diff --git a/.github/workflows/_build_and_publish_documentation.yml b/.github/workflows/_build_and_publish_documentation.yml
index 4f33efb4..97cf1e95 100644
--- a/.github/workflows/_build_and_publish_documentation.yml
+++ b/.github/workflows/_build_and_publish_documentation.yml
@@ -12,72 +12,62 @@ jobs:
name: Build and publish documentation in combined version (farn, dictIO, ospx)
runs-on: ubuntu-latest
steps:
- # Checkout farn (active branch)
- - name: Checkout farn (active branch)
+ - name: Checkout active branch
uses: actions/checkout@v5
with:
lfs: true
- - name: prepare farn
+ # ---- BEGIN: Extra steps to merge the documentation of the sub-packages dictIO and ospx into the farn documentation ----
+ - name: Copy farn README and CHANGELOG to docs/source
run: |
cp -v -f README.md docs/source/README_farn.md
cp -v -f CHANGELOG.md docs/source/CHANGELOG_farn.md
sed -i '1 s/Changelog/farn/' docs/source/CHANGELOG_farn.md
-
- # Create temporary subfolders to hold the checked out sub-packages
- - name: Create temporary subfolders
+ - name: Create temporary subfolders for dictIO and ospx
run: |
mkdir dictIO
mkdir ospx
-
- # Checkout dictIO (same branch as the one that triggered the workflow here in farn)
- name: Checkout dictIO (same branch as in farn)
uses: actions/checkout@v5
with:
+ lfs: true
repository: 'dnv-opensource/dictIO'
ref: ${{github.ref}}
path: dictIO
- lfs: true
- - name: Prepare dictIO
+ - name: Copy dictIO README and CHANGELOG to docs/source
run: |
rm -rf dictIO/.git/
cp -v -f dictIO/README.md dictIO/docs/source/README_dictIO.md
cp -v -f dictIO/CHANGELOG.md dictIO/docs/source/CHANGELOG_dictIO.md
sed -i '1 s/Changelog/dictIO/' dictIO/docs/source/CHANGELOG_dictIO.md
-
- # Checkout ospx (same branch as the one that triggered the workflow here in farn)
- name: Checkout ospx (same branch as in farn)
uses: actions/checkout@v5
with:
+ lfs: true
repository: 'dnv-opensource/ospx'
ref: ${{github.ref}}
path: ospx
- lfs: true
- - name: Prepare ospx
+ - name: Copy ospx README and CHANGELOG to docs/source
run: |
rm -rf ospx/.git/
cp -v -f ospx/README.md ospx/docs/source/README_ospx.md
cp -v -f ospx/CHANGELOG.md ospx/docs/source/CHANGELOG_ospx.md
sed -i '1 s/Changelog/ospx/' ospx/docs/source/CHANGELOG_ospx.md
-
- # merge sub-packages into root
- - name: merge sub-packages
+ - name: Merge sub-packages dictIO and ospx into root
run: |
cp -v -n -r dictIO/* .
cp -v -n -r ospx/* .
-
- # replace TOC files by its combined versions
- - name: replace TOC files
+ - name: replace TOC files in docs/source by its combined versions
run: |
cp -v -f docs/source/combined/* docs/source
rm -v -r docs/source/combined
-
+ # ---- END: Extra steps to merge the documentation of the sub-packages dictIO and ospx into the farn documentation ----
- name: Install uv
uses: astral-sh/setup-uv@v7
with:
enable-cache: true
- cache-dependency-glob: "uv.lock"
+ cache-dependency-glob: 'uv.lock'
- name: Install the project
- run: uv sync -U
+ run: uv sync --frozen
- name: Print debugging information
run: |
echo "github.ref:" ${{github.ref}}
diff --git a/.github/workflows/_build_and_publish_documentation.yml.original_single_repo_version.disabled b/.github/workflows/_build_and_publish_documentation.yml.original_single_repo_version.disabled
index 3f39aa7b..8df022f1 100644
--- a/.github/workflows/_build_and_publish_documentation.yml.original_single_repo_version.disabled
+++ b/.github/workflows/_build_and_publish_documentation.yml.original_single_repo_version.disabled
@@ -13,20 +13,16 @@ jobs:
runs-on: ubuntu-latest
steps:
- name: Checkout active branch
- uses: actions/checkout@v4
+ uses: actions/checkout@v5
with:
lfs: true
- name: Install uv
- uses: astral-sh/setup-uv@v5
+ uses: astral-sh/setup-uv@v7
with:
enable-cache: true
- cache-dependency-glob: "uv.lock"
- - name: Set up Python
- uses: actions/setup-python@v5
- with:
- python-version-file: "pyproject.toml"
+ cache-dependency-glob: 'uv.lock'
- name: Install the project
- run: uv sync --upgrade
+ run: uv sync --frozen
- name: Print debugging information
run: |
echo "github.ref:" ${{github.ref}}
diff --git a/.github/workflows/_build_package.yml b/.github/workflows/_build_package.yml
index c48c122e..509ec20a 100644
--- a/.github/workflows/_build_package.yml
+++ b/.github/workflows/_build_package.yml
@@ -15,7 +15,7 @@ jobs:
uses: astral-sh/setup-uv@v7
with:
enable-cache: true
- cache-dependency-glob: "uv.lock"
+ cache-dependency-glob: 'uv.lock'
- name: Build source distribution and wheels
run: uv build
- name: Check build artifacts
diff --git a/.github/workflows/_code_quality.yml b/.github/workflows/_code_quality.yml
index 321bcb3e..6d7f696a 100644
--- a/.github/workflows/_code_quality.yml
+++ b/.github/workflows/_code_quality.yml
@@ -13,7 +13,7 @@ jobs:
uses: astral-sh/setup-uv@v7
with:
enable-cache: true
- cache-dependency-glob: "uv.lock"
+ cache-dependency-glob: 'uv.lock'
- name: Install the project
run: uv sync -U
- name: Run ruff format
@@ -29,7 +29,7 @@ jobs:
uses: astral-sh/setup-uv@v7
with:
enable-cache: true
- cache-dependency-glob: "uv.lock"
+ cache-dependency-glob: 'uv.lock'
- name: Install the project
run: uv sync -U
- name: Run ruff check
@@ -45,7 +45,7 @@ jobs:
uses: astral-sh/setup-uv@v7
with:
enable-cache: true
- cache-dependency-glob: "uv.lock"
+ cache-dependency-glob: 'uv.lock'
- name: Install the project
run: uv sync -U
- name: Run pyright
@@ -61,7 +61,7 @@ jobs:
uses: astral-sh/setup-uv@v7
with:
enable-cache: true
- cache-dependency-glob: "uv.lock"
+ cache-dependency-glob: 'uv.lock'
- name: Install the project
run: uv sync -U
- name: Run mypy
diff --git a/.github/workflows/_test.yml b/.github/workflows/_test.yml
index 1850affb..3c34a4f1 100644
--- a/.github/workflows/_test.yml
+++ b/.github/workflows/_test.yml
@@ -7,6 +7,7 @@ jobs:
name: Test (Python ${{ matrix.python }}, ${{ matrix.os }})
runs-on: ${{ matrix.os }}
strategy:
+ fail-fast: true
matrix:
os: [ubuntu-latest, windows-latest, macos-latest]
python: ['3.11', '3.12', '3.13', '3.14']
@@ -17,7 +18,7 @@ jobs:
uses: astral-sh/setup-uv@v7
with:
enable-cache: true
- cache-dependency-glob: "uv.lock"
+ cache-dependency-glob: 'uv.lock'
- name: Install the project
run: uv sync -p ${{ matrix.python }} -U --no-dev
- name: Run pytest
diff --git a/.github/workflows/_test_future.yml b/.github/workflows/_test_future.yml
index b3bb7fd9..80b10f0d 100644
--- a/.github/workflows/_test_future.yml
+++ b/.github/workflows/_test_future.yml
@@ -9,6 +9,7 @@ jobs:
continue-on-error: true
runs-on: ${{ matrix.os }}
strategy:
+ fail-fast: true
matrix:
os: [ubuntu-latest, windows-latest]
python:
@@ -21,7 +22,18 @@ jobs:
uses: astral-sh/setup-uv@v7
with:
enable-cache: true
- cache-dependency-glob: "uv.lock"
+ cache-dependency-glob: 'uv.lock'
+ - name: Remove Python upper version constraint from pyproject.toml
+ shell: pwsh
+ run: |
+ $File = Get-Item pyproject.toml
+ $Content = Get-Content $File -Raw
+ [regex]$RequiresPythonPattern = '(?=]{1,2}\s?\d+\.\d+\.?\d*\.?[\d\w]*\s?)(,\s?[<=]{1,2}\s?\d+\.?\d*\.?\d*\.?[\d\w]*\s?)?(")'
+ if ($Content -match $RequiresPythonPattern) {
+ $RequiresPythonFound = $Matches[0]
+ $RequiresPythonReplacement = $Matches[1] + $Matches[3]
+ $Content -Replace $RequiresPythonFound, $RequiresPythonReplacement | Set-Content $File -NoNewline
+ }
- name: Install the project
run: uv sync -p ${{ matrix.python.uvpy }} -U --no-dev
- name: Run pytest
diff --git a/.gitignore b/.gitignore
index 63f89273..d4144e5a 100644
--- a/.gitignore
+++ b/.gitignore
@@ -91,7 +91,7 @@ ipython_config.py
# It is generally recommended to include `uv.lock` in version control.
# However, in case of collaboration, if having platform-specific dependencies or dependencies
# having no cross-platform support, `uv` might install dependencies in one environment that don't work in another.
-# In such case, `uv.lock` should be added to `.gitignore`
+# In such case, `uv.lock` should be added to `.gitignore` (and, as such, excluded from version control).
# uv.lock
# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index c7ca41c9..80216739 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -9,7 +9,7 @@ repos:
- id: check-toml
- id: check-merge-conflict
- repo: https://github.com/astral-sh/ruff-pre-commit
- rev: v0.15.1
+ rev: v0.15.9
hooks:
- id: ruff-format
- id: ruff-check
diff --git a/.vscode/launch.json b/.vscode/launch.json
index 215d34d7..48299a63 100644
--- a/.vscode/launch.json
+++ b/.vscode/launch.json
@@ -19,7 +19,11 @@
"autoReload": {
"enable": true
},
+ "subProcess": true,
"justMyCode": true,
+ "redirectOutput": true, // pipe stdout/stderr to Debug Console
+ "showReturnValue": true,
+ "logToFile": false, // set true temporarily when diagnosing debugger issues
},
{
"name": "Python: Current File, cwd = file dir",
@@ -28,10 +32,14 @@
"cwd": "${fileDirname}", // working dir = dir where current file is
"program": "${file}",
"console": "integratedTerminal",
- "justMyCode": true,
"autoReload": {
"enable": true
},
+ "subProcess": true,
+ "justMyCode": true,
+ "redirectOutput": true,
+ "showReturnValue": true,
+ "logToFile": false,
},
{
"name": "Python: Current File, cwd = workspace root folder",
@@ -43,14 +51,18 @@
"autoReload": {
"enable": true
},
+ "subProcess": true,
"justMyCode": true,
+ "redirectOutput": true,
+ "showReturnValue": true,
+ "logToFile": false,
},
{
"name": "farn test sample and generate test_farnDict",
"type": "debugpy",
"request": "launch",
"cwd": "${workspaceFolder}\\tests\\test_working_directory",
- "program": "${workspaceFolder}\\src\\farn\\cli\\farn.py",
+ "program": "${workspaceFolder}\\src\\farn\\cli\\__main__.py",
"args": [
"test_farnDict",
"--sample",
@@ -60,14 +72,18 @@
"autoReload": {
"enable": true
},
+ "subProcess": true,
"justMyCode": true,
+ "redirectOutput": true,
+ "showReturnValue": true,
+ "logToFile": false,
},
{
"name": "farn test generate test_farnDict",
"type": "debugpy",
"request": "launch",
"cwd": "${workspaceFolder}\\tests\\test_working_directory",
- "program": "${workspaceFolder}\\src\\farn\\cli\\farn.py",
+ "program": "${workspaceFolder}\\src\\farn\\cli\\__main__.py",
"args": [
"test_farnDict",
"-g",
@@ -76,14 +92,18 @@
"autoReload": {
"enable": true
},
+ "subProcess": true,
"justMyCode": true,
+ "redirectOutput": true,
+ "showReturnValue": true,
+ "logToFile": false,
},
{
"name": "farn test execute test_farnDict",
"type": "debugpy",
"request": "launch",
"cwd": "${workspaceFolder}\\tests\\test_working_directory",
- "program": "${workspaceFolder}\\src\\farn\\cli\\farn.py",
+ "program": "${workspaceFolder}\\src\\farn\\cli\\__main__.py",
"args": [
"sampled.test_farnDict",
"-e",
@@ -93,14 +113,18 @@
"autoReload": {
"enable": true
},
+ "subProcess": true,
"justMyCode": true,
+ "redirectOutput": true,
+ "showReturnValue": true,
+ "logToFile": false,
},
{
"name": "farn test sample test_farnDict_v4",
"type": "debugpy",
"request": "launch",
"cwd": "${workspaceFolder}\\tests\\test_working_directory",
- "program": "${workspaceFolder}\\src\\farn\\cli\\farn.py",
+ "program": "${workspaceFolder}\\src\\farn\\cli\\__main__.py",
"args": [
"test_farnDict_v4",
"--sample",
@@ -109,14 +133,18 @@
"autoReload": {
"enable": true
},
+ "subProcess": true,
"justMyCode": true,
+ "redirectOutput": true,
+ "showReturnValue": true,
+ "logToFile": false,
},
{
"name": "farn test generate test_farnDict_v4",
"type": "debugpy",
"request": "launch",
"cwd": "${workspaceFolder}\\tests\\test_working_directory",
- "program": "${workspaceFolder}\\src\\farn\\cli\\farn.py",
+ "program": "${workspaceFolder}\\src\\farn\\cli\\__main__.py",
"args": [
"sampled.test_farnDict_v4",
"-g",
@@ -125,14 +153,18 @@
"autoReload": {
"enable": true
},
+ "subProcess": true,
"justMyCode": true,
+ "redirectOutput": true,
+ "showReturnValue": true,
+ "logToFile": false,
},
{
"name": "farn test sample and generate test_farnDict_v4",
"type": "debugpy",
"request": "launch",
"cwd": "${workspaceFolder}\\tests\\test_working_directory",
- "program": "${workspaceFolder}\\src\\farn\\cli\\farn.py",
+ "program": "${workspaceFolder}\\src\\farn\\cli\\__main__.py",
"args": [
"test_farnDict_v4",
"--sample",
@@ -142,14 +174,18 @@
"autoReload": {
"enable": true
},
+ "subProcess": true,
"justMyCode": true,
+ "redirectOutput": true,
+ "showReturnValue": true,
+ "logToFile": false,
},
{
"name": "farn test execute test_farnDict_v4",
"type": "debugpy",
"request": "launch",
"cwd": "${workspaceFolder}\\tests\\test_working_directory",
- "program": "${workspaceFolder}\\src\\farn\\cli\\farn.py",
+ "program": "${workspaceFolder}\\src\\farn\\cli\\__main__.py",
"args": [
"sampled.test_farnDict_v4",
"-e",
@@ -159,14 +195,18 @@
"autoReload": {
"enable": true
},
+ "subProcess": true,
"justMyCode": true,
+ "redirectOutput": true,
+ "showReturnValue": true,
+ "logToFile": false,
},
{
"name": "farn test generate test_farnDict logfile in subdir",
"type": "debugpy",
"request": "launch",
"cwd": "${workspaceFolder}\\tests\\test_working_directory",
- "program": "${workspaceFolder}\\src\\farn\\cli\\farn.py",
+ "program": "${workspaceFolder}\\src\\farn\\cli\\__main__.py",
"args": [
"test_farnDict",
"-g",
@@ -179,7 +219,11 @@
"autoReload": {
"enable": true
},
+ "subProcess": true,
"justMyCode": true,
+ "redirectOutput": true,
+ "showReturnValue": true,
+ "logToFile": false,
},
]
}
\ No newline at end of file
diff --git a/.vscode/settings.json b/.vscode/settings.json
index f48f8042..efe9d309 100644
--- a/.vscode/settings.json
+++ b/.vscode/settings.json
@@ -49,4 +49,4 @@
"mypy-type-checker.reportingScope": "custom",
"mypy-type-checker.preferDaemon": true,
"ruff.configurationPreference": "filesystemFirst",
-}
\ No newline at end of file
+}
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 3dfb1ee2..0e66c983 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -8,6 +8,30 @@ The changelog format is based on [Keep a Changelog](https://keepachangelog.com/e
* -/-
+## [0.5.0] - 2026-04-09
+
+### BREAKING Changes
+* Moved module `farn.run.utils.threading` to `farn.utils.threading`
+* Renamed and moved module `farn.run.subProcess` to `farn.utils.sub_process`
+* Renamed and moved module `farn.run.batchProcess` to `farn.batch.batch_processor`
+* Renamed module `farn.sampling.sampling` to `farn.sampling.discrete` (because the only class it actually contains is `DiscreteSampling`
+
+### Changed
+* Updated code base with latest changes in python_project_template v0.2.10
+* Python modules: Changed `__ALL__` to `__all__` (lowercase, PEP8 and PEP257 compliant).
+
+### Dependencies
+* .pre-commit-config.yaml: Updated rev of ruff-pre-commit to v0.15.9
+* Updated to dictIO>=0.4.4
+* Updated to numpy>=2.4
+* Updated to ospx>=0.3.5
+* Updated to pytest-cov>=7.1
+* Updated to ruff>=0.15.9
+* Updated to scipy>=1.17.1
+* Updated to sphinx-argparse-cli>=1.21.3
+* Updated to types-lxml>=2026.2
+
+
## [0.4.4] - 2026-03-17
### Solved
diff --git a/LICENSE b/LICENSE
index 90b0cc37..8f54c6d1 100644
--- a/LICENSE
+++ b/LICENSE
@@ -1,6 +1,6 @@
MIT License
-Copyright (c) 2024 [DNV](https://www.dnv.com) [open source](https://github.com/dnv-opensource)
+Copyright (c) 2026 [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
diff --git a/README.md b/README.md
index 5943e6e2..0a9f1466 100644
--- a/README.md
+++ b/README.md
@@ -26,13 +26,8 @@ farn
```sh
pip install farn
```
-farn requires the following two (sub-)packages:
-1. [dictIO][dictIO_docs]: foundation package, enabling farn to handle configuration files in dictIO dict file format.
-2. [ospx][ospx_docs]: extension package, enabling farn to generate OSP (co-)simulation files.
-However, both get installed automatically with farn (just pip install farn and you're done).
-
-## Usage Example
+## Usage
farn provides both an API for use inside Python as well as a CLI for shell execution of core functions.
@@ -48,7 +43,7 @@ The above task can also be invoked from the command line, using the 'farn' comma
farn farnDict --sample --generate
```
-_For more examples and usage, please refer to [farn's documentation][farn_docs]._
+_For more examples and usage, please refer to farn's [documentation][farn_docs]._
Further, the [farn-demo][farn_demo_repo] repository on GitHub is an excellent place for a jumpstart into farn.
Simply clone the [farn-demo][farn_demo_repo] repository to your local machine and click through the demos and related READMEs, by recommendation in the following sequence:
@@ -87,7 +82,7 @@ uv self update
```
### 2. Install Python
-This project requires Python 3.10 or later.
+This project requires Python 3.11 or later.
If you don't already have a compatible version installed on your machine, the probably most comfortable way to install Python is through `uv`:
```sh
uv python install
@@ -111,15 +106,18 @@ cd farn
```
### 4. Install dependencies
-Run `uv sync` to create a virtual environment and install all project dependencies into it:
+Run `uv sync -U` to create a virtual environment and install all project dependencies into it:
```sh
-uv sync
+uv sync -U
```
> **Note**: Using `--no-dev` will omit installing development dependencies.
+> **Explanation**: The `-U` option stands for `--update`. It forces `uv` to fetch and install the latest versions of all dependencies,
+> ensuring that your environment is up-to-date.
+
> **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`.
+> `uv sync -U` the first time. Optionally, you can create your own virtual environment using e.g. `uv venv`, before running
+> `uv sync -U`.
### 5. (Optional) Activate the virtual environment
When using `uv`, there is in almost all cases no longer a need to manually activate the virtual environment.
@@ -197,7 +195,7 @@ Distributed under the MIT license. See [LICENSE](LICENSE.md) for more informatio
For your contribution, please make sure you follow the [STYLEGUIDE](STYLEGUIDE.md) before creating the Pull Request.
-[dictIO_docs]: https://dnv-opensource.github.io/dictIO/README.html
-[ospx_docs]: https://dnv-opensource.github.io/ospx/README.html
[farn_docs]: https://dnv-opensource.github.io/farn/README.html
[farn_demo_repo]: https://github.com/dnv-opensource/farn-demo
+[dictIO_docs]: https://dnv-opensource.github.io/dictIO/README.html
+[ospx_docs]: https://dnv-opensource.github.io/ospx/README.html
diff --git a/docs/source/cli.batchProcess.rst b/docs/source/cli.batchProcess.rst
index 23e7516a..7e7d18e2 100644
--- a/docs/source/cli.batchProcess.rst
+++ b/docs/source/cli.batchProcess.rst
@@ -1,3 +1,3 @@
-.. sphinx_argparse_cli::
- :module: farn.run.cli.batchProcess
- :func: _argparser
+.. sphinx_argparse_cli::
+ :module: farn.cli.batchProcess
+ :func: _argparser
diff --git a/docs/source/combined/cli.sub.dictIO.rst b/docs/source/combined/cli.sub.dictIO.rst
index 4191b176..4af6f0de 100644
--- a/docs/source/combined/cli.sub.dictIO.rst
+++ b/docs/source/combined/cli.sub.dictIO.rst
@@ -4,4 +4,4 @@ dictIO
.. toctree::
:maxdepth: 3
- cli.dict_parser
+ cli.__main__
diff --git a/docs/source/combined/cli.sub.farn.rst b/docs/source/combined/cli.sub.farn.rst
index be3a008d..881cc079 100644
--- a/docs/source/combined/cli.sub.farn.rst
+++ b/docs/source/combined/cli.sub.farn.rst
@@ -1,8 +1,8 @@
-farn
-----
-
-.. toctree::
- :maxdepth: 3
-
- cli.farn
- cli.batchProcess
+farn
+----
+
+.. toctree::
+ :maxdepth: 3
+
+ cli.__main__
+ cli.batchProcess
diff --git a/docs/source/farn.rst b/docs/source/farn.rst
index 703e23c3..78ac0e39 100644
--- a/docs/source/farn.rst
+++ b/docs/source/farn.rst
@@ -9,8 +9,8 @@ Subpackages
:template: custom-module.rst
:recursive:
+ farn.batch
farn.core
- farn.run
farn.sampling
farn.utils
diff --git a/docs/source/farn_example.md b/docs/source/farn_example.md
index 0aefe80d..90303724 100644
--- a/docs/source/farn_example.md
+++ b/docs/source/farn_example.md
@@ -1,181 +1,180 @@
-# Example of farn API usage
-
-The following gives an example of how the farn API can be used in conjunction with OSP cosim and the ospx package.
-
-## Case
-
-Case is a simple dataclass designed to hold case-specific information as instance attributes.
-Below example uses the most typical / important ones:
-
-~~~py
-from pathlib import Path
-from typing import Dict, List
-from farn.core import Case, Parameter
-
-case_name: str = "test_001"
-
-case_folder: Path = Path("path/to/your/experiment/cases") / case_name
-
-case_parameters: List[Parameter] = [
- Parameter("x1", 1.0),
- Parameter("x2", 2.0),
- Parameter("x3", 3.0),
-]
-
-command_sets: Dict[str, List[str]] = {
- "prepare": [
- "copy path/to/template/dir/caseDict .", # copy a (case-agnostic) ospx config file from a template directory into the case folder
- "dictParser caseDict", # parse the ospx config file. This will make it case-specific
- "ospCaseBuilder parsed.caseDict", # build the (case-specific) OspSystemStructure.xml
- ],
- "run": [
- "cosim run OspSystemStructure.xml -b 0 -d 10", # run OSP cosim
- ],
- "post": [
- "watchCosim -d watchDict", # optional post-processing. watchCosim creates a sub-folder 'results' in the case folder
- ],
-}
-
-case: Case = Case(
- case=case_name,
- path=case_folder,
- is_leaf=True,
- parameters=case_parameters,
- command_sets=command_sets,
-)
-~~~
-
-
-## Cases
-
-Many farn functions expect not a single Case object, but a list of Case objects passed in.
-So, even if you create only a single Case object, you will likely need to wrap it in a Cases list for processing.
-
-~~~py
-from farn.core import Cases
-
-cases: Cases = Cases()
-cases.append(case)
-~~~
-
-## Create case folder(s)
-
-~~~py
-from farn.farn import create_case_folders
-
-_ = create_case_folders(cases)
-~~~
-
-## Create paramDict file in case folder(s)
-
-It is a convention used by both farn and ospx that a 'paramDict' file is expected to exist in the case folder
-which contains the case-specific values of all varied parameters.
-create_param_dict_files() will create this paramDict file in the case folder(s):
-
-~~~py
-from farn.farn import create_param_dict_files
-
-_ = create_param_dict_files(cases)
-~~~
-
-
-## Prepare OSP simulation case(s)
-
-Execute the command_set that performs preparatory tasks in your case folder(s).
-
-~~~py
-from farn.farn import execute_command_set
-
-_ = execute_command_set(
- cases=cases,
- command_set="prepare",
-)
-~~~
-
-
-## Run OSP simulation case(s)
-
-Execute the command_set that actually runs your simulation case(s).
-
-~~~py
-_ = execute_command_set(
- cases=cases,
- command_set="run",
-)
-~~~
-
-## Execute post-processing (optional)
-
-Execute the command_set that performs post-processing tasks in your case folder(s) (if any).
-
-~~~py
-_ = execute_command_set(
- cases=cases,
- command_set="post",
-)
-~~~
-
-## Read results
-
-Reading results after your simulation cases finished can be rather individual and there will surely be multiple ways to accomplish this.
-Two exemplary ways being
-
-a) You can read the *.csv files that cosim.exe generates, i.e. by reading them into a Pandas DataFrame.
-
-b) In case you executed watchCosim as a post-processing step, a sub-folder 'results' will exist in each case folder that contains the results additionally as a resultDict file.
-
-Variant a) is less complex and can be done with Pandas (no example given here).
-Variant b) offers some additional possibilities but requires also additional code.
-Below hence an example for variant b), i.e. how to read a resultDict file generated by watchCosim
-
-~~~py
-from typing import Any, Dict, List
-from pandas import DataFrame, Series
-from dictIO import DictReader
-from dictIO.utils.path import relative_path
-
-# @NOTE: Adjust 'component_name' and 'variable_name' to what is defined in your (FMU) model
-# @NOTE: 'y' is just an example. Add mappings for more column names / variables as you like and need.
-mapping: Dict[str, Dict[str, Any]] = {
- "y": { # column name you want to map a variable to
- "key": "component_name|variable_name:latestValue", # variable in FMU
- "unit": 1, # usually 1, unless you want to apply a scaling factor
- }
-}
-
-# column names
-names: List[str] = [name for name in mapping if not re.search("(^_|COMMENT)", name)]
-
-series: Dict[str, Series] = {
- "path": Series(data=None, dtype=dtype(str), name="path"),
-}
-
-for index, case in cases:
-
- case_folder: Path = case.path
- result_folder: Path = case_folder / "results"
- result_dict_file: Path = result_folder / "watchDict-test_project-resultDict" # adapt to output of watchCosim.
-
- series["path"].loc[index] = str(relative_path(Path.cwd(), case_folder))
-
- result_dict = DictReader.read(result_dict_file, includes=False, comments=False)
-
- for name in names:
- value: Any = None
- value_eval_string = "result_dict['" + "']['".join(mapping[name]["key"].split(":")) + "']"
- try:
- value = eval(value_eval_string)
- except Exception:
- logger.warning(f'"{value_eval_string}" not in {result_dict_file}')
- continue
-
- if name not in series:
- series[name] = Series(data=None, dtype=dtype(type(value)), name=name)
-
- if value is not None:
- series[name].loc[index] = value
-
-df: DataFrame = DataFrame(data=series)
-
-df.set_index("path", inplace=True) # optional. Makes the 'path' column the DataFrame's index
-~~~
\ No newline at end of file
+# Example of farn API usage
+
+The following gives an example of how the farn API can be used in conjunction with OSP cosim and the ospx package.
+
+## Case
+
+Case is a simple dataclass designed to hold case-specific information as instance attributes.
+Below example uses the most typical / important ones:
+
+~~~py
+from pathlib import Path
+from typing import Dict, List
+from farn.core import Case, Parameter
+
+case_name: str = "test_001"
+
+case_folder: Path = Path("path/to/your/experiment/cases") / case_name
+
+case_parameters: List[Parameter] = [
+ Parameter("x1", 1.0),
+ Parameter("x2", 2.0),
+ Parameter("x3", 3.0),
+]
+
+command_sets: Dict[str, List[str]] = {
+ "prepare": [
+ "copy path/to/template/dir/caseDict .", # copy a (case-agnostic) ospx config file from a template directory into the case folder
+ "dictParser caseDict", # parse the ospx config file. This will make it case-specific
+ "ospCaseBuilder parsed.caseDict", # build the (case-specific) OspSystemStructure.xml
+ ],
+ "run": [
+ "cosim run OspSystemStructure.xml -b 0 -d 10", # run OSP cosim
+ ],
+ "post": [
+ "watchCosim -d watchDict", # optional post-processing. watchCosim creates a sub-folder 'results' in the case folder
+ ],
+}
+
+case: Case = Case(
+ case=case_name,
+ path=case_folder,
+ is_leaf=True,
+ parameters=case_parameters,
+ command_sets=command_sets,
+)
+~~~
+
+
+## Cases
+
+Many farn functions expect not a single Case object, but a list of Case objects passed in.
+So, even if you create only a single Case object, you will likely need to wrap it in a Cases list for processing.
+
+~~~py
+from farn.core import Cases
+
+cases: Cases = Cases()
+cases.append(case)
+~~~
+
+## Create case folder(s)
+
+~~~py
+from farn import create_case_folders
+
+_ = create_case_folders(cases)
+~~~
+
+## Create paramDict file in case folder(s)
+
+It is a convention used by both farn and ospx that a 'paramDict' file is expected to exist in the case folder
+which contains the case-specific values of all varied parameters.
+create_param_dict_files() will create this paramDict file in the case folder(s):
+
+~~~py
+from farn import create_param_dict_files
+
+_ = create_param_dict_files(cases)
+~~~
+
+
+## Prepare OSP simulation case(s)
+
+Execute the command_set that performs preparatory tasks in your case folder(s).
+
+~~~py
+from farn import execute_command_set
+
+_ = execute_command_set(
+ cases=cases,
+ command_set="prepare",
+)
+~~~
+
+
+## Run OSP simulation case(s)
+
+Execute the command_set that actually runs your simulation case(s).
+
+~~~py
+_ = execute_command_set(
+ cases=cases,
+ command_set="run",
+)
+~~~
+
+## Execute post-processing (optional)
+
+Execute the command_set that performs post-processing tasks in your case folder(s) (if any).
+
+~~~py
+_ = execute_command_set(
+ cases=cases,
+ command_set="post",
+)
+~~~
+
+## Read results
+
+Reading results after your simulation cases finished can be rather individual and there will surely be multiple ways to accomplish this.
+Two exemplary ways being
+
+a) You can read the *.csv files that cosim.exe generates, i.e. by reading them into a Pandas DataFrame.
+
+b) In case you executed watchCosim as a post-processing step, a sub-folder 'results' will exist in each case folder that contains the results additionally as a resultDict file.
+
+Variant a) is less complex and can be done with Pandas (no example given here).
+Variant b) offers some additional possibilities but requires also additional code.
+Below hence an example for variant b), i.e. how to read a resultDict file generated by watchCosim
+
+~~~py
+from typing import Any, Dict, List
+from pandas import DataFrame, Series
+from dictIO import DictReader
+from dictIO.utils.path import relative_path
+
+# @NOTE: Adjust 'component_name' and 'variable_name' to what is defined in your (FMU) model
+# @NOTE: 'y' is just an example. Add mappings for more column names / variables as you like and need.
+mapping: Dict[str, Dict[str, Any]] = {
+ "y": { # column name you want to map a variable to
+ "key": "component_name|variable_name:latestValue", # variable in FMU
+ "unit": 1, # usually 1, unless you want to apply a scaling factor
+ }
+}
+
+# column names
+names: List[str] = [name for name in mapping if not re.search("(^_|COMMENT)", name)]
+
+series: Dict[str, Series] = {
+ "path": Series(data=None, dtype=dtype(str), name="path"),
+}
+
+for index, case in cases:
+ case_folder: Path = case.path
+ result_folder: Path = case_folder / "results"
+ result_dict_file: Path = result_folder / "watchDict-test_project-resultDict" # adapt to output of watchCosim.
+
+ series["path"].loc[index] = str(relative_path(Path.cwd(), case_folder))
+
+ result_dict = DictReader.read(result_dict_file, includes=False, comments=False)
+
+ for name in names:
+ value: Any = None
+ value_eval_string = "result_dict['" + "']['".join(mapping[name]["key"].split(":")) + "']"
+ try:
+ value = eval(value_eval_string)
+ except Exception:
+ logger.warning(f'"{value_eval_string}" not in {result_dict_file}')
+ continue
+
+ if name not in series:
+ series[name] = Series(data=None, dtype=dtype(type(value)), name=name)
+
+ if value is not None:
+ series[name].loc[index] = value
+
+df: DataFrame = DataFrame(data=series)
+
+df.set_index("path", inplace=True) # optional. Makes the 'path' column the DataFrame's index
+~~~
diff --git a/pyproject.toml b/pyproject.toml
index 1b35dd1f..6efc1e02 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -11,7 +11,6 @@ only-include = [
".coveragerc",
".editorconfig",
".pre-commit-config.yaml",
- "manage.py",
"pyproject.toml",
"pytest.ini",
"ruff.toml",
@@ -23,6 +22,9 @@ packages = [
"src/farn",
]
+[tool.hatch.metadata]
+allow-direct-references = true
+
[project]
name = "farn"
version = "0.4.4"
@@ -61,16 +63,16 @@ classifiers = [
]
dependencies = [
"lxml>=6.0",
- "numpy>=2.3",
- "scipy>=1.17.0",
+ "numpy>=2.4",
+ "scipy>=1.17.1",
"pandas>=3.0",
"matplotlib>=3.10",
"pillow>=12.1",
"pyDOE3>=1.6.2",
"psutil>=7.2",
"hilbertcurve>=2.0",
- "dictIO>=0.4.3",
- "ospx>=0.3.3",
+ "dictIO>=0.4.4",
+ "ospx>=0.3.5",
]
[project.urls]
@@ -84,24 +86,24 @@ Changelog = "https://github.com/dnv-opensource/farn/blob/main/CHANGELOG.md"
[dependency-groups]
dev = [
"pytest>=9.0",
- "pytest-cov>=7.0",
- "ruff>=0.15.1",
+ "pytest-cov>=7.1",
+ "ruff>=0.15.9",
"pyright>=1.1.408",
"mypy>=1.19.1",
"sourcery>=1.43.0",
"pre-commit>=4.5",
"Sphinx>=9.0",
- "sphinx-argparse-cli>=1.20.1",
+ "sphinx-argparse-cli>=1.21.3",
"sphinx-autodoc-typehints>=3.6",
"sphinxcontrib-mermaid>=2.0",
"myst-parser>=5.0",
"furo>=2025.12",
- "nbconvert>=7.17",
"jupyter>=1.1.1",
- "jupyter-client>=8.8",
+ "nbconvert>=7.17",
"pandas-stubs>=3.0",
+ "types-lxml>=2026.2",
+ "scipy-stubs>=1.17.1",
"types-psutil>=7.2",
- "types-lxml>=2026.1",
]
[tool.uv]
@@ -118,7 +120,7 @@ required-environments = [
[project.scripts]
farn = "farn.cli.__main__:main"
-batchProcess = "farn.run.cli.batchProcess:main"
+batchProcess = "farn.cli.batchProcess:main"
[tool.mypy]
@@ -151,6 +153,7 @@ exclude = [
"**/__pycache__",
"**/.*",
".venv",
+ "src/folder_to_be_excluded",
]
typeCheckingMode = "basic"
diff --git a/ruff.toml b/ruff.toml
index 4e4405ab..1e984ec8 100644
--- a/ruff.toml
+++ b/ruff.toml
@@ -27,6 +27,7 @@ ignore = [
"PLR0911", # Too many return statements <- @TODO: reactivate and resolve @CLAROS, 2024-10-21
"PLR0912", # Too many branches <- @TODO: reactivate and resolve @CLAROS, 2024-10-21
"PLR0915", # Too many statements <- @TODO: reactivate and resolve @CLAROS, 2024-10-21
+
# Ruff lint rules considered as too strict and hence ignored
"FIX002", # Line contains TODO, consider resolving the issue
"TD003", # Missing issue link on the line following a TODO
@@ -150,20 +151,24 @@ raises-require-match-for = [
"T201", # `print` found
"E402", # Module level import not at top of cell
]
+# utils/logging specific ignores
+"**/utils/logging.py" = [
+ "A005", # Module `logging` shadows a Python standard-library module
+]
# docs/source/conf.py specific ignores
"docs/source/conf.py" = [
"INP001", # File is part of an implicit namespace package. Add an `__init__.py`. (NOTE: conf.py is not intended to be a module, __init__.py hence not required.)
"A001", # Variable {name} is shadowing a Python builtin
"D100", # Missing docstring in public module
]
-# utils/*.py specific ignores
-"**/utils/*.py" = [
- "A005", # Module {name} shadows a Python standard-library module (applies to logging.py, threading.py, os.py)
+# types.py specific ignores
+"**/types.py" = [
+ "A005", # Module `types` shadows a Python standard-library module
]
-
[lint.pydocstyle]
convention = "numpy"
[format]
docstring-code-format = true
+# preview = true # uncomment to enable preview features of Ruff formatter (https://docs.astral.sh/ruff/formatter/#preview-features)
diff --git a/src/farn/__init__.py b/src/farn/__init__.py
index df493505..dff397f6 100644
--- a/src/farn/__init__.py
+++ b/src/farn/__init__.py
@@ -1,11 +1,21 @@
"""farn package."""
-from .farn import (
- run_farn as run_farn,
- create_samples as create_samples,
- create_cases as create_cases,
- create_case_folders as create_case_folders,
- create_param_dict_files as create_param_dict_files,
- create_case_list_files as create_case_list_files,
- execute_command_set as execute_command_set,
+from farn.farn import (
+ run_farn,
+ create_samples,
+ create_cases,
+ create_case_folders,
+ create_param_dict_files,
+ create_case_list_files,
+ execute_command_set,
)
+
+__all__ = [
+ "create_case_folders",
+ "create_case_list_files",
+ "create_cases",
+ "create_param_dict_files",
+ "create_samples",
+ "execute_command_set",
+ "run_farn",
+]
diff --git a/src/farn/batch/__init__.py b/src/farn/batch/__init__.py
new file mode 100644
index 00000000..ebec34db
--- /dev/null
+++ b/src/farn/batch/__init__.py
@@ -0,0 +1 @@
+from farn.batch.batch_processor import AsyncBatchProcessor
diff --git a/src/farn/run/batchProcess.py b/src/farn/batch/batch_processor.py
similarity index 95%
rename from src/farn/run/batchProcess.py
rename to src/farn/batch/batch_processor.py
index bf7ee8e4..ed5b07e5 100644
--- a/src/farn/run/batchProcess.py
+++ b/src/farn/batch/batch_processor.py
@@ -3,8 +3,8 @@
from psutil import cpu_count
-from farn.run.subProcess import execute_in_sub_process
-from farn.run.utils.threading import JobQueue, Worker
+from farn.utils.sub_process import execute_in_sub_process
+from farn.utils.threading import JobQueue, Worker
logger = logging.getLogger(__name__)
diff --git a/src/farn/cli/__init__.py b/src/farn/cli/__init__.py
index e69de29b..753505c9 100644
--- a/src/farn/cli/__init__.py
+++ b/src/farn/cli/__init__.py
@@ -0,0 +1 @@
+"""Command line interfaces."""
diff --git a/src/farn/cli/__main__.py b/src/farn/cli/__main__.py
index 6d7ba4ed..e3ea01da 100644
--- a/src/farn/cli/__main__.py
+++ b/src/farn/cli/__main__.py
@@ -1,10 +1,10 @@
#!/usr/bin/env python
-# coding utf-8
+"""farn command line interface."""
import argparse
import logging
-import sys
-from argparse import ArgumentParser
+import pprint
+from importlib import metadata
from pathlib import Path
from farn import run_farn
@@ -13,8 +13,17 @@
logger = logging.getLogger(__name__)
+def _get_version() -> str:
+ """Return the installed package version, or a safe fallback if unavailable."""
+ try:
+ return metadata.version("farn")
+ except metadata.PackageNotFoundError:
+ # Fallback when package metadata is not available (e.g. running from source)
+ return "farn (version unknown)"
+
+
def _argparser() -> argparse.ArgumentParser:
- parser = ArgumentParser(
+ parser = argparse.ArgumentParser(
prog="farn",
usage="%(prog)s farn_dict_file [options [args]]",
epilog="_________________farn___________________",
@@ -92,7 +101,7 @@ def _argparser() -> argparse.ArgumentParser:
"-q",
"--quiet",
action="store_true",
- help="console output will be quiet.",
+ help=("console output will be quiet."),
default=False,
)
@@ -100,7 +109,7 @@ def _argparser() -> argparse.ArgumentParser:
"-v",
"--verbose",
action="store_true",
- help="console output will be verbose.",
+ help=("console output will be verbose."),
default=False,
)
@@ -123,30 +132,32 @@ def _argparser() -> argparse.ArgumentParser:
required=False,
)
+ _ = parser.add_argument(
+ "-V",
+ "--version",
+ action="version",
+ version=_get_version(),
+ )
+
return parser
def main() -> None:
- """Entry point for console script as configured in setup.cfg.
+ """Entry point for console script as configured in pyproject.toml.
Runs the command line interface and parses arguments and options entered on the console.
"""
parser = _argparser()
- try:
- args = parser.parse_args()
- except Exception: # noqa: BLE001
- parser.print_help()
- sys.exit(0)
+ args = parser.parse_args()
# Configure Logging
# ..to console
- log_level_console: str = (
- "INFO" # default would usually be 'WARNING', but for farn it makes sense to set default level to 'INFO'
- )
+ # NOTE: Default would usually be 'WARNING', but for farn it makes sense to set default level to 'INFO'
+ log_level_console: str = "INFO"
if any([args.quiet, args.verbose]):
log_level_console = "ERROR" if args.quiet else log_level_console
log_level_console = "DEBUG" if args.verbose else log_level_console
- # ..to file
+ # ..to file
log_file: Path | None = Path(args.log) if args.log else None
log_level_file: str = args.log_level
configure_logging(log_level_console, log_file, log_level_file)
@@ -158,28 +169,31 @@ def main() -> None:
batch: bool = args.batch
test: bool = args.test
- # catch missing arguments {sample, generate, command}
- # and drop an error
- # as one of them IS required
- if not sample and not generate and command is None:
+ # Ensure that at least one of the arguments {sample, generate, command} is given.
+ # (minimum one of them is required)
+ # Drop an error if not.
+ if not (sample or generate or command):
parser.print_help()
logger.error("farn: none of the required options given: '--sample' or '--generate' or '--execute'")
# Check whether farn dict file exists
if not farn_dict_file.is_file():
logger.error(f"farn: File {farn_dict_file} not found.")
- # easter egg: Generate Barnsley fern
- # _generate_barnsley_fern() # noqa: ERA001
return
+ # Print the parsed commandline arguments for documentation and debugging purposes.
+ # The arguments will be split into one argument per line, if possible.
+ # If extracting a mapping from `args` fails, fall back to its string representation.
+ _indent: str = " " * 13
+ try:
+ _arg_mapping = vars(args)
+ except TypeError:
+ _arg_mapping = {"args": str(args)}
+ _formatted_args = pprint.pformat(_arg_mapping, sort_dicts=True)
+ _indented_args = "\n".join(f"{_indent}{line}" for line in _formatted_args.splitlines())
logger.info(
- f"Start farn.py with following arguments:\n"
- f"\t farn_dict_file: \t{farn_dict_file}\n"
- f"\t sample: \t\t{sample}\n"
- f"\t generate: \t\t{generate}\n"
- f"\t command: \t\t{command}\n"
- f"\t batch: \t\t\t{batch}\n"
- f"\t test: \t\t\t{test}"
+ "Start farn.py with following arguments:\n%s\n",
+ _indented_args,
)
# Invoke API
diff --git a/src/farn/run/cli/batchProcess.py b/src/farn/cli/batchProcess.py
similarity index 68%
rename from src/farn/run/cli/batchProcess.py
rename to src/farn/cli/batchProcess.py
index 3b3d693d..7008e901 100644
--- a/src/farn/run/cli/batchProcess.py
+++ b/src/farn/cli/batchProcess.py
@@ -1,18 +1,29 @@
#!/usr/bin/env python
+"""batchProcess command line interface."""
import argparse
import logging
-from argparse import ArgumentParser
+import pprint
+from importlib import metadata
from pathlib import Path
-from farn.run.batchProcess import AsyncBatchProcessor
+from farn.batch.batch_processor import AsyncBatchProcessor
from farn.utils.logging import configure_logging
logger = logging.getLogger(__name__)
+def _get_version() -> str:
+ """Return the installed package version, or a safe fallback if unavailable."""
+ try:
+ return metadata.version("farn")
+ except metadata.PackageNotFoundError:
+ # Fallback when package metadata is not available (e.g. running from source)
+ return "farn (version unknown)"
+
+
def _argparser() -> argparse.ArgumentParser:
- parser = ArgumentParser(
+ parser = argparse.ArgumentParser(
prog="batchProcess",
usage="%(prog)s caseList [options [args]]",
epilog="_________________batchProcess___________________",
@@ -22,8 +33,8 @@ def _argparser() -> argparse.ArgumentParser:
)
_ = parser.add_argument(
- "caseList",
- metavar="caseList",
+ "case_list_file",
+ metavar="case_list_file",
type=str,
help="name of the text file containing all paths of the cases to be processed.",
)
@@ -31,7 +42,7 @@ def _argparser() -> argparse.ArgumentParser:
_ = parser.add_argument(
"-e",
"--execute",
- metavar="CMD",
+ metavar="command",
action="store",
type=str,
help=(
@@ -99,11 +110,18 @@ def _argparser() -> argparse.ArgumentParser:
required=False,
)
+ _ = parser.add_argument(
+ "-V",
+ "--version",
+ action="version",
+ version=_get_version(),
+ )
+
return parser
def main() -> None:
- """Entry point for console script as configured in setup.cfg.
+ """Entry point for console script as configured in pyproject.toml.
Runs the command line interface and parses arguments and options entered on the console.
"""
@@ -121,16 +139,31 @@ def main() -> None:
log_level_file: str = args.log_level
configure_logging(log_level_console, log_file, log_level_file)
- case_list_file: Path = Path(args.caseList)
+ case_list_file: Path = Path(args.case_list_file)
command: str = args.execute
timeout: int = args.timeout
max_number_of_cpus: int = args.cpu
- # Check whether caselist file exists
+ # Check whether case list file exists
if not case_list_file.is_file():
- logger.error(f"runCases.py: File {case_list_file} not found.")
+ logger.error(f"batchProcess.py: File {case_list_file} not found.")
return
+ # Print the parsed commandline arguments for documentation and debugging purposes.
+ # The arguments will be split into one argument per line, if possible.
+ # If extracting a mapping from `args` fails, fall back to its string representation.
+ _indent: str = " " * 13
+ try:
+ _arg_mapping = vars(args)
+ except TypeError:
+ _arg_mapping = {"args": str(args)}
+ _formatted_args = pprint.pformat(_arg_mapping, sort_dicts=True)
+ _indented_args = "\n".join(f"{_indent}{line}" for line in _formatted_args.splitlines())
+ logger.info(
+ "Start batchProcess.py with following arguments:\n%s\n",
+ _indented_args,
+ )
+
# Invoke API
batch_processor: AsyncBatchProcessor = AsyncBatchProcessor(
case_list_file=case_list_file,
diff --git a/src/farn/core/__init__.py b/src/farn/core/__init__.py
index 04969f08..92aad9e3 100644
--- a/src/farn/core/__init__.py
+++ b/src/farn/core/__init__.py
@@ -1,6 +1,6 @@
-from farn.core.parameter import Parameter as Parameter
+from farn.core.parameter import Parameter
from farn.core.case import (
- CaseStatus as CaseStatus,
- Case as Case,
- Cases as Cases,
+ CaseStatus,
+ Case,
+ Cases,
)
diff --git a/src/farn/core/case.py b/src/farn/core/case.py
index 31185bc6..1a9f9899 100644
--- a/src/farn/core/case.py
+++ b/src/farn/core/case.py
@@ -18,11 +18,11 @@
from numpy import ndarray
from pandas import DataFrame, Series
-from farn.core import Parameter
+from farn.core.parameter import Parameter
-__ALL__ = [
- "CaseStatus",
+__all__ = [
"Case",
+ "CaseStatus",
"Cases",
]
diff --git a/src/farn/core/parameter.py b/src/farn/core/parameter.py
index 52f37826..6020280f 100644
--- a/src/farn/core/parameter.py
+++ b/src/farn/core/parameter.py
@@ -2,7 +2,7 @@
import numpy as np
-__ALL__ = ["Parameter"]
+__all__ = ["Parameter"]
logger = logging.getLogger(__name__)
diff --git a/src/farn/farn.py b/src/farn/farn.py
index 0853caf0..c9ddf6c2 100644
--- a/src/farn/farn.py
+++ b/src/farn/farn.py
@@ -1,3 +1,5 @@
+"""farn API."""
+
import logging
import os
import platform
@@ -12,20 +14,20 @@
from dictIO import DictReader, DictWriter, SDict, create_target_file_name
from dictIO.utils.strings import remove_quotes
+from farn.batch.batch_processor import AsyncBatchProcessor
from farn.core import Case, Cases, Parameter
-from farn.run.batchProcess import AsyncBatchProcessor
-from farn.run.subProcess import execute_in_sub_process
from farn.utils.logging import plural
from farn.utils.os import append_system_variable
+from farn.utils.sub_process import execute_in_sub_process
-__ALL__ = [
- "run_farn",
- "create_samples",
- "create_cases",
+__all__ = [
"create_case_folders",
- "create_param_dict_files",
"create_case_list_files",
+ "create_cases",
+ "create_param_dict_files",
+ "create_samples",
"execute_command_set",
+ "run_farn",
]
logger = logging.getLogger(__name__)
@@ -160,7 +162,7 @@ def create_samples(farn_dict: SDict[str, Any]) -> None:
farn_dict : SDict[str, Any]
farn dict the samples shall be created in
"""
- from farn.sampling.sampling import DiscreteSampling # noqa: PLC0415
+ from farn.sampling.discrete import DiscreteSampling # noqa: PLC0415
if "_layers" not in farn_dict:
logger.error(f"no '_layers' element in farn dict {farn_dict.name}. Sampling not possible.")
diff --git a/src/farn/run/__init__.py b/src/farn/run/__init__.py
deleted file mode 100644
index e69de29b..00000000
diff --git a/src/farn/run/cli/__init__.py b/src/farn/run/cli/__init__.py
deleted file mode 100644
index e69de29b..00000000
diff --git a/src/farn/run/utils/__init__.py b/src/farn/run/utils/__init__.py
deleted file mode 100644
index e69de29b..00000000
diff --git a/src/farn/sampling/__init__.py b/src/farn/sampling/__init__.py
index e69de29b..8ad47bcb 100644
--- a/src/farn/sampling/__init__.py
+++ b/src/farn/sampling/__init__.py
@@ -0,0 +1 @@
+from farn.sampling.discrete import DiscreteSampling
diff --git a/src/farn/sampling/sampling.py b/src/farn/sampling/discrete.py
similarity index 98%
rename from src/farn/sampling/sampling.py
rename to src/farn/sampling/discrete.py
index a59ab8cf..cf5b4618 100644
--- a/src/farn/sampling/sampling.py
+++ b/src/farn/sampling/discrete.py
@@ -393,13 +393,16 @@ def _generate_values_using_uniform_lhs_sampling(self) -> np.ndarray[Any, np.dtyp
criterion="corr" if self.number_of_fields > 1 else None,
random_state=self.seed,
)
-
+ if lhs_distribution is None:
+ msg: str = "lhs_distribution is None. This should not happen. Check pyDOE3.lhs function."
+ logger.error(msg)
+ raise ValueError(msg)
_range_lower_bounds: np.ndarray[Any, np.dtype[np.float64]] = np.array([r[0] for r in self.ranges])
_range_upper_bounds: np.ndarray[Any, np.dtype[np.float64]] = np.array([r[1] for r in self.ranges])
loc: np.ndarray[Any, np.dtype[np.float64]] = _range_lower_bounds
scale: np.ndarray[Any, np.dtype[np.float64]] = _range_upper_bounds - _range_lower_bounds
- sample_set: np.ndarray[Any, np.dtype[np.float64]] = uniform(loc=loc, scale=scale).ppf(lhs_distribution) # pyright: ignore[reportUnknownMemberType]
+ sample_set: np.ndarray[Any, np.dtype[np.float64]] = uniform(loc=loc, scale=scale).ppf(lhs_distribution)
return sample_set
@@ -414,6 +417,10 @@ def _generate_values_using_normal_lhs_sampling(self) -> np.ndarray[Any, np.dtype
criterion="corr" if self.number_of_fields > 1 else None,
random_state=self.seed,
)
+ if lhs_distribution is None:
+ msg: str = "lhs_distribution is None. This should not happen. Check pyDOE3.lhs function."
+ logger.error(msg)
+ raise ValueError(msg)
# criterion: a string that tells lhs how to sample the points
# (default: None, which simply randomizes the points within the intervals)
# - center|c: center the points within the sampling intervals
@@ -425,7 +432,7 @@ def _generate_values_using_normal_lhs_sampling(self) -> np.ndarray[Any, np.dtype
# std of type scalar (scale) or vector (stretch, scale), no rotation
_std: np.ndarray[Any, np.dtype[np.float64]] = np.array(self.std)
- sample_set: np.ndarray[Any, np.dtype[np.float64]] = norm(loc=self.mean, scale=_std).ppf(lhs_distribution) # pyright: ignore[reportUnknownMemberType]
+ sample_set: np.ndarray[Any, np.dtype[np.float64]] = norm(loc=self.mean, scale=_std).ppf(lhs_distribution)
return sample_set
diff --git a/src/farn/utils/__init__.py b/src/farn/utils/__init__.py
index e69de29b..a7cdd247 100644
--- a/src/farn/utils/__init__.py
+++ b/src/farn/utils/__init__.py
@@ -0,0 +1 @@
+"""Utilities for farn."""
diff --git a/src/farn/run/subProcess.py b/src/farn/utils/sub_process.py
similarity index 100%
rename from src/farn/run/subProcess.py
rename to src/farn/utils/sub_process.py
diff --git a/src/farn/run/utils/threading.py b/src/farn/utils/threading.py
similarity index 100%
rename from src/farn/run/utils/threading.py
rename to src/farn/utils/threading.py
diff --git a/tests/.gitignore b/tests/.gitignore
index 7afaac4d..918c5117 100644
--- a/tests/.gitignore
+++ b/tests/.gitignore
@@ -1,2 +1,2 @@
temp_*
-~$temp*
+~$temp*
\ No newline at end of file
diff --git a/tests/__init__.py b/tests/__init__.py
deleted file mode 100644
index e69de29b..00000000
diff --git a/tests/cli/test_farn_cli.py b/tests/cli/test_farn_cli.py
index 929d5d4e..9bfdcffe 100644
--- a/tests/cli/test_farn_cli.py
+++ b/tests/cli/test_farn_cli.py
@@ -7,7 +7,7 @@
import pytest
from farn.cli import __main__
-from farn.cli.__main__ import _argparser, main
+from farn.cli.__main__ import _argparser, _get_version, main
# *****Test commandline interface (CLI)************************************************************
@@ -81,6 +81,23 @@ def test_cli(
raise TypeError
+@pytest.mark.parametrize("flag", ["-V", "--version"])
+def test_cli_version(
+ flag: str,
+ monkeypatch: pytest.MonkeyPatch,
+ capsys: pytest.CaptureFixture[str],
+):
+ # Prepare
+ monkeypatch.setattr(sys, "argv", ["farn", flag])
+ parser = _argparser()
+ # Execute & Assert
+ with pytest.raises(SystemExit) as exc_info:
+ _ = parser.parse_args()
+ assert exc_info.value.code == 0
+ captured = capsys.readouterr()
+ assert _get_version() in captured.out
+
+
# *****Ensure the CLI correctly configures logging*************************************************
diff --git a/tests/conftest.py b/tests/conftest.py
index cd7cb547..3e5d7df7 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -1,3 +1,5 @@
+"""Test configuration and fixtures."""
+
import logging
import os
from pathlib import Path
@@ -7,24 +9,29 @@
@pytest.fixture(scope="session", autouse=True)
-def chdir() -> None:
+def chdir():
"""
Fixture that changes the current working directory to the 'test_working_directory' folder.
- This fixture is automatically used for the entire package.
+ This fixture is automatically used for the entire session.
"""
+ original_cwd = Path.cwd()
os.chdir(Path(__file__).parent.absolute() / "test_working_directory")
+ try:
+ yield
+ finally:
+ os.chdir(original_cwd) # reset to original working directory after tests
@pytest.fixture(scope="session", autouse=True)
def test_dir() -> Path:
"""
Fixture that returns the absolute path of the directory containing the current file.
- This fixture is automatically used for the entire package.
+ This fixture is automatically used for the entire session.
"""
return Path(__file__).parent.absolute()
-output_dirs = [
+output_dirs: list[str] = [
"cases",
"cases_one_layer",
"cases_two_layers",
@@ -36,7 +43,7 @@ def test_dir() -> Path:
"results",
"templates",
]
-output_files = [
+output_files: list[str] = [
"sampled*",
"queueList*",
"*.copy",
@@ -65,7 +72,8 @@ def _remove_output_dirs_and_files() -> None:
for pattern in output_files:
for file in Path.cwd().glob(pattern):
_file = Path(file)
- _file.unlink(missing_ok=True)
+ if _file.is_file():
+ _file.unlink(missing_ok=True)
@pytest.fixture(autouse=True)
diff --git a/tests/test_sampling.py b/tests/test_sampling.py
index 9aecb50b..e0ed63d7 100644
--- a/tests/test_sampling.py
+++ b/tests/test_sampling.py
@@ -3,7 +3,7 @@
import numpy as np
import pytest
-from farn.sampling.sampling import DiscreteSampling
+from farn.sampling.discrete import DiscreteSampling
def test_fixed_sampling_one_param() -> None:
diff --git a/tests/test_working_directory/.gitignore b/tests/test_working_directory/.gitignore
index 6e4e6e55..05d5e5bc 100644
--- a/tests/test_working_directory/.gitignore
+++ b/tests/test_working_directory/.gitignore
@@ -1,10 +1,7 @@
-/cases_expected/
-/cases_expected/*
-/cases/
-/cases/*
-/logs/
-/logs/*
-/caseList*
-/queueList_*
-/sampled*
-/parsed*
+cases_expected
+cases
+logs
+caseList*
+queueList_*
+sampled*
+parsed*
diff --git a/uv.lock b/uv.lock
index cfb8206c..d03373d9 100644
--- a/uv.lock
+++ b/uv.lock
@@ -41,15 +41,15 @@ wheels = [
[[package]]
name = "anyio"
-version = "4.12.1"
+version = "4.13.0"
source = { registry = "https://pypi.org/simple" }
dependencies = [
{ name = "idna" },
{ name = "typing-extensions", marker = "python_full_version < '3.13'" },
]
-sdist = { url = "https://files.pythonhosted.org/packages/96/f0/5eb65b2bb0d09ac6776f2eb54adee6abe8228ea05b20a5ad0e4945de8aac/anyio-4.12.1.tar.gz", hash = "sha256:41cfcc3a4c85d3f05c932da7c26d0201ac36f72abd4435ba90d0464a3ffed703", size = 228685, upload-time = "2026-01-06T11:45:21.246Z" }
+sdist = { url = "https://files.pythonhosted.org/packages/19/14/2c5dd9f512b66549ae92767a9c7b330ae88e1932ca57876909410251fe13/anyio-4.13.0.tar.gz", hash = "sha256:334b70e641fd2221c1505b3890c69882fe4a2df910cba14d97019b90b24439dc", size = 231622, upload-time = "2026-03-24T12:59:09.671Z" }
wheels = [
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+ { url = "https://files.pythonhosted.org/packages/da/42/e921fccf5015463e32a3cf6ee7f980a6ed0f395ceeaa45060b61d86486c2/anyio-4.13.0-py3-none-any.whl", hash = "sha256:08b310f9e24a9594186fd75b4f73f4a4152069e3853f1ed8bfbf58369f4ad708", size = 114353, upload-time = "2026-03-24T12:59:08.246Z" },
]
[[package]]
@@ -128,20 +128,20 @@ wheels = [
[[package]]
name = "async-lru"
-version = "2.2.0"
+version = "2.3.0"
source = { registry = "https://pypi.org/simple" }
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+sdist = { url = "https://files.pythonhosted.org/packages/e8/1f/989ecfef8e64109a489fff357450cb73fa73a865a92bd8c272170a6922c2/async_lru-2.3.0.tar.gz", hash = "sha256:89bdb258a0140d7313cf8f4031d816a042202faa61d0ab310a0a538baa1c24b6", size = 16332, upload-time = "2026-03-19T01:04:32.413Z" }
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+ { url = "https://files.pythonhosted.org/packages/e5/e2/c2e3abf398f80732e58b03be77bde9022550d221dd8781bf586bd4d97cc1/async_lru-2.3.0-py3-none-any.whl", hash = "sha256:eea27b01841909316f2cc739807acea1c623df2be8c5cfad7583286397bb8315", size = 8403, upload-time = "2026-03-19T01:04:30.883Z" },
]
[[package]]
name = "attrs"
-version = "25.4.0"
+version = "26.1.0"
source = { registry = "https://pypi.org/simple" }
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@@ -273,91 +273,91 @@ wheels = [
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