Merge pull request #623 from oist/develop-main

Merge release ver1.1.0
oist · Dec 21, 2023 · b9901fc · b9901fc
2 parents 825f3c0 + f5544e0
commit b9901fc
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diff --git a/.codespellignore b/.codespellignore
@@ -0,0 +1,5 @@
+createR
+afterAll
+xdescribe
+optinist
+Optinist
diff --git a/.github/workflows/codespell.yml b/.github/workflows/codespell.yml
@@ -0,0 +1,10 @@
+name: Codespell
+on:
+  pull_request:
+
+jobs:
+  codespell:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: codespell-project/actions-codespell@v2
diff --git a/.github/workflows/linters.yml b/.github/workflows/linters.yml
@@ -37,3 +37,5 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - uses: psf/black@stable
+        with:
+          version: "~= 23.11"
diff --git a/.github/workflows/test.yml → .github/workflows/tests.yml b/.github/workflows/test.yml → .github/workflows/tests.yml
@@ -1,10 +1,12 @@
-name: CI
+name: Tests
 
 on:
-  push:
-    branches: [ main ]
   pull_request:
-    branches: [ main ]
+    branches:
+      - main
+      - develop-main
+    paths-ignore:
+      - 'docs/**'
 
   workflow_dispatch:
 
@@ -17,7 +19,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
 
-      - name: Run a one-line script
+      - name: Run test_run command
         shell: bash
         run: |
           make test_run
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -6,8 +6,6 @@ repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.4.0
     hooks:
-    -   id: check-added-large-files
-        exclude: frontend/build
     -   id: check-toml
     -   id: check-yaml
         args:
@@ -26,3 +24,9 @@ repos:
     rev: 6.1.0
     hooks:
     -   id: flake8
+-   repo: https://github.com/codespell-project/codespell
+    rev: v2.2.4
+    hooks:
+    -   id: codespell
+        additional_dependencies:
+        -   tomli
diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -11,4 +11,4 @@ sphinx:
   configuration: docs/conf.py
 python:
   install:
-  - requirements: docs/requirements.txt
+  - requirements: docs/requirements.txt
diff --git a/.vscode/extensions.json b/.vscode/extensions.json
@@ -2,6 +2,8 @@
   "recommendations": [
     "ms-python.black-formatter",
     "ms-python.flake8",
-    "ms-python.isort"
+    "ms-python.isort",
+    "dbaeumer.vscode-eslint",
+    "esbenp.prettier-vscode"
   ]
 }
diff --git a/.vscode/settings.example.json b/.vscode/settings.example.json
@@ -10,6 +10,7 @@
       "source.organizeImports": true
     }
   },
+  "eslint.workingDirectories": ["frontend"],
   "flake8.args": ["--config=.flake8"],
   // NOTE: Uncomment following line and fix "optinist_dev" to your conda env name
   // "flake8.path": ["conda", "run", "-n", "optinist_dev", "python", "-m", "flake8"],

diff --git a/Makefile b/Makefile
@@ -31,7 +31,7 @@ build_frontend:
 .PHONY: docs
 docs:
 	rm -rf docs/_build/
-	# pip install -e '.[doc]'
+	poetry install --with doc --no-root
 	# sphinx-apidoc -f -o ./docs/_build/modules ./studio
 	sphinx-autobuild -b html docs docs/_build --port 8001
 
@@ -42,24 +42,21 @@ dockerhub:
 
 .PHONY: local_build
 local_build:
-	cd frontend
-	yarn install && yarn build
-	cd ../
-	pip install .
+	cd frontend && yarn install --ignore-scripts && yarn build
+	poetry build
 
 .PHONY: upload_testpypi
 upload_testpypi:
-	python -m build
-	twine upload --repository testpypi dist/*
+	poetry publish -r testpypi
 
-.PHONY: test_pypi
-test_pypi:
-	python3 -m pip install --index-url https://test.pypi.org/simple/ studio
+.PHONY: install_testpypi
+install_testpypi:
+	pip install --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple/ optinist
+	pip show optinist
 
 .PHONY: push_pypi
 push_pypi:
-	twine upload --repository pypi dist/*
-
+	poetry publish
 
 .PHONY: format
 format:

diff --git a/README.md b/README.md
@@ -41,7 +41,7 @@ OptiNiSt also supports reproducibility of scientific research, standardization o
 
 ### Postprocessing
 - [x] Basic Neural Analysis(Event Trigger Average...)
-- [x] Dimenstion Reduction(PCA...)
+- [x] Dimension Reduction(PCA...)
 - [x] Neural Decoding(LDA...)
 - [x] Neural Population Analysis(Correlation...)
 
@@ -85,7 +85,7 @@ 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. 
+- 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>
@@ -99,7 +99,7 @@ https://optinist.readthedocs.io/en/latest/
 </p>
 
 ### Record
-- OptiNiSt 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>
@@ -118,8 +118,8 @@ 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  
+[[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
 

diff --git a/docker-compose.dev.yml b/docker-compose.dev.yml
@@ -8,20 +8,22 @@ services:
     working_dir: /app
     volumes:
       - .:/app
+      - ../optinist-docker-volumes/studio_data/:/app/studio_data
     ports:
-      - "8000:8000"
-    command: python main.py --reload --host 0.0.0.0 --port 8000
+      - "127.0.0.1:8000:8000"
+    command: poetry run python main.py --reload --host 0.0.0.0 --port 8000
     environment:
       PYTHONPATH: /app/
       TZ: Asia/Tokyo
+      OPTINIST_DIR: /app/studio_data
 
   studio-dev-fe:
-    image: node:16.20.1-alpine
+    image: node:20.8.0-alpine3.18
     working_dir: /app/frontend
     volumes:
       - ./frontend/:/app/frontend/
     ports:
-      - "3000:3000"
+      - "127.0.0.1:3000:3000"
     command: ash -c 'yarn install && yarn start'
     environment:
       TZ: Asia/Tokyo
diff --git a/docker-compose.test.yml b/docker-compose.test.yml
@@ -10,11 +10,9 @@ services:
     environment:
       PYTHONPATH: .
       TZ: Asia/Tokyo
+    command: bash -c "poetry install --no-root --with test && poetry run python3 -m pytest -s ."
     volumes:
-      - ./studio:/app/studio
-      - ./conda/yaml:/app/conda/yaml
-      - ./studio/test_data:/tmp/studio
-      - ./frontend/build:/app/frontend/build
+      - .:/app
 
   test_studio_frontend:
     image: test_studio_frontend

diff --git a/docker-compose.yml b/docker-compose.yml
@@ -11,8 +11,8 @@ services:
       - ../optinist-docker-volumes/logs/:/app/logs
       - ../optinist-docker-volumes/studio_data/:/app/studio_data
     ports:
-      - "8000:8000"
-    command: python main.py --host 0.0.0.0 --port 8000
+      - "127.0.0.1:8000:8000"
+    command: poetry run python main.py --host 0.0.0.0 --port 8000
     environment:
       PYTHONPATH: /app/
       TZ: Asia/Tokyo

diff --git a/docs/_static/record/components/table.png b/docs/_static/record/components/table.png
diff --git a/docs/_static/record/components/details.png → docs/_static/record/details.png b/docs/_static/record/components/details.png → docs/_static/record/details.png
diff --git a/docs/_static/tutorials/fig42_workflownwb.png → docs/_static/record/download_buttons.png b/docs/_static/tutorials/fig42_workflownwb.png → docs/_static/record/download_buttons.png
diff --git a/docs/_static/record/error_message.png b/docs/_static/record/error_message.png
diff --git a/docs/_static/tutorials/fig41_reproduce.png → docs/_static/record/reproduce_button.png b/docs/_static/tutorials/fig41_reproduce.png → docs/_static/record/reproduce_button.png
diff --git a/docs/_static/record/table.png b/docs/_static/record/table.png
diff --git a/docs/_static/record/whole.png b/docs/_static/record/whole.png
diff --git a/docs/_static/tutorials/ETA.png b/docs/_static/tutorials/ETA.png
diff --git a/docs/_static/tutorials/PCA.png b/docs/_static/tutorials/PCA.png
diff --git a/docs/_static/tutorials/add_modules.png b/docs/_static/tutorials/add_modules.png
diff --git a/docs/_static/tutorials/caiman_sample_pipeline.png b/docs/_static/tutorials/caiman_sample_pipeline.png
diff --git a/docs/_static/tutorials/check_csv.png b/docs/_static/tutorials/check_csv.png
diff --git a/docs/_static/tutorials/delete_ROI.png b/docs/_static/tutorials/delete_ROI.png
diff --git a/docs/_static/tutorials/download_workflow_config.png b/docs/_static/tutorials/download_workflow_config.png
diff --git a/docs/_static/tutorials/fig10.1_buttons.png b/docs/_static/tutorials/fig10.1_buttons.png
diff --git a/docs/_static/tutorials/fig10_parameters.png b/docs/_static/tutorials/fig10_parameters.png
diff --git a/docs/_static/tutorials/fig11_runall.png b/docs/_static/tutorials/fig11_runall.png
diff --git a/docs/_static/tutorials/fig12.00_hdfnode.png b/docs/_static/tutorials/fig12.00_hdfnode.png
diff --git a/docs/_static/tutorials/fig12.01_hdfnode2.png b/docs/_static/tutorials/fig12.01_hdfnode2.png
diff --git a/docs/_static/tutorials/fig12.02_hdfs2p.png b/docs/_static/tutorials/fig12.02_hdfs2p.png
diff --git a/docs/_static/tutorials/fig12.03_hdfcaiman.png b/docs/_static/tutorials/fig12.03_hdfcaiman.png
diff --git a/docs/_static/tutorials/fig12.04_behaviornode.png b/docs/_static/tutorials/fig12.04_behaviornode.png
diff --git a/docs/_static/tutorials/fig12.05_behaviornode2.png b/docs/_static/tutorials/fig12.05_behaviornode2.png
diff --git a/docs/_static/tutorials/fig12.06_etaworkflow.png b/docs/_static/tutorials/fig12.06_etaworkflow.png
diff --git a/docs/_static/tutorials/fig12.07_etamean.png b/docs/_static/tutorials/fig12.07_etamean.png
diff --git a/docs/_static/tutorials/fig12.08_resulthdf.png b/docs/_static/tutorials/fig12.08_resulthdf.png
diff --git a/docs/_static/tutorials/fig13_nwbsnakemake.png b/docs/_static/tutorials/fig13_nwbsnakemake.png
diff --git a/docs/_static/tutorials/fig1_console.png b/docs/_static/tutorials/fig1_console.png
diff --git a/docs/_static/tutorials/fig20_initialize.png b/docs/_static/tutorials/fig20_initialize.png
diff --git a/docs/_static/tutorials/fig21_loadmovie.png b/docs/_static/tutorials/fig21_loadmovie.png
diff --git a/docs/_static/tutorials/fig22_movie.png b/docs/_static/tutorials/fig22_movie.png
diff --git a/docs/_static/tutorials/fig2_open.png b/docs/_static/tutorials/fig2_open.png
diff --git a/docs/_static/tutorials/fig30_saving.png b/docs/_static/tutorials/fig30_saving.png
diff --git a/docs/_static/tutorials/fig40_recordall.png b/docs/_static/tutorials/fig40_recordall.png
diff --git a/docs/_static/tutorials/fig4_algorithms.png b/docs/_static/tutorials/fig4_algorithms.png
diff --git a/docs/_static/tutorials/fig5_imagenode2.png b/docs/_static/tutorials/fig5_imagenode2.png
diff --git a/docs/_static/tutorials/fig6_suite2p.png b/docs/_static/tutorials/fig6_suite2p.png
diff --git a/docs/_static/tutorials/fig7_suite2p2.png b/docs/_static/tutorials/fig7_suite2p2.png
diff --git a/docs/_static/tutorials/fig8_suite2pcaiman.png b/docs/_static/tutorials/fig8_suite2pcaiman.png
diff --git a/docs/_static/tutorials/fig9_workflowbranch.png b/docs/_static/tutorials/fig9_workflowbranch.png
diff --git a/docs/_static/tutorials/import_workflow.png b/docs/_static/tutorials/import_workflow.png
diff --git a/docs/_static/tutorials/lccd_sample_pipeline.png b/docs/_static/tutorials/lccd_sample_pipeline.png
diff --git a/docs/_static/tutorials/load_sample_data.png b/docs/_static/tutorials/load_sample_data.png
diff --git a/docs/_static/tutorials/play_vid.png b/docs/_static/tutorials/play_vid.png
diff --git a/docs/_static/tutorials/sample_pipelines.png b/docs/_static/tutorials/sample_pipelines.png
diff --git a/docs/_static/tutorials/show_fluorescence.png b/docs/_static/tutorials/show_fluorescence.png
diff --git a/docs/_static/tutorials/suite2p_sample_pipeline.png b/docs/_static/tutorials/suite2p_sample_pipeline.png
diff --git a/docs/_static/visualize/add_column.png b/docs/_static/visualize/add_column.png
diff --git a/docs/_static/visualize/components/add_column.png b/docs/_static/visualize/components/add_column.png
diff --git a/docs/_static/visualize/components/customize_param.png b/docs/_static/visualize/components/customize_param.png
diff --git a/docs/_static/visualize/components/select_output_item.png b/docs/_static/visualize/components/select_output_item.png
diff --git a/docs/_static/visualize/components/set_display_box.png b/docs/_static/visualize/components/set_display_box.png
diff --git a/docs/_static/visualize/customize_param.png b/docs/_static/visualize/customize_param.png
diff --git a/docs/_static/tutorials/fig29_dragselect.png → docs/_static/visualize/drag_select.png b/docs/_static/tutorials/fig29_dragselect.png → docs/_static/visualize/drag_select.png
diff --git a/...ic/tutorials/edit-roi/add_roi_clicked.png → ...ic/visualize/edit-roi/add_roi_clicked.png b/...ic/tutorials/edit-roi/add_roi_clicked.png → ...ic/visualize/edit-roi/add_roi_clicked.png
diff --git a/docs/_static/tutorials/edit-roi/box.png → docs/_static/visualize/edit-roi/box.png b/docs/_static/tutorials/edit-roi/box.png → docs/_static/visualize/edit-roi/box.png
diff --git a/.../tutorials/edit-roi/cell_roi_selected.png → .../visualize/edit-roi/cell_roi_selected.png b/.../tutorials/edit-roi/cell_roi_selected.png → .../visualize/edit-roi/cell_roi_selected.png
diff --git a/...edit-roi/roi_selected_merge_or_delete.png → ...edit-roi/roi_selected_merge_or_delete.png b/...edit-roi/roi_selected_merge_or_delete.png → ...edit-roi/roi_selected_merge_or_delete.png
diff --git a/docs/_static/tutorials/fig27_fluo.png → docs/_static/visualize/fluo.png b/docs/_static/tutorials/fig27_fluo.png → docs/_static/visualize/fluo.png
diff --git a/docs/_static/visualize/imaging_rate.png b/docs/_static/visualize/imaging_rate.png
diff --git a/docs/_static/visualize/movie_index.png b/docs/_static/visualize/movie_index.png
diff --git a/...static/visualize/components/ref_image.png → docs/_static/visualize/ref_image.png b/...static/visualize/components/ref_image.png → docs/_static/visualize/ref_image.png
diff --git a/docs/_static/tutorials/fig26_roi.png → docs/_static/visualize/roi.png b/docs/_static/tutorials/fig26_roi.png → docs/_static/visualize/roi.png
diff --git a/docs/_static/tutorials/fig28_roifluo.png → docs/_static/visualize/roi_fluo.png b/docs/_static/tutorials/fig28_roifluo.png → docs/_static/visualize/roi_fluo.png
diff --git a/docs/_static/visualize/save_fig.png b/docs/_static/visualize/save_fig.png
diff --git a/docs/_static/tutorials/fig24_selectitem.png → docs/_static/visualize/select_item.png b/docs/_static/tutorials/fig24_selectitem.png → docs/_static/visualize/select_item.png
diff --git a/docs/_static/visualize/select_output_item.png b/docs/_static/visualize/select_output_item.png
diff --git a/docs/_static/tutorials/fig25_selectroi.png → docs/_static/visualize/select_roi.png b/docs/_static/tutorials/fig25_selectroi.png → docs/_static/visualize/select_roi.png
diff --git a/docs/_static/visualize/set_display_box.png b/docs/_static/visualize/set_display_box.png
diff --git a/docs/_static/tutorials/fig23_twobox.png → docs/_static/visualize/twobox.png b/docs/_static/tutorials/fig23_twobox.png → docs/_static/visualize/twobox.png
diff --git a/docs/_static/visualize/whole.png b/docs/_static/visualize/whole.png
diff --git a/docs/_static/workflow/add_algorithm.png b/docs/_static/workflow/add_algorithm.png
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diff --git a/docs/_static/workflow/components/add_algorithm.png b/docs/_static/workflow/components/add_algorithm.png
diff --git a/docs/_static/workflow/components/connect_edge.png b/docs/_static/workflow/components/connect_edge.png
diff --git a/docs/_static/workflow/components/imageList.png b/docs/_static/workflow/components/imageList.png
diff --git a/docs/_static/workflow/components/imageNode.png b/docs/_static/workflow/components/imageNode.png
diff --git a/docs/_static/workflow/connect_edge.png b/docs/_static/workflow/connect_edge.png
diff --git a/docs/_static/workflow/create_new_workflow.png b/docs/_static/workflow/create_new_workflow.png
diff --git a/...tatic/workflow/components/csv_connect.png → docs/_static/workflow/csv_connect.png b/...tatic/workflow/components/csv_connect.png → docs/_static/workflow/csv_connect.png
diff --git a/docs/_static/workflow/download_workflow_config.png b/docs/_static/workflow/download_workflow_config.png
diff --git a/...static/workflow/components/flow_chart.png → docs/_static/workflow/flow_chart.png b/...static/workflow/components/flow_chart.png → docs/_static/workflow/flow_chart.png
diff --git a/docs/_static/workflow/imageList.png b/docs/_static/workflow/imageList.png
diff --git a/docs/_static/tutorials/fig3_imagenode.png → docs/_static/workflow/image_node.png b/docs/_static/tutorials/fig3_imagenode.png → docs/_static/workflow/image_node.png
diff --git a/docs/_static/workflow/import_workflow.png b/docs/_static/workflow/import_workflow.png
diff --git a/docs/_static/workflow/nwb_settings.png b/docs/_static/workflow/nwb_settings.png
diff --git a/...ow/components/put_folder_to_input_dir.png → ...atic/workflow/put_folder_to_input_dir.png b/...ow/components/put_folder_to_input_dir.png → ...atic/workflow/put_folder_to_input_dir.png
diff --git a/docs/_static/workflow/run_after.png b/docs/_static/workflow/run_after.png
diff --git a/docs/_static/workflow/run_before.png b/docs/_static/workflow/run_before.png
diff --git a/docs/_static/workflow/run_buttons.png b/docs/_static/workflow/run_buttons.png
diff --git a/...ic/workflow/components/run_checkpoint.png → docs/_static/workflow/run_checkpoint.png b/...ic/workflow/components/run_checkpoint.png → docs/_static/workflow/run_checkpoint.png
diff --git a/...static/workflow/components/run_finish.png → docs/_static/workflow/run_finish.png b/...static/workflow/components/run_finish.png → docs/_static/workflow/run_finish.png
diff --git a/.../_static/workflow/components/run_name.png → docs/_static/workflow/run_name.png b/.../_static/workflow/components/run_name.png → docs/_static/workflow/run_name.png
diff --git a/...static/workflow/components/run_output.png → docs/_static/workflow/run_output.png b/...static/workflow/components/run_output.png → docs/_static/workflow/run_output.png
diff --git a/..._static/workflow/components/run_start.png → docs/_static/workflow/run_start.png b/..._static/workflow/components/run_start.png → docs/_static/workflow/run_start.png
diff --git a/docs/_static/workflow/components/running.png → docs/_static/workflow/running.png b/docs/_static/workflow/components/running.png → docs/_static/workflow/running.png
diff --git a/.../_static/workflow/components/setparam.png → docs/_static/workflow/setparam.png b/.../_static/workflow/components/setparam.png → docs/_static/workflow/setparam.png
diff --git a/docs/_static/workflow/snakemake_settings.png b/docs/_static/workflow/snakemake_settings.png
diff --git a/docs/_static/workflow/whole.png b/docs/_static/workflow/whole.png
diff --git a/docs/conf.py b/docs/conf.py
@@ -7,8 +7,6 @@
 import os
 from datetime import datetime
 
-from sphinx_pyproject import SphinxConfig
-
 # -- Path setup --------------------------------------------------------------
 
 # If extensions (or modules to document with autodoc) are in another directory,
@@ -18,11 +16,10 @@
 
 
 # -- Project information -----------------------------------------------------
-config = SphinxConfig("../pyproject.toml", globalns=globals())
 project = "OptiNiSt"
 copyright = f"{datetime.today().year}, OIST"
 author = ""
-release = ".".join(config.version.split(".")[:2])
+release = "1.1.0"
 
 # -- readthedocs -------------------------------------------------------------
 on_rtd = os.environ.get("READTHEDOCS", None) == "True"
@@ -46,6 +43,7 @@
     "sphinx.ext.autosummary",
     "sphinx.ext.extlinks",
     "sphinx.ext.autodoc.typehints",
+    "sphinx_copybutton",
 ]
 
 # Tell myst-parser to assign header anchors for h1-h3.

diff --git a/docs/for_developers/architecture.md b/docs/for_developers/architecture.md
@@ -0,0 +1,61 @@
+## Architecture
+### Frontend
+- language: TypeScript
+- environment: Node.js (v20)
+- framework: React (v18)
+- middleware: Redux, Redux Toolkit, React Router
+
+#### Directory structure
+Following is the summary of directory structure.
+
+- frontend
+  - src
+    - api: handle API requests.
+    - components: React components.
+    - const: constants.
+    - pages: Components set as `element` in `Route` component of react-router.
+    - store: Redux store.
+      - slice
+        - Some
+          - SomeActions.ts: create actions like async thunk from api response.
+          - SomeSelectors.ts: select state from store.
+          - SomeSlice.ts: define reducers.
+          - SomeType.ts: define data type.
+          - SomeUtils.ts: define utility functions if needed.
+    - style: extra css files.
+    - utils: common utility functions.
+
+- api, components, store/slice directories are separated by its domain.
+
+### Backend
+- language: Python (v3.8)
+- framework: FastAPI
+- handle workflow by snakemake.
+
+#### Directory structure
+Following is the summary of directory structure.
+- studio
+  - alembic: files for database migration. database is used in multi-user mode.
+  - app
+    - `Snakefile`: File read by snakemake. It defines how to run workflow by language like Python.
+    - common: common modules(not for specific domain)
+      - core: define core functions.
+      - dataclass: define dataclasses that are passed between nodes or used as visualize outputs.
+      - db: database general configuration.
+      - models: database models.
+      - routers: define fastapi routers.
+      - schemas: define pydantic schemas for api requests and responses.
+      - wrappers: functions for algorithm nodes.
+    - optinist: modules specific to calcium imaging data processing domain. It has same structure as common.
+  - config: configuration files.
+    - `standalone-logging.yaml`: logging config for standalone mode. In standalone mode, logs are sent to streams.
+    - `logging.yaml`: logging config for multi-user mode. In multi-user mode, logs are sent to file (in `logs` dir). log file rotation settings are included.
+      - you can manage log configurations by editing these files.
+    - auth: put Firebase authentication secret files.
+    - docker: backend Dockerfiles for each environment.
+  - test_data: test data for unit tests.
+  - tests: unit tests.
+  - `__main__.py`: entry point of backend in production.
+  - `__main_unit__.py`: core main unit. called by `studio/__main__.py` and `main.py`.
+- `main.py`: entry point of backend in development.
+- `run_cluster.py`: entry point for CLI run.
diff --git a/docs/for_developers/index.rst b/docs/for_developers/index.rst
@@ -0,0 +1,16 @@
+.. _for_developers:
+
+***************
+FOR DEVELOPERS
+***************
+
+OptiNiSt welcomes your contributions.
+See the following guidelines before submitting Pull Requests.
+
+.. toctree::
+  :maxdepth: 2
+
+  style
+  pull_request
+  architecture
+  test
diff --git a/docs/for_developers/pull_request.md b/docs/for_developers/pull_request.md
@@ -0,0 +1,18 @@
+## Pull Request
+- GitHub Pull Request page
+  - [https://github.com/oist/optinist/pulls](https://github.com/oist/optinist/pulls)
+
+### Pre Commit
+- run following command before your first commit
+  ```
+  pre-commit install
+  ```
+  - Once installed, it automatically checks your coding style on every commits.
+
+### Branch rules
+- You can submit Pull Request by pushing new branch.
+  - Make sure the base branch is `develop-main`, and PR is to `develop-main`.
+  - You can't push to the `develop-main` branch directly, the branch is protected.
+  - Make sure new branch name is in following format (`xxx` is the name of the feature or bug you are working on.).
+    - `feature/xxx`
+    - `fix/xxx`
diff --git a/docs/utils/contributing.md → docs/for_developers/style.md b/docs/utils/contributing.md → docs/for_developers/style.md
@@ -1,16 +1,4 @@
-(Contributing)=
-# Contributing to OptiNiSt
-OptiNiSt welcomes your contributions.
-See the following guidelines before submitting Pull Requests.
-
-## Coding Style
-### Pre Commit
-- run following command before your first commit
-  ```
-  pre-commit install
-  ```
-  - Once installed, it automatically checkes your code style on every commits.
-
+## Style Guides
 ### Python
 - Format all files using [black](https://black.readthedocs.io/en/stable/#).
 - Check the code for problems using [flake8](https://pypi.org/project/flake8/).
@@ -19,7 +7,14 @@ See the following guidelines before submitting Pull Requests.
 - Sort your import using [isort](https://github.com/PyCQA/isort).
 - These guides are checked by pre-commits, github workflow on submitting Pull Requests.
 
-#### VSCode Settings
+### TypeScript
+- Format all files using [prettier](https://prettier.io/).
+  - Rules are defined in `frontend/.prettierrc.json`.
+- Check the code for problems using [eslint](https://eslint.org/).
+  - Rules are defined in `frontend/.eslintrc.json`.
+
+### Editor support
+#### VSCode
 - If you are using VSCode, you can use features (like format/lint on save) by installing and activating the extensions in `.vscode/extensions.json`.
 - For these extensions, we provide example settings in `.vscode/settings.example.json`
   - To use this,