MAINT: Update testing (use Black, Ruff, precommit hook)

.github/workflows/check_linting.yml

@@ -1,22 +1,22 @@
-name: PEP8 Compliance, Spellcheck, & Docstring
+name: Style, Spellcheck, & Docstring
 
 on: pull_request
 
 jobs:
-  linting:
+  style:
+    name: Style
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
-    - name: Set up Python 3.x
-      uses: actions/setup-python@v4
-      with:
-        python-version: "3.x"
-    - name: Install dependencies
-      run: pip install -r requirements_testing.txt
-    - name: Run flake8
-      run: flake8 pylossless docs --exclude pylossless/__init__.py
-    - name: Run Codespell
-      run: codespell pylossless docs --skip docs/source/generated
-    - name: Check Numpy Format Docstring
-      run: pydocstyle pylossless
-
+      - uses: actions/checkout@v3
+        with:
+          python-version: "3.11"
+      - uses: psf/black@stable
+      - uses: pre-commit/[email protected]
+      - name: Install dependencies
+        run: pip install -r requirements_testing.txt
+      # Run Ruff
+      - name: Run Ruff
+        run: ruff pylossless
+      # Run Codespell
+      - name: Run Codespell
+        run: codespell pylossless docs

.github/workflows/main_pylossless-qc-demo.yml

@@ -0,0 +1,63 @@
+# Docs for the Azure Web Apps Deploy action: https://github.com/Azure/webapps-deploy
+# More GitHub Actions for Azure: https://github.com/Azure/actions
+# More info on Python, GitHub Actions, and Azure App Service: https://aka.ms/python-webapps-actions
+
+name: Build and deploy Python app to Azure Web App - pylossless-qc-demo
+
+on:
+  push:
+    branches:
+      - main
+  workflow_dispatch:
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Set up Python version
+        uses: actions/setup-python@v1
+        with:
+          python-version: '3.7'
+
+      - name: Create and start virtual environment
+        run: |
+          python -m venv venv
+          source venv/bin/activate
+      
+      - name: Install dependencies
+        run: pip install -r requirements.txt
+
+      # Optional: Add step to run tests here (PyTest, Django test suites, etc.)
+
+      - name: Upload artifact for deployment jobs
+        uses: actions/upload-artifact@v2
+        with:
+          name: python-app
+          path: |
+            . 
+            !venv/
+
+  deploy:
+    runs-on: ubuntu-latest
+    needs: build
+    environment:
+      name: 'Production'
+      url: ${{ steps.deploy-to-webapp.outputs.webapp-url }}
+
+    steps:
+      - name: Download artifact from build job
+        uses: actions/download-artifact@v2
+        with:
+          name: python-app
+          path: .
+
+      - name: 'Deploy to Azure Web App'
+        uses: azure/webapps-deploy@v2
+        id: deploy-to-webapp
+        with:
+          app-name: 'pylossless-qc-demo'
+          slot-name: 'Production'
+          publish-profile: ${{ secrets.AZUREAPPSERVICE_PUBLISHPROFILE_B1F7B3988A884792AC90F3E962E01A2B }}

.github/workflows/test_pipeline.yml

@@ -1,28 +1,34 @@
 name: Test pipeline
 
-on: pull_request
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
 
 jobs:
   test:
-    runs-on: ubuntu-latest
+    runs-on: macos-latest
     steps:
-    - uses: actions/checkout@v3
-    - name: Set up Python 3.x
-      uses: actions/setup-python@v4
-      with:
-        python-version: "3.x"
-    - name: Install Pylossless & Deps
-      run: pip install -e .
-    - name: Install testing dependencies
-      run: pip install -r requirements_testing.txt
-    - name: Install QC depedencies
-      run: pip install -r requirements_qc.txt      
-    - name: install openneuro
-      run: pip install openneuro-py
-    - name: Test Pipeline
-      run: | 
-        coverage run -m pytest
-    - name: Upload coverage to codecov
-      uses: codecov/codecov-action@v3
-      with:
+      - uses: actions/checkout@v3
+      - name: Set up Python 3.x
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.x"
+      - name: Install Pylossless & Deps
+        run: pip install -e .
+      - name: Install testing dependencies
+        run: pip install -r requirements_testing.txt
+      - name: Install QC depedencies
+        run: pip install -r requirements_qc.txt
+      - name: install openneuro
+        run: pip install openneuro-py
+      - name: Test Pipeline
+        run: |
+          coverage run -m pytest
+      - name: Upload coverage to codecov
+        uses: codecov/codecov-action@v3
+        with:
           token: ${{secrets.CODECOV_TOKEN}}

.pre-commit-config.yaml

@@ -0,0 +1,24 @@
+repos:
+  - repo: https://github.com/psf/black
+    rev: 23.7.0
+    hooks:
+      - id: black
+        args: [--quiet]
+
+  # Ruff linter
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.0.286
+    hooks:
+      - id: ruff
+        name: ruff
+        files: ^pylossless/
+
+  # Codespell
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.2.5
+    hooks:
+      - id: codespell
+        additional_dependencies:
+          - tomli
+        files: ^pylossless/|^docs/
+        types_or: [python, bib, rst, inc]

docs/examples/usage.py

@@ -17,5 +17,6 @@
 # Then, we import the function we need.
 # For use in jupyter notebooks, We just need to import a single function.
 from pylossless.dash.app import get_app
+
 app = get_app(kind="jupyter")
 app.run_server(mode="inline")

docs/source/conf.py

@@ -9,15 +9,15 @@
 # -- Project information -----------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
 
-project = 'pyLossless'
+project = "pyLossless"
 copyright = "2023, Huberty, Scott; O'Reilly, Christian; Desjardins, James"
 author = "Huberty, Scott; O'reilly, Christian"
-release = '0.1'
+release = "0.1"
 
 
 # Point Sphinx.ext.autodoc to the our python modules (two parent directories
 # from this dir)
-sys.path.insert(0, os.path.abspath('../..'))
+sys.path.insert(0, os.path.abspath("../.."))
 
 # -- General configuration ---------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
@@ -29,13 +29,15 @@
 # gallery for: building tutorial .rst files from python files
 # sphinxemoji So we can use emoji's in docs.
 # sphinx design to support certain directives, like ::grid etc.
-extensions = ['sphinx.ext.intersphinx',
-              'sphinx.ext.autodoc',
-              'numpydoc',
-              'sphinx.ext.todo',
-              'sphinx_gallery.gen_gallery',
-              'sphinxemoji.sphinxemoji',
-              "sphinx_design"]
+extensions = [
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.autodoc",
+    "numpydoc",
+    "sphinx.ext.todo",
+    "sphinx_gallery.gen_gallery",
+    "sphinxemoji.sphinxemoji",
+    "sphinx_design",
+]
 
 # Allows us to use the ..todo:: directive
 todo_include_todos = True
@@ -44,45 +46,43 @@
 # Source directory of python file tutorials and the target
 # directory for the converted rST files
 sphinx_gallery_conf = {
-     'examples_dirs': '../examples',   # path to your example scripts
-     'gallery_dirs': './generated/auto_tutorials',  # path to save tutorials
+    "examples_dirs": "../examples",  # path to your example scripts
+    "gallery_dirs": "./generated/auto_tutorials",  # path to save tutorials
 }
 
-templates_path = ['_templates']
+templates_path = ["_templates"]
 exclude_patterns = []
 
 # -- Intersphinx configuration -----------------------------------------------
 
 intersphinx_mapping = {
-    'python': ('https://docs.python.org/3', None),
-    'numpy': ('https://numpy.org/doc/stable/', None),
-    'pandas': ('https://pandas.pydata.org/docs/', None),
-    'xarray': ('https://docs.xarray.dev/en/stable/', None),
-    'mne': ('https://mne.tools/dev', None),
-    'mne_icalabel': ('https://mne.tools/mne-icalabel/dev', None)
+    "python": ("https://docs.python.org/3", None),
+    "numpy": ("https://numpy.org/doc/stable/", None),
+    "pandas": ("https://pandas.pydata.org/docs/", None),
+    "xarray": ("https://docs.xarray.dev/en/stable/", None),
+    "mne": ("https://mne.tools/dev", None),
+    "mne_icalabel": ("https://mne.tools/mne-icalabel/dev", None),
 }
 
 # -- Options for HTML output -------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
 
-html_theme = 'pydata_sphinx_theme'
-html_static_path = ['_static']
+html_theme = "pydata_sphinx_theme"
+html_static_path = ["_static"]
 html_theme_options = {
-   "logo": {
-      "image_light": "logo-lightmode_color.png",
-      "image_dark": "logo_white.png",
-   }
+    "logo": {
+        "image_light": "logo-lightmode_color.png",
+        "image_dark": "logo_white.png",
+    }
 }
 
 # user made CSS to customize look
 html_css_files = [
-    'css/custom.css',
+    "css/custom.css",
 ]
 
 # Custom sidebar templates, maps document names to template names.
-html_sidebars = {
-    "index": ["search-field.html", "sidebar-nav-bs", 'globaltoc.html']
-}
+html_sidebars = {"index": ["search-field.html", "sidebar-nav-bs", "globaltoc.html"]}
 
 # NumPyDoc configuration -----------------------------------------------------
 
@@ -96,7 +96,7 @@
 numpydoc_xref_param_type = True
 numpydoc_validate = True
 # Only generate documentation for public members
-autodoc_default_flags = ['members', 'undoc-members', 'inherited-members']
+autodoc_default_flags = ["members", "undoc-members", "inherited-members"]
 numpydoc_class_members_toctree = False
 
 numpydoc_xref_aliases = {
@@ -126,5 +126,5 @@
     "in",
     "dtype",
     "object",
-    "LosslessPipeline"
+    "LosslessPipeline",
 }

docs/source/contributing.rst

@@ -113,7 +113,7 @@ Viewing the docs locally
 
 The built documentation is placed in ``docs/build``. You should not
 change any files in this directory. If you want to view the documentation
-locally, simply click on the ``docs/build/html/index.rst`` file from your
+locally, simply click on the ``docs/build/html/index.html`` file from your
 file browser or open it with the command line:
 
 If you are in the ``docs`` directory:

docs/source/install.rst

@@ -4,15 +4,26 @@
 Installation
 ============
 
-****************************************
-Install via :code:`pip` or :code:`conda`
-****************************************
+To stay up to date with the latest version of pyLossless, we recommend that you install
+the package from the github repository. This will allow you to easily update to the
+latest version of pyLossless as we continue to develop it.
 
 .. hint::
     To use pyLossless you need to have the ``git`` command line tool installed.
     If you are not sure, see this
     `tutorial
-    <https://git-scm.com/book/en/v2/Getting-Started-Installing-Git>`__
+    <https://mne.tools/stable/install/contributing.html>`__
+
+
+Once you have git installed and configured, and before creating your local copy
+of the codebase, go to the `PyLossless GitHub <https://github.com/lina-usc/pylossless>`_
+page and create a
+`fork <https://docs.github.com/en/get-started/quickstart/fork-a-repo>`_ into your GitHub
+user account.
+
+****************************************
+Install via :code:`pip` or :code:`conda`
+****************************************
 
 Pylossless requires Python version |min_python_version| or higher. If you
 need to install Python, please see `MNE-Pythons guide to installing Python
@@ -63,4 +74,26 @@ or via :code:`conda`:
    $ conda develop ./pylossless
 
 
-That's it! You are now ready to use pyLossless.
+That's it! You are now ready to use pyLossless.
+
+Additional Requirements for Development
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+If you plan on contributing to the development of pyLossless, you will need to install
+some additional dependencies so that you can run tests and build the documentation
+locally. The code below will install the additional dependencies as well as the
+pre-commit hooks that we use to ensure that all code is formatted correctly. Make sure
+that you have activated your ``pylossless`` environment and are inside the pylossless
+git repository directory, before running the code below:
+
+.. code-block:: console
+
+   $ pip install -r requirements_testing.txt
+   $ pip install -r docs/requirements_doc.txt
+   $ pre-commit run -a
+
+PyLossless uses `black <https://github.com/psf/black>`_ style formatting. If you are
+using Visual Studio Code, you can also install the black extension to automatically
+format your code. See the instructions at this
+`link 
+<https://dev.to/adamlombard/how-to-use-the-black-python-code-formatter-in-vscode-3lo0>`_