[13-1, 14] Change definition of scaling factor `alpha` , add center and approximations for Hermite functions, add Fourier transform utility functions #15

MothNik · 2024-07-30T12:05:02Z

This pull request

💥 Breaking changes

transitions the definition of the scaling parameter alpha of the dilated Hermite functions from x / alpha to x * alpha which is not backwards-compatible
updates all documentation and test files for the new definition of alpha
renames hermite_functions._interface to hermite_functions._func_interface

🦾 Features/Enhancements

adds the module fourier_transform._fft_utils (with test suite) for an object-oriented interface to Fourier transforms as well as easy conversions between discrete and continuous Fourier transforms
implements support for all kinds of x, n, alpha, and x_center for the Hermite functions by making the type checking less rigid (especially worth to mention are Pandas Series and Python Array support for x)
makes tests for type handling of input validation for Hermite functions more dynamic and safer
adds an x_center to the Hermite functions to shift them in x-direction and adds it to documentation and tests
adds hermite_functions._approximations (with test suite) that offers 3 functions to easily approximate the positions of
- the largest zero
- the largest extremum
- the numerical fadeout point
of the first 100 000 Hermite functions together with scripts (developer-only (see ✍️ Documentation)) to generate the reference data

✍️ Documentation

adds a custom Matplotlib style to make the plots look more consistent
updates the content of the example plots to be more informative
puts proper titles on the example plots and aligns their visual appearance
gives example plots better names that include the index of the example they are from
adds a section to the README that explains the new _approximations module
made all plot saves in example scripts developer-only and added a note to the README that they need to be enabled by setting an environment variable

🪛 Internal changes

removed redundant Numba-jitted code for Hermite functions and made Numba jit-compile the existing NumPy-function instead
moves input validation of Hermite functions to hermite_functions._validate
makes input validation of Hermite functions smarter in terms of type handling

- first test of a GitHub CI for testing

- fixed wrong pip install and python versions in CI ?

- fixed loading of test files that do not contain test but dependencies that cannot be loaded ?

- 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

- test whether Cython build can be removed from GitHub actions for testing ?

- reverted removal of Cython for testing

- 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

- changed CI pipeline target branches

- augmented CI checks with format, type, and lint checks

- fixed CI pipeline wrong folder include ? BLD: - added isort check

- fixed broken `isort` usage in CI?

- fixed missing `isort` dependency in CI? - fixed wrong import sort order in Cython Hermite functions

- fixed missing `colorama` dependency for `isort` in CI ?

- type-ignored Cython import that was not properly resolved by `pyright` ?

- fixed missing import of Cython module for `pyright` in CI ?

- again trying to resolve the wrong import error of Cython module by `pyright` in CI ?

- fixed wrong `pyright` Cython import error of Cython import in CI

- removed pushes to `develop` from the GitHub CI actions

- added missing comma to the name of the GitHub CI action

* 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

- added `mypy` to CI pipeline BUG: - fixed type error that `mypy` uncovered for the `filename_parameters_mapping` for the Hermite function reference generation

- test if CI can still pass ?

- CI apparently still runs; removed check

- added `pycodestyle` as a part of the CI checks BUG: - fixed a line too long error revealed by `pycodestyle`

- added CI test status to `README` ?

- added functions that help for computing discrete/continuous Fourier transforms (`fourier_transform._fft_utils`) TST: - implemented a test suite for `fourier_transform._fft_utils`

DOC: - updated equations with new definitions of $\alpha$ - updated `README` with new equations and added respective reference that these definitions are based on

- 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`

- CI tests fixed `black` formatting after confirming that it works - `isort` is the next to check

- fixed `isort` CI failure after confirming that it works - `pyright` is the next to check

- temporarily broke `isort` CI check again to check its output

- fixed `isort` problem again - checking for reasons why `pyright`-check fails by running it separately without output ?

- 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

- 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 ?

- going back to the start for tests after `mypy` also stopped CI correctly - starting with `black` test

- `black` successfully stopped the CI without customised handling - `isort` is the next to check without customised handling

- also `isort` stops the CI on failure - next to check is `pyright`

- reverted GitHub CI to its original working state

codecov · 2024-07-30T12:08:21Z

Codecov Report

All modified and coverable lines are covered by tests ✅

Files	Coverage Δ
...rc/robust_hermite_ft/fourier_transform/__init__.py	`100.00% <100.00%> (ø)`
.../robust_hermite_ft/fourier_transform/_fft_utils.py	`100.00% <100.00%> (ø)`
...rc/robust_hermite_ft/hermite_functions/__init__.py	`100.00% <100.00%> (ø)`
...st_hermite_ft/hermite_functions/_approximations.py	`100.00% <100.00%> (ø)`
...st_hermite_ft/hermite_functions/_func_interface.py	`100.00% <100.00%> (ø)`
...rmite_functions/_hermite_largest_extrema_spline.py	`100.00% <100.00%> (ø)`
...hermite_functions/_hermite_largest_roots_spline.py	`100.00% <100.00%> (ø)`
...obust_hermite_ft/hermite_functions/_numba_funcs.py	`100.00% <100.00%> (ø)`
...obust_hermite_ft/hermite_functions/_numpy_funcs.py	`100.00% <ø> (ø)`
...c/robust_hermite_ft/hermite_functions/_validate.py	`100.00% <100.00%> (ø)`

- updated `README` with new CI commands

- 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

- fixed missing `pandas` dependency for GitHub CI

- fixed type incompatibility that caused `mypy` to crash the GitHub CI

- fixed missing coverage for default and error handling of FFT utility functions

- arranged legend of plot for special points of Hermite functions in a better position

MothNik

Checked on top of CI checks

- removed unnecessary list parametrization for orthonormality test of Hermite functions

MothNik added 30 commits July 20, 2024 19:25

BLD:

4e8f44d

- first test of a GitHub CI for testing

FIX:

9f84d93

- fixed wrong pip install and python versions in CI ?

FIX:

5e201f0

- fixed loading of test files that do not contain test but dependencies that cannot be loaded ?

BUG:

408d818

- 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:

d8f158d

- test whether Cython build can be removed from GitHub actions for testing ?

TST:

2132928

- reverted removal of Cython for testing

PKG:

08849e4

- 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:

ff9d285

- changed CI pipeline target branches

Merge remote-tracking branch 'origin/main' into develop

3f07f43

BLD:

4ca0611

- augmented CI checks with format, type, and lint checks

BUG:

5da4991

- fixed CI pipeline wrong folder include ? BLD: - added isort check

BUG:

e813f7c

- fixed broken `isort` usage in CI?

FIX:

af55627

- fixed missing `isort` dependency in CI? - fixed wrong import sort order in Cython Hermite functions

FIX:

8cb691c

- fixed missing `colorama` dependency for `isort` in CI ?

FIX:

c1e1737

- type-ignored Cython import that was not properly resolved by `pyright` ?

FIX:

54cdf10

- fixed missing import of Cython module for `pyright` in CI ?

FIX:

912259d

- again trying to resolve the wrong import error of Cython module by `pyright` in CI ?

FIX:

973bde4

- fixed wrong `pyright` Cython import error of Cython import in CI

BLD:

fd4fe7f

- removed pushes to `develop` from the GitHub CI actions

BLD:

0b49758

- added missing comma to the name of the GitHub CI action

Merge branch 'main' into develop

0dc5225

Merge branch 'main' into develop

457479d

BLD:

5bd6eae

- added `mypy` to CI pipeline BUG: - fixed type error that `mypy` uncovered for the `filename_parameters_mapping` for the Hermite function reference generation

wip:

5b91333

- test if CI can still pass ?

wip:

35dafc5

- CI apparently still runs; removed check

BLD:

913fb68

- added `pycodestyle` as a part of the CI checks BUG: - fixed a line too long error revealed by `pycodestyle`

DOC:

43940a2

- added CI test status to `README` ?

ENH:

9573890

- 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

285178a

DOC: - updated equations with new definitions of $\alpha$ - updated `README` with new equations and added respective reference that these definitions are based on

MothNik added 11 commits July 30, 2024 13:02

BLD:

0013c14

- CI tests fixed `black` formatting after confirming that it works - `isort` is the next to check

BLD:

5d06d33

- fixed `isort` CI failure after confirming that it works - `pyright` is the next to check

BLD:

a4f13a6

- temporarily broke `isort` CI check again to check its output

BLD:

4a7896d

- fixed `isort` problem again - checking for reasons why `pyright`-check fails by running it separately without output ?

BLD:

5401719

- 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:

e6ae861

- 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:

7d48768

- going back to the start for tests after `mypy` also stopped CI correctly - starting with `black` test

BLD:

ffffcd1

- `black` successfully stopped the CI without customised handling - `isort` is the next to check without customised handling

BLD:

e60a349

- also `isort` stops the CI on failure - next to check is `pyright`

BLD:

f0ac7b5

- reverted GitHub CI to its original working state

MothNik added ✍️ documentation Improvements or additions to documentation 💪 enhancement New feature or request ✅❌ tests Everything related to maintaining or improving tests and coverage 💥 breaks old funcionality Changes that break old functionality labels Jul 30, 2024

MothNik self-assigned this Jul 30, 2024

MothNik linked an issue Jul 30, 2024 that may be closed by this pull request

🤕🔨 Change definition of the alpha-parameter to be more Fourier-friendly #14

Closed

MothNik added 6 commits July 30, 2024 17:11

DOC:

58f1f4b

- updated `README` with new CI commands

BUG:

0ac95fa

- fixed missing `pandas` dependency for GitHub CI

BUG:

34e48ce

- fixed type incompatibility that caused `mypy` to crash the GitHub CI

TST:

df6ac6b

- fixed missing coverage for default and error handling of FFT utility functions

DOC:

7c6f2b8

- arranged legend of plot for special points of Hermite functions in a better position

MothNik commented Jul 30, 2024

View reviewed changes

TST:

cf318e3

- removed unnecessary list parametrization for orthonormality test of Hermite functions

MothNik merged commit 3c663ba into main Jul 30, 2024
5 checks passed

MothNik linked an issue Jul 30, 2024 that may be closed by this pull request

🧮〰️ Implement Robust Weighted Least Squares Regression-based Fourier transform #13

Open

MothNik mentioned this pull request Aug 2, 2024

🤦 Revert change of definition of alpha #19

Closed

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[13-1, 14] Change definition of scaling factor `alpha` , add center and approximations for Hermite functions, add Fourier transform utility functions #15

[13-1, 14] Change definition of scaling factor `alpha` , add center and approximations for Hermite functions, add Fourier transform utility functions #15

MothNik commented Jul 30, 2024 •

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[13-1, 14] Change definition of scaling factor alpha , add center and approximations for Hermite functions, add Fourier transform utility functions #15

[13-1, 14] Change definition of scaling factor alpha , add center and approximations for Hermite functions, add Fourier transform utility functions #15

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MothNik commented Jul 30, 2024 • edited Loading

💥 Breaking changes

🦾 Features/Enhancements

✍️ Documentation

🪛 Internal changes

codecov bot commented Jul 30, 2024 • edited Loading

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[13-1, 14] Change definition of scaling factor `alpha` , add center and approximations for Hermite functions, add Fourier transform utility functions #15

[13-1, 14] Change definition of scaling factor `alpha` , add center and approximations for Hermite functions, add Fourier transform utility functions #15

MothNik commented Jul 30, 2024 •

edited

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codecov bot commented Jul 30, 2024 •

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