Merge pull request #193 from arayabrain/release/server-production-deploy

Release version 1.0.0
arayabrain · Sep 15, 2023 · 42005b5 · 42005b5
2 parents 6cfe6d8 + 4fca36c
commit 42005b5
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diff --git a/setup.cfg → .flake8 b/setup.cfg → .flake8
@@ -1,6 +1,4 @@
 [flake8]
-max-line-length = 88
+exclude = build, .git
 extend-ignore = E203, W503
-
-[isort]
-profile = black
+max-line-length = 88
diff --git a/.github/dependabot.yml b/.github/dependabot.yml
@@ -0,0 +1,19 @@
+# To get started with Dependabot version updates, you'll need to specify which
+# package ecosystems to update and where the package manifests are located.
+# Please see the documentation for all configuration options:
+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+  - package-ecosystem: "npm"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+  - package-ecosystem: "pip"
+    directory: "/"
+    schedule:
+      interval: "weekly"
diff --git a/.github/workflows/linters.yml b/.github/workflows/linters.yml
@@ -31,7 +31,7 @@ jobs:
       - uses: liskin/gh-problem-matcher-wrap@d8afa2cfb66dd3f982b1950429e652bc14d0d7d2
         with:
           linters: isort
-          run: isort --check --diff optinist
+          run: isort --check --diff studio
   black:
     runs-on: ubuntu-latest
     steps:

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -15,7 +15,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - name: Run a one-line script
         shell: bash

diff --git a/.gitignore b/.gitignore
@@ -2,26 +2,31 @@
 __pycache__
 .ipynb_checkpoints
 .vscode/*
+.idea
 !.vscode/settings.json
 !.vscode/extensions.json
 dist
 /build
-optinist/frontend
 
-optinist.extensions.yaml
-optinist.namespace.yaml
+*.extensions.yaml
+*.namespace.yaml
 
 files/*
 Pipfile.lock
-optinist.egg-info
+*.egg-info
 .tox
 .snakemake
 .pytest_cache
 
-optinist/config.yaml
+studio/test_data/output
+studio/notebooks
+studio/config.production*
 
 docs/_build
-
-optinist/notebooks
 conda/envs/*
-tensorflow-2.4.1-py3-none-any.whl
+tensorflow-2.4.1-py3-none-any.whl
+
+.env*
+!*.env.example
+
+process.lock
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -0,0 +1,27 @@
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+default_language_version:
+    python: python3.8
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    hooks:
+    -   id: check-added-large-files
+    -   id: check-toml
+    -   id: check-yaml
+        args:
+        -   --unsafe
+    -   id: end-of-file-fixer
+    -   id: trailing-whitespace
+-   repo: https://github.com/pycqa/isort
+    rev: 5.12.0
+    hooks:
+    -   id: isort
+-   repo: https://github.com/psf/black
+    rev: 23.3.0
+    hooks:
+    -   id: black
+-   repo: https://github.com/pycqa/flake8
+    rev: 6.0.0
+    hooks:
+    -   id: flake8
diff --git a/Dockerfile-test b/Dockerfile-test
diff --git a/MANIFEST.in b/MANIFEST.in
diff --git a/Makefile b/Makefile
@@ -1,37 +1,38 @@
 .PHONY: test_run
 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_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
+	docker-compose -f docker-compose.test.yml down --rmi all --volumes --remove-orphans
+	docker-compose -f docker-compose.test.yml rm -f
+	docker-compose -f docker-compose.test.yml build test_studio
+	docker-compose -f docker-compose.test.yml build test_studio_frontend
+	docker-compose -f docker-compose.test.yml run test_studio
+	docker-compose -f docker-compose.test.yml run test_studio_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_optinist
-	docker-compose -f docker-compose.yml run test_optinist
+	docker-compose -f docker-compose.test.yml down --rmi all --volumes --remove-orphans
+	docker-compose -f docker-compose.test.yml rm -f
+	docker-compose -f docker-compose.test.yml build test_studio
+	docker-compose -f docker-compose.test.yml run test_studio
 
 .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_optinist_frontend
-	docker-compose -f docker-compose.yml run test_optinist_frontend
+	docker-compose -f docker-compose.test.yml down --rmi all --volumes --remove-orphans
+	docker-compose -f docker-compose.test.yml rm -f
+	docker-compose -f docker-compose.test.yml build test_studio_frontend
+	docker-compose -f docker-compose.test.yml run test_studio_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_optinist_frontend
-	docker-compose -f docker-compose.yml run build_optinist_frontend
+	docker-compose -f docker-compose.test.yml down --rmi all --volumes --remove-orphans
+	docker-compose -f docker-compose.test.yml rm -f
+	docker-compose -f docker-compose.test.yml build build_studio_frontend
+	docker-compose -f docker-compose.test.yml run build_studio_frontend
 
 .PHONY: docs
 docs:
 	rm -rf docs/_build/
-	# sphinx-apidoc -f -o ./docs/_build/modules ./optinist
+	pip install -e '.[doc]'
+	# sphinx-apidoc -f -o ./docs/_build/modules ./studio
 	sphinx-autobuild -b html docs docs/_build --port 8001
 
 .PHONY: dockerhub
@@ -41,25 +42,27 @@ dockerhub:
 
 .PHONY: local_build
 local_build:
-	cp -r frontend/build optinist/frontend/build
+	cd frontend
+	yarn install && yarn build
+	cd ../
 	pip install .
 
 .PHONY: upload_testpypi
 upload_testpypi:
-	mkdir -p optinist/frontend/build
-	cp -r frontend/build optinist/frontend/
-	python setup.py sdist
+	python -m build
 	twine upload --repository testpypi dist/*
 
 .PHONY: test_pypi
 test_pypi:
-	python3 -m pip install --index-url https://test.pypi.org/simple/ optinist
+	python3 -m pip install --index-url https://test.pypi.org/simple/ studio
 
 .PHONY: push_pypi
 push_pypi:
 	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
+
+.PHONY: format
+format:
+	black studio *.py
+	isort studio *.py
+	flake8 studio *.py
diff --git a/README.md b/README.md
@@ -1,52 +1,23 @@
-# optinist <img src="docs/_static/optinist.png" width="250" title="optinist" alt="optinist" align="right" vspace = "50">
-
+# Studio
 <p align="center">
     <a>
        <img src="https://img.shields.io/badge/-Python-F9DC3E.svg?logo=python&style=flat">
     </a>
     <a>
       <img src="https://img.shields.io/badge/-TypeScript-007ACC.svg?logo=typescript&style=flat&logoColor=white">
     </a>
-    <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/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/optinist">
-      <img alt="" src="https://badge.fury.io/py/optinist.svg">
+    <a href="https://github.com/arayabrain/optinist-for-server">
+      <img alt="" src="https://img.shields.io/github/repo-size/arayabrain/optinist-for-server">
     </a>
-    <a href="https://github.com/oist/optinist">
-      <img alt="" src="https://img.shields.io/github/repo-size/oist/optinist">
+    <a href="https://github.com/arayabrain/optinist-for-server">
+      <img alt="" src="https://img.shields.io/github/stars/arayabrain/optinist-for-server?style=social">
     </a>
-    <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/optinist">
-      <img alt="" src="https://img.shields.io/github/forks/oist/optinist?style=social">
+    <a href="https://github.com/arayabrain/optinist-for-server">
+      <img alt="" src="https://img.shields.io/github/forks/arayabrain/optinist-for-server?style=social">
     </a>
 </p>
 
-OptiNiSt(Optical Neuroimage Studio) is a GUI based workflow pipeline tools for processing two-photon calcium imaging data.
-
-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.
-
-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...)
-- [x] Dimenstion Reduction(PCA...)
-- [x] Neural Decoding(LDA...)
-- [x] Neural Population Analysis(Correlation...)
-
-### Saving Format
-- [x] [NWB](https://github.com/NeurodataWithoutBorders/pynwb)
+Studio is a platform for sharing datasets, analyzing data of marmoset brain. Analysis using pipeline is based on OptiNiSt(Optical Neuroimage Studio), a GUI based workflow pipeline tools for processing two-photon calcium imaging data.
 
 
 ## Key Features
@@ -59,77 +30,24 @@ OptiNiSt also supports reproducibility of scientific research, standardization o
 ### :rocket: Managing Workflows
 - **recording and reproducing**: OptiNiSt records and reproduces the workflow pipelines easily.
 
-
-## Installation
-Need anaconda or miniconda environment.
-```
-conda create -n optinist python=3.8
-conda activate optinist
-```
-
-Install from pip.
-```
-pip install optinist
-```
-
-launch.
-```
-run_optinist
-```
-
-Open browser. http://localhost:8000
-
-## Documentation
-https://optinist.readthedocs.io/en/latest/
-
-
-## Using GUI
-### Workflow
-- 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
-- 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
-- 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>
-
-
-
 ## Contributors
 ### Proposers
-Kenji Doya, Yukako Yamane [OIST Neural Computation Unit](https://groups.oist.jp/ncu)
-
-### Main Developers
-[Shogo Akiyama](https://github.com/ShogoAkiyama), [Yoshifumi Takeshima](https://github.com/Yoshifumi14)
+Kenichi Ohki [University of Tokyo](https://physiol1.m.u-tokyo.ac.jp/ern24596/)
 
-### Support Developers
-[Tatsuya Tanabe](https://github.com/ttya16), [Yosuke Kaneko](https://github.com/toto-maru), [Syuya Saeki](https://github.com/hiiaka)
+### Developers
+[Keita Matsumoto](https://github.com/emuemuJP), [Nobuo Kawada](https://github.com/itutu-tienday), [Rei Hashimoto](https://github.com/ReiHashimoto)
 
 
 ## 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
+[[Optinist]](https://github.com/oist/optinist)
 
 <!-- ## Citing the Project
 To cite this repository in publications:
 ```
-@misc{OptiNiSt,
+@misc{Studio,
   author = {name},
   title = {title},
-  year = {2022},
+  year = {2023},
   publisher = {},
   journal = {},
   howpublished = {},