fucciphase 0.0.1__tar.gz

fucciphase-0.0.1/.copier-answers.yml

@@ -0,0 +1,18 @@
+# Do not edit - changes here will be overwritten by Copier
+_commit: v1.0
+_src_path: gh:pydev-guide/pyrepo-copier
+author_email: first.last@example.com
+author_name: Joran Deschamps
+git_versioning: true
+github_username: jdeschamps
+mode: tooling
+module_name: fucciphase
+project_license: BSD-3-Clause
+project_name: fucciphase
+project_short_description: Cell cycle analysis plugin.
+test_pre_release: true
+use_black: true
+use_mypy: true
+use_pre_commit: true
+use_ruff: true
+

fucciphase-0.0.1/.github/ISSUE_TEMPLATE.md

@@ -0,0 +1,15 @@
+* fucciphase version:
+* Python version:
+* Operating System:
+
+### Description
+
+Describe what you were trying to get done.
+Tell us what happened, what went wrong, and what you expected to happen.
+
+### What I Did
+
+```
+Paste the command(s) you ran and the output.
+If there was a crash, please include the traceback here.
+```

fucciphase-0.0.1/.github/TEST_FAIL_TEMPLATE.md

@@ -0,0 +1,12 @@
+---
+title: "{{ env.TITLE }}"
+labels: [bug]
+---
+The {{ workflow }} workflow failed on {{ date | date("YYYY-MM-DD HH:mm") }} UTC
+
+The most recent failing test was on {{ env.PLATFORM }} py{{ env.PYTHON }}
+with commit: {{ sha }}
+
+Full run: https://github.com/{{ repo }}/actions/runs/{{ env.RUN_ID }}
+
+(This post will be updated if another test fails, as long as this issue remains open.)

fucciphase-0.0.1/.github/dependabot.yml

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+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    commit-message:
+      prefix: "ci(dependabot):"

fucciphase-0.0.1/.github/workflows/ci.yml

@@ -0,0 +1,107 @@
+name: CI
+
+on:
+  push:
+    branches:
+      - main
+    tags:
+      - "v*"
+  pull_request:
+  workflow_dispatch:
+  schedule:
+    # run every week (for --pre release tests)
+    - cron: "0 0 * * 0"
+
+jobs:
+  check-manifest:
+    # check-manifest is a tool that checks that all files in version control are
+    # included in the sdist (unless explicitly excluded)
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v5
+      - run: pipx run check-manifest
+
+  test:
+    name: ${{ matrix.platform }} (${{ matrix.python-version }})
+    runs-on: ${{ matrix.platform }}
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
+        platform: [ubuntu-latest, macos-latest, windows-latest]
+
+    steps:
+      - name: 🛑 Cancel Previous Runs
+        uses: styfle/cancel-workflow-action@0.12.1
+        with:
+          access_token: ${{ github.token }}
+
+      - uses: actions/checkout@v5
+
+      - name: 🐍 Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v6
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache-dependency-path: "pyproject.toml"
+          cache: "pip"
+
+      - name: Install Dependencies
+        run: |
+          python -m pip install -U pip
+          # if running a cron job, we add the --pre flag to test against pre-releases
+          python -m pip install .[test] ${{ github.event_name == 'schedule' && '--pre' || ''  }}
+
+      - name: 🧪 Run Tests
+        run: pytest --color=yes --cov --cov-report=xml --cov-report=term-missing
+
+      # If something goes wrong with --pre tests, we can open an issue in the repo
+      - name: 📝 Report --pre Failures
+        if: failure() && github.event_name == 'schedule'
+        uses: JasonEtco/create-an-issue@v2
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          PLATFORM: ${{ matrix.platform }}
+          PYTHON: ${{ matrix.python-version }}
+          RUN_ID: ${{ github.run_id }}
+          TITLE: "[test-bot] pip install --pre is failing"
+        with:
+          filename: .github/TEST_FAIL_TEMPLATE.md
+          update_existing: true
+
+      - name: Coverage
+        uses: codecov/codecov-action@v5
+
+  deploy:
+    name: Release
+    needs: test
+    if: success() && startsWith(github.ref, 'refs/tags/') && github.event_name != 'schedule'
+    runs-on: ubuntu-latest
+
+    permissions:
+      # IMPORTANT: this permission is mandatory for trusted publishing
+      id-token: write
+
+      # This permission allows writing releases
+      contents: write
+
+    steps:
+      - uses: actions/checkout@v5
+        with:
+          fetch-depth: 0
+
+      - name: Set up Python
+        uses: actions/setup-python@v6
+        with:
+          python-version: "3.10"
+
+      - name: Build
+        run: |
+          python -m pip install build
+          python -m build
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+
+      - uses: softprops/action-gh-release@v2
+        with:
+          generate_release_notes: true

fucciphase-0.0.1/.gitignore

@@ -0,0 +1,123 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+
+.DS_Store
+
+# 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/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# dotenv
+.env
+
+# virtualenv
+.venv
+venv/
+ENV/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+
+# ruff
+.ruff_cache/
+
+# IDE settings
+.vscode/
+.idea/
+
+# images generated by examples
+example/*.pdf
+example/*.svg
+example/*.png
+
+# vim files
+*.swp
+
+# Sphinx files
+make.bat
+_build/

fucciphase-0.0.1/.pre-commit-config.yaml

@@ -0,0 +1,37 @@
+# enable pre-commit.ci at https://pre-commit.ci/
+# it adds:
+# 1. auto fixing pull requests
+# 2. auto updating the pre-commit configuration
+ci:
+  autoupdate_schedule: monthly
+  autofix_commit_msg: "style(pre-commit.ci): auto fixes [...]"
+  autoupdate_commit_msg: "ci(pre-commit.ci): autoupdate"
+
+repos:
+  - repo: https://github.com/abravalheri/validate-pyproject
+    rev: v0.24.1
+    hooks:
+      - id: validate-pyproject
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.12.11
+    hooks:
+      - id: ruff
+        types_or: [python, pyi, jupyter]
+        args: [--fix]
+      - id: ruff-format
+
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.17.1
+    hooks:
+      - id: mypy
+        files: "^src/"
+        additional_dependencies:
+          - numpy
+          - pandas
+
+  # strip out jupyter notebooks
+  - repo: https://github.com/kynan/nbstripout
+    rev: 0.8.1
+    hooks:
+      - id: nbstripout

fucciphase-0.0.1/LICENSE

@@ -0,0 +1,29 @@
+BSD 3-Clause License
+
+Copyright (c) 2023, Joran Deschamps
+Copyright (c) 2023, Julius Zimmermann (contributor)
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

fucciphase-0.0.1/PKG-INFO

@@ -0,0 +1,137 @@
+Metadata-Version: 2.4
+Name: fucciphase
+Version: 0.0.1
+Summary: Cell cycle analysis plugin.
+Project-URL: homepage, https://github.com/nobias-ht/fucciphase
+Project-URL: repository, https://github.com/nobias-ht/fucciphase
+Author-email: Joran Deschamps <joran.deschamps@fht.org>
+License: BSD-3-Clause
+License-File: LICENSE
+Classifier: Development Status :: 3 - Alpha
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Requires-Python: >=3.8
+Requires-Dist: dtaidistance
+Requires-Dist: lineagetree<1.5.0
+Requires-Dist: matplotlib
+Requires-Dist: monotonic-derivative
+Requires-Dist: numpy
+Requires-Dist: openpyxl
+Requires-Dist: pandas
+Requires-Dist: scipy
+Requires-Dist: svgwrite
+Provides-Extra: dev
+Requires-Dist: ipython; extra == 'dev'
+Requires-Dist: mypy; extra == 'dev'
+Requires-Dist: pdbpp; extra == 'dev'
+Requires-Dist: pre-commit; extra == 'dev'
+Requires-Dist: rich; extra == 'dev'
+Requires-Dist: ruff; extra == 'dev'
+Provides-Extra: doc
+Requires-Dist: sphinx; extra == 'doc'
+Provides-Extra: jupyter
+Requires-Dist: jupyter; extra == 'jupyter'
+Provides-Extra: test
+Requires-Dist: pytest; extra == 'test'
+Requires-Dist: pytest-cov; extra == 'test'
+Description-Content-Type: text/markdown
+
+# fucciphase
+
+[![License](https://img.shields.io/pypi/l/fucciphase.svg?color=green)](https://github.com/Synthetic-Physiology-Lab/fucciphase/raw/main/LICENSE)
+[![PyPI](https://img.shields.io/pypi/v/fucciphase.svg?color=green)](https://pypi.org/project/fucciphase)
+[![Python Version](https://img.shields.io/pypi/pyversions/fucciphase.svg?color=green)](https://python.org)
+[![CI](https://github.com/Synthetic-Physiology-Lab/fucciphase/actions/workflows/ci.yml/badge.svg)](https://github.com/Synthetic-Physiology-Lab/fucciphase/actions/workflows/ci.yml)
+[![codecov](https://codecov.io/gh/Synthetic-Physiology-Lab/fucciphase/branch/main/graph/badge.svg)](https://codecov.io/gh/Synthetic-Physiology-Lab/fucciphase)
+[![pre-commit.ci status](https://results.pre-commit.ci/badge/github/Synthetic-Physiology-Lab/fucciphase/main.svg)](https://results.pre-commit.ci/latest/github/Synthetic-Physiology-Lab/fucciphase/main)
+
+FUCCI cell cycle analysis plugin.
+Obtain cell cycle information from FUCCI fluorescence intensities.
+
+## Installation
+
+The best way to run fucciphase is to install it in a virtual conda environment.
+Make sure that git is installed and can be called from the command line.
+
+(SOON) To install from pip:
+
+```bash
+pip install fucciphase
+```
+
+If you wish to install it from source:
+    
+```bash
+git clone https://github.com/Synthetic-Physiology-Lab/fucciphase
+cd fucciphase
+pip install -e .
+```
+
+The installation should not take longer than a few seconds (depending on your internet connection).
+
+To use the notebooks, also install jupyter:
+    
+```bash
+pip install jupyter
+```
+
+## Usage
+
+Fucci phase currently supports loading a 
+[TrackMate](https://imagej.net/plugins/trackmate/) XML file:
+
+```python
+from fucciphase import process_trackmate
+from fucciphase.sensor import get_fuccisa_default_sensor
+
+trackmate_xml = "path/to/trackmate.xml"
+channel1 = "MEAN_INTENSITY_CH3"
+channel2 = "MEAN_INTENSITY_CH4"
+
+sensor = get_fuccisa_default_sensor()
+
+df = process_trackmate(trackmate_xml,
+                       channels=[channel1, channel2],
+		       sensor=sensor,
+                       thresholds=[0.1, 0.1])
+print(df)
+```
+
+The TrackMate XML is converted to a [Pandas](https://pandas.pydata.org/) DataFrame.
+Thus, in general data (e.g., stored in a CSV or XLSX file) that can be parsed into
+a DataFrame is supported.
+
+Have a look at the examples in the `example` folder to get more information!
+
+The runtime of the scripts depends on your datasize. 2D samples with a few hundred to a few thousand cells
+can be processed in a few minutes. Visualization in Napari can take a bit longer.
+Standard processing does not require a powerful computer.
+Make sure that you have sufficient RAM to load videos for visualization in Napari.
+
+## Development
+
+To develop fucciphase, clone the repository, install fucciphase in your environment
+and install the pre-commit hooks:
+
+```bash
+git clone https://github.com/Synthetic-Physiology-Lab/fucciphase
+cd fucciphase
+pip install -e ".[test, dev]"
+pre-commit install
+```
+
+If you want to build the documentation, replace the abovementioned pip install by:
+```bash
+pip install -e ".[test, dev, doc]"
+```
+
+## Cite us
+
+Di Sante, M., Pezzotti, M., Zimmermann, J., Enrico, A., Deschamps, J., Balmas, E.,
+Becca, S., Solito, S., Reali, A., Bertero, A., Jug, F. and Pasqualini, F.S., 2025.
+CALIPERS: Cell cycle-aware live imaging for phenotyping experiments and regeneration studies.
+bioRxiv, https://doi.org/10.1101/2024.12.19.629259 

fucciphase-0.0.1/README.md

@@ -0,0 +1,95 @@
+# fucciphase
+
+[![License](https://img.shields.io/pypi/l/fucciphase.svg?color=green)](https://github.com/Synthetic-Physiology-Lab/fucciphase/raw/main/LICENSE)
+[![PyPI](https://img.shields.io/pypi/v/fucciphase.svg?color=green)](https://pypi.org/project/fucciphase)
+[![Python Version](https://img.shields.io/pypi/pyversions/fucciphase.svg?color=green)](https://python.org)
+[![CI](https://github.com/Synthetic-Physiology-Lab/fucciphase/actions/workflows/ci.yml/badge.svg)](https://github.com/Synthetic-Physiology-Lab/fucciphase/actions/workflows/ci.yml)
+[![codecov](https://codecov.io/gh/Synthetic-Physiology-Lab/fucciphase/branch/main/graph/badge.svg)](https://codecov.io/gh/Synthetic-Physiology-Lab/fucciphase)
+[![pre-commit.ci status](https://results.pre-commit.ci/badge/github/Synthetic-Physiology-Lab/fucciphase/main.svg)](https://results.pre-commit.ci/latest/github/Synthetic-Physiology-Lab/fucciphase/main)
+
+FUCCI cell cycle analysis plugin.
+Obtain cell cycle information from FUCCI fluorescence intensities.
+
+## Installation
+
+The best way to run fucciphase is to install it in a virtual conda environment.
+Make sure that git is installed and can be called from the command line.
+
+(SOON) To install from pip:
+
+```bash
+pip install fucciphase
+```
+
+If you wish to install it from source:
+    
+```bash
+git clone https://github.com/Synthetic-Physiology-Lab/fucciphase
+cd fucciphase
+pip install -e .
+```
+
+The installation should not take longer than a few seconds (depending on your internet connection).
+
+To use the notebooks, also install jupyter:
+    
+```bash
+pip install jupyter
+```
+
+## Usage
+
+Fucci phase currently supports loading a 
+[TrackMate](https://imagej.net/plugins/trackmate/) XML file:
+
+```python
+from fucciphase import process_trackmate
+from fucciphase.sensor import get_fuccisa_default_sensor
+
+trackmate_xml = "path/to/trackmate.xml"
+channel1 = "MEAN_INTENSITY_CH3"
+channel2 = "MEAN_INTENSITY_CH4"
+
+sensor = get_fuccisa_default_sensor()
+
+df = process_trackmate(trackmate_xml,
+                       channels=[channel1, channel2],
+		       sensor=sensor,
+                       thresholds=[0.1, 0.1])
+print(df)
+```
+
+The TrackMate XML is converted to a [Pandas](https://pandas.pydata.org/) DataFrame.
+Thus, in general data (e.g., stored in a CSV or XLSX file) that can be parsed into
+a DataFrame is supported.
+
+Have a look at the examples in the `example` folder to get more information!
+
+The runtime of the scripts depends on your datasize. 2D samples with a few hundred to a few thousand cells
+can be processed in a few minutes. Visualization in Napari can take a bit longer.
+Standard processing does not require a powerful computer.
+Make sure that you have sufficient RAM to load videos for visualization in Napari.
+
+## Development
+
+To develop fucciphase, clone the repository, install fucciphase in your environment
+and install the pre-commit hooks:
+
+```bash
+git clone https://github.com/Synthetic-Physiology-Lab/fucciphase
+cd fucciphase
+pip install -e ".[test, dev]"
+pre-commit install
+```
+
+If you want to build the documentation, replace the abovementioned pip install by:
+```bash
+pip install -e ".[test, dev, doc]"
+```
+
+## Cite us
+
+Di Sante, M., Pezzotti, M., Zimmermann, J., Enrico, A., Deschamps, J., Balmas, E.,
+Becca, S., Solito, S., Reali, A., Bertero, A., Jug, F. and Pasqualini, F.S., 2025.
+CALIPERS: Cell cycle-aware live imaging for phenotyping experiments and regeneration studies.
+bioRxiv, https://doi.org/10.1101/2024.12.19.629259 

fucciphase-0.0.1/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     = .
+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)

fucciphase-0.0.1/doc/api.rst

@@ -0,0 +1,28 @@
+.. _API:
+
+API reference
+=============
+
+High-level API
+--------------
+
+.. automodule:: fucciphase.fucci_phase
+     :members:
+
+Compute phases
+--------------
+
+.. automodule:: fucciphase.phase
+     :members:
+
+Plots
+-----
+
+.. automodule:: fucciphase.plot
+     :members:
+
+Input/Output
+------------
+
+.. automodule:: fucciphase.io
+     :members:

fucciphase-0.0.1/doc/conf.py

@@ -0,0 +1,31 @@
+# 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
+
+project = "fucciphase"
+project_copyright = "2023, Joran Deschamps, Julius Zimmermann (contributor)"
+author = "Joran Deschamps"
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = []
+
+templates_path = ["_templates"]
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
+
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = "alabaster"
+html_static_path = ["_static"]
+
+extensions = [
+    "sphinx.ext.autodoc",
+    "sphinx.ext.napoleon",
+]  # support for NumPy and Google style docstrings

fucciphase-0.0.1/doc/examples/examples.rst

@@ -0,0 +1,9 @@
+.. _examples:
+
+Examples
+========
+
+.. toctree::
+   :maxdepth: 1
+
+   simulator

fucciphase-0.0.1/doc/examples/simulator.rst

@@ -0,0 +1,6 @@
+.. _Simulator:
+
+Simulator
+=========
+
+TODO