updated with latest changes in python_project_template

.gitignore

@@ -143,9 +143,6 @@ cython_debug/
 # PyCharm
 .idea
 
-# modules
-modules.txt
-
 # VS Code
 .vscode/*
 !.vscode/settings.json
@@ -154,3 +151,8 @@ modules.txt
 !.vscode/extensions.json
 !.vscode/*.code-snippets
 
+# Cmake generated files
+CMakeUserPresets.json
+
+# modules
+modules.txt

.vscode/extensions.json

@@ -11,6 +11,8 @@
         "sourcery.sourcery",
         "njpwerner.autodocstring",
         "editorconfig.editorconfig",
+        "ms-toolsai.jupyter",
+        "ms-toolsai.jupyter-renderers",
         "ms-python.mypy-type-checker",
     ],
     // List of extensions recommended by VS Code that should not be recommended for users of this workspace.

.vscode/settings.json

@@ -26,7 +26,7 @@
     "python.analysis.inlayHints.functionReturnTypes": false,
     "python.analysis.inlayHints.pytestParameters": true,
     "python.terminal.executeInFileDir": true,
-    "python.terminal.activateEnvironment": true,
+    "python.terminal.activateEnvironment": false,
     "python.terminal.activateEnvInCurrentTerminal": false,
     "python.analysis.packageIndexDepths": [
         {
@@ -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",
 }

README.md

@@ -1,5 +1,5 @@
 # farn-demo
-demo cases to get started with [farn][farn_docs]
+Demo cases to get started with [farn][farn_docs].
 
 
 ## Development Setup
@@ -69,36 +69,25 @@ C:\path\of\your\choice\osp\cosim\bin
 ### 5. Clone the repository
 Clone the farn-demo repository into your local development directory:
 ```sh
-git clone https://github.com/dnv-innersource/farn-demo path/to/your/dev/farn-demo
+git clone https://github.com/dnv-opensource/farn-demo path/to/your/dev/farn-demo
+```
+Change into the project directory after cloning:
+```sh
+cd farn-demo
 ```
 
 ### 6. Install dependencies
 Run `uv sync` to create a virtual environment and install all project dependencies into it:
 ```sh
 uv sync
 ```
+> **Note**: Using `--no-dev` will omit installing development dependencies.
 
-### 7. (Optional) Install CUDA support
-Run `uv sync` with option `--extra cuda` to in addition install torch with CUDA support:
-```sh
-uv sync --extra cuda
-```
-
-Alternatively, you can manually install torch with CUDA support.
-_Note 1_: Do this preferably _after_ running `uv sync`. That way you ensure a virtual environment exists, which is a prerequisite before you install torch with CUDA support using below `uv pip install` command.
-
-To manually install torch with CUDA support, generate a `uv pip install` command matching your local machine's operating system using the wizard on the official [PyTorch website](https://pytorch.org/get-started/locally/).
-_Note_: As we use `uv` as package manager, remember to replace `pip` in the command generated by the wizard with `uv pip`.
-
-If you are on Windows, the resulting `uv pip install` command will most likely look something like this:
-```sh
-uv pip install torch torchvision torchaudio --index-url https://download.pytorch.org/whl/cu124
-```
+> **Note**: `uv` will create a new virtual environment called `.venv` in the project root directory when running
+> `uv sync` the first time. Optionally, you can create your own virtual environment using e.g. `uv venv`, before running
+> `uv sync`.
 
-_Hint:_ If you are unsure which cuda version to indicate in above `uv pip install .. /cuXXX` command, you can use the shell command `nvidia-smi` on your local system to find out the cuda version supported by the current graphics driver installed on your system. When then generating the `uv pip install` command with the wizard from the [PyTorch website](https://pytorch.org/get-started/locally/), select the cuda version that matches the major version of what your graphics driver supports (major version must match, minor version may deviate).
-
-
-### 8. (Optional) Activate the virtual environment
+### 7. (Optional) Activate the virtual environment
 When using `uv`, there is in almost all cases no longer a need to manually activate the virtual environment. <br>
 `uv` will find the `.venv` virtual environment in the working directory or any parent directory, and activate it on the fly whenever you run a command via `uv` inside your project folder structure:
 ```sh
@@ -117,6 +106,54 @@ To manually activate the virtual environment, run one of the "known" legacy comm
 source .venv/bin/activate
 ```
 
+### 8. Install pre-commit hooks
+The `.pre-commit-config.yaml` file in the project root directory contains a configuration for pre-commit hooks.
+To install the pre-commit hooks defined therein in your local git repository, run:
+```sh
+uv run pre-commit install
+```
+
+All pre-commit hooks configured in `.pre-commit-config.yaml` will now run each time you commit changes.
+
+pre-commit can also manually be invoked, at anytime, using:
+```sh
+uv run pre-commit run --all-files
+```
+
+To skip the pre-commit validation on commits (e.g. when intentionally committing broken code), run:
+```sh
+uv run git commit -m <MSG> --no-verify
+```
+
+To update the hooks configured in `.pre-commit-config.yaml` to their newest versions, run:
+```sh
+uv run pre-commit autoupdate
+```
+
+## Meta
+
+Copyright (c) 2024 [DNV](https://www.dnv.com) SE. All rights reserved.
+
+Frank Lumpitzsch - [@LinkedIn](https://www.linkedin.com/in/frank-lumpitzsch-23013196/) - [email protected]
+
+Claas Rostock - [@LinkedIn](https://www.linkedin.com/in/claasrostock/?locale=en_US) - [email protected]
+
+Seunghyeon Yoo - [@LinkedIn](https://www.linkedin.com/in/seunghyeon-yoo-3625173b/) - [email protected]
+
+Distributed under the MIT license. See [LICENSE](LICENSE.md) for more information.
+
+[https://github.com/dnv-opensource/farn-demo](https://github.com/dnv-opensource/farn-demo)
+
+## Contributing
+
+1. Fork it (<https://github.com/dnv-opensource/farn-demo/fork>)
+2. Create an issue in your GitHub repo
+3. Create your branch based on the issue number and type (`git checkout -b issue-name`)
+4. Evaluate and stage the changes you want to commit (`git add -i`)
+5. Commit your changes (`git commit -am 'place a descriptive commit message here'`)
+6. Push to the branch (`git push origin issue-name`)
+7. Create a new Pull Request in GitHub
+
 
 ## farn Documentation on GitHub
 

farn/hilbert_farnDict

@@ -34,7 +34,7 @@ _layers
             );
             _includeBoundingBox        true;
             _numberOfSamples        20;
-			// upscale re-sampling: _numberOfSamples += _numberOfSamples-1  
+			// upscale re-sampling: _numberOfSamples += _numberOfSamples-1
 			_iterationDepth			5;
         }
         _comment              'hilbert sampling demo case dividend / (minuend - subtrahend) and filtering avoiding div_by_zero';
@@ -60,9 +60,9 @@ _layers
             );
 			resampleRun
             (
-				'if not exist results (if not exist *.csv (cosim run OspSystemStructure.xml -b 0 -d 10) )' 
+				'if not exist results (if not exist *.csv (cosim run OspSystemStructure.xml -b 0 -d 10) )'
             );
-			
+
             runjob
             (
                 .\winjob.cmd

pyproject.toml

@@ -1,34 +1,78 @@
 [project]
 name = "farn-demo"
-version = "0.4.0"
-description = "examples of how to use the farn package."
+version = "0.4.1"
+description = "Demo cases to get started with farn."
 readme = "README.md"
-requires-python = ">= 3.10"
+requires-python = ">= 3.10, < 3.14"
 license = { file = "LICENSE" }
+authors = [
+    { name = "Frank Lumpitzsch", email = "[email protected]" },
+    { name = "Claas Rostock", email = "[email protected]" },
+    { name = "Seunghyeon Yoo", email = "[email protected]" },
+]
+maintainers = [
+    { name = "Claas Rostock", email = "[email protected]" },
+]
+keywords = [
+    "farn",
+    "OSP",
+    "fmi",
+]
+classifiers = [
+    "Development Status :: 5 - Production/Stable",
+    "License :: OSI Approved :: MIT License",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+    "Operating System :: Microsoft :: Windows",
+    "Operating System :: POSIX :: Linux",
+    "Operating System :: MacOS",
+    "Environment :: Console",
+    "Intended Audience :: Developers",
+    "Intended Audience :: Science/Research",
+    "Topic :: Scientific/Engineering",
+    "Topic :: Software Development :: Libraries :: Python Modules",
+]
 dependencies = [
     "farn>=0.4.1",
 ]
 
-[tool.uv]
-dev-dependencies = [
+[project.urls]
+Homepage = "https://github.com/dnv-opensource/farn"
+Documentation = "https://dnv-opensource.github.io/farn/README.html"
+Repository = "https://github.com/dnv-opensource/farn.git"
+Issues = "https://github.com/dnv-opensource/farn/issues"
+Changelog = "https://github.com/dnv-opensource/farn/blob/main/CHANGELOG.md"
+
+
+[dependency-groups]
+dev = [
     "ruff>=0.9.2",
     "pyright>=1.1.392",
     "mypy>=1.14",
     "sourcery>=1.31",
+    "pre-commit>=4.0",
     "pandas-stubs>=2.2",
     "types-psutil>=6.1",
     "types-lxml>=2024.12",
 ]
 
+[tool.uv]
+default-groups = [
+    "dev",
+]
+native-tls = true
+
 [tool.mypy]
 plugins = [
     "numpy.typing.mypy_plugin",
 ]
 mypy_path = "stubs"
 files = [
-    "src",
-    "tests",
-    "demos",
+    "farn",
+    "importSystemStructure",
+    "ospCaseBuilder",
 ]
 exclude = [
     "^src/folder_to_be_excluded/",
@@ -39,18 +83,23 @@ disable_error_code = [
     "import-untyped",
 ]
 
+
 [tool.pyright]
 stubPath = "stubs"
 include = [
     "farn",
     "importSystemStructure",
     "ospCaseBuilder",
 ]
+exclude = [
+    "src/folder_to_be_excluded",
+]
+
 typeCheckingMode = "basic"
 useLibraryCodeForTypes = true
 reportMissingParameterType = "error"
 reportUnknownParameterType = "warning"
-reportUnknownMemberType = "warning" # consider to set to `false` if you work a lot with matplotlib and pandas, which are both not properly typed and known to trigger this warning
+reportUnknownMemberType = "warning"                # consider to set to `false` if you work a lot with matplotlib and pandas, which are both not properly typed and known to trigger this warning
 reportMissingTypeArgument = "error"
 reportPropertyTypeMismatch = "error"
 reportFunctionMemberAccess = "warning"

ruff.toml

@@ -4,6 +4,7 @@ exclude = [
     "dist",
     "*cache",
     "**/__pycache__",
+    "src/folder_to_be_excluded",
 ]
 src = [
     "farn",
@@ -34,8 +35,6 @@ ignore = [
     "D213", # Multi-line docstring summary should start at the second line
     "N999", # Invalid module name
     # Ruff lint rules considered as too strict and hence ignored
-    "ANN101",  # Missing type annotation for `self` argument in instance methods (NOTE: also listed as deprecated by Ruff)
-    "ANN102",  # Missing type annotation for `cls` argument in class methods (NOTE: also listed as deprecated by Ruff)
     "FIX002",  # Line contains TODO, consider resolving the issue
     "TD003",   # Missing issue link on the line following a TODO
     "S101",    # Use of assert detected
@@ -45,6 +44,9 @@ 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,
@@ -53,9 +55,9 @@ ignore = [
     # -> Listed here for easy access and reference.
     # (uncomment to ignore)
     # "N803",   # Argument name should be lowercase (NOTE: ignore to allow capital arguments (e.g X) in scientific code)
-    "N806", # Variable in function should be lowercase (NOTE: ignore to allow capital variables (e.g X) in scientific code)
-    # "TCH002", # Move third-party import into a type-checking block
-    # "TCH003", # Move standard library import into a type-checking block
+    # "N806",   # Variable in function should be lowercase (NOTE: ignore to allow capital variables (e.g X) in scientific code)
+    # "TC002", # Move third-party import into a type-checking block
+    # "TC003", # Move standard library import into a type-checking block
 
     # Ruff lint rules known to be in conflict with Ruff formatter.
     # https://docs.astral.sh/ruff/formatter/#conflicting-lint-rules
@@ -86,8 +88,6 @@ allowed-confusables = [
 [lint.pep8-naming]
 ignore-names = [
     "test_*",
-    "setUp",
-    "tearDown",
 ]
 
 [lint.pylint]
@@ -106,8 +106,9 @@ raises-require-match-for = [
 [lint.per-file-ignores]
 # `__init__.py` specific ignores
 "__init__.py" = [
-    "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
+    "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
 ]
 # `tests` specific ignores
 "tests/**/*" = [
@@ -118,6 +119,8 @@ 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
     "TRY004",  # Prefer `TypeError` exception for invalid type