pyretis.inout.report package¶

This package contains methods for generating reports.

The reports will typically summarise the results from different analysis and present it as a text file, pdf or web-page.

Package structure¶

Modules¶

__init__.py: This file. Handles imports for PyRETIS and defines a method for writing a report to a file.
markup.py (pyretis.inout.report.markup): This module defines some methods for generating simple tables and formatting numbers for rst and latex.
report.py (pyretis.inout.report.report): General methods for generating reports.
report_md.py (pyretis.inout.report.report_md): This module defines the molecular dynamics reports. Specifically it defines the report that is made based on results from a MD Flux simulations.
report_path.py (pyretis.inout.report.report_path): This module defines the reports for path simulations like TIS and RETIS.

Important methods defined here¶

generate_report (generate_report()): Method for generating reports.

Folders¶

templates: A folder containing templates for generating reports.

pyretis.inout.report.markup module¶

Some common functions for generating simple tables and numbers.

This module contains some common functions for the generation of reports. The functions defined here are typically used to format numbers and generate tables for the reports.

Important methods defined here¶

generate_rst_table (generate_rst_table()): Generate reStructuredText for a table.
generate_latex_table (generate_latex_table()): Generate latex code for a table.
latexify_number (latexify_number()): Change exponential notation into something nicer for latex.

pyretis.inout.report.markup.generate_latex_table(table, title, headings, fixnum=None)[source]¶

Generate latex code for a table.

This function will generate latex code for a table. The table is given with a title, headings for the columns and the contents of the table. For latex we might wish to make some numbers more pretty by removing exponential notation: i.e. 1.e-10 can be replaced by 1.0 \times 10^{-10} (which should render like $1.0 \times 10^{-10}$ ).

Parameters:	table (list of lists) – table[i][j] is the contents of column j of row i of the table. title (string) – The header/title for the table. headings (list of strings) – These are the headings for each table column. fixnum (list of integers, optional) – These integers identify the columns where latexify_number is to be applied.

pyretis.inout.report.markup.generate_rst_table(table, title, headings)[source]¶

Generate reStructuredText for a table.

This is a general function to generate a table in reStructuredText. The table is specified with a title, headings for the columns and the contents of the columns and rows.

Parameters:	table (list of lists) – table[i][j] is the contents of column j of row i of the table. title (string) – The header/title for the table. headings (list of strings) – These are the headings for each table column.

pyretis.inout.report.markup.latexify_number(str_float)[source]¶

Change exponential notation into something nicer for latex.

This will change exponential notation, e.g 1.2e-03, into 1.2 \times 10^{-3} for latex output which should be rendered like $1.2 \times 10^{-3}$ .

Parameters:	str_float (string) – This is the string representation of a float.
Returns:	out (string) – A formatted string for latex.

pyretis.inout.report.report module¶

General functions for generating reports.

This module contains some general functions for report generation. These functions are used by the specific report generators to format the reports.

Important methods defined here¶

get_template (get_template()): Returns the template for a specific output format and report type.
render_report (render_report()): Render a report using a template and jinja2.
generate_report (generate_report()): Generate a specific report from analysis output.

pyretis.inout.report.report._rst_to_html(rst)[source]¶

Convert a reStrcuturedText string to simple HTML.

Parameters:	rst (string) – The string to convert.
Returns:	out (string) – A HTML document corresponding to the input reStructuredText.

pyretis.inout.report.report.generate_report(report_type, analysis_results, output, template=None)[source]¶

Generate a report of a given type with the given analysis results.

Parameters:

Parameters:	report_type (string) – Selects the kind of report we want. analysis_results (dict) – The results from running the analysis. output (string) – Output format for the report. template (string, optional) – The full path to the template to use. If not given/found, the defaults in :py:const`._TEMPLATES` will be used. This is handled by `get_template()`.
Returns:	out[0] (string) – This is the generated report in the desired format out[1] (string) – This is an extension which can be used when writing the report to a file.

report_type (string) – Selects the kind of report we want.
analysis_results (dict) – The results from running the analysis.
output (string) – Output format for the report.
template (string, optional) – The full path to the template to use. If not given/found, the defaults in :py:const`._TEMPLATES` will be used. This is handled by get_template().

Returns:

out[0] (string) – This is the generated report in the desired format
out[1] (string) – This is an extension which can be used when writing the report to a file.

pyretis.inout.report.report.get_template(output, report_type, template=None)[source]¶

Return the template to use for a specified output format.

The output is one of the defined output types, for instance ‘rst’ for restructured text or ‘latex’ for latex. Different report types will have different templates and the report types must also be specified here.

Parameters:

Parameters:	output (string) – This string selects the output format for the template, i.e., rst, html, latex, tex. template (string, optional) – The full path to the template to use. If not given/found, the defaults in `_TEMPLATES` will be used. report_type (string) – This is the type of report we are doing, e.g. TIS or MD.
Returns:	out[0] (string) – Filename of template to use. out[1] (string) – The path to the template to use.

output (string) – This string selects the output format for the template, i.e., rst, html, latex, tex.
template (string, optional) – The full path to the template to use. If not given/found, the defaults in _TEMPLATES will be used.
report_type (string) – This is the type of report we are doing, e.g. TIS or MD.

Returns:

out[0] (string) – Filename of template to use.
out[1] (string) – The path to the template to use.

pyretis.inout.report.report.render_report(report, output, template, path)[source]¶

Render a report using a template and jinja2.

The report is given as a dictionary which is used to fill in a template with jinja2. The template is given as a string (a file name) with a path to the template. The output can also be specified here and this is only used to convert to HTML if that is the desired output.

Parameters:

Parameters:	report (dict) – This dict contains the data to be reported. It is assumed that this dict matches the specified template. output (string) – This is the desired output format. Here it’s used only for generating HTML as this is done via rst. template (string) – This is the template to use (the file name). path (string) – This is the template file to use (its full path).
Returns:	out[0] (string) – The generated report in the desired format. out[1] (string) – The file extension (i.e. file type) for the generated report.

report (dict) – This dict contains the data to be reported. It is assumed that this dict matches the specified template.
output (string) – This is the desired output format. Here it’s used only for generating HTML as this is done via rst.
template (string) – This is the template to use (the file name).
path (string) – This is the template file to use (its full path).

Returns:

out[0] (string) – The generated report in the desired format.
out[1] (string) – The file extension (i.e. file type) for the generated report.

Note

The parameters template and path are typically obtained by a call to get_template().

pyretis.inout.report.report_md module¶

Functions for generating reports.

The reports are useful for displaying results from the analysis.

Important methods defined here¶

generate_report_mdflux (generate_report_mdflux()): Generate a report for a MD flux simulation.

pyretis.inout.report.report_md._table_md_efficiency(results, fmt='rst')[source]¶

Generate table with MD-flux results for efficiencies and correlations.

Parameters:

Parameters:	results (dict) – These are the results obtained by `analyse_flux()`. fmt (string, optional) – Determines if we create reStructuredText (‘rst’) or latex (‘tex’).
Returns:	out[0] (list of strings) – These are the rows of the table. out[1] (string) – This is a string in the desired format which represents the table.

results (dict) – These are the results obtained by analyse_flux().
fmt (string, optional) – Determines if we create reStructuredText (‘rst’) or latex (‘tex’).

Returns:

out[0] (list of strings) – These are the rows of the table.
out[1] (string) – This is a string in the desired format which represents the table.

pyretis.inout.report.report_md._table_md_flux(results, fmt='rst')[source]¶

Generate the table for the MD-flux results.

Parameters:

Parameters:	results (dict) – These are the results obtained by `analyse_flux()`. fmt (string, optional) – Determines if we create reStructuredText (‘rst’) or latex (‘tex’).
Returns:	out[0] (list of strings) – These are the rows of the table. out[1] (string) – This is a string in the desired format which represents the table.

results (dict) – These are the results obtained by analyse_flux().
fmt (string, optional) – Determines if we create reStructuredText (‘rst’) or latex (‘tex’).

Returns:

out[0] (list of strings) – These are the rows of the table.
out[1] (string) – This is a string in the desired format which represents the table.

pyretis.inout.report.report_md._table_md_flux_cycles(results, fmt='rst')[source]¶

Generate a table for the MD-flux results for cycle numbers.

The table will display the number of steps in state A, state B, overall state A and B and the total number of MD cycles.

Parameters:

Parameters:	results (dict) – These are the results obtained by `analyse_flux()`. fmt (string, optional) – Determines if we create reStructuredText (‘rst’) or latex (‘tex’).
Returns:	out[0] (list of strings) – These are the rows of the table. out[1] (string) – This is a string in the desired format which represents the table.

results (dict) – These are the results obtained by analyse_flux().
fmt (string, optional) – Determines if we create reStructuredText (‘rst’) or latex (‘tex’).

Returns:

out[0] (list of strings) – These are the rows of the table.
out[1] (string) – This is a string in the desired format which represents the table.

pyretis.inout.report.report_md.generate_report_mdflux(analysis, output='rst')[source]¶

Generate a report for a MD flux simulation.

Parameters:	analysis (dict) – This is the output from the analysis. output (string, optional) – This is the desired output format. It must match one of the formats defined in `pyretis.inout.report.report.__TEMPLATES`. Default is ‘rst’ (reStructuredText).
Returns:	out (dictionary) – The generated report as a string.

pyretis.inout.report.report_path module¶

Method for generating reports from path sampling simulations.

The reports are useful for displaying results from the analysis.

Important methods defined here¶

generate_report_tis (generate_report_tis()): Generate a report for the overall results from a TIS simulation.
generate_report_tis_path (generate_report_tis_path()): Generate a report for a single TIS simulation.
generate_report_retis (generate_report_retis()): Generate a report for the overall results from a RETIS simulation.

pyretis.inout.report.report_path._get_path_figures(figures)[source]¶

Return path figures from a dict of figures.

This method extracts figures from results and makes them available to the report.

Parameters:	figures (dict) – The figures generated by the analysis.
Returns:	path_figures (dict) – A dict which can be used in the report.

pyretis.inout.report.report_path._table_efficiencies(results, fmt='rst')[source]¶

Generate table for efficiencies.

This table will display results for the efficiencies, acceptance ratios and correlation.

Parameters:

Parameters:	results (list of dicts) – The dictionaries are the results obtained from the analysis. fmt (string, optional) – Determines if we create reStructuredText (‘rst’) or latex (‘tex’).
Returns:	out[0] (list of strings) – These are the rows of the table. out[1] (string) – This is a string in reStructuredText format which represents the table.

results (list of dicts) – The dictionaries are the results obtained from the analysis.
fmt (string, optional) – Determines if we create reStructuredText (‘rst’) or latex (‘tex’).

Returns:

out[0] (list of strings) – These are the rows of the table.
out[1] (string) – This is a string in reStructuredText format which represents the table.

pyretis.inout.report.report_path._table_interface(results, fmt='rst')[source]¶

Generate the table for the interfaces.

This table will display the location of the different interfaces.

Parameters:

Parameters:	results (list of dicts) – These are the results of the analysis. fmt (string, optional) – Determines if we create reStructuredText (‘rst’) or latex (‘tex’).
Returns:	out[0] (list of strings) – These are the rows of the table. out[1] (string) – This is a string in the desired format which represents the table.

results (list of dicts) – These are the results of the analysis.
fmt (string, optional) – Determines if we create reStructuredText (‘rst’) or latex (‘tex’).

Returns:

out[0] (list of strings) – These are the rows of the table.
out[1] (string) – This is a string in the desired format which represents the table.

pyretis.inout.report.report_path._table_interface0(results, fmt='rst')[source]¶

Generate the table for the [0^-] ensemble.

This table will display the location of the different interfaces.

Parameters:

Parameters:	results (list of dicts) – These are the results of the analysis. fmt (string, optional) – Determines if we create reStructuredText (‘rst’) or latex (‘tex’).
Returns:	out[0] (list of strings) – These are the rows of the table. out[1] (string) – This is a string in the desired format which represents the table.

results (list of dicts) – These are the results of the analysis.
fmt (string, optional) – Determines if we create reStructuredText (‘rst’) or latex (‘tex’).

Returns:

out[0] (list of strings) – These are the rows of the table.
out[1] (string) – This is a string in the desired format which represents the table.

pyretis.inout.report.report_path._table_interface_repptis(results, fmt='rst')[source]¶

Generate the table for the interfaces.

This table will display the location of the different interfaces.

Parameters:

Parameters:	results (list of dicts) – These are the results of the analysis. fmt (string, optional) – Determines if we create reStructuredText (‘rst’) or latex (‘tex’).
Returns:	out[0] (list of strings) – These are the rows of the table. out[1] (string) – This is a string in the desired format which represents the table.

results (list of dicts) – These are the results of the analysis.
fmt (string, optional) – Determines if we create reStructuredText (‘rst’) or latex (‘tex’).

Returns:

out[0] (list of strings) – These are the rows of the table.
out[1] (string) – This is a string in the desired format which represents the table.

pyretis.inout.report.report_path._table_probability(results, fmt='rst')[source]¶

Generate the table for the probabilities.

This table will display the crossing probabilities with uncertainties.

Parameters:

Parameters:	results (list of dicts) – The dictionaries are the results obtained from the analysis. fmt (string, optional) – Determines if we create reStructuredText (‘rst’) or latex (‘tex’).
Returns:	out[0] (list of strings) – These are the rows of the table. out[1] (string) – This is a string in reStructuredText format which represents the table.

results (list of dicts) – The dictionaries are the results obtained from the analysis.
fmt (string, optional) – Determines if we create reStructuredText (‘rst’) or latex (‘tex’).

Returns:

out[0] (list of strings) – These are the rows of the table.
out[1] (string) – This is a string in reStructuredText format which represents the table.

pyretis.inout.report.report_path._table_probability_repptis(results, fmt='rst')[source]¶

Generate the table for the probabilities.

This table will display the crossing probabilities with uncertainties.

Parameters:

Parameters:	results (list of dicts) – The dictionaries are the results obtained from the analysis. fmt (string, optional) – Determines if we create reStructuredText (‘rst’) or latex (‘tex’).
Returns:	out[0] (list of strings) – These are the rows of the table. out[1] (string) – This is a string in reStructuredText format which represents the table.

results (list of dicts) – The dictionaries are the results obtained from the analysis.
fmt (string, optional) – Determines if we create reStructuredText (‘rst’) or latex (‘tex’).

Returns:

out[0] (list of strings) – These are the rows of the table.
out[1] (string) – This is a string in reStructuredText format which represents the table.

pyretis.inout.report.report_path._table_summary(report, fmt='rst')[source]¶

Generate table with summary of main results.

This table will display results for the crossing probability, the initial flux and rate constant.

Parameters:

Parameters:	report (dict) – Dict with current report. We use the information in this dictionary to generate the table. fmt (string, optional) – Determines if we create reStructuredText (‘rst’) or latex (‘tex’).
Returns:	out[0] (list of strings) – These are the rows of the table. out[1] (string) – This is a string in reStructuredText format which represents the table.

report (dict) – Dict with current report. We use the information in this dictionary to generate the table.
fmt (string, optional) – Determines if we create reStructuredText (‘rst’) or latex (‘tex’).

Returns:

out[0] (list of strings) – These are the rows of the table.
out[1] (string) – This is a string in reStructuredText format which represents the table.

pyretis.inout.report.report_path.generate_report_retis(analysis, output='rst')[source]¶

Generate a report for the over-all results from a RETIS simulation.

Parameters:

Parameters:	analysis (dict) – This is the output from the analysis. output (string, optional) – This is the desired output format. It must match one of the formats defined in `pyretis.inout.report.report._TEMPLATES`. Default is ‘rst’ (reStructuredText).
Returns:	out[0] (string) – The generated report in the desired format. out[1] (string) – The file extension (i.e. file type) for the generated report.

analysis (dict) – This is the output from the analysis.
output (string, optional) – This is the desired output format. It must match one of the formats defined in pyretis.inout.report.report._TEMPLATES. Default is ‘rst’ (reStructuredText).

Returns:

out[0] (string) – The generated report in the desired format.
out[1] (string) – The file extension (i.e. file type) for the generated report.

pyretis.inout.report.report_path.generate_report_tis(analysis, output='rst')[source]¶

Generate a report for the over-all results from a TIS simulation.

Parameters:

Parameters:	analysis (dict) – This is the output from the analysis. output (string, optional) – This is the desired output format. It must match one of the formats defined in `pyretis.inout.report.report._TEMPLATES`. Default is ‘rst’ (reStructuredText).
Returns:	out[0] (string) – The generated report in the desired format. out[1] (string) – The file extension (i.e. file type) for the generated report.

analysis (dict) – This is the output from the analysis.
output (string, optional) – This is the desired output format. It must match one of the formats defined in pyretis.inout.report.report._TEMPLATES. Default is ‘rst’ (reStructuredText).

Returns:

out[0] (string) – The generated report in the desired format.
out[1] (string) – The file extension (i.e. file type) for the generated report.

pyretis.inout.report.report_path.generate_report_tis_path(analysis, output='rst')[source]¶

Generate a report for a single TIS simulation.

Parameters:

Parameters:	analysis (dict) – This is the output from the analysis. output (string, optional) – This is the desired output format. It must match one of the formats defined in `pyretis.inout.report.report._TEMPLATES`. Default is ‘rst’ (reStructuredText).
Returns:	out[0] (string) – The generated report in the desired format. out[1] (string) – The file extension (i.e. file type) for the generated report.

analysis (dict) – This is the output from the analysis.
output (string, optional) – This is the desired output format. It must match one of the formats defined in pyretis.inout.report.report._TEMPLATES. Default is ‘rst’ (reStructuredText).

Returns:

out[0] (string) – The generated report in the desired format.
out[1] (string) – The file extension (i.e. file type) for the generated report.