ModOpt v1.5 release (#108)

* added workflows * test update to deploy test results from fork * fix typo * test commands copied from yaml * removed test deployment * Pyralid style update (#104) * first iteration of pyralid style update * updated progress on pyralid style refactor * further updates * latest update * all tests passing locally * all doctests passing locally * removed autodoc files * updated refactoring * test pull_request_target and add main branch * added logo and fixed link to api docs * added develop branch to CI * updated workflow * test PR review * reverted to standard PR directive * updated readme * test deploy test results from fork * attempt to fix fomatting * removed test deployment * added #97 GPU compatibility in consistent style * additional clean up * more clean up * fixed mistake * Update modopt/interface/errors.py Co-authored-by: Zaccharie Ramzi <zaccharie.ramzi@gmail.com> * Update modopt/tests/test_opt.py Co-authored-by: Zaccharie Ramzi <zaccharie.ramzi@gmail.com> * Update modopt/tests/test_opt.py Co-authored-by: Zaccharie Ramzi <zaccharie.ramzi@gmail.com> * Update modopt/tests/test_opt.py Co-authored-by: Zaccharie Ramzi <zaccharie.ramzi@gmail.com> * Update modopt/tests/test_opt.py Co-authored-by: Zaccharie Ramzi <zaccharie.ramzi@gmail.com> * Update modopt/tests/test_opt.py Co-authored-by: Zaccharie Ramzi <zaccharie.ramzi@gmail.com> * Update modopt/tests/test_math.py Co-authored-by: Zaccharie Ramzi <zaccharie.ramzi@gmail.com> * Update modopt/tests/test_math.py Co-authored-by: Zaccharie Ramzi <zaccharie.ramzi@gmail.com> * removed doc requirements from basic test suite * removed contents as they are now automatically generated on GitHub * fix GPU bug in PowerMethod * Update modopt/tests/test_opt.py Co-authored-by: Zaccharie Ramzi <zaccharie.ramzi@gmail.com> * Update modopt/tests/test_opt.py Co-authored-by: Zaccharie Ramzi <zaccharie.ramzi@gmail.com> * Update modopt/tests/test_opt.py Co-authored-by: Zaccharie Ramzi <zaccharie.ramzi@gmail.com> * Update modopt/tests/test_opt.py Co-authored-by: Zaccharie Ramzi <zaccharie.ramzi@gmail.com> * Update modopt/tests/test_opt.py Co-authored-by: Zaccharie Ramzi <zaccharie.ramzi@gmail.com> * Update modopt/tests/test_opt.py Co-authored-by: Zaccharie Ramzi <zaccharie.ramzi@gmail.com> * Update modopt/tests/test_opt.py Co-authored-by: Zaccharie Ramzi <zaccharie.ramzi@gmail.com> * Update modopt/tests/test_opt.py Co-authored-by: Zaccharie Ramzi <zaccharie.ramzi@gmail.com> * Update modopt/tests/test_opt.py Co-authored-by: Zaccharie Ramzi <zaccharie.ramzi@gmail.com> * Update modopt/tests/test_opt.py Co-authored-by: Zaccharie Ramzi <zaccharie.ramzi@gmail.com> * Update modopt/tests/test_opt.py Co-authored-by: Zaccharie Ramzi <zaccharie.ramzi@gmail.com> * Update modopt/tests/test_opt.py Co-authored-by: Zaccharie Ramzi <zaccharie.ramzi@gmail.com> * Update modopt/tests/test_opt.py Co-authored-by: Zaccharie Ramzi <zaccharie.ramzi@gmail.com> * Update modopt/tests/test_opt.py Co-authored-by: Zaccharie Ramzi <zaccharie.ramzi@gmail.com> * Update modopt/tests/test_opt.py Co-authored-by: Zaccharie Ramzi <zaccharie.ramzi@gmail.com> * renamed dummy functions in test_opt.py Co-authored-by: Zaccharie Ramzi <zaccharie.ramzi@gmail.com> * Release cleanup (#109) * cleaned up readme * cleaned up api docs Co-authored-by: Zaccharie Ramzi <zaccharie.ramzi@gmail.com>
CEA-COSMIC · Mar 31, 2021 · 616c9e7 · 616c9e7
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commit 616c9e7
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diff --git a/.github/workflows/cd-build.yml b/.github/workflows/cd-build.yml
@@ -0,0 +1,87 @@
+name: CD
+
+on:
+  push:
+    branches:
+     - master
+     - main
+
+jobs:
+
+  coverage:
+    name: Deploy Coverage Results
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+
+      - name: Set up Conda with Python 3.8
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          auto-update-conda: true
+          python-version: 3.8
+          auto-activate-base: false
+
+      - name: Install dependencies
+        shell: bash -l {0}
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install -r develop.txt
+          python -m pip install twine
+          python -m pip install .
+
+      - name: Run Tests
+        shell: bash -l {0}
+        run: |
+          python setup.py test
+
+      - name: Check distribution
+        shell: bash -l {0}
+        run: |
+          python setup.py sdist
+          twine check dist/*
+
+      - 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()
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+
+      - name: Set up Conda with Python 3.8
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          auto-update-conda: true
+          python-version: 3.8
+          auto-activate-base: false
+
+      - name: Install dependencies
+        shell: bash -l {0}
+        run: |
+          conda install -c conda-forge pandoc
+          python -m pip install --upgrade pip
+          python -m pip install -r docs/requirements.txt
+          python -m pip install .
+
+      - name: Build API documentation
+        shell: bash -l {0}
+        run: |
+          sphinx-apidoc -t docs/_templates -feTMo docs/source modopt
+          sphinx-build -E docs/source docs/_build
+
+      - name: Deploy API documentation
+        uses: peaceiris/actions-gh-pages@v3.5.9
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: docs/_build
diff --git a/.github/workflows/ci-build.yml b/.github/workflows/ci-build.yml
@@ -0,0 +1,126 @@
+name: CI
+
+on:
+  pull_request:
+    branches:
+     - develop
+     - master
+     - main
+
+jobs:
+  test-full:
+    name: Full Test Suite
+    runs-on: ${{ matrix.os }}
+
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+        python-version: [3.8]
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+
+      - name: Report WPS Errors
+        uses: wemake-services/wemake-python-styleguide@0.14.1
+        continue-on-error: true
+        with:
+          reporter: 'github-pr-review'
+          path: './modopt'
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Set up Conda with Python ${{ matrix.python-version }}
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          auto-update-conda: true
+          python-version: ${{ matrix.python-version }}
+          auto-activate-base: false
+
+      - name: Check Conda
+        shell: bash -l {0}
+        run: |
+          conda info
+          conda list
+          python --version
+
+      - name: Install Dependencies
+        shell: bash -l {0}
+        run: |
+          python --version
+          python -m pip install --upgrade pip
+          python -m pip install -r develop.txt
+          python -m pip install -r docs/requirements.txt
+          python -m pip install astropy scikit-image scikit-learn
+          python -m pip install twine
+          python -m pip install .
+
+      - name: Run Tests
+        shell: bash -l {0}
+        run: |
+          export PATH=/usr/share/miniconda/bin:$PATH
+          python setup.py test
+
+      - name: Save Test Results
+        if: always()
+        uses: actions/upload-artifact@v2
+        with:
+          name: unit-test-results-${{ matrix.os }}-${{ matrix.python-version }}
+          path: pytest.xml
+
+      - name: Check Distribution
+        shell: bash -l {0}
+        run: |
+          python setup.py sdist
+          twine check dist/*
+
+      - name: Check API Documentation build
+        shell: bash -l {0}
+        run: |
+          conda install -c conda-forge pandoc
+          sphinx-apidoc -t docs/_templates -feTMo docs/source modopt
+          sphinx-build -b doctest -E docs/source docs/_build
+
+      - name: Upload Coverage to Codecov
+        uses: codecov/codecov-action@v1
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          file: coverage.xml
+          flags: unittests
+
+  test-basic:
+    name: Basic Test Suite
+    runs-on: ${{ matrix.os }}
+
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+        python-version: [3.6, 3.7, 3.9]
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+
+      - name: Set up Conda with Python ${{ matrix.python-version }}
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          auto-update-conda: true
+          python-version: ${{ matrix.python-version }}
+          auto-activate-base: false
+
+      - name: Install Dependencies
+        shell: bash -l {0}
+        run: |
+          python --version
+          python -m pip install --upgrade pip
+          python -m pip install -r develop.txt
+          python -m pip install astropy scikit-image scikit-learn
+          python -m pip install .
+
+      - name: Run Tests
+        shell: bash -l {0}
+        run: |
+          export PATH=/usr/share/miniconda/bin:$PATH
+          python setup.py test
diff --git a/.gitignore b/.gitignore
@@ -1,21 +1,142 @@
-# Ignore Python compilation
-*.pyc
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
 
-# Ignore scripts
-*.sh
+# C extensions
+*.so
 
-# Ignore cache
-*.cache/
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+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.
+*.manifest
+*.spec
 
-# Ignore coverage tests
+# Installer logs
+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/
+cover/
+pytest.xml
 
-# Ignore installation
-.eggs/
-modopt.egg-info/
-dist/
-build/
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+docs/source/fortuna.*
+docs/source/scripts.*
+docs/source/*.nblink
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+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
+
+# 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
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
 
-# Ignore pypi config
-.pypirc
+# Cython debug symbols
+cython_debug/
diff --git a/.pylintrc b/.pylintrc
@@ -0,0 +1,2 @@
+[MASTER]
+ignore-patterns=**/docs/**/*.py
diff --git a/.pyup.yml b/.pyup.yml
@@ -0,0 +1,11 @@
+# autogenerated pyup.io config file
+# see https://pyup.io/docs/configuration/ for all available options
+
+schedule: ''
+update: all
+label_prs: update
+assignees: sfarrens
+requirements:
+  - requirements.txt
+  - develop.txt
+  - docs/requirements.txt