FitBenchmarking 1.3.0__tar.gz → 1.4.0__tar.gz

{fitbenchmarking-1.3.0 → fitbenchmarking-1.4.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: FitBenchmarking
-Version: 1.3.0
+Version: 1.4.0
 Summary: FitBenchmarking: A tool for comparing fitting software
 Project-URL: Homepage, https://fitbenchmarking.github.io
 Project-URL: Documentation, https://fitbenchmarking.readthedocs.io/en/stable
@@ -13,7 +13,7 @@ Keywords: benchmark,comparison,fitting,least squares,optimisation
 Classifier: License :: OSI Approved :: BSD License
 Classifier: Operating System :: OS Independent
 Classifier: Programming Language :: Python :: 3
-Requires-Python: >=3.9.1
+Requires-Python: >=3.10.1
 Requires-Dist: codecarbon<2.7,>=2.5.1
 Requires-Dist: configparser
 Requires-Dist: dash
@@ -23,11 +23,11 @@ Requires-Dist: lxml
 Requires-Dist: matplotlib>=2.0
 Requires-Dist: numpy
 Requires-Dist: pandas>=1.3
-Requires-Dist: plotly>=5.0.0
-Requires-Dist: scipy>=0.18
+Requires-Dist: plotly>=6.6.0
+Requires-Dist: scipy<1.16.0,>=0.18
 Requires-Dist: tqdm>=4.60
 Provides-Extra: bumps
-Requires-Dist: bumps>=0.9.0; extra == 'bumps'
+Requires-Dist: bumps<1.0.0; extra == 'bumps'
 Provides-Extra: dev
 Requires-Dist: coverage[toml]>=6.3; extra == 'dev'
 Requires-Dist: coveralls; extra == 'dev'
@@ -40,10 +40,12 @@ Requires-Dist: pytest-cov>=4.0.0; extra == 'dev'
 Requires-Dist: ruff; extra == 'dev'
 Provides-Extra: dfo
 Requires-Dist: dfo-ls; extra == 'dfo'
+Provides-Extra: galahad
+Requires-Dist: galahad-optrove; extra == 'galahad'
 Provides-Extra: gofit
 Requires-Dist: gofit; extra == 'gofit'
 Provides-Extra: gradient-free
-Requires-Dist: gradient-free-optimizers; extra == 'gradient-free'
+Requires-Dist: gradient-free-optimizers[sklearn]; extra == 'gradient-free'
 Provides-Extra: hogben
 Requires-Dist: hogben; extra == 'hogben'
 Provides-Extra: levmar
@@ -69,22 +71,22 @@ Requires-Dist: sasmodels; extra == 'sas'
 Requires-Dist: tinycc; (platform_system == 'Windows') and extra == 'sas'
 Description-Content-Type: text/markdown
 
-[![Build Status](https://img.shields.io/github/actions/workflow/status/fitbenchmarking/fitbenchmarking/release.yml?style=flat-square)](https://github.com/fitbenchmarking/fitbenchmarking/actions/workflows/release.yml?query=branch%3Av1.3.0)
-[![Tests Status](https://img.shields.io/github/actions/workflow/status/fitbenchmarking/fitbenchmarking/main.yml?label=tests&style=flat-square)](https://github.com/fitbenchmarking/fitbenchmarking/actions/workflows/main.yml?query=branch%3Av1.3.0)
+[![Build Status](https://img.shields.io/github/actions/workflow/status/fitbenchmarking/fitbenchmarking/release.yml?style=flat-square)](https://github.com/fitbenchmarking/fitbenchmarking/actions/workflows/release.yml?query=branch%3Av1.4.0)
+[![Tests Status](https://img.shields.io/github/actions/workflow/status/fitbenchmarking/fitbenchmarking/main.yml?label=tests&style=flat-square)](https://github.com/fitbenchmarking/fitbenchmarking/actions/workflows/main.yml?query=branch%3Av1.4.0)
 [![Install Status](https://img.shields.io/github/actions/workflow/status/fitbenchmarking/fitbenchmarking/install.yml?label=install&style=flat-square)](https://github.com/fitbenchmarking/fitbenchmarking/actions/workflows/install.yml)
-[![Documentation Status](https://img.shields.io/readthedocs/fitbenchmarking/v1.3.0?style=flat-square)](https://fitbenchmarking.readthedocs.io/en/v1.3.0)
+[![Documentation Status](https://img.shields.io/readthedocs/fitbenchmarking/v1.4.0?style=flat-square)](https://fitbenchmarking.readthedocs.io/en/v1.4.0)
 [![Coverage Status](https://img.shields.io/coveralls/github/fitbenchmarking/fitbenchmarking.svg?style=flat-square)](https://coveralls.io/github/fitbenchmarking/fitbenchmarking)
 [![Chat](https://img.shields.io/badge/chat-CompareFitMinimizers-lightgrey.svg?style=flat-square&logo=slack)](https://slack.com/)
-[![Zenodo](https://img.shields.io/badge/Zenodo-10.5281/zenodo.14224242-blue.svg?style=flat-square)](https://doi.org/10.5281/zenodo.14224242)
+[![Zenodo](https://img.shields.io/badge/Zenodo-10.5281/zenodo.15546207-blue.svg?style=flat-square)](https://zenodo.org/records/15546207)
 [![JOSS](https://img.shields.io/badge/JOSS-10.21105/joss.03127-brightgreen.svg?style=flat-square)](https://doi.org/10.21105/joss.03127)
 # FitBenchmarking
 
 FitBenchmarking is an open source tool for comparing different minimizers/fitting frameworks. FitBenchmarking is cross platform and we support Windows, Linux and Mac OS. For questions, feature requests or any other inquiries, please open an issue on GitHub.
 
-- **Installation Instructions:** https://fitbenchmarking.readthedocs.io/en/v1.3.0/users/install_instructions/index.html
-- **User Documentation & Example Usage:** https://fitbenchmarking.readthedocs.io/en/v1.3.0/users/index.html
-- **Community Guidelines:** https://fitbenchmarking.readthedocs.io/en/v1.3.0/contributors/guidelines.html
-- **Automated Tests:** Run via GitHub Actions, https://github.com/fitbenchmarking/fitbenchmarking/actions, and tests are documented at https://fitbenchmarking.readthedocs.io/en/v1.3.0/users/tests.html
+- **Installation Instructions:** https://fitbenchmarking.readthedocs.io/en/v1.4.0/users/install_instructions/index.html
+- **User Documentation & Example Usage:** https://fitbenchmarking.readthedocs.io/en/v1.4.0/users/index.html
+- **Community Guidelines:** https://fitbenchmarking.readthedocs.io/en/v1.4.0/contributors/guidelines.html
+- **Automated Tests:** Run via GitHub Actions, https://github.com/fitbenchmarking/fitbenchmarking/actions, and tests are documented at https://fitbenchmarking.readthedocs.io/en/v1.4.0/users/tests.html
 
 The package is the result of a collaboration between STFC’s Scientific Computing Department and ISIS Neutron and Muon Facility and the Diamond Light Source. We also would like to acknowledge support from:
 

{fitbenchmarking-1.3.0 → fitbenchmarking-1.4.0}/README.md

@@ -1,19 +1,19 @@
-[![Build Status](https://img.shields.io/github/actions/workflow/status/fitbenchmarking/fitbenchmarking/release.yml?style=flat-square)](https://github.com/fitbenchmarking/fitbenchmarking/actions/workflows/release.yml?query=branch%3Av1.3.0)
-[![Tests Status](https://img.shields.io/github/actions/workflow/status/fitbenchmarking/fitbenchmarking/main.yml?label=tests&style=flat-square)](https://github.com/fitbenchmarking/fitbenchmarking/actions/workflows/main.yml?query=branch%3Av1.3.0)
+[![Build Status](https://img.shields.io/github/actions/workflow/status/fitbenchmarking/fitbenchmarking/release.yml?style=flat-square)](https://github.com/fitbenchmarking/fitbenchmarking/actions/workflows/release.yml?query=branch%3Av1.4.0)
+[![Tests Status](https://img.shields.io/github/actions/workflow/status/fitbenchmarking/fitbenchmarking/main.yml?label=tests&style=flat-square)](https://github.com/fitbenchmarking/fitbenchmarking/actions/workflows/main.yml?query=branch%3Av1.4.0)
 [![Install Status](https://img.shields.io/github/actions/workflow/status/fitbenchmarking/fitbenchmarking/install.yml?label=install&style=flat-square)](https://github.com/fitbenchmarking/fitbenchmarking/actions/workflows/install.yml)
-[![Documentation Status](https://img.shields.io/readthedocs/fitbenchmarking/v1.3.0?style=flat-square)](https://fitbenchmarking.readthedocs.io/en/v1.3.0)
+[![Documentation Status](https://img.shields.io/readthedocs/fitbenchmarking/v1.4.0?style=flat-square)](https://fitbenchmarking.readthedocs.io/en/v1.4.0)
 [![Coverage Status](https://img.shields.io/coveralls/github/fitbenchmarking/fitbenchmarking.svg?style=flat-square)](https://coveralls.io/github/fitbenchmarking/fitbenchmarking)
 [![Chat](https://img.shields.io/badge/chat-CompareFitMinimizers-lightgrey.svg?style=flat-square&logo=slack)](https://slack.com/)
-[![Zenodo](https://img.shields.io/badge/Zenodo-10.5281/zenodo.14224242-blue.svg?style=flat-square)](https://doi.org/10.5281/zenodo.14224242)
+[![Zenodo](https://img.shields.io/badge/Zenodo-10.5281/zenodo.15546207-blue.svg?style=flat-square)](https://zenodo.org/records/15546207)
 [![JOSS](https://img.shields.io/badge/JOSS-10.21105/joss.03127-brightgreen.svg?style=flat-square)](https://doi.org/10.21105/joss.03127)
 # FitBenchmarking
 
 FitBenchmarking is an open source tool for comparing different minimizers/fitting frameworks. FitBenchmarking is cross platform and we support Windows, Linux and Mac OS. For questions, feature requests or any other inquiries, please open an issue on GitHub.
 
-- **Installation Instructions:** https://fitbenchmarking.readthedocs.io/en/v1.3.0/users/install_instructions/index.html
-- **User Documentation & Example Usage:** https://fitbenchmarking.readthedocs.io/en/v1.3.0/users/index.html
-- **Community Guidelines:** https://fitbenchmarking.readthedocs.io/en/v1.3.0/contributors/guidelines.html
-- **Automated Tests:** Run via GitHub Actions, https://github.com/fitbenchmarking/fitbenchmarking/actions, and tests are documented at https://fitbenchmarking.readthedocs.io/en/v1.3.0/users/tests.html
+- **Installation Instructions:** https://fitbenchmarking.readthedocs.io/en/v1.4.0/users/install_instructions/index.html
+- **User Documentation & Example Usage:** https://fitbenchmarking.readthedocs.io/en/v1.4.0/users/index.html
+- **Community Guidelines:** https://fitbenchmarking.readthedocs.io/en/v1.4.0/contributors/guidelines.html
+- **Automated Tests:** Run via GitHub Actions, https://github.com/fitbenchmarking/fitbenchmarking/actions, and tests are documented at https://fitbenchmarking.readthedocs.io/en/v1.4.0/users/tests.html
 
 The package is the result of a collaboration between STFC’s Scientific Computing Department and ISIS Neutron and Muon Facility and the Diamond Light Source. We also would like to acknowledge support from:
 

{fitbenchmarking-1.3.0 → fitbenchmarking-1.4.0}/fitbenchmarking/cli/checkpoint_handler.py

@@ -11,6 +11,7 @@ import os
 import sys
 import textwrap
 from argparse import ArgumentParser, RawDescriptionHelpFormatter
+from collections import defaultdict
 
 from fitbenchmarking.cli.exception_handler import exception_handler
 from fitbenchmarking.core.results_output import (
@@ -155,6 +156,20 @@ def generate_report(options_file="", additional_options=None, debug=False):
     checkpoint = Checkpoint(options=options)
     results, unselected_minimizers, failed_problems, config = checkpoint.load()
 
+    # Update options.software and options.minimizers
+    # so that they hold the correct values rather than
+    # the default. This update is necessary for processing
+    # the multstart plots.
+    set_minimizers = defaultdict(set)
+    for results_list in results.values():
+        for r in results_list:
+            set_minimizers[r.software].add(r.minimizer)
+    minimizers = defaultdict(
+        list, {k: list(v) for k, v in set_minimizers.items()}
+    )
+    options.software = list(minimizers.keys())
+    options.minimizers = minimizers
+
     all_dirs = []
     pp_dfs_all_prob_sets = {}
     for label in results:

{fitbenchmarking-1.3.0 → fitbenchmarking-1.4.0}/fitbenchmarking/cli/main.py

@@ -178,6 +178,14 @@ of the Fitbenchmarking docs. """
         help="Set the port for Dash.",
     )
 
+    parser.add_argument(
+        "--ip_address",
+        metavar="IP_ADDRESS",
+        type=str,
+        default="",
+        help="Set the ip address for Dash.",
+    )
+
     make_plots_group = parser.add_mutually_exclusive_group()
     make_plots_group.add_argument(
         "--make_plots",
@@ -296,7 +304,8 @@ of the Fitbenchmarking docs. """
         default="",
         help=(
             "Specify the minimum level of logging to display "
-            "on console during runtime."
+            "on console during runtime. Can be any of: "
+            "NOTSET, DEBUG, INFO, WARNING, ERROR, CRITICAL ."
         ),
     )
     parser.add_argument(
@@ -304,7 +313,10 @@ of the Fitbenchmarking docs. """
         "--external_output",
         metavar="EXTERNAL_OUTPUT",
         default="",
-        help="Select the amount of information displayed from third-parties.",
+        help=(
+            "Select the amount of information displayed from third-parties. "
+            "Can be any of: display, log_only, debug."
+        ),
     )
 
     parser.add_argument(
@@ -312,7 +324,7 @@ of the Fitbenchmarking docs. """
         default=False,
         action="store_true",
         help=(
-            "Load results from the checkpoint and generate"
+            "Load results from the checkpoint and generate "
             "reports. Will not run any new tests."
         ),
     )
@@ -340,7 +352,7 @@ of the Fitbenchmarking docs. """
         "--check_jacobian",
         action="store_true",
         help=(
-            "Use this option to check the jacobian against"
+            "Use this option to check the jacobian against "
             "a finite difference approximation."
         ),
     )
@@ -541,6 +553,7 @@ def main():
         "run_name": args.run_name,
         "runtime_metric": args.runtime_metric,
         "port": args.port,
+        "ip_address": args.ip_address,
     }
 
     # Check if make_plots in options.py should be overridden, and if so,

{fitbenchmarking-1.3.0 → fitbenchmarking-1.4.0}/fitbenchmarking/controllers/base_controller.py

@@ -46,7 +46,7 @@ class Controller:
     #:     - ``general`` - minimizers which solve a generic `min f(x)`
     #:     - ``simplex`` - derivative free simplex based algorithms
     #:       e.g. Nelder-Mead
-    #:     - ``trust_region`` - algorithms which emply a trust region approach
+    #:     - ``trust_region`` - algorithms which employ a trust region approach
     #:     - ``levenberg-marquardt`` - minimizers that use the
     #:       Levenberg-Marquardt algorithm
     #:     - ``gauss_newton`` - minimizers that use the Gauss Newton algorithm
@@ -62,7 +62,7 @@ class Controller:
     #:
     #: The ``algorithm_check`` dictionary is used to determine which minimizers
     #: to run given the ``algorithm_type`` selected in Fitting Options.
-    #: For guidance on how to catagorise minimizers, see the Optimization
+    #: For guidance on how to categorise minimizers, see the Optimization
     #: Algorithms section of the FitBenchmarking docs.
     algorithm_check = {
         "all": [],

{fitbenchmarking-1.3.0 → fitbenchmarking-1.4.0}/fitbenchmarking/controllers/galahad_controller.py

@@ -3,7 +3,7 @@ Implements a controller for the GALAHAD fitting software.
 """
 
 from contextlib import suppress
-from typing import Any, Callable
+from typing import TYPE_CHECKING, Any
 
 import numpy as np
 from galahad import arc, bgo, dgo, nls, trb, tru
@@ -11,6 +11,9 @@ from galahad import arc, bgo, dgo, nls, trb, tru
 from fitbenchmarking.controllers.base_controller import Controller
 from fitbenchmarking.utils.exceptions import IncompatibleMinimizerError
 
+if TYPE_CHECKING:
+    from collections.abc import Callable
+
 
 class GalahadController(Controller):
     """
@@ -94,15 +97,23 @@ class GalahadController(Controller):
         x_u = np.array(x_u)
 
         opts = self._module.initialize()
+
+        if minimizer in ["arc", "nls"]:
+            opts["glrt_options"]["impose_descent"] = False
+
         kwargs: dict[str, Any] = {
             "options": opts,
         }
 
         if minimizer in ["arc", "tru"]:
+            if not has_hessian:
+                raise IncompatibleMinimizerError(
+                    "Requires hessian information (for now)"
+                )
             kwargs.update(
                 {
                     "n": self._num_vars,
-                    "H_type": "dense" if has_hessian else "absent",
+                    "H_type": "dense",
                     "H_ne": 10,
                     "H_row": None,
                     "H_col": None,
@@ -123,7 +134,7 @@ class GalahadController(Controller):
                 }
             )
 
-        elif minimizer in ["nls"]:
+        elif minimizer == "nls":
             if not has_hessian:
                 raise IncompatibleMinimizerError(
                     "Requires hessian information (for now)"
@@ -178,7 +189,7 @@ class GalahadController(Controller):
                 "eval_g": self._jacobian,
                 "eval_h": self._hessian,
             }
-        elif self._minimizer in ["nls"]:
+        elif self._minimizer == "nls":
             m = self.data_x.shape[0]
             kwargs = {
                 "n": self._num_vars,

{fitbenchmarking-1.3.0 → fitbenchmarking-1.4.0}/fitbenchmarking/controllers/gradient_free_controller.py

@@ -125,7 +125,7 @@ class GradientFreeController(Controller):
         }
 
         self.iteration_count = 1000
-        self.initialize = {"warm_start": param_dict}
+        self.initialize = {"warm_start": [param_dict]}
 
     def _feval(self, p):
         """
@@ -152,7 +152,7 @@ class GradientFreeController(Controller):
 
         method_to_call = getattr(gfo, self.minimizer)
 
-        opt = method_to_call(self.search_space)
+        opt = method_to_call(self.search_space, initialize=self.initialize)
         opt.search(self._feval, n_iter=self.iteration_count, verbosity=False)
         self.results = opt.best_para
         self._status = 0 if self.results is not None else 1

{fitbenchmarking-1.3.0 → fitbenchmarking-1.4.0}/fitbenchmarking/controllers/mantid_controller.py

@@ -3,7 +3,6 @@ Implements a controller for the Mantid fitting software.
 """
 
 from itertools import repeat
-from typing import Union
 
 import numpy as np
 from mantid import simpleapi as msapi
@@ -85,6 +84,7 @@ class MantidController(Controller):
     ]
 
     support_for_bounds = True
+    incompatible_problems = ["sscanss"]
 
     def __init__(self, cost_func):
         """
@@ -125,6 +125,8 @@ class MantidController(Controller):
         )
 
         if self.problem.multifit:
+            if self.data_x[0].dtype not in [float, int]:
+                self.data_x = [np.array(range(len(d))) for d in self.data_x]
             # len(data_obj) will be equal to dataset count
             data_obj = [
                 msapi.CreateWorkspace(
@@ -142,6 +144,8 @@ class MantidController(Controller):
                 for i, v in enumerate(data_obj[1:])
             }
         else:
+            if self.data_x.dtype not in [float, int]:
+                self.data_x = np.array(range(len(self.data_x)))
             data_obj = msapi.CreateWorkspace(
                 DataX=self.data_x, DataY=self.data_y, DataE=self.data_e
             )
@@ -405,11 +409,11 @@ class MantidController(Controller):
     # =====================
     def eval_chisq(
         self,
-        params: Union[float, list[float]],
-        x: Union[np.ndarray, list[np.ndarray], None] = None,
-        y: Union[np.ndarray, list[np.ndarray], None] = None,
-        e: Union[np.ndarray, list[np.ndarray], None] = None,
-    ) -> Union[np.ndarray, list[np.ndarray]]:
+        params: float | list[float],
+        x: np.ndarray | list[np.ndarray] | None = None,
+        y: np.ndarray | list[np.ndarray] | None = None,
+        e: np.ndarray | list[np.ndarray] | None = None,
+    ) -> np.ndarray | list[np.ndarray]:
         """
         Computes the chisq value.
         If multi-fit inputs will be lists and this will return a list of chi

{fitbenchmarking-1.3.0 → fitbenchmarking-1.4.0}/fitbenchmarking/controllers/theseus_controller.py

@@ -2,8 +2,12 @@
 Implements a controller for the Theseus fitting software.
 """
 
-from collections.abc import Sequence
-from typing import Optional
+from __future__ import annotations
+
+from typing import TYPE_CHECKING
+
+if TYPE_CHECKING:
+    from collections.abc import Sequence
 
 import numpy as np
 import theseus as th
@@ -24,8 +28,8 @@ class TheseusCostFunction(th.CostFunction):
         var: list[th.Vector],
         auxvar: Sequence[th.Variable],
         dim: int,
-        cost_weight: Optional[th.CostWeight] = None,
-        name: Optional[str] = None,
+        cost_weight: th.CostWeight | None = None,
+        name: str | None = None,
     ):
         if cost_weight is None:
             cost_weight = th.ScaleCostWeight(1.0)
@@ -79,7 +83,7 @@ class TheseusCostFunction(th.CostFunction):
         """
         return self._dim
 
-    def _copy_impl(self, new_name: Optional[str] = None):
+    def _copy_impl(self, new_name: str | None = None):
         return TheseusCostFunction(  # type: ignore
             var=[v.copy() for v in self.var],
             auxvar=[v.copy() for v in self.auxvar],

{fitbenchmarking-1.3.0 → fitbenchmarking-1.4.0}/fitbenchmarking/core/fitting_benchmarking.py

@@ -108,13 +108,14 @@ class Fit:
             try:
                 with self._grabbed_output:
                     parsed = parse_problem_file(p, self._options)
-                    parsed.correct_data()
             except FitBenchmarkException as e:
                 LOGGER.info("Could not parse problem from: %s", p)
                 LOGGER.warning(e)
             else:
-                name_count[parsed.name] = name_count.get(parsed.name, 0) + 1
-                problems.append((p, parsed))
+                for fp in parsed:
+                    fp.correct_data()
+                    name_count[fp.name] = name_count.get(fp.name, 0) + 1
+                    problems.append((p, fp))
 
         LOGGER.info("Running problems")
 
@@ -141,7 +142,7 @@ class Fit:
 
                 info_str = (
                     f" Running data from: {os.path.basename(fname)}"
-                    f" {i + 1}/{len(problem_group)} "
+                    f" {i + 1}/{len(problems)} "
                 )
                 LOGGER.info("\n%s", "#" * len(info_str))
                 LOGGER.info(info_str)
@@ -413,7 +414,7 @@ class Fit:
                         LOGGER.info(
                             "%sJacobian: %s",
                             self._logger_prefix * 5,
-                            jacobian.name() if jacobian.name() else "default",
+                            jacobian.name() or "default",
                         )
 
                     if (

{fitbenchmarking-1.3.0 → fitbenchmarking-1.4.0}/fitbenchmarking/core/results_output.py

@@ -9,7 +9,6 @@ import platform
 import re
 import webbrowser
 from shutil import copytree
-from typing import Optional, Union
 
 import pandas as pd
 from dash import Dash, dcc, html
@@ -164,7 +163,7 @@ def preprocess_data(results: list[FittingResult]):
     col_sections = ["costfun"]
 
     # Generate the columns, category, and row tags and sort
-    rows: Union[list[str], set[str]] = set()
+    rows: list[str] | set[str] = set()
     columns = {}
     for r in results:
         # Error 4 means none of the jacobians ran so can't infer the
@@ -192,7 +191,7 @@ def preprocess_data(results: list[FittingResult]):
     }
 
     # Build the sorted results dictionary
-    sorted_results: dict[str, dict[str, list[Optional[FittingResult]]]] = {
+    sorted_results: dict[str, dict[str, list[FittingResult | None]]] = {
         r.strip(":"): {
             k: [None for _ in category] for k, category in columns.items()
         }
@@ -363,7 +362,6 @@ def create_plots(options, results, best_results, figures_dir):
     """
     for best_dict, prob_result in zip(best_results.values(), results.values()):
         plot_dict = {}
-        initial_guess_path = {}
         data = {}
 
         # Create a dataframe for each problem
@@ -439,9 +437,6 @@ def create_plots(options, results, best_results, figures_dir):
                     result.figure_error = str(e)
                 continue
 
-            # Create a plot showing the initial guess and get filename
-            initial_guess_path[cf] = plot.plot_initial_guess(data[cf])
-
             # Get filenames of best plot first
             # If none of the fits succeeded, params could be None
             # Otherwise, add the best fit to the plot
@@ -452,7 +447,6 @@ def create_plots(options, results, best_results, figures_dir):
                 best_dict[
                     cf
                 ].figure_error = "Minimizer failed to produce any parameters"
-            best_dict[cf].start_figure_link = initial_guess_path[cf]
             plot_dict[cf] = plot
 
             plot_paths = plot.plotly_fit(data[cf])
@@ -469,7 +463,6 @@ def create_plots(options, results, best_results, figures_dir):
                     result.figure_error = (
                         "Minimizer failed to produce any parameters"
                     )
-                result.start_figure_link = initial_guess_path[cf]
 
         # For each result, if it succeeded and produced posterior pdf estimates
         # for each parameter, create histogram plots and add plot links to the
@@ -634,7 +627,7 @@ def open_browser(output_file: str, options, pp_dfs_all_prob_sets) -> None:
         )
 
     if options.run_dash:
-        run_dash_app(options, pp_dfs_all_prob_sets)
+        prepare_dash_app_and_run(options, pp_dfs_all_prob_sets)
 
 
 def update_warning(solvers, max_solvers):
@@ -754,10 +747,10 @@ def display_page(
     return html.Div(new_layout)
 
 
-def run_dash_app(options, pp_dfs_all_prob_sets) -> None:
+def prepare_dash_app_and_run(options, pp_dfs_all_prob_sets) -> None:
     """
-    Runs the Dash app to produce the interactive performance profile
-    plots.
+    Prepares the Dash app to produce the interactive performance profile
+    plots, and calls the function to run it.
 
     :param options: The user options for the benchmark.
     :type options: fitbenchmarking.utils.options.Options
@@ -866,4 +859,18 @@ def run_dash_app(options, pp_dfs_all_prob_sets) -> None:
         )
     )
 
-    app.run(port=options.port)
+    run_dash_app(app=app, host=options.ip_address, port=options.port)
+
+
+def run_dash_app(app, host, port):
+    """
+    Runs the Dash app.
+
+    :param host: The dash app to run
+    :type host: dash.dash.Dash
+    :param host: The ip address where to run the app.
+    :type host: str
+    :param port: The port where to run the app.
+    :type port: str
+    """
+    app.run(host=host, port=port)

{fitbenchmarking-1.3.0 → fitbenchmarking-1.4.0}/fitbenchmarking/cost_func/base_cost_func.py

@@ -3,7 +3,7 @@ Implements the base class for the cost function class.
 """
 
 from abc import ABCMeta, abstractmethod
-from typing import TYPE_CHECKING, Optional
+from typing import TYPE_CHECKING
 
 from fitbenchmarking.utils.exceptions import IncompatibleMinimizerError
 
@@ -32,7 +32,7 @@ class CostFunc:
         self.problem: FittingProblem = problem
 
         # The Jacobian object to evaluate
-        self.jacobian: Optional[Jacobian] = None
+        self.jacobian: Jacobian | None = None
 
         # The Hessian object to evaluate
         self.hessian = None

{fitbenchmarking-1.3.0 → fitbenchmarking-1.4.0}/fitbenchmarking/cost_func/nlls_base_cost_func.py

@@ -77,8 +77,10 @@ class BaseNLLSCostFunc(CostFunc):
         Uses the Jacobian of the model to evaluate the Jacobian of the
         cost function, :math:`\\nabla_p F(r(x,y,p))`, at the given
         parameters.
+
         :param params: The parameters at which to calculate Jacobians
         :type params: list
+
         :return: evaluated Jacobian of the cost function
         :rtype: 1D numpy array
         """

{fitbenchmarking-1.3.0 → fitbenchmarking-1.4.0}/fitbenchmarking/parsing/base_parser.py

@@ -5,6 +5,8 @@ Implements the base Parser as a Context Manager.
 import contextlib
 from abc import ABCMeta, abstractmethod
 
+from fitbenchmarking.parsing.fitting_problem import FittingProblem
+
 
 class Parser:
     """
@@ -56,7 +58,7 @@ class Parser:
             self.file.close()
 
     @abstractmethod
-    def parse(self):
+    def parse(self) -> FittingProblem | list[FittingProblem]:
         """
         Parse the file into a FittingProblem.