pyVertexModel 1.0.2.dev0__tar.gz

pyvertexmodel-1.0.2.dev0/.gitattributes

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+.tif filter=lfs diff=lfs merge=lfs -text
+*.tif filter=lfs diff=lfs merge=lfs -text

pyvertexmodel-1.0.2.dev0/.github/ISSUE_TEMPLATE/bug_report.md

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+---
+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.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**Desktop (please complete the following information):**
+ - OS: [e.g. iOS]
+ - Browser [e.g. chrome, safari]
+ - Version [e.g. 22]
+
+**Smartphone (please complete the following information):**
+ - Device: [e.g. iPhone6]
+ - OS: [e.g. iOS8.1]
+ - Browser [e.g. stock browser, safari]
+ - Version [e.g. 22]
+
+**Additional context**
+Add any other context about the problem here.

pyvertexmodel-1.0.2.dev0/.github/ISSUE_TEMPLATE/feature_request.md

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+---
+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.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

pyvertexmodel-1.0.2.dev0/.github/workflows/tests.yaml

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+name: Run Python Tests
+
+on:
+  workflow_dispatch:
+  push:
+    branches: [ main megha]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Set up Python 3.9
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.9
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install -r requirements.txt
+
+    - name: Build Cython extensions
+      run: |
+        python setup.py build_ext --inplace
+
+    - name: Run tests
+      run: |
+        pip install pytest pytest-cov
+        pytest Tests/ -k "not filename" --doctest-modules --junitxml=test-results.xml --cov . --cov-report=xml --cov-report=html
+      continue-on-error: true
+
+    - name: Upload coverage reports to Codecov
+      uses: codecov/codecov-action@v4.0.1
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}
+        slug: Pablo1990/pyVertexModel
+
+    - name: Coveralls
+      uses: coverallsapp/github-action@v2
+      with:
+        file: coverage.xml
+
+    - name: TestForest Dashboard
+      uses: test-summary/action@v2.3
+      with:
+        paths: "test-results.xml"
+

pyvertexmodel-1.0.2.dev0/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+src/pyVertexModel/Kg/build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+.DS_Store
+
+*.png
+
+src/pyVertexModel/Kg/kg_functions.c
+
+*.html
+
+*.csv
+
+*.lcov
+
+Result/*
+
+.idea/*
+
+src/pyVertexModel/Result/*
+
+*.xz
+
+data/
+
+.nextflow/
+
+.idea/misc.xml
+
+*.db
+
+*.o
+
+Input
+
+*.xlsx

pyvertexmodel-1.0.2.dev0/.idea/.gitignore

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+# Default ignored files
+/shelf/
+/workspace.xml
+# Editor-based HTTP Client requests
+/httpRequests/
+# Datasource local storage ignored files
+/dataSources/
+/dataSources.local.xml
+# GitHub Copilot persisted chat sessions
+/copilot/chatSessions

pyvertexmodel-1.0.2.dev0/.idea/inspectionProfiles/profiles_settings.xml

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+<component name="InspectionProjectProfileManager">
+  <settings>
+    <option name="USE_PROJECT_PROFILE" value="false" />
+    <version value="1.0" />
+  </settings>
+</component>

pyvertexmodel-1.0.2.dev0/.idea/modules.xml

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+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="ProjectModuleManager">
+    <modules>
+      <module fileurl="file://$PROJECT_DIR$/.idea/pyVertexModel.iml" filepath="$PROJECT_DIR$/.idea/pyVertexModel.iml" />
+    </modules>
+  </component>
+</project>

pyvertexmodel-1.0.2.dev0/.idea/other.xml

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+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="PySciProjectComponent">
+    <option name="PY_SCI_VIEW" value="true" />
+    <option name="PY_INTERACTIVE_PLOTS_SUGGESTED" value="true" />
+  </component>
+</project>

pyvertexmodel-1.0.2.dev0/.idea/pyVertexModel.iml

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+<?xml version="1.0" encoding="UTF-8"?>
+<module type="PYTHON_MODULE" version="4">
+  <component name="NewModuleRootManager">
+    <content url="file://$MODULE_DIR$">
+      <excludeFolder url="file://$MODULE_DIR$/Result" />
+    </content>
+    <orderEntry type="jdk" jdkName="pyVertexModel" jdkType="Python SDK" />
+    <orderEntry type="sourceFolder" forTests="false" />
+  </component>
+  <component name="PackageRequirementsSettings">
+    <option name="removeUnused" value="true" />
+    <option name="keepMatchingSpecifier" value="false" />
+  </component>
+  <component name="PyDocumentationSettings">
+    <option name="renderExternalDocumentation" value="true" />
+  </component>
+</module>

pyvertexmodel-1.0.2.dev0/.idea/vcs.xml

@@ -0,0 +1,6 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="VcsDirectoryMappings">
+    <mapping directory="" vcs="Git" />
+  </component>
+</project>

pyvertexmodel-1.0.2.dev0/.python-version

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+3.10

pyvertexmodel-1.0.2.dev0/.run/analyse_simulations.run.xml

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+<component name="ProjectRunConfigurationManager">
+  <configuration default="false" name="analyse_simulations" type="PythonConfigurationType" factoryName="Python" singleton="false" nameIsGenerated="true">
+    <module name="pyVertexModel" />
+    <option name="ENV_FILES" value="" />
+    <option name="INTERPRETER_OPTIONS" value="" />
+    <option name="PARENT_ENVS" value="true" />
+    <envs>
+      <env name="PYTHONUNBUFFERED" value="1" />
+    </envs>
+    <option name="SDK_HOME" value="" />
+    <option name="WORKING_DIRECTORY" value="$PROJECT_DIR$/src/pyVertexModel/analysis" />
+    <option name="IS_MODULE_SDK" value="true" />
+    <option name="ADD_CONTENT_ROOTS" value="true" />
+    <option name="ADD_SOURCE_ROOTS" value="true" />
+    <EXTENSION ID="PythonCoverageRunConfigurationExtension" runner="coverage.py" />
+    <option name="SCRIPT_NAME" value="$PROJECT_DIR$/src/pyVertexModel/analysis/analyse_simulations.py" />
+    <option name="PARAMETERS" value="build_ext --inplace" />
+    <option name="SHOW_COMMAND_LINE" value="false" />
+    <option name="EMULATE_TERMINAL" value="false" />
+    <option name="MODULE_MODE" value="false" />
+    <option name="REDIRECT_INPUT" value="false" />
+    <option name="INPUT_FILE" value="" />
+    <method v="2" />
+  </configuration>
+</component>

pyvertexmodel-1.0.2.dev0/CODE_OF_CONDUCT.md

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+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, religion, or sexual identity
+and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+  and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the
+  overall community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or
+  advances of any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email
+  address, without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, and will communicate reasons for moderation
+decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when
+an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official e-mail address,
+posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the community leaders responsible for enforcement at
+mailto:pablovm1990@gmail.com.
+All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series
+of actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or
+permanent ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior,  harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within
+the community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.0, available at
+https://www.contributor-covenant.org/version/2/0/code_of_conduct.html.
+
+Community Impact Guidelines were inspired by [Mozilla's code of conduct
+enforcement ladder](https://github.com/mozilla/diversity).
+
+[homepage]: https://www.contributor-covenant.org
+
+For answers to common questions about this code of conduct, see the FAQ at
+https://www.contributor-covenant.org/faq. Translations are available at
+https://www.contributor-covenant.org/translations.

pyvertexmodel-1.0.2.dev0/LICENSE

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+MIT License
+
+Copyright (c) 2023 Pablo Vicente Munuera
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

pyvertexmodel-1.0.2.dev0/PKG-INFO

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+Metadata-Version: 2.4
+Name: pyVertexModel
+Version: 1.0.2.dev0
+Home-page: 
+License-File: LICENSE
+Requires-Dist: cython
+Requires-Dist: numpy
+Requires-Dist: scipy
+Requires-Dist: pillow
+Requires-Dist: scikit-image
+Requires-Dist: cython
+Requires-Dist: vtk
+Requires-Dist: pandas
+Requires-Dist: networkx
+Requires-Dist: pyvista
+Requires-Dist: scikit-learn
+Requires-Dist: matplotlib
+Dynamic: license-file

pyvertexmodel-1.0.2.dev0/README.md

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+![logo.png](logo.png)
+
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.17649953.svg)](https://doi.org/10.5281/zenodo.17649953)
+[![Coverage Status](https://coveralls.io/repos/github/Pablo1990/pyVertexModel/badge.svg?branch=main)](https://coveralls.io/github/Pablo1990/pyVertexModel?branch=main)
+[![codecov](https://codecov.io/gh/Pablo1990/pyVertexModel/graph/badge.svg?token=AKGWS79Z61)](https://codecov.io/gh/Pablo1990/pyVertexModel)
+
+pyVertexModel is versatile 3D vertex model to model tissue and cell mechanics, in particular, regarding tissue repair.
+
+Please, to ensure you use a polished version, use the 'paper' version/branch: https://github.com/Pablo1990/pyVertexModel/tree/paper 
+
+## Environment
+
+```bash
+conda create -n pyVertexModel python=3.9
+conda activate pyVertexModel
+pip install -r requirements.txt
+```
+
+## Usage
+The first time you run the code, you need to compile the cython code. To do so, run the following commands:
+```bash
+python setup.py build_ext --inplace
+```
+
+To run the code, you can use the following command:
+```bash
+python main.py
+```
+
+To run the tests, we use 'tox':
+```bash
+tox
+```
+
+## Changing the parameters
+You can change the parameters of the model in the `parameters/set.py` file. At the moment, you should change it under 
+the 'wing_disc()' function.
+
+Each simulation will be saved in a different folder in the `results` directory. The name of the folder will be the date and time of the simulation.
+
+## Help
+
+For any issues with the code, you can put an issue in the repository.
+For other matters, you can contact Pablo Vicente Munuera (p.munuera@ucl.ac.uk).
+

pyvertexmodel-1.0.2.dev0/SECURITY.md

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+# Security Policy
+
+There should not be any breach of your data or security issue with this project

pyvertexmodel-1.0.2.dev0/Tests/__init__.py

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+import os
+
+TEST_DIRECTORY = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))