farn

All notable changes to the farn project will be documented in this file.
The changelog format is based on Keep a Changelog.

Unreleased

-/-

[0.4.0] - 2024-11-11

Breaking changes

  • The code has been adapted to dictIO 0.4.0
    dictIO 0.4.0 introduced some breaking changes. With the current release 0.4.0 of farn, the code base has been adapted to these in changes.
    The most prominent change being that class dictIO.CppDict has been replaced by class dictIO.SDict.

Changed

  • Changed from pip/tox to uv as package manager

  • README.md : Completely rewrote section “Development Setup”, introducing uv as package manager.

  • Changed publishing workflow to use OpenID Connect (Trusted Publisher Management) when publishing to PyPI

  • Updated copyright statement

  • VS Code settings: Turned off automatic venv activation

  • Replaced black formatter with ruff formatter

Solved

  • Sphinx documentation: Resolved issue that documentation of class members was generated twice.

Added

  • Sphinx documentation: Added extension to support Markdown-based diagrams created with Mermaid.

  • Added mypy as static type checker (in addition to pyright)

GitHub workflows

  • (all workflows): Adapted to use uv as package manager

  • _test_future.yml : updated Python version to 3.13.0-alpha - 3.13.0

  • _test_future.yml : updated name of test job to ‘test313’

Dependencies

  • Updated to dictIO>=0.4.0 (from dictIO>=0.3.4)

  • Updated to ospx>=0.3.0 (from ospx>=0.2.14)

  • Updated to ruff>=0.6.3 (from ruff==0.4.2)

  • Updated to pyright>=1.1.378 (from pyright==1.1.360)

  • Updated to sourcery>=1.22 (from sourcery==1.16)

  • Updated to pytest>=8.3 (from pytest>=8.2)

  • Updated to Sphinx>=8.0 (from Sphinx>=7.3)

  • Updated to sphinx-argparse-cli>=1.17 (from sphinx-argparse-cli>=1.16)

  • Updated to myst-parser>=4.0 (from myst-parser>=3.0)

  • Updated to furo>=2024.8 (from furo>=2024.5)

  • updated to setup-python@v5 (from setup-python@v4)

  • updated to actions-gh-pages@v4 (from actions-gh-pages@v3)

  • updated to upload-artifact@v4 (from upload-artifact@v3)

  • Updated to download-artifact@v4 (from download-artifact@v3)

  • updated to checkout@v4 (from checkout@v3)

0.3.7 - 2024-05-22

Dependencies

  • updated to ruff==0.4.2 (from ruff==0.2.1)

  • updated to pyright==1.1.360 (from pyright==1.1.350)

  • updated to sourcery==1.16 (from sourcery==1.15)

  • updated to lxml>=5.2 (from lxml>=5.1)

  • updated to types-lxml>=2024.4 (from types-lxml>=5.1)

  • updated to scipy>=1.13 (from scipy>=1.12)

  • updated to Pillow>=10.3 (from Pillow>=10.2)

  • updated to pytest>=8.2 (from pytest>=7.4)

  • updated to pytest-cov>=5.0 (from pytest-cov>=4.1)

  • updated to Sphinx>=7.3 (from Sphinx>=7.2)

  • updated to sphinx-argparse-cli>=1.15 (from sphinx-argparse-cli>=1.11)

  • updated to myst-parser>=3.0 (from myst-parser>=2.0)

  • updated to furo>=2024.4 (from furo>=2023.9.10)

  • updated to dictIO>=0.3.4 (from dictIO>=0.3.3)

  • updated to ospx>=0.2.14 (from ospx>=0.2.13)

  • updated to numpy>=1.26,<2.0 (from numpy>=1.26)

  • updated to matplotlib>=3.9 (from matplotlib>=3.8)

  • removed black

Changed

  • replaced black formatter with ruff formatter

  • Changed publishing workflow to use OpenID Connect (Trusted Publisher Management) when publishing to PyPI

  • Updated copyright statement

  • VS Code settings: Turned off automatic venv activation

Added

  • farn.core.case.Case: Added method add_parameters(), which allows to manually add user-defined parameters to a Case.

0.3.6 - 2024-02-21

Added

  • README.md : Under Development Setup, added a step to install current package in “editable” mode, using the pip install -e option. This removes the need to manually add /src to the PythonPath environment variable in order for debugging and tests to work.

Removed

  • VS Code settings: Removed the setting which added the /src folder to PythonPath. This is no longer necessary. Installing the project itself as a package in “editable” mode, using the pip install -e option, solves the issue and removes the need to manually add /src to the PythonPath environment variable.

Changed

  • Moved all project configuration from setup.cfg to pyproject.toml

  • Moved all tox configuration from setup.cfg to tox.ini.

  • Moved pytest configuration from pyproject.toml to pytest.ini

  • Deleted setup.cfg

Dependencies

  • updated to black[jupyter]==24.1 (from black[jupyter]==23.12)

  • updated to version: ‘==24.1’ (from version: ‘==23.12’)

  • updated to ruff==0.2.1 (from ruff==0.1.8)

  • updated to pyright==1.1.350 (from pyright==1.1.338)

  • updated to sourcery==1.15 (from sourcery==1.14)

  • updated to lxml>=5.1 (from lxml>=4.9)

  • updated to scipy>=1.12 (from scipy>=1.11)

  • updated to pandas>=2.2 (from pandas>=2.1)

  • updated to Pillow>=10.2 (from Pillow>=10.1)

  • -/-

0.3.5 - 2024-01-09

Changed

  • farn/sampling/sampling.py:

    • _generate_values_using_uniform_lhs_sampling(): replaced SALib latin with pyDOE2 lhs

    • _generate_values_using_sobol_sampling(): replaced sobol-seq with scipy.stats.qmc.sobol

    • removed orphaned _cov argument from normalLhs sampling

Dependencies

  • Upgraded from pyDOE2>=1.3 to pyDOE3>=1.0

  • Removed SALib and sobol-seq

  • Updated to dictIO>=0.3.1 and ospx>=0.2.12

  • Updated other dependencies to latest versions

0.3.4 - 2023-09-25

Dependencies

  • Updated dependencies to latest versions

0.3.3 - 2023-06-22

Changed

  • Modularized GitHub workflows

  • Changed default Python version in GitHub workflows from 3.10 to 3.11

Dependencies

  • updated to dictIO>=0.2.8 and ospx>=0.2.10

  • requirements-dev.txt: Updated dependencies to latest versions

0.3.2 - 2023-05-04

Changed

  • dependencies: updated dependencies to latest versions

0.3.1 - 2023-01-11

Changed

  • Added missing DocStrings for public classes, methods and functions

  • Changed links to package documentation to open README.html, not the default index page

  • data classes: changed initialisation of mutable types to use default_factory

  • ruff: added rule-set “B” (flake8-bugbear)

Dependencies

  • updated to dictIO>=0.2.6 and ospx>=0.2.8

0.3.0 - 2023-01-09

v0.3.0 is a major update comprising one breaking change (see below). Users are encouraged to update to this version.

Breaking Change

  • Moved classes ‘Case’ and ‘Parameter’ from farn.farn to farn.core
    As a consequence, if you imported these classes in your code, you need to adapt the respective import statements. I.e.
    old

    from farn.farn import Case, Parameter

    new

    from farn.core import Case, Parameter

Added

  • Added a ‘Cases’ class, acting as a container for Case instances. Cases inherits from List[Case] and can hence transparently be used as a Python list type. However, Cases provides additional convenience methods to export the attributes of all contained Case instances to a pandas DataFrame (Cases.to_pandas()) or to a numpy ndarray (Cases.to_numpy())

    Cases is located in the farn.core sub-package and can be imported from there, i.e:

    from farn.core import Case, Cases, Parameter

0.2.7 - 2023-01-04

Changed

  • Linter: Migrated from flake8 to ruff.
    (Added ruff; removed flake8 and isort)

  • Adjusted GitHub CI workflow accordingly.
    (Added ruff job; removed flake8 and isort jobs)

  • VS Code settings: Adjusted Pylance configuration

Added

  • Added a batch file ‘qa.bat’ in root folder to ease local execution of code quality checks

Dependencies

  • updated to dictIO>=0.2.5 and ospx>=0.2.7

0.2.6 - 2022-12-12

Dependencies

  • updated to ospx>=0.2.6

0.2.5 - 2022-12-12

Changed

  • Moved dev-only dependencies from requirements.txt to requirements-dev.txt

  • farn/__init__.py : ensured that imported symbols get also exported
    (added “as” clause -> “from x import y as y” instead of only “from x import y”)

  • sampling.py: refactored for cleaner code

  • Configured code quality tools flake8, black, isort, pyright

  • Improved code quality, resolving all warnings and errors flagged by the configured code quality tools (flake8, black, isort, pyright, sourcery)

Added

  • Added GitHub workflow ‘main.yml’ for continuous integration (runs all CI tasks except Sphinx)

    • format checks: black, isort

    • lint check: flake8, flake8-bugbear

    • type check: pyright

    • test: uses tox to run pytest on {Windows, Linux, MacOS} with {py39, py310}

    • publish: publishing to PyPI (runs only on push of new tag vx.x.x, and after all other jobs succeeded)

    • merge_to_release_branch: merge tagged commit to release branch (runs after publish)

Dependencies

  • updated to dictIO>=0.2.4

0.2.4 - 2022-12-01

Changed

  • Code formatting: Changed from yapf to black

  • STYLEGUIDE.md : Adjusted to match black formatting

  • VS Code settings: Updated to use black as formatter

  • requirements.txt: Updated dependencies to their most recent versions

  • GitHub actions (yml files): Updated following actions to their most recent versions:

    • checkout@v1 -> checkout@v3

    • setup-python@v2 -> setup-python@v4

    • cache@v2 -> cache@v3

Added

  • Added sourcery configuration (.sourcery.yaml)

  • Added py.typed file into the package root folder and included it setup.cfg as package_data

0.2.3 - 2022-11-08

Changed

  • sampling.py: sampling adapted, removed unused (and non-preferable) options

  • dependencies:

    • upgraded to dictIO >= 0.2.2 (now supporting references and expressions in JSON dicts)

    • upgraded to ospx >= 0.2.4

    • changed from pyDOE>=0.3.8 to pyDOE2>=1.3.0

0.2.2 - 2022-10-05

Changed

  • dependencies:

    • upgraded to ospx >= 0.2.3

0.2.1 - 2022-10-01

Changed

  • dependencies:

    • upgraded to dictIO >= 0.2.0

    • upgraded to ospx >= 0.2.1

0.2.0 - 2022-09-28

Changed

  • Dependencies:

    • upgraded to ospx >= 0.2.0

    • upgraded to dictIO >= 0.1.2

0.1.2 - 2022-08-19

Changed

  • farn.py:

    • create_samples(): Removed undocumented return value ‘layers’. This was simply wrong. create_samples() is not meant to return anything.

  • subProcess.py:

    • Changed level of ‘per case’ log messages from INFO to DEBUG, to reduce cluttering of log.

Added

  • farn CLI (and farn.run_farn() API):

    • EXPERIMENTAL FEATURE: Added –batch option. Default is False. The batch option lets farn execute commands in batch mode, i.e. asynchroneous instead of sequential.

Fixed

  • sampling.py:

    • uniformLhs sampling: Corrected the BoundingBox code for the case where Lhs sampling is requested with only one single parameter varied (i.e. 1-dimensional Lhs)

  • farn.py:

    • Additional log file handler for farn gets registered only once. Multiple calls to _configure_additional_logging_handler_exclusively_for_farn() will not create multiple handlers, if the file handler for the log file already exists.

0.1.1 - 2022-05-30

Changed

  • Sphinx documentation: Added Changelogs (for combined documentation)

  • updated dependency ospx to version >=0.1.1

0.1.0 - 2022-05-28

Changed

  • Simplified imports from namespace farn. Example:

    • Old (<= v0.0.22):

      from farn.farn import run_farn

    • New:

      from farn import run_farn

  • Use new simplified imports from namespace dictIO (using updated version of dictIO package)

  • farn.py

    • Renamed following functions:

      • run_sampling() -> create_samples()

      • generate_samples_for_layer() -> create_samples_in_layer()

      • register_cases() -> create_cases()

      • generate_case_folder_structure() -> create_case_folders()

      • generate_case_lists() -> create_case_list_files()

      • _create_param_dict_file_in_case_folders() -> create_param_dict_files()

      • _execute_command_set_in_case_folders() -> execute_command_set()

    • Introduced Dataclass ‘Parameter’

    • Removed method add_uservars() in dataclass Case (moved the respective code into create_cases() )

    • run_farn(): Removed the ignore_errors argument

    • farnDict ‘_samples’ section -> changed naming of ‘_names’ element to ‘_case_name’, to improve clarity of its meaning

    • Smaller refactorings to improve code clarity and testability

  • cli/farn.py

    • Removed the -i / –ignore-errors argument

0.0.22 - 2022-05-09

  • First public release

0.0.17 - 2022-02-14

Added

  • Added support for Python 3.10