From ab9c0b0eb7dbd9ed143398363a77e33d07be940d Mon Sep 17 00:00:00 2001 From: Joris Snellenburg Date: Sun, 22 Mar 2026 12:03:54 +0100 Subject: [PATCH 1/8] Update dependencies and fix js errors For up to python 3.12 compatibility --- pyparamgui/__init__.py | 5 +- pyparamgui/static/form.js | 351 +++--- pyproject.toml | 11 +- uv.lock | 2445 +++++++++++++++++++++++++++++++++++++ 4 files changed, 2647 insertions(+), 165 deletions(-) create mode 100644 uv.lock diff --git a/pyparamgui/__init__.py b/pyparamgui/__init__.py index e087c69..0dac3fd 100644 --- a/pyparamgui/__init__.py +++ b/pyparamgui/__init__.py @@ -11,9 +11,12 @@ __all__ = ["Widget"] """ Package Usage: - %env ANYWIDGET_HMR=1 from pyparamgui import Widget widget = Widget() widget + +Frontend development in JupyterLab only: + %env ANYWIDGET_HMR=1 + from pyparamgui import Widget """ diff --git a/pyparamgui/static/form.js b/pyparamgui/static/form.js index 5b237e6..fc3b695 100644 --- a/pyparamgui/static/form.js +++ b/pyparamgui/static/form.js @@ -25,7 +25,7 @@ function createTextFormGroup(labelText, inputId, inputName, inputValue) { formGroup.appendChild(label); formGroup.appendChild(input); - return formGroup; + return { formGroup, input }; } /** @@ -60,7 +60,50 @@ function createCheckboxFormGroup( formGroup.appendChild(label); formGroup.appendChild(input); - return formGroup; + return { formGroup, input }; +} + +function appendTextFormGroup(form, labelText, inputId, inputName, inputValue) { + const { formGroup, input } = createTextFormGroup( + labelText, + inputId, + inputName, + inputValue, + ); + form.appendChild(formGroup); + return input; +} + +function appendCheckboxFormGroup( + form, + labelText, + inputId, + inputName, + inputChecked = false, +) { + const { formGroup, input } = createCheckboxFormGroup( + labelText, + inputId, + inputName, + inputChecked, + ); + form.appendChild(formGroup); + return input; +} + +function parseNumberList(value) { + return value.split(",").map((part) => parseFloat(part.trim())); +} + +function createSimulationId() { + if ( + globalThis.crypto && + typeof globalThis.crypto.randomUUID === "function" + ) { + return globalThis.crypto.randomUUID(); + } + + return `${Date.now()}-${Math.random().toString(16).slice(2)}`; } /** @@ -87,11 +130,11 @@ function createCheckboxFormGroup( */ function convertInputs(inputs) { try { - const decay_rates = inputs.decay_rates.split(",").map(parseFloat); - const amplitude = inputs.amplitude.split(",").map(parseFloat); - const location = inputs.location.split(",").map(parseFloat); - const width = inputs.width.split(",").map(parseFloat); - const skewness = inputs.skewness.split(",").map(parseFloat); + const decay_rates = parseNumberList(inputs.decay_rates); + const amplitude = parseNumberList(inputs.amplitude); + const location = parseNumberList(inputs.location); + const width = parseNumberList(inputs.width); + const skewness = parseNumberList(inputs.skewness); const timepoints_max = parseInt(inputs.timepoints_max, 10); const timepoints_stepsize = parseFloat(inputs.timepoints_stepsize); const wavelength_min = parseFloat(inputs.wavelength_min); @@ -216,190 +259,176 @@ function displaySimulationMessage(parentElement) { function render({ model, el }) { const form = document.createElement("form"); - form.appendChild( - createTextFormGroup( - "Decay rates:", - "decay_rates_input", - "decay_rates_input", - "0.055, 0.005", - ), + const decayRatesInput = appendTextFormGroup( + form, + "Decay rates:", + "decay_rates_input", + "decay_rates_input", + "0.055, 0.005", ); form.appendChild(document.createElement("hr")); - form.appendChild( - createTextFormGroup( - "Amplitudes:", - "amplitude_input", - "amplitude_input", - "1., 1.", - ), + const amplitudeInput = appendTextFormGroup( + form, + "Amplitudes:", + "amplitude_input", + "amplitude_input", + "1., 1.", ); - form.appendChild( - createTextFormGroup( - "Location (mean) of spectra:", - "location_input", - "location_input", - "22000, 20000", - ), + const locationInput = appendTextFormGroup( + form, + "Location (mean) of spectra:", + "location_input", + "location_input", + "22000, 20000", ); - form.appendChild( - createTextFormGroup( - "Width of spectra:", - "width_input", - "width_input", - "4000, 3500", - ), + const widthInput = appendTextFormGroup( + form, + "Width of spectra:", + "width_input", + "width_input", + "4000, 3500", ); - form.appendChild( - createTextFormGroup( - "Skewness of spectra:", - "skewness_input", - "skewness_input", - "0.1, -0.1", - ), + const skewnessInput = appendTextFormGroup( + form, + "Skewness of spectra:", + "skewness_input", + "skewness_input", + "0.1, -0.1", ); form.appendChild(document.createElement("hr")); - form.appendChild( - createTextFormGroup( - "Timepoints, max:", - "timepoints_max_input", - "timepoints_max_input", - "80", - ), + const timepointsMaxInput = appendTextFormGroup( + form, + "Timepoints, max:", + "timepoints_max_input", + "timepoints_max_input", + "80", ); - form.appendChild( - createTextFormGroup( - "Stepsize:", - "timepoints_stepsize_input", - "timepoints_stepsize_input", - "1", - ), + const timepointsStepsizeInput = appendTextFormGroup( + form, + "Stepsize:", + "timepoints_stepsize_input", + "timepoints_stepsize_input", + "1", ); form.appendChild(document.createElement("hr")); - form.appendChild( - createTextFormGroup( - "Wavelength Min:", - "wavelength_min_input", - "wavelength_min_input", - "400", - ), + const wavelengthMinInput = appendTextFormGroup( + form, + "Wavelength Min:", + "wavelength_min_input", + "wavelength_min_input", + "400", ); - form.appendChild( - createTextFormGroup( - "Wavelength Max:", - "wavelength_max_input", - "wavelength_max_input", - "600", - ), + const wavelengthMaxInput = appendTextFormGroup( + form, + "Wavelength Max:", + "wavelength_max_input", + "wavelength_max_input", + "600", ); - form.appendChild( - createTextFormGroup( - "Stepsize:", - "wavelength_stepsize_input", - "wavelength_stepsize_input", - "5", - ), + const wavelengthStepsizeInput = appendTextFormGroup( + form, + "Stepsize:", + "wavelength_stepsize_input", + "wavelength_stepsize_input", + "5", ); form.appendChild(document.createElement("hr")); - form.appendChild( - createTextFormGroup( - "Std.dev. noise:", - "stdev_noise_input", - "stdev_noise_input", - "0.01", - ), + const stdevNoiseInput = appendTextFormGroup( + form, + "Std.dev. noise:", + "stdev_noise_input", + "stdev_noise_input", + "0.01", ); - form.appendChild( - createTextFormGroup("Seed:", "seed_input", "seed_input", "123"), + const seedInput = appendTextFormGroup( + form, + "Seed:", + "seed_input", + "seed_input", + "123", ); form.appendChild(document.createElement("hr")); - form.appendChild( - createCheckboxFormGroup( - "Add Gaussian IRF:", - "add_gaussian_irf_input", - "add_gaussian_irf_input", - ), + const addGaussianIrfInput = appendCheckboxFormGroup( + form, + "Add Gaussian IRF:", + "add_gaussian_irf_input", + "add_gaussian_irf_input", ); - form.appendChild( - createTextFormGroup( - "IRF location:", - "irf_location_input", - "irf_location_input", - "3", - ), + const irfLocationInput = appendTextFormGroup( + form, + "IRF location:", + "irf_location_input", + "irf_location_input", + "3", ); - form.appendChild( - createTextFormGroup( - "IRF width:", - "irf_width_input", - "irf_width_input", - "1", - ), + const irfWidthInput = appendTextFormGroup( + form, + "IRF width:", + "irf_width_input", + "irf_width_input", + "1", ); form.appendChild(document.createElement("hr")); - form.appendChild( - createCheckboxFormGroup( - "Use Sequential Scheme:", - "use_sequential_scheme_input", - "use_sequential_scheme_input", - ), + const useSequentialSchemeInput = appendCheckboxFormGroup( + form, + "Use Sequential Scheme:", + "use_sequential_scheme_input", + "use_sequential_scheme_input", ); form.appendChild(document.createElement("hr")); - form.appendChild( - createTextFormGroup( - "Model File Name:", - "model_file_name_input", - "model_file_name_input", - "model.yml", - ), + const modelFileNameInput = appendTextFormGroup( + form, + "Model File Name:", + "model_file_name_input", + "model_file_name_input", + "model.yml", ); - form.appendChild( - createTextFormGroup( - "Parameter File Name:", - "parameter_file_name_input", - "parameter_file_name_input", - "parameters.csv", - ), + const parameterFileNameInput = appendTextFormGroup( + form, + "Parameter File Name:", + "parameter_file_name_input", + "parameter_file_name_input", + "parameters.csv", ); - form.appendChild( - createTextFormGroup( - "Data File Name:", - "data_file_name_input", - "data_file_name_input", - "dataset.nc", - ), + const dataFileNameInput = appendTextFormGroup( + form, + "Data File Name:", + "data_file_name_input", + "data_file_name_input", + "dataset.nc", ); form.appendChild(document.createElement("hr")); - form.appendChild( - createCheckboxFormGroup( - "Visualize Data:", - "visualize_data_input", - "visualize_data_input", - true, - ), + const visualizeDataInput = appendCheckboxFormGroup( + form, + "Visualize Data:", + "visualize_data_input", + "visualize_data_input", + true, ); el.appendChild(form); const btn = document.createElement("button"); + btn.type = "button"; btn.textContent = "Simulate"; btn.addEventListener("click", function (event) { event.preventDefault(); const inputs = { - decay_rates: decay_rates_input.value, - amplitude: amplitude_input.value, - location: location_input.value, - width: width_input.value, - skewness: skewness_input.value, - timepoints_max: timepoints_max_input.value, - timepoints_stepsize: timepoints_stepsize_input.value, - wavelength_min: wavelength_min_input.value, - wavelength_max: wavelength_max_input.value, - wavelength_stepsize: wavelength_stepsize_input.value, - stdev_noise: stdev_noise_input.value, - seed: seed_input.value, - irf_location: irf_location_input.value, - irf_width: irf_width_input.value, + decay_rates: decayRatesInput.value, + amplitude: amplitudeInput.value, + location: locationInput.value, + width: widthInput.value, + skewness: skewnessInput.value, + timepoints_max: timepointsMaxInput.value, + timepoints_stepsize: timepointsStepsizeInput.value, + wavelength_min: wavelengthMinInput.value, + wavelength_max: wavelengthMaxInput.value, + wavelength_stepsize: wavelengthStepsizeInput.value, + stdev_noise: stdevNoiseInput.value, + seed: seedInput.value, + irf_location: irfLocationInput.value, + irf_width: irfWidthInput.value, }; const convertedInputs = convertInputs(inputs); if (!convertedInputs) return; @@ -419,18 +448,18 @@ function render({ model, el }) { model.set("wavelength_stepsize_input", convertedInputs.wavelength_stepsize); model.set("stdev_noise_input", convertedInputs.stdev_noise); model.set("seed_input", convertedInputs.seed); - model.set("add_gaussian_irf_input", add_gaussian_irf_input.checked); + model.set("add_gaussian_irf_input", addGaussianIrfInput.checked); model.set("irf_location_input", convertedInputs.irf_location); model.set("irf_width_input", convertedInputs.irf_width); model.set( "use_sequential_scheme_input", - use_sequential_scheme_input.checked, + useSequentialSchemeInput.checked, ); - model.set("model_file_name_input", model_file_name_input.value); - model.set("parameter_file_name_input", parameter_file_name_input.value); - model.set("data_file_name_input", data_file_name_input.value); - model.set("visualize_data", visualize_data_input.checked); - model.set("simulate", self.crypto.randomUUID()); + model.set("model_file_name_input", modelFileNameInput.value); + model.set("parameter_file_name_input", parameterFileNameInput.value); + model.set("data_file_name_input", dataFileNameInput.value); + model.set("visualize_data", visualizeDataInput.checked); + model.set("simulate", createSimulationId()); model.save_changes(); diff --git a/pyproject.toml b/pyproject.toml index 98082cb..079f850 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -17,7 +17,7 @@ license = { file = "LICENSE" } authors = [ 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"sha256:978b6acb018770554f8fd964af4eb02f9bcc165d4085dbb7326190d92aa74bcf", size = 3111388, upload-time = "2026-02-13T22:20:50.18Z" } +wheels = [ + { url = "https://files.pythonhosted.org/packages/99/92/545eb2ca17fc0e05456728d7e4378bfee48d66433ae3b7e71948e46826fb/xarray-2026.2.0-py3-none-any.whl", hash = "sha256:e927d7d716ea71dea78a13417970850a640447d8dd2ceeb65c5687f6373837c9", size = 1405358, upload-time = "2026-02-13T22:20:47.847Z" }, +] From 8622be0a309195c94b77222ec356362117c4870e Mon Sep 17 00:00:00 2001 From: Joris Snellenburg Date: Sun, 22 Mar 2026 12:08:43 +0100 Subject: [PATCH 2/8] Add uv usage instructions - Include steps to run directly from remote source - Add instructions for running from a local copy - Show how to add as a dependency to existing projects --- README.md | 32 ++++++++++++++++++++++++++++++++ 1 file changed, 32 insertions(+) diff --git a/README.md b/README.md index 17b5d46..b593a1c 100644 --- a/README.md +++ b/README.md @@ -16,6 +16,38 @@ A pyglotaran based jupyter notebook widget for teaching parameter estimation examples. It can simulate data, visualize it and create related model.yml, parameters.csv and dataset.nc files. It is supposed to help students learn about the basics of the pyglotaran ecosystem. +## Usage + +### Option 1: Run directly from GitHub with uv + +Install and run PyParamGUI directly from the repository without cloning: + +```bash +uv run --with "pyparamgui @ git+https://github.com/glotaran/PyParamGUI" --with jupyter jupyter lab +``` + +### Option 2: Run from a local clone + +Clone the repository and run with the local source: + +```bash +uv run --with . --with jupyter jupyter lab +``` + +### Option 3: Add to an existing uv project + +Add PyParamGUI as a dependency to your project: + +```bash +uv add pyparamgui @ git+https://github.com/glotaran/PyParamGUI +``` + +Then run Jupyter Lab in your project environment: + +```bash +uv run jupyter lab +``` + ## Contributors ✨ Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/docs/en/emoji-key)): From bd8627cdc9e4c17d795a768894b41ac746152bdb Mon Sep 17 00:00:00 2001 From: Joris Snellenburg Date: Sun, 22 Mar 2026 12:12:16 +0100 Subject: [PATCH 3/8] Remove unneeded env var mention Was tested to not be needed anymore --- pyparamgui/__init__.py | 4 ---- 1 file changed, 4 deletions(-) diff --git a/pyparamgui/__init__.py b/pyparamgui/__init__.py index 0dac3fd..93ef10f 100644 --- a/pyparamgui/__init__.py +++ b/pyparamgui/__init__.py @@ -15,8 +15,4 @@ widget = Widget() widget - -Frontend development in JupyterLab only: - %env ANYWIDGET_HMR=1 - from pyparamgui import Widget """ From 54e1f6e1899c9f7199792b5a691764db9bb50104 Mon Sep 17 00:00:00 2001 From: Joris Snellenburg Date: Sun, 22 Mar 2026 19:59:53 +0100 Subject: [PATCH 4/8] Fix (pre-commit) isssues and address review comments --- .pre-commit-config.yaml | 16 +++---- README.md | 6 +-- pyparamgui/generator.py | 18 ++++---- pyparamgui/schema.py | 68 +++++++++++++++++++----------- pyparamgui/static/form.js | 14 ++----- pyparamgui/widget.py | 69 ++++++++++++++++++++----------- pyproject.toml | 87 +++++++++++++++++---------------------- tests/test_simulate.py | 4 +- 8 files changed, 153 insertions(+), 129 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 6b48cbb..06ba757 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -3,12 +3,12 @@ repos: # FORMATTER # ################### - repo: https://github.com/tox-dev/pyproject-fmt - rev: "2.1.4" + rev: "v2.20.0" hooks: - id: pyproject-fmt - repo: https://github.com/pre-commit/pre-commit-hooks - rev: v4.6.0 + rev: v6.0.0 hooks: - id: check-ast - id: check-builtin-literals @@ -20,7 +20,7 @@ repos: args: [--fix=lf] - repo: https://github.com/PyCQA/docformatter - rev: 06907d0 + rev: v1.7.7 hooks: - id: docformatter additional_dependencies: [tomli] @@ -43,7 +43,7 @@ repos: ################### - repo: https://github.com/astral-sh/ruff-pre-commit # Ruff version. - rev: v0.5.1 + rev: v0.15.7 hooks: - id: ruff name: "ruff sort imports" @@ -58,7 +58,7 @@ repos: name: "ruff lint" - repo: https://github.com/pre-commit/mirrors-mypy - rev: v1.10.1 + rev: v1.19.1 hooks: - id: mypy exclude: "docs" @@ -68,7 +68,7 @@ repos: # LINTER DOCS # ################### - repo: https://github.com/PyCQA/flake8 - rev: 7.1.0 + rev: 7.3.0 hooks: - id: flake8 alias: flake8-docs @@ -91,7 +91,7 @@ repos: pass_filenames: false - repo: https://github.com/codespell-project/codespell - rev: v2.3.0 + rev: v2.4.2 hooks: - id: codespell types: [file] @@ -100,6 +100,6 @@ repos: exclude: ^examples/ - repo: https://github.com/rhysd/actionlint - rev: "v1.7.1" + rev: "v1.7.11" hooks: - id: actionlint diff --git a/README.md b/README.md index b593a1c..871f967 100644 --- a/README.md +++ b/README.md @@ -23,7 +23,7 @@ A pyglotaran based jupyter notebook widget for teaching parameter estimation exa Install and run PyParamGUI directly from the repository without cloning: ```bash -uv run --with "pyparamgui @ git+https://github.com/glotaran/PyParamGUI" --with jupyter jupyter lab +uv run --with "pyparamgui @ git+https://github.com/glotaran/pyparamgui" --with jupyter jupyter lab ``` ### Option 2: Run from a local clone @@ -39,7 +39,7 @@ uv run --with . --with jupyter jupyter lab Add PyParamGUI as a dependency to your project: ```bash -uv add pyparamgui @ git+https://github.com/glotaran/PyParamGUI +uv add "pyparamgui @ git+https://github.com/glotaran/pyparamgui" ``` Then run Jupyter Lab in your project environment: @@ -58,7 +58,7 @@ Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/d - +
Anmol Bhatia
Anmol Bhatia
💻		Anmol Bhatia
Anmol Bhatia
💻
diff --git a/pyparamgui/generator.py b/pyparamgui/generator.py index 9d49b6b..219cd0c 100644 --- a/pyparamgui/generator.py +++ b/pyparamgui/generator.py @@ -38,8 +38,8 @@ def _generate_decay_model( dict[str, Any] The generated model dictionary. """ - compartments = [f"species_{i+1}" for i in range(nr_compartments)] - rates = [f"rates.species_{i+1}" for i in range(nr_compartments)] + compartments = [f"species_{i + 1}" for i in range(nr_compartments)] + rates = [f"rates.species_{i + 1}" for i in range(nr_compartments)] model: dict[str, Any] = { "megacomplex": { @@ -56,18 +56,18 @@ def _generate_decay_model( "megacomplex_spectral": { "type": "spectral", "shape": { - compartment: f"shape_species_{i+1}" + compartment: f"shape_species_{i + 1}" for i, compartment in enumerate(compartments) }, } } model["shape"] = { - f"shape_species_{i+1}": { + f"shape_species_{i + 1}": { "type": "skewed-gaussian", - "amplitude": f"shapes.species_{i+1}.amplitude", - "location": f"shapes.species_{i+1}.location", - "width": f"shapes.species_{i+1}.width", - "skewness": f"shapes.species_{i+1}.skewness", + "amplitude": f"shapes.species_{i + 1}.amplitude", + "location": f"shapes.species_{i + 1}.location", + "width": f"shapes.species_{i + 1}.width", + "skewness": f"shapes.species_{i + 1}.skewness", } for i in range(nr_compartments) } @@ -275,4 +275,4 @@ def generate_model_yml(*, generator_name: str, generator_arguments: GeneratorArg ) raise ValueError(msg) model = generators[generator_name](**generator_arguments) - return cast(str, write_dict(model)) + return cast("str", write_dict(model)) diff --git a/pyparamgui/schema.py b/pyparamgui/schema.py index 260177c..4f46f43 100644 --- a/pyparamgui/schema.py +++ b/pyparamgui/schema.py @@ -15,7 +15,8 @@ class KineticParameters(BaseModel): Attributes ---------- - decay_rates (list[float]): List of decay rates. + decay_rates : list[float] + List of decay rates. """ decay_rates: list[float] @@ -26,10 +27,14 @@ class SpectralParameters(BaseModel): Attributes ---------- - amplitude (list[float]): List of amplitudes. - location (list[float]): List of locations. - width (list[float]): List of widths. - skewness (list[float]): List of skewness values. + amplitude : list[float] + List of amplitudes. + location : list[float] + List of locations. + width : list[float] + List of widths. + skewness : list[float] + List of skewness values. """ amplitude: list[float] @@ -43,8 +48,10 @@ class TimeCoordinates(BaseModel): Attributes ---------- - timepoints_max (int): Maximum number of time points. - timepoints_stepsize (float): Step size between time points. + timepoints_max : int + Maximum number of time points. + timepoints_stepsize : float + Step size between time points. """ timepoints_max: int @@ -56,9 +63,12 @@ class SpectralCoordinates(BaseModel): Attributes ---------- - wavelength_min (int): Minimum wavelength. - wavelength_max (int): Maximum wavelength. - wavelength_stepsize (float): Step size between wavelengths. + wavelength_min : int + Minimum wavelength. + wavelength_max : int + Maximum wavelength. + wavelength_stepsize : float + Step size between wavelengths. """ wavelength_min: int @@ -100,12 +110,14 @@ class Settings(BaseModel): Attributes ---------- - stdev_noise (float): Standard deviation of the noise to be added to the simulation data. - seed (int): Seed for the random number generator to ensure reproducibility. - add_gaussian_irf (bool): Whether to add a Gaussian IRF to the simulation. - Default is False. - use_sequential_scheme (bool): Whether to use a sequential scheme in the simulation. - Default is False. + stdev_noise : float + Standard deviation of the noise to be added to the simulation data. + seed : int + Seed for the random number generator to ensure reproducibility. + add_gaussian_irf : bool + Whether to add a Gaussian IRF to the simulation. Default is False. + use_sequential_scheme : bool + Whether to use a sequential scheme in the simulation. Default is False. """ stdev_noise: float @@ -119,8 +131,10 @@ class IRF(BaseModel): Attributes ---------- - center (float): The center position of the IRF. - width (float): The width of the IRF. + center : float + The center position of the IRF. + width : float + The width of the IRF. """ center: float @@ -132,13 +146,17 @@ class SimulationConfig(BaseModel): Attributes ---------- - kinetic_parameters (KineticParameters): Kinetic parameters for the simulation. - spectral_parameters (SpectralParameters): Spectral parameters for the simulation. - coordinates (Dict[str, np.ndarray]): Dictionary containing the time and spectral axes as - numpy arrays. - settings (Settings): Other settings for the simulation, including noise standard deviation, - random seed, and flags for adding Gaussian IRF and using a sequential scheme. - irf (IRF): Instrument Response Function (IRF) settings, e.g. center position and width. + kinetic_parameters : KineticParameters + Kinetic parameters for the simulation. + spectral_parameters : SpectralParameters + Spectral parameters for the simulation. + coordinates : dict[str, np.ndarray] + Dictionary containing the time and spectral axes as numpy arrays. + settings : Settings + Other settings for the simulation, including noise standard deviation, + random seed, and flags for adding Gaussian IRF and using a sequential scheme. + irf : IRF + Instrument Response Function (IRF) settings, e.g. center position and width. """ kinetic_parameters: KineticParameters diff --git a/pyparamgui/static/form.js b/pyparamgui/static/form.js index fc3b695..5650d2c 100644 --- a/pyparamgui/static/form.js +++ b/pyparamgui/static/form.js @@ -6,7 +6,7 @@ * @param {string} inputName - The name attribute for the input element. * @param {string} inputValue - The initial value for the input element. * - * @returns {HTMLDivElement} The form group element containing the label and input. + * @returns {{ formGroup: HTMLDivElement, input: HTMLInputElement }} An object containing the form group element and text input. */ function createTextFormGroup(labelText, inputId, inputName, inputValue) { const formGroup = document.createElement("div"); @@ -36,7 +36,7 @@ function createTextFormGroup(labelText, inputId, inputName, inputValue) { * @param {string} inputName - The name attribute for the input element. * @param {boolean} [inputChecked=false] - The initial checked state for the checkbox. * - * @returns {HTMLDivElement} The form group element containing the label and checkbox input. + * @returns {{ formGroup: HTMLDivElement, input: HTMLInputElement }} An object containing the form group element and checkbox input. */ function createCheckboxFormGroup( labelText, @@ -96,10 +96,7 @@ function parseNumberList(value) { } function createSimulationId() { - if ( - globalThis.crypto && - typeof globalThis.crypto.randomUUID === "function" - ) { + if (globalThis.crypto && typeof globalThis.crypto.randomUUID === "function") { return globalThis.crypto.randomUUID(); } @@ -451,10 +448,7 @@ function render({ model, el }) { model.set("add_gaussian_irf_input", addGaussianIrfInput.checked); model.set("irf_location_input", convertedInputs.irf_location); model.set("irf_width_input", convertedInputs.irf_width); - model.set( - "use_sequential_scheme_input", - useSequentialSchemeInput.checked, - ); + model.set("use_sequential_scheme_input", useSequentialSchemeInput.checked); model.set("model_file_name_input", modelFileNameInput.value); model.set("parameter_file_name_input", parameterFileNameInput.value); model.set("data_file_name_input", dataFileNameInput.value); diff --git a/pyparamgui/widget.py b/pyparamgui/widget.py index c11476b..0af4798 100644 --- a/pyparamgui/widget.py +++ b/pyparamgui/widget.py @@ -25,29 +25,52 @@ class Widget(anywidget.AnyWidget): Attributes ---------- - _esm (pathlib.Path): Path to the JavaScript file for the widget. - _css (pathlib.Path): Path to the CSS file for the widget. - decay_rates_input (traitlets.List): List of decay rates as floats. - amplitude_input (traitlets.List): List of amplitudes as floats. - location_input (traitlets.List): List of locations as floats. - width_input (traitlets.List): List of widths as floats. - skewness_input (traitlets.List): List of skewness values as floats. - timepoints_max_input (traitlets.Int): Maximum number of timepoints. - timepoints_stepsize_input (traitlets.Float): Step size for timepoints. - wavelength_min_input (traitlets.Float): Minimum wavelength value. - wavelength_max_input (traitlets.Float): Maximum wavelength value. - wavelength_stepsize_input (traitlets.Float): Step size for wavelength. - stdev_noise_input (traitlets.Float): Standard deviation of noise. - seed_input (traitlets.Int): Seed for random number generation. - add_gaussian_irf_input (traitlets.Bool): Flag to add Gaussian IRF. - irf_location_input (traitlets.Float): Location of the IRF center. - irf_width_input (traitlets.Float): Width of the IRF. - use_sequential_scheme_input (traitlets.Bool): Flag to use sequential scheme. - model_file_name_input (traitlets.Unicode): Name of the model file. - parameter_file_name_input (traitlets.Unicode): Name of the parameter file. - data_file_name_input (traitlets.Unicode): Name of the data file. - simulate (traitlets.Unicode): Trigger for simulation. - visualize_data (traitlets.Bool): Flag to visualize data. + _esm : pathlib.Path + Path to the JavaScript file for the widget. + _css : pathlib.Path + Path to the CSS file for the widget. + decay_rates_input : traitlets.List + List of decay rates as floats. + amplitude_input : traitlets.List + List of amplitudes as floats. + location_input : traitlets.List + List of locations as floats. + width_input : traitlets.List + List of widths as floats. + skewness_input : traitlets.List + List of skewness values as floats. + timepoints_max_input : traitlets.Int + Maximum number of timepoints. + timepoints_stepsize_input : traitlets.Float + Step size for timepoints. + wavelength_min_input : traitlets.Float + Minimum wavelength value. + wavelength_max_input : traitlets.Float + Maximum wavelength value. + wavelength_stepsize_input : traitlets.Float + Step size for wavelength. + stdev_noise_input : traitlets.Float + Standard deviation of noise. + seed_input : traitlets.Int + Seed for random number generation. + add_gaussian_irf_input : traitlets.Bool + Flag to add Gaussian IRF. + irf_location_input : traitlets.Float + Location of the IRF center. + irf_width_input : traitlets.Float + Width of the IRF. + use_sequential_scheme_input : traitlets.Bool + Flag to use sequential scheme. + model_file_name_input : traitlets.Unicode + Name of the model file. + parameter_file_name_input : traitlets.Unicode + Name of the parameter file. + data_file_name_input : traitlets.Unicode + Name of the data file. + simulate : traitlets.Unicode + Trigger for simulation. + visualize_data : traitlets.Bool + Flag to visualize data. """ _esm: pathlib.Path = pathlib.Path(__file__).parent / "static" / "form.js" diff --git a/pyproject.toml b/pyproject.toml index 079f850..9bb97c9 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -5,7 +5,6 @@ requires = [ ] [project] - name = "pyparamgui" description = "pyglotaran notebook widgets for teaching parameter estimation examples" readme = "README.md" @@ -13,7 +12,6 @@ keywords = [ "pyparamgui", ] license = { file = "LICENSE" } - authors = [ { name = "Anmol Bhatia", email = "anmolbhatia05@gmail.com " }, ] @@ -31,7 +29,6 @@ classifiers = [ dynamic = [ "version", ] - dependencies = [ "anywidget==0.9.13", "pydantic==2.8.2", @@ -63,14 +60,15 @@ urls.Homepage = "https://github.com/glotaran/pyparamgui" urls.Source = "https://github.com/glotaran/pyparamgui" urls.Tracker = "https://github.com/glotaran/pyparamgui/issues" -[tool.hatch.version] -path = "pyparamgui/__init__.py" - -[tool.hatch.build.targets.sdist] -include = [ "/pyparamgui", "/tests" ] +[dependency-groups] +dev = [ + "ipykernel>=7.2", +] -[tool.hatch.envs.default] -features = [ "dev" ] +[tool.hatch] +build.targets.sdist.include = [ "/pyparamgui", "/tests" ] +envs.default.features = [ "dev" ] +version.path = "pyparamgui/__init__.py" [tool.docformatter] black = true @@ -79,13 +77,22 @@ wrap-descriptions = 99 [tool.pydoclint] skip-checking-short-docstrings = false -style = 'numpy' -exclude = '^(docs/|tests?/)' +style = "numpy" +exclude = "^(docs/|tests?/)" require-return-section-when-returning-nothing = false allow-init-docstring = true -[tool.pytest.ini_options] -addopts = [ +[tool.mypy] +exclude = "^docs/" +ignore_missing_imports = true +scripts_are_modules = true +show_error_codes = true +warn_unused_configs = true +warn_unused_ignores = true +strict_equality = true + +[tool.pytest] +ini_options.addopts = [ "--cov=pyparamgui", "--cov-report=term", "--cov-report=xml", @@ -93,52 +100,34 @@ addopts = [ "--cov-config=pyproject.toml", ] -[tool.coverage.run] -branch = true -omit = [ - 'pyparamgui/__init__.py', - 'tests/*', +[tool.coverage] +run.branch = true +run.omit = [ + "pyparamgui/__init__.py", + "tests/*", # comment the above line if you want to see if all tests did run ] - -[tool.coverage.report] # Regexes for lines to exclude from consideration -exclude_lines = [ - # Have to re-enable the standard pragma - 'pragma: no cover', - +report.exclude_lines = [ # Don't complain about missing debug-only code: - 'def __repr__', - 'if self\.debug', - - # Don't complain if tests don't hit defensive assertion code: - 'raise AssertionError', - 'raise NotImplementedError', + "def __repr__", + "if __name__ == .__main__.:", # Don't complain if non-runnable code isn't run: - 'if 0:', - 'if __name__ == .__main__.:', + "if 0:", + "if self\\.debug", # only accessible during typechecking - 'if TYPE_CHECKING:', -] + "if TYPE_CHECKING:", + # Have to re-enable the standard pragma + "pragma: no cover", -[tool.mypy] -exclude = "^docs/" -ignore_missing_imports = true -scripts_are_modules = true -show_error_codes = true -warn_unused_configs = true -warn_unused_ignores = true -strict_equality = true + # Don't complain if tests don't hit defensive assertion code: + "raise AssertionError", + "raise NotImplementedError", +] # For now this is not used because pydoclint does not support toml when used with flake8 - [tool.interrogate] exclude = [ "docs", "tests" ] ignore-init-module = true fail-under = 100 - -[dependency-groups] -dev = [ - "ipykernel>=7.2.0", -] diff --git a/tests/test_simulate.py b/tests/test_simulate.py index fbb44c6..db96a59 100644 --- a/tests/test_simulate.py +++ b/tests/test_simulate.py @@ -36,13 +36,13 @@ def _create_mock_widget(): return widget -@pytest.fixture() +@pytest.fixture def mock_widget(): """Return a mock Widget for testing.""" return _create_mock_widget() -@pytest.fixture() +@pytest.fixture def temp_dir(): """Create a temporary directory for testing.""" with tempfile.TemporaryDirectory() as tmpdirname: From 57d79b11b8dae0ed8052624b6ef8ecea46568bfc Mon Sep 17 00:00:00 2001 From: Joris Snellenburg Date: Sun, 22 Mar 2026 21:22:23 +0100 Subject: [PATCH 5/8] Also update this not that we used it, but at least be consistent --- requirements_pinned.txt | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/requirements_pinned.txt b/requirements_pinned.txt index 573b71a..14909c9 100644 --- a/requirements_pinned.txt +++ b/requirements_pinned.txt @@ -3,6 +3,6 @@ pydantic==2.8.2 anywidget==0.9.13 -pyglotaran==0.7.2 -pyglotaran_extras==0.7.2 +pyglotaran==0.7.4 +pyglotaran_extras==0.7.4 pyyaml==6.0.1 From 9b643a54729d47a9f3116cecb75a83a6d08ff966 Mon Sep 17 00:00:00 2001 From: Sebastian Weigand Date: Sun, 22 Mar 2026 21:49:14 +0100 Subject: [PATCH 6/8] =?UTF-8?q?=E2=AC=86=EF=B8=8F=20Bump=20pydantic=20for?= =?UTF-8?q?=20python=203.14=20support?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- pyproject.toml | 2 +- requirements_pinned.txt | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 9bb97c9..49adbc2 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -31,7 +31,7 @@ dynamic = [ ] dependencies = [ "anywidget==0.9.13", - "pydantic==2.8.2", + "pydantic==2.12.5", "pyglotaran==0.7.4", "pyglotaran-extras==0.7.4", "pyyaml==6.0.1", diff --git a/requirements_pinned.txt b/requirements_pinned.txt index 14909c9..2b5fde2 100644 --- a/requirements_pinned.txt +++ b/requirements_pinned.txt @@ -1,7 +1,7 @@ # runtime requirements # pinned so the bot can create PRs to test with new versions -pydantic==2.8.2 +pydantic==2.12.5 anywidget==0.9.13 pyglotaran==0.7.4 pyglotaran_extras==0.7.4 From d048a530cae51e8bc88a35e23006c0125d62bd62 Mon Sep 17 00:00:00 2001 From: Sebastian Weigand Date: Sun, 22 Mar 2026 21:49:41 +0100 Subject: [PATCH 7/8] =?UTF-8?q?=F0=9F=9A=87=E2=AC=86=EF=B8=8F=20Add=20more?= =?UTF-8?q?=20python=20version=20to=20CI=20test=20matrix?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- .github/workflows/test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 39c4491..9a980e8 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -66,7 +66,7 @@ jobs: strategy: matrix: os: [ubuntu-latest, windows-latest, macOS-latest] - python-version: ["3.10", "3.11"] + python-version: ["3.10", "3.11", "3.12", "3.13", "3.14"] steps: - name: Check out repo From b67c3b46659906a8cd915d0c726fd82863bc3b55 Mon Sep 17 00:00:00 2001 From: Sebastian Weigand Date: Sun, 22 Mar 2026 21:55:09 +0100 Subject: [PATCH 8/8] =?UTF-8?q?=F0=9F=A9=B9=20Raise=20upper=20supported=20?= =?UTF-8?q?version?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- pyproject.toml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 49adbc2..b69da0c 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -15,7 +15,7 @@ license = { file = "LICENSE" } authors = [ { name = "Anmol Bhatia", email = "anmolbhatia05@gmail.com " }, ] -requires-python = ">=3.10,<3.13" +requires-python = ">=3.10,<3.15" classifiers = [ "Development Status :: 2 - Pre-Alpha", "Intended Audience :: Developers", @@ -25,6 +25,8 @@ classifiers = [ "Programming Language :: Python :: 3.10", "Programming Language :: Python :: 3.11", "Programming Language :: Python :: 3.12", + "Programming Language :: Python :: 3.13", + "Programming Language :: Python :: 3.14", ] dynamic = [ "version",