Merge pull request #2 from arayabrain/feature/fetch-upstream-main

fetch upstream main

.github/workflows/linters.yml

@@ -0,0 +1,39 @@
+name: Python Linters
+on:
+  pull_request:
+    paths-ignore:
+      - 'docs/**'
+      - 'notebooks/**'
+      - 'frontend/**'
+      - 'sample_data/**'
+
+jobs:
+  flake8:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        with:
+          python-version: '3.8'
+      - run: python -m pip install flake8
+      - uses: liskin/gh-problem-matcher-wrap@d8afa2cfb66dd3f982b1950429e652bc14d0d7d2
+        with:
+          linters: flake8
+          run: flake8
+  isort:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        with:
+          python-version: '3.8'
+      - run: python -m pip install isort
+      - uses: liskin/gh-problem-matcher-wrap@d8afa2cfb66dd3f982b1950429e652bc14d0d7d2
+        with:
+          linters: isort
+          run: isort --check --diff optinist
+  black:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: psf/black@stable

.gitignore

@@ -3,6 +3,7 @@ __pycache__
 .ipynb_checkpoints
 .vscode/*
 !.vscode/settings.json
+!.vscode/extensions.json
 dist
 /build
 optinist/frontend

.readthedocs.yaml

@@ -0,0 +1,14 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+version: 2
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.11"
+sphinx:
+  configuration: docs/conf.py
+python:
+  install:
+  - requirements: docs/requirements.txt

.vscode/extensions.json

@@ -0,0 +1,7 @@
+{
+  "recommendations": [
+    "ms-python.black-formatter",
+    "ms-python.flake8",
+    "ms-python.isort"
+  ]
+}

.vscode/settings.json

@@ -3,5 +3,16 @@
     "frontend/build/**": true,
     "build/**": true
   },
+  "[python]": {
+    "editor.defaultFormatter": "ms-python.black-formatter",
+    "editor.formatOnSave": true,
+    "editor.codeActionsOnSave": {
+      "source.organizeImports": true
+    }
+  },
+  "python.linting.enabled": true,
+  "python.linting.lintOnSave": true,
+  "python.linting.pylintEnabled": false,
+  "python.linting.flake8Enabled": true,
   "esbonio.sphinx.confDir": ""
 }

Dockerfile

@@ -1,23 +1,12 @@
-FROM python:3.9.7-slim
+FROM --platform=linux/amd64 python:3.8.16-slim
 
 COPY requirements.txt /app/requirements.txt
 
 RUN apt-get --allow-releaseinfo-change update && \
-    apt-get install --no-install-recommends -y git gcc g++ libgl1 libgl1-mesa-dev && \
+    apt-get install --no-install-recommends -y gcc g++ libgl1 libgl1-mesa-dev && \
     pip3 install --no-cache-dir --upgrade pip && \
     pip3 install --no-cache-dir -r /app/requirements.txt && \
-    pip3 install --no-cache-dir \
-        cython==0.29.30 \
-        holoviews==1.14.9 \
-        ipyparallel==8.4.1 \
-        matplotlib==3.5.2 \
-        opencv-python==4.6.0.66 \
-        scikit-image==0.18.0 \
-        scikit-learn==1.1.1 \
-        tensorflow==2.9.1 && \
-        watershed==2.2.2 \
-    pip3 install --no-cache-dir git+https://github.com/flatironinstitute/CaImAn.git@914324989443fac5d481ef32aad4f327701294a8#egg=caiman && \
-    apt-get purge git -y && apt-get autoremove -y && apt-get clean && rm -rf /root/.cache/pip/*
+    apt-get clean && rm -rf /root/.cache/pip/*
 
 RUN mkdir -p /root/miniconda3 && \
     apt-get install --no-install-recommends -y wget && \
@@ -31,7 +20,7 @@ RUN mkdir -p /root/miniconda3 && \
     conda clean -y --tarballs
 
 COPY frontend/build /app/frontend/build
-COPY studio /app/studio
+COPY optinist /app/optinist
 COPY main.py /app/main.py
 
 ENV PATH $PATH:/root/miniconda3/bin

Dockerfile-test

@@ -1,4 +1,4 @@
-FROM python:3.9.7-slim
+FROM --platform=linux/amd64 python:3.8.16-slim
 
 COPY requirements.txt /app/requirements.txt
 

Makefile

@@ -2,57 +2,64 @@
 test_run:
 	docker-compose -f docker-compose.yml down --rmi all --volumes --remove-orphans
 	docker-compose -f docker-compose.yml rm -f
-	docker-compose -f docker-compose.yml build test_studio
-	docker-compose -f docker-compose.yml build test_studio_frontend
-	docker-compose -f docker-compose.yml run test_studio
-	docker-compose -f docker-compose.yml run test_studio_frontend
+	docker-compose -f docker-compose.yml build test_optinist
+	docker-compose -f docker-compose.yml build test_optinist_frontend
+	docker-compose -f docker-compose.yml run test_optinist
+	docker-compose -f docker-compose.yml run test_optinist_frontend
 
 .PHONY: test_python
 test_python:
 	docker-compose -f docker-compose.yml down --rmi all --volumes --remove-orphans
 	docker-compose -f docker-compose.yml rm -f
-	docker-compose -f docker-compose.yml build test_studio
-	docker-compose -f docker-compose.yml run test_studio
+	docker-compose -f docker-compose.yml build test_optinist
+	docker-compose -f docker-compose.yml run test_optinist
 
 .PHONY: test_frontend
 test_frontend:
 	docker-compose -f docker-compose.yml down --rmi all --volumes --remove-orphans
 	docker-compose -f docker-compose.yml rm -f
-	docker-compose -f docker-compose.yml build test_studio_frontend
-	docker-compose -f docker-compose.yml run test_studio_frontend
+	docker-compose -f docker-compose.yml build test_optinist_frontend
+	docker-compose -f docker-compose.yml run test_optinist_frontend
 
 .PHONY: build_frontend
 build_frontend:
 	docker-compose -f docker-compose.yml down --rmi all --volumes --remove-orphans
 	docker-compose -f docker-compose.yml rm -f
-	docker-compose -f docker-compose.yml build build_studio_frontend
-	docker-compose -f docker-compose.yml run build_studio_frontend
+	docker-compose -f docker-compose.yml build build_optinist_frontend
+	docker-compose -f docker-compose.yml run build_optinist_frontend
 
 .PHONY: docs
 docs:
 	rm -rf docs/_build/
-	# sphinx-apidoc -f -o ./docs/_build/modules ./studio
+	# sphinx-apidoc -f -o ./docs/_build/modules ./optinist
 	sphinx-autobuild -b html docs docs/_build --port 8001
 
 .PHONY: dockerhub
 dockerhub:
-	docker build --rm -t oistncu/studio:latest . --platform=linux/amd64
-	docker push oistncu/studio:latest
+	docker build --rm -t oistncu/optinist:latest . --platform=linux/amd64
+	docker push oistncu/optinist:latest
 
 .PHONY: local_build
 local_build:
-	cp -r frontend/build studio/frontend/build
+	cp -r frontend/build optinist/frontend/build
 	pip install .
 
 .PHONY: upload_testpypi
 upload_testpypi:
+	mkdir -p optinist/frontend/build
+	cp -r frontend/build optinist/frontend/
 	python setup.py sdist
 	twine upload --repository testpypi dist/*
 
 .PHONY: test_pypi
 test_pypi:
-	python3 -m pip install --index-url https://test.pypi.org/simple/ studio
+	python3 -m pip install --index-url https://test.pypi.org/simple/ optinist
 
 .PHONY: push_pypi
 push_pypi:
-	twine upload --repository pypi dist/*
+	twine upload --repository pypi dist/*
+
+.PHONY: test_doc
+test_doc:
+	python3 -m pip install -r docs/requirements.txt
+	sphinx-autobuild -b html docs docs/_build --port 8001

README.md

@@ -1,4 +1,4 @@
-# studio <img src="docs/_static/studio.png" width="250" title="studio" alt="studio" align="right" vspace = "50">
+# optinist <img src="docs/_static/optinist.png" width="250" title="optinist" alt="optinist" align="right" vspace = "50">
 
 <p align="center">
     <a>
@@ -7,36 +7,37 @@
     <a>
       <img src="https://img.shields.io/badge/-TypeScript-007ACC.svg?logo=typescript&style=flat&logoColor=white">
     </a>
-    <a href="https://pypi.org/project/studio">
-        <img alt="PYPI" src="https://static.pepy.tech/personalized-badge/studio?period=total&units=international_system&left_color=black&right_color=blue&left_text=Downloads(PYPI)">
+    <a href="https://pypi.org/project/optinist">
+        <img alt="PYPI" src="https://static.pepy.tech/personalized-badge/optinist?period=total&units=international_system&left_color=black&right_color=blue&left_text=Downloads(PYPI)">
     </a>
-    <a href="https://pypi.org/project/studio">
-        <img alt="PYPI" src="https://static.pepy.tech/personalized-badge/studio?period=week&units=international_system&left_color=black&right_color=blue&left_text=Downloads/week(PYPI)">
+    <a href="https://pypi.org/project/optinist">
+        <img alt="PYPI" src="https://static.pepy.tech/personalized-badge/optinist?period=week&units=international_system&left_color=black&right_color=blue&left_text=Downloads/week(PYPI)">
     </a>
-    <a href="https://pypi.org/project/studio">
-      <img alt="" src="https://badge.fury.io/py/studio.svg">
+    <a href="https://pypi.org/project/optinist">
+      <img alt="" src="https://badge.fury.io/py/optinist.svg">
     </a>
-    <a href="https://github.com/oist/studio">
-      <img alt="" src="https://img.shields.io/github/repo-size/oist/studio">
+    <a href="https://github.com/oist/optinist">
+      <img alt="" src="https://img.shields.io/github/repo-size/oist/optinist">
     </a>
-    <a href="https://github.com/oist/studio">
-      <img alt="" src="https://img.shields.io/github/stars/oist/studio?style=social">
+    <a href="https://github.com/oist/optinist">
+      <img alt="" src="https://img.shields.io/github/stars/oist/optinist?style=social">
     </a>
-    <a href="https://github.com/oist/studio">
-      <img alt="" src="https://img.shields.io/github/forks/oist/studio?style=social">
+    <a href="https://github.com/oist/optinist">
+      <img alt="" src="https://img.shields.io/github/forks/oist/optinist?style=social">
     </a>
 </p>
 
-studio(Optical Neuroimage Studio) is a GUI based workflow pipeline tools for processing two-photon calcium imaging data.
+OptiNiSt(Optical Neuroimage Studio) is a GUI based workflow pipeline tools for processing two-photon calcium imaging data.
 
-studio helps researchers try multiple data analysis methods, visualize the results, and construct the data analysis pipelines easily and quickly on GUI. studio's data-saving format follows NWB standards.
+OptiNiSt helps researchers try multiple data analysis methods, visualize the results, and construct the data analysis pipelines easily and quickly on GUI. OptiNiSt's data-saving format follows NWB standards.
 
-studio also supports reproducibility of scientific research, standardization of analysis protocols, and developments of novel analysis tools as plug-in.
+OptiNiSt also supports reproducibility of scientific research, standardization of analysis protocols, and developments of novel analysis tools as plug-in.
 
 ## Support library
 ### ROI detection
 - [x] [Suite2p](https://github.com/MouseLand/suite2p)
 - [x] [CaImAn](https://github.com/flatironinstitute/CaImAn)
+- [x] [LCCD](https://github.com/magnetizedCell/lccd-python)
 
 ### Postprocessing
 - [x] Basic Neural Analysis(Event Trigger Average...)
@@ -50,55 +51,55 @@ studio also supports reproducibility of scientific research, standardization of
 
 ## Key Features
 ### :beginner: Easy-To-Create Workflow
-- **zero-knowledge of coding**: studio allows you to create analysis pipelines easily on the GUI.
+- **zero-knowledge of coding**: OptiNiSt allows you to create analysis pipelines easily on the GUI.
 
 ### :zap: Visualizing analysis results
-- **quick visualization**: studio supports you visualize the analysis results by plotly.
+- **quick visualization**: OptiNiSt supports you visualize the analysis results by plotly.
 
 ### :rocket: Managing Workflows
-- **recording and reproducing**: studio records and reproduces the workflow pipelines easily.
+- **recording and reproducing**: OptiNiSt records and reproduces the workflow pipelines easily.
 
 
 ## Installation
 Need anaconda or miniconda environment.
 ```
-conda create -n studio python=3.8
-conda activate studio
+conda create -n optinist python=3.8
+conda activate optinist
 ```
 
 Install from pip.
 ```
-pip install studio
+pip install optinist
 ```
 
 launch.
 ```
-run_studio
+run_optinist
 ```
 
 Open browser. http://localhost:8000
 
 ## Documentation
-https://studio.readthedocs.io/en/latest/
+https://optinist.readthedocs.io/en/latest/
 
 
 ## Using GUI
 ### Workflow
-- studio allows you to make your analysis pipelines by graph style using nodes and edges on GUI. Parameters for each analysis are easily changeable. 
+- OptiNiSt allows you to make your analysis pipelines by graph style using nodes and edges on GUI. Parameters for each analysis are easily changeable. 
 <p align="center">
   <img width="400px" src="docs/_static/workflow/whole.png" alt="workflow" />
 </p>
 
 
 
 ### Visualize
-- studio allows you to visualize the analysis results with one click by plotly. It supports a variety of plotting styles.
+- OptiNiSt allows you to visualize the analysis results with one click by plotly. It supports a variety of plotting styles.
 <p align="center">
   <img width="400px" src="docs/_static/visualize/whole.png" alt="visualize" />
 </p>
 
 ### Record
-- studio supports you in recording and reproducing workflow pipelines in an organized manner. 
+- OptiNiSt supports you in recording and reproducing workflow pipelines in an organized manner. 
 <p align="center">
   <img width="400px" src="docs/_static/record/whole.png" alt="record" />
 </p>
@@ -119,12 +120,13 @@ Kenji Doya, Yukako Yamane [OIST Neural Computation Unit](https://groups.oist.jp/
 ## References
 [[Suite2p]](https://github.com/MouseLand/suite2p) Marius Pachitariu, Carsen Stringer, Mario Dipoppa, Sylvia Schröder, L. Federico Rossi, Henry Dalgleish, Matteo Carandini, Kenneth D. Harris. "Suite2p: beyond 10,000 neurons with standard two-photon microscopy". 2017  
 [[CaImAn]](https://github.com/flatironinstitute/CaImAn) Andrea Giovannucci Is a corresponding author, Johannes Friedrich, Pat Gunn, Jérémie Kalfon, Brandon L Brown, Sue Ann Koay, Jiannis Taxidis, Farzaneh Najafi, Jeffrey L Gauthier, Pengcheng Zhou, Baljit S Khakh, David W Tank, Dmitri B Chklovskii, Eftychios A Pnevmatikakis. "CaImAn: An open source tool for scalable Calcium Imaging data Analysis". 2019  
+[[LCCD]](https://github.com/magnetizedCell/lccd-python) Tsubasa Ito, Keisuke Ota, Kanako Ueno, Yasuhiro Oisi, Chie Matsubara, Kenta Kobayashi, Masamichi Ohkura, Junichi Nakai, Masanori Murayama, Toru Aonishi, "Low computational-cost cell detection method for calcium imaging data", 2022
 [[PyNWB]](https://github.com/NeurodataWithoutBorders/pynwb) Oliver Rübel, Andrew Tritt, Ryan Ly, Benjamin K. Dichter, Satrajit Ghosh, Lawrence Niu, Ivan Soltesz, Karel Svoboda, Loren Frank, Kristofer E. Bouchard, "The Neurodata Without Borders ecosystem for neurophysiological data science", bioRxiv 2021.03.13.435173, March 15, 2021
 
 <!-- ## Citing the Project
 To cite this repository in publications:
 ```
-@misc{studio,
+@misc{OptiNiSt,
   author = {name},
   title = {title},
   year = {2022},

docker-compose.yml

@@ -1,32 +1,32 @@
 version: "3.8"
 services:
-  test_studio:
-    image: test_studio
-    container_name: test_studio
+  test_optinist:
+    image: test_optinist
+    container_name: test_optinist
     build:
       context: .
       dockerfile: Dockerfile-test
     environment:
       PYTHONPATH: .
       TZ: Asia/Tokyo
     volumes:
-      - ./studio:/app/studio
+      - ./optinist:/app/optinist
       - ./conda/yaml:/app/conda/yaml
-      - ./studio/test_data:/tmp/studio
+      - ./optinist/test_data:/tmp/optinist
 
-  test_studio_frontend:
-    image: test_studio_frontend
-    container_name: test_studio_frontend
+  test_optinist_frontend:
+    image: test_optinist_frontend
+    container_name: test_optinist_frontend
     build:
       context: ./frontend
       dockerfile: Dockerfile-test
     environment:
       TZ: Asia/Tokyo
     command: yarn test:ci
 
-  build_studio_frontend:
-    image: build_studio_frontend
-    container_name: build_studio_frontend
+  build_optinist_frontend:
+    image: build_optinist_frontend
+    container_name: build_optinist_frontend
     build:
       context: ./frontend
       dockerfile: Dockerfile-build