Merge pull request #1 from JakobEliasWagner/wip-inital-setup

Wip inital setup

.github/workflows/ci.yml

@@ -0,0 +1,104 @@
+name: CI
+
+on: [ push ]
+
+jobs:
+  hooks:
+
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.11'
+          architecture: 'x64'
+      - name: Display Python version
+        run: python -c "import sys; print(sys.version)"
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r requirements.txt
+
+  test:
+
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.11'
+          architecture: 'x64'
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r requirements.txt
+      - name: Test with pytest and build coverage reports
+        run: |
+          pytest test --cov=src --cov-report=html:codecov --cov-report=json
+      - name: Upload coverage data
+        uses: actions/upload-artifact@v3
+        with:
+          name: covdata
+          path: |
+            coverage.json
+      - name: package coverage report
+        run: |
+          zip -r coverage_report.zip codecov
+      - name: Upload coverage report
+        uses: actions/upload-artifact@v3
+        with:
+          name: covdata-html
+          path: coverage_report.zip
+
+
+  coverage-reports:
+    name: coverage
+    needs: test
+    if: ${{ github.ref == 'refs/heads/master' }}
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@master
+        name: Checkout
+      - name: Download coverage data
+        uses: actions/download-artifact@v3
+        with:
+          name: covdata
+      - name: Download coverage report
+        uses: actions/download-artifact@v3
+        with:
+          name: covdata-html
+      - name: Unpack coverage report and move into sphinx
+        run: |
+          unzip coverage_report.zip
+          mv codecov doc/source/_static/codecov
+      - name: build website for detailed coverage
+        run: |
+          pip install sphinx
+          sphinx-build -M html doc/source doc/build
+      - name: deploy website
+        uses: peaceiris/actions-gh-pages@v3
+        with:
+          publish_branch: deployed-pages
+          github_token: ${{ secrets.DEPLOY_TOKEN }}
+          publish_dir: doc/build/html/
+          force_orphan: true
+      - name: Create json for badge
+        run: |
+          export TOTAL=$(python -c "import json;print(json.load(open('coverage.json'))['totals']['percent_covered_display'])")
+          echo "total=$TOTAL" >> $GITHUB_ENV
+          echo "### Total coverage: ${TOTAL}%" >> $GITHUB_STEP_SUMMARY
+      - name: Make badge
+        uses: schneegans/[email protected]
+        with:
+          auth: ${{ secrets.GIST_TOKEN }}
+          gistID: 715271f51dd7b16c37fcf84c79dcb31a
+          filename: covbadge.json
+          label: Coverage
+          message: ${{ env.total }}%
+          minColorRange: 50
+          maxColorRange: 95
+          valColorRange: ${{ env.total }}

.gitignore

@@ -27,8 +27,6 @@ share/python-wheels/
 MANIFEST
 
 # PyInstaller
-#  Usually these files are written by a python script from a template
-#  before PyInstaller builds the exe, so as to inject date/other infos into it.
 *.manifest
 *.spec
 
@@ -82,31 +80,7 @@ target/
 profile_default/
 ipython_config.py
 
-# pyenv
-#   For a library or package, you might want to ignore these files since the code is
-#   intended to run in multiple environments; otherwise, check them in:
-# .python-version
-
-# pipenv
-#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
-#   However, in case of collaboration, if having platform-specific dependencies or dependencies
-#   having no cross-platform support, pipenv may install dependencies that don't work, or not
-#   install all needed dependencies.
-#Pipfile.lock
-
-# poetry
-#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
-#   This is especially recommended for binary packages to ensure reproducibility, and is more
-#   commonly ignored for libraries.
-#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
-#poetry.lock
-
 # pdm
-#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
-#pdm.lock
-#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
-#   in version control.
-#   https://pdm.fming.dev/#use-with-ide
 .pdm.toml
 
 # PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
@@ -152,9 +126,19 @@ dmypy.json
 # Cython debug symbols
 cython_debug/
 
-# PyCharm
-#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
-#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
-#  and can be added to the global gitignore or merged into this file.  For a more nuclear
-#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
-#.idea/
+# IntelliJ
+out/
+
+# mpeltonen/sbt-idea plugin
+.idea_modules/
+
+# JIRA plugin
+atlassian-ide-plugin.xml
+
+# Cursive Clojure plugin
+.idea/replstate.xml
+
+# SonarLint plugin
+.idea/sonarlint/
+
+.idea

.pre-commit-config.yaml

@@ -0,0 +1,29 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v2.3.0
+    hooks:
+      - id: check-yaml
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+      - id: check-case-conflict
+      - id: check-merge-conflict
+      - id: no-commit-to-branch
+  - repo: https://github.com/psf/black
+    rev: 22.10.0
+    hooks:
+      - id: black
+  - repo: https://github.com/pycqa/flake8
+    rev: 3.9.2
+    hooks:
+      - id: flake8
+  - repo: https://github.com/pycqa/isort
+    rev: 5.12.0
+    hooks:
+      - id: isort
+        name: isort (python)
+      - id: isort
+        name: isort (cython)
+        types: [ cython ]
+      - id: isort
+        name: isort (pyi)
+        types: [ pyi ]

README.md

@@ -1 +1,32 @@
-# Neural-Operators
+# Neural-Operators
+*Master's Thesis by Jakob Wagner*
+
+[![Python 3.8](https://img.shields.io/badge/Python-3.11-blue)](https://www.python.org/downloads/release/python-3110/)
+[![Code Coverage](https://img.shields.io/endpoint?url=https://gist.githubusercontent.com/JakobEliasWagner/715271f51dd7b16c37fcf84c79dcb31a/raw/e1ecebc4ebfaac81fe3225be6d84ebe1069231c2/covbadge.json)](https://jakobeliaswagner.github.io/Neural-Operators/_static/codecov/index.html)
+[![Documentation](https://img.shields.io/badge/Documentation-FF7043)](https://jakobeliaswagner.github.io/Neural-Operators/index.html)
+[![Linkedin](https://img.shields.io/badge/-LinkedIn-blue?style=flat&logo=linkedin)](https://www.linkedin.com/in/jakob-wagner-65b9871a9/)
+
+## Setup
+I recommend setting up a python venv.
+
+Install the required packages and libraries
+```shell
+pip install -r requirements.txt
+```
+
+## Hooks
+Install the pre-commit package manager:
+```shell
+pip install pre-commit
+```
+Install the git hook scripts
+```shell
+pre-commit install
+```
+now `pre-commit` will run automatically on `git commit `.
+
+## Tests
+Run tests
+```shell
+pytest test/
+```

doc/Makefile

@@ -0,0 +1,12 @@
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

doc/make.bat

@@ -0,0 +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

doc/source/conf.py

@@ -0,0 +1,19 @@
+import os
+import sys
+
+sys.path.insert(0, os.path.abspath(os.path.join("..", "..", "src")))
+
+# -- Project information -----------------------------------------------------
+project = "Neural Operators"
+copyright = "2023, Jakob Wagner"
+author = "Jakob Wagner"
+
+# -- General configuration ---------------------------------------------------
+extensions = ["sphinx.ext.autodoc"]
+
+templates_path = ["_templates"]
+exclude_patterns = []
+
+# -- Options for HTML output -------------------------------------------------
+html_theme = "alabaster"
+html_static_path = ["_static"]

doc/source/coverage.rst

@@ -0,0 +1,4 @@
+Code Coverage
+=============
+
+ For an in detail report on the code coverage `click here <_static/codecov/index.html>`_.

doc/source/index.rst

@@ -0,0 +1,6 @@
+Neural Operators
+============================================
+.. toctree::
+   :maxdepth: 2
+
+   coverage

pyproject.toml

@@ -0,0 +1,12 @@
+[tool.black]
+line-length = 79
+
+[tool.isort]
+profile = "black"
+multi_line_output = 3
+include_trailing_comma = true
+force_grid_wrap = 0
+use_parentheses = true
+ensure_newline_before_comments = true
+line_length = 79
+skip_glob = [".github/*", ".idea/*", ".pytest_cache/*", "data/*", "docs/*", "models/*", "venv/*"]

requirements.txt

@@ -0,0 +1,3 @@
+pre-commit
+pytest
+pytest-cov

src/dummy.py

@@ -0,0 +1,2 @@
+def tmp_dummy_function(x: int, y: int) -> int:
+    return x + y

test/test_dummy.py

@@ -0,0 +1,5 @@
+from src.dummy import tmp_dummy_function
+
+
+def test_dummy_function():
+    assert tmp_dummy_function(1, 2) == 3

test/test_pytest.py

@@ -0,0 +1,6 @@
+def test_assert_true():
+    """
+    Make sure pytest is running correctly
+    :return:
+    """
+    assert True