diff --git a/.pylintrc b/.pylintrc index 4ca30150d..2071e00c3 100644 --- a/.pylintrc +++ b/.pylintrc @@ -105,6 +105,7 @@ disable= # We anticipate #3512 where it will become optional fixme, E0401, # Import is not at the top of the file + R6002, # Old typing definition [REPORTS] diff --git a/CHANGELOG.md b/CHANGELOG.md index 8c982482f..c4eafaf03 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,6 +4,16 @@ > See also: [https://github.com/Anselmoo/spectrafit/releases][1] +## v0.9.0 + +--- + +- Adding Python 3.10 support +- Adding [Athena file][19] support +- Increasing code quality by using [`pylint`][18] +- Adding plugin support for `SpectraFit` + - Starting with input file converter + ## v0.8.6 --- @@ -202,3 +212,5 @@ [15]: https://pypi.org/project/spectrafit/ [16]: https://docs.scipy.org/doc/scipy/reference/generated/scipy.signal.find_peaks.html [17]: https://prettier.io +[18]: https://github.com/PyCQA/pylint +[19]: http://bruceravel.github.io/demeter/documents/Athena/index.html diff --git a/Examples/example_8_summary.toml b/Examples/example_8_summary.toml new file mode 100644 index 000000000..e26566b94 --- /dev/null +++ b/Examples/example_8_summary.toml @@ -0,0 +1,400 @@ +infile = "athena.nor" +outfile = "example_8" +input = "example_8.json" +oversampling = false +energy_start = 5440 +energy_stop = 5520 +smooth = 0 +shift = 0 +column = [ 0, 1,] +separator = "\\s+" +decimal = "." +comment = "#" +global = 0 +autopeak = false +noplot = false +version = false +verbose = 0 +timestamp = "2022-06-26 12:35:11" +ID = "e5c7fc20-bd57-4578-abbf-7736cef3be9b" +user_name = "user_name" +user_system = "user_system" +used_version = "0.9.0" + +[description] +project_name = "Template" +project_details = "Template for testing" +keywords = [ "2D-Spectra", "fitting", "curve-fitting", "peak-fitting", "spectrum",] + +[minimizer] +nan_policy = "propagate" +calc_covar = true + +[optimizer] +max_nfev = 1000 +method = "leastsq" + +[report] +min_correl = 0.0 + +[data_statistic] +0 = [ 393.0, 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+[fit_insights.variables.gaussian_center_5] +init_value = 5483 +model_value = 5481.724992617458 +best_value = 5481.724992617458 + +[fit_insights.variables.gaussian_fwhmg_5] +init_value = 3 +model_value = 4.1240411794396445 +best_value = 4.1240411794396445 + +[fit_insights.variables.gaussian_amplitude_6] +init_value = 4 +model_value = 1.2428818045605532 +best_value = 1.2428818045605532 + +[fit_insights.variables.gaussian_center_6] +init_value = 5494 +model_value = 5493.950495823278 +best_value = 5493.950495823278 + +[fit_insights.variables.gaussian_fwhmg_6] +init_value = 3 +model_value = 4.749999999999982 +best_value = 4.749999999999982 + +[fit_insights.variables.atan_amplitude_7] +init_value = 1 +model_value = 1.0784237600535795 +best_value = 1.0784237600535795 + +[fit_insights.variables.atan_center_7] +init_value = 5483 +model_value = 5483.0 +best_value = 5483.0 + +[fit_insights.variables.atan_sigma_7] +init_value = 0.01 +model_value = 0.7490707110057951 +best_value = 0.7490707110057951 + +[fit_insights.correlations.pseudovoigt_amplitude_1] + +[fit_insights.correlations.pseudovoigt_center_1] + +[fit_insights.correlations.pseudovoigt_fwhmg_1] + +[fit_insights.correlations.pseudovoigt_fwhml_1] + +[fit_insights.correlations.pseudovoigt_amplitude_2] + +[fit_insights.correlations.pseudovoigt_center_2] + +[fit_insights.correlations.pseudovoigt_fwhmg_2] + +[fit_insights.correlations.pseudovoigt_fwhml_2] + +[fit_insights.correlations.pseudovoigt_amplitude_3] + +[fit_insights.correlations.pseudovoigt_center_3] + +[fit_insights.correlations.pseudovoigt_fwhmg_3] + +[fit_insights.correlations.pseudovoigt_fwhml_3] + +[fit_insights.correlations.gaussian_amplitude_4] + +[fit_insights.correlations.gaussian_center_4] + +[fit_insights.correlations.gaussian_fwhmg_4] + +[fit_insights.correlations.gaussian_amplitude_5] + +[fit_insights.correlations.gaussian_center_5] + +[fit_insights.correlations.gaussian_fwhmg_5] + +[fit_insights.correlations.gaussian_amplitude_6] + +[fit_insights.correlations.gaussian_center_6] + +[fit_insights.correlations.gaussian_fwhmg_6] + +[fit_insights.correlations.atan_amplitude_7] + +[fit_insights.correlations.atan_center_7] + +[fit_insights.correlations.atan_sigma_7] + +[peaks.1.pseudovoigt.amplitude] +max = 4 +min = 0 +vary = true +value = 1 + +[peaks.1.pseudovoigt.center] +max = 5470 +min = 5460 +vary = true +value = 5468 + +[peaks.1.pseudovoigt.fwhmg] +max = 2.75 +min = 0.001 +vary = true +value = 1.0 + +[peaks.1.pseudovoigt.fwhml] +max = 2.75 +min = 0.001 +vary = true +value = 1.0 + +[peaks.2.pseudovoigt.amplitude] +max = 4 +min = 0 +vary = true +value = 1 + +[peaks.2.pseudovoigt.center] +max = 5470 +min = 5465 +vary = true +value = 5469 + +[peaks.2.pseudovoigt.fwhmg] +max = 2.75 +min = 0.001 +vary = true +value = 1.0 + +[peaks.2.pseudovoigt.fwhml] +max = 2.75 +min = 0.001 +vary = true +value = 1.0 + +[peaks.3.pseudovoigt.amplitude] +max = 4 +min = 0 +vary = true +value = 1 + +[peaks.3.pseudovoigt.center] +max = 5480 +min = 5470 +vary = true +value = 5473 + +[peaks.3.pseudovoigt.fwhmg] +max = 3.75 +min = 0.1 +vary = true +value = 1 + +[peaks.3.pseudovoigt.fwhml] +max = 3.75 +min = 0.1 +vary = true +value = 1 + +[peaks.4.gaussian.amplitude] +max = 10 +min = 0.1 +vary = true +value = 3 + +[peaks.4.gaussian.center] +max = 5485 +min = 5475 +vary = true +value = 5478 + +[peaks.4.gaussian.fwhmg] +max = 4 +min = 0.1 +vary = true +value = 1 + +[peaks.5.gaussian.amplitude] +max = 10 +min = 0.1 +vary = true +value = 4 + +[peaks.5.gaussian.center] +max = 5498 +min = 5480 +vary = true +value = 5483 + +[peaks.5.gaussian.fwhmg] +max = 4.75 +min = 0.1 +vary = true +value = 3 + +[peaks.6.gaussian.amplitude] +max = 10 +min = 0.1 +vary = true +value = 4 + +[peaks.6.gaussian.center] +max = 5498 +min = 5493 +vary = true +value = 5494 + +[peaks.6.gaussian.fwhmg] +max = 4.75 +min = 0.1 +vary = true +value = 3 + +[peaks.7.atan.amplitude] +max = 5 +min = 0 +vary = true +value = 1 + +[peaks.7.atan.center] +max = 5500 +min = 5483 +vary = true +value = 5481 + +[peaks.7.atan.sigma] +max = 0.75 +min = 0.001 +vary = true +value = 0.01 diff --git a/docs/contact.md b/docs/contact.md index 490e75dc4..d86164c6f 100644 --- a/docs/contact.md +++ b/docs/contact.md @@ -1,4 +1,5 @@ ## Contact us at ... - [Issue-Board](https://github.com/Anselmoo/spectrafit/issues) +- [Project-Board](https://github.com/Anselmoo/spectrafit/projects/1) - Discussion-Board might come later ... diff --git a/docs/plugins/spectrafit-converter.md b/docs/plugins/spectrafit-converter.md new file mode 100644 index 000000000..873c438d4 --- /dev/null +++ b/docs/plugins/spectrafit-converter.md @@ -0,0 +1,1854 @@ +With the command `spectrafit-converter` input and output files can be converted. The supported file formats are: + +1. `.json` +2. `.yaml` +3. `.toml` + +```shell + ❯ spectrafit-converter -h + usage: spectrafit-converter [-h] [-f {lock,ymltoml,yaml,json}] infile + + Converter for 'SpectraFit' input and output files. + + positional arguments: + infile Filename of the 'SpectraFit' input or output file. + + options: + -h, --help show this help message and exit + -f {lock,ymltoml,yaml,json}, --format {lock,ymltoml,yaml,json} + File format for the conversion. + +``` + +=== "File Change from `json` to `lock`" + + !!! info + + The file format change can be also applied to the `.json`-output to the more human-readable `lock`-file-format, which is a `.toml` file. + + Both output files are provided as: + + * example_8_summary.json + * example_8_summary.lock + +=== "JSON" + + ```json + { + "infile": "athena.nor", + "outfile": "example_8", + "input": "example_8.json", + "oversampling": false, + "energy_start": 5440, + "energy_stop": 5520, + "smooth": 0, + "shift": 0, + "column": [0, 1], + "separator": "\\s+", + "decimal": ".", + "header": null, + "comment": "#", + "global": 0, + "autopeak": false, + "noplot": false, + "version": false, + "verbose": 0, + "description": { + "project_name": "Template", + "project_details": "Template for testing", + "keywords": [ + "2D-Spectra", + "fitting", + "curve-fitting", + "peak-fitting", + "spectrum" + ] + }, + "minimizer": { + "nan_policy": "propagate", + "calc_covar": true + }, + "optimizer": { + "max_nfev": 1000, + "method": "leastsq" + }, + "report": { + "min_correl": 0.0 + }, + "conf_interval": null, + "peaks": { + "1": { + "pseudovoigt": { + "amplitude": { + "max": 4, + "min": 0, + "vary": true, + "value": 1 + }, + "center": { + "max": 5470, + "min": 5460, + "vary": true, + "value": 5468 + }, + "fwhmg": { + "max": 2.75, + "min": 0.001, + "vary": true, + "value": 1.0 + }, + "fwhml": { + "max": 2.75, + "min": 0.001, + "vary": true, + "value": 1.0 + } + } + }, + "2": { + "pseudovoigt": { + "amplitude": { + "max": 4, + "min": 0, + "vary": true, + "value": 1 + }, + "center": { + "max": 5470, + "min": 5465, + "vary": true, + "value": 5469 + }, + "fwhmg": { + "max": 2.75, + "min": 0.001, + "vary": true, + "value": 1.0 + }, + "fwhml": { + "max": 2.75, + "min": 0.001, + "vary": true, + "value": 1.0 + } + } + }, + "3": { + "pseudovoigt": { + "amplitude": { + "max": 4, + "min": 0, + "vary": true, + "value": 1 + }, + "center": { + "max": 5480, + "min": 5470, + "vary": true, + "value": 5473 + }, + "fwhmg": { + "max": 3.75, + "min": 0.1, + "vary": true, + "value": 1 + }, + "fwhml": { + "max": 3.75, + "min": 0.1, + "vary": true, + "value": 1 + } + } + }, + "4": { + "gaussian": { + "amplitude": { + "max": 10, + "min": 0.1, + "vary": true, + "value": 3 + }, + "center": { + "max": 5485, + "min": 5475, + "vary": true, + "value": 5478 + }, + "fwhmg": { + "max": 4, + "min": 0.1, + "vary": true, + "value": 1 + } + } + }, + "5": { + "gaussian": { + "amplitude": { + "max": 10, + "min": 0.1, + "vary": true, + "value": 4 + }, + "center": { + "max": 5498, + "min": 5480, + "vary": true, + "value": 5483 + }, + "fwhmg": { + "max": 4.75, + "min": 0.1, + "vary": true, + "value": 3 + } + } + }, + "6": { + "gaussian": { + "amplitude": { + "max": 10, + "min": 0.1, + "vary": true, + "value": 4 + }, + "center": { + "max": 5498, + "min": 5493, + "vary": true, + "value": 5494 + }, + "fwhmg": { + "max": 4.75, + "min": 0.1, + "vary": true, + "value": 3 + } + } + }, + "7": { + "atan": { + "amplitude": { + "max": 5, + "min": 0, + "vary": true, + "value": 1 + }, + "center": { + "max": 5500, + "min": 5483, + "vary": true, + "value": 5481 + }, + "sigma": { + "max": 0.75, + "min": 0.001, + "vary": true, + "value": 0.01 + } + } + } + }, + "timestamp": "2022-06-26 12:35:11", + "ID": "e5c7fc20-bd57-4578-abbf-7736cef3be9b", + "user_name": "user_name", + "user_system": "user_system", + "used_version": "0.9.0", + "data_statistic": { + "0": [ + 393.0, 5493.268875318066, 70.85455926057932, 5263.8492, 5439.3992, + 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project_name = "Template" + project_details = "Template for testing" + keywords = [ "2D-Spectra", "fitting", "curve-fitting", "peak-fitting", "spectrum",] + + [minimizer] + nan_policy = "propagate" + calc_covar = true + + [optimizer] + max_nfev = 1000 + method = "leastsq" + + [report] + min_correl = 0.0 + + [data_statistic] + 0 = [ 393.0, 5493.268875318066, 70.85455926057932, 5263.8492, 5439.3992, 5449.2004400000005, 5459.00094, 5468.80008, 5478.5995, 5488.40074, 5498.20038, 5526.97246, 5602.409339999999, 5707.751,] + 1 = [ 393.0, 0.5559652545537828, 0.5000826290756465, -0.0015911817, 0.0011720014800000002, 0.003939243640000001, 0.012118344800000002, 0.11680503600000006, 0.55104052, 0.983449568, 1.0087658400000001, 1.04338526, 1.12497912, 1.2670019,] + + [linear_correlation] + energy = [ 1.0, 0.8935483804274674, 0.014165493917872009, 0.8994185246507211, -0.08246614304287148, -0.05776360778162228, 0.04606936027745239, 0.05426690223694854, 0.13152358463255703, 0.3565816542879464, 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0.0744198775097722, 0.08016640148299946, 0.08678237893702904, 0.09455846159894472, 0.10381854271718445, 0.115137930941325, 0.12895510537206828, 0.14632074337329493, 0.16864768851714007, 0.1980878943642129, 0.23853836290240887, 0.29353365116177793, 0.3712384891638708, 0.4715897596186985, 0.5847690231931497, 0.6892197128444592, 0.7709839871250703, 0.83039552595971, 0.8730991185003477, 0.9044232442090606, 0.9280439919975729, 0.9462996095463007, 0.9607455590626317, 0.9724528909534325, 0.9820979104737809, 0.9901635950269833, 0.9970115343486721, 1.002889372061163, 1.0079867923692056, 1.012442667657563, 1.0163815263243314, 1.0198782805406956, 1.0230075241470533, 1.0258238529255068, 1.0283658319667748, 1.0306776037439533, 1.0327848712802061, 1.0347156968732825, 1.0364742242858793, 1.0381149672118775, 1.0396298073202925, 1.0410369721203856, 1.042345989689725, 1.043555442842206, 1.044696392912147, 1.0457677405947312, 1.046770977180337, 1.0477068859350114, 1.048597113307248, 1.0494376386653905, 1.0502318850679817, 1.0509783035541564, 1.0516921199152156, 1.0523703433410703, 1.0530082960450058, 1.0536220168611887, 1.0542073002524035, 1.054759987834216, 1.0552930352100218, 1.0558034257490165, 1.0562861007644435, 1.0567537420746898, 1.057202759290147, 1.0576286987365169, 1.0580417693579116, 1.05843504309784, 1.0588174765920297, 1.0591821146127258, 1.0595367773181141, 1.0598750063540652, 1.0602050863270371, 1.06052039695601, 1.0608278762656094, 1.0611218410545253, 1.0614098657099427, 1.0616850908818294, 1.061954722779951, 1.062212953162244, 1.0624632163293728, 1.062708371043094, 1.0629436925393998, 1.0631745157062626, 1.0633961035946267, 1.063611774201365, 1.0638235829371996, 1.0640268454496244, 1.064224842698698, 1.0644194530283535, 1.0646067262447143, 1.0647893485517375, 1.0649671383814954, 1.0651422050781973, 1.0653109061432329, 1.065475507661714, 1.0656375553134998, 1.0657942969222531, 1.0659468807843688, 1.0660960596272866, 1.0667902196830066, 1.0674181726528138, 1.067991186069206, 1.0685138799632483, 1.068994320798989, 1.0694356214358438, 1.0698430284901264, 1.0702194835741392, 1.0705697251238486, 1.0708950625885092, 1.0711984632971308,] + + [fit_insights.configurations] + fitting_method = "leastsq" + function_evals = 1000 + data_points = 267 + variable_names = [ "pseudovoigt_amplitude_1", "pseudovoigt_center_1", "pseudovoigt_fwhmg_1", "pseudovoigt_fwhml_1", "pseudovoigt_amplitude_2", "pseudovoigt_center_2", "pseudovoigt_fwhmg_2", "pseudovoigt_fwhml_2", "pseudovoigt_amplitude_3", "pseudovoigt_center_3", "pseudovoigt_fwhmg_3", "pseudovoigt_fwhml_3", "gaussian_amplitude_4", "gaussian_center_4", "gaussian_fwhmg_4", "gaussian_amplitude_5", "gaussian_center_5", "gaussian_fwhmg_5", "gaussian_amplitude_6", "gaussian_center_6", "gaussian_fwhmg_6", "atan_amplitude_7", "atan_center_7", "atan_sigma_7",] + variable_numbers = 24 + degree_of_freedom = 243 + + [fit_insights.statistics] + chi-square = 0.19287134070118112 + reduced_chi_square = 0.0007937092209925148 + akaike_information = -1883.2058200035844 + bayesian_information = -1797.1118522019785 + + [fit_insights.errorbars] + at_boundary = "atan_center_7" + at_initial_value = "atan_center_7" + + [fit_insights.covariance_matrix] + + [fit_insights.variables.pseudovoigt_amplitude_1] + init_value = 1 + model_value = 6.887357351104129e-11 + best_value = 6.887357351104129e-11 + + [fit_insights.variables.pseudovoigt_center_1] + init_value = 5468 + model_value = 5468.054405630964 + best_value = 5468.054405630964 + + [fit_insights.variables.pseudovoigt_fwhmg_1] + init_value = 1.0 + model_value = 0.1897199824713271 + best_value = 0.1897199824713271 + + [fit_insights.variables.pseudovoigt_fwhml_1] + init_value = 1.0 + model_value = 1.8340047382909581 + best_value = 1.8340047382909581 + + [fit_insights.variables.pseudovoigt_amplitude_2] + init_value = 1 + model_value = 1.5312014287723803 + best_value = 1.5312014287723803 + + [fit_insights.variables.pseudovoigt_center_2] + init_value = 5469 + model_value = 5468.965365073547 + best_value = 5468.965365073547 + + [fit_insights.variables.pseudovoigt_fwhmg_2] + init_value = 1.0 + model_value = 2.1735730746400175 + best_value = 2.1735730746400175 + + [fit_insights.variables.pseudovoigt_fwhml_2] + init_value = 1.0 + model_value = 1.429425183820899 + best_value = 1.429425183820899 + + [fit_insights.variables.pseudovoigt_amplitude_3] + init_value = 1 + model_value = 1.4124892488220628 + best_value = 1.4124892488220628 + + [fit_insights.variables.pseudovoigt_center_3] + init_value = 5473 + model_value = 5475.767047063245 + best_value = 5475.767047063245 + + [fit_insights.variables.pseudovoigt_fwhmg_3] + init_value = 1 + model_value = 0.10000000837664919 + best_value = 0.10000000837664919 + + [fit_insights.variables.pseudovoigt_fwhml_3] + init_value = 1 + model_value = 3.7499977334701127 + best_value = 3.7499977334701127 + + [fit_insights.variables.gaussian_amplitude_4] + init_value = 3 + model_value = 0.6090009741875487 + best_value = 0.6090009741875487 + + [fit_insights.variables.gaussian_center_4] + init_value = 5478 + model_value = 5477.92439530641 + best_value = 5477.92439530641 + + [fit_insights.variables.gaussian_fwhmg_4] + init_value = 1 + model_value = 2.5805286730950385 + best_value = 2.5805286730950385 + + [fit_insights.variables.gaussian_amplitude_5] + init_value = 4 + model_value = 3.2112928728775594 + best_value = 3.2112928728775594 + + [fit_insights.variables.gaussian_center_5] + init_value = 5483 + model_value = 5481.724992617458 + best_value = 5481.724992617458 + + [fit_insights.variables.gaussian_fwhmg_5] + init_value = 3 + model_value = 4.1240411794396445 + best_value = 4.1240411794396445 + + [fit_insights.variables.gaussian_amplitude_6] + init_value = 4 + model_value = 1.2428818045605532 + best_value = 1.2428818045605532 + + [fit_insights.variables.gaussian_center_6] + init_value = 5494 + model_value = 5493.950495823278 + best_value = 5493.950495823278 + + [fit_insights.variables.gaussian_fwhmg_6] + init_value = 3 + model_value = 4.749999999999982 + best_value = 4.749999999999982 + + [fit_insights.variables.atan_amplitude_7] + init_value = 1 + model_value = 1.0784237600535795 + best_value = 1.0784237600535795 + + [fit_insights.variables.atan_center_7] + init_value = 5483 + model_value = 5483.0 + best_value = 5483.0 + + [fit_insights.variables.atan_sigma_7] + init_value = 0.01 + model_value = 0.7490707110057951 + best_value = 0.7490707110057951 + + [fit_insights.correlations.pseudovoigt_amplitude_1] + + [fit_insights.correlations.pseudovoigt_center_1] + + [fit_insights.correlations.pseudovoigt_fwhmg_1] + + [fit_insights.correlations.pseudovoigt_fwhml_1] + + [fit_insights.correlations.pseudovoigt_amplitude_2] + + [fit_insights.correlations.pseudovoigt_center_2] + + [fit_insights.correlations.pseudovoigt_fwhmg_2] + + [fit_insights.correlations.pseudovoigt_fwhml_2] + + [fit_insights.correlations.pseudovoigt_amplitude_3] + + [fit_insights.correlations.pseudovoigt_center_3] + + [fit_insights.correlations.pseudovoigt_fwhmg_3] + + [fit_insights.correlations.pseudovoigt_fwhml_3] + + [fit_insights.correlations.gaussian_amplitude_4] + + [fit_insights.correlations.gaussian_center_4] + + [fit_insights.correlations.gaussian_fwhmg_4] + + [fit_insights.correlations.gaussian_amplitude_5] + + [fit_insights.correlations.gaussian_center_5] + + [fit_insights.correlations.gaussian_fwhmg_5] + + [fit_insights.correlations.gaussian_amplitude_6] + + [fit_insights.correlations.gaussian_center_6] + + [fit_insights.correlations.gaussian_fwhmg_6] + + [fit_insights.correlations.atan_amplitude_7] + + [fit_insights.correlations.atan_center_7] + + [fit_insights.correlations.atan_sigma_7] + + [peaks.1.pseudovoigt.amplitude] + max = 4 + min = 0 + vary = true + value = 1 + + [peaks.1.pseudovoigt.center] + max = 5470 + min = 5460 + vary = true + value = 5468 + + [peaks.1.pseudovoigt.fwhmg] + max = 2.75 + min = 0.001 + vary = true + value = 1.0 + + [peaks.1.pseudovoigt.fwhml] + max = 2.75 + min = 0.001 + vary = true + value = 1.0 + + [peaks.2.pseudovoigt.amplitude] + max = 4 + min = 0 + vary = true + value = 1 + + [peaks.2.pseudovoigt.center] + max = 5470 + min = 5465 + vary = true + value = 5469 + + [peaks.2.pseudovoigt.fwhmg] + max = 2.75 + min = 0.001 + vary = true + value = 1.0 + + [peaks.2.pseudovoigt.fwhml] + max = 2.75 + min = 0.001 + vary = true + value = 1.0 + + [peaks.3.pseudovoigt.amplitude] + max = 4 + min = 0 + vary = true + value = 1 + + [peaks.3.pseudovoigt.center] + max = 5480 + min = 5470 + vary = true + value = 5473 + + [peaks.3.pseudovoigt.fwhmg] + max = 3.75 + min = 0.1 + vary = true + value = 1 + + [peaks.3.pseudovoigt.fwhml] + max = 3.75 + min = 0.1 + vary = true + value = 1 + + [peaks.4.gaussian.amplitude] + max = 10 + min = 0.1 + vary = true + value = 3 + + [peaks.4.gaussian.center] + max = 5485 + min = 5475 + vary = true + value = 5478 + + [peaks.4.gaussian.fwhmg] + max = 4 + min = 0.1 + vary = true + value = 1 + + [peaks.5.gaussian.amplitude] + max = 10 + min = 0.1 + vary = true + value = 4 + + [peaks.5.gaussian.center] + max = 5498 + min = 5480 + vary = true + value = 5483 + + [peaks.5.gaussian.fwhmg] + max = 4.75 + min = 0.1 + vary = true + value = 3 + + [peaks.6.gaussian.amplitude] + max = 10 + min = 0.1 + vary = true + value = 4 + + [peaks.6.gaussian.center] + max = 5498 + min = 5493 + vary = true + value = 5494 + + [peaks.6.gaussian.fwhmg] + max = 4.75 + min = 0.1 + vary = true + value = 3 + + [peaks.7.atan.amplitude] + max = 5 + min = 0 + vary = true + value = 1 + + [peaks.7.atan.center] + max = 5500 + min = 5483 + vary = true + value = 5481 + + [peaks.7.atan.sigma] + max = 0.75 + min = 0.001 + vary = true + value = 0.01 + ``` diff --git a/mkdocs.yaml b/mkdocs.yaml index 684a4d07e..ef3c8d484 100644 --- a/mkdocs.yaml +++ b/mkdocs.yaml @@ -151,6 +151,8 @@ nav: - Solvers: doc/solver.md - Fitting: doc/fitting.md - Statistics: doc/statistics.md + - Plugins: + - File-Format-Conversion: plugins/spectrafit-converter.md - API: - SpectraFit: api/spectrafit_api.md - Plotting: api/plotting_api.md diff --git a/poetry.lock b/poetry.lock index 5c021371d..4fdbf3a2f 100644 --- a/poetry.lock +++ b/poetry.lock @@ -11,7 +11,7 @@ name = "argcomplete" version = "2.0.0" description = "Bash tab completion for argparse" category = "dev" -optional = false +optional = true python-versions = ">=3.6" [package.dependencies] @@ -118,23 +118,6 @@ python-versions = ">=3.7" [package.dependencies] black = ">=19.3b0" -[[package]] -name = "cachecontrol" -version = "0.12.11" -description = "httplib2 caching for requests" -category = "dev" -optional = true -python-versions = ">=3.6" - -[package.dependencies] -lockfile = {version = ">=0.9", optional = true, markers = "extra == \"filecache\""} -msgpack = ">=0.5.2" -requests = "*" - -[package.extras] -filecache = ["lockfile (>=0.9)"] -redis = ["redis (>=2.10.5)"] - [[package]] name = "cached-property" version = "1.5.2" @@ -148,7 +131,7 @@ name = "certifi" version = "2022.6.15" description = "Python package for providing Mozilla's CA Bundle." category = "dev" -optional = false +optional = true python-versions = ">=3.6" [[package]] @@ -164,7 +147,7 @@ name = "chardet" version = "4.0.0" description = "Universal encoding detector for Python 2 and 3" category = "dev" -optional = false +optional = true python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" [[package]] @@ -172,7 +155,7 @@ name = "charset-normalizer" version = "2.0.12" description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet." category = "dev" -optional = false +optional = true python-versions = ">=3.5.0" [package.extras] @@ -256,26 +239,12 @@ category = "main" optional = false python-versions = ">=3.6" -[[package]] -name = "cyclonedx-python-lib" -version = "2.6.0" -description = "A library for producing CycloneDX SBOM (Software Bill of Materials) files." -category = "dev" -optional = true -python-versions = ">=3.6,<4.0" - -[package.dependencies] -importlib-metadata = {version = ">=3.4", markers = "python_version < \"3.8\""} -packageurl-python = ">=0.9" -sortedcontainers = ">=2.4.0,<3.0.0" -toml = ">=0.10.0,<0.11.0" - [[package]] name = "datamodel-code-generator" version = "0.13.0" description = "Datamodel Code Generator" category = "dev" -optional = false +optional = true python-versions = ">=3.6.1,<4.0.0" [package.dependencies] @@ -287,7 +256,10 @@ isort = ">=4.3.21,<6.0" jinja2 = ">=2.10.1,<4.0" openapi-spec-validator = ">=0.2.8,<0.4" prance = ">=0.18.2,<1.0" -pydantic = {version = ">=1.5.1,<2.0", extras = ["email"], markers = "python_version < \"3.10\""} +pydantic = [ + {version = ">=1.5.1,<2.0", extras = ["email"], markers = "python_version < \"3.10\""}, + {version = ">=1.9.0,<2.0", extras = ["email"], markers = "python_version >= \"3.10\""}, +] PySnooper = ">=0.4.1,<2.0.0" toml = ">=0.10.0,<1.0.0" typed-ast = [ @@ -322,7 +294,7 @@ name = "dnspython" version = "2.2.1" description = "DNS toolkit" category = "dev" -optional = false +optional = true python-versions = ">=3.6,<4.0" [package.extras] @@ -338,7 +310,7 @@ name = "email-validator" version = "1.2.1" description = "A robust email syntax and deliverability validation library." category = "dev" -optional = false +optional = true python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7" [package.dependencies] @@ -391,20 +363,6 @@ python-versions = ">=3.7" docs = ["furo (>=2021.8.17b43)", "sphinx (>=4.1)", "sphinx-autodoc-typehints (>=1.12)"] testing = ["covdefaults (>=1.2.0)", "coverage (>=4)", "pytest (>=4)", "pytest-cov", "pytest-timeout (>=1.4.2)"] -[[package]] -name = "flake8" -version = "4.0.1" -description = "the modular source code checker: pep8 pyflakes and co" -category = "dev" -optional = false -python-versions = ">=3.6" - -[package.dependencies] -importlib-metadata = {version = "<4.3", markers = "python_version < \"3.8\""} -mccabe = ">=0.6.0,<0.7.0" -pycodestyle = ">=2.8.0,<2.9.0" -pyflakes = ">=2.4.0,<2.5.0" - [[package]] name = "fonttools" version = "4.33.3" @@ -440,7 +398,7 @@ name = "genson" version = "1.2.2" description = "GenSON is a powerful, user-friendly JSON Schema generator." category = "dev" -optional = false +optional = true python-versions = "*" [[package]] @@ -457,24 +415,6 @@ python-dateutil = ">=2.8.1" [package.extras] dev = ["twine", "markdown", "flake8", "wheel"] -[[package]] -name = "html5lib" -version = "1.1" -description = "HTML parser based on the WHATWG HTML specification" -category = "dev" -optional = true -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" - -[package.dependencies] -six = ">=1.9" -webencodings = "*" - -[package.extras] -all = ["genshi", "chardet (>=2.2)", "lxml"] -chardet = ["chardet (>=2.2)"] -genshi = ["genshi"] -lxml = ["lxml"] - [[package]] name = "htmlmin" version = "0.1.12" @@ -499,31 +439,32 @@ name = "idna" version = "3.3" description = "Internationalized Domain Names in Applications (IDNA)" category = "dev" -optional = false +optional = true python-versions = ">=3.5" [[package]] name = "importlib-metadata" -version = "4.2.0" +version = "4.12.0" description = "Read metadata from Python packages" category = "main" optional = false -python-versions = ">=3.6" +python-versions = ">=3.7" [package.dependencies] typing-extensions = {version = ">=3.6.4", markers = "python_version < \"3.8\""} zipp = ">=0.5" [package.extras] -docs = ["sphinx", "jaraco.packaging (>=8.2)", "rst.linker (>=1.9)"] -testing = ["pytest (>=4.6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "packaging", "pep517", "pyfakefs", "flufl.flake8", "pytest-black (>=0.3.7)", "pytest-mypy", "importlib-resources (>=1.3)"] +docs = ["sphinx", "jaraco.packaging (>=9)", "rst.linker (>=1.9)"] +perf = ["ipython"] +testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.3)", "packaging", "pyfakefs", "flufl.flake8", "pytest-perf (>=0.9.2)", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)", "importlib-resources (>=1.3)"] [[package]] name = "inflect" version = "5.6.0" description = "Correctly generate plurals, singular nouns, ordinals, indefinite articles; convert numbers to words" category = "dev" -optional = false +optional = true python-versions = ">=3.7" [package.extras] @@ -543,7 +484,7 @@ name = "isodate" version = "0.6.1" description = "An ISO 8601 date/time/duration parser and formatter" category = "dev" -optional = false +optional = true python-versions = "*" [package.dependencies] @@ -590,7 +531,7 @@ name = "jsonschema" version = "3.2.0" description = "An implementation of JSON Schema validation for Python" category = "dev" -optional = false +optional = true python-versions = "*" [package.dependencies] @@ -636,14 +577,6 @@ numpy = ">=1.18" scipy = ">=1.4" uncertainties = ">=3.0.1" -[[package]] -name = "lockfile" -version = "0.12.2" -description = "Platform-independent file locking module" -category = "dev" -optional = true -python-versions = "*" - [[package]] name = "markdown" version = "3.3.5" @@ -835,14 +768,6 @@ python-versions = ">=3.7" mkdocstrings = ">=0.18" pytkdocs = ">=0.14" -[[package]] -name = "msgpack" -version = "1.0.4" -description = "MessagePack serializer" -category = "dev" -optional = true -python-versions = "*" - [[package]] name = "mypy" version = "0.961" @@ -908,7 +833,7 @@ name = "openapi-schema-validator" version = "0.1.6" description = "OpenAPI schema validation for Python" category = "dev" -optional = false +optional = true python-versions = ">= 2.7, != 3.0.*, != 3.1.*, != 3.2.*, != 3.3.*, != 3.4.*" [package.dependencies] @@ -926,7 +851,7 @@ name = "openapi-spec-validator" version = "0.3.3" description = "OpenAPI 2.0 (aka Swagger) and OpenAPI 3.0 spec validator" category = "dev" -optional = false +optional = true python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" [package.dependencies] @@ -950,17 +875,6 @@ python-versions = ">=3.6" [package.dependencies] et-xmlfile = "*" -[[package]] -name = "packageurl-python" -version = "0.9.9" -description = "A purl aka. Package URL parser and builder" -category = "dev" -optional = true -python-versions = ">=3.6" - -[package.extras] -test = ["isort", "pytest"] - [[package]] name = "packaging" version = "21.3" @@ -985,6 +899,7 @@ numpy = [ {version = ">=1.17.3", markers = "platform_machine != \"aarch64\" and platform_machine != \"arm64\" and python_version < \"3.10\""}, {version = ">=1.19.2", markers = "platform_machine == \"aarch64\" and python_version < \"3.10\""}, {version = ">=1.20.0", markers = "platform_machine == \"arm64\" and python_version < \"3.10\""}, + {version = ">=1.21.0", markers = "python_version >= \"3.10\""}, ] python-dateutil = ">=2.7.3" pytz = ">=2017.3" @@ -1027,49 +942,6 @@ python-versions = ">=3.7" docs = ["olefile", "sphinx (>=2.4)", "sphinx-copybutton", "sphinx-issues (>=3.0.1)", "sphinx-removed-in", "sphinx-rtd-theme (>=1.0)", "sphinxext-opengraph"] tests = ["check-manifest", "coverage", "defusedxml", "markdown2", "olefile", "packaging", "pyroma", "pytest", "pytest-cov", "pytest-timeout"] -[[package]] -name = "pip-api" -version = "0.0.29" -description = "An unofficial, importable pip API" -category = "dev" -optional = true -python-versions = ">=3.7" - -[[package]] -name = "pip-audit" -version = "2.3.4" -description = "A tool for scanning Python environments for known vulnerabilities" -category = "dev" -optional = true -python-versions = ">=3.7" - -[package.dependencies] -CacheControl = {version = ">=0.12.10", extras = ["filecache"]} -cyclonedx-python-lib = ">=2.0.0,<2.5.0 || >2.5.0" -html5lib = ">=1.1" -packaging = ">=21.0.0" -pip-api = ">=0.0.28" -resolvelib = ">=0.8.0" -rich = ">=12.4" -toml = ">=0.10" - -[package.extras] -dev = ["build", "black (>=22.3.0)", "bump (>=1.3.2)", "coverage", "flake8", "interrogate", "isort", "mypy", "pdoc3", "pretend", "pytest", "pytest-cov", "types-html5lib", "types-requests", "types-toml"] - -[[package]] -name = "pip-licenses" -version = "3.5.4" -description = "Dump the software license list of Python packages 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version = "^2.3.4", optional = true } - flake8 = "^4.0.1" + # flake8 = "^4.0.1" + importlib-metadata = "^4.12.0" [build-system] @@ -95,9 +94,10 @@ build-backend = "poetry.core.masonry.api" [tool.poetry.scripts] spectrafit = "spectrafit.spectrafit:command_line_runner" +spectrafit-converter = "spectrafit.plugins.converter:command_line_runner" [tool.poetry.extras] -dev = ["pip-license", "pip-audit"] +dev = ["datamodel-code-generator"] [tool.isort] profile = "black" diff --git a/spectrafit/plugins/__init__.py b/spectrafit/plugins/__init__.py new file mode 100644 index 000000000..fa9a00efd --- /dev/null +++ b/spectrafit/plugins/__init__.py @@ -0,0 +1 @@ +"""Plugins for SpectraFit.""" diff --git a/spectrafit/plugins/converter.py b/spectrafit/plugins/converter.py new file mode 100644 index 000000000..354f4dda2 --- /dev/null +++ b/spectrafit/plugins/converter.py @@ -0,0 +1,78 @@ +"""Convert the input and output files to the preferred file format.""" +import argparse +import json + +from pathlib import Path +from typing import Any +from typing import Dict + +import toml +import yaml + +from spectrafit.tools import read_input_file + + +choices = ["json", "yaml", "yml", "toml", "lock"] + + +def get_args() -> Dict[str, Any]: + """Get the arguments from the command line. + + Returns: + Dict[str, Any]: Return the input file arguments as a dictionary without + additional information beyond the command line arguments. + """ + parser = argparse.ArgumentParser( + description="Converter for 'SpectraFit' input and output files." + ) + parser.add_argument( + "infile", type=Path, help="Filename of the 'SpectraFit' input or output file." + ) + parser.add_argument( + "-f", + "--format", + help="File format for the conversion.", + type=str, + choices=choices, + ) + return vars(parser.parse_args()) + + +def convert(args: Dict[str, Any]) -> None: + """Convert the input file to the output file. + + Args: + args (Dict[str, Any]): The input file arguments as a dictionary with + additional information beyond the command line arguments. + + Raises: + ValueError: If the input file format is identical with the output format. + ValueError: If the output file format is not supported. + """ + if args["infile"].suffix[1:] == args["format"]: + raise ValueError( + f"The input file suffix '{args['infile'].suffix[1:]}' is similar to the" + f" output file format '{args['format']}'." + "Please use a different output file suffix." + ) + + if args["format"] not in choices: + raise ValueError(f"The output file format '{args['format']}' is not supported.") + + data = read_input_file(args["infile"]) + + if args["format"] == "json": + # Convert the input file to a JSON file + with open(args["infile"].with_suffix(".json"), "w", encoding="utf8") as f: + json.dump(data, f, indent=4) + elif args["format"] == "yaml": + with open(args["infile"].with_suffix(".yaml"), "w", encoding="utf8") as f: + yaml.dump(data, f, default_flow_style=False) + elif args["format"] in ["toml", "lock"]: + with open(args["infile"].with_suffix(".toml"), "w", encoding="utf8") as f: + toml.dump(data, f) + + +def command_line_runner() -> None: + """Run the converter via cmd commands.""" + convert(get_args()) diff --git a/spectrafit/plugins/test/__init__.py b/spectrafit/plugins/test/__init__.py new file mode 100644 index 000000000..6b59cbb2a --- /dev/null +++ b/spectrafit/plugins/test/__init__.py @@ -0,0 +1 @@ +"""Test of the SpectraFit plugins.""" diff --git a/spectrafit/plugins/test/test_converter.py b/spectrafit/plugins/test/test_converter.py new file mode 100644 index 000000000..75f88d47f --- /dev/null +++ b/spectrafit/plugins/test/test_converter.py @@ -0,0 +1,104 @@ +"""Test of the converter plugin.""" + +import json + +from pathlib import Path +from tempfile import TemporaryDirectory + +import pytest +import toml +import yaml + +from spectrafit.plugins.converter import convert + + +def test_cmd_converter(script_runner) -> None: + """Test the converter plugin.""" + ret = script_runner.run("spectrafit-converter", "-h") + + assert ret.success + assert "Converter for 'SpectraFit' input and output files." in ret.stdout + assert ret.stderr == "" + + +def test_raise_input_output(): + """Test raise error input format is similar to ouptut.""" + args = { + "infile": Path("tests/data/input/input_1.yaml"), + "format": "yaml", + } + with pytest.raises(ValueError) as excinfo: + convert(args) + + assert ( + "The input file suffix 'yaml' is similar to the output file format 'yaml'." + in str(excinfo.value) + ) + + +def test_raise_no_guilty_ouput(): + """Test illegal output format.""" + args = { + "infile": Path("tests/data/input/input_1.yaml"), + "format": "illegal", + } + with pytest.raises(ValueError) as excinfo: + convert(args) + assert "The output file format 'illegal' is not supported." in str(excinfo.value) + + +def test_json_conversion(): + """Test json to yaml conversion.""" + with TemporaryDirectory() as tmpdir: + infile = Path(tmpdir) / "input_1.json" + + # write input json + with open(infile, "w", encoding="utf8") as f: + json.dump({"a": 1, "b": 2}, f) + args = { + "infile": infile, + "format": "yaml", + } + convert(args) + with open(infile.with_suffix(".yaml"), encoding="utf8") as f: + data = yaml.safe_load(f) + + assert data == {"a": 1, "b": 2} + + +def test_yaml_conversion(): + """Test yaml to json conversion.""" + with TemporaryDirectory() as tmpdir: + infile = Path(tmpdir) / "input_1.yaml" + + # write input yaml + with open(infile, "w", encoding="utf8") as f: + yaml.dump({"a": 1, "b": 2}, f) + args = { + "infile": infile, + "format": "toml", + } + convert(args) + with open(infile.with_suffix(".toml"), encoding="utf8") as f: + data = toml.load(f) + + assert data == {"a": 1, "b": 2} + + +def test_toml_conversion(): + """Test toml to json conversion.""" + with TemporaryDirectory() as tmpdir: + infile = Path(tmpdir) / "input_1.toml" + + # write input toml + with open(infile, "w", encoding="utf8") as f: + toml.dump({"a": 1, "b": 2}, f) + args = { + "infile": infile, + "format": "json", + } + convert(args) + with open(infile.with_suffix(".json"), encoding="utf8") as f: + data = json.load(f) + + assert data == {"a": 1, "b": 2} diff --git a/spectrafit/tools.py b/spectrafit/tools.py index 87acdf160..c960303a6 100644 --- a/spectrafit/tools.py +++ b/spectrafit/tools.py @@ -451,13 +451,15 @@ def save_as_csv(self) -> None: def save_as_json(self) -> None: """Save the fitting result as json file.""" if self.args["outfile"]: - with open(Path(f"{self.args['outfile']}_summary.json"), "w") as f: + with open( + Path(f"{self.args['outfile']}_summary.json"), "w", encoding="utf8" + ) as f: json.dump(self.args, f, indent=4) else: raise FileNotFoundError("No output file provided!") -def read_input_file(fname: str) -> MutableMapping[str, Any]: +def read_input_file(fname: Path) -> MutableMapping[str, Any]: """Read the input file. Read the input file as `toml`, `json`, or `yaml` files and return as a dictionary. @@ -473,15 +475,15 @@ def read_input_file(fname: str) -> MutableMapping[str, Any]: information beyond the command line arguments. """ - _fname = Path(fname) + fname = Path(fname) - if _fname.suffix == ".toml": + if fname.suffix == ".toml": args = toml.load(fname) - elif _fname.suffix == ".json": - with open(_fname, "r") as f: + elif fname.suffix == ".json": + with open(fname, "r", encoding="utf8") as f: args = json.load(f) - elif _fname.suffix in [".yaml", ".yml"]: - with open(_fname, "r") as f: + elif fname.suffix in [".yaml", ".yml"]: + with open(fname, "r", encoding="utf8") as f: args = yaml.load(f, Loader=yaml.FullLoader) else: raise OSError( @@ -514,7 +516,7 @@ def load_data(args: Dict[str, str]) -> pd.DataFrame: try: if args["global"]: return pd.read_csv( - Path(args["infile"]), + args["infile"], sep=args["separator"], header=args["header"], dtype=np.float64, @@ -522,7 +524,7 @@ def load_data(args: Dict[str, str]) -> pd.DataFrame: comment=args["comment"], ) return pd.read_csv( - Path(args["infile"]), + args["infile"], sep=args["separator"], header=args["header"], usecols=args["column"],