Add initial structure to repository (#1)

* Add actions/setup-python

* More updates

* Add coverage report

Author: jorgensd

.github/workflows/test_package.yml

@@ -0,0 +1,78 @@
+name: Test package
+
+on:
+  push:
+    # The CI is executed on every push on every branch
+    branches:
+      - "**"
+  pull_request:
+    # The CI is executed on every pull request to the main branch
+    branches:
+      - main
+
+  schedule:
+    # The CI is executed every day at 8am
+    - cron: "0 8 * * *"
+jobs:
+  check-code:
+    # This skips running the test if '[ci skip]' or '[skip ci]' is in the commit message
+    # if: "!(contains(github.event.head_commit.message, '[ci skip]') || contains(github.event.head_commit.message, '[skip ci]'))"
+
+    # Choose which operating system to run on, for more options see:
+    # https://docs.github.com/en/actions/using-github-hosted-runners/about-github-hosted-runners#supported-runners-and-hardware-resources
+    runs-on: ubuntu-22.04
+
+    steps:
+      # This action sets the current path to the root of your github repo
+      - uses: actions/checkout@v3
+      
+      - uses: actions/setup-python@v4
+        with:
+          python-version: '3.10' 
+
+      - name: "Install code"
+        run: pip install .[test,docs]
+
+      - name: Flake8 code
+        run: flake8 .
+
+      - name: Mypy check
+        run: |
+           pip install mypy
+           python -m mypy . --exclude=build
+
+      - name: Generate coverage report
+        run: python -m pytest --cov=mypackage test
+
+      - name: Generate html report
+        run: python -m coverage html
+           
+      - name: Upload coverage report as artifact
+        uses: actions/upload-artifact@v3
+        with:
+          name: code-coverage-report
+          path: htmlcov
+          if-no-files-found: error
+
+  test-code:
+    # This code depends on the result of check-code
+    needs: check-code
+    runs-on: ${{ matrix.os }}
+    
+    strategy:
+      matrix:
+        os: [ubuntu-22.04, windows-latest, macos-12]    
+    
+    steps:
+      - uses: actions/setup-python@v4
+        with:
+          python-version: '3.10' 
+
+      - uses: actions/checkout@v3
+    
+      - name: "Install mypackage"
+        run: pip install .[test]
+
+      - name: Run tests
+        run: |
+          python -m pytest test/

README.md

@@ -1 +1,7 @@
-# reproducibility
+# reproducibility
+
+This repository is a template for how to set up a reproducible python environment with GitHub.
+
+## Python-packaging
+
+To be able to create a python package, we need a folder with the name of the package (in this repository `mypackage`), and a `pyproject.toml` file.

mypackage/__init__.py

@@ -0,0 +1,9 @@
+
+# Copyright (C) 2022 Jørgen Schartum Dokken
+#
+# This file is part of my_package
+# SPDX-License-Identifier:    MIT
+
+from .functions import addition
+
+__all__ = ["addition"]

mypackage/functions.py

@@ -0,0 +1,16 @@
+
+
+# Copyright (C) 2022 Jørgen Schartum Dokken
+#
+# This file is part of mypackage
+# SPDX-License-Identifier:    MIT
+
+def addition(a: int, b: int) -> int:
+    """ Computes a+b """
+    return a + b
+
+
+def print_add(a: int, b: int) -> int:
+    c = a + b
+    print(c)
+    return c

pyproject.toml

@@ -0,0 +1,39 @@
+[build-system]
+requires = ["setuptools>=62.1.0", "wheel"]
+
+
+[project]
+name = "mypackage"
+authors = [
+    {name = "Jørgen S. Dokken", email = "dokken@simula.no"}
+    ]
+version = "0.1.0"  
+description = "Minimal package for adding two numbers"
+readme = "README.md"
+requires-python = ">=3.8"
+license = {file = "LICENSE"}
+dependencies = [
+    'numpy'
+]
+
+
+[project.optional-dependencies]
+test = [
+   "flake8",
+   "mypy",
+   "pytest",
+   "pytest-cov"
+]
+
+docs = [
+    "Sphinx",
+    "jupyter-book",
+    "pandoc"
+]
+
+[tool.mypy]
+ignore_missing_imports = true
+exclude = [
+    "docs/",
+    "build/"
+]

setup.cfg

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+# flake8 does not support, see:
+# https://github.com/PyCQA/flake8/issues/234
+[flake8]
+exclude = docs
+max-line-length = 100
+
+

test/test_code.py

@@ -0,0 +1,12 @@
+# Copyright (C) 2022 Jørgen Schartum Dokken
+#
+# This file is part of my_package
+# SPDX-License-Identifier:    MIT
+
+from mypackage import addition
+
+
+def test_addition():
+    a = 5
+    b = 3
+    assert addition(a, b) == a + b