Iddefix

*Coming soon!*

🚀 New Features
* Smart Bound Determination (SBD):
* Method `to_table()` to display the estimated parameter bounds.
* Custom scale factors for Rs, Q, and fres: `Rs_bounds`, `Q_bounds`, `fres_bounds` for init.

* Utils:
* Integration of [`neffint`](https://github.com/ImpedanCEI/neffint) for non-equidistant Fourier transforms inside functions:
- `compute_neffint()`: alternative to compute FFT.
- `compute_ineffint()`: allows going from impedance to Wake potential, alternative to iFFT.
- `compute_deconvolution()`: Allows going from wake potential to impedance using `FFT(wake)/FFT(charge_distribution)`. Assumes charge distribution is a Gaussian with `sigmaz` specified by the user in [s].
* File I/O:
* `read_txt()`: reads ASCII `.txt` files into arrays or dicts.
* `save_txt()`: exports x/y data to formatted `.txt` files.

* Framework:
* In `run_minimization_algorithm()`, the argument `margin` now supports a list of independent values for `[Rs, Q, fres]`, allowing finer control over parameter variations during optimization.
* Updated docstrings for `EvolutionaryAlgorithm` methods for better documentation and clarity.
* Check if beam sigma parameter is not passed when using wake potential functions and print a warning

* Solvers:
* Implemented `pymoo`'s CMA-ES algorithm (`run_cmaes()`) as an alternative global optimization solver.
* Added `run_pymoo_cmaes_solver()` for CMA-ES optimization using `pymoo`, with support for custom population size, sigma, and stopping criteria.
* Included an example integrating CMA-ES with previous optimization workflows.

💗 Other Tag Highlights
* 🔁 Nightly tests with GitHub Actions:
- 001 -> Compare `neffint`, FFT, and analytical methods.
* 📁 Examples:
- 004a: Fit directly the wake potential data with wake potential resonator formalism
- 004b: Fit impedance from wake potential data using `compute_deconvolution()`
- 005: Examples using `pymoo`'s CMA-ES algorithm

🐛 Bugfixes
* SBD: Method `find()` now updates `parameterBounds` in `self`.
* Trimmed trailing whitespaces for improved code readability.


👋👩‍💻New Contributors
* babreufig - Implemented the CMA-ES algorithm using `pymoo`

📝Full changelog
`git log v0.0.2... --date=short --pretty=format:"* %ad %d %s (%aN)" | copy`
* 2025-03-26 Little timing comparison between CMAES and DE (Bernardo Abreu Figueiredo)
* 2025-03-26 Added two more examples to notebook (Bernardo Abreu Figueiredo)
* 2025-03-17 fix/feat: Check if sigma is not passed, and use the sigma value in self or default and print warning (elenafuengar)
* 2025-03-17 feature: add functions to read and write to .txt files (elenafuengar)
* 2025-03-16 build: include pymoo (optional) (elenafuengar)
* 2025-03-16 docs: Update readme (elenafuengar)
* 2025-03-16 fix: add `OptimizationProblem` class inside pymoo routine for import handling and clarity (elenafuengar)
* 2025-03-16 docs: update release.md (elenafuengar)
* 2025-03-16 docs: add docstring and error handling for pymoo imports (elenafuengar)
* 2025-03-16 Merge pull request 3 from babreufig/main (Elena de la Fuente García)
* 2025-03-12 Implemented CMA-ES and added one mixed example of previous notebooks (Bernardo Abreu Figueiredo)
* 2025-03-12 Trimmed trailing whitespaces (Bernardo Abreu Figueiredo)
* 2025-03-11 docs: update docstrings inside EvolutionaryAlgorithm methods (elenafuengar)
* 2025-03-11 docs: update release.md (elenafuengar)
* 2025-03-11 feature: allow different margins for Rs, Q and fres when running the minimization algorithm (elenafuengar)
* 2025-03-10 docs: prepare for 0.1.0 release (elenafuengar)
* 2025-03-10 docs: include call to new method `SBD.to_table()` (elenafuengar)
* 2025-03-10 docs: add docstring (elenafuengar)
* 2025-03-10 feature: add custom scaling factors for Rs, Q, fres in init (elenafuengar)
* 2025-03-10 fix: `find()` method was not updating paramBounds in self (elenafuengar)
* 2025-03-10 feature: add method to display parameter bounds as a table (elenafuengar)
* 2025-02-28 style: adding wake with lines plot (elenafuengar)
* 2025-02-24 fix: change/remove units (elenafuengar)
* 2025-02-11 test: use iddefix new `compute_neffint` and `compute_ineffint` functions (elenafuengar)
* 2025-02-11 feature: functions to compute fft and ifft using `neffint` (elenafuengar)
* 2025-02-11 test: add adaptative frequency refining (elenafuengar)
* 2025-02-11 docs: fix typo, update notebook list, new RTD version (elenafuengar)

Changelog since v0.0.1 tag
`git log v0.0.1... --date=short --pretty=format:"* %ad %d %s (%aN)" | copy `

* 2025-02-06 (HEAD -> main, origin/main, origin/HEAD) fix: remove tests outputs from remote (elenafuengar)
* 2025-02-06 new: add text 001 to compare analytical, fft and neffint fft methods (elenafuengar)
* 2025-02-05 docs: add publications (elenafuengar)
* 2025-02-04 update: add partially and fully decayed impedance to result comparison (elenafuengar)
* 2025-02-04 update: use fitFunction argument in notebook (elenafuengar)
* 2025-02-04 fix: initialize attributes to None (elenafuengar)
* 2025-02-04 new: generalize parameters and docstring for impedance or wake or wake potential fit function modes (elenafuengar)
* 2025-02-03 add changelog (elenafuengar)
* 2025-02-03 add example using directly the wake resonator formalism as fit function for the EA (elenafuengar)
* 2025-02-03 add deconvolution routine (elenafuengar)
* 2025-02-03 use multithreaded sum for 10x speedup! (elenafuengar)
* 2025-02-03 feature: make sigma an optional argument for wake potential so it is suitable for using it as a fitFunction in the evolutionary algorithm (elenafuengar)
* 2025-02-01 use ML jargon (elenafuengar)
* 2025-01-31 use new framework methods, add real and imaginary check, update units, cosmetic changes (elenafuengar)
* 2025-01-31 more error handling and bugfix in get_impedance_from_fitFunction (elenafuengar)
* 2025-01-31 change units of time data to [s] (elenafuengar)
* 2025-01-30 add docstring to class (elenafuengar)
* 2025-01-30 add new methods for impedance and wakes to the example (elenafuengar)
* 2025-01-30 remove warning (elenafuengar)
* 2025-01-30 cosmetic changes and adding the new methods to get impedance and wake from the DE class (elenafuengar)
* 2025-01-30 change Nres to N_resonators for readability (elenafuengar)
* 2025-01-30 add new methods for impedance and wakes to the example (elenafuengar)
* 2025-01-30 add markdown format to print, change flag to `use minimization` and minor bugfixes (elenafuengar)
* 2025-01-30 add n_wake_potential for longitudinal and transverse (elenafuengar)
* 2025-01-30 feature: Add methods to get wakes, impedance and wake potential to the Evolutionary Algorithm class using the computed evolutionary or minimization algorithms (elenafuengar)
* 2025-01-29 change from wake potential to wake function (elenafuengar)
* 2025-01-29 update docstring, allow for ndarray in `minimum_peak_height`, add more parameters to tweak scipys find_peaks, change numbering of peaks to start in 1 (elenafuengar)
* 2025-01-29 Update README.md (Elena de la Fuente García)
* 2025-01-29 Update 004_sps_transition.ipynb (Elena de la Fuente García)
* 2025-01-29 Update 003_beam_wire_scanner.ipynb (Elena de la Fuente García)
* 2025-01-29 Update 002_extrapolation_sim_data.ipynb (Elena de la Fuente García)
* 2025-01-29 Update 001_analytical_resonator.ipynb (Elena de la Fuente García)
* 2025-01-29 Update README.md (Elena de la Fuente García)
* 2025-01-28 Update 004_sps_transition.ipynb (Elena de la Fuente García)
* 2025-01-28 small refactor: moving helper functions and adding the compute fft function to utils.py (elenafuengar)
* 2025-01-28 bump python version to 3.11 (elenafuengar)
* 2025-01-28 Update 004_sps_transition.ipynb (Elena de la Fuente García)
* 2025-01-28 Update 003_beam_wire_scanner.ipynb (Elena de la Fuente García)
* 2025-01-28 Update 002_extrapolation_sim_data.ipynb (Elena de la Fuente García)
* 2025-01-28 Update 001_analytical_resonator.ipynb (Elena de la Fuente García)
* 2025-01-28 reorganize badges (elenafuengar)
* 2025-01-28 solve security vulnerability (elenafuengar)
* 2025-01-28 add fork upstream to readme (elenafuengar)
* 2025-01-27 First version of the documentation (elenafuengar)
* 2025-01-27 update gitignore (elenafuengar)
* 2025-01-27 put logo inside docs/ (elenafuengar)
* 2025-01-27 Update README.md (Elena de la Fuente García)
* 2025-01-27 (tag: v0.0.2) Update 003_beam_wire_scanner.ipynb (Elena de la Fuente García)
* 2025-01-27 prepare 0.0.2 release (elenafuengar)
* 2025-01-27 add Nres as attribute (elenafuengar)
* 2025-01-24 Move out from dict to ndarray for passing params (Elena de la Fuente García)
* 2025-01-24 Move out from dict to ndarray to pass params (Elena de la Fuente García)
* 2025-01-24 small fix (Elena de la Fuente García)
* 2025-01-24 move out from dict to ndarray to pass params (Elena de la Fuente García)
* 2025-01-24 move out from dict to ndarray to pass FitFunction params (Elena de la Fuente García)
* 2025-01-24 add stopping criteria if convergence>1 (elenafuengar)
* 2025-01-24 add ndarray option for resonator parameters (elenafuengar)
* 2025-01-24 Update README.md (MaltheRaschke)
* 2025-01-24 Update theory.md (MaltheRaschke)
* 2025-01-24 Progress bar update to convergence based (Malthe Raschke Nielsen)
* 2025-01-24 Update README.md (MaltheRaschke)
* 2025-01-23 minor updates and fixes (Malthe Raschke Nielsen)
* 2025-01-23 Added 004 example and data (Malthe Raschke Nielsen)
* 2025-01-22 Minor changes and fixes (Malthe Raschke Nielsen)
* 2025-01-21 updating examples + new 003 example for beam wire scanner (Malthe Raschke Nielsen)
* 2025-01-21 Edit of init to include SBD (Malthe Raschke Nielsen)
* 2025-01-21 Smart bound determination code added to IDDEFIX (Malthe Raschke Nielsen)
* 2025-01-21 New example. CST cavity simulation (Malthe Raschke Nielsen)
* 2025-01-21 time_data and wake_data to be none (Malthe Raschke Nielsen)
* 2025-01-20 Rename files (Malthe Raschke Nielsen)
* 2025-01-20 add tqdm progress bar to pyfde solvers (elenafuengar)
* 2025-01-20 bugfix: rework progress bar for scipy.diferential_evolution() (elenafuengar)
* 2025-01-20 impedance data added for accelerator cavity sim. by CST (Malthe Raschke Nielsen)
* 2025-01-20 Updated - draft for finished notebook (Malthe Raschke Nielsen)
* 2025-01-20 change 'hyperparameters' to 'evolutionParameters' as hyperparameters was used in wrong context. New variable name is more fitting (Malthe Raschke Nielsen)
* 2025-01-20 updating 001 example notebook - cleared outputs. (Malthe Raschke Nielsen)
* 2025-01-20 updating 001 example notebook + code notes in framework. No need for WP data and time data. (Malthe Raschke Nielsen)
* 2025-01-20 correcting from genetic to evolutionary (Malthe Raschke Nielsen)
* 2025-01-17 added analytical res. parameters (Malthe Raschke Nielsen)
* 2025-01-17 Changed genetic algorihm to evolutionary and differential evolution (Malthe Raschke Nielsen)
* 2025-01-17 Remove all old examples (Malthe Raschke Nielsen)
* 2025-01-17 Starting the first example (Malthe Raschke Nielsen)
* 2025-01-17 fix import issues (elenafuengar)
* 2025-01-17 docs placeholders (elenafuengar)
* 2025-01-17 update to Sebastiens new logo (elenafuengar)
* 2024-12-13 Update README.md (MaltheRaschke)
* 2024-11-27 change homepage for pipy (elenafuengar)
* 2024-11-27 Name changes for pypi (Malthe Raschke Nielsen)

Changelog since v0.0.1 tag
`git log v0.0.1... --date=short --pretty=format:"* %ad %d %s (%aN)" | copy `

* 2025-02-03 (HEAD -> main, origin/main, origin/HEAD) add example using directly the wake resonator formalism as fit function for the EA (elenafuengar)
* 2025-02-03 add deconvolution routine (elenafuengar)
* 2025-02-03 use multithreaded sum for 10x speedup! (elenafuengar)
* 2025-02-03 feature: make sigma an optional argument for wake potential so it is suitable for using it as a fitFunction in the evolutionary algorithm (elenafuengar)
* 2025-02-01 use ML jargon (elenafuengar)
* 2025-01-31 use new framework methods, add real and imaginary check, update units, cosmetic changes (elenafuengar)
* 2025-01-31 more error handling and bugfix in get_impedance_from_fitFunction (elenafuengar)
* 2025-01-31 change units of time data to [s] (elenafuengar)
* 2025-01-30 add docstring to class (elenafuengar)
* 2025-01-30 add new methods for impedance and wakes to the example (elenafuengar)
* 2025-01-30 remove warning (elenafuengar)
* 2025-01-30 cosmetic changes and adding the new methods to get impedance and wake from the DE class (elenafuengar)
* 2025-01-30 change Nres to N_resonators for readability (elenafuengar)
* 2025-01-30 add new methods for impedance and wakes to the example (elenafuengar)
* 2025-01-30 add markdown format to print, change flag to `use minimization` and minor bugfixes (elenafuengar)
* 2025-01-30 add n_wake_potential for longitudinal and transverse (elenafuengar)
* 2025-01-30 feature: Add methods to get wakes, impedance and wake potential to the Evolutionary Algorithm class using the computed evolutionary or minimization algorithms (elenafuengar)
* 2025-01-29 change from wake potential to wake function (elenafuengar)
* 2025-01-29 update docstring, allow for ndarray in `minimum_peak_height`, add more parameters to tweak scipys find_peaks, change numbering of peaks to start in 1 (elenafuengar)
* 2025-01-29 Update README.md (Elena de la Fuente García)
* 2025-01-29 Update 004_sps_transition.ipynb (Elena de la Fuente García)
* 2025-01-29 Update 003_beam_wire_scanner.ipynb (Elena de la Fuente García)
* 2025-01-29 Update 002_extrapolation_sim_data.ipynb (Elena de la Fuente García)
* 2025-01-29 Update 001_analytical_resonator.ipynb (Elena de la Fuente García)
* 2025-01-29 Update README.md (Elena de la Fuente García)
* 2025-01-28 Update 004_sps_transition.ipynb (Elena de la Fuente García)
* 2025-01-28 small refactor: moving helper functions and adding the compute fft function to utils.py (elenafuengar)
* 2025-01-28 bump python version to 3.11 (elenafuengar)
* 2025-01-28 Update 004_sps_transition.ipynb (Elena de la Fuente García)
* 2025-01-28 Update 003_beam_wire_scanner.ipynb (Elena de la Fuente García)
* 2025-01-28 Update 002_extrapolation_sim_data.ipynb (Elena de la Fuente García)
* 2025-01-28 Update 001_analytical_resonator.ipynb (Elena de la Fuente García)
* 2025-01-28 reorganize badges (elenafuengar)
* 2025-01-28 solve security vulnerability (elenafuengar)
* 2025-01-28 add fork upstream to readme (elenafuengar)
* 2025-01-27 First version of the documentation (elenafuengar)
* 2025-01-27 update gitignore (elenafuengar)
* 2025-01-27 put logo inside docs/ (elenafuengar)
* 2025-01-27 Update README.md (Elena de la Fuente García)
* 2025-01-27 (tag: v0.0.2) Update 003_beam_wire_scanner.ipynb (Elena de la Fuente García)
* 2025-01-27 prepare 0.0.2 release (elenafuengar)
* 2025-01-27 add Nres as attribute (elenafuengar)
* 2025-01-24 Move out from dict to ndarray for passing params (Elena de la Fuente García)
* 2025-01-24 Move out from dict to ndarray to pass params (Elena de la Fuente García)
* 2025-01-24 small fix (Elena de la Fuente García)
* 2025-01-24 move out from dict to ndarray to pass params (Elena de la Fuente García)
* 2025-01-24 move out from dict to ndarray to pass FitFunction params (Elena de la Fuente García)
* 2025-01-24 add stopping criteria if convergence>1 (elenafuengar)
* 2025-01-24 add ndarray option for resonator parameters (elenafuengar)
* 2025-01-24 Update README.md (MaltheRaschke)
* 2025-01-24 Update theory.md (MaltheRaschke)
* 2025-01-24 Progress bar update to convergence based (Malthe Raschke Nielsen)
* 2025-01-24 Update README.md (MaltheRaschke)
* 2025-01-23 minor updates and fixes (Malthe Raschke Nielsen)
* 2025-01-23 Added 004 example and data (Malthe Raschke Nielsen)
* 2025-01-22 Minor changes and fixes (Malthe Raschke Nielsen)
* 2025-01-21 updating examples + new 003 example for beam wire scanner (Malthe Raschke Nielsen)
* 2025-01-21 Edit of init to include SBD (Malthe Raschke Nielsen)
* 2025-01-21 Smart bound determination code added to IDDEFIX (Malthe Raschke Nielsen)
* 2025-01-21 New example. CST cavity simulation (Malthe Raschke Nielsen)
* 2025-01-21 time_data and wake_data to be none (Malthe Raschke Nielsen)
* 2025-01-20 Rename files (Malthe Raschke Nielsen)
* 2025-01-20 add tqdm progress bar to pyfde solvers (elenafuengar)
* 2025-01-20 bugfix: rework progress bar for scipy.diferential_evolution() (elenafuengar)
* 2025-01-20 impedance data added for accelerator cavity sim. by CST (Malthe Raschke Nielsen)
* 2025-01-20 Updated - draft for finished notebook (Malthe Raschke Nielsen)
* 2025-01-20 change 'hyperparameters' to 'evolutionParameters' as hyperparameters was used in wrong context. New variable name is more fitting (Malthe Raschke Nielsen)
* 2025-01-20 updating 001 example notebook - cleared outputs. (Malthe Raschke Nielsen)
* 2025-01-20 updating 001 example notebook + code notes in framework. No need for WP data and time data. (Malthe Raschke Nielsen)
* 2025-01-20 correcting from genetic to evolutionary (Malthe Raschke Nielsen)
* 2025-01-17 added analytical res. parameters (Malthe Raschke Nielsen)
* 2025-01-17 Changed genetic algorihm to evolutionary and differential evolution (Malthe Raschke Nielsen)
* 2025-01-17 Remove all old examples (Malthe Raschke Nielsen)
* 2025-01-17 Starting the first example (Malthe Raschke Nielsen)
* 2025-01-17 fix import issues (elenafuengar)
* 2025-01-17 docs placeholders (elenafuengar)
* 2025-01-17 update to Sebastiens new logo (elenafuengar)
* 2024-12-13 Update README.md (MaltheRaschke)
* 2024-11-27 change homepage for pipy (elenafuengar)
* 2024-11-27 Name changes for pypi (Malthe Raschke Nielsen)