physioblocks 1.0.0__tar.gz

physioblocks-1.0.0/.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,28 @@
+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behavior:
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Desktop (please complete the following information):**
+ - OS: [e.g. iOS]
+ - Version [e.g. 22]
+
+**(Optional) Additional Information**
+Here you can add additional information, screenshots, links to external projects, articles, etc

physioblocks-1.0.0/.github/ISSUE_TEMPLATE/documentation.md

@@ -0,0 +1,17 @@
+---
+name: Documentation
+about: Request changes or additions to the documentation
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Description**
+Describe here the issue with the documentation. It can be a section that is not clear enough, a mistake, typo, etc, or even a request for a full section that you think is missing.
+
+**(Optional) Suggestions**
+Here, you can provide suggestions that would solve the documentation issue.
+
+**(Optional) Additional Information**
+Here you can add additional information, screenshots, links to external projects, articles, etc

physioblocks-1.0.0/.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,20 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**(Optional) Additional Information**
+Here you can add additional information, screenshots, links to external projects, articles, etc

physioblocks-1.0.0/.gitignore

@@ -0,0 +1,7 @@
+.DS_Store
+.coverage
+.vscode
+.tox
+.python-version
+__pycache__
+dist

physioblocks-1.0.0/.gitlab/issue_templates/Bug.md

@@ -0,0 +1,23 @@
+### Description
+
+<!-- Short bug description -->
+
+### Steps to reproduce
+
+<!-- Describe how to reproduce the bug step by step -->
+
+### Expected Behavior
+
+<!-- Describe the expected behavior WITHOUT the bug -->
+
+### (Optional) Additional Information
+
+<!-- Here you can add additional information, screenshots, links to external projects, code samples, articles, etc -->
+
+### (Optional) Suggestions
+
+<!-- Here you can suggest fixes ideas -->
+
+
+/label ~"bug"
+/assign @cdrieu

physioblocks-1.0.0/.gitlab/issue_templates/Documentation.md

@@ -0,0 +1,14 @@
+### Description
+
+<!-- Description of the changes required -->
+
+### (Optional) Suggestions
+
+<!-- Here, you can provide suggestions, screenshots, drafts, etc -->
+
+### (Optional) Additional Information
+
+<!-- Here you can add additional information, screenshots, links to external projects, code samples, articles, etc -->
+
+/label ~"doc"
+/assign @cdrieu

physioblocks-1.0.0/.gitlab/issue_templates/Feature.md

@@ -0,0 +1,19 @@
+### Use Case
+
+<!-- Describe the problem the new feature should solve -->
+
+### Solution
+
+<!-- Describe what the feature should do to solve the problem -->
+
+### (Optional) Alternatives
+
+<!-- Alternatives solutions to consider -->
+
+### (Optional) Additional Information
+
+<!-- Here you can add additional information, screenshots, links to external projects, code samples, articles, etc -->
+
+
+/label ~"feature"
+/assign @cdrieu

physioblocks-1.0.0/.gitlab-ci.yml

@@ -0,0 +1,148 @@
+
+variables:
+  DEBIAN_PYENV_TAG: $CI_REGISTRY_IMAGE:debian-pyenv
+  DEBIAN_LATEX_TAG: $CI_REGISTRY_IMAGE:debian-latex
+
+# Build containers
+docker debian pyenv:
+  image: docker:20.10.16
+  stage: .pre
+  tags:
+    - ci.inria.fr
+    - small
+  rules:
+    - changes:
+      - docker/**/*
+      when: always
+    - when: manual
+      allow_failure: true
+  before_script:
+    - docker login -u $CI_REGISTRY_USER -p $CI_REGISTRY_PASSWORD $CI_REGISTRY
+  script:
+    - docker image build -t $DEBIAN_PYENV_TAG -f ./docker/pyenv/Dockerfile .
+    - docker push $DEBIAN_PYENV_TAG
+
+docker debian latex:
+  image: docker:20.10.16
+  stage: .pre
+  tags:
+    - ci.inria.fr
+    - small 
+  rules:
+    - changes:
+      - docker/**/*
+      when: always
+    - when: manual
+      allow_failure: true
+  needs: ["docker debian pyenv"]
+  before_script:
+    - docker login -u $CI_REGISTRY_USER -p $CI_REGISTRY_PASSWORD $CI_REGISTRY
+  script:
+    - docker image build -t $DEBIAN_LATEX_TAG -f ./docker/latex/Dockerfile --build-arg BASE_IMAGE_TAG=$DEBIAN_PYENV_TAG .
+    - docker push $DEBIAN_LATEX_TAG
+
+# Build Package
+build debian:
+  image: $DEBIAN_PYENV_TAG
+  stage: build
+  tags:
+    - ci.inria.fr
+    - large
+  script: 
+    - pip install --upgrade pip
+    - pip install --upgrade build
+    - python -m build
+  artifacts:
+    paths:
+      - dist/
+
+# Run tests on debian
+test debian:
+  image: $DEBIAN_PYENV_TAG
+  stage: test
+  tags:
+    - ci.inria.fr
+    - small
+  script:
+    - pip install .[tox]
+    - tox
+  artifacts:
+    paths:
+      - htmlcov
+
+# Run reference simulation and trace the comparison with the reference
+test references debian:
+  image: $DEBIAN_PYENV_TAG
+  stage: test
+  tags:
+    - ci.inria.fr
+    - large
+  script:
+    - pip install .
+    - python -m physioblocks.launcher.configure -d ./launcher
+    - python -m physioblocks.launcher references/circulation_alone_sim.jsonc -d launcher -t --compare tests/tests_references/circulation_alone/ref_circulation_alone_sim.csv -s Circulation
+    - python -m physioblocks.launcher references/spherical_heart_sim.jsonc -d launcher -t --compare tests/tests_references/spherical_heart/ref_spherical_heart_sim.csv -s SphericalHeart
+    - python -m physioblocks.launcher references/spherical_heart_respiration_sim.jsonc -d launcher -t --compare tests/tests_references/spherical_heart/ref_spherical_heart_respiration_sim.csv -s SphericalHeartRespiration
+  artifacts:
+    paths:
+      - launcher/simulations
+
+test windows:
+  stage: test
+  tags:
+    - windows
+  script:
+    - pip install .[tox]
+    - tox
+
+# Run reference simulation and trace the comparison with the reference
+test references windows:
+  stage: test
+  tags:
+    - windows
+  script:
+    - pip install .
+    - python -m physioblocks.launcher.configure -d ./launcher 
+    - python -m physioblocks.launcher references/circulation_alone_sim.jsonc -d launcher -t --compare tests/tests_references/circulation_alone/ref_circulation_alone_sim.csv -s Circulation
+    - python -m physioblocks.launcher references/spherical_heart_sim.jsonc -d launcher -t --compare tests/tests_references/spherical_heart/ref_spherical_heart_sim.csv -s SphericalHeart
+    - python -m physioblocks.launcher references/spherical_heart_respiration_sim.jsonc -d launcher -t --compare tests/tests_references/spherical_heart/ref_spherical_heart_respiration_sim.csv -s SphericalHeartRespiration
+  artifacts:
+    paths:
+      - launcher/simulations
+
+# Build documentation and deploy to Pages
+pages:
+  image: $DEBIAN_LATEX_TAG
+  stage: deploy
+  tags:
+    - ci.inria.fr
+    - large
+  script:
+    - pip install .[doc]
+    - cd doc
+    - make html
+    - mv build/html ../public/
+  artifacts:
+    paths:
+      - public
+  rules:
+    - if: $CI_COMMIT_TAG
+
+publish package:
+  image: $DEBIAN_LATEX_TAG
+  stage: deploy
+  tags:
+    - ci.inria.fr
+    - large
+  variables:
+    TWINE_USERNAME: __token__
+    TWINE_PASSWORD: ${PYPI_TOKEN}
+  script:
+    - pip install twine
+    - pip install --upgrade twine 
+    - python -m twine upload --repository pypi dist/* 
+  artifacts:
+    paths:
+      - dist/
+  rules:
+    - if: $CI_COMMIT_TAG

physioblocks-1.0.0/PKG-INFO

@@ -0,0 +1,127 @@
+Metadata-Version: 2.4
+Name: physioblocks
+Version: 1.0.0
+Dynamic: Author
+Dynamic: Author-email
+Dynamic: License
+Dynamic: License-Expression
+Summary: Physioblocks allows the simulation of dynamical models of physiological systems
+Project-URL: Homepage, https://github.com/physioblocks/physioblocks
+Project-URL: Documentation, https://physioblocks.gitlabpages.inria.fr/physioblocks/
+Project-URL: Issues, https://github.com/physioblocks/physioblocks/issues
+Project-URL: Discussions, https://github.com/physioblocks/physioblocks/discussions
+License-File: licenses/GPL-3.0-only.txt
+License-File: licenses/LGPL-3.0-only.txt
+Keywords: block diagram,cardiovascular modeling,dynamical systems,physiology
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: GNU Lesser General Public License v3 (LGPLv3)
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Classifier: Topic :: Scientific/Engineering :: Mathematics
+Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
+Requires-Python: >=3.10
+Requires-Dist: numpy
+Requires-Dist: pandas
+Requires-Dist: plotly
+Requires-Dist: pyarrow
+Requires-Dist: regex
+Requires-Dist: scipy
+Provides-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'
+Requires-Dist: ruff; extra == 'quality'
+Provides-Extra: test
+Requires-Dist: coverage; extra == 'test'
+Requires-Dist: pytest>=8; extra == 'test'
+Provides-Extra: tox
+Requires-Dist: tox>=4; extra == 'tox'
+Description-Content-Type: text/markdown
+
+# PhysioBlocks
+
+PhysioBlocks allows the simulation of dynamical models of physiological systems.
+
+## User Levels
+
+They are several use cases for PhysioBlocks depending on the user profile:
+
+* __Level 1:__ Configure and run physiological systems simulation (for pre-existing systems)
+* __Level 2:__ Create new systems with existing blocks without writing code
+* __Level 3:__ Write and add new blocks to the library.
+
+## Principle
+
+* A __Net__ (system) is built from __Nodes__ and __Blocks__ connected by those nodes.
+* At each node in the net, connected blocks share __Degrees of Freedom__ (ex: pressure) and send __Fluxes__ that verify Kirchhoff Law.
+* __ModelComponents__ concatenate blocks equations to the global system (if necessary, for modularity purposes within the block)
+
+## Interactions
+
+__Level 1:__ Configure and run a simulation : JSON
+* Update the model parameters
+
+__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
+* Declare the quantities to use in the model
+* Write the fluxes and equations
+
+## Documentation
+
+Here are the links to the sections of the [full documentation](https://physioblocks.gitlabpages.inria.fr/physioblocks/):
+* [Installation](https://physioblocks.gitlabpages.inria.fr/physioblocks/installation.html)
+* [User Guide](https://physioblocks.gitlabpages.inria.fr/physioblocks/user_guide.html)
+* [Library](https://physioblocks.gitlabpages.inria.fr/physioblocks/library.html)
+* [API Reference](https://physioblocks.gitlabpages.inria.fr/physioblocks/api_reference.html)
+
+## Quick start
+
+Complete instructions are available in the [documentation](https://physioblocks.gitlabpages.inria.fr/physioblocks/). This instructions will enable you to launch a reference simulation.
+
+### Installation
+
+This project requires a recent version of python installed.
+Then: 
+```
+    pip install physioblocks
+```
+
+### Configuration
+
+To configure PhysioBlocks Launcher:
+
+```
+# Create an empty folder where you want to store simulations results.
+mkdir $LAUNCHER_FOLDER_PATH$
+
+# Configure the folder
+python -m physioblocks.launcher.configure -d $LAUNCHER_FOLDER_PATH$ -v
+```
+
+### Launch a simulation
+
+With a Launcher folder configured:
+
+```
+# Move to your configured launcher folder
+cd $LAUNCHER_FOLDER_PATH$
+
+#  Launch a reference simulation
+python -m physioblocks.launcher references/spherical_heart_sim.jsonc -v -t -s QuickStart
+
+# This can take some time.
+```
+
+
+Results will be available in the `$LAUNCHER_FOLDER_PATH$/simulations/QuickStart` series folder.

physioblocks-1.0.0/README.md

@@ -0,0 +1,79 @@
+# PhysioBlocks
+
+PhysioBlocks allows the simulation of dynamical models of physiological systems.
+
+## User Levels
+
+They are several use cases for PhysioBlocks depending on the user profile:
+
+* __Level 1:__ Configure and run physiological systems simulation (for pre-existing systems)
+* __Level 2:__ Create new systems with existing blocks without writing code
+* __Level 3:__ Write and add new blocks to the library.
+
+## Principle
+
+* A __Net__ (system) is built from __Nodes__ and __Blocks__ connected by those nodes.
+* At each node in the net, connected blocks share __Degrees of Freedom__ (ex: pressure) and send __Fluxes__ that verify Kirchhoff Law.
+* __ModelComponents__ concatenate blocks equations to the global system (if necessary, for modularity purposes within the block)
+
+## Interactions
+
+__Level 1:__ Configure and run a simulation : JSON
+* Update the model parameters
+
+__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
+* Declare the quantities to use in the model
+* Write the fluxes and equations
+
+## Documentation
+
+Here are the links to the sections of the [full documentation](https://physioblocks.gitlabpages.inria.fr/physioblocks/):
+* [Installation](https://physioblocks.gitlabpages.inria.fr/physioblocks/installation.html)
+* [User Guide](https://physioblocks.gitlabpages.inria.fr/physioblocks/user_guide.html)
+* [Library](https://physioblocks.gitlabpages.inria.fr/physioblocks/library.html)
+* [API Reference](https://physioblocks.gitlabpages.inria.fr/physioblocks/api_reference.html)
+
+## Quick start
+
+Complete instructions are available in the [documentation](https://physioblocks.gitlabpages.inria.fr/physioblocks/). This instructions will enable you to launch a reference simulation.
+
+### Installation
+
+This project requires a recent version of python installed.
+Then: 
+```
+    pip install physioblocks
+```
+
+### Configuration
+
+To configure PhysioBlocks Launcher:
+
+```
+# Create an empty folder where you want to store simulations results.
+mkdir $LAUNCHER_FOLDER_PATH$
+
+# Configure the folder
+python -m physioblocks.launcher.configure -d $LAUNCHER_FOLDER_PATH$ -v
+```
+
+### Launch a simulation
+
+With a Launcher folder configured:
+
+```
+# Move to your configured launcher folder
+cd $LAUNCHER_FOLDER_PATH$
+
+#  Launch a reference simulation
+python -m physioblocks.launcher references/spherical_heart_sim.jsonc -v -t -s QuickStart
+
+# This can take some time.
+```
+
+
+Results will be available in the `$LAUNCHER_FOLDER_PATH$/simulations/QuickStart` series folder.

physioblocks-1.0.0/doc/.gitignore

@@ -0,0 +1 @@
+build

physioblocks-1.0.0/doc/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

physioblocks-1.0.0/doc/build/html/.buildinfo

@@ -0,0 +1,4 @@
+# Sphinx build info version 1
+# This file records the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: efd432c11c801e0d2c433b68089ef1c3
+tags: 645f666f9bcd5a90fca523b33c5a78b7