Merge branch 'develop-main' into use-absolute-path-import

.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

.gitignore

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

.vscode/extensions.json

@@ -0,0 +1,7 @@
+{
+  "recommendations": [
+    "ms-python.black-formatter",
+    "ms-python.flake8",
+    "ms-python.isort"
+  ]
+}

.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": ""
 }

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,
+}

docs/utils/contributing.md

@@ -0,0 +1,13 @@
+# Contributing to OptiNiSt
+OptiNiSt welcomes your contributions.
+See the following guidelines before submitting Pull Requests.
+
+## Coding Style
+### Python
+- Format all files using [black](https://black.readthedocs.io/en/stable/#).
+- Check the code for problems using [flake8](https://pypi.org/project/flake8/).
+  - Some excluded rules are contained in `setup.cfg`.
+  - These exclusion are to avoid conflicts between black and flake8.
+- Sort your import using [isort](https://github.com/PyCQA/isort).
+- These guides are checked by workflows on submitting Pull Requests.
+- If you are using VSCode, you can follow the above guidelines by installing and activating the extensions in `.vscode/extensions.json`.

docs/utils/index.rst

@@ -8,4 +8,5 @@ OTHER
 
   add_algorithm
   cui_execution
-  implemented_analysis
+  implemented_analysis
+  contributing

main.py

@@ -6,4 +6,5 @@
 # run backend main module.
 if __name__ == "__main__":
     from optinist.__main_unit__ import main
-    main(develop_mode = True)
+
+    main(develop_mode=True)

optinist/__main__.py

@@ -1,4 +1,5 @@
 # run backend main module.
 if __name__ == "__main__":
     from optinist.__main_unit__ import main
+
     main()

optinist/__main_unit__.py

@@ -1,23 +1,16 @@
+import argparse
+import os
+
+import uvicorn
 from fastapi import FastAPI, Request
 from fastapi.staticfiles import StaticFiles
 from fastapi.templating import Jinja2Templates
-
-import os
-import argparse
-import uvicorn
 from starlette.middleware.cors import CORSMiddleware
-from optinist.api.dir_path import DIRPATH as OPTINIST_DIRPATH
-from optinist.routers import (
-    files,
-    run,
-    params,
-    outputs,
-    algolist,
-    hdf5,
-    experiment,
-)
+
 from optinist.api.config.config_reader import ConfigReader
+from optinist.api.dir_path import DIRPATH as OPTINIST_DIRPATH
 from optinist.api.utils.filepath_creater import join_filepath
+from optinist.routers import algolist, experiment, files, hdf5, outputs, params, run
 
 app = FastAPI(docs_url="/docs", openapi_url="/openapi")
 app.include_router(algolist.router)
@@ -63,14 +56,33 @@ def main(develop_mode: bool = False):
     args = parser.parse_args()
 
     # set fastapi@uvicorn logging config.
-    logging_config_path = join_filepath([OPTINIST_DIRPATH.ROOT_DIR, 'app_config', 'logging.yaml'])
+    logging_config_path = join_filepath(
+        [OPTINIST_DIRPATH.ROOT_DIR, "app_config", "logging.yaml"]
+    )
     logging_config = ConfigReader.read(logging_config_path)
     fastapi_logging_config = uvicorn.config.LOGGING_CONFIG
-    fastapi_logging_config["formatters"]["default"]["fmt"] = logging_config["fastapi_logging_config"]["default_fmt"]
-    fastapi_logging_config["formatters"]["access"]["fmt"] = logging_config["fastapi_logging_config"]["access_fmt"]
+    fastapi_logging_config["formatters"]["default"]["fmt"] = logging_config[
+        "fastapi_logging_config"
+    ]["default_fmt"]
+    fastapi_logging_config["formatters"]["access"]["fmt"] = logging_config[
+        "fastapi_logging_config"
+    ]["access_fmt"]
 
     if develop_mode:
         reload_options = {"reload_dirs": ["optinist"]} if args.reload else {}
-        uvicorn.run("optinist.__main_unit__:app", host=args.host, port=args.port, log_config=fastapi_logging_config, reload=args.reload, **reload_options)
+        uvicorn.run(
+            "optinist.__main_unit__:app",
+            host=args.host,
+            port=args.port,
+            log_config=fastapi_logging_config,
+            reload=args.reload,
+            **reload_options,
+        )
     else:
-        uvicorn.run("optinist.__main_unit__:app", host=args.host, port=args.port, log_config=fastapi_logging_config, reload=False)
+        uvicorn.run(
+            "optinist.__main_unit__:app",
+            host=args.host,
+            port=args.port,
+            log_config=fastapi_logging_config,
+            reload=False,
+        )

optinist/api/config/config_reader.py

@@ -1,4 +1,5 @@
 import os
+
 import yaml
 
 

optinist/api/config/config_writer.py

@@ -1,9 +1,6 @@
 import yaml
 
-from optinist.api.utils.filepath_creater import (
-    create_directory,
-    join_filepath
-)
+from optinist.api.utils.filepath_creater import create_directory, join_filepath
 
 
 class ConfigWriter:

optinist/api/dataclass/bar.py

@@ -7,16 +7,16 @@
 
 
 class BarData(BaseData):
-    def __init__(self, data, index=None, file_name='bar'):
+    def __init__(self, data, index=None, file_name="bar"):
         super().__init__(file_name)
         data = np.array(data)
 
-        assert data.ndim <= 2, 'Bar Dimension Error'
+        assert data.ndim <= 2, "Bar Dimension Error"
 
         if data.ndim == 1:
             data = data[np.newaxis]
 
-        assert data.ndim == 2, 'Bar Dimesion is not 2'
+        assert data.ndim == 2, "Bar Dimesion is not 2"
 
         self.data = data
 

optinist/api/dataclass/csv.py

@@ -2,13 +2,12 @@
 import pandas as pd
 
 from optinist.api.dataclass.base import BaseData
-
 from optinist.api.utils.filepath_creater import create_directory, join_filepath
 from optinist.api.utils.json_writer import JsonWriter
 
 
 class CsvData(BaseData):
-    def __init__(self, data, params, file_name='csv'):
+    def __init__(self, data, params, file_name="csv"):
         super().__init__(file_name)
 
         if isinstance(data, str):
@@ -33,6 +32,5 @@ def save_json(self, json_dir):
 
         for i, data in enumerate(self.data):
             JsonWriter.write_as_split(
-                join_filepath([self.json_path, f'{str(i)}.json']),
-                data
+                join_filepath([self.json_path, f"{str(i)}.json"]), data
             )