From 622a0a4ed374bac0260b072026171b53a62c0c67 Mon Sep 17 00:00:00 2001 From: biosimulatorsdaemon Date: Wed, 18 Aug 2021 05:08:24 +0000 Subject: [PATCH] Updating compiled documentation --- docs/_static/documentation_options.js | 2 +- docs/about.html | 2 +- docs/genindex.html | 16 +++- docs/index.html | 2 +- docs/installation.html | 2 +- docs/py-modindex.html | 2 +- docs/search.html | 2 +- docs/searchindex.js | 2 +- docs/source/biosimulators_xpp.html | 108 +++++++++++++++++++++----- docs/tutorial.html | 8 +- 10 files changed, 113 insertions(+), 33 deletions(-) diff --git a/docs/_static/documentation_options.js b/docs/_static/documentation_options.js index 6e1f597..110c119 100644 --- a/docs/_static/documentation_options.js +++ b/docs/_static/documentation_options.js @@ -1,6 +1,6 @@ var DOCUMENTATION_OPTIONS = { URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'), - VERSION: '0.0.1', + VERSION: '0.0.2', LANGUAGE: 'en', COLLAPSE_INDEX: false, BUILDER: 'html', diff --git a/docs/about.html b/docs/about.html index e5485e4..27ce335 100644 --- a/docs/about.html +++ b/docs/about.html @@ -5,7 +5,7 @@ - About BioSimulators-XPP — BioSimulators-XPP 0.0.1 documentation + About BioSimulators-XPP — BioSimulators-XPP 0.0.2 documentation diff --git a/docs/genindex.html b/docs/genindex.html index 855ff21..8495723 100644 --- a/docs/genindex.html +++ b/docs/genindex.html @@ -5,7 +5,7 @@ - Index — BioSimulators-XPP 0.0.1 documentation + Index — BioSimulators-XPP 0.0.2 documentation @@ -160,12 +160,20 @@

B

E

@@ -180,7 +188,7 @@

G

diff --git a/docs/index.html b/docs/index.html index 061dbba..85ffe7f 100644 --- a/docs/index.html +++ b/docs/index.html @@ -5,7 +5,7 @@ - BioSimulators-XPP documentation — BioSimulators-XPP 0.0.1 documentation + BioSimulators-XPP documentation — BioSimulators-XPP 0.0.2 documentation diff --git a/docs/installation.html b/docs/installation.html index 9b41846..aa9778c 100644 --- a/docs/installation.html +++ b/docs/installation.html @@ -5,7 +5,7 @@ - Installation instructions — BioSimulators-XPP 0.0.1 documentation + Installation instructions — BioSimulators-XPP 0.0.2 documentation diff --git a/docs/py-modindex.html b/docs/py-modindex.html index 3d11e4a..ab5c83e 100644 --- a/docs/py-modindex.html +++ b/docs/py-modindex.html @@ -5,7 +5,7 @@ - Python Module Index — BioSimulators-XPP 0.0.1 documentation + Python Module Index — BioSimulators-XPP 0.0.2 documentation diff --git a/docs/search.html b/docs/search.html index dd8e257..0c98e40 100644 --- a/docs/search.html +++ b/docs/search.html @@ -5,7 +5,7 @@ - Search — BioSimulators-XPP 0.0.1 documentation + Search — BioSimulators-XPP 0.0.2 documentation diff --git a/docs/searchindex.js b/docs/searchindex.js index 906ff25..327990e 100644 --- a/docs/searchindex.js +++ b/docs/searchindex.js @@ -1 +1 @@ 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Quick search

biosimulators_xpp package

+
+
+biosimulators_xpp.exec_sed_task(task, variables, log=None)[source]
+

Execute a task and save its results

+
+
Parameters
+
    +

  • task (Task) – task

    • +

  • variables (list of Variable) – variables that should be recorded

    • +

  • log (TaskLog, optional) – log for the task

    • +
+
+
Returns
+

VariableResults: results of variables +TaskLog: log

+
+
Return type
+

tuple

+
+
Raises
+

NotImplementedError –

    +

  • Task requires a time course that XPP doesn’t support + * Task requires an algorithm that XPP doesn’t support

    • +
+

+
+
+
+ +
+
+biosimulators_xpp.exec_sedml_docs_in_combine_archive(archive_filename, out_dir, return_results=False, report_formats=None, plot_formats=None, bundle_outputs=None, keep_individual_outputs=None, raise_exceptions=True)[source]
+

Execute the SED tasks defined in a COMBINE/OMEX archive and save the outputs

+
+
Parameters
+
    +

  • archive_filename (str) – path to COMBINE/OMEX archive

    • +

  • out_dir (str) –

    path to store the outputs of the archive

    +
      +

    • CSV: directory in which to save outputs to files +{ out_dir }/{ relative-path-to-SED-ML-file-within-archive }/{ report.id }.csv

      • +

    • HDF5: directory in which to save a single HDF5 file ({ out_dir }/reports.h5), +with reports at keys { relative-path-to-SED-ML-file-within-archive }/{ report.id } within the HDF5 file

      • +
    +

    • +

  • return_results (bool, optional) – whether to return the result of each output of each SED-ML file

    • +

  • report_formats (list of ReportFormat, optional) – report format (e.g., csv or h5)

    • +

  • plot_formats (list of VizFormat, optional) – report format (e.g., pdf)

    • +

  • bundle_outputs (bool, optional) – if True, bundle outputs into archives for reports and plots

    • +

  • keep_individual_outputs (bool, optional) – if True, keep individual output files

    • +

  • raise_exceptions (bool, optional) – whether to raise exceptions

    • +
+
+
Returns
+

    +

  • SedDocumentResults: results

    • +

  • CombineArchiveLog: log

    • +
+

+
+
Return type
+

tuple

+
+
+
+ +
+
+biosimulators_xpp.get_simulator_version()[source]
+

Get the installed version of XPP

+
+
Returns
+

version

+
+
Return type
+

str

+
+
+
+

Submodules

@@ -162,7 +242,7 @@

Submodules
-biosimulators_xpp.core.exec_sedml_docs_in_combine_archive(archive_filename, out_dir, report_formats=None, plot_formats=None, bundle_outputs=None, keep_individual_outputs=None)[source]
+biosimulators_xpp.core.exec_sedml_docs_in_combine_archive(archive_filename, out_dir, return_results=False, report_formats=None, plot_formats=None, bundle_outputs=None, keep_individual_outputs=None, raise_exceptions=True)[source]

Execute the SED tasks defined in a COMBINE/OMEX archive and save the outputs

Parameters
@@ -176,17 +256,23 @@

Submodules{ relative-path-to-SED-ML-file-within-archive }/{ report.id } within the HDF5 file

+

  • return_results (bool, optional) – whether to return the result of each output of each SED-ML file

  • report_formats (list of ReportFormat, optional) – report format (e.g., csv or h5)

  • plot_formats (list of VizFormat, optional) – report format (e.g., pdf)

  • bundle_outputs (bool, optional) – if True, bundle outputs into archives for reports and plots

  • keep_individual_outputs (bool, optional) – if True, keep individual output files

    • +

  • raise_exceptions (bool, optional) – whether to raise exceptions

    • Returns
    -

    log

    +

      +

    • SedDocumentResults: results

      • +

    • CombineArchiveLog: log

      • +
    +

    Return type
    -

    CombineArchiveLog

    +

    tuple

    @@ -299,20 +385,6 @@

    Submodules -
    -biosimulators_xpp.utils.get_xpp_version()[source]
    -

    Get the installed version of XPP

    -
    -
    Returns
    -

    version

    -
    -
    Return type
    -

    str

    -
    -
    -
    -
    biosimulators_xpp.utils.set_up_simulation(sed_sim, xpp_sim)[source]
    diff --git a/docs/tutorial.html b/docs/tutorial.html index c664dec..5064146 100644 --- a/docs/tutorial.html +++ b/docs/tutorial.html @@ -5,7 +5,7 @@ - Tutorial — BioSimulators-XPP 0.0.1 documentation + Tutorial — BioSimulators-XPP 0.0.2 documentation @@ -121,17 +121,17 @@

    Models (XPP)

    Simulation experiments (SED-ML, KISAO)

    -

    BioSimulators-XPP can execute simulation experiments encoded in SED-ML, using KiSAO to indicate specific algorithms and their parameters. Information about the algorithms (KiSAO terms), algorithm parameters (KiSAO terms), and outputs (XML XPaths for variables) supported by BioSimulators-XPP is available from the BioSimulators registry.

    +

    BioSimulators-XPP can execute simulation experiments encoded in SED-ML, using KiSAO to indicate specific algorithms and their parameters. Information about the algorithms (KiSAO terms), algorithm parameters (KiSAO terms), and outputs (names for variables) supported by BioSimulators-XPP is available from the BioSimulators registry.

    Example COMBINE/OMEX archives

    -

    Examples of COMBINE/OMEX archives for logical simulations which BioSimulators-XPP can execute are available in the BioSimulators test suite.

    +

    Examples of COMBINE/OMEX archives for simulations which BioSimulators-XPP can execute are available in the BioSimulators test suite.

    Command-line program

    The command-line program can be used to execute COMBINE/OMEX archives that describe simulations as illustrated below.

    -
    usage: xpp [-h] [-d] [-q] -i ARCHIVE [-o OUT_DIR] [-v]
+
    usage: biosimulators-xpp [-h] [-d] [-q] -i ARCHIVE [-o OUT_DIR] [-v]
 
 BioSimulators-compliant command-line interface to the XPP <http://www.math.pitt.edu/~bard/xpp/xpp.html> simulation program.