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Merge pull request #482 from oist/develop-main
import develop-main
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‎.github/workflows/linters.yml

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

‎.gitignore

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

‎.vscode/extensions.json

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{
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"recommendations": [
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"ms-python.black-formatter",
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"ms-python.flake8",
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"ms-python.isort"
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]
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}

‎.vscode/settings.json

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

‎docs/conf.py

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import os
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import sys
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from datetime import datetime
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sys.path.insert(0, os.path.abspath('../'))
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from optinist.version import VERSION, VERSION_SHORT
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sys.path.insert(0, os.path.abspath("../"))
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from optinist.version import VERSION, VERSION_SHORT # noqa: E402
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# -- Path setup --------------------------------------------------------------
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# -- Project information -----------------------------------------------------
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project = 'OptiNiSt'
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project = "OptiNiSt"
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copyright = f"{datetime.today().year}, OIST"
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author = ''
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author = ""
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version = VERSION_SHORT
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release = VERSION
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# -- readthedocs -------------------------------------------------------------
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on_rtd = os.environ.get('READTHEDOCS', None) == 'True'
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on_rtd = os.environ.get("READTHEDOCS", None) == "True"
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# -- General configuration ---------------------------------------------------
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master_doc = 'index'
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master_doc = "index"
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# Add any Sphinx extension module names here, as strings. They can be
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# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
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"sphinx.ext.intersphinx",
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"sphinx.ext.mathjax",
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"sphinx.ext.viewcode",
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'sphinx.ext.napoleon',
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'sphinx.ext.coverage',
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'sphinxcontrib.apidoc',
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'sphinx_autodoc_typehints',
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'myst_parser',
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'sphinx.ext.autosectionlabel',
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'sphinx.ext.autosummary',
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'sphinx.ext.extlinks',
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'sphinx.ext.autodoc.typehints'
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"sphinx.ext.napoleon",
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"sphinx.ext.coverage",
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"sphinxcontrib.apidoc",
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"sphinx_autodoc_typehints",
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"myst_parser",
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"sphinx.ext.autosectionlabel",
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"sphinx.ext.autosummary",
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"sphinx.ext.extlinks",
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"sphinx.ext.autodoc.typehints",
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]
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# Tell myst-parser to assign header anchors for h1-h3.
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suppress_warnings = ["myst.header"]
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# Add any paths that contain templates here, relative to this directory.
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templates_path = ['_templates']
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templates_path = ["_templates"]
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# List of patterns, relative to source directory, that match files and
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# directories to ignore when looking for source files.
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# This pattern also affects html_static_path and html_extra_path.
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exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store', 'tests', '*test*']
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exclude_patterns = ["_build", "Thumbs.db", ".DS_Store", "tests", "*test*"]
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source_suffix = [".rst", ".md"]
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# The theme to use for HTML and HTML Help pages. See the documentation for
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# a list of builtin themes.
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#
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html_theme = 'sphinx_rtd_theme'
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html_theme = "sphinx_rtd_theme"
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# Add any paths that contain custom static files (such as style sheets) here,
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# relative to this directory. They are copied after the builtin static files,
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# so a file named "default.css" will overwrite the builtin "default.css".
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html_static_path = ['_static']
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html_logo = '_static/optinist.png'
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html_favicon = '_static/favicon.ico'
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html_static_path = ["_static"]
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html_logo = "_static/optinist.png"
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html_favicon = "_static/favicon.ico"
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# disable document page source link
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html_show_sourcelink = False
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autosummary_generate = True
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html_theme_options = {
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'canonical_url': '',
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'logo_only': False,
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'display_version': True,
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'prev_next_buttons_location': 'top',
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'style_external_links': False,
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'style_nav_header_background': '#C3EBE1',
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"canonical_url": "",
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"logo_only": False,
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"display_version": True,
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"prev_next_buttons_location": "top",
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"style_external_links": False,
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"style_nav_header_background": "#C3EBE1",
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# Toc options
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'collapse_navigation': True,
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'sticky_navigation': True,
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'navigation_depth': 4,
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'includehidden': True,
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'titles_only': False,
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}
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"collapse_navigation": True,
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"sticky_navigation": True,
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"navigation_depth": 4,
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"includehidden": True,
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"titles_only": False,
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}

‎docs/index.rst

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contain the root `toctree` directive.
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OptiNiSt - Calcium Imaging Pipeline Tool
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===================================
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==========================================
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**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.
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‎docs/installation/docker_for_developer.md

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Docker for Developer (recommended)
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Docker for Developer
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=================
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```{contents}

‎docs/installation/linux_for_developer.md ‎docs/installation/each_platforms_for_developer.md

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Linux for Developer (recommended)
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Each Platforms for Developer
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=================
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```{contents}
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### Install Tools
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#### Install Anaconda
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Install [Anaconda for Windows](https://www.anaconda.com/products/individual)
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- Unix-like platforms
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- Linux
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- [Install Tools](linux.md#install-tools)
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- Windows WSL
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- [Install Tools](windows.md#install-tools-1)
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- Mac
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- [Install Tools](mac.md#install-tools)
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- Windows
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- [Install Tools](windows.md#install-tools)
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### Clone repository
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### Create anaconda environment
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```
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conda create -n optinist python=3.8
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conda activate optinist
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conda create -n optinist_dev python=3.8
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conda activate optinist_dev
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```
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```
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conda config --set channel_priority strict
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```
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### Install requirements
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### Set saving directory
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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.
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```bash
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```
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export OPTINIST_DIR="your_saving_dir"
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```
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<!--
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## 2. Create virtualenv
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### 2. Create virtualenv
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Under maintenance...
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-->

‎docs/installation/each_platforms_for_developer_use_mamba.md

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Each Platforms for Developer (Use Mamba)
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=================
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```{contents}
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:depth: 4
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```
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## Installation
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We introduce how to install optinist for developer.
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We have developed optinist python(backend) and typescript(frontend), so you need to make both environment.
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Please follow instructions below.
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## 1. Make backend environment
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### Install Tools
17+
18+
- Unix-like platforms
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- Linux
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- [Install Tools](linux.md#install-tools)
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- Windows WSL
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- [Install Tools](windows.md#install-tools-1)
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- Mac
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- [Install Tools](mac.md#install-tools)
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- Windows
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- *Under construction.
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28+
#### Install Mamba
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- Unix-like platforms
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- https://mamba.readthedocs.io/en/latest/installation.html
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- Use Mambaforge
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- https://github.com/conda-forge/miniforge#mambaforge
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- Install
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- for Linux
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```
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curl -L -O "https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-$(uname)-$(uname -m).sh"
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bash Mambaforge-$(uname)-$(uname -m).sh
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# restart shell, and check mamba installed. (show version)
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mamba --version
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```
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- for Mac (fixed with x86_64)
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```
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curl -L -O "https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-$(uname)-x86_64.sh"
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bash Mambaforge-$(uname)-x86_64.sh
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# restart shell, and check mamba installed. (show version)
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mamba --version
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```
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- Windows
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- *Under construction.
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### Clone repository
55+
56+
```
57+
git clone https://github.com/oist/optinist.git
58+
cd ./optinist
59+
```
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### Create mamba(anaconda) environment
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<!--
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mamba create -c conda-forge -c bioconda -n optinist_dev python=3.8 snakemake
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-->
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```
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mamba create -n optinist_dev python=3.8
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conda activate optinist_dev
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```
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```
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conda config --set channel_priority strict
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```
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- Note:
77+
- If mamba is already installed, snakamake prefers to use mamba over conda.
78+
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### Install requirements
81+
82+
```
83+
pip install -r requirements.txt
84+
```
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### Set saving directory
87+
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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.
89+
```
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export OPTINIST_DIR="your_saving_dir"
91+
```
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<!--
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## 2. Create virtualenv
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96+
Under maintenance...
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-->
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## 2. Run backend
100+
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```
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python main.py
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```
104+
- `python main.py` log is as blow:
105+
```
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$ run_optinist
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INFO: Will watch for changes in these directories: ['/home/oist/optinist/backend']
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INFO: Uvicorn running on http://0.0.0.0:8000 (Press CTRL+C to quit)
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INFO: Started reloader process [6520] using statreload
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INFO: Started server process [6557]
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INFO: Waiting for application startup.
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INFO: Application startup complete.
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```
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- Launch browser, and go to http://localhost:8000
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It opens correctly!
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Done!

‎docs/installation/index.rst

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:caption: Installation (for Developer)
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docker_for_developer
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linux_for_developer
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windows_for_developer
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mac_for_developer
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each_platforms_for_developer
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.. each_platforms_for_developer_use_mamba

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