-uv@v2
+        uses: astral-sh/setup-uv@v5
         with:
           enable-cache: true
           cache-dependency-glob: "uv.lock"
@@ -47,7 +47,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - name: Install uv
-        uses: astral-sh/setup-uv@v2
+        uses: astral-sh/setup-uv@v5
         with:
           enable-cache: true
           cache-dependency-glob: "uv.lock"
@@ -66,7 +66,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - name: Install uv
-        uses: astral-sh/setup-uv@v2
+        uses: astral-sh/setup-uv@v5
         with:
           enable-cache: true
           cache-dependency-glob: "uv.lock"

.github/workflows/_test.yml

@@ -18,9 +18,9 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - name: Install uv
-        uses: astral-sh/setup-uv@v2
+        uses: astral-sh/setup-uv@v5
         with:
-          enable-cache: true
+          enable-cache: false
           cache-dependency-glob: "uv.lock"
       - name: Install Python ${{ matrix.python.version }}
         uses: actions/setup-python@v5

.github/workflows/_test_future.yml

@@ -19,9 +19,9 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - name: Install uv
-        uses: astral-sh/setup-uv@v2
+        uses: astral-sh/setup-uv@v5
         with:
-          enable-cache: true
+          enable-cache: false
           cache-dependency-glob: "uv.lock"
       - name: Install Python ${{ matrix.python.version }}
         uses: actions/setup-python@v5

.pre-commit-config.yaml

@@ -9,13 +9,12 @@ repos:
       - id: check-toml
       - id: check-merge-conflict
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.8.3
+    rev: v0.9.2
     hooks:
       - id: ruff-format
       - id: ruff
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.13.0
+    rev: v1.14.1
     hooks:
       - id: mypy
-        additional_dependencies: [numpy==1.26.4, torch==2.4.1]
 exclude: '(.venv|.*_cache)/.*'

.vscode/launch.json

@@ -63,4 +63,4 @@
             "justMyCode": true,
         },
     ]
-}
+}

.vscode/settings.json

@@ -47,6 +47,6 @@
     ],
     "mypy-type-checker.importStrategy": "fromEnvironment",
     "mypy-type-checker.reportingScope": "workspace",
-    "mypy-type-checker.preferDaemon": false,
+    "mypy-type-checker.preferDaemon": true,
     "ruff.configurationPreference": "filesystemFirst",
 }

CHANGELOG.md

@@ -5,7 +5,25 @@ The changelog format is based on [Keep a Changelog](https://keepachangelog.com/e
 
 ## [Unreleased]
 
+### Added
+* pyproject.toml : Added keywords
+
+### Changed
+* Updated multiple files to latest changes changes in python_project_template
+
+### Solved
+* Resolved issues raised by `ruff` 0.9.2
+
+### Dependencies
+* Updated to matplotlib>=3.10  (from matplotlib>=3.9)
+* Updated to sphinx-autodoc-typehints>=3.0  (from sphinx-autodoc-typehints>=2.5)
+* Updated to pyarrow>=19.0  (from pyarrow>=18.1)
+* Updated to mypy>=1.14  (from mypy>=1.13)
+* Updated to setup-uv@v5  (from setup-uv@v2)
+
+
 ## [0.1.1] - 2024-12-27
+
 ### Added:
 Major addition of new qoi method `MarginalCDFExtrapolation`. The following helpers are alse added.
 * `utils/numerical_precision`: quantify the precision possible with different datatypes

CITATION.cff

@@ -1,31 +1,35 @@
-cff-version: 1.2.0
 title: Axtreme
-message: Ax for Extremes
+version: 0.1.1
+abstract: >-
+  A toolkit for estimating the long term behaviour
+  (extremes) of expensive, stochastic, black box functions.
 type: software
 authors:
-  - name: DNV
-    address: 'Veritasveien 1, 1363 Høvik'
-    city: Oslo
+  - name: DNV AS
+    address: 'Veritasveien 1'
+    post-code: '1363'
+    city: Høvik
+    country: NO
     website: 'https://www.dnv.com/'
   - given-names: Sebastian
     family-names: Winter
-    email: [email protected]
     affiliation: DNV
+    email: [email protected]
   - given-names: Kristoffer
     family-names: Skare
-    email: [email protected]
     affiliation: DNV
+    email: [email protected]
   - given-names: Magnus
     family-names: Kristiansen
-    email: [email protected]
     affiliation: DNV
-abstract: >-
-  A toolkit for estimating the long term behaviour
-  (extremes) of expensive, stochastic, black box functions.
+    email: [email protected]
 keywords:
   - Design of Experiments
   - Active Learning
   - Extreme Response
 license: MIT
-url: "https://github.com/dnv-opensource/axtreme"
-version: 0.1.1
+license-url: 'https://dnv-opensource.github.io/axtreme/LICENSE.html'
+url: 'https://dnv-opensource.github.io/axtreme/README.html'
+repository-code: 'https://github.com/dnv-opensource/axtreme'
+message: 'Please cite this software using these metadata.'
+cff-version: 1.2.0

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2024 [DNV](https://www.dnv.com) [open source](https://github.com/dnv-opensource)
+Copyright (c) 2025 [DNV](https://www.dnv.com) [open source](https://github.com/dnv-opensource)
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

README.md

@@ -65,7 +65,7 @@ uv sync
 > **Note**: Using `--no-dev` will omit installing development dependencies.
 
 > **Note**: `uv` will create a new virtual environment called `.venv` in the project root directory when running
-> `uv sync` for the first time. Optionally, you can create your own using e.g. `uv venv`, before running
+> `uv sync` the first time. Optionally, you can create your own virtual environment using e.g. `uv venv`, before running
 > `uv sync`.
 
 ### 5. (Optional) Install CUDA support

docs/source/axtreme.rst

@@ -1,5 +1,5 @@
 axtreme package
-==================
+===============
 
 Subpackages
 -----------

docs/source/conf.py

@@ -23,7 +23,7 @@
 
 project = "axtreme"
 copyright = "2024, DNV AS. All rights reserved."
-author = "Sebastian Winter, Kristoffer Skare"
+author = "Sebastian Winter, Kristoffer Skare, Magnus Kristiansen"
 
 # The full version, including alpha/beta/rc tags
 release = "0.1.1"
@@ -33,11 +33,10 @@
 
 extensions = [
     "myst_parser",
-    "sphinx.ext.autodoc",  # upgrade to autodoc2if want to you myst markup in docstings
+    "sphinx.ext.autodoc",
     "sphinx.ext.napoleon",
     "sphinx_argparse_cli",
     "sphinx.ext.mathjax",
-    "matplotlib.sphinxext.plot_directive",
     "sphinx.ext.autosummary",
     "sphinx.ext.todo",
     "sphinxcontrib.mermaid",
@@ -74,9 +73,6 @@
 autodoc_default_options = {
     "member-order": "groupwise",
     "undoc-members": True,
-    # "special-members": True,
-    # TODO(sw 2024-12-5): using "inherited-members" might be a more elegant want to achieve the below.
-    # "exclude-members": "__weakref__, __init__, __annotations__, __abstractmethods__, __module__, __parameters__, __subclasshook__",
     "exclude-members": "__weakref__",
 }
 autodoc_preserve_defaults = True

docs/source/index.rst

@@ -23,7 +23,6 @@ axtreme Documentation
    LICENSE
 
 
-
 Indices and tables
 ==================
 

pyproject.toml

@@ -10,6 +10,9 @@ only-include = [
     "tests",
     ".coveragerc",
     ".editorconfig",
+    ".pre-commit-config.yaml",
+    "manage.py",
+    "pyproject.toml",
     "pytest.ini",
     "ruff.toml",
     "uv.lock",
@@ -37,6 +40,9 @@ maintainers = [
     { name = "Jorge Luis Mendez", email = "[email protected]" },
 ]
 keywords = [
+    "Design of Experiments",
+    "Active Learning",
+    "Extreme Response",
 ]
 classifiers = [
     "Development Status :: 3 - Alpha",
@@ -53,8 +59,8 @@ classifiers = [
     "Topic :: Software Development :: Libraries :: Python Modules",
 ]
 dependencies = [
-    "numpy>=1.26,<2.0",
-    "matplotlib>=3.9",
+    "numpy>=1.26, <2.0",
+    "matplotlib>=3.10",
     "statsmodels>=0.14.4",
     "filterpy>=1.4.5",
     "numba>=0.60.0",
@@ -80,20 +86,20 @@ Changelog = "https://github.com/dnv-opensource/axtreme/blob/main/CHANGELOG.md"
 dev = [
     "pytest>=8.3",
     "pytest-cov>=6.0",
-    "ruff>=0.8.3",
-    "pyright>=1.1.390",
-    "mypy>=1.13",
-    "sourcery>=1.27",
+    "ruff>=0.9.2",
+    "pyright>=1.1.392",
+    "mypy>=1.14",
+    "sourcery>=1.31",
     "pre-commit>=4.0",
     "Sphinx>=8.1",
     "sphinx-argparse-cli>=1.19",
-    "sphinx-autodoc-typehints>=2.5",
+    "sphinx-autodoc-typehints>=3.0",
     "sphinxcontrib-mermaid>=1.0.0",
     "myst-parser>=4.0",
     "furo>=2024.8",
     "jupyter>=1.1",
     "pandas-stubs>=2.2",
-    "pyarrow>=18.1",
+    "pyarrow>=19.0",
 ]
 
 [tool.uv]

pytest.ini

@@ -1,7 +1,7 @@
 [pytest]
 testpaths =
     tests
-addopts = --strict-markers --verbose
+addopts = --strict-markers --verbose --durations=10
 xfail_strict = True
 filterwarnings =
   # Filter out parameters and sklearn deprecation warnings.

ruff.toml

@@ -33,6 +33,9 @@ ignore = [
     "TRY003",  # Avoid specifying long messages outside the exception class
     "PLR1711", # Useless `return` statement at end of function
     "G00",     # Logging statement uses string formatting ('G00' covers all rules flagging string formatting in logging, e.g. G001, G002, etc.)
+    "S311",    # Standard pseudo-random generators are not suitable for cryptographic purposes
+    "PLW0603", # Using the global statement to update {name} is discouraged
+    "PYI041",  # Use `float` instead of `int | float`
 
     # Ruff lint rules recommended to keep enabled,
     # but which are typical candidates you might have a need to ignore,
@@ -74,8 +77,6 @@ allowed-confusables = [
 [lint.pep8-naming]
 ignore-names = [
     "test_*",
-    "setUp",
-    "tearDown",
 ]
 
 [lint.pylint]
@@ -94,7 +95,7 @@ raises-require-match-for = [
 [lint.per-file-ignores]
 # `__init__.py` specific ignores
 "__init__.py" = [
-    "D104",    # Missing docstring in public package
+    "D104",    # Missing docstring in public package  <- @TODO: Reactivate and resolve  @ ClaasRostock, 2025-01-20
     "F401",    # {name} imported but unused (NOTE: ignored as imports in `__init__.py` files are almost never used inside the module, but are intended for namespaces)
     "I001",    # Import block is un-sorted or un-formatted
     "PLC0414", # Import alias does not rename original package
@@ -108,9 +109,11 @@ raises-require-match-for = [
     "PLR2004", # Magic value used in comparison
     "ANN201",  # Missing return type annotation for public function
     "ANN202",  # Missing return type annotation for private function
+    "ARG001",  # Unused function argument: {name}
+    "ARG002",  # Unused method argument: {name}
     "INP001",  # File is part of an implicit namespace package. Add an `__init__.py`. (NOTE: tests are not intended to be a module, __init__.py hence not required.)
     "SLF001",  # Private member accessed
-    "N802",    # Function name should be lowercase
+    "N802",    # Function name should be lowercase  <- @TODO: Reactivate and resolve  @ ClaasRostock, 2025-01-20
     "TRY004",  # Prefer `TypeError` exception for invalid type
 ]
 # `stubs` specific ignores
@@ -139,6 +142,7 @@ raises-require-match-for = [
 ]
 # `tutorials` specific ignores
 "tutorials/**/*" = [
+    "D",       # Missing docstrings
     "S101",    # Use of assert detected
     "PLR2004", # Magic value used in comparison
     "INP001",  # File is part of an implicit namespace package. Add an `__init__.py`. (NOTE: tutorials are not intended to be a module, __init__.py hence not required.)
@@ -154,6 +158,11 @@ raises-require-match-for = [
     "N803", # allow capital variables (e.g X). The botorch interface requireds this
     "N806", # allow capital variables (e.g X). The botorch interface requireds this
 ]
+# utils/logging specific ignores
+"**/utils/logging.py" = [
+    "A005", # Module `logging` shadows a Python standard-library module
+]
+
 
 [lint.pydocstyle]
 convention = "google"

src/axtreme/data/batch_invariant_sampler.py

@@ -111,7 +111,7 @@ def __init__(self, sampler: Sampler[int] | Iterable[int], batch_shape: torch.Siz
         if partial_batch_data_len % batch_shape[0] != 0:
             msg = (
                 f"Final batch will have {partial_batch_data_len} items,"
-                f" which does not fit into batch shape {torch.Size([*batch_shape[:-1] , -1])}"
+                f" which does not fit into batch shape {torch.Size([*batch_shape[:-1], -1])}"
             )
             raise ValueError(msg)
 

src/axtreme/eval/qoi_helpers.py

@@ -66,7 +66,7 @@ def plot_col_histogram(df: pd.DataFrame, ax: Axes, col_name: str = "mean", brute
         f"mean of dist {values.mean():.3f}."
         f" std of dist {values.std():.3f},"
         # Protect against divide by error error
-        f"C.o.V {values.std()/ values.mean() if values.mean() > 1e-2 else np.nan:.3f}"  # noqa: PLR2004
+        f"C.o.V {values.std() / values.mean() if values.mean() > 1e-2 else np.nan:.3f}"  # noqa: PLR2004
     )
     _ = ax.set_title(title_str)
     _ = ax.set_ylabel("density")