merging with develop-main

README.md

@@ -34,90 +34,104 @@ OptiNiSt helps researchers try multiple data analysis methods, visualize the res
 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] Dimension Reduction(PCA...)
 - [x] Neural Decoding(LDA...)
 - [x] Neural Population Analysis(Correlation...)
 
 ### Saving Format
-- [x] [NWB](https://github.com/NeurodataWithoutBorders/pynwb)
 
+- [x] [NWB](https://github.com/NeurodataWithoutBorders/pynwb)
 
 ## Key Features
+
 ### :beginner: Easy-To-Create Workflow
+
 - **zero-knowledge of coding**: OptiNiSt allows you to create analysis pipelines easily on the GUI.
 
 ### :zap: Visualizing analysis results
+
 - **quick visualization**: OptiNiSt supports you visualize the analysis results by plotly.
 
 ### :rocket: Managing Workflows
-- **recording and reproducing**: OptiNiSt records and reproduces the workflow pipelines easily.
 
+- **recording and reproducing**: OptiNiSt records and reproduces the workflow pipelines easily.
 
 ## Installation
-Need anaconda or miniconda environment.
+
+Need anaconda or miniconda or miniforge 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/
 
+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)
 
 ### Support Developers
-[Tatsuya Tanabe](https://github.com/ttya16), [Yosuke Kaneko](https://github.com/toto-maru), [Syuya Saeki](https://github.com/hiiaka)
 
+[Tatsuya Tanabe](https://github.com/ttya16), [Yosuke Kaneko](https://github.com/toto-maru), [Syuya Saeki](https://github.com/hiiaka)
 
 ## 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

docs/conf.py

@@ -19,7 +19,7 @@
 project = "OptiNiSt"
 copyright = f"{datetime.today().year}, OIST"
 author = ""
-release = "1.2.1"
+release = "1.3.0"
 
 # -- readthedocs -------------------------------------------------------------
 on_rtd = os.environ.get("READTHEDOCS", None) == "True"

docs/installation/docker.md

@@ -22,7 +22,7 @@ Please follow instructions below.
 ### Make Docker Image
 
 Pull the latest docker image from docker hub.
-```
+```bash
 docker pull oistncu/optinist
 ```
 Start docker container.

docs/installation/docker_developer.md

@@ -19,20 +19,20 @@ Please follow instructions below.
 
 ### Clone repository
 
-```
+```bash
 git clone https://github.com/oist/optinist.git
 cd ./optinist
 ```
 
 - copy config files
-  ```
+  ```bash
   cp studio/config/.env.example studio/config/.env
   cp frontend/.env.example frontend/.env
   ```
 
 ### Start Docker Container
 
-```
+```bash
 docker compose -f docker-compose.dev.yml up
 ```
 

docs/installation/linux.md

@@ -23,46 +23,50 @@ Please follow instructions below.
 #### Install gcc, g++
 
 - For install CaImAn, you need to install gcc and g++.
-```
+
+```bash
 sudo apt install gcc g++
 ```
 
 #### Install Anaconda
 
-```
+```bash
 # *The latest version of the module is ok.
-wget https://repo.anaconda.com/archive/Anaconda3-2022.10-Linux-x86_64.sh
-bash Anaconda3-2022.10-Linux-x86_64.sh
+ANACONDA_VERSION=2022.10
+wget https://repo.anaconda.com/archive/Anaconda3-${ANACONDA_VERSION}-Linux-x86_64.sh
+bash Anaconda3-${ANACONDA_VERSION}-Linux-x86_64.sh
 ```
 
-### Create Anaconda Environment
+### Create Conda Environment
 
-```
+```bash
 conda create -n optinist python=3.8
 conda activate optinist
 ```
 
-
 ### Install Library
 
-```
+```bash
 pip install optinist
 ```
 
 ### Set Saving Directory
 
 Optinist default saving directory is `/tmp/studio`. If you reboot your PC, this repogitory content is deleted. And setting the saving directory in environment path.
-```
+
+```bash
 export OPTINIST_DIR="your_saving_dir"
 ```
 
 ## 2. Run Backend
 
-```
+```bash
 run_optinist
 ```
+
 - `run_optinist` log is as blow:
-```
+
+```bash
 $ run_optinist
 INFO:     Will watch for changes in these directories: ['/home/oist/optinist/backend']
 INFO:     Uvicorn running on http://0.0.0.0:8000 (Press CTRL+C to quit)
@@ -71,6 +75,7 @@ INFO:     Started server process [6557]
 INFO:     Waiting for application startup.
 INFO:     Application startup complete.
 ```
+
 - Launch browser, and go to http://localhost:8000
 
 Done!

docs/installation/mac.md

@@ -46,49 +46,53 @@ Please follow instructions below.
 
            arch -x86_64 /usr/bin/env bash
 
-   3. Download and install Miniconda:
+   3. Download and install Miniforge:
+
+      - Miniforge: https://github.com/conda-forge/miniforge
 
         .. code-block:: bash
 
-           curl -O https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh
+           curl -L -O "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-x86_64.sh"
 
-           bash Miniconda3-latest-MacOSX-x86_64.sh
+           bash Miniforge3-$(uname)-x86_64.sh
 
-           /Users/MYUSERNAME/miniconda3/bin/conda init
+           $HOME/miniforge3/bin/conda init
 
            conda activate
 
+           conda config --set channel_priority flexible
+
    Now continue creating the optinist environment using conda
 ```
 
-### Create Anaconda Environment
+### Create Conda Environment
 
-```
+```bash
 conda create -n optinist python=3.8
 conda activate optinist
 ```
 
 
 ### Install Library
 
-```
+```bash
 pip install optinist
 ```
 
 ### Set Saving Directory
 
 Optinist default saving directory is `/tmp/studio`. If you reboot your PC, this repogitory content is deleted. And setting the saving directory in environment path.
-```
+```bash
 export OPTINIST_DIR="your_saving_dir"
 ```
 
 ## 2. Run Backend
 
-```
+```bash
 run_optinist
 ```
 - `run_optinist` log is as blow:
-```
+```bash
 $ run_optinist
 INFO:   Will watch for changes in these directories: [‘/Users/oist/optinist/backend’]
 INFO:   Uvicorn running on http://0.0.0.0:8000 (Press CTRL+C to quit)

docs/installation/native_platforms_developer.md

@@ -34,13 +34,13 @@ Get node with version 20
 You can also install node via [nvm](https://github.com/nvm-sh/nvm)
 
 After install node, install yarn.
-```
+```bash
 npm install -g yarn
 ```
 
 ### Clone Repository
 
-```
+```bash
 git clone https://github.com/oist/optinist.git
 cd ./optinist
 ```
@@ -51,20 +51,25 @@ cd ./optinist
   cp frontend/.env.example frontend/.env
   ```
 
-### Create Anaconda Environment
+### Create Conda Environment
 
-```
+```bash
 conda create -n optinist_dev python=3.8 poetry
 conda activate optinist_dev
 ```
 
-```
-conda config --set channel_priority strict
-```
+- for *Miniconda*
+  ```bash
+  conda config --set channel_priority strict
+  ```
+- for *Miniforge*
+  ```bash
+  conda config --set channel_priority flexible
+  ```
 
 ### Install Requirements
 
-```
+```bash
 poetry install --no-root --with dev
 ```
 
@@ -73,17 +78,18 @@ If you will make PRs, please see the [](for_developers) section.
 ### Set Saving Directory
 
 Optinist default saving directory is `/tmp/studio`. If you reboot your PC, this repogitory content is deleted. And setting the saving directory in environment path.
-```
+
+```bash
 export OPTINIST_DIR="your_saving_dir"
 ```
 
 ## 2. Run Backend
 
-```
+```bash
 python main.py
 ```
 - `python main.py` log is as blow:
-```
+```bash
 $ run_optinist
 INFO:     Will watch for changes in these directories: ['/home/oist/optinist/backend']
 INFO:     Uvicorn running on http://0.0.0.0:8000 (Press CTRL+C to quit)
@@ -99,13 +105,13 @@ INFO:     Application startup complete.
 
 Open new terminal window, and go to `frontend` directory.
 
-```
+```bash
 # from optinist root directory
 cd frontend
 ```
 
 Then install packages and run.
-```
+```bash
 yarn install
 yarn start
 ```