FitBenchmarking 1.2.0__tar.gz → 1.3.0__tar.gz

{fitbenchmarking-1.2.0 → fitbenchmarking-1.3.0}/PKG-INFO

@@ -1,13 +1,14 @@
-Metadata-Version: 2.3
+Metadata-Version: 2.4
 Name: FitBenchmarking
-Version: 1.2.0
+Version: 1.3.0
 Summary: FitBenchmarking: A tool for comparing fitting software
 Project-URL: Homepage, https://fitbenchmarking.github.io
 Project-URL: Documentation, https://fitbenchmarking.readthedocs.io/en/stable
 Project-URL: Repository, https://github.com/fitbenchmarking/fitbenchmarking
 Project-URL: Release Notes, https://github.com/fitbenchmarking/fitbenchmarking/releases
 Project-URL: Issues, https://github.com/fitbenchmarking/fitbenchmarking/issues
-Author: FitBenchmarkign Team
+Author: FitBenchmarking Team
+License-File: LICENSE.txt
 Keywords: benchmark,comparison,fitting,least squares,optimisation
 Classifier: License :: OSI Approved :: BSD License
 Classifier: Operating System :: OS Independent
@@ -68,22 +69,22 @@ 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%3Av1.2.0)
-[![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%3Av1.2.0)
+[![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%3Av1.3.0)
+[![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)
 [![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/v1.2.0?style=flat-square)](https://fitbenchmarking.readthedocs.io/en/v1.2.0)
+[![Documentation Status](https://img.shields.io/readthedocs/fitbenchmarking/v1.3.0?style=flat-square)](https://fitbenchmarking.readthedocs.io/en/v1.3.0)
 [![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.11198140-blue.svg?style=flat-square)](https://doi.org/10.5281/zenodo.11198140)
+[![Zenodo](https://img.shields.io/badge/Zenodo-10.5281/zenodo.14224242-blue.svg?style=flat-square)](https://doi.org/10.5281/zenodo.14224242)
 [![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/v1.2.0/users/install_instructions/index.html
-- **User Documentation & Example Usage:** https://fitbenchmarking.readthedocs.io/en/v1.2.0/users/index.html
-- **Community Guidelines:** https://fitbenchmarking.readthedocs.io/en/v1.2.0/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/v1.2.0/users/tests.html
+- **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
 
 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-1.2.0 → fitbenchmarking-1.3.0}/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%3Av1.2.0)
-[![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%3Av1.2.0)
+[![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%3Av1.3.0)
+[![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)
 [![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/v1.2.0?style=flat-square)](https://fitbenchmarking.readthedocs.io/en/v1.2.0)
+[![Documentation Status](https://img.shields.io/readthedocs/fitbenchmarking/v1.3.0?style=flat-square)](https://fitbenchmarking.readthedocs.io/en/v1.3.0)
 [![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.11198140-blue.svg?style=flat-square)](https://doi.org/10.5281/zenodo.11198140)
+[![Zenodo](https://img.shields.io/badge/Zenodo-10.5281/zenodo.14224242-blue.svg?style=flat-square)](https://doi.org/10.5281/zenodo.14224242)
 [![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/v1.2.0/users/install_instructions/index.html
-- **User Documentation & Example Usage:** https://fitbenchmarking.readthedocs.io/en/v1.2.0/users/index.html
-- **Community Guidelines:** https://fitbenchmarking.readthedocs.io/en/v1.2.0/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/v1.2.0/users/tests.html
+- **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
 
 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-1.2.0 → fitbenchmarking-1.3.0}/fitbenchmarking/cli/checkpoint_handler.py

@@ -142,7 +142,7 @@ def generate_report(options_file="", additional_options=None, debug=False):
     :type options_file: str, optional
     :param additional_options: Extra options for the reporting.
                                Available keys are:
-                                   filename (str): The checkpoint file to use.
+                               filename (str): The checkpoint file to use.
     :type additional_options: dict, optional
     """
     if additional_options is None:
@@ -185,46 +185,65 @@ def merge_data_sets(
 ):
     """
     Combine multiple checkpoint files into one following these rules:
-     1) The output will be the same as combining them one at a time in
-        sequence. i.e. A + B + C = (A + B) + C
-        The rules from here on will only reference A and B as the relation is
-        recursive.
-     2) Datasets
-         2a) Datasets in A and B are identical if they agree on the label
-         2b) If A and B contain identical datasets, the problems and results
-             are combined as below.
-             The remainder of these rules assume that A and B are identical
-             datasets as the alternative is trivial.
-     3) Problems
-         3a) If problems in A and B agree on name, ini_params, ini_y, x, y,
-             and e then these problems are considered identical.
-         3b) If A and B share identical problems, the details not specified in
-             3a are taken from A.
-         3c) If problems in A and B are not identical but share a name, the
-             name of the project in B should be updated to "<problem_name>*".
-     4) Results
-         4a) If results in A and B have identical problems and agree on name,
-             software_tag, minimizer_tag, jacobian_tag, hessian_tag, and
-             costfun_tag they are considered identical.
-         4b) If A an B share identical results, the details not specified in 4a
-             are taken from A if strategy is 'first', or B if strategy is
-             'last'.
-     5) As tables are grids of results, combining arbitrary results can lead to
-        un-table-able checkpoint files.
-        This occurs when the problems in A and B are not all identical and the
-        set of combinations of software_tag, minimizer_tag, jacobian_tag,
-        hessian_tag, and costfun_tag for which there are results in each of A
-        and B are not identical.
-        E.g. B has a problem not in A and uses a minimizer for which there are
-             no results in A.
-         5a) If the resulting checkpoint file would have the above issue, the
-             checkpoints are incompatible.
-         5b) Incompatible checkpoint files can be combined but should raise
-             warnings and mark the dataset in the checkpoint file.
-             Note: Some datasets may be incompatible where others can be
-                   successfully combined.
-     6) Unselected minimizers and failed problems will be discarded when
-        combining.
+
+    1) The output will be the same as combining them one at a time in
+       sequence. i.e. A + B + C = (A + B) + C
+
+        **Note:** The rules from here on will only reference A and B as
+        the relation is recursive.
+
+    2) Datasets
+
+        2a) Datasets in A and B are identical if they agree on the label
+
+        2b) If A and B contain identical datasets, the problems and results
+        are combined as below.
+
+        **Note:** The remainder of these rules assume that A and B are
+        identical datasets as the alternative is trivial.
+
+    3) Problems
+
+        3a) If problems in A and B agree on name, ini_params, ini_y, x, y,
+        and e then these problems are considered identical.
+
+        3b)If A and B share identical problems, the details not specified in
+        3a are taken from A.
+
+        3c) If problems in A and B are not identical but share a name, the
+        name of the project in B should be updated to "<problem_name>*".
+
+    4) Results
+
+        4a) If results in A and B have identical problems and agree on name,
+        software_tag, minimizer_tag, jacobian_tag, hessian_tag, and
+        costfun_tag they are considered identical.
+
+        4b) If A an B share identical results, the details not specified in 4a
+        are taken from A if strategy is 'first', or B if strategy is 'last'.
+
+    5) As tables are grids of results, combining arbitrary results can lead to
+       un-table-able checkpoint files.
+
+       This occurs when the problems in A and B are not all identical and the
+       set of combinations of software_tag, minimizer_tag, jacobian_tag,
+       hessian_tag, and costfun_tag for which there are results in each of A
+       and B are not identical.
+
+       **E.g.** B has a problem not in A and uses a minimizer for which there
+       are no results in A.
+
+            5a) If the resulting checkpoint file would have the above issue,
+            the checkpoints are incompatible.
+
+            5b) Incompatible checkpoint files can be combined but should raise
+            warnings and mark the dataset in the checkpoint file.
+
+        **Note:** Some datasets may be incompatible where others can be
+        successfully combined.
+
+    6) Unselected minimizers and failed problems will be discarded when
+       combining.
 
     :param files: The files to combine.
     :type files: list[str]

{fitbenchmarking-1.2.0 → fitbenchmarking-1.3.0}/fitbenchmarking/cli/main.py

@@ -122,8 +122,7 @@ of the Fitbenchmarking docs. """
         type=str,
         default=[],
         help=(
-            "Select what type of algorithm is used within a specific "
-            "software."
+            "Select what type of algorithm is used within a specific software."
         ),
     )
     parser.add_argument(
@@ -179,8 +178,8 @@ of the Fitbenchmarking docs. """
         help="Set the port for Dash.",
     )
 
-    group1 = parser.add_mutually_exclusive_group()
-    group1.add_argument(
+    make_plots_group = parser.add_mutually_exclusive_group()
+    make_plots_group.add_argument(
         "--make_plots",
         action="store_true",
         help=(
@@ -188,7 +187,7 @@ of the Fitbenchmarking docs. """
             "during runtime."
         ),
     )
-    group1.add_argument(
+    make_plots_group.add_argument(
         "--dont_make_plots",
         action="store_true",
         help=(
@@ -197,8 +196,8 @@ of the Fitbenchmarking docs. """
         ),
     )
 
-    group2 = parser.add_mutually_exclusive_group()
-    group2.add_argument(
+    results_browser_group = parser.add_mutually_exclusive_group()
+    results_browser_group.add_argument(
         "--results_browser",
         action="store_true",
         help=(
@@ -207,7 +206,7 @@ of the Fitbenchmarking docs. """
             "of a fit benchmark."
         ),
     )
-    group2.add_argument(
+    results_browser_group.add_argument(
         "--no_results_browser",
         action="store_true",
         help=(
@@ -217,8 +216,8 @@ of the Fitbenchmarking docs. """
         ),
     )
 
-    group3 = parser.add_mutually_exclusive_group()
-    group3.add_argument(
+    pbar_group = parser.add_mutually_exclusive_group()
+    pbar_group.add_argument(
         "--pbar",
         action="store_true",
         help=(
@@ -226,7 +225,7 @@ of the Fitbenchmarking docs. """
             "see the progress bar during runtime."
         ),
     )
-    group3.add_argument(
+    pbar_group.add_argument(
         "--no_pbar",
         action="store_true",
         help=(
@@ -269,8 +268,8 @@ of the Fitbenchmarking docs. """
         help="Specify the file path to write the logs to.",
     )
 
-    group2 = parser.add_mutually_exclusive_group()
-    group2.add_argument(
+    append_log_group = parser.add_mutually_exclusive_group()
+    append_log_group.add_argument(
         "--append_log",
         action="store_true",
         help=(
@@ -280,7 +279,7 @@ of the Fitbenchmarking docs. """
             "subsequent run."
         ),
     )
-    group2.add_argument(
+    append_log_group.add_argument(
         "--overwrite_log",
         action="store_true",
         help=(
@@ -318,8 +317,8 @@ of the Fitbenchmarking docs. """
         ),
     )
 
-    group4 = parser.add_mutually_exclusive_group()
-    group4.add_argument(
+    run_dash_group = parser.add_mutually_exclusive_group()
+    run_dash_group.add_argument(
         "--run_dash",
         action="store_true",
         help=(
@@ -327,7 +326,7 @@ of the Fitbenchmarking docs. """
             "interactive plots."
         ),
     )
-    group4.add_argument(
+    run_dash_group.add_argument(
         "--dont_run_dash",
         action="store_true",
         help=(
@@ -335,6 +334,23 @@ of the Fitbenchmarking docs. """
             "run dash for interactive plots."
         ),
     )
+
+    jacobian_check_group = parser.add_mutually_exclusive_group()
+    jacobian_check_group.add_argument(
+        "--check_jacobian",
+        action="store_true",
+        help=(
+            "Use this option to check the jacobian against"
+            "a finite difference approximation."
+        ),
+    )
+    jacobian_check_group.add_argument(
+        "--dont_check_jacobian",
+        action="store_true",
+        help=(
+            "Use this option if you have decided not to check the jacobian."
+        ),
+    )
     return parser
 
 
@@ -347,7 +363,7 @@ def run(problem_sets, additional_options=None, options_file="", debug=False):
     :param problem_sets: The paths to directories containing problem_sets.
     :type problem_sets: list of str
     :param additional_options: A dictionary of options input by the
-    user into the command line.
+                               user into the command line.
     :type additional_options: dict
     :param options_file: The path to an options file, defaults to ''.
     :type options_file: str, optional
@@ -383,76 +399,85 @@ def run(problem_sets, additional_options=None, options_file="", debug=False):
     pp_dfs_all_prob_sets = {}
     cp = Checkpoint(options=options)
 
-    for sub_dir in problem_sets:
-        # Create full path for the directory that holds a group of
-        # problem definition files
-        data_dir = os.path.join(current_path, sub_dir)
-
-        test_data = glob.glob(data_dir + "/*.*")
-
-        if not test_data:
-            LOGGER.warning("Problem set %s not found", data_dir)
-            continue
-
-        # generate group label/name used for problem set
-        try:
-            with open(
-                os.path.join(data_dir, "META.txt"), encoding="utf-8"
-            ) as f:
-                label = f.readline().strip("\n")
-        except OSError:
-            label = sub_dir.replace("/", "_")
-
-        LOGGER.info("Running the benchmarking on the %s problem set", label)
-        fit = Fit(
-            options=options, data_dir=data_dir, label=label, checkpointer=cp
-        )
-        results, failed_problems, unselected_minimizers = fit.benchmark()
-
-        # If a result has error flag 4 then the result contains dummy values,
-        # if this is the case for all results then output should not be
-        # produced as results tables won't show meaningful values.
-        all_dummy_results_flag = True
-        for result in results:
-            if result.error_flag != 4:
-                all_dummy_results_flag = False
-                break
-
-        # If the results are an empty list then this means that all minimizers
-        # raise an exception and the tables will produce errors if they run
-        # for that problem set.
-        if not results or all_dummy_results_flag:
-            message = (
-                "\nWARNING: \nThe user chosen options and/or problem "
-                " setup resulted in all minimizers and/or parsers "
-                "raising an exception. Because of this, results for "
-                f"the {label} problem set will not be displayed. "
-                "Please see the logs for more detail on why this is "
-                "the case."
+    try:
+        for sub_dir in problem_sets:
+            # Create full path for the directory that holds a group of
+            # problem definition files
+            data_dir = os.path.join(current_path, sub_dir)
+
+            test_data = glob.glob(data_dir + "/*.*")
+
+            if not test_data:
+                LOGGER.warning("Problem set %s not found", data_dir)
+                continue
+
+            # generate group label/name used for problem set
+            try:
+                with open(
+                    os.path.join(data_dir, "META.txt"), encoding="utf-8"
+                ) as f:
+                    label = f.readline().strip("\n")
+            except OSError:
+                label = sub_dir.replace("/", "_")
+
+            LOGGER.info(
+                "Running the benchmarking on the %s problem set", label
             )
-            LOGGER.warning(message)
-        else:
-            LOGGER.info("Producing output for the %s problem set", label)
-            # Display the runtime and accuracy results in a table
-            group_results_dir, pp_dfs = save_results(
-                group_name=label,
-                results=results,
+            fit = Fit(
                 options=options,
-                failed_problems=failed_problems,
-                unselected_minimizers=unselected_minimizers,
-                config=cp.config,
-            )
-
-            pp_dfs_all_prob_sets[label] = pp_dfs
-
-            LOGGER.info("Completed benchmarking for %s problem set", sub_dir)
-            group_results_dir = os.path.relpath(
-                path=group_results_dir, start=options.results_dir
+                data_dir=data_dir,
+                label=label,
+                checkpointer=cp,
             )
-            result_dir.append(group_results_dir)
-            group_labels.append(label)
-
-    cp.finalise()
+            results, failed_problems, unselected_minimizers = fit.benchmark()
+
+            # If a result has error flag 4 then the result contains dummy
+            # values, if this is the case for all results then output should
+            # not be produced as results tables won't show meaningful values.
+            all_dummy_results_flag = True
+            for result in results:
+                if result.error_flag != 4:
+                    all_dummy_results_flag = False
+                    break
+
+            # If the results are an empty list then this means that all
+            # minimizers raise an exception and the tables will produce
+            # errors if they run for that problem set.
+            if not results or all_dummy_results_flag:
+                message = (
+                    "\nWARNING: \nThe user chosen options and/or problem "
+                    " setup resulted in all minimizers and/or parsers "
+                    "raising an exception. Because of this, results for "
+                    f"the {label} problem set will not be displayed. "
+                    "Please see the logs for more detail on why this is "
+                    "the case."
+                )
+                LOGGER.warning(message)
+            else:
+                LOGGER.info("Producing output for the %s problem set", label)
+                # Display the runtime and accuracy results in a table
+                group_results_dir, pp_dfs = save_results(
+                    group_name=label,
+                    results=results,
+                    options=options,
+                    failed_problems=failed_problems,
+                    unselected_minimizers=unselected_minimizers,
+                    config=cp.config,
+                )
+
+                pp_dfs_all_prob_sets[label] = pp_dfs
+
+                LOGGER.info(
+                    "Completed benchmarking for %s problem set", sub_dir
+                )
+                group_results_dir = os.path.relpath(
+                    path=group_results_dir, start=options.results_dir
+                )
+                result_dir.append(group_results_dir)
+                group_labels.append(label)
+
+    finally:
+        cp.finalise()
 
     # Check result_dir is non empty before producing output
     if not result_dir:
@@ -539,6 +564,13 @@ def main():
     elif args.dont_run_dash:
         options_dictionary["run_dash"] = False
 
+    # Check if check_jacobian in options.py should be overridden, and if so,
+    # add to options_dictionary
+    if args.check_jacobian:
+        options_dictionary["check_jacobian"] = True
+    elif args.dont_check_jacobian:
+        options_dictionary["check_jacobian"] = False
+
     # Check if benchmark in options.py should be overridden, and if so,
     # add to options_dictionary
     if args.pbar:

{fitbenchmarking-1.2.0 → fitbenchmarking-1.3.0}/fitbenchmarking/controllers/base_controller.py

@@ -3,6 +3,7 @@ Implements the base class for the fitting software controllers.
 """
 
 from abc import ABCMeta, abstractmethod
+from typing import TYPE_CHECKING
 
 import numpy as np
 from scipy.optimize import curve_fit
@@ -13,9 +14,13 @@ from fitbenchmarking.utils.exceptions import (
     IncompatibleJacobianError,
     IncompatibleMinimizerError,
     IncompatibleProblemError,
+    MissingBoundsError,
     UnknownMinimizerError,
 )
 
+if TYPE_CHECKING:
+    from fitbenchmarking.cost_func.base_cost_func import CostFunc
+
 
 class Controller:
     """
@@ -80,9 +85,10 @@ class Controller:
     #: for the specific software are able to use jacobian
     #: information.
     #:
-    #: - ``jacobian_enabled_solvers``: a list of minimizers in a specific
-    #: software that allow Jacobian information to be passed
-    #: into the fitting algorithm
+    #: - ``jacobian_enabled_solvers``: a list of minimizers in a
+    #:   specific software that allow Jacobian information to
+    #:   be passed into the fitting algorithm
+    #:
     jacobian_enabled_solvers = []
 
     #: Within the controller class, you must define the list
@@ -90,9 +96,10 @@ class Controller:
     #: for the specific software are able to use hessian
     #: information.
     #:
-    #: - ``hessian_enabled_solvers``: a list of minimizers in a specific
-    #: software that allow Hessian information to be passed
-    #: into the fitting algorithm
+    #: - ``hessian_enabled_solvers``: a list of minimizers in a
+    #:   specific software that allow Hessian information to
+    #:   be passed into the fitting algorithm
+    #:
     hessian_enabled_solvers = []
 
     #: Within the controller class, you must define the list
@@ -100,15 +107,29 @@ class Controller:
     #: for the specific software offer support for sparse
     #: jacobians.
     #:
-    #: - ``sparsity_enabled_solvers``: a list of minimizers in a specific
-    #: software that allow sparsity structure to be passed
-    #: into the fitting algorithm
+    #: - ``sparsity_enabled_solvers``: a list of minimizers in a
+    #:   specific software that allow sparsity structure to be
+    #:   passed into the fitting algorithm
+    #:
     sparsity_enabled_solvers = []
 
     #: A name to be used in tables. If this is set to None it will be inferred
     #: from the class name.
     controller_name = None
 
+    #: Used to check whether the fitting software has support for
+    #: bounded problems, set as True if at least some minimizers
+    #: in the fitting software have support for bounds
+    support_for_bounds = False
+
+    #: Used to check whether the selected minimizers is compatible with
+    #: problems that have parameter bounds
+    no_bounds_minimizers = []
+
+    #: Used to check whether the selected minimizer is compatible with
+    #: problems that don't have parameter bounds
+    bounds_required_minimizers = []
+
     #: A list of incompatible problem formats for this controller.
     incompatible_problems = []
 
@@ -124,7 +145,7 @@ class Controller:
         :type cost_func: subclass of
                 :class:`~fitbenchmarking.cost_func.base_cost_func.CostFunc`
         """
-        self.cost_func = cost_func
+        self.cost_func: CostFunc = cost_func
         # Problem: The problem object from parsing
         self.problem = self.cost_func.problem
 
@@ -155,15 +176,6 @@ class Controller:
         # Flag: error handling flag
         self._flag = None
 
-        # Used to check whether the selected minimizers is compatible with
-        # problems that have parameter bounds
-        self.no_bounds_minimizers = []
-
-        # Used to check whether the fitting software has support for
-        # bounded problems, set as True if at least some minimizers
-        # in the fitting software have support for bounds
-        self.support_for_bounds = False
-
         # The timer used to check if the 'max_runtime' is exceeded.
         self.timer = cost_func.problem.timer
 
@@ -178,6 +190,9 @@ class Controller:
         # save number of function evaluations
         self.func_evals = None
 
+        # set default chain length for Bayesian minimizers
+        self.chain_length = 100000
+
     @property
     def flag(self):
         """
@@ -442,16 +457,21 @@ class Controller:
                           options
         :type minimizer: str
         """
-
-        if (
+        if self.value_ranges is not None and (
             self.support_for_bounds is False
             or minimizer in self.no_bounds_minimizers
         ):
-            message = (
+            raise IncompatibleMinimizerError(
                 "The selected minimizer does not currently support "
                 "problems with parameter bounds"
             )
-            raise IncompatibleMinimizerError(message)
+
+        if minimizer in self.bounds_required_minimizers and (
+            self.value_ranges is None or np.any(np.isinf(self.value_ranges))
+        ):
+            raise MissingBoundsError(
+                f"{minimizer} requires finite bounds on all parameters"
+            )
 
     def check_bounds_respected(self):
         """