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[13-2, 16, 19, 21, 22] Bring
main up to date with develop (#24)
* BLD: - first test of a GitHub CI for testing * FIX: - fixed wrong pip install and python versions in CI ? * FIX: - fixed loading of test files that do not contain test but dependencies that cannot be loaded ? * BUG: - escaped imports of unaccessible dependencies for test-file generation in GitHub CI tests by making the `if __name__ == "__main__"` include these imports and function definitions * TST: - test whether Cython build can be removed from GitHub actions for testing ? * TST: - reverted removal of Cython for testing * PKG: - moved the full package back into an `src`-folder BLD: - updated `pyproject.toml` and `setup.py` to account for the movement to the `src`-folder - removed dedicated Cython build from CI test pipeline * BLD: - changed CI pipeline target branches * BLD: - augmented CI checks with format, type, and lint checks * BUG: - fixed CI pipeline wrong folder include ? BLD: - added isort check * BUG: - fixed broken `isort` usage in CI? * FIX: - fixed missing `isort` dependency in CI? - fixed wrong import sort order in Cython Hermite functions * FIX: - fixed missing `colorama` dependency for `isort` in CI ? * FIX: - type-ignored Cython import that was not properly resolved by `pyright` ? * FIX: - fixed missing import of Cython module for `pyright` in CI ? * FIX: - again trying to resolve the wrong import error of Cython module by `pyright` in CI ? * FIX: - fixed wrong `pyright` Cython import error of Cython import in CI * BLD: - removed pushes to `develop` from the GitHub CI actions * BLD: - added missing comma to the name of the GitHub CI action * [10 develop] Add coverage to CI pipeline (#11) * DOC: - added Python versions and `black` code style to `README` * DOC: - added `isort` badge to `README` * TST: - added `--no-jit`-flag to `pytest` to enable proper coverage of Numba functions * tmp: - first test of CI with coverage report ? * BUG: - fixed failure of `pytest-xdist` and `pytest-cov` in GitHub CI (works locally) ? * BUG: - fixed accidentally placed `\` for `./tests` in coverage CI action ? * BUG: - added codecov to CI pipeline ? * TST: - tried to readd `pytest-xdist` for coverage reports ? * wip: - reset example Jupyter notebook number 3 * MAINT: - made `_get_num_workers` a function of the `_utils`-model TST: - increased coverage to 100% by testing `np.float32` x-values for the Hermite functions was well as super negative numbers of requested workers * DOC: - added setup, installation, and development instructions to `README` * DOC: - switched back from `README.rst` to `README.md` BLD: - made CI pipeline push actions apply to the main branch only * [Pre-16] Add Makefile (#17) * BLD: - added initial version of Makefile and based GitHub CI on it ? * BUG: - fixed type in `pip install` in `Makefile` for GitHub CI * BLD: - added plain install to Makefile - removed current branch from GitHub CI trigger on push DOC: - added Makefile instructions to `README` * [13-2] Implement class interface to Hermite functions (#18) * BLD: - added `mypy` to CI pipeline BUG: - fixed type error that `mypy` uncovered for the `filename_parameters_mapping` for the Hermite function reference generation * wip: - test if CI can still pass ? * wip: - CI apparently still runs; removed check * BLD: - added `pycodestyle` as a part of the CI checks BUG: - fixed a line too long error revealed by `pycodestyle` * DOC: - added CI test status to `README` ? * ENH: - added functions that help for computing discrete/continuous Fourier transforms (`fourier_transform._fft_utils`) TST: - implemented a test suite for `fourier_transform._fft_utils` * Issue 14 #14 DOC: - updated equations with new definitions of $\alpha$ - updated `README` with new equations and added respective reference that these definitions are based on * Issue 14 #14 MAINT: - removed redundant Numba version of the legacy Hermite functions and `jit`-compiled the NumPy-version instead - fixed minor documentation issues * Issue 14 #14 MAINT: - adapted interface to Hermite functions to the new definition of $\alpha$ in terms of both implementation and docs * Issue 14 #14 DOC: - updated example scripts and resulting plots with new definition of $\alpha$ * Issue 14 #14 TST: - generated new references files for testing the new definition of $\alpha$ for the Hermite functions - adapted Hermite function tests to properly run for the new definition of $\alpha$ - configured Hermite function tests via global constants and kept comments in them more vague - made test for Cramér's inequality of the Hermite functions ensure that the boundary value is not only an upper bound but actually reached - changed `requirements` for GitHub CI because with a re-arrangement of the `if __name__ == "__main__"` in the Hermite function reference generation file, `sympy` and `tqdm` became CI requirements as well * BUG: - fixed failing `ruff` for too long line in docstring of new `_fft_utils` BLD: - temporarily enabled CI on push to current branch to check if it still passes after an adaption in `pyright` * Issue 14 #14 BLD: - disabled GitHub CI on push to the current branch again after verifying that it still runs * Issue 13 #13 (3) ENH: - added `x_center` to the Hermite function basis for shifting the Hermite functions in x-direction - added input validation for `x_center` MAINT: - renamed `hermite_functions._interface` to `hermite_functions._func_interface` to prepare for the class interface - made type handling of Hermite function input validation smarter and safer by first converting to the target type and then testing only for this one - made argument types for `x` of the Hermite functions broader by also including lists and tuples TST: - made input validation tests for Hermite functions be executed before the Hermite function reference tests - made input validation tests for Hermite functions not only check failure but also success cases - added tests for the new `x_center` and ensured that it does not modify the original `x`-values for the Hermite functions (after this causes some problems) DOC: - updated all equations and the `README` to clarify the new `x_center` for the Hermite functions - updated installation commands (also mentioned venv activation) and test/check commands in `README` * DOC: - added y-axis to Hermite-function-scale-effect-plot - fixed first vertical x-axis for order `n=0` not showing in the plot at all * Issue #13 (3) MAINT: - moved Hermite function input validation to dedicated file ENH: - pushed forgotten files that add `x_center` to Hermite functions TST: - pushed forgotten files that test the new `x_center` of the Hermite functions and improved the testing of the Hermite function input validation * TST: - split up tests for Hermite functions into dedicated test files to be more flexible * Issue #13 (3) DOC: - added common matplotlib style to unify all plots - updated example scripts with new matplotlib style - added shifted center to Hermite function example 01 * DOC: - made example plots 01 and 02 for Hermite functions more visually appealing/less overwhelming * Issue #13 (6.1) ENH: - added auxiliary script that auto-generates a Python file with spline coefficients for almost exactly evaluating the largest zero (= outermost roots) of the Hermite functions up to order ~100_000 * Issue #13 (6.1) MAINT: - refactored the reference creation for the largest roots of the Hermite functions to not minimize the relative but the absolute error - relaxed permitted absolute error in reference creation for the largest roots of the Hermite functions because the SciPy-reference is not that accurate DOC: - mentioned that the SciPy-reference for the largest roots of the Hermite functions is not perfectly accurate * Issue #13 (6) ENH: - added script to create reference data for the largest extrema of the Hermite functions - added new `_approximations`-module for Hermite functions that offers approximations for their largest roots, largest extrema, and fadeout points TST: - added tests for the new `_approximations`-module DOC: - added legend to first plot in script that creates reference data for the largest roots of the Hermite functions * MAINT: - refactored the reference data generation for the largest roots and extrema of the Hermite functions to fit the splines based on relative errors - updated reference data and plots created by these scripts - made this reference data generation a developer-only script TST: - made test for largest root of Hermite functions more meaningful by adapting the tolerance for checking to the actual magnitude of the root position - made test for largest extremum of Hermite functions more meaningful by checking the y-values (and not the x-values) of the extremum against a numerical optimisation (also with magnitude-adaptive tolerances) * DOC: - made all plot saves in examples available for developers only - aligned plots in terms of visuals (especially titles and sizes) - updated `README` with new plots and developer-only environment variable * BLD: - added additional scripts checks to GitHub CI - made all tools cause actual failures rather than just printing test output ? - broke CI on purpose, by badly formatting `auxiliary_scripts\02_hermite_functions_largest_extremum.py` and `src\robust_hermite_ft\hermite_functions\_c_hermite.pyx` * BLD: - CI tests fixed `black` formatting after confirming that it works - `isort` is the next to check * BLD: - fixed `isort` CI failure after confirming that it works - `pyright` is the next to check * BLD: - temporarily broke `isort` CI check again to check its output * BLD: - fixed `isort` problem again - checking for reasons why `pyright`-check fails by running it separately without output ? * BLD: - fixed `pyright` error handling in CI - `mypy` is the next one to check, but for now it's checked whether it just runs through even though there is an error * BLD: - pushing updated CI workflow file for properly testing that `mypy` just runs through - added `matplotlib` to CI requirements to avoid `pyright` from throwing an error ? * BLD: - going back to the start for tests after `mypy` also stopped CI correctly - starting with `black` test * BLD: - `black` successfully stopped the CI without customised handling - `isort` is the next to check without customised handling * BLD: - also `isort` stops the CI on failure - next to check is `pyright` * BLD: - reverted GitHub CI to its original working state * DOC: - updated `README` with new CI commands * ENH: - Hermite functions now support all kinds of real numeric scalars/Arrays as `x`-values, integer scalars as `n`-values, and real numeric scalars for `alpha` and `x_center` after making the input validation way more relaxed and smarter TST: - test for Hermite function input validation now covers Python and Numpy scalars individually and on top of that also includes Pandas series and Python Arrays - test for data link to original `x` in Hermite functions now evaluates dynamically whether memory is shared by checking if changes in the copy/view are reflected in the original - added a completely new test set whether the Hermite functions yield the same results for all different kinds of `x`-values, `n`-values, `alpha`- and `x-center` values * BUG: - fixed missing `pandas` dependency for GitHub CI * BUG: - fixed type incompatibility that caused `mypy` to crash the GitHub CI * TST: - fixed missing coverage for default and error handling of FFT utility functions * DOC: - arranged legend of plot for special points of Hermite functions in a better position * TST: - removed unnecessary list parametrization for orthonormality test of Hermite functions * DEV: - fixed wrong wording of static type check in Makefile - added combined check for all checks to Makefile * ENH: - improved typing to given `dtype` type hint for Arrays in Hermite functions * ENH: - added check that the `x` for Hermite function computations holds at least 1 entry TST: - extended input validation test for Hermite functions to cover the "at least 1 element in x" failure case * ENH: - made integer type hinting of Hermite functions more consistent - added option to disable input validation of Hermite functions * DOC: - added complete check make command to `README` * Issue #13 (7, 8) ENH: - made `x_center` a float-only in the internals of the Hermite functions TST: - moved tests for function interface of the Hermite functions to a dedicated test file that can be distinguished from the tests for the class interface DEV: - added make command for running a single test * DEV: - made names of test commands in Makefile more descriptive in terms of coverage - updated GitHub CI and `README` accordingly * ENH: - finalised proper type handling of the parameters of the Hermite functions in `_func_interface` and `_approximations` - removed checks for `x_center is None` for the Hermite function that are now obsolete given that it's always a float * Issue #13 (7, 9) ENH: - implemented a class interface to the Hermite functions that can compute them in the time/space and frequency domain with in principle arbitrary parameters Issue #13 (8) TST: - added extensive tests for the new class interface to the Hermite functions * Issue #13 (7, 9) ENH: - added static method `eval` to `HermiteFunctionBasis` and made this the central computation method where `HermiteFunctionsBasis` (especially `__call__`) wraps around Issue #13 (8) TST: - made tests for `HermiteFunctionBasis` properly cover both the static method `eval` and the magic method `__call__` via the parametrised tests * [19] Rechange definition of `alpha` in Hermite functions back to a denominator; made Hermite function definition only real for the time/space domain (#20) * # Issue 19 MAINT: - refactored all Hermite functions computations (except for the class interface) to handle the new old definition of the scaling parameter alpha for `x / alpha` rather than the former `alpha * x` TST: - regenerated symbolic reference files for Hermite functions to reflect the new definition of alpha - reflected new definition of alpha in all Hermite function tests - improved test variable naming of global constants - made x-value computation of the orthonormality test of the Hermite functions based on an approximation of the fadeout points and the order to lower the computational load while ensuring that the x-values are always properly created in a dynamic fashion - made Cramér's inequality check for Hermite functions checked with relative rather than absolute tolerance * Issue #19 DEV: - added auxiliary script that creates images of the equations used for documenting the package - added a make command to update all the equation images via this script DOC: - incorporated the new definition of the scaling factor alpha of the Hermite functions (not `alpha * x` but now `alpha / x` again) in the documentation - cleaned up documentation equation images and plots - linked all new equations and plots properly in the `README` and docstrings * BUG: - updated fontsize of equations to ensure they are properly rendered in `README` (not pixely) ? * BUG: - made equation images in `README` not pixely ? * BUG: - made equation images in `README` not pixely (new resolution) ? * BUG: - made equation images in `README` not pixely pt.3 ? * BUG: - made equation images in `README` not pixely pt.4 ? * BUG: - made equation images in `README` not pixely pt.5 (transition to SVG) ? * BUG: - made equation images in `README` not pixely pt.5 (SVG with reduced fontsize) ? * BUG: - made equation images in `README` not pixely pt.6 (SVG with even more fontsize reduction) ? * BUG: - made equation images in `README` not pixely pt.7 (SVG with even more fontsize reduction) ? * DOC: - fully transitioned to `.svg` instead of `.png` based documentation - added plain definition of Hermite functions and polynomials to script that creates/updates equation images * BUG: - fixed too small equations in `README` ? * BUG: - fixed too small font of equation images in `README` * Issue #19 MAINT: - adapted definition of the Hermite function class interface to make the time/space domain real-valued only TST: - adapted output dtypes of the Hermite class interface to the new definition that the time/space domain has to be real-valued only DOC: - added LaTeX equation images for the Hermite functions and their Fourier transforms * Issue #19 DOC: - added example for the Fourier transforms of the Hermite functions with the new definition of `alpha` - made the Fourier transform of the Hermite functions part of the `README` - updated all plots because an axis label size changed * BUG: - fixed typo in `README` * ENH: - made validation functions for Hermite function input public - made validation input for `x_center` for Hermite functions more generic * ENH: - made typing of input validation of Hermite functions indicate `Any` instead of any specified types * DOC: - changed colors of example 4 plots * DOC: - removed Fourier transform of Hermite functions from examples and `README` * ENH: - made input validation of Hermite functions more flexible for the `x_center` by just handling it as an offset of a certain axis * Issue #13 (7 - 9) ENH: - actually a downwards enhancement - removed the direct Fourier transform of the Hermite function class interface - adapted all implementations, documentations, and tests to this new stripped down version of the class interface - included class interface into function interface test for the Hermite functions and therefore renamed the test file from `function_interface` to `implementations` * [21, 22] Remaned package to `robust_fourier`; dropped Cython implementation of Hermite functions (#23) * Issue #22 MAINT: - dropped Cython implementation of Hermite functions (also `cython-lint` as a check in the CI) * Issue #22 MAINT: - removed `Cython` and `psutil` from the requirements * Issue #22 MAINT: - completely dropped Cython implementation of all Hermite functions in the whole package Issue #23 MAINT: - renamed package from `robust_hermite_ft` to `robust_fourier` * BUG: - raised coverage to 100% again by conducting type error check for the `jit` property of the Hermite function class interface * BUG: - fix `black` check crashing the CI because of missing empty line * Issue #22 MAINT: - relaxed upper bound on NumPy version (now also v2 will be allowed) * BUG: - fixed wrong hashtag in test file * BUG: - fixed NumPy v2 deprecated `trapz` * BUG: - fixed wrong `README`-file in `pyproject.toml`
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