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mh105 committed Oct 23, 2022
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57 changes: 57 additions & 0 deletions .github/workflows/pr-pytest-conda.yml
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@@ -0,0 +1,57 @@
name: Pull Request Tests

on:
pull_request:
branches:
- master

jobs:
build:
name: build-${{ matrix.os }}
runs-on: ${{ matrix.os }}
strategy:
matrix:
os: ["ubuntu-latest", "macos-latest", "windows-latest"]
steps:
- uses: actions/[email protected]

- name: Install Conda environment with Micromamba
uses: mamba-org/provision-with-micromamba@main
with:
cache-env: true
environment-file: environment.yml
environment-name: pot

- name: Micromamba info
shell: bash -l {0}
run: |
micromamba info
- name: Micromamba list
shell: bash -l {0}
run: |
micromamba list
- name: Check python version
shell: bash -l {0}
run: |
python --version
- name: Install somata
shell: bash -l {0}
run: |
pip install -e .
- name: Lint with flake8
shell: bash -l {0}
run: |
micromamba install flake8
# 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
shell: bash -l {0}
run: |
pytest
57 changes: 57 additions & 0 deletions .github/workflows/push-pytest-conda.yml
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name: Push Tests on Linux

on:
push:
branches:
- master

jobs:
build:
name: build-${{ matrix.os }}
runs-on: ${{ matrix.os }}
strategy:
matrix:
os: ["ubuntu-latest"]
steps:
- uses: actions/[email protected]

- name: Install Conda environment with Micromamba
uses: mamba-org/provision-with-micromamba@main
with:
cache-env: true
environment-file: environment.yml
environment-name: pot

- name: Micromamba info
shell: bash -l {0}
run: |
micromamba info
- name: Micromamba list
shell: bash -l {0}
run: |
micromamba list
- name: Check python version
shell: bash -l {0}
run: |
python --version
- name: Install somata
shell: bash -l {0}
run: |
pip install -e .
- name: Lint with flake8
shell: bash -l {0}
run: |
micromamba install flake8
# 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
shell: bash -l {0}
run: |
pytest
63 changes: 10 additions & 53 deletions .gitignore
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@@ -1,32 +1,15 @@
# MacOS Finder
.DS_Store
._.DS_Store

# Byte-compiled / optimized / DLL files
__pycache__/
*.py[cod]
*$py.class
.pytest_cache
.idea

# C extensions
*.so

# Distribution / packaging
.Python
build/
develop-eggs/
dist/
downloads/
eggs/
.eggs/
lib/
lib64/
parts/
sdist/
var/
wheels/
pip-wheel-metadata/
share/python-wheels/
*.egg-info/
.installed.cfg
*.egg
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.
Expand All @@ -37,19 +20,8 @@ MANIFEST
pip-log.txt
pip-delete-this-directory.txt

# Unit test / coverage reports
htmlcov/
.tox/
.nox/
.coverage
.coverage.*
.cache
nosetests.xml
coverage.xml
*.cover
*.py,cover
.hypothesis/
.pytest_cache/
# Pip install egg
*.egg-info

# Translations
*.mo
Expand All @@ -68,14 +40,13 @@ instance/
# Scrapy stuff:
.scrapy

# Sphinx documentation
docs/_build/

# PyBuilder
target/

# Jupyter Notebook
.ipynb_checkpoints
.iml
.xml

# IPython
profile_default/
Expand All @@ -94,13 +65,6 @@ ipython_config.py
# PEP 582; used by e.g. github.com/David-OConnor/pyflow
__pypackages__/

# Celery stuff
celerybeat-schedule
celerybeat.pid

# SageMath parsed files
*.sage.py

# Environments
.env
.venv
Expand All @@ -110,13 +74,6 @@ ENV/
env.bak/
venv.bak/

# Spyder project settings
.spyderproject
.spyproject

# Rope project settings
.ropeproject

# mkdocs documentation
/site

Expand Down
43 changes: 26 additions & 17 deletions LICENSE
Original file line number Diff line number Diff line change
@@ -1,21 +1,30 @@
MIT License
BSD 3-Clause Clear License

Copyright (c) 2021 Mingjian He
Copyright (c) 2022, Patrick L. Purdon
All rights reserved.

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:
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:

The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.
1. Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer.

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.
2. Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.

3. Neither the name of the copyright holder nor the names of its
contributors may be used to endorse or promote products derived from
this software without specific prior written permission.

NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE GRANTED BY
THIS LICENSE. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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