Merge pull request #482 from oist/develop-main

import develop-main
oist · May 8, 2023 · 3ab617b · 3ab617b
2 parents 40bd530 + 5488cc2
commit 3ab617b
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diff --git a/.github/workflows/linters.yml b/.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
diff --git a/.gitignore b/.gitignore
@@ -3,6 +3,7 @@ __pycache__
 .ipynb_checkpoints
 .vscode/*
 !.vscode/settings.json
+!.vscode/extensions.json
 dist
 /build
 optinist/frontend

diff --git a/.vscode/extensions.json b/.vscode/extensions.json
@@ -0,0 +1,7 @@
+{
+  "recommendations": [
+    "ms-python.black-formatter",
+    "ms-python.flake8",
+    "ms-python.isort"
+  ]
+}
diff --git a/.vscode/settings.json b/.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": ""
 }
diff --git a/docs/conf.py b/docs/conf.py
@@ -7,8 +7,9 @@
 import os
 import sys
 from datetime import datetime
-sys.path.insert(0, os.path.abspath('../'))
-from optinist.version import VERSION, VERSION_SHORT
+
+sys.path.insert(0, os.path.abspath("../"))
+from optinist.version import VERSION, VERSION_SHORT  # noqa: E402
 
 # -- Path setup --------------------------------------------------------------
 
@@ -20,17 +21,17 @@
 
 # -- Project information -----------------------------------------------------
 
-project = 'OptiNiSt'
+project = "OptiNiSt"
 copyright = f"{datetime.today().year}, OIST"
-author = ''
+author = ""
 version = VERSION_SHORT
 release = VERSION
 
 # -- readthedocs -------------------------------------------------------------
-on_rtd = os.environ.get('READTHEDOCS', None) == 'True'
+on_rtd = os.environ.get("READTHEDOCS", None) == "True"
 
 # -- General configuration ---------------------------------------------------
-master_doc = 'index'
+master_doc = "index"
 
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
@@ -40,15 +41,15 @@
     "sphinx.ext.intersphinx",
     "sphinx.ext.mathjax",
     "sphinx.ext.viewcode",
-    'sphinx.ext.napoleon',
-    'sphinx.ext.coverage',
-    'sphinxcontrib.apidoc',
-    'sphinx_autodoc_typehints',
-    'myst_parser',
-    'sphinx.ext.autosectionlabel',
-    'sphinx.ext.autosummary',
-    'sphinx.ext.extlinks',
-    'sphinx.ext.autodoc.typehints'
+    "sphinx.ext.napoleon",
+    "sphinx.ext.coverage",
+    "sphinxcontrib.apidoc",
+    "sphinx_autodoc_typehints",
+    "myst_parser",
+    "sphinx.ext.autosectionlabel",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.extlinks",
+    "sphinx.ext.autodoc.typehints",
 ]
 
 # Tell myst-parser to assign header anchors for h1-h3.
@@ -57,12 +58,12 @@
 suppress_warnings = ["myst.header"]
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path.
-exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store', 'tests', '*test*']
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store", "tests", "*test*"]
 
 source_suffix = [".rst", ".md"]
 
@@ -71,31 +72,31 @@
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'sphinx_rtd_theme'
+html_theme = "sphinx_rtd_theme"
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
-html_logo = '_static/optinist.png'
-html_favicon = '_static/favicon.ico'
+html_static_path = ["_static"]
+html_logo = "_static/optinist.png"
+html_favicon = "_static/favicon.ico"
 
 # disable document page source link
 html_show_sourcelink = False
 
 autosummary_generate = True
 
 html_theme_options = {
-    'canonical_url': '',
-    'logo_only': False,
-    'display_version': True,
-    'prev_next_buttons_location': 'top',
-    'style_external_links': False,
-    'style_nav_header_background': '#C3EBE1',
+    "canonical_url": "",
+    "logo_only": False,
+    "display_version": True,
+    "prev_next_buttons_location": "top",
+    "style_external_links": False,
+    "style_nav_header_background": "#C3EBE1",
     # Toc options
-    'collapse_navigation': True,
-    'sticky_navigation': True,
-    'navigation_depth': 4,
-    'includehidden': True,
-    'titles_only': False,
-}
+    "collapse_navigation": True,
+    "sticky_navigation": True,
+    "navigation_depth": 4,
+    "includehidden": True,
+    "titles_only": False,
+}
diff --git a/docs/index.rst b/docs/index.rst
@@ -4,7 +4,7 @@
   contain the root `toctree` directive.
 
 OptiNiSt - Calcium Imaging Pipeline Tool
-===================================
+==========================================
 
 **OptiNiSt(Optical Neuroimage Studio)** helps researchers try multiple data analysis methods, visualize the results, and construct the data analysis pipelines easily and quickly. OptiNiSt's data-saving format follows NWB standards.
 

diff --git a/docs/installation/docker_for_developer.md b/docs/installation/docker_for_developer.md
@@ -1,4 +1,4 @@
-Docker for Developer (recommended)
+Docker for Developer
 =================
 
 ```{contents}

diff --git a/docs/installation/linux_for_developer.md → ...tallation/each_platforms_for_developer.md b/docs/installation/linux_for_developer.md → ...tallation/each_platforms_for_developer.md
@@ -1,4 +1,4 @@
-Linux for Developer (recommended)
+Each Platforms for Developer
 =================
 
 ```{contents}
@@ -15,9 +15,15 @@ Please follow instructions below.
 
 ### Install Tools
 
-#### Install Anaconda
-
-Install [Anaconda for Windows](https://www.anaconda.com/products/individual)
+- Unix-like platforms
+  - Linux
+    - [Install Tools](linux.md#install-tools)
+  - Windows WSL
+    - [Install Tools](windows.md#install-tools-1)
+  - Mac
+    - [Install Tools](mac.md#install-tools)
+- Windows
+    - [Install Tools](windows.md#install-tools)
 
 ### Clone repository
 
@@ -29,8 +35,12 @@ cd ./optinist
 ### Create anaconda environment
 
 ```
-conda create -n optinist python=3.8
-conda activate optinist
+conda create -n optinist_dev python=3.8
+conda activate optinist_dev
+```
+
+```
+conda config --set channel_priority strict
 ```
 
 ### Install requirements
@@ -42,12 +52,12 @@ pip install -r requirements.txt
 ### Set saving directory
 
 Optinist default saving directory is `/tmp/optinist`. 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. Create virtualenv
+### 2. Create virtualenv
 
 Under maintenance...
 -->

diff --git a/docs/installation/each_platforms_for_developer_use_mamba.md b/docs/installation/each_platforms_for_developer_use_mamba.md
@@ -0,0 +1,118 @@
+Each Platforms for Developer (Use Mamba)
+=================
+
+```{contents}
+:depth: 4
+```
+
+## Installation
+
+We introduce how to install optinist for developer.
+We have developed optinist python(backend) and typescript(frontend), so you need to make both environment.
+Please follow instructions below.
+
+## 1. Make backend environment
+
+### Install Tools
+
+- Unix-like platforms
+  - Linux
+    - [Install Tools](linux.md#install-tools)
+  - Windows WSL
+    - [Install Tools](windows.md#install-tools-1)
+  - Mac
+    - [Install Tools](mac.md#install-tools)
+- Windows
+  - *Under construction.
+
+#### Install Mamba
+
+- Unix-like platforms
+  - https://mamba.readthedocs.io/en/latest/installation.html
+    - Use Mambaforge
+      - https://github.com/conda-forge/miniforge#mambaforge
+    - Install
+      - for Linux
+        ```
+        curl -L -O "https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-$(uname)-$(uname -m).sh"
+        bash Mambaforge-$(uname)-$(uname -m).sh
+
+        # restart shell, and check mamba installed. (show version)
+        mamba --version
+        ```
+      - for Mac (fixed with x86_64)
+        ```
+        curl -L -O "https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-$(uname)-x86_64.sh"
+        bash Mambaforge-$(uname)-x86_64.sh
+
+        # restart shell, and check mamba installed. (show version)
+        mamba --version
+        ```
+- Windows
+  - *Under construction.
+
+### Clone repository
+
+```
+git clone https://github.com/oist/optinist.git
+cd ./optinist
+```
+
+### Create mamba(anaconda) environment
+
+<!--
+mamba create -c conda-forge -c bioconda -n optinist_dev python=3.8 snakemake
+-->
+
+```
+mamba create -n optinist_dev python=3.8
+conda activate optinist_dev
+```
+
+```
+conda config --set channel_priority strict
+```
+
+- Note:
+  - If mamba is already installed, snakamake prefers to use mamba over conda.
+
+
+### Install requirements
+
+```
+pip install -r requirements.txt
+```
+
+### Set saving directory
+
+Optinist default saving directory is `/tmp/optinist`. If you reboot your PC, this repogitory content is deleted. And setting the saving directory in environment path.
+```
+export OPTINIST_DIR="your_saving_dir"
+```
+
+<!--
+## 2. Create virtualenv
+
+Under maintenance...
+-->
+
+## 2. Run backend
+
+```
+python main.py
+```
+- `python main.py` log is as blow:
+```
+$ 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)
+INFO:     Started reloader process [6520] using statreload
+INFO:     Started server process [6557]
+INFO:     Waiting for application startup.
+INFO:     Application startup complete.
+```
+- Launch browser, and go to http://localhost:8000
+
+It opens correctly!
+
+Done!
diff --git a/docs/installation/index.rst b/docs/installation/index.rst
@@ -16,6 +16,5 @@ Installation
   :caption: Installation (for Developer)
 
   docker_for_developer
-  linux_for_developer
-  windows_for_developer
-  mac_for_developer
+  each_platforms_for_developer
+..  each_platforms_for_developer_use_mamba