smfbursts 0.1.2__tar.gz

smfbursts-0.1.2/.github/workflows/test.yml

@@ -0,0 +1,109 @@
+name: Tests
+
+on: [push, pull_request]
+
+jobs:
+  Download:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v6
+      - uses: conda-incubator/setup-miniconda@v4
+        with:
+          auto-update-conda: true
+          channels: conda-forge
+          python-version: "3.12"
+          activate-environment: test
+      - name: Install Pooch
+        shell: bash -l {0}
+        run: conda install -c conda-forge pooch
+      - name: Download Files
+        shell: bash -l {0}
+        run: |
+          cd tests
+          python fetch_files.py
+      - uses: actions/cache@v6
+        id: filecache
+        with:
+          path: ./tests/data
+          enableCrossOsArchive: true
+          key: testfiles
+
+  TestProject:
+    needs: Download
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, windows-latest, macos-latest]
+        python-version: ["3.10", "3.12", "3.14"]
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          persist-credentials: false
+          fetch-depth: 0
+      - name: Restore Cached Files
+        id: cache-action
+        uses: actions/cache/restore@v6
+        with:
+          path: ./tests/data
+          key: testfiles
+          enableCrossOsArchive: true
+      - name: Install Conda
+        uses: conda-incubator/setup-miniconda@v4
+        with:
+          auto-update-conda: true
+          channels: conda-forge
+          python-version: ${{ matrix.python-version }}
+          activate_environment: test
+      - name: Apple Silicon Oddities
+        if: matrix.os == 'macos-latest'
+        shell: bash -l {0}
+        run: |
+          brew install c-blosc hdf5
+          export HDF5_DIF=/opt/homebrew/opt/hdf5
+          export BLOSC_DIR=/opt/homebrew/opt/c-blosc
+      - name: Install Dependencies
+        shell: bash -l {0}
+        run: |
+          conda install -c conda-forge pip
+          python -m pip install setuptools build
+          conda install -c conda-forge pytest numpy numba scipy pandas matplotlib pytables msgpack-python phconvert
+      - name: Install Project
+        shell: bash -l {0}
+        run:
+          pip install .
+      - name: Test Project
+        shell: bash -l {0}
+        run: |
+          cd tests
+          pytest
+  BuildWheels:
+    name: Build wheels on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    needs: TestProject
+    strategy:
+      matrix:
+        os: [ubuntu-latest, ubuntu-24.04-arm, windows-latest, windows-11-arm, macos-15-intel, macos-14]
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          persist-credentials: false
+          fetch-depth: 0
+      - name: Restore Cached Files
+        id: cache-action
+        uses: actions/cache/restore@v6
+        with:
+          path: ./tests/data
+          key: testfiles
+          enableCrossOsArchive: true
+      - name: Build wheels
+        uses: pypa/cibuildwheel@v4.2.0
+        env:
+          CIBW_SKIP: "cp310-win_arm64"
+          CIBW_TEST_REQUIRES: pytest matplotlib
+          CIBW_TEST_COMMAND: cd {package}/tests; pytest test_tables.py test_TypeValidator.py test_immutabledata.py test_diskdict.py test_gates.py test_phsel.py test_multifit.py
+          CIBW_CACHE_PATH: $GITHUB_WORKSPACE/tests/data
+          CIBW_TEST_SKIP: "*win* cp315-macosx_arm64 cp315t-macosx_* cp315t-manylinux_aarch64 *musllinux* cp315t-manylinux_x86_64"
+      - uses: actions/upload-artifact@v4
+        with:
+          name: cibw-wheels-${{ matrix.os }}-${{ strategy.job-index }}
+          path: ./wheelhouse/*.whl

smfbursts-0.1.2/.gitignore

@@ -0,0 +1,13 @@
+.ipynb_checkpoints/
+build/
+dist/
+*.so
+*.egg
+*.egg-info
+*.whl
+*.hdf5
+*.spc
+*.set
+__pycache__
+data
+/docs/build

smfbursts-0.1.2/.readthedocs.yaml

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+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the OS, Python version, and other tools you might need
+build:
+  os: ubuntu-24.04
+  tools:
+    python: "3.13"
+
+# Build documentation in the "docs/" directory with Sphinx
+sphinx:
+   configuration: docs/source/conf.py
+
+# Optionally, but recommended,
+# declare the Python requirements required to build your documentation
+# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
+python: 
+   install:
+   - requirements: docs/source/requirements.txt
+   - method: pip
+     path: .
+        

smfbursts-0.1.2/LICENSE.txt

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) [year] [fullname]
+
+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.

smfbursts-0.1.2/MANIFEST.in

@@ -0,0 +1,4 @@
+include LICENSE.txt
+include README.md
+include smfbursts/cfuncs/smfbursts_burstwise.h
+include smfbursts/fcs.py

smfbursts-0.1.2/PKG-INFO

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+Metadata-Version: 2.4
+Name: smfbursts
+Version: 0.1.2
+Summary: Burst analysis toolkit for single and multi-spot smFRET data.
+Author-email: Antonio Ingargiola <tritemio@gmail.com>, Paul David Harris <harripd@gmail.com>
+License-Expression: MIT
+Project-URL: Homepage, http://opensmfs.github.io/smfBursts/
+Project-URL: Documentation, https://smfbursts.readthedocs.io/en/latest/
+Project-URL: Issues, https://github.com/OpenSMFS/smfBursts/
+Project-URL: Repository, https://github.com/OpenSMFS/smfBursts/issues
+Keywords: single-molecule FRET,smFRET,burst-analysis,biophysics
+Classifier: Intended Audience :: Science/Research
+Classifier: Operating System :: OS Independent
+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
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE.txt
+Requires-Dist: numpy>=1.20
+Requires-Dist: pandas>=2.0
+Requires-Dist: scipy>=1.2
+Requires-Dist: tables>=3.5
+Requires-Dist: msgpack>=1.0
+Requires-Dist: phconvert>=0.8
+Requires-Dist: pyFCS>=0.1.3
+Provides-Extra: scientific
+Requires-Dist: jupyter; extra == "scientific"
+Requires-Dist: matplotlib>=3.0.1; extra == "scientific"
+Dynamic: license-file
+
+# smfBursts
+
+[![Tests](https://github.com/OpenSMFS/smfBursts/actions/workflows/test.yml/badge.svg)](https://github.com/OpenSMFS/smfBursts/actions)
+[![Documentations Status](https://readthedocs.org/projects/smfbursts/badge?version=latest)](https://smfbursts.readthedocs.io/en/latest/?badge=latest)
+
+## Project Description
+
+smfBursts is an open source package for analysis of freely-diffusing single molecule experiments, with a focus on burst-wise analysis techniques.
+
+The goal is to be easy to use, easy to reproduce, and easy to communicate
+
+While initially designed for FRET based experiments,
+it supports any number of spectral, as well as polarization based detection channels,
+as well as any number of excitation channels.
+
+### smfBursts and Reproducibility
+
+smfBursts is an effort to bring 
+[reproducible computing](http://dx.doi.org/10.1371/journal.pcbi.1003285)
+to the field of single-molecule confocal microscopy.
+smfBursts records all instructions with their thresholds and other parameters
+in special `Param` objects, which have a standard text representation,
+so that exact computations can be unambiguously reproduced.
+
+smfBursts provides tutorials for use with
+[Jupyter Notebooks](https://jupyter.org),
+and plotting relies on the ubiquitous python plotting library
+[matplotlib](https://matplotlib.org/)
+
+## Supported Features
+
+smfBursts provides algorithms for the following analysis methods
+- Backgrounds estimation as a function of time
+- Sliding-window bursts earch with adaptive (background-dependent) rate-threshold
+- Multi-channel burst search with logical combinations of bursts, extending DCBS
+- Burst corrections based on [Hellenkamp et. al.](https://doi.org/10.1038/s41592-018-0085-0), and the flexibility to specify corrections for other excitation/detector schemes with more channels and polarization (MFD)
+- Flexible and reproducible burst selection based on logical operations on arbitrary numbers of gates
+- Large suite of burst statistics, such as E, S, peak rate, brightness, mean fluorescence lifetime, etc.
+
+
+## Install
+
+smfBursts is available on pypi, install with
+
+```bash
+pip install smfbursts
+```
+
+hopefully soon smfbursts will also be available on conda-forge
+
+```bash
+conda install smfbursts -c conda-forge
+```
+
+## License and Copyrights
+
+License: MIT
+
+You can find a full copy fo the license in the file LICENSE.txt
+
+### A request from the developer
+
+Be nice, give credit and give back.
+
+That is the basic philosophy I would like users of this package to adopt.
+
+If you are a lab group, a company selling equipment or whoever/whatever else,
+if you can make use of smfBursts, I want you to use it,
+but please don't box people out, and give me the proper citation.
+I chose the MIT license because I didn't want to scare anyone (especially companies) away because of strong copyleft licenses like GPL.
+
+MIT basically lets anyone do pretty much whatever they want with this code.
+I would however ask people to use this in a more copyleft way, making sure to give credit, and make open source what they develop off of it.
+
+Open source is incredibly valuable to the scientific community.
+It makes analysis transparent and reproducible.
+There's nothing more frustrating than reading in a paper
+that the analysis was done with some black box piece of software.
+Open source lets use your new methods,
+and let's us understand what you are doing, and check your work.
+
+So if you are doing science, or selling to those doing science, I ask you keep that in mind.
+
+If you don't act that way, the MIT license can't stop you,
+but you will get me wagging a finger at you in conversation.

smfbursts-0.1.2/README.md

@@ -0,0 +1,85 @@
+# smfBursts
+
+[![Tests](https://github.com/OpenSMFS/smfBursts/actions/workflows/test.yml/badge.svg)](https://github.com/OpenSMFS/smfBursts/actions)
+[![Documentations Status](https://readthedocs.org/projects/smfbursts/badge?version=latest)](https://smfbursts.readthedocs.io/en/latest/?badge=latest)
+
+## Project Description
+
+smfBursts is an open source package for analysis of freely-diffusing single molecule experiments, with a focus on burst-wise analysis techniques.
+
+The goal is to be easy to use, easy to reproduce, and easy to communicate
+
+While initially designed for FRET based experiments,
+it supports any number of spectral, as well as polarization based detection channels,
+as well as any number of excitation channels.
+
+### smfBursts and Reproducibility
+
+smfBursts is an effort to bring 
+[reproducible computing](http://dx.doi.org/10.1371/journal.pcbi.1003285)
+to the field of single-molecule confocal microscopy.
+smfBursts records all instructions with their thresholds and other parameters
+in special `Param` objects, which have a standard text representation,
+so that exact computations can be unambiguously reproduced.
+
+smfBursts provides tutorials for use with
+[Jupyter Notebooks](https://jupyter.org),
+and plotting relies on the ubiquitous python plotting library
+[matplotlib](https://matplotlib.org/)
+
+## Supported Features
+
+smfBursts provides algorithms for the following analysis methods
+- Backgrounds estimation as a function of time
+- Sliding-window bursts earch with adaptive (background-dependent) rate-threshold
+- Multi-channel burst search with logical combinations of bursts, extending DCBS
+- Burst corrections based on [Hellenkamp et. al.](https://doi.org/10.1038/s41592-018-0085-0), and the flexibility to specify corrections for other excitation/detector schemes with more channels and polarization (MFD)
+- Flexible and reproducible burst selection based on logical operations on arbitrary numbers of gates
+- Large suite of burst statistics, such as E, S, peak rate, brightness, mean fluorescence lifetime, etc.
+
+
+## Install
+
+smfBursts is available on pypi, install with
+
+```bash
+pip install smfbursts
+```
+
+hopefully soon smfbursts will also be available on conda-forge
+
+```bash
+conda install smfbursts -c conda-forge
+```
+
+## License and Copyrights
+
+License: MIT
+
+You can find a full copy fo the license in the file LICENSE.txt
+
+### A request from the developer
+
+Be nice, give credit and give back.
+
+That is the basic philosophy I would like users of this package to adopt.
+
+If you are a lab group, a company selling equipment or whoever/whatever else,
+if you can make use of smfBursts, I want you to use it,
+but please don't box people out, and give me the proper citation.
+I chose the MIT license because I didn't want to scare anyone (especially companies) away because of strong copyleft licenses like GPL.
+
+MIT basically lets anyone do pretty much whatever they want with this code.
+I would however ask people to use this in a more copyleft way, making sure to give credit, and make open source what they develop off of it.
+
+Open source is incredibly valuable to the scientific community.
+It makes analysis transparent and reproducible.
+There's nothing more frustrating than reading in a paper
+that the analysis was done with some black box piece of software.
+Open source lets use your new methods,
+and let's us understand what you are doing, and check your work.
+
+So if you are doing science, or selling to those doing science, I ask you keep that in mind.
+
+If you don't act that way, the MIT license can't stop you,
+but you will get me wagging a finger at you in conversation.

smfbursts-0.1.2/docs/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)

smfbursts-0.1.2/docs/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd