Merge pull request #2 from fish-quant/develop

v0.1.0

Author: Henley13

.codecov.yml

@@ -0,0 +1,26 @@
+comment: false
+
+ignore:
+  - "setup.py"
+  - "scripts"
+  - "data"
+
+coverage:
+  status:
+    project:
+      default:
+        # Commits pushed to master should not make the overall project
+        # coverage decrease by more than 1%:
+        target: auto
+        threshold: 1%
+    patch:
+      default:
+        # Be tolerant on slight code coverage diff on PRs to limit
+        # noisy red coverage status on github PRs.
+        # Note The coverage stats are still uploaded
+        # to codecov so that PR reviewers can see uncovered lines
+        # in the github diff if they install the codecov browser
+        # extension:
+        # https://github.com/codecov/browser-extension
+        target: auto
+        threshold: 1%

.gitignore

@@ -5,8 +5,9 @@
 .idea/
 
 # folders
-playground/
+notebooks/
 data/
+images/others/
 
 # ### General python stuff ###
 

.readthedocs.yml

@@ -0,0 +1,23 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+   builder: html
+   configuration: docs/source/conf.py
+
+# Optionally build your docs in additional formats such as PDF
+formats:
+   - pdf
+
+# Optionally set the version of Python and requirements required to build your docs
+python:
+   version: 3.6
+   install:
+   - requirements: requirements_docs.txt
+   - method: pip
+     path: .

.travis.yml

@@ -0,0 +1,15 @@
+language: python
+
+python:
+    - "3.6"
+    - "3.7"
+    - "3.8"
+    - "3.9"
+
+install:
+    - pip install -r requirements.txt
+    - pip install -r requirements_dev.txt
+
+script:
+    - pytest --cov=./
+    - codecov

MANIFEST.in

@@ -0,0 +1 @@
+include images/*

Makefile

@@ -0,0 +1,2 @@
+init:
+    pip install -r requirements.txt

README.md

@@ -1,26 +1,38 @@
 # Sim-FISH
 
-[![License](https://img.shields.io/badge/license-BSD%203--Clause-green)](https://github.com/fish-quant/big-fish/blob/master/LICENSE)
-[![Python 3.6](https://img.shields.io/badge/python-3.6-blue.svg)](https://www.python.org/downloads/release/python-360/)
+[![PyPI version](https://badge.fury.io/py/sim-fish.svg)](https://badge.fury.io/py/sim-fish)
+[![Build Status](https://travis-ci.com/fish-quant/sim-fish.svg?branch=main)](https://travis-ci.com/fish-quant/sim-fish)
+[![Documentation Status](https://readthedocs.org/projects/sim-fish/badge/?version=stable)](https://sim-fish.readthedocs.io/en/latest/?badge=stable)
+[![codecov](https://codecov.io/gh/fish-quant/sim-fish/branch/main/graph/badge.svg)](https://codecov.io/gh/fish-quant/sim-fish)
+[![License](https://img.shields.io/badge/license-BSD%203--Clause-green)](https://github.com/fish-quant/sim-fish/blob/main/LICENSE)
+[![Python version](https://img.shields.io/pypi/pyversions/sim-fish.svg)](https://pypi.python.org/pypi/sim-fish/)
 
 **Sim-FISH** is a python package to **simulate smFISH images**. The package allows the user simulate and localize spots, cells and nuclei. The ultimate goal is to provide toy images to **experiment, train and evaluate smFISH statistical analysis**.
 
+User can simulate images of spots and clusters with different level of noise...
+
+| Spots | Clustered  spots |
+| ------------- | ------------- |
+| ![](images/plot_spot.png "Spots") | ![](images/plot_cluster_zoom.png "Clustered spots") |
+
+... or localization patterns within  subcellular regions.
+
+| Perinuclear pattern | Foci pattern |
+| ------------- | ------------- |
+| ![](images/perinuclear_1_300.png "Perinuclear pattern") | ![](images/foci_1_300.png "Foci pattern") |
 
 ## Installation
 
 ### Dependencies
 
 Sim-FISH requires Python 3.6 or newer. Additionally, it has the following dependencies:
 
-- numpy (== 1.16.0)
-- scipy (== 1.4.1)
-- scikit-learn (== 0.20.2)
-- scikit-image (== 0.14.2)
-- matplotlib (== 3.0.2)
-- pandas (== 0.24.0)
-- mrc (== 0.1.5)
-
-Updated dependencies might break.
+- big-fish (>= 0.6.1)
+- joblib (>= 0.13.2)
+- numpy (>= 1.16.0)
+- scikit-image (>= 0.14.2)
+- matplotlib (>= 3.0.2)
+- pandas (>= 0.24.0)
 
 ### Virtual environment
 
@@ -33,9 +45,13 @@ source activate simfish_env
 
 We recommend two options to then install Sim-FISH in your virtual environment.
 
-#### Download the package from PyPi (not available yet)
+#### Download the package from PyPi
 
+Use the package manager [pip](https://pip.pypa.io/en/stable/) to install Sim-FISH. In a terminal run the command:
 
+```bash
+pip install sim-fish
+```
 
 #### Clone package from Github
 
@@ -49,30 +65,27 @@ pip install .
 
 ## Usage
 
+Sim-FISH provides a toolbox to simulate smFISH images. A complete [documentation](https://sim-fish.readthedocs.io/en/stable/) is available online. 
 
+This package is part of the [FISH-Quant](https://fish-quant.github.io/) framework.
 
 ## Support
 
 If you have any question relative to the repository, please open an [issue](https://github.com/fish-quant/sim-fish/issues). You can also contact [Arthur Imbert](mailto:arthur.imbert@mines-paristech.fr).
 
 ## Roadmap (suggestion)
 
-Version 0.1.0:
-- I/O routines.
-- Random spot simulation in 2D and 3D.
-- Clustered spot simulation in 2D and 3D.
-- Allow benchmark and valuation pipeline.
-
 Version 0.Y.0:
-- Noise simulation.
-- Localized spot simulation in 2D. 
+- Improve background noise simulation.
+- Improve PSF simulation.
 - Cell and nucleus simulation in 2D.
-- Localized spot simulation in 3D. 
 - Cell and nucleus simulation in 3D.
+- Allow benchmark and valuation pipeline.
+- Add simulation of colocalized spots
+- Add examples
 
 Version 1.0.0:
 - Complete code coverage.
-- Add sphinx documentation.
 
 ## Development
 
@@ -89,3 +102,23 @@ git checkout develop
 ### Contributing
 
 [Pull requests](https://github.com/fish-quant/sim-fish/pulls) are welcome. For major changes, please open an [issue](https://github.com/fish-quant/sim-fish/issues) first to discuss what you would like to change.
+
+### Testing
+
+Please make sure to update tests as appropriate if you open a pull request. You can install exacts dependencies and specific version of [pytest](https://docs.pytest.org/en/latest/) by running the following command:
+
+```bash
+pip install -r requirements_dev.txt
+```
+
+To perform unit tests, run : 
+
+```bash
+pytest simfish
+```
+
+## Citation
+
+If you exploit this package for your work, please cite:
+
+> Arthur Imbert, Wei Ouyang, Adham Safieddine, Emeline Coleno, Christophe Zimmer, Edouard Bertrand, Thomas Walter, Florian Mueller. FISH-quant v2: a scalable and modular analysis tool for smFISH image analysis. bioRxiv (2021) https://doi.org/10.1101/2021.07.20.453024

build_package.sh

@@ -0,0 +1,9 @@
+#!/bin/bash
+
+rm -r build/*
+rm -r dist/*
+
+pip install --upgrade pip setuptools wheel twine
+
+python setup.py sdist bdist_wheel
+twine upload dist/*

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)

docs/README.md

@@ -0,0 +1,5 @@
+# Documentation for Sim-FISH
+
+[![Documentation Status](https://readthedocs.org/projects/sim-fish/badge/?version=stable)](https://sim-fish.readthedocs.io/en/latest/?badge=stable)
+
+This folder gathers the materials for the online [documentation](https://sim-fish.readthedocs.io/en/stable/).