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205 improve documentation on entry points #225

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merged 13 commits into from
Oct 10, 2019
Merged

205 improve documentation on entry points #225

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8465943
Fix indentation linting complaints
AndrewLister-STFC Sep 11, 2019
7108555
Re-insert API functions as I missed the useage in expert example
AndrewLister-STFC Sep 12, 2019
95b4240
Insert fitbenchmarking path into mantid script as crashes
AndrewLister-STFC Sep 12, 2019
ed921d1
Issue #205: Readability of code improvements and docstrings updated
AndrewLister-STFC Sep 12, 2019
b745846
Merge branch 'master' into 205_improve_documentation_on_entry_points
AndrewLister-STFC Sep 12, 2019
b98886f
Issue #205: Further tidy up of example scripts as discussed in workshop
AndrewLister-STFC Sep 17, 2019
d7987e5
Issue #205: Remove concept of blocks in problem_groups.
AndrewLister-STFC Sep 17, 2019
10ca91a
Issue #205: Fix comments from review
AndrewLister-STFC Sep 18, 2019
40e51e6
Merge branch 'master' into 205_improve_documentation_on_entry_points
Anders-Markvardsen Sep 23, 2019
3a5fda0
Merge branch 'master' into 205_improve_documentation_on_entry_points
AndrewLister-STFC Sep 26, 2019
efc959d
Merge branch 'master' into 205_improve_documentation_on_entry_points
Anders-Markvardsen Oct 9, 2019
dec6855
remove mention of "blocks" from comment
AndrewLister-STFC Oct 10, 2019
f54747a
Issue #205: Remove unneccesary function
AndrewLister-STFC Oct 10, 2019
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33 changes: 19 additions & 14 deletions example_scripts/example_runScripts.py
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -9,8 +9,8 @@
import sys
import glob

from fitbenchmarking.fitting_benchmarking import do_fitting_benchmark as fitBenchmarking
from fitbenchmarking.results_output import save_results_tables as printTables
from fitbenchmarking.fitting_benchmarking import fitbenchmark_group
from fitbenchmarking.results_output import save_results_tables


def main(args):
Expand Down Expand Up @@ -56,10 +56,10 @@ def main(args):
# e.g. lower that 1.1 -> light yellow, higher than 3 -> dark red
# Change these values to suit your needs
color_scale = [(1.1, 'ranking-top-1'),
(1.33, 'ranking-top-2'),
(1.75, 'ranking-med-3'),
(3, 'ranking-low-4'),
(float('nan'), 'ranking-low-5')]
(1.33, 'ranking-top-2'),
(1.75, 'ranking-med-3'),
(3, 'ranking-low-4'),
(float('nan'), 'ranking-low-5')]

# ADD WHICH PROBLEM SETS TO TEST AGAINST HERE
# Do this, in this example file, by selecting sub-folders in benchmark_probs_dir
Expand All @@ -82,16 +82,21 @@ def main(args):
continue

print('\nRunning the benchmarking on the {} problem set\n'.format(label))
results_per_group, results_dir = fitBenchmarking(group_name=label, software_options=software_options,
data_dir=data_dir,
use_errors=use_errors, results_dir=results_dir)
results, results_dir = \
fitbenchmark_group(group_name=label,
software_options=software_options,
data_dir=data_dir,
use_errors=use_errors,
results_dir=results_dir)

print('\nProducing output for the {} problem set\n'.format(label))
for _, group_results in enumerate(results_per_group):
# Display the runtime and accuracy results in a table
printTables(software_options, group_results,
group_name=label, use_errors=use_errors,
color_scale=color_scale, results_dir=results_dir)
# Display the runtime and accuracy results in a table
save_results_tables(software_options=software_options,
results_per_test=results,
group_name=label,
use_errors=use_errors,
color_scale=color_scale,
results_dir=results_dir)

print('\nCompleted benchmarking for {} problem set\n'.format(sub_dir))

Expand Down
25 changes: 15 additions & 10 deletions example_scripts/example_runScripts_SasView.py
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Original file line number Diff line number Diff line change
Expand Up @@ -34,8 +34,8 @@
'******************************************')
sys.exit()

from fitbenchmarking.fitting_benchmarking import do_fitting_benchmark as fitBenchmarking
from fitbenchmarking.results_output import save_results_tables as printTables
from fitbenchmarking.fitting_benchmarking import fitbenchmark_group
from fitbenchmarking.results_output import save_results_tables

# SPECIFY THE SOFTWARE/PACKAGE CONTAINING THE MINIMIZERS YOU WANT TO BENCHMARK
software = ['sasview']
Expand Down Expand Up @@ -100,15 +100,20 @@
data_dir = os.path.join(benchmark_probs_dir, sub_dir)

print('\nRunning the benchmarking on the {} problem set\n'.format(label))
results_per_group, results_dir = fitBenchmarking(group_name=label, software_options=software_options,
data_dir=data_dir,
use_errors=use_errors, results_dir=results_dir)
results, results_dir = fitbenchmark_group(group_name=label,
software_options=software_options,
data_dir=data_dir,
use_errors=use_errors,
results_dir=results_dir)

print('\nProducing output for the {} problem set\n'.format(label))
for idx, group_results in enumerate(results_per_group):
# Display the runtime and accuracy results in a table
printTables(software_options, group_results,
group_name=label, use_errors=use_errors,
color_scale=color_scale, results_dir=results_dir)

# Display the runtime and accuracy results in a table
save_results_tables(software_options=software_options,
results_per_test=results,
group_name=label,
use_errors=use_errors,
color_scale=color_scale,
results_dir=results_dir)

print('\nCompleted benchmarking for {} problem set\n'.format(sub_dir))
47 changes: 24 additions & 23 deletions example_scripts/example_runScripts_expert.py
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Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,7 @@
import sys
import glob

from fitbenchmarking.fitting_benchmarking import do_benchmarking
from fitbenchmarking.fitting_benchmarking import _benchmark
from fitbenchmarking.utils import misc
from fitbenchmarking.utils import create_dirs
from fitbenchmarking.results_output import save_tables, generate_tables, \
Expand Down Expand Up @@ -90,10 +90,11 @@ def main(argv):
# Processes software_options dictionary into Fitbenchmarking format
minimizers, software = misc.get_minimizers(software_options)

# Sets up the problem groups specified by the user by providing
# Sets up the problem group specified by the user by providing
# a respective data directory.
problem_groups = misc.setup_fitting_problems(data_dir, group_name)
problem_group = misc.setup_fitting_problems(data_dir)

# Create output dirs
results_dir = create_dirs.results(results_dir)
group_results_dir = create_dirs.group_results(results_dir, group_name)

Expand All @@ -102,35 +103,35 @@ def main(argv):
group_results_dir, use_errors)

# Loops through group of problems and benchmark them
prob_results = do_benchmarking(user_input, problem_groups, group_name)
prob_results = _benchmark(user_input, problem_group)

print('\nProducing output for the {} problem set\n'.format(group_name))
for idx, group_results in enumerate(prob_results):
# Creates the results directory where the tables are located
tables_dir = create_dirs.restables_dir(results_dir, group_name)

if isinstance(software, list):
minimizers = sum(minimizers, [])
# Creates the results directory where the tables are located
tables_dir = create_dirs.restables_dir(results_dir, group_name)

# Creates the problem names with links to the visual display pages
# in rst
linked_problems = visual_pages.create_linked_probs(group_results,
group_name, results_dir)
if isinstance(software, list):
minimizers = sum(minimizers, [])

# Generates accuracy and runtime normalised tables and summary tables
norm_acc_rankings, norm_runtimes, sum_cells_acc, sum_cells_runtime = generate_tables(group_results, minimizers)
# Creates the problem names with links to the visual display pages
# in rst
linked_problems = visual_pages.create_linked_probs(prob_results,
group_name, results_dir)

# Creates an accuracy table
acc_tbl = create_acc_tbl(minimizers, linked_problems, norm_acc_rankings, use_errors, color_scale)
# Generates accuracy and runtime tables and summary tables
acc_rankings, runtimes, sum_cells_acc, sum_cells_runtime = generate_tables(prob_results, minimizers)

# Creates an runtime table
runtime_tbl = create_runtime_tbl(minimizers, linked_problems, norm_runtimes, use_errors, color_scale)
# Creates an accuracy table
acc_tbl = create_acc_tbl(minimizers, linked_problems, acc_rankings, use_errors, color_scale)

# Saves accuracy minimizer results
save_tables(tables_dir, acc_tbl, use_errors, group_name, 'acc')
# Creates an runtime table
runtime_tbl = create_runtime_tbl(minimizers, linked_problems, runtimes, use_errors, color_scale)

# Saves runtime minimizer results
save_tables(tables_dir, runtime_tbl, use_errors, group_name, 'runtime')
# Saves accuracy minimizer results
save_tables(tables_dir, acc_tbl, use_errors, group_name, 'acc')

# Saves runtime minimizer results
save_tables(tables_dir, runtime_tbl, use_errors, group_name, 'runtime')

print('\nCompleted benchmarking for {} problem set\n'.format(sub_dir))

Expand Down
39 changes: 22 additions & 17 deletions example_scripts/example_runScripts_mantid.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -14,16 +14,16 @@

try:
import mantid.simpleapi as msapi
except:
except ImportError:
print('******************************************\n'
'Mantid is not yet installed on your computer\n'
'To install, go to the directory where setup.py is located and simply type:\n'
'python setup.py install externals -s mantid\n'
'******************************************')
sys.exit()

from fitbenchmarking.fitting_benchmarking import do_fitting_benchmark as fitBenchmarking
from fitbenchmarking.results_output import save_results_tables as printTables
from fitbenchmarking.fitting_benchmarking import fitbenchmark_group
from fitbenchmarking.results_output import save_results_tables


def main(argv):
Expand All @@ -33,7 +33,7 @@ def main(argv):

# User defined minimizers
custom_minimizers = {"mantid": ["Levenberg-Marquardt"],
"scipy": ["lm", "trf", "dogbox"]}
"scipy": ["lm", "trf", "dogbox"]}
# custom_minimizers = None

# SPECIFY THE MINIMIZERS YOU WANT TO BENCHMARK, AND AS A MINIMUM FOR THE SOFTWARE YOU SPECIFIED ABOVE
Expand All @@ -53,7 +53,7 @@ def main(argv):
# Benchmark problem directories
fitbenchmarking_folder = os.path.abspath(os.path.join(current_path, os.pardir))
benchmark_probs_dir = os.path.join(fitbenchmarking_folder,
'benchmark_problems')
'benchmark_problems')

"""
Modify results_dir to specify where the results of the fit should be saved
Expand All @@ -69,10 +69,10 @@ def main(argv):
# e.g. lower that 1.1 -> light yellow, higher than 3 -> dark red
# Change these values to suit your needs
color_scale = [(1.1, 'ranking-top-1'),
(1.33, 'ranking-top-2'),
(1.75, 'ranking-med-3'),
(3, 'ranking-low-4'),
(float('nan'), 'ranking-low-5')]
(1.33, 'ranking-top-2'),
(1.75, 'ranking-med-3'),
(3, 'ranking-low-4'),
(float('nan'), 'ranking-low-5')]

# ADD WHICH PROBLEM SETS TO TEST AGAINST HERE
# Do this, in this example file, by selecting sub-folders in benchmark_probs_dir
Expand All @@ -93,16 +93,21 @@ def main(argv):
continue

print('\nRunning the benchmarking on the {} problem set\n'.format(label))
results_per_group, results_dir = fitBenchmarking(group_name=label, software_options=software_options,
data_dir=data_dir,
use_errors=use_errors, results_dir=results_dir)
results, results_dir = fitbenchmark_group(group_name=label,
software_options=software_options,
data_dir=data_dir,
use_errors=use_errors,
results_dir=results_dir)

print('\nProducing output for the {} problem set\n'.format(label))
for idx, group_results in enumerate(results_per_group):
# Display the runtime and accuracy results in a table
printTables(software_options, group_results,
group_name=label, use_errors=use_errors,
color_scale=color_scale, results_dir=results_dir)

# Display the runtime and accuracy results in a table
save_results_tables(software_options=software_options,
results_per_test=results,
group_name=label,
use_errors=use_errors,
color_scale=color_scale,
results_dir=results_dir)

print('\nCompleted benchmarking for {} problem set\n'.format(sub_dir))

Expand Down
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