Merge pull request #17 from spirosmaggioros/test_cases

Documentation update | Added test cases | Updated docstrings

.github/CONTRIBUTE/contribute.md

@@ -16,13 +16,15 @@
         def your_function(param1: type, param2: type, ...) -> return_type:
             """
                 Describe briefly what your function does
+                :param param1: Describe what param1 is used for.
+                :type param1: type of param1
+                :param param2: Describe what param2 is used for.
+                :type param2: type of param2
+                etc.
+
+                :return: Explain what your function returns
+                :rtype: return type of the function
 
-                Args:
-                    param1(type): Describe what param1 is used for.
-                    param2(type): Describe what param2 is used for.
-                    etc.
-                Return:
-                    return_type: Explain what your function returns.
             """
     ```
     - For classes:
@@ -31,19 +33,14 @@
             """
                 Describe briefly what your class does
 
-                Static attributes:
-                    param1(type): Explain what param1 is used for.
-                    param2(type): Explain what param2 is used for.
-                    etc.
-                
-                Methods:
-                    func1(param1, param2, ...):
-                        Here you have to explain what func1 does using the tutorial above.
-                    You have to do the same for every function.
-                
-                Note that you can add more docstrings inside function if you wish.
+                :param param1: Explain what param1 is used for.
+                :type param1: type of param1
+                :param param2: Explain what param2 is used for.
+                :type param2: type of param2 
+                etc.
+
             """
-        def __init__(self, param1: type, param2: type, ...):
+        def __init__(self, param1: type, param2: type, ...) -> None:
             ...
 
         def func1(self, param1: type, param2: type, ...) -> return_type: 
@@ -58,4 +55,4 @@
 
 * You can find all the existing model weights at the [mdl](../../spare_scores/mdl/) folder.
 
-* All the code that is used for the documentation is located at the [contents](../../docs/source/) folder and you can manually add more.
+* All the code that is used for the documentation is located at the [contents](../../docs/source/) folder and you can manually add more.

.github/workflows/python-publish.yml

@@ -0,0 +1,40 @@
+name: Upload Python Package
+
+on: workflow_dispatch
+
+permissions:
+  contents: read
+  id-token: write  # Allow GitHub to mint tokens
+
+jobs:
+  pypi-publish:
+    name: Upload release to PyPI
+    runs-on: ubuntu-latest  # Can use macos-latest if needed
+
+    steps:
+    - name: Checkout repo
+      uses: actions/checkout@v2
+
+    - name: Set up Python
+      uses: actions/setup-python@v3
+      with:
+        python-version: '3.x'
+
+    - name: Install dependencies
+      run: |
+        pip install setuptools
+        pip install twine
+        pip install wheel
+        sudo apt-get install jq
+
+    - name: Clean previous builds
+      run: rm -rf dist
+
+    - name: Build package
+      run: python setup.py sdist bdist_wheel
+
+    - name: Publish package to PyPI
+      env:
+        TWINE_USERNAME: __token__
+        TWINE_PASSWORD: ${{ secrets.PYPI_API_TOKEN }}
+      run: twine upload --repository-url https://upload.pypi.org/legacy/ dist/*

.github/workflows/sphinx-docs.yml

@@ -1,35 +1,37 @@
-name: Docs
+name: Deploy static cntent to Pages
 on:
   push:
-    branches:
-      - "main"
-  pull_request:
-  workflow_dispatch:
-
-
+    branches: ["main"]
+
 jobs:
   build-docs:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
-      - uses: actions/setup-python@v3
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
         with:
-          python-version: '3.8'
+          python-version: '3.12'
+      - name: Activate conda
+        run: |
+          conda create -n spare python=3.8
+          conda run -n spare conda install pip
+          conda run -n spare pip install spare_scores
       - name: Install dependencies
         run: |
           pip install -e .
-          pip install sphinx sphinx_rtd_theme sphinx-tabs
+          pip install sphinx sphinx_rtd_theme sphinx-tabs sphinx_toolbox
       - name: Sphinx build
         run: |
+          sphinx-apidoc -o docs spare_scores/
           cd docs/
-          sphinx-apidoc -o ./source ../spare_scores
-          sphinx-build source _build
+          make html
           cd ..
+
       - name: Upload pages artifact
-        uses: actions/upload-pages-artifact@v1
+        uses: actions/upload-pages-artifact@v3
 
         with:
-          path: docs/_build
+          path: docs/_build/html
           retention-days: 90
 
   deploy-docs:
@@ -52,5 +54,5 @@ jobs:
     steps:
      - name: Deploy artifact to GitHub Pages
        id: deployment
-       uses: actions/deploy-pages@v1
+       uses: actions/deploy-pages@v4
 

.pre-commit-config.yaml

@@ -0,0 +1,19 @@
+repos:
+  - repo: https://github.com/ambv/black
+    rev: 24.3.0
+    hooks:
+    - id: black
+  - repo: https://github.com/pycqa/isort
+    rev: 5.11.5
+    hooks:
+    - id: isort
+      args: ["--profile", "black"]
+  - repo: https://github.com/pycqa/flake8
+    rev: 5.0.4
+    hooks:
+    - id: flake8
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v0.991
+    hooks:
+      - id: mypy
+        args: ["--ignore-missing-imports"]

dev-dependencies.txt

@@ -18,7 +18,7 @@ jsonschema==4.17.3
 kiwisolver==1.4.4
 matplotlib==3.7.1
 msgpack==1.0.5
-numpy==1.23.5
+numpy==1.26.4
 packaging==23.1
 pandas==2.0.3
 Pillow==9.5.0
@@ -36,12 +36,11 @@ requests==2.31.0
 scikit-learn==0.24.2
 scipy==1.8.0
 six==1.16.0
--e git+https://github.com/georgeaidinis/spare_score@3055a393e7aad704dd00dd378e45d695d99deebd#egg=spare_scores
 threadpoolctl==3.1.0
 tomli==2.0.1
 torch==2.3.1
 typing_extensions==4.7.0
 tzdata==2023.3
 urllib3==2.0.3
 zipp==3.15.0
-setuptools==70.3.0
+setuptools==59.8.0

docs/Makefile

@@ -5,8 +5,8 @@
 # from the environment for the first two.
 SPHINXOPTS    ?=
 SPHINXBUILD   ?= sphinx-build
-SOURCEDIR     = source
-BUILDDIR      = build
+SOURCEDIR     = .
+BUILDDIR      = _build
 
 # Put it first so that "make" without argument is like "make help".
 help:

docs/source/conf.py → docs/conf.py

@@ -6,24 +6,36 @@
 # -- Project information -----------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
 
-project = 'spare_scores'
-copyright = '2023, Ashish Singh'
-author = 'Ashish Singh'
-release = '0.1'
+import os
+import sys
+
+sys.path.insert(0, os.path.abspath("../spare_scores/"))
+
+project = "spare-scores"
+copyright = "2024, Gyujoon Hwang, George Aidinis"
+author = "Gyujoon Hwang, George Aidinis"
+release = "2024"
 
 # -- General configuration ---------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
 
-extensions = []
-
-templates_path = ['_templates']
-exclude_patterns = []
+extensions = [
+    "sphinx.ext.todo",
+    "sphinx.ext.viewcode",
+    "sphinx.ext.autodoc",
+    "sphinx_toolbox.sidebar_links",
+    "sphinx_toolbox.github",
+]
 
+templates_path = ["_templates"]
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
 
 
 # -- Options for HTML output -------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
 
-# html_theme = 'alabaster'
-html_theme = 'sphinx_rtd_theme'
-html_static_path = ['_static']
+github_username = "CBICA"
+github_repository = "github.com/CBICA/spare_score"
+
+html_theme = "sphinx_rtd_theme"
+html_static_path = ["_static"]

docs/index.rst

@@ -0,0 +1,20 @@
+.. spare-scores documentation master file, created by
+   sphinx-quickstart on Mon Jul 15 15:13:44 2024.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to spare-scores's documentation!
+========================================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
+
+

docs/make.bat

@@ -1,35 +1,35 @@
-@ECHO OFF
-
-pushd %~dp0
-
-REM Command file for Sphinx documentation
-
-if "%SPHINXBUILD%" == "" (
-	set SPHINXBUILD=sphinx-build
-)
-set SOURCEDIR=source
-set BUILDDIR=build
-
-%SPHINXBUILD% >NUL 2>NUL
-if errorlevel 9009 (
-	echo.
-	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
-	echo.installed, then set the SPHINXBUILD environment variable to point
-	echo.to the full path of the 'sphinx-build' executable. Alternatively you
-	echo.may add the Sphinx directory to PATH.
-	echo.
-	echo.If you don't have Sphinx installed, grab it from
-	echo.https://www.sphinx-doc.org/
-	exit /b 1
-)
-
-if "%1" == "" goto help
-
-%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
-goto end
-
-:help
-%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
-
-:end
-popd
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=.
+set BUILDDIR=_build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

docs/modules.rst

@@ -0,0 +1,7 @@
+spare_scores
+============
+
+.. toctree::
+   :maxdepth: 4
+
+   spare_scores