FitBenchmarking 1.4.0__tar.gz → 1.6.0__tar.gz

{fitbenchmarking-1.4.0 → fitbenchmarking-1.6.0}/.gitignore

@@ -14,4 +14,5 @@ docs/source/contributors/module_index
 .vscode/
 .eggs/
 *.out
+*.diff
 powermetrics_log.txt

{fitbenchmarking-1.4.0 → fitbenchmarking-1.6.0}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.4
+Metadata-Version: 2.5
 Name: FitBenchmarking
-Version: 1.4.0
+Version: 1.6.0
 Summary: FitBenchmarking: A tool for comparing fitting software
 Project-URL: Homepage, https://fitbenchmarking.github.io
 Project-URL: Documentation, https://fitbenchmarking.readthedocs.io/en/stable
@@ -13,21 +13,24 @@ 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: >=3.10.1
-Requires-Dist: codecarbon<2.7,>=2.5.1
+Requires-Python: >=3.11
+Requires-Dist: codecarbon>=3.2.6
 Requires-Dist: configparser
 Requires-Dist: dash
+Requires-Dist: dash-bootstrap-components
 Requires-Dist: docutils
 Requires-Dist: jinja2
 Requires-Dist: lxml
 Requires-Dist: matplotlib>=2.0
 Requires-Dist: numpy
 Requires-Dist: pandas>=1.3
-Requires-Dist: plotly>=6.6.0
-Requires-Dist: scipy<1.16.0,>=0.18
+Requires-Dist: plotly>=7.0.0
+Requires-Dist: scipy>=1.16
 Requires-Dist: tqdm>=4.60
+Provides-Extra: aoclda
+Requires-Dist: aoclda; (platform_system == 'Linux') and extra == 'aoclda'
 Provides-Extra: bumps
-Requires-Dist: bumps<1.0.0; extra == 'bumps'
+Requires-Dist: bumps; extra == 'bumps'
 Provides-Extra: dev
 Requires-Dist: coverage[toml]>=6.3; extra == 'dev'
 Requires-Dist: coveralls; extra == 'dev'
@@ -46,6 +49,8 @@ Provides-Extra: gofit
 Requires-Dist: gofit; extra == 'gofit'
 Provides-Extra: gradient-free
 Requires-Dist: gradient-free-optimizers[sklearn]; extra == 'gradient-free'
+Provides-Extra: gvar
+Requires-Dist: gvar; extra == 'gvar'
 Provides-Extra: hogben
 Requires-Dist: hogben; extra == 'hogben'
 Provides-Extra: levmar
@@ -53,9 +58,6 @@ Requires-Dist: levmar; extra == 'levmar'
 Provides-Extra: lmfit
 Requires-Dist: emcee>=3.1.0; extra == 'lmfit'
 Requires-Dist: lmfit; extra == 'lmfit'
-Provides-Extra: mantid
-Requires-Dist: h5py<3,>=2.10.0; extra == 'mantid'
-Requires-Dist: pyyaml>=5.4.1; extra == 'mantid'
 Provides-Extra: matlab
 Requires-Dist: dill; extra == 'matlab'
 Provides-Extra: minuit
@@ -67,14 +69,14 @@ Requires-Dist: numdifftools; extra == 'numdifftools'
 Provides-Extra: paramonte
 Requires-Dist: paramonte; extra == 'paramonte'
 Provides-Extra: sas
-Requires-Dist: sasmodels; extra == 'sas'
+Requires-Dist: sasmodels==1.0.12; 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%3Av1.4.0)
-[![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)
+[![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%3Av1.6.0)
+[![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%3Av1.6.0)
 [![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/v1.4.0?style=flat-square)](https://fitbenchmarking.readthedocs.io/en/v1.4.0)
+[![Documentation Status](https://img.shields.io/readthedocs/fitbenchmarking/v1.6.0?style=flat-square)](https://fitbenchmarking.readthedocs.io/en/v1.6.0)
 [![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.15546207-blue.svg?style=flat-square)](https://zenodo.org/records/15546207)
@@ -83,10 +85,11 @@ Description-Content-Type: text/markdown
 
 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/v1.4.0/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
+- [Installation Instructions](https://fitbenchmarking.readthedocs.io/en/v1.6.0)
+ > **Note:** Please ensure that you are using the latest version of FitBenchmarking in order to stay up to date with security fixes.
+- [User Documentation & Example Usage](https://fitbenchmarking.readthedocs.io/en/v1.6.0)
+- [Community Guidelines](https://fitbenchmarking.readthedocs.io/en/v1.6.0)
+- Automated Tests are [run via GitHub Actions](https://github.com/fitbenchmarking/fitbenchmarking/actions), please see [our documentation](https://fitbenchmarking.readthedocs.io/en/v1.6.0) for more information.
 
 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-1.4.0 → fitbenchmarking-1.6.0}/README.md

@@ -1,7 +1,7 @@
-[![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)
+[![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%3Av1.6.0)
+[![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%3Av1.6.0)
 [![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/v1.4.0?style=flat-square)](https://fitbenchmarking.readthedocs.io/en/v1.4.0)
+[![Documentation Status](https://img.shields.io/readthedocs/fitbenchmarking/v1.6.0?style=flat-square)](https://fitbenchmarking.readthedocs.io/en/v1.6.0)
 [![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.15546207-blue.svg?style=flat-square)](https://zenodo.org/records/15546207)
@@ -10,10 +10,11 @@
 
 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/v1.4.0/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
+- [Installation Instructions](https://fitbenchmarking.readthedocs.io/en/v1.6.0)
+ > **Note:** Please ensure that you are using the latest version of FitBenchmarking in order to stay up to date with security fixes.
+- [User Documentation & Example Usage](https://fitbenchmarking.readthedocs.io/en/v1.6.0)
+- [Community Guidelines](https://fitbenchmarking.readthedocs.io/en/v1.6.0)
+- Automated Tests are [run via GitHub Actions](https://github.com/fitbenchmarking/fitbenchmarking/actions), please see [our documentation](https://fitbenchmarking.readthedocs.io/en/v1.6.0) for more information.
 
 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-1.4.0 → fitbenchmarking-1.6.0}/fitbenchmarking/cli/checkpoint_handler.py

@@ -20,8 +20,11 @@ from fitbenchmarking.core.results_output import (
     save_results,
 )
 from fitbenchmarking.utils.checkpoint import Checkpoint
+from fitbenchmarking.utils.log import get_logger
 from fitbenchmarking.utils.options import find_options_file
 
+LOGGER = get_logger()
+
 
 def get_parser() -> ArgumentParser:
     """
@@ -188,7 +191,17 @@ def generate_report(options_file="", additional_options=None, debug=False):
         all_dirs.append(directory)
 
     index_page = create_index_page(options, list(results), all_dirs)
-    open_browser(index_page, options, pp_dfs_all_prob_sets)
+
+    # flatten results dictionary because open_browser expects a list of
+    # fitting results
+
+    flat_results = [
+        result for result_list in results.values() for result in result_list
+    ]
+
+    open_browser(
+        index_page, options, pp_dfs_all_prob_sets, results=flat_results
+    )
 
 
 @exception_handler
@@ -270,19 +283,20 @@ def merge_data_sets(
     :param debug: Enable debugging output.
     :type debug: bool
     """
+
     if len(files) < 2:
         return
 
-    print(f"Loading {files[0]}...")
+    LOGGER.info("Loading %s...", files[0])
     with open(files[0], encoding="utf-8") as f:
         A = json.load(f)
     for to_merge in files[1:]:
-        print(f"Merging {to_merge}...")
+        LOGGER.info("Merging %s...", to_merge)
         with open(to_merge, encoding="utf-8") as f:
             B = json.load(f)
         A = merge(A, B, strategy=strategy)
 
-    print(f"Writing to {output}...")
+    LOGGER.info("Writing to %s...", output)
     with open(output, "w", encoding="utf-8") as f:
         json.dump(A, f, indent=2)
 

{fitbenchmarking-1.4.0 → fitbenchmarking-1.6.0}/fitbenchmarking/cli/exception_handler.py

@@ -35,7 +35,7 @@ def exception_handler(f):
             if debug:
                 raise
 
-            LOGGER.error(str(e))
+            LOGGER.error(e, exc_info=debug)
             sys.exit(1)
 
         except Exception as e:
@@ -43,7 +43,7 @@ def exception_handler(f):
             if debug:
                 raise
 
-            LOGGER.error(str(e))
+            LOGGER.error(e, exc_info=debug)
             sys.exit(1)
 
     return wrapped

{fitbenchmarking-1.4.0 → fitbenchmarking-1.6.0}/fitbenchmarking/cli/main.py

@@ -366,6 +366,80 @@ of the Fitbenchmarking docs. """
     return parser
 
 
+def parse_options_from_cli(args: argparse.Namespace) -> dict:
+    """
+    parse the command line options, and apply any options which should override
+    the options file or default options.
+    :param args: The command line arguments.
+    :type args: argparse.Namespace
+
+    :return: A dictionary of options to be used in the benchmarking run.
+    :rtype: dict
+    """
+
+    # Dictionary of options which can be set via argparse
+    # rather than from an ini file or from the default options
+    options_dictionary = {
+        "results_dir": args.results_dir,
+        "num_runs": args.num_runs,
+        "algorithm_type": args.algorithm_type,
+        "software": args.software,
+        "jac_method": args.jac_method,
+        "cost_func_type": args.cost_func_type,
+        "comparison_mode": args.comparison_mode,
+        "table_type": args.table_type,
+        "file_name": args.logging_file_name,
+        "level": args.level,
+        "external_output": args.external_output,
+        "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,
+    # add to options_dictionary
+    if args.make_plots:
+        options_dictionary["make_plots"] = True
+    elif args.dont_make_plots:
+        options_dictionary["make_plots"] = False
+
+    # Check if results_browser in options.py should be overridden, and if so,
+    # add to options_dictionary
+    if args.results_browser:
+        options_dictionary["results_browser"] = True
+    elif args.no_results_browser:
+        options_dictionary["results_browser"] = False
+
+    # Check if run_dash in options.py should be overridden, and if so,
+    # add to options_dictionary
+    if args.run_dash:
+        options_dictionary["run_dash"] = True
+    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:
+        options_dictionary["pbar"] = True
+    elif args.no_pbar:
+        options_dictionary["pbar"] = False
+
+    # Check if log_append in options.py should be overridden, and if so,
+    # add to options_dictionary
+    if args.append_log:
+        options_dictionary["append"] = True
+    elif args.overwrite_log:
+        options_dictionary["append"] = False
+    return options_dictionary
+
+
 @exception_handler
 def run(problem_sets, additional_options=None, options_file="", debug=False):
     """
@@ -410,7 +484,7 @@ def run(problem_sets, additional_options=None, options_file="", debug=False):
     result_dir = []
     pp_dfs_all_prob_sets = {}
     cp = Checkpoint(options=options)
-
+    results = {}
     try:
         for sub_dir in problem_sets:
             # Create full path for the directory that holds a group of
@@ -510,9 +584,8 @@ def run(problem_sets, additional_options=None, options_file="", debug=False):
             "You can also set 'results_dir' in an options file.",
             options.results_dir,
         )
-
     index_page = create_index_page(options, group_labels, result_dir)
-    open_browser(index_page, options, pp_dfs_all_prob_sets)
+    open_browser(index_page, options, pp_dfs_all_prob_sets, results=results)
 
 
 def main():
@@ -524,84 +597,25 @@ def main():
 
     if len(sys.argv) == 1:
         if not args.problem_sets[0].exists():
-            print(
+            LOGGER.error(
                 "The default problem set has either been "
                 "deleted or moved. Please specify a file "
                 "path to a different problem set with the "
                 "-p option."
             )
             sys.exit(1)
-        print(
+        LOGGER.info(
             "Running NIST average_difficulty problem set "
             "with scipy minimizers \n"
         )
 
-    # Dictionary of options which can be set via argparse
-    # rather than from an ini file or from the default options
-    options_dictionary = {
-        "results_dir": args.results_dir,
-        "num_runs": args.num_runs,
-        "algorithm_type": args.algorithm_type,
-        "software": args.software,
-        "jac_method": args.jac_method,
-        "cost_func_type": args.cost_func_type,
-        "comparison_mode": args.comparison_mode,
-        "table_type": args.table_type,
-        "file_name": args.logging_file_name,
-        "level": args.level,
-        "external_output": args.external_output,
-        "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,
-    # add to options_dictionary
-    if args.make_plots:
-        options_dictionary["make_plots"] = True
-    elif args.dont_make_plots:
-        options_dictionary["make_plots"] = False
-
-    # Check if results_browser in options.py should be overridden, and if so,
-    # add to options_dictionary
-    if args.results_browser:
-        options_dictionary["results_browser"] = True
-    elif args.no_results_browser:
-        options_dictionary["results_browser"] = False
-
-    # Check if run_dash in options.py should be overridden, and if so,
-    # add to options_dictionary
-    if args.run_dash:
-        options_dictionary["run_dash"] = True
-    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:
-        options_dictionary["pbar"] = True
-    elif args.no_pbar:
-        options_dictionary["pbar"] = False
-
-    # Check if log_append in options.py should be overridden, and if so,
-    # add to options_dictionary
-    if args.append_log:
-        options_dictionary["append"] = True
-    elif args.overwrite_log:
-        options_dictionary["append"] = False
+    options_dictionary = parse_options_from_cli(args)
 
     if args.load_checkpoint:
         generate_report(
             options_file=args.options_file,
             additional_options=options_dictionary,
+            debug=args.debug_mode,
         )
     else:
         run(