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Merged
heberlr merged 14 commits into from
Nov 10, 2025
Merged

Release 1.2.2 – Documentation and Example Updates #17

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b28389b
fix: format INI file for better readability and consistency
heberlr Nov 7, 2025
5e72476
feat: add cooperative cancellation support in Bayesian optimization p…
heberlr Nov 7, 2025
5965399
feat: implement run/cancel functionality for Bayesian optimization ca…
heberlr Nov 7, 2025
05395f8
fix: clarify heuristic nature of AIC-style criterion in process_db_fi…
heberlr Nov 7, 2025
a241406
fix: improve formatting of INI parameters for better readability
heberlr Nov 10, 2025
74a836d
fix: include GitHub link in version string for documentation
heberlr Nov 10, 2025
6cafd65
Added test to download PhysiCell if not already present.
heberlr Nov 10, 2025
c008eac
fix: enhance simulation logging and adjust download behavior for privacy
heberlr Nov 10, 2025
e74a763
fix: update release preparation instructions in pyproject.toml for cl…
heberlr Nov 10, 2025
064d634
fix: update release version in documentation to v1.2.2
heberlr Nov 10, 2025
e864db3
release v1.2.2
heberlr Nov 10, 2025
dc41fa5
fix: update documentation steps for rebuilding to correct numbering
heberlr Nov 10, 2025
6c425ec
Merge pull request #16 from heberlr/dev_heber
heberlr Nov 10, 2025
37a1e9e
Update PyPI badge version date
heberlr Nov 10, 2025
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2 changes: 1 addition & 1 deletion README.md
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Expand Up @@ -6,7 +6,7 @@

[![Run Unit Tests](https://github.com/heberlr/UQ_PhysiCell/actions/workflows/test-examples.yml/badge.svg)](https://github.com/heberlr/UQ_PhysiCell/actions/workflows/test-examples.yml)
[![Documentation Status](https://readthedocs.org/projects/uq-physicell/badge/?version=latest)](https://uq-physicell.readthedocs.io/en/latest/?badge=latest)
[![PyPI](https://badge.fury.io/py/uq-physicell.svg?updated=20241106)](https://badge.fury.io/py/uq-physicell)
[![PyPI](https://badge.fury.io/py/uq-physicell.svg?updated=20251110)](https://badge.fury.io/py/uq-physicell)
[![Python](https://img.shields.io/badge/Python-%3E%3D3.10-blue?logo=python&logoColor=green)](https://python.org)

UQ-PhysiCell is a comprehensive framework for performing uncertainty quantification and parameter calibration of PhysiCell models. It provides sophisticated tools for model analysis, calibration, and model selection.
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8 changes: 6 additions & 2 deletions doc/about.md
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Expand Up @@ -24,9 +24,13 @@ configfile_ref = config/PhysiCell_settings.xml
numreplicates = 2
parameters = {
'.//save/SVG/enable': 'false',
'.//save/full_data/interval': '360', ".//cell_definitions/cell_definition[@name='macrophage']/phenotype/cell_interactions/live_phagocytosis_rates/phagocytosis_rate[@name='epithelial_infected']": [None, 'mac_phag_rate_infected'], ".//cell_definitions/cell_definition[@name='macrophage']/phenotype/motility/migration_bias": [None, 'mac_motility_bias']}
'.//save/full_data/interval': '360',
".//cell_definitions/cell_definition[@name='macrophage']/phenotype/cell_interactions/live_phagocytosis_rates/phagocytosis_rate[@name='epithelial_infected']": [None, 'mac_phag_rate_infected'],
".//cell_definitions/cell_definition[@name='macrophage']/phenotype/motility/migration_bias": [None, 'mac_motility_bias']}
rulesfile_ref = config/cell_rules.csv
parameters_rules = {'epithelial,virus,increases,transform to epithelial_infected,saturation': [None, 'epi2infected_sat'], 'epithelial,virus,increases,transform to epithelial_infected,half_max': [None, 'epi2infected_hfm']}
parameters_rules = {
'epithelial,virus,increases,transform to epithelial_infected,saturation': [None, 'epi2infected_sat'],
'epithelial,virus,increases,transform to epithelial_infected,half_max': [None, 'epi2infected_hfm']}
```
You can initialize the model structure, print information, and run a simulation as follows:
```python
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2 changes: 1 addition & 1 deletion doc/index.md
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Expand Up @@ -2,7 +2,7 @@

Welcome to the UQ-PhysiCell documentation! This project provides uncertainty quantification tools for PhysiCell models.

**Release:** [v1.2.1](https://github.com/heberlr/UQ_PhysiCell/releases/tag/v1.2.1)
**Release:** [v1.2.2 (GitHub link)](https://github.com/heberlr/UQ_PhysiCell/releases/tag/v1.2.2 (GitHub link))

```{note}
This readthedocs documentation is under active development.
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2 changes: 1 addition & 1 deletion doc/rebuild_docs.sh
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Expand Up @@ -123,7 +123,7 @@ VERSION=$(python -c "try:
except ImportError:
print('unknown')
")
VERSION_STR="v$VERSION"
VERSION_STR="v$VERSION (GitHub link)"
VERSION_REF="https://github.com/heberlr/UQ_PhysiCell/releases/tag/$VERSION_STR"
print_status "Building documentation for UQ-PhysiCell version: $VERSION"

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37 changes: 8 additions & 29 deletions examples/ex1_print.ipynb
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Expand Up @@ -23,7 +23,7 @@
"metadata": {},
"outputs": [],
"source": [
"from uq_physicell import PhysiCell_Model"
"from uq_physicell import PhysiCell_Model, get_physicell"
]
},
{
Expand All @@ -44,6 +44,8 @@
"name": "stdout",
"output_type": "stream",
"text": [
"PhysiCell already exists at: PhysiCell-master\n",
"Skipping download. Use force_download=True to override.\n",
"Compiling PhysiCell model: ./PhysiCell-master/virus-sample...\n",
"PhysiCell path: PhysiCell-master\n",
"Model path: PhysiCell-master/sample_projects/virus_macrophage\n",
Expand All @@ -54,34 +56,8 @@
"cp ./user_projects/../sample_projects/virus_macrophage/Makefile .\n",
"cp ./user_projects/../sample_projects/virus_macrophage/config/* ./config/ \n",
"cp ./user_projects/../sample_projects/virus_macrophage/custom_modules/* ./custom_modules/ \n",
"g++-14 -march=native -O3 -fomit-frame-pointer -fopenmp -m64 -std=c++11 -c ./custom_modules/custom.cpp\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"clang: warning: overriding deployment version from '16.0' to '26.0' [-Woverriding-deployment-version]\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"g++-14 -march=native -O3 -fomit-frame-pointer -fopenmp -m64 -std=c++11 -o virus-sample BioFVM_vector.o BioFVM_mesh.o BioFVM_microenvironment.o BioFVM_solvers.o BioFVM_matlab.o BioFVM_utilities.o BioFVM_basic_agent.o BioFVM_MultiCellDS.o BioFVM_agent_container.o pugixml.o PhysiCell_phenotype.o PhysiCell_cell_container.o PhysiCell_standard_models.o PhysiCell_cell.o PhysiCell_custom.o PhysiCell_utilities.o PhysiCell_constants.o PhysiCell_signal_behavior.o PhysiCell_rules.o PhysiCell_basic_signaling.o PhysiCell_SVG.o PhysiCell_pathology.o PhysiCell_MultiCellDS.o PhysiCell_various_outputs.o PhysiCell_pugixml.o PhysiCell_settings.o PhysiCell_geometry.o custom.o main.cpp \n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"clang: warning: overriding deployment version from '16.0' to '26.0' [-Woverriding-deployment-version]\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"/opt/homebrew/bin/g++-15 -march=native -O3 -fomit-frame-pointer -fopenmp -m64 -std=c++11 -c ./custom_modules/custom.cpp\n",
"/opt/homebrew/bin/g++-15 -march=native -O3 -fomit-frame-pointer -fopenmp -m64 -std=c++11 -o virus-sample BioFVM_vector.o BioFVM_mesh.o BioFVM_microenvironment.o BioFVM_solvers.o BioFVM_matlab.o BioFVM_utilities.o BioFVM_basic_agent.o BioFVM_MultiCellDS.o BioFVM_agent_container.o pugixml.o PhysiCell_phenotype.o PhysiCell_cell_container.o PhysiCell_standard_models.o PhysiCell_cell.o PhysiCell_custom.o PhysiCell_utilities.o PhysiCell_constants.o PhysiCell_signal_behavior.o PhysiCell_rules.o PhysiCell_basic_signaling.o PhysiCell_SVG.o PhysiCell_pathology.o PhysiCell_MultiCellDS.o PhysiCell_various_outputs.o PhysiCell_pugixml.o PhysiCell_settings.o PhysiCell_geometry.o custom.o main.cpp \n",
"make name \n",
"\n",
"Executable name is virus-sample\n",
Expand Down Expand Up @@ -110,6 +86,9 @@
"fileName = \"Model_Struct.ini\" # Configuration file path\n",
"key_model = \"physicell_model\" # Name of model strucure in the config file\n",
"\n",
"# Get PhysiCell, if not exist, it will be downloaded - Alternatively, you can change the paths in the Model_Struct.ini file to a PhysiCell folder on your system.\n",
"get_physicell(target_dir=\".\")\n",
"\n",
"# Generate the model exploration structure physicell_model.\n",
"PhysiCellModel = PhysiCell_Model(fileName, key_model)\n",
"\n",
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63 changes: 36 additions & 27 deletions examples/ex2_runModel.ipynb
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Expand Up @@ -29,6 +29,8 @@
"name": "stdout",
"output_type": "stream",
"text": [
"PhysiCell already exists at: PhysiCell-master\n",
"Skipping download. Use force_download=True to override.\n",
"\t> Constructor PhysiCell_Model: physicell_model_2 at Model_Struct.ini...\n",
"\t\t>> Reading config file: Model_Struct.ini ...\n",
"\t\t>> Checking executable format ...\n",
Expand All @@ -38,12 +40,16 @@
}
],
"source": [
"from uq_physicell import PhysiCell_Model\n",
"from uq_physicell import PhysiCell_Model, get_physicell\n",
"from uq_physicell.utils import summ_func_FinalPopLiveDead\n",
"import numpy as np\n",
"\n",
"fileName = \"Model_Struct.ini\"\n",
"key_model = \"physicell_model_2\"\n",
"\n",
"# Get PhysiCell, if not exist, it will be downloaded - Alternatively, you can change the paths in the Model_Struct.ini file to a PhysiCell folder on your system.\n",
"get_physicell(target_dir=\".\")\n",
"\n",
"# Create the structure of model exploration\n",
"PhysiCellModel = PhysiCell_Model(fileName, key_model, verbose=True)"
]
Expand Down Expand Up @@ -74,7 +80,8 @@
"\t\t\t>>> Setting up XML input...\n",
"\t\t\t>>> Generating XML file config2/config_S000000_00.xml ...\n",
"\t\t>> Running model ...\n",
"Registered process 0_0 with PID 77361\n",
"Registered process 0_0 with PID 61436 - running simulation ...\n",
"\t\t>> Simulation completed successfully!\n",
"\t\t>> Removing config files ...\n"
]
}
Expand Down Expand Up @@ -110,9 +117,10 @@
"\t\t\t>>> Setting up XML input...\n",
"\t\t\t>>> Generating XML file config2/config_S000000_00.xml ...\n",
"\t\t>> Running model ...\n",
"Registered process 0_0 with PID 77408\n",
"Registered process 0_0 with PID 61470 - running simulation ...\n",
"\t\t>> Simulation completed successfully!\n",
"\t\t>> Removing config files ...\n",
"\t\t>> Running summary function: <function summ_func_FinalPopLiveDead at 0x11e40b100> ...\n",
"\t\t>> Running summary function: <function summ_func_FinalPopLiveDead at 0x11fac31a0> ...\n",
"\t\t\t>>> Returning summary data ...\n"
]
},
Expand Down Expand Up @@ -155,7 +163,7 @@
" <td>0</td>\n",
" <td>50</td>\n",
" <td>0</td>\n",
" <td>20.119688</td>\n",
" <td>20.553828</td>\n",
" <td>0.75</td>\n",
" <td>0.5</td>\n",
" </tr>\n",
Expand All @@ -165,7 +173,7 @@
],
"text/plain": [
" time sampleID replicateID live_cells dead_cells run_time_sec \\\n",
"0 2880.01 0 0 50 0 20.119688 \n",
"0 2880.01 0 0 50 0 20.553828 \n",
"\n",
" viral_replication_rate min_virion_count \n",
"0 0.75 0.5 "
Expand Down Expand Up @@ -206,9 +214,10 @@
"\t\t\t>>> Setting up XML input...\n",
"\t\t\t>>> Generating XML file config2/config_S000001_00.xml ...\n",
"\t\t>> Running model ...\n",
"Registered process 1_0 with PID 78228\n",
"Registered process 1_0 with PID 61500 - running simulation ...\n",
"\t\t>> Simulation completed successfully!\n",
"\t\t>> Removing config files ...\n",
"\t\t>> Running summary function: <function custom_summary_func at 0x14ef62700> ...\n",
"\t\t>> Running summary function: <function custom_summary_func at 0x1557132e0> ...\n",
"\t\t\t>>> Returning summary data ...\n"
]
},
Expand Down Expand Up @@ -251,7 +260,7 @@
" <td>0</td>\n",
" <td>1060</td>\n",
" <td>0</td>\n",
" <td>0.000008</td>\n",
" <td>0.000007</td>\n",
" <td>0.8</td>\n",
" <td>0.55</td>\n",
" </tr>\n",
Expand All @@ -260,9 +269,9 @@
" <td>360.0</td>\n",
" <td>1</td>\n",
" <td>0</td>\n",
" <td>50</td>\n",
" <td>72</td>\n",
" <td>0</td>\n",
" <td>5.718475</td>\n",
" <td>5.493968</td>\n",
" <td>0.8</td>\n",
" <td>0.55</td>\n",
" </tr>\n",
Expand All @@ -273,7 +282,7 @@
" <td>0</td>\n",
" <td>50</td>\n",
" <td>0</td>\n",
" <td>7.785989</td>\n",
" <td>7.771156</td>\n",
" <td>0.8</td>\n",
" <td>0.55</td>\n",
" </tr>\n",
Expand All @@ -284,7 +293,7 @@
" <td>0</td>\n",
" <td>50</td>\n",
" <td>0</td>\n",
" <td>9.892772</td>\n",
" <td>10.041700</td>\n",
" <td>0.8</td>\n",
" <td>0.55</td>\n",
" </tr>\n",
Expand All @@ -295,7 +304,7 @@
" <td>0</td>\n",
" <td>50</td>\n",
" <td>0</td>\n",
" <td>12.036282</td>\n",
" <td>12.299380</td>\n",
" <td>0.8</td>\n",
" <td>0.55</td>\n",
" </tr>\n",
Expand All @@ -306,7 +315,7 @@
" <td>0</td>\n",
" <td>50</td>\n",
" <td>0</td>\n",
" <td>14.214356</td>\n",
" <td>14.533652</td>\n",
" <td>0.8</td>\n",
" <td>0.55</td>\n",
" </tr>\n",
Expand All @@ -317,7 +326,7 @@
" <td>0</td>\n",
" <td>50</td>\n",
" <td>0</td>\n",
" <td>16.376806</td>\n",
" <td>16.705065</td>\n",
" <td>0.8</td>\n",
" <td>0.55</td>\n",
" </tr>\n",
Expand All @@ -328,7 +337,7 @@
" <td>0</td>\n",
" <td>50</td>\n",
" <td>0</td>\n",
" <td>18.623699</td>\n",
" <td>18.924461</td>\n",
" <td>0.8</td>\n",
" <td>0.55</td>\n",
" </tr>\n",
Expand All @@ -339,7 +348,7 @@
" <td>0</td>\n",
" <td>50</td>\n",
" <td>0</td>\n",
" <td>20.752024</td>\n",
" <td>21.094291</td>\n",
" <td>0.8</td>\n",
" <td>0.55</td>\n",
" </tr>\n",
Expand All @@ -349,15 +358,15 @@
],
"text/plain": [
" time sampleID replicateID live_cells dead_cells run_time_sec \\\n",
"0 0.0 1 0 1060 0 0.000008 \n",
"1 360.0 1 0 50 0 5.718475 \n",
"2 720.0 1 0 50 0 7.785989 \n",
"3 1080.0 1 0 50 0 9.892772 \n",
"4 1440.0 1 0 50 0 12.036282 \n",
"5 1800.0 1 0 50 0 14.214356 \n",
"6 2160.0 1 0 50 0 16.376806 \n",
"7 2520.0 1 0 50 0 18.623699 \n",
"8 2880.0 1 0 50 0 20.752024 \n",
"0 0.0 1 0 1060 0 0.000007 \n",
"1 360.0 1 0 72 0 5.493968 \n",
"2 720.0 1 0 50 0 7.771156 \n",
"3 1080.0 1 0 50 0 10.041700 \n",
"4 1440.0 1 0 50 0 12.299380 \n",
"5 1800.0 1 0 50 0 14.533652 \n",
"6 2160.0 1 0 50 0 16.705065 \n",
"7 2520.0 1 0 50 0 18.924461 \n",
"8 2880.0 1 0 50 0 21.094291 \n",
"\n",
" viral_replication_rate min_virion_count \n",
"0 0.8 0.55 \n",
Expand Down
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