Initial commit

.github/workflows/test.yml

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+name: test
+
+on: [push]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
+
+    steps:
+    - name: Git checkout
+      uses: actions/checkout@v4
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install requirements
+      run: |
+        sudo apt-get install -y openmpi-bin libopenmpi-dev libfftw3-dev libfftw3-mpi-dev
+        python -m pip install --upgrade pip
+        pip install .[test]
+        pip list
+
+    - name: Lint with flake8
+      run: |
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+
+    - name: Test with pytest
+      run: |
+        pytest

.gitignore

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+*~
+*.pyc
+*.cpython*.so
+__pycache__
+../build
+dist
+*egg-info
+*.pyc
+
+

AUTHORS

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+Lars Pastewka <[email protected]>

CHANGELOG.md

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+This file lists all changes to the code
+
+v0.0.1
+------
+
+* Initial release

LICENSE.md

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+MIT License
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.md

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+# Skeleton
+
+Skeleton for numerical projects with Python. This skeleton uses [numpy](https://numpy.org/) and [pytest](https://pytest.org). Rename the `python_skeleton` subdirectory to your module name.
+
+## Tests
+
+Before being able to run tests, you need to execute
+```python
+pip install -e .[test] 
+```
+to editably install the code.

maintenance/copyright.py

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+#
+#
+
+
+import os
+import sys
+from collections import defaultdict
+from datetime import datetime
+from subprocess import Popen, PIPE
+
+root = os.path.dirname(sys.argv[0])
+
+
+def read_authors(fn):
+    return {email.strip('<>'): name for name, email in
+            [line.rsplit(maxsplit=1) for line in open(fn, 'r')]}
+
+
+def parse_git_log(log, authors):
+    committers = defaultdict(set)
+    author = None
+    date = None
+    for line in log.decode('utf-8').split('\n'):
+        if line.startswith('commit'):
+            if date is not None and author is not None:
+                committers[author].add(date.year)
+        elif line.startswith('Author:'):
+            email = line.rsplit('<', maxsplit=1)[1][:-1]
+        elif line.startswith('Date:'):
+            date = datetime.strptime(line[5:].rsplit(maxsplit=1)[0].strip(),
+                                     '%a %b %d %H:%M:%S %Y')
+            try:
+                author = authors[email]
+            except KeyError:
+                author = email
+        elif 'copyright' in line.lower() or 'license' in line.lower():
+            date = None
+    if date is not None:
+        committers[author].add(date.year)
+    return committers
+
+
+def pretty_years(years):
+    years = sorted(years)
+    prev_year = prev_out = years[0]
+    s = '{}'.format(prev_year)
+    for year in years[1:]:
+        if year - prev_year > 1:
+            if year - prev_out > 1:
+                if prev_year == prev_out:
+                    s = '{}, {}'.format(s, year)
+                else:
+                    s = '{}-{}, {}'.format(s, prev_year, year)
+            else:
+                s = '{}, {}'.format(s, prev_year)
+            prev_out = year
+        prev_year = year
+    if prev_year - prev_out == 1:
+        s = '{}-{}'.format(s, prev_year)
+    elif prev_year - prev_out > 1:
+        s = '{}, {}'.format(s, prev_year)
+    return s
+
+
+authors = read_authors('{}/../AUTHORS'.format(root))
+
+process = Popen(['git', 'log', '--follow', sys.argv[1]], stdout=PIPE,
+                stderr=PIPE)
+stdout, stderr = process.communicate()
+committers = parse_git_log(stdout, authors)
+
+prefix = 'Copyright'
+for name, years in committers.items():
+    print('{} {} {}'.format(prefix, pretty_years(years), name))
+    prefix = ' ' * len(prefix)
+print()

maintenance/replace_header.py

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+#
+#
+
+
+import sys
+
+file_lines = open(sys.argv[1], 'r').readlines()
+header_lines = sys.stdin.readlines()
+
+while file_lines[0].startswith('#'):
+    file_lines = file_lines[1:]
+
+file_lines.insert(0, '#\n')
+for header_line in header_lines[::-1]:
+    file_lines.insert(0, '# {}'.format(header_line).strip() + '\n')
+file_lines.insert(0, '#\n')
+
+open(sys.argv[1], 'w').writelines(file_lines)

maintenance/update_license_headers.sh

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+#! /bin/sh
+# Updates all Python files with license taken from README.md and copyright information obtained from the git log.
+
+for fn in setup.py `find python_skeleton test -name "*.py"`; do
+  echo $fn
+  python3 maintenance/copyright.py $fn | cat - LICENSE.md | python3 maintenance/replace_header.py $fn
+done

pyproject.toml

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+[build-system]
+requires = ["flit_core>=3.2"]
+build-backend = "flit_core.buildapi"
+
+[project]
+name = "python-skeleton"
+description = "Python skeleton project"
+readme = "README.md"
+license = { file = "LICENSE.md" }
+authors = [
+    { name = "Lars Pastewka", email = "[email protected]" }
+]
+classifiers = [
+    "Development Status :: 2 - Pre-Alpha",
+    "Programming Language :: Python"
+]
+requires-python = ">=3.8.0"
+dynamic = [ "version" ]
+dependencies = [
+    "numpy",
+    "scipy"
+]
+
+[project.optional-dependencies]
+test = [
+    "flake8",
+    "pytest",
+    "pytest-cov",
+    "pytest-flake8"
+]
+
+[tool.pytest.ini_options]
+pythonpath = [
+  "."
+]
+
+[project.urls]
+documentation = "https://imtek-simulation.github.io/python-skeleton/"
+repository = "https://github.com/imtek-simulation/python-skeleton"
+changelog = "https://github.com/imtek-simulation/python-skeleton/blob/master/CHANGELOG.md"

python_skeleton/__init__.py

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+#
+# Copyright 2021 Lars Pastewka
+#
+# MIT License
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in all
+# copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.
+#
+
+"""
+The entry point for the code
+"""
+
+__version__ = '0.0.1'
+
+def hello_world():
+	return "Hello world!"

test/test_hello_world.py

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+#
+# Copyright 2021 Lars Pastewka
+#
+# MIT License
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in all
+# copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.
+#
+
+"""
+Tests the hello world function
+"""
+
+from python_skeleton import hello_world
+
+
+def test_hello_world():
+    assert hello_world() == 'Hello world!'