diff --git a/bio_compose/_VERSION b/bio_compose/_VERSION index 7d85683..d1d899f 100644 --- a/bio_compose/_VERSION +++ b/bio_compose/_VERSION @@ -1 +1 @@ -0.5.4 +0.5.5 diff --git a/documentation/build/doctrees/bio_compose.doctree b/documentation/build/doctrees/bio_compose.doctree index 79ef7b5..b538d58 100644 Binary files a/documentation/build/doctrees/bio_compose.doctree and b/documentation/build/doctrees/bio_compose.doctree differ diff --git a/documentation/build/doctrees/environment.pickle b/documentation/build/doctrees/environment.pickle index b815bb9..bb5aa4b 100644 Binary files a/documentation/build/doctrees/environment.pickle and b/documentation/build/doctrees/environment.pickle differ diff --git a/documentation/build/html/_modules/bio_compose/verifier.html b/documentation/build/html/_modules/bio_compose/verifier.html index b6c32ea..1e67c8f 100644 --- a/documentation/build/html/_modules/bio_compose/verifier.html +++ b/documentation/build/html/_modules/bio_compose/verifier.html @@ -644,6 +644,10 @@
[docs]
def rmse(self, *args, **kwargs):
+ """Visualize root-mean-square error scoring for this verification result data.
+ :param kwargs: (`Union[Tuple[int, int], List[str], str]`) kwargs for `Verifier.visualize_rmse`: fig_dimensions, color_mapping, save_dest.
+
+ """
from functools import partial
return self.verifier.visualize_rmse(self.job_id, **kwargs)
diff --git a/documentation/build/html/bio_compose.html b/documentation/build/html/bio_compose.html
index 96dfb90..01db3a2 100644
--- a/documentation/build/html/bio_compose.html
+++ b/documentation/build/html/bio_compose.html
@@ -471,7 +471,9 @@ Submodules
rmse(*args, **kwargs)[source]
-
+Visualize root-mean-square error scoring for this verification result data.
+:param kwargs: (Union[Tuple[int, int], List[str], str]) kwargs for Verifier.visualize_rmse: fig_dimensions, color_mapping, save_dest.
+
diff --git a/documentation/build/html/searchindex.js b/documentation/build/html/searchindex.js
index 4a4c63a..ae8a4d9 100644
--- a/documentation/build/html/searchindex.js
+++ b/documentation/build/html/searchindex.js
@@ -1 +1 @@
-Search.setIndex({"alltitles": {"API Documentation": [[3, null]], "BioCompose documentation": [[1, null]], "Contents": [[1, null]], "Installation": [[2, null]], "Module contents": [[0, "module-bio_compose"]], "Simulation Runs": [[5, null]], "Submodules": [[0, "submodules"]], "Verification": [[6, null]], "bio_compose": [[0, null]], "bio_compose.bundles module": [[0, "module-bio_compose.bundles"]], "bio_compose.composer module": [[0, "module-bio_compose.composer"]], "bio_compose.data_model module": [[0, "module-bio_compose.data_model"]], "bio_compose.processing_tools module": [[0, "module-bio_compose.processing_tools"]], "bio_compose.runner module": [[0, "module-bio_compose.runner"]], "bio_compose.verifier module": [[0, "module-bio_compose.verifier"]]}, "docnames": ["bio_compose", "index", "installation", "modules", "simple_example", "simulation_runs", "verification"], "envversion": {"sphinx": 62, "sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.viewcode": 1}, "filenames": ["bio_compose.rst", "index.rst", "installation.rst", "modules.rst", "simple_example.rst", "simulation_runs.rst", "verification.rst"], "indexentries": {"add_emitter_node() (bio_compose.bundles.biobundle method)": [[0, "bio_compose.bundles.BioBundle.add_emitter_node", false]], "api (class in bio_compose.data_model)": [[0, "bio_compose.data_model.Api", false]], "bio_compose": [[0, "module-bio_compose", false]], "bio_compose.bundles": [[0, "module-bio_compose.bundles", false]], "bio_compose.composer": [[0, "module-bio_compose.composer", false]], "bio_compose.data_model": [[0, "module-bio_compose.data_model", false]], "bio_compose.processing_tools": [[0, "module-bio_compose.processing_tools", false]], "bio_compose.runner": [[0, "module-bio_compose.runner", false]], "bio_compose.verifier": [[0, "module-bio_compose.verifier", false]], "biobundle (class in bio_compose.bundles)": [[0, "bio_compose.bundles.BioBundle", false]], "composer (class in bio_compose.composer)": [[0, "bio_compose.composer.Composer", false]], "data (bio_compose.composer.composer attribute)": [[0, "bio_compose.composer.Composer.data", false]], "endpoint_root (bio_compose.composer.composer attribute)": [[0, "bio_compose.composer.Composer.endpoint_root", false]], "error (bio_compose.data_model.requesterror attribute)": [[0, "bio_compose.data_model.RequestError.error", false]], "export_csv() (bio_compose.data_model.api method)": [[0, "bio_compose.data_model.Api.export_csv", false]], "export_plot() (bio_compose.data_model.api method)": [[0, "bio_compose.data_model.Api.export_plot", false]], "fetch_job() (in module bio_compose.data_model)": [[0, "bio_compose.data_model.fetch_job", false]], "generate_color_gradient() (in module bio_compose.processing_tools)": [[0, "bio_compose.processing_tools.generate_color_gradient", false]], "generate_node() (bio_compose.bundles.biobundle method)": [[0, "bio_compose.bundles.BioBundle.generate_node", false]], "generate_port_spec() (bio_compose.bundles.biobundle method)": [[0, "bio_compose.bundles.BioBundle.generate_port_spec", false]], "generate_simularium_file() (bio_compose.runner.simulationrunner method)": [[0, "bio_compose.runner.SimulationRunner.generate_simularium_file", false]], "get_compatible() (bio_compose.verifier.verifier method)": [[0, "bio_compose.verifier.Verifier.get_compatible", false]], "get_job_signature() (in module bio_compose.processing_tools)": [[0, "bio_compose.processing_tools.get_job_signature", false]], "get_job_status() (bio_compose.data_model.api method)": [[0, "bio_compose.data_model.Api.get_job_status", false]], "get_observables() (bio_compose.data_model.api method)": [[0, "bio_compose.data_model.Api.get_observables", false]], "get_output() (bio_compose.data_model.api method)": [[0, "bio_compose.data_model.Api.get_output", false]], "get_rmse() (bio_compose.verifier.verifier method)": [[0, "bio_compose.verifier.Verifier.get_rmse", false]], "module": [[0, "module-bio_compose", false], [0, "module-bio_compose.bundles", false], [0, "module-bio_compose.composer", false], [0, "module-bio_compose.data_model", false], [0, "module-bio_compose.processing_tools", false], [0, "module-bio_compose.runner", false], [0, "module-bio_compose.verifier", false]], "observables() (bio_compose.verifier.verificationresult method)": [[0, "bio_compose.verifier.VerificationResult.observables", false]], "read_observables() (bio_compose.data_model.api method)": [[0, "bio_compose.data_model.Api.read_observables", false]], "requesterror (class in bio_compose.data_model)": [[0, "bio_compose.data_model.RequestError", false]], "rmse() (bio_compose.verifier.verificationresult method)": [[0, "bio_compose.verifier.VerificationResult.rmse", false]], "run_composition() (bio_compose.composer.composer method)": [[0, "bio_compose.composer.Composer.run_composition", false]], "run_simulation() (in module bio_compose)": [[0, "bio_compose.run_simulation", false]], "run_smoldyn_simulation() (bio_compose.runner.simulationrunner method)": [[0, "bio_compose.runner.SimulationRunner.run_smoldyn_simulation", false]], "run_utc_simulation() (bio_compose.runner.simulationrunner method)": [[0, "bio_compose.runner.SimulationRunner.run_utc_simulation", false]], "save_plot() (in module bio_compose.data_model)": [[0, "bio_compose.data_model.save_plot", false]], "select_observables() (bio_compose.data_model.api method)": [[0, "bio_compose.data_model.Api.select_observables", false]], "simulationresult (class in bio_compose.runner)": [[0, "bio_compose.runner.SimulationResult", false]], "simulationrunner (class in bio_compose.runner)": [[0, "bio_compose.runner.SimulationRunner", false]], "submitted_jobs (bio_compose.composer.composer attribute)": [[0, "bio_compose.composer.Composer.submitted_jobs", false]], "test_verifier() (in module bio_compose.verifier)": [[0, "bio_compose.verifier.test_verifier", false]], "to_dict() (bio_compose.data_model.requesterror method)": [[0, "bio_compose.data_model.RequestError.to_dict", false]], "verificationresult (class in bio_compose.verifier)": [[0, "bio_compose.verifier.VerificationResult", false]], "verifier (class in bio_compose.verifier)": [[0, "bio_compose.verifier.Verifier", false]], "verify() (in module bio_compose)": [[0, "bio_compose.verify", false]], "verify_omex() (bio_compose.verifier.verifier method)": [[0, "bio_compose.verifier.Verifier.verify_omex", false]], "verify_sbml() (bio_compose.verifier.verifier method)": [[0, "bio_compose.verifier.Verifier.verify_sbml", false]], "visualize() (bio_compose.runner.simulationresult method)": [[0, "bio_compose.runner.SimulationResult.visualize", false]], "visualize_comparison() (bio_compose.verifier.verifier method)": [[0, "bio_compose.verifier.Verifier.visualize_comparison", false]], "visualize_observables() (bio_compose.runner.simulationrunner method)": [[0, "bio_compose.runner.SimulationRunner.visualize_observables", false]], "visualize_observables() (bio_compose.verifier.verifier method)": [[0, "bio_compose.verifier.Verifier.visualize_observables", false]], "visualize_outputs() (bio_compose.verifier.verifier method)": [[0, "bio_compose.verifier.Verifier.visualize_outputs", false]], "visualize_rmse() (bio_compose.verifier.verifier method)": [[0, "bio_compose.verifier.Verifier.visualize_rmse", false]]}, "objects": {"": [[0, 0, 0, "-", "bio_compose"]], "bio_compose": [[0, 0, 0, "-", "bundles"], [0, 0, 0, "-", "composer"], [0, 0, 0, "-", "data_model"], [0, 0, 0, "-", "processing_tools"], [0, 4, 1, "", "run_simulation"], [0, 0, 0, "-", "runner"], [0, 0, 0, "-", "verifier"], [0, 4, 1, "", "verify"]], "bio_compose.bundles": [[0, 1, 1, "", "BioBundle"]], "bio_compose.bundles.BioBundle": [[0, 2, 1, "", "add_emitter_node"], [0, 2, 1, "", "generate_node"], [0, 2, 1, "", "generate_port_spec"]], "bio_compose.composer": [[0, 1, 1, "", "Composer"]], "bio_compose.composer.Composer": [[0, 3, 1, "", "data"], [0, 3, 1, "", "endpoint_root"], [0, 2, 1, "", "run_composition"], [0, 3, 1, "", "submitted_jobs"]], "bio_compose.data_model": [[0, 1, 1, "", "Api"], [0, 1, 1, "", "RequestError"], [0, 4, 1, "", "fetch_job"], [0, 4, 1, "", "save_plot"]], "bio_compose.data_model.Api": [[0, 2, 1, "", "export_csv"], [0, 2, 1, "", "export_plot"], [0, 2, 1, "", "get_job_status"], [0, 2, 1, "", "get_observables"], [0, 2, 1, "", "get_output"], [0, 2, 1, "", "read_observables"], [0, 2, 1, "", "select_observables"]], "bio_compose.data_model.RequestError": [[0, 3, 1, "", "error"], [0, 2, 1, "", "to_dict"]], "bio_compose.processing_tools": [[0, 4, 1, "", "generate_color_gradient"], [0, 4, 1, "", "get_job_signature"]], "bio_compose.runner": [[0, 1, 1, "", "SimulationResult"], [0, 1, 1, "", "SimulationRunner"]], "bio_compose.runner.SimulationResult": [[0, 2, 1, "", "visualize"]], "bio_compose.runner.SimulationRunner": [[0, 2, 1, "", "generate_simularium_file"], [0, 2, 1, "", "run_smoldyn_simulation"], [0, 2, 1, "", "run_utc_simulation"], [0, 2, 1, "", "visualize_observables"]], "bio_compose.verifier": [[0, 1, 1, "", "VerificationResult"], [0, 1, 1, "", "Verifier"], [0, 4, 1, "", "test_verifier"]], "bio_compose.verifier.VerificationResult": [[0, 2, 1, "", "observables"], [0, 2, 1, "", "rmse"]], "bio_compose.verifier.Verifier": [[0, 2, 1, "", "get_compatible"], [0, 2, 1, "", "get_rmse"], [0, 2, 1, "", "verify_omex"], [0, 2, 1, "", "verify_sbml"], [0, 2, 1, "", "visualize_comparison"], [0, 2, 1, "", "visualize_observables"], [0, 2, 1, "", "visualize_outputs"], [0, 2, 1, "", "visualize_rmse"]]}, "objnames": {"0": ["py", "module", "Python module"], "1": ["py", "class", "Python class"], "2": ["py", "method", "Python method"], "3": ["py", "attribute", "Python attribute"], "4": ["py", "function", "Python function"]}, "objtypes": {"0": "py:module", "1": "py:class", "2": "py:method", "3": "py:attribute", "4": "py:function"}, "terms": {"": 0, "0": [0, 5, 6], "02": 5, "1": 0, "10": [0, 5], "100": [5, 6], "1000": [5, 6], "2": 0, "25": 0, "3": 0, "4": 0, "5": 0, "6": 0, "8": 0, "A": 0, "If": [0, 2], "NOT": 0, "OR": [0, 5], "One": 0, "The": 0, "To": 2, "_": 0, "_steady_st": 0, "absolut": 0, "access": 0, "achiev": 6, "add_emitter_nod": [0, 3], "address": 0, "aforement": 0, "again": 0, "all": [0, 6], "alreadi": 0, "although": 0, "amici": [0, 6], "an": 0, "analysi": 0, "ani": 0, "antimoni": 0, "api": [0, 1], "ar": [0, 2], "arbitrari": 0, "archiv": 0, "arg": 0, "argument": 0, "arrai": 0, "aspect": 0, "associ": 0, "assum": 0, "atol": 0, "attempt": 0, "base": 0, "been": 0, "being": 0, "between": 0, "bio": [2, 5, 6], "bio_check": 0, "bio_compos": [1, 3, 5, 6], "biobundl": [0, 3], "biocompos": 0, "biolog": 1, "biosimul": 2, "blue": 0, "bool": 0, "box": 0, "box_siz": 0, "brownian": 0, "bundl": 3, "calcul": 0, "call": 0, "callabl": 0, "can": [0, 2, 5, 6], "cd": 2, "check": 0, "choic": 0, "clash": 0, "class": 0, "clone": 2, "code": 0, "collect": 0, "color": 0, "color_map": 0, "column": 0, "com": 2, "combin": 0, "command": 2, "compar": 0, "comparison": 0, "comparison_id": 0, "comparison_typ": 0, "compat": 0, "complet": 0, "compos": [2, 3, 5, 6], "composit": [0, 1], "config": 0, "configur": [0, 5], "confirm": 0, "contain": 0, "content": 3, "convert": 0, "copasi": [0, 5, 6], "cours": 0, "creat": 1, "csv": 0, "csv_path": 0, "current": 0, "data": [0, 3], "data_model": 3, "data_nam": 0, "datafram": 0, "decor": 0, "default": 0, "defin": 0, "deriv": 0, "destin": 0, "determin": 0, "dict": 0, "dictionari": 0, "directori": 0, "disposit": 0, "distanc": 0, "doc": 0, "doe": 0, "domain": 0, "download": 0, "download_dest": 0, "dt": [0, 5], "durat": [0, 5, 6], "dynam": 1, "e": [0, 2], "each": 0, "easili": 0, "either": [0, 5], "emitted_schema": 0, "emitter_address_id": 0, "end": 0, "endpoint": 0, "endpoint_root": [0, 3], "entir": 0, "entrypoint": 0, "error": [0, 3, 6], "etc": 0, "exclud": 0, "execut": [0, 1], "expect": 0, "expected_result": 0, "export": 0, "export_csv": [0, 3], "export_plot": [0, 3], "extract": 0, "fals": 0, "featur": 0, "fetch": 0, "fetch_job": [0, 3], "few": 6, "field": 0, "fig": 0, "fig_dimens": 0, "figsiz": 0, "figur": 0, "file": [0, 5, 6], "filenam": 0, "filepath": [0, 5, 6], "flatten": 0, "flavor": 0, "float": 0, "follow": [0, 2], "form": 0, "format": 0, "from": [0, 2, 5, 6], "func": 0, "fundament": 0, "g": 0, "gener": 0, "generate_color_gradi": [0, 3], "generate_nod": [0, 3], "generate_port_spec": [0, 3], "generate_simularium_fil": [0, 3], "get": 0, "get_compat": [0, 3], "get_job_signatur": [0, 3], "get_job_statu": [0, 3], "get_observ": [0, 3], "get_output": [0, 3], "get_rms": [0, 3], "get_verify_output": 0, "git": 2, "github": 2, "given": 0, "gradient": 0, "green": 0, "grid": 0, "ground": 0, "group": 0, "ha": [0, 5], "handl": 0, "have": 0, "header": 0, "heatmap": 0, "hex": 0, "highli": 0, "histor": 0, "horizont": 0, "hspace": 0, "http": [0, 2], "hue": 0, "i": 0, "id": 0, "identifi": 0, "implement": 0, "import": [5, 6], "in_progress": 0, "includ": 0, "include_output": 0, "index": 0, "infer": 0, "inform": 0, "inherit": 0, "input": 0, "input_port": 0, "instal": 1, "instanc": 0, "int": 0, "interact": 0, "introspect": 1, "involv": [0, 6], "ioerror": 0, "its": 0, "job": 0, "job_id": 0, "json": 0, "keep": 0, "kei": 0, "keyword": 0, "kwarg": 0, "last": 0, "line": 0, "list": 0, "load": 0, "locat": 0, "mai": 0, "map": 0, "matplotlib": 0, "matrix": 0, "mean": [0, 6], "memory_stor": 0, "method": [0, 5], "model": 0, "modul": 3, "more": 0, "motion": 0, "multipl": 0, "must": 0, "my": 6, "n_step": [5, 6], "name": 0, "nativ": 0, "necessari": 0, "new": 0, "node_nam": 0, "node_typ": 0, "none": 0, "note": 0, "notebook": 0, "num_point": 0, "number": 0, "object": 0, "observ": [0, 3, 6], "occur": 0, "od": 0, "omex": [0, 6], "omex_filepath": 0, "one": 0, "onli": 0, "option": 0, "org": 0, "output": 0, "output_end": 0, "output_port": 0, "output_start": 0, "own": 0, "packag": 0, "pairwis": 0, "param": 0, "paramet": 0, "pars": 0, "pass": 0, "path": [0, 5, 6], "pd": 0, "pdf": 0, "pend": 0, "pertain": 0, "pip": 2, "pleas": 0, "plot": 0, "point": 0, "polymorph": 0, "port_param": 0, "posit": 0, "process": 0, "processing_tool": 3, "provid": 0, "proxim": 0, "pyplot": 0, "quasi": 0, "rais": 0, "read": 0, "read_observ": [0, 3], "recommend": 0, "record": 0, "red": 0, "referenc": 0, "rel": 0, "report": 0, "repositori": 2, "reproduc": 1, "request": 0, "requesterror": [0, 3], "respect": 0, "respons": 0, "rest": 0, "result": [0, 5], "return": 0, "rmse": [0, 3, 6], "root": [0, 6], "row": 0, "rtol": 0, "run": [0, 1, 6], "run_composit": [0, 3], "run_simul": [0, 3, 5], "run_smoldyn_simul": [0, 3], "run_utc_simul": [0, 3], "runner": 3, "save": [0, 6], "save_dest": [0, 6], "save_plot": [0, 3], "sbml": [0, 5, 6], "sbml_filepath": 0, "score": [0, 6], "second": 0, "see": 0, "select": 0, "select_observ": [0, 3], "selection_list": 0, "seri": 0, "servic": 0, "should": 0, "simpl": 6, "simul": [0, 1, 6], "simularium": 0, "simulationresult": [0, 3], "simulationrunn": [0, 3], "singleton": 0, "size": 0, "smoldyn": [0, 5], "smoldyn_configuration_filepath": 0, "smoldyn_output_filepath": 0, "smoldynmanu": 0, "so": 0, "sourc": [0, 2], "space": 0, "speci": 0, "specif": 0, "specifi": 0, "squar": [0, 6], "standard": 0, "start": 0, "start_tim": [5, 6], "state": 0, "statu": 0, "steadi": 0, "step": [0, 6], "stop": 0, "str": 0, "string": 0, "submiss": 0, "submit": 0, "submitted_job": [0, 3], "submodul": 3, "subplot": 0, "support": 0, "system": 1, "tag": 0, "tellurium": [0, 6], "test_verifi": [0, 3], "thi": 0, "throw": 0, "time": 0, "time_stop": 0, "timestep": 0, "tip": 0, "to_dict": [0, 3], "toler": 0, "trajectori": 0, "treat": 0, "true": 0, "try": 0, "tupl": 0, "txt": 5, "type": 0, "uniform": 0, "uniqu": 0, "upon": 0, "us": [0, 2, 5], "use_grid": 0, "user": 0, "utc": 0, "uuid": 0, "valid": [0, 5, 6], "valu": 0, "verif": [0, 1], "verifi": [3, 6], "verificationresult": [0, 3], "verify_": 0, "verify_omex": [0, 3], "verify_sbml": [0, 3], "version": 0, "visual": [0, 3, 6], "visualize_": 0, "visualize_comparison": [0, 3], "visualize_observ": [0, 3], "visualize_output": [0, 3], "visualize_rms": [0, 3], "where": 0, "whether": 0, "which": 0, "wish": 0, "within": 0, "www": 0, "xml": [5, 6], "yet": 0, "you": [0, 2], "your": 0, "your_project": 2}, "titles": ["bio_compose", "BioCompose documentation", "Installation", "API Documentation", "<no title>", "Simulation Runs", "Verification"], "titleterms": {"api": 3, "bio_compos": 0, "biocompos": 1, "bundl": 0, "compos": 0, "content": [0, 1], "data_model": 0, "document": [1, 3], "instal": 2, "modul": 0, "processing_tool": 0, "run": 5, "runner": 0, "simul": 5, "submodul": 0, "verif": 6, "verifi": 0}})
\ No newline at end of file
+Search.setIndex({"alltitles": {"API Documentation": [[3, null]], "BioCompose documentation": [[1, null]], "Contents": [[1, null]], "Installation": [[2, null]], "Module contents": [[0, "module-bio_compose"]], "Simulation Runs": [[5, null]], "Submodules": [[0, "submodules"]], "Verification": [[6, null]], "bio_compose": [[0, null]], "bio_compose.bundles module": [[0, "module-bio_compose.bundles"]], "bio_compose.composer module": [[0, "module-bio_compose.composer"]], "bio_compose.data_model module": [[0, "module-bio_compose.data_model"]], "bio_compose.processing_tools module": [[0, "module-bio_compose.processing_tools"]], "bio_compose.runner module": [[0, "module-bio_compose.runner"]], "bio_compose.verifier module": [[0, "module-bio_compose.verifier"]]}, "docnames": ["bio_compose", "index", "installation", "modules", "simple_example", "simulation_runs", "verification"], "envversion": {"sphinx": 62, "sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.viewcode": 1}, "filenames": ["bio_compose.rst", "index.rst", "installation.rst", "modules.rst", "simple_example.rst", "simulation_runs.rst", "verification.rst"], "indexentries": {"add_emitter_node() (bio_compose.bundles.biobundle method)": [[0, "bio_compose.bundles.BioBundle.add_emitter_node", false]], "api (class in bio_compose.data_model)": [[0, "bio_compose.data_model.Api", false]], "bio_compose": [[0, "module-bio_compose", false]], "bio_compose.bundles": [[0, "module-bio_compose.bundles", false]], "bio_compose.composer": [[0, "module-bio_compose.composer", false]], "bio_compose.data_model": [[0, "module-bio_compose.data_model", false]], "bio_compose.processing_tools": [[0, "module-bio_compose.processing_tools", false]], "bio_compose.runner": [[0, "module-bio_compose.runner", false]], "bio_compose.verifier": [[0, "module-bio_compose.verifier", false]], "biobundle (class in bio_compose.bundles)": [[0, "bio_compose.bundles.BioBundle", false]], "composer (class in bio_compose.composer)": [[0, "bio_compose.composer.Composer", false]], "data (bio_compose.composer.composer attribute)": [[0, "bio_compose.composer.Composer.data", false]], "endpoint_root (bio_compose.composer.composer attribute)": [[0, "bio_compose.composer.Composer.endpoint_root", false]], "error (bio_compose.data_model.requesterror attribute)": [[0, "bio_compose.data_model.RequestError.error", false]], "export_csv() (bio_compose.data_model.api method)": [[0, "bio_compose.data_model.Api.export_csv", false]], "export_plot() (bio_compose.data_model.api method)": [[0, "bio_compose.data_model.Api.export_plot", false]], "fetch_job() (in module bio_compose.data_model)": [[0, "bio_compose.data_model.fetch_job", false]], "generate_color_gradient() (in module bio_compose.processing_tools)": [[0, "bio_compose.processing_tools.generate_color_gradient", false]], "generate_node() (bio_compose.bundles.biobundle method)": [[0, "bio_compose.bundles.BioBundle.generate_node", false]], "generate_port_spec() (bio_compose.bundles.biobundle method)": [[0, "bio_compose.bundles.BioBundle.generate_port_spec", false]], "generate_simularium_file() (bio_compose.runner.simulationrunner method)": [[0, "bio_compose.runner.SimulationRunner.generate_simularium_file", false]], "get_compatible() (bio_compose.verifier.verifier method)": [[0, "bio_compose.verifier.Verifier.get_compatible", false]], "get_job_signature() (in module bio_compose.processing_tools)": [[0, "bio_compose.processing_tools.get_job_signature", false]], "get_job_status() (bio_compose.data_model.api method)": [[0, "bio_compose.data_model.Api.get_job_status", false]], "get_observables() (bio_compose.data_model.api method)": [[0, "bio_compose.data_model.Api.get_observables", false]], "get_output() (bio_compose.data_model.api method)": [[0, "bio_compose.data_model.Api.get_output", false]], "get_rmse() (bio_compose.verifier.verifier method)": [[0, "bio_compose.verifier.Verifier.get_rmse", false]], "module": [[0, "module-bio_compose", false], [0, "module-bio_compose.bundles", false], [0, "module-bio_compose.composer", false], [0, "module-bio_compose.data_model", false], [0, "module-bio_compose.processing_tools", false], [0, "module-bio_compose.runner", false], [0, "module-bio_compose.verifier", false]], "observables() (bio_compose.verifier.verificationresult method)": [[0, "bio_compose.verifier.VerificationResult.observables", false]], "read_observables() (bio_compose.data_model.api method)": [[0, "bio_compose.data_model.Api.read_observables", false]], "requesterror (class in bio_compose.data_model)": [[0, "bio_compose.data_model.RequestError", false]], "rmse() (bio_compose.verifier.verificationresult method)": [[0, "bio_compose.verifier.VerificationResult.rmse", false]], "run_composition() (bio_compose.composer.composer method)": [[0, "bio_compose.composer.Composer.run_composition", false]], "run_simulation() (in module bio_compose)": [[0, "bio_compose.run_simulation", false]], "run_smoldyn_simulation() (bio_compose.runner.simulationrunner method)": [[0, "bio_compose.runner.SimulationRunner.run_smoldyn_simulation", false]], "run_utc_simulation() (bio_compose.runner.simulationrunner method)": [[0, "bio_compose.runner.SimulationRunner.run_utc_simulation", false]], "save_plot() (in module bio_compose.data_model)": [[0, "bio_compose.data_model.save_plot", false]], "select_observables() (bio_compose.data_model.api method)": [[0, "bio_compose.data_model.Api.select_observables", false]], "simulationresult (class in bio_compose.runner)": [[0, "bio_compose.runner.SimulationResult", false]], "simulationrunner (class in bio_compose.runner)": [[0, "bio_compose.runner.SimulationRunner", false]], "submitted_jobs (bio_compose.composer.composer attribute)": [[0, "bio_compose.composer.Composer.submitted_jobs", false]], "test_verifier() (in module bio_compose.verifier)": [[0, "bio_compose.verifier.test_verifier", false]], "to_dict() (bio_compose.data_model.requesterror method)": [[0, "bio_compose.data_model.RequestError.to_dict", false]], "verificationresult (class in bio_compose.verifier)": [[0, "bio_compose.verifier.VerificationResult", false]], "verifier (class in bio_compose.verifier)": [[0, "bio_compose.verifier.Verifier", false]], "verify() (in module bio_compose)": [[0, "bio_compose.verify", false]], "verify_omex() (bio_compose.verifier.verifier method)": [[0, "bio_compose.verifier.Verifier.verify_omex", false]], "verify_sbml() (bio_compose.verifier.verifier method)": [[0, "bio_compose.verifier.Verifier.verify_sbml", false]], "visualize() (bio_compose.runner.simulationresult method)": [[0, "bio_compose.runner.SimulationResult.visualize", false]], "visualize_comparison() (bio_compose.verifier.verifier method)": [[0, "bio_compose.verifier.Verifier.visualize_comparison", false]], "visualize_observables() (bio_compose.runner.simulationrunner method)": [[0, "bio_compose.runner.SimulationRunner.visualize_observables", false]], "visualize_observables() (bio_compose.verifier.verifier method)": [[0, "bio_compose.verifier.Verifier.visualize_observables", false]], "visualize_outputs() (bio_compose.verifier.verifier method)": [[0, "bio_compose.verifier.Verifier.visualize_outputs", false]], "visualize_rmse() (bio_compose.verifier.verifier method)": [[0, "bio_compose.verifier.Verifier.visualize_rmse", false]]}, "objects": {"": [[0, 0, 0, "-", "bio_compose"]], "bio_compose": [[0, 0, 0, "-", "bundles"], [0, 0, 0, "-", "composer"], [0, 0, 0, "-", "data_model"], [0, 0, 0, "-", "processing_tools"], [0, 4, 1, "", "run_simulation"], [0, 0, 0, "-", "runner"], [0, 0, 0, "-", "verifier"], [0, 4, 1, "", "verify"]], "bio_compose.bundles": [[0, 1, 1, "", "BioBundle"]], "bio_compose.bundles.BioBundle": [[0, 2, 1, "", "add_emitter_node"], [0, 2, 1, "", "generate_node"], [0, 2, 1, "", "generate_port_spec"]], "bio_compose.composer": [[0, 1, 1, "", "Composer"]], "bio_compose.composer.Composer": [[0, 3, 1, "", "data"], [0, 3, 1, "", "endpoint_root"], [0, 2, 1, "", "run_composition"], [0, 3, 1, "", "submitted_jobs"]], "bio_compose.data_model": [[0, 1, 1, "", "Api"], [0, 1, 1, "", "RequestError"], [0, 4, 1, "", "fetch_job"], [0, 4, 1, "", "save_plot"]], "bio_compose.data_model.Api": [[0, 2, 1, "", "export_csv"], [0, 2, 1, "", "export_plot"], [0, 2, 1, "", "get_job_status"], [0, 2, 1, "", "get_observables"], [0, 2, 1, "", "get_output"], [0, 2, 1, "", "read_observables"], [0, 2, 1, "", "select_observables"]], "bio_compose.data_model.RequestError": [[0, 3, 1, "", "error"], [0, 2, 1, "", "to_dict"]], "bio_compose.processing_tools": [[0, 4, 1, "", "generate_color_gradient"], [0, 4, 1, "", "get_job_signature"]], "bio_compose.runner": [[0, 1, 1, "", "SimulationResult"], [0, 1, 1, "", "SimulationRunner"]], "bio_compose.runner.SimulationResult": [[0, 2, 1, "", "visualize"]], "bio_compose.runner.SimulationRunner": [[0, 2, 1, "", "generate_simularium_file"], [0, 2, 1, "", "run_smoldyn_simulation"], [0, 2, 1, "", "run_utc_simulation"], [0, 2, 1, "", "visualize_observables"]], "bio_compose.verifier": [[0, 1, 1, "", "VerificationResult"], [0, 1, 1, "", "Verifier"], [0, 4, 1, "", "test_verifier"]], "bio_compose.verifier.VerificationResult": [[0, 2, 1, "", "observables"], [0, 2, 1, "", "rmse"]], "bio_compose.verifier.Verifier": [[0, 2, 1, "", "get_compatible"], [0, 2, 1, "", "get_rmse"], [0, 2, 1, "", "verify_omex"], [0, 2, 1, "", "verify_sbml"], [0, 2, 1, "", "visualize_comparison"], [0, 2, 1, "", "visualize_observables"], [0, 2, 1, "", "visualize_outputs"], [0, 2, 1, "", "visualize_rmse"]]}, "objnames": {"0": ["py", "module", "Python module"], "1": ["py", "class", "Python class"], "2": ["py", "method", "Python method"], "3": ["py", "attribute", "Python attribute"], "4": ["py", "function", "Python function"]}, "objtypes": {"0": "py:module", "1": "py:class", "2": "py:method", "3": "py:attribute", "4": "py:function"}, "terms": {"": 0, "0": [0, 5, 6], "02": 5, "1": 0, "10": [0, 5], "100": [5, 6], "1000": [5, 6], "2": 0, "25": 0, "3": 0, "4": 0, "5": 0, "6": 0, "8": 0, "A": 0, "If": [0, 2], "NOT": 0, "OR": [0, 5], "One": 0, "The": 0, "To": 2, "_": 0, "_steady_st": 0, "absolut": 0, "access": 0, "achiev": 6, "add_emitter_nod": [0, 3], "address": 0, "aforement": 0, "again": 0, "all": [0, 6], "alreadi": 0, "although": 0, "amici": [0, 6], "an": 0, "analysi": 0, "ani": 0, "antimoni": 0, "api": [0, 1], "ar": [0, 2], "arbitrari": 0, "archiv": 0, "arg": 0, "argument": 0, "arrai": 0, "aspect": 0, "associ": 0, "assum": 0, "atol": 0, "attempt": 0, "base": 0, "been": 0, "being": 0, "between": 0, "bio": [2, 5, 6], "bio_check": 0, "bio_compos": [1, 3, 5, 6], "biobundl": [0, 3], "biocompos": 0, "biolog": 1, "biosimul": 2, "blue": 0, "bool": 0, "box": 0, "box_siz": 0, "brownian": 0, "bundl": 3, "calcul": 0, "call": 0, "callabl": 0, "can": [0, 2, 5, 6], "cd": 2, "check": 0, "choic": 0, "clash": 0, "class": 0, "clone": 2, "code": 0, "collect": 0, "color": 0, "color_map": 0, "column": 0, "com": 2, "combin": 0, "command": 2, "compar": 0, "comparison": 0, "comparison_id": 0, "comparison_typ": 0, "compat": 0, "complet": 0, "compos": [2, 3, 5, 6], "composit": [0, 1], "config": 0, "configur": [0, 5], "confirm": 0, "contain": 0, "content": 3, "convert": 0, "copasi": [0, 5, 6], "cours": 0, "creat": 1, "csv": 0, "csv_path": 0, "current": 0, "data": [0, 3], "data_model": 3, "data_nam": 0, "datafram": 0, "decor": 0, "default": 0, "defin": 0, "deriv": 0, "destin": 0, "determin": 0, "dict": 0, "dictionari": 0, "directori": 0, "disposit": 0, "distanc": 0, "doc": 0, "doe": 0, "domain": 0, "download": 0, "download_dest": 0, "dt": [0, 5], "durat": [0, 5, 6], "dynam": 1, "e": [0, 2], "each": 0, "easili": 0, "either": [0, 5], "emitted_schema": 0, "emitter_address_id": 0, "end": 0, "endpoint": 0, "endpoint_root": [0, 3], "entir": 0, "entrypoint": 0, "error": [0, 3, 6], "etc": 0, "exclud": 0, "execut": [0, 1], "expect": 0, "expected_result": 0, "export": 0, "export_csv": [0, 3], "export_plot": [0, 3], "extract": 0, "fals": 0, "featur": 0, "fetch": 0, "fetch_job": [0, 3], "few": 6, "field": 0, "fig": 0, "fig_dimens": 0, "figsiz": 0, "figur": 0, "file": [0, 5, 6], "filenam": 0, "filepath": [0, 5, 6], "flatten": 0, "flavor": 0, "float": 0, "follow": [0, 2], "form": 0, "format": 0, "from": [0, 2, 5, 6], "func": 0, "fundament": 0, "g": 0, "gener": 0, "generate_color_gradi": [0, 3], "generate_nod": [0, 3], "generate_port_spec": [0, 3], "generate_simularium_fil": [0, 3], "get": 0, "get_compat": [0, 3], "get_job_signatur": [0, 3], "get_job_statu": [0, 3], "get_observ": [0, 3], "get_output": [0, 3], "get_rms": [0, 3], "get_verify_output": 0, "git": 2, "github": 2, "given": 0, "gradient": 0, "green": 0, "grid": 0, "ground": 0, "group": 0, "ha": [0, 5], "handl": 0, "have": 0, "header": 0, "heatmap": 0, "hex": 0, "highli": 0, "histor": 0, "horizont": 0, "hspace": 0, "http": [0, 2], "hue": 0, "i": 0, "id": 0, "identifi": 0, "implement": 0, "import": [5, 6], "in_progress": 0, "includ": 0, "include_output": 0, "index": 0, "infer": 0, "inform": 0, "inherit": 0, "input": 0, "input_port": 0, "instal": 1, "instanc": 0, "int": 0, "interact": 0, "introspect": 1, "involv": [0, 6], "ioerror": 0, "its": 0, "job": 0, "job_id": 0, "json": 0, "keep": 0, "kei": 0, "keyword": 0, "kwarg": 0, "last": 0, "line": 0, "list": 0, "load": 0, "locat": 0, "mai": 0, "map": 0, "matplotlib": 0, "matrix": 0, "mean": [0, 6], "memory_stor": 0, "method": [0, 5], "model": 0, "modul": 3, "more": 0, "motion": 0, "multipl": 0, "must": 0, "my": 6, "n_step": [5, 6], "name": 0, "nativ": 0, "necessari": 0, "new": 0, "node_nam": 0, "node_typ": 0, "none": 0, "note": 0, "notebook": 0, "num_point": 0, "number": 0, "object": 0, "observ": [0, 3, 6], "occur": 0, "od": 0, "omex": [0, 6], "omex_filepath": 0, "one": 0, "onli": 0, "option": 0, "org": 0, "output": 0, "output_end": 0, "output_port": 0, "output_start": 0, "own": 0, "packag": 0, "pairwis": 0, "param": 0, "paramet": 0, "pars": 0, "pass": 0, "path": [0, 5, 6], "pd": 0, "pdf": 0, "pend": 0, "pertain": 0, "pip": 2, "pleas": 0, "plot": 0, "point": 0, "polymorph": 0, "port_param": 0, "posit": 0, "process": 0, "processing_tool": 3, "provid": 0, "proxim": 0, "pyplot": 0, "quasi": 0, "rais": 0, "read": 0, "read_observ": [0, 3], "recommend": 0, "record": 0, "red": 0, "referenc": 0, "rel": 0, "report": 0, "repositori": 2, "reproduc": 1, "request": 0, "requesterror": [0, 3], "respect": 0, "respons": 0, "rest": 0, "result": [0, 5], "return": 0, "rmse": [0, 3, 6], "root": [0, 6], "row": 0, "rtol": 0, "run": [0, 1, 6], "run_composit": [0, 3], "run_simul": [0, 3, 5], "run_smoldyn_simul": [0, 3], "run_utc_simul": [0, 3], "runner": 3, "save": [0, 6], "save_dest": [0, 6], "save_plot": [0, 3], "sbml": [0, 5, 6], "sbml_filepath": 0, "score": [0, 6], "second": 0, "see": 0, "select": 0, "select_observ": [0, 3], "selection_list": 0, "seri": 0, "servic": 0, "should": 0, "simpl": 6, "simul": [0, 1, 6], "simularium": 0, "simulationresult": [0, 3], "simulationrunn": [0, 3], "singleton": 0, "size": 0, "smoldyn": [0, 5], "smoldyn_configuration_filepath": 0, "smoldyn_output_filepath": 0, "smoldynmanu": 0, "so": 0, "sourc": [0, 2], "space": 0, "speci": 0, "specif": 0, "specifi": 0, "squar": [0, 6], "standard": 0, "start": 0, "start_tim": [5, 6], "state": 0, "statu": 0, "steadi": 0, "step": [0, 6], "stop": 0, "str": 0, "string": 0, "submiss": 0, "submit": 0, "submitted_job": [0, 3], "submodul": 3, "subplot": 0, "support": 0, "system": 1, "tag": 0, "tellurium": [0, 6], "test_verifi": [0, 3], "thi": 0, "throw": 0, "time": 0, "time_stop": 0, "timestep": 0, "tip": 0, "to_dict": [0, 3], "toler": 0, "trajectori": 0, "treat": 0, "true": 0, "try": 0, "tupl": 0, "txt": 5, "type": 0, "uniform": 0, "union": 0, "uniqu": 0, "upon": 0, "us": [0, 2, 5], "use_grid": 0, "user": 0, "utc": 0, "uuid": 0, "valid": [0, 5, 6], "valu": 0, "verif": [0, 1], "verifi": [3, 6], "verificationresult": [0, 3], "verify_": 0, "verify_omex": [0, 3], "verify_sbml": [0, 3], "version": 0, "visual": [0, 3, 6], "visualize_": 0, "visualize_comparison": [0, 3], "visualize_observ": [0, 3], "visualize_output": [0, 3], "visualize_rms": [0, 3], "where": 0, "whether": 0, "which": 0, "wish": 0, "within": 0, "www": 0, "xml": [5, 6], "yet": 0, "you": [0, 2], "your": 0, "your_project": 2}, "titles": ["bio_compose", "BioCompose documentation", "Installation", "API Documentation", "<no title>", "Simulation Runs", "Verification"], "titleterms": {"api": 3, "bio_compos": 0, "biocompos": 1, "bundl": 0, "compos": 0, "content": [0, 1], "data_model": 0, "document": [1, 3], "instal": 2, "modul": 0, "processing_tool": 0, "run": 5, "runner": 0, "simul": 5, "submodul": 0, "verif": 6, "verifi": 0}})
\ No newline at end of file