physioblocks 1.2.0__tar.gz → 2.0.0__tar.gz

{physioblocks-1.2.0 → physioblocks-2.0.0}/.gitlab-ci.yml

@@ -67,8 +67,11 @@ test debian:
     - pip install .[tox]
     - tox
   artifacts:
+    when: always
     paths:
       - htmlcov
+      - tests/tests_references/artifacts
+      - doc/build/html
 
 # Run reference simulation and trace the comparison with the reference
 test references debian:
@@ -80,9 +83,10 @@ test references debian:
   script:
     - pip install .
     - python -m physioblocks.launcher.configure -d ./launcher
-    - python -m physioblocks.launcher tests/tests_references/circulation_alone/circulation_alone_sim_compare_reference.jsonc -d launcher -s Circulation
-    - python -m physioblocks.launcher tests/tests_references/spherical_heart/spherical_heart_sim_compare_reference.jsonc -d launcher  -s SphericalHeart
-    - python -m physioblocks.launcher tests/tests_references/spherical_heart/spherical_heart_respiration_sim_compare_reference.jsonc -d launcher -s SphericalHeartRespiration
+    - python -m physioblocks.launcher tests/tests_references/circulation_alone/circulation_alone_forward_sim_compare_reference.jsonc -d launcher -s Circulation
+    - python -m physioblocks.launcher tests/tests_references/circulation_alone/circulation_alone_estimation_sim_compare_reference.jsonc -d launcher -s CirculationEstimation
+    - python -m physioblocks.launcher tests/tests_references/spherical_heart/spherical_heart_forward_sim_compare_reference.jsonc -d launcher  -s SphericalHeart
+    - python -m physioblocks.launcher tests/tests_references/spherical_heart/spherical_heart_estimation_sim_compare_reference.jsonc -d launcher -s SphericalHeartEstimation
   artifacts:
     paths:
       - launcher/simulations
@@ -94,6 +98,12 @@ test windows:
   script:
     - pip install .[tox]
     - tox
+  artifacts:
+    when: always
+    paths:
+      - htmlcov
+      - tests/tests_references/artifacts
+      - doc/build/html
 
 # Run reference simulation and trace the comparison with the reference
 test references windows:
@@ -103,9 +113,10 @@ test references windows:
   script:
     - pip install .
     - python -m physioblocks.launcher.configure -d ./launcher
-    - python -m physioblocks.launcher tests/tests_references/circulation_alone/circulation_alone_sim_compare_reference.jsonc -d launcher -s Circulation
-    - python -m physioblocks.launcher tests/tests_references/spherical_heart/spherical_heart_sim_compare_reference.jsonc -d launcher  -s SphericalHeart
-    - python -m physioblocks.launcher tests/tests_references/spherical_heart/spherical_heart_respiration_sim_compare_reference.jsonc -d launcher -s SphericalHeartRespiration
+    - python -m physioblocks.launcher tests/tests_references/circulation_alone/circulation_alone_forward_sim_compare_reference.jsonc -d launcher -s Circulation
+    - python -m physioblocks.launcher tests/tests_references/circulation_alone/circulation_alone_estimation_sim_compare_reference.jsonc -d launcher -s CirculationEstimation
+    - python -m physioblocks.launcher tests/tests_references/spherical_heart/spherical_heart_forward_sim_compare_reference.jsonc -d launcher  -s SphericalHeart
+    - python -m physioblocks.launcher tests/tests_references/spherical_heart/spherical_heart_estimation_sim_compare_reference.jsonc -d launcher -s SphericalHeartEstimation
   artifacts:
     paths:
       - launcher/simulations
@@ -119,9 +130,8 @@ pages:
     - large
   script:
     - pip install .[doc]
-    - cd doc
-    - make html
-    - mv build/html ../public/
+    - sphinx-build -b html doc/source/ doc/build/html/
+    - mv doc/build/html public/
   artifacts:
     paths:
       - public

{physioblocks-1.2.0 → physioblocks-2.0.0}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.4
+Metadata-Version: 2.5
 Name: physioblocks
-Version: 1.2.0
+Version: 2.0.0
 Dynamic: Author
 Dynamic: Author-email
 Dynamic: License
@@ -34,8 +34,8 @@ Requires-Dist: regex
 Requires-Dist: rich
 Requires-Dist: scipy
 Provides-Extra: doc
+Requires-Dist: pydata-sphinx-theme; extra == 'doc'
 Requires-Dist: sphinx; extra == 'doc'
-Requires-Dist: sphinx-rtd-theme; extra == 'doc'
 Requires-Dist: sphinxcontrib-tikz; extra == 'doc'
 Provides-Extra: quality
 Requires-Dist: mypy; extra == 'quality'
@@ -67,10 +67,10 @@ They are several use cases for PhysioBlocks depending on the user profile:
 
 ## Interactions
 
-__Level 1:__ Configure and run a simulation : JSON
+__Level 1:__ Configure and run a simulation: JSON
 * Update the model parameters
 
-__Level 2:__ Create Nets : JSON
+__Level 2:__ Create Nets: JSON
 * Declare the nodes, the blocks, and the block - nodes connections
 
 __Level 3:__ Write and add models to the library: Python
@@ -122,7 +122,7 @@ python -m physioblocks.launcher references/spherical_heart_sim.jsonc -v -s Quick
 ```
 
 
-Results will be available in the `$LAUNCHER_FOLDER_PATH$/simulations/QuickStart` series folder:
+Results will be available in the `$LAUNCHER_FOLDER_PATH/simulations/QuickStart` series folder:
 * the csv files contain the simulation results.
 * the html files allow you to visualize the results.
 * the log and json files are here for debug purposes.

{physioblocks-1.2.0 → physioblocks-2.0.0}/README.md

@@ -18,10 +18,10 @@ They are several use cases for PhysioBlocks depending on the user profile:
 
 ## Interactions
 
-__Level 1:__ Configure and run a simulation : JSON
+__Level 1:__ Configure and run a simulation: JSON
 * Update the model parameters
 
-__Level 2:__ Create Nets : JSON
+__Level 2:__ Create Nets: JSON
 * Declare the nodes, the blocks, and the block - nodes connections
 
 __Level 3:__ Write and add models to the library: Python
@@ -73,7 +73,7 @@ python -m physioblocks.launcher references/spherical_heart_sim.jsonc -v -s Quick
 ```
 
 
-Results will be available in the `$LAUNCHER_FOLDER_PATH$/simulations/QuickStart` series folder:
+Results will be available in the `$LAUNCHER_FOLDER_PATH/simulations/QuickStart` series folder:
 * the csv files contain the simulation results.
 * the html files allow you to visualize the results.
 * the log and json files are here for debug purposes.

physioblocks-2.0.0/doc/.gitignore

@@ -0,0 +1,2 @@
+build
+simulations_results

physioblocks-1.2.0/doc/source/api_reference/io.rst → physioblocks-2.0.0/doc/source/api_reference.rst

@@ -24,21 +24,14 @@
 .. You should have received a copy of the GNU Lesser General Public License along with
 .. PhysioBlocks. If not, see <https://www.gnu.org/licenses/>.
 
-*********
-IO Module
-*********
+.. _api_reference :
 
-.. automodule:: physioblocks.io
-    :members:
+#############
+API Reference
+#############
 
-Configuration
-=============
+.. autosummary::
+   :toctree: _autosummary
+   :recursive:
 
-.. automodule:: physioblocks.io.configuration
-    :members:
-
-Aliases
-=======
-
-.. automodule:: physioblocks.io.aliases
-    :members:
+   physioblocks

physioblocks-2.0.0/doc/source/conf.py

@@ -0,0 +1,200 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+import shutil
+import subprocess
+import sys
+import warnings
+from pathlib import Path
+
+from sphinx.application import Sphinx
+
+import physioblocks
+from physioblocks.launcher.constants import (
+    LAUNCHER_SERIES_DIR_NAME,
+    LAUNCHER_USER_ALIASES_DIR_NAME,
+    LAUNCHER_USER_LIBRARY_DIR_NAME,
+)
+
+project = physioblocks.__name__
+copyright = physioblocks.__copyright__
+author = str(physioblocks.__authors__)
+release = physioblocks.__version__
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+
+extensions = [
+    "sphinx.ext.autodoc",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.napoleon",
+    "sphinx.ext.intersphinx",
+    "sphinxcontrib.tikz",
+]
+autosummary_generate = True
+autodoc_default_options = {
+    "members": True,
+    "member-order": "bysource",
+    "ignore-module-all": True,
+}
+autosummary_ignore_module_all = True
+
+# Mappings for sphinx.ext.intersphinx. Projects have to have Sphinx-generated doc!
+intersphinx_mapping = {
+    "python": ("https://docs.python.org/3/", None),
+    "numpy": ("https://numpy.org/doc/stable/", None),
+}
+
+tikz_latex_preamble = "\\usepackage[siunitx, RPvoltages]{circuitikz}"
+
+add_module_names = False
+pygments_style = "sphinx"
+exclude_patterns = []
+mathjax3_config = {"chtml": {"displayAlign": "center"}}
+
+napoleon_custom_sections = [
+    "Scheme",
+    "Fluxes",
+    "Discretization",
+    "Internal Equations",
+    "Saved Quantities",
+    "Configuration",
+    "Aliases",
+]
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = "pydata_sphinx_theme"
+html_static_path = ["_static"]
+
+
+# NamedTuple fields are already documented in the "Attributes" section.
+def _skip_namedtuple_fields(app, what, name, obj, skip, options):
+    if (obj.__doc__ or "").startswith("Alias for field number"):
+        return True
+    return None
+
+
+def _on_builder_inited(app: Sphinx):
+    # Generate the example results if 'run-example' is set to true. Default is True
+    if app.config.run_examples:
+        _run_examples(app.srcdir, app.outdir)
+
+
+def _run_examples(exec_dir: Path, out_dir: Path):
+    # Initialize the launcher folder
+    temp_launcher_folder = exec_dir / "_simulations"
+    _initialize_launcher_folder(exec_dir, temp_launcher_folder)
+
+    try:
+        # Initialize example folder
+        example_configurations_folder = exec_dir / "examples" / "configurations"
+        example_configurations_folder.mkdir(exist_ok=True)
+
+        example_library_folder = exec_dir / "examples" / "library"
+        example_library_folder.mkdir(exist_ok=True)
+        shutil.copytree(
+            example_library_folder,
+            temp_launcher_folder / LAUNCHER_USER_LIBRARY_DIR_NAME,
+            dirs_exist_ok=True,
+        )
+
+        example_aliases_folder = exec_dir / "examples" / "aliases"
+        example_aliases_folder.mkdir(exist_ok=True)
+        shutil.copytree(
+            example_aliases_folder,
+            temp_launcher_folder / LAUNCHER_USER_ALIASES_DIR_NAME,
+            dirs_exist_ok=True,
+        )
+
+        output_simulation_folder = out_dir
+
+        # run example simulations
+        _generate_simulation_results(
+            exec_dir,
+            example_configurations_folder,
+            temp_launcher_folder,
+            output_simulation_folder,
+        )
+
+    finally:
+        shutil.rmtree(temp_launcher_folder)
+
+
+def _initialize_launcher_folder(exec_dir: Path, path: Path):
+    # Initialized a result folder
+    exit_code = subprocess.call(
+        [
+            sys.executable,
+            "-m",
+            "physioblocks.launcher.configure",
+            "-d",
+            str(path),
+        ],
+        cwd=exec_dir,
+    )
+    if exit_code != 0:
+        warnings.warn("Launcher configuration failed", stacklevel=2)
+
+
+def _generate_simulation_results(
+    exec_dir: Path,
+    configurations_folder: Path,
+    launcher_folder: Path,
+    output_folder: Path,
+):
+    configurations = [
+        file
+        for file in configurations_folder.rglob("*")
+        if file.suffix in {".json", ".jsonc"}
+    ]
+    for configuration in sorted(configurations):
+        series_name = configuration.name.removesuffix(configuration.suffix)
+        series_path = launcher_folder / LAUNCHER_SERIES_DIR_NAME / series_name
+
+        # Run simulation
+        exit_code = subprocess.call(
+            [
+                sys.executable,
+                "-m",
+                "physioblocks.launcher",
+                str(configuration),
+                "-d",
+                str(launcher_folder),
+                "-s",
+                series_name,
+            ],
+            cwd=exec_dir,
+        )
+        if exit_code != 0:
+            warnings.warn(
+                f"Simulation for configuration at {configuration} failed",
+                stacklevel=2,
+            )
+
+        # copy the html to the output folder
+        rel_config = configuration.relative_to(configurations_folder)
+        html_folder: Path = output_folder / rel_config.with_suffix("")
+        html_folder.mkdir(exist_ok=True, parents=True)
+        for file in series_path.rglob("*"):
+            if file.suffix == ".html":
+                shutil.copy(file, html_folder)
+
+
+def setup(app: Sphinx):
+    app.add_config_value(
+        "run_examples",
+        default=True,
+        rebuild="html",
+        types=(bool),
+        description="Generate the simulations results for documentation examples.",
+    )
+    app.connect("autodoc-skip-member", _skip_namedtuple_fields)
+    app.connect("builder-inited", _on_builder_inited)

physioblocks-2.0.0/doc/source/examples/aliases/flow_pulse_function.json

@@ -0,0 +1,7 @@
+{
+    "type": "piecewise_linear_periodic",
+    "evaluation_quantities": {"time": "time"},
+    "period": 1.0,
+    "points_abscissas": [0.0, 0.075, 0.135, 0.140, 0.275],
+    "points_ordinates": [0.0, 0.0, 0.5e-3, 0.5e-3, 0.0]
+}

physioblocks-2.0.0/doc/source/examples/aliases/simple_circulation_net.json

@@ -0,0 +1,29 @@
+{
+    "type": "net",
+    "nodes": ["A", "B", "C"],
+    "flux_dof_definitions": {"flow": "pressure"},
+    "blocks": {
+        "RC_1": {
+            "type": "rc_block",
+            "flux_type": "flow",
+            "resistance": "Ra",
+            "capacitance": "Ca",
+            "nodes":
+            {
+                "1": "B",
+                "2": "A"
+            }
+        },
+        "RC_2": {
+            "type": "rc_block",
+            "flux_type": "flow",
+            "resistance": "Rb",
+            "capacitance": "Cb",
+            "nodes":
+            {
+                "1": "C",
+                "2": "B"
+            }
+        }
+    }
+}

physioblocks-2.0.0/doc/source/examples/configurations/user_guide/level_2/create_simulation/simple_circulation.jsonc

@@ -0,0 +1,144 @@
+{
+    "type": "forward_simulation",
+    "solver": {
+        "type": "newton_solver",
+        "tolerance": 1e-9,
+        "iteration_max": 2
+    },
+    "time": {
+        "type": "range",
+        "start": 0.0,
+        "length": 30.0,
+        "step_size": 0.001
+    },
+    "simulation_options": {
+        "min_step": 6.25e-5
+    },
+    "net": {
+        "type": "net",
+        "flux_dof_definitions": {
+            "flow": "pressure"
+        },
+        "nodes": ["A", "B", "C"],
+        "blocks": {
+            "RC_1": {
+                "type": "rc_block",
+                "flux_type": "flow",
+                "resistance": "Ra",
+                "capacitance": "Ca",
+                "nodes":
+                {
+                    "1": "B",
+                    "2": "A"
+                }
+            },
+            "RC_2": {
+                "type": "rc_block",
+                "flux_type": "flow",
+                "resistance": "Rb",
+                "capacitance": "Cb",
+                "nodes":
+                {
+                    "1": "C",
+                    "2": "B"
+                }
+            }
+        },
+        "boundaries_conditions": {
+            "C": [
+                {
+                    "type": "condition",
+                    "condition_type": "pressure",
+                    "condition_id": "C.pressure"
+                }
+            ],
+            "A": [
+                {
+                    "type": "condition",
+                    "condition_type": "flow",
+                    "condition_id": "A.flow"
+                }
+            ]
+        }
+    },
+    "state": {
+        "A.pressure": {
+            "type": "quantity",
+            "value": 8e3,
+            "magnitude": 1e5
+        },
+        "B.pressure": {
+            "type": "quantity",
+            "value": 8e3,
+            "magnitude": 1e5
+        }
+    },
+    "parameters": {
+        "Ca": 2.0e-10,
+        "Ra": 8.0e6,
+        "Cb": 1.7e-08,
+        "Rb": 1.0e8,
+        "C.pressure": 1.6e3,
+        "sin_period": 0.80
+    },
+    "update_functions": {
+        "A.flow": {
+            "type": "sinus_offset",
+            "evaluation_quantities": {"time": "time"},
+            "offset_value": 1.0e-3,
+            "amplitude": 1.0e-3,
+            "frequency": {
+                "type": "product",
+                "factors": [1.0],
+                "inverses": ["sin_period"]
+            },
+            "phase_shift": 0.0
+        }
+    },
+    "output_functions":{
+        "A.flow": {"type": "watch_quantity", "evaluation_quantities": {"quantity": "A.flow"}},
+        "Ca.volume_stored": {
+            "type": "product",
+            "factors": ["Ca", "A.pressure"],
+            "evaluation_quantities": {"A.pressure": "A.pressure"}
+        }
+    },
+    // We did not define preprocesses for the simulation.
+    // "preprocesses": {}
+    "postprocesses": {
+        "conversion": {
+            "type": "conversion_process",
+            "conversion_factors": {
+                "A.flow": 1.0e6, // from m3/s to mL/s
+                "Ca.volume_stored": 1.0e6, // from m3 to mL
+                "A.pressure": 0.00750062, // from Pa to mmHg
+                "B.pressure": 0.00750062 // from Pa to mmHg
+            },
+            "inputs": ["main"],
+            "outputs": ["main_medical_units"]
+        }
+    },
+    "plots": {
+        "pressures": {
+            "type": "plot",
+            "abscissas": "time",
+            "subplots": ["A.pressure", "B.pressure"],
+            "inputs": ["main_medical_units"]
+        },
+        "main_medical_units": {
+            "type": "plot",
+            "abscissas": "time",
+            "inputs": ["main_medical_units"],
+            "layout": {
+                "xaxis1_title": "time (s)",
+                "yaxis1_title": "pressure (mmHg)",
+                "xaxis2_title": "time (s)",
+                "yaxis2_title": "pressure (mmHg)",
+                "xaxis3_title": "time (s)",
+                "yaxis3_title": "flux (mL/s)",
+                "xaxis4_title": "time (s)",
+                "yaxis4_title": "pressure (mL)"
+            }
+        }
+    }
+}

physioblocks-2.0.0/doc/source/examples/configurations/user_guide/level_2/estimation/1_synthetic_data.jsonc

@@ -0,0 +1,73 @@
+{
+    "type": "default_forward_simulation",
+    "solver": {"type": "linear_solver"},
+    "time": {
+        "start": -10.0,
+        "step_size": 0.001,
+        "length": 20.0
+    },
+    "net": {
+        "type": "simple_circulation_net",
+        "boundaries_conditions": {
+            "C": [{
+                "type": "condition",
+                "condition_type": "pressure",
+                "condition_id": "C.pressure"
+            }],
+            "A": [{
+                "type": "condition",
+                "condition_type": "flow",
+                "condition_id": "A.flow"
+            }]
+        }
+    },
+    "state": {
+        "A.pressure": {
+            "type": "quantity",
+            "value": 8e3,
+            "magnitude": 1e5
+        },
+        "B.pressure": {
+            "type": "quantity",
+            "value": 8e3,
+            "magnitude": 1e5
+        }
+    },
+    "parameters": {
+        "Ca": 2.0e-10,
+        "Ra": 8.0e6,
+        "Cb": 1.7e-08,
+        "Rb": 1.0e8,
+        "C.pressure": 1.6e3
+    },
+    "update_functions": {
+        "A.flow": {"type": "flow_pulse_function"}
+    },
+    "postprocesses": {
+        "remove_transition": {
+            "type": "drop_process",
+            "inputs": ["main"],
+            "outputs": ["synthetic_data"],
+            "columns":["B.pressure"],
+            "abscissas_name": "time",
+            "abscissas_interval": [-10.0001, -0.0001]
+        },
+        "copy": {
+            "type": "write_process",
+            "inputs": ["synthetic_data"],
+            "destinations": ["simulations_results/user_guide/level_2/estimation/1_synthetic_data/synthetic_data.csv"]
+        }
+    },
+    "plots": {
+        "synthetic_data": {
+            "type": "plot",
+            "abscissas": "time",
+            "inputs": ["synthetic_data"],
+            "subplots": ["A.pressure"],
+            "layout": {
+                "xaxis_title": "time (s)",
+                "yaxis_title": "pressure (Pa)"
+            }
+        }
+    }
+}