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Merging for a new release #188

Merged
merged 8 commits into from
Jan 5, 2024
Merged

Merging for a new release #188

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c71d125
add pysap logo
paquiteau Feb 21, 2022
90d531f
Merge pull request #171 from paquiteau/develop
philouc Feb 21, 2022
b66338f
Support to ET data and TIF files (#176)
philouc May 2, 2022
1dc42cf
Unified docs for PySAP (#174)
sfarrens Jun 29, 2022
f5abaf3
Sparse2D version 3 (#183)
sfarrens Jan 19, 2023
92f3cdb
removed pre-installation of pybind11
sfarrens Feb 3, 2023
2e26a71
Merge pull request #186 from sfarrens/pybind11_update
paquiteau Feb 4, 2023
d841ba0
Updated docs (#179)
sfarrens Apr 14, 2023
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92 changes: 81 additions & 11 deletions .github/workflows/cd-build.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -16,28 +16,98 @@ jobs:
- name: Checkout
uses: actions/checkout@v2

- name: Set up Conda with Python 3.8
uses: conda-incubator/setup-miniconda@v2
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v4
with:
auto-update-conda: true
python-version: 3.8
auto-activate-base: false
python-version: ${{ matrix.python-version }}

- name: Check Python Version
run: python --version

- name: Install Package Dependencies
shell: bash -l {0}
run: |
python --version
python -m pip install --upgrade pip
python -m pip install nose nose-exclude coverage pycodestyle
python -m pip install -r develop.txt

- name: Install PySAP
run: python -m pip install .

- name: Run Tests
shell: bash -l {0}
run: |
python setup.py nosetests
run: python -m pytest

- name: Upload coverage to Codecov
uses: codecov/codecov-action@v1
with:
token: ${{ secrets.CODECOV_TOKEN }}
file: coverage.xml
flags: unittests

api:
name: Deploy API Documentation
needs: coverage
runs-on: ubuntu-latest
if: success()

env:
gh_root: https://github.com/CEA-COSMIC/
tag_path: /archive/refs/tags/
sphinx_opts: -t docs/_templates -feTMo docs/source

steps:
- name: Checkout
uses: actions/checkout@v2

- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v4
with:
python-version: ${{ matrix.python-version }}

- name: Check Python Version
run: python --version

- name: Install dependencies
run: |
python -m pip install --upgrade pip
python -m pip install pandoc
python -m pip install -r docs/requirements.txt
python -m pip install .

- name: Download plug-ins
if: ${{ inputs.build_plugins }}
run: |
while read _plugin; do
plugin_name="$(echo ${_plugin} | awk -F== '{print $1}')"
plugin_version="$(echo ${_plugin} | awk -F== '{print $2}')"
wget ${gh_root}${plugin_name}${tag_path}${plugin_version}.tar.gz -O ${plugin_name}.tar.gz
done < plugins.txt
for file in *.tar.gz; do tar xzf "$file"; done
rm *.tar.gz

- name: Extract plug-in examples
if: ${{ inputs.build_examples }}
run: |
while read _plugin; do
plugin_name="$(echo ${_plugin} | awk -F== '{print $1}')"
cp -r ${plugin_name}-*/examples examples/${plugin_name} || echo "Warning: no examples found for ${plugin_name}"
done < plugins.txt

- name: Build PySAP source files
run: sphinx-apidoc ${sphinx_opts} pysap

- name: Build plug-in source files
if: ${{ inputs.build_plugins }}
run: |
while read _plugin; do
plugin_name="$(echo ${_plugin} | awk -F== '{print $1}')"
package_name="$(echo ${plugin_name} | awk -F- '{print $2}')"
sphinx-apidoc ${sphinx_opts} ${plugin_name}-*/${package_name}
done < plugins.txt

- name: Build API documentation
run: sphinx-build -E docs/source docs/_build

- name: Deploy API documentation
uses: peaceiris/[email protected]
with:
github_token: ${{ secrets.GITHUB_TOKEN }}
publish_dir: docs/_build
86 changes: 86 additions & 0 deletions .github/workflows/check-docs.yml
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@@ -0,0 +1,86 @@
name: Check Docs Manually

on:
workflow_dispatch:
inputs:
build_plugins:
description: 'Build API Docs with Plug-Ins'
required: true
default: true
type: boolean
build_examples:
description: 'Build API Docs with Examples'
required: true
default: true
type: boolean

jobs:

api:
name: Check API Documentation
runs-on: ubuntu-latest

env:
gh_root: https://github.com/CEA-COSMIC/
tag_path: /archive/refs/tags/
sphinx_opts: -t docs/_templates -feTMo docs/source

steps:
- name: Checkout
uses: actions/checkout@v2

- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v4
with:
python-version: ${{ matrix.python-version }}

- name: Check Python Version
run: python --version

- name: Install dependencies
run: |
python -m pip install --upgrade pip
python -m pip install pandoc
python -m pip install -r docs/requirements.txt
python -m pip install .

- name: Download plug-ins
if: ${{ inputs.build_plugins }}
run: |
while read _plugin; do
plugin_name="$(echo ${_plugin} | awk -F== '{print $1}')"
plugin_version="$(echo ${_plugin} | awk -F== '{print $2}')"
wget ${gh_root}${plugin_name}${tag_path}${plugin_version}.tar.gz -O ${plugin_name}.tar.gz
done < plugins.txt
for file in *.tar.gz; do tar xzf "$file"; done
rm *.tar.gz

- name: Extract plug-in examples
if: ${{ inputs.build_examples }}
run: |
while read _plugin; do
plugin_name="$(echo ${_plugin} | awk -F== '{print $1}')"
cp -r ${plugin_name}-*/examples examples/${plugin_name} || echo "Warning: no examples found for ${plugin_name}"
done < plugins.txt

- name: Build PySAP source files
run: sphinx-apidoc ${sphinx_opts} pysap

- name: Build plug-in source files
if: ${{ inputs.build_plugins }}
run: |
while read _plugin; do
plugin_name="$(echo ${_plugin} | awk -F== '{print $1}')"
package_name="$(echo ${plugin_name} | awk -F- '{print $2}')"
sphinx-apidoc ${sphinx_opts} ${plugin_name}-*/${package_name}
done < plugins.txt

- name: Build API documentation
run: sphinx-build -E docs/source docs/_build

- name: Archive API build
uses: actions/upload-artifact@v2
with:
name: api-docs
retention-days: 14
path: docs/_build
78 changes: 38 additions & 40 deletions .github/workflows/ci-build.yml
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Expand Up @@ -16,63 +16,55 @@ jobs:
fail-fast: false
matrix:
os: [ubuntu-latest, macos-latest]
python-version: [3.8]
python-version: ["3.10"]

steps:
- name: Checkout
uses: actions/checkout@v2
uses: actions/checkout@v3

- name: Set up Conda with Python ${{ matrix.python-version }}
uses: conda-incubator/setup-miniconda@v2
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v4
with:
auto-update-conda: true
python-version: ${{ matrix.python-version }}
auto-activate-base: false

- name: Check Conda
shell: bash -l {0}
run: |
conda info
conda list
python --version
- name: Check Python Version
run: python --version

- name: Install macOS Dependencies
shell: bash -l {0}
if: runner.os == 'macOS'
run: |
brew install libomp
brew tap sfarrens/sf
brew install bigmac libomp

- name: Install Package Dependencies
shell: bash -l {0}
run: |
python --version
python -m pip install --upgrade pip
python -m pip install nose nose-exclude coverage pycodestyle
python -m pip install -r develop.txt
python -m pip install twine

- name: Run Tests
shell: bash -l {0}
- name: Install PySAP
run: python -m pip install .

- name: Check PySAP Installation
run: |
python setup.py nosetests
pycodestyle pysap --ignore="E121,E123,E126,E226,E24,E704,E402,E731,E722,E741,W503,W504,W605"
pycodestyle examples --ignore="E121,E123,E126,E226,E24,E704,E402,E731,E741,W503,W504,W605"
python -c "import pysparse"
python -c "import pysap; print(pysap.info())"

- name: Run Tests
run: python -m pytest

- name: Save Test Results
if: always()
uses: actions/upload-artifact@v2
with:
name: unit-test-results-${{ matrix.os }}-${{ matrix.python-version }}
path: nosetests.xml
path: pytest.xml

- name: Run Examples
continue-on-error: true
shell: bash -l {0}
run: |
python -m pip install .
python pysap/test/test_examples.py
run: python pysap/test/test_examples.py

- name: Check Distribution
shell: bash -l {0}
run: |
python setup.py sdist
twine check dist/*
Expand All @@ -92,33 +84,39 @@ jobs:
fail-fast: false
matrix:
os: [ubuntu-latest, macos-latest]
python-version: [3.6, 3.7, 3.9]
python-version: ["3.7", "3.8", "3.9"]

steps:
- name: Checkout
uses: actions/checkout@v2

- name: Set up Conda with Python ${{ matrix.python-version }}
uses: conda-incubator/setup-miniconda@v2
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v4
with:
auto-update-conda: true
python-version: ${{ matrix.python-version }}
auto-activate-base: false

- name: Check Python Version
run: python --version

- name: Install macOS Dependencies
shell: bash -l {0}
if: runner.os == 'macOS'
run: |
brew install libomp
brew tap sfarrens/sf
brew install bigmac libomp

- name: Install Package Dependencies
shell: bash -l {0}
run: |
python --version
python -m pip install --upgrade pip
python -m pip install nose nose-exclude coverage pycodestyle
python -m pip install -r develop.txt

- name: Run Tests
shell: bash -l {0}
- name: Install PySAP
run: python -m pip install .

- name: Check PySAP Installation
run: |
python setup.py nosetests
python -c "import pysparse"
python -c "import pysap; print(pysap.info())"

- name: Run Tests
run: python -m pytest
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