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brandonwillardbrandonwillard
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Updates post org transfer
1 parent 48e1c73 commit 201082f

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‎.gitattributes

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aesara_hmc/_version.py export-subst
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aehmc/_version.py export-subst

‎.github/FUNDING.yml

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github: numfocus

‎.github/PULL_REQUEST_TEMPLATE.md

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**Thank you for opening a PR!**
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Here are a few important guidelines and requirements to check before your PR can be merged:
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+ [ ] There is an informative high-level description of the changes.
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+ [ ] The description and/or commit message(s) references the relevant GitHub issue(s).
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+ [ ] [`pre-commit`](https://pre-commit.com/#installation) is installed and [set up](https://pre-commit.com/#3-install-the-git-hook-scripts).
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+ [ ] The commit messages follow [these guidelines](https://tbaggery.com/2008/04/19/a-note-about-git-commit-messages.html).
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+ [ ] The commits correspond to [relevant logical changes](https://wiki.openstack.org/wiki/GitCommitMessages#Structural_split_of_changes).
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+ [ ] The commits correspond to [_relevant logical changes_](https://wiki.openstack.org/wiki/GitCommitMessages#Structural_split_of_changes), and there are **no commits that fix changes introduced by other commits in the same branch/BR**. If your commit description starts with "Fix...", then you're probably making this mistake.
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+ [ ] There are tests covering the changes introduced in the PR.
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Don't worry, your PR doesn't need to be in perfect order to submit it. As development progresses and/or reviewers request changes, you can always [rewrite the history](https://git-scm.com/book/en/v2/Git-Tools-Rewriting-History#_rewriting_history) of your feature/PR branches.

‎.github/SECURITY.md

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To report a security vulnerability to Aesara, please go to
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https://tidelift.com/security and see the instructions there.
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‎.github/workflows/pypi.yml

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on:
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push:
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branches:
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- master
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- main
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- auto-release
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pull_request:
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branches: [master]
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branches: [main]
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release:
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types: [published]
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jobs:
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build:
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# Disabled
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if: false
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name: Build source distribution
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runs-on: ubuntu-latest
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steps:
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- name: Build the sdist
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run: |
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python setup.py sdist
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- name: Check that the sdist build installs
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- name: Check the sdist installs and imports
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run: |
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mkdir -p test-sdist
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cd test-sdist
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python -m venv venv-sdist
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venv-sdist/bin/python -m pip install ../dist/aesara-hmc-*
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venv-sdist/bin/python -m pip install ../dist/aehmc-*.tar.gz
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venv-sdist/bin/python -c "import aehmc;print(aehmc.__version__)"
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- uses: actions/upload-artifact@v2
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with:
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name: artifact
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name: Upload to PyPI on release
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needs: [build]
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runs-on: ubuntu-latest
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# Disabled
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if: false
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# if: github.event_name == 'release' && github.event.action == 'published'
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if: github.event_name == 'release' && github.event.action == 'published'
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steps:
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- uses: actions/download-artifact@v2
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with:

‎.github/workflows/python-tests.yml

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‎.github/workflows/test.yml

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name: Tests
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on:
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push:
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branches:
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- main
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- checks
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pull_request:
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branches:
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- main
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jobs:
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changes:
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name: "Check for changes"
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runs-on: ubuntu-latest
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outputs:
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changes: ${{ steps.changes.outputs.src }}
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steps:
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- uses: actions/checkout@v2
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with:
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fetch-depth: 0
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- uses: dorny/paths-filter@v2
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id: changes
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with:
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filters: |
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python: &python
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- 'aehmc/**/*.py'
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- 'tests/**/*.py'
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- 'aehmc/**/*.pyx'
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- 'tests/**/*.pyx'
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- '*.py'
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src:
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- *python
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- 'aehmc/**/*.c'
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- 'tests/**/*.c'
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- 'aehmc/**/*.h'
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- 'tests/**/*.h'
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- '.github/**/*.yml'
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- 'setup.cfg'
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- 'requirements.txt'
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- '.coveragerc'
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style:
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name: Check code style
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needs: changes
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runs-on: ubuntu-latest
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if: ${{ needs.changes.outputs.changes == 'true' }}
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steps:
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- uses: actions/checkout@v2
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- uses: actions/setup-python@v2
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- uses: pre-commit/[email protected]
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test:
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name: "Test py${{ matrix.python-version }}: ${{ matrix.part }}"
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needs:
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- changes
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- style
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runs-on: ubuntu-latest
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if: ${{ needs.changes.outputs.changes == 'true' && needs.style.result == 'success' }}
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strategy:
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fail-fast: true
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matrix:
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python-version: ["3.6", "3.7"]
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fast-compile: [0]
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float32: [0]
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part:
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- "tests"
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steps:
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- uses: actions/checkout@v2
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with:
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fetch-depth: 0
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- name: Set up Python ${{ matrix.python-version }}
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uses: conda-incubator/setup-miniconda@v2
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with:
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mamba-version: "*"
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channels: conda-forge,defaults
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channel-priority: true
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python-version: ${{ matrix.python-version }}
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auto-update-conda: true
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- name: Create matrix id
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id: matrix-id
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env:
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MATRIX_CONTEXT: ${{ toJson(matrix) }}
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run: |
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echo $MATRIX_CONTEXT
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export MATRIX_ID=`echo $MATRIX_CONTEXT | md5sum | cut -c 1-32`
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echo $MATRIX_ID
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echo "::set-output name=id::$MATRIX_ID"
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- name: Install dependencies
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shell: bash -l {0}
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run: |
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mamba install --yes -q "python~=${PYTHON_VERSION}=*_cpython" mkl numpy scipy pip mkl-service
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pip install -q -r requirements.txt
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mamba list && pip freeze
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python -c 'import aesara; print(aesara.config.__str__(print_doc=False))'
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python -c 'import aesara; assert(aesara.config.blas__ldflags != "")'
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env:
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PYTHON_VERSION: ${{ matrix.python-version }}
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- name: Run tests
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shell: bash -l {0}
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run: |
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if [[ $FAST_COMPILE == "1" ]]; then export AESARA_FLAGS=$AESARA_FLAGS,mode=FAST_COMPILE; fi
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if [[ $FLOAT32 == "1" ]]; then export AESARA_FLAGS=$AESARA_FLAGS,floatX=float32; fi
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export AESARA_FLAGS=$AESARA_FLAGS,warn__ignore_bug_before=all,on_opt_error=raise,on_shape_error=raise,gcc__cxxflags=-pipe
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python -m pytest -x -r A --verbose --cov=aehmc --cov-report=xml:coverage/coverage-${MATRIX_ID}.xml --no-cov-on-fail $PART
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env:
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MATRIX_ID: ${{ steps.matrix-id.outputs.id }}
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MKL_THREADING_LAYER: GNU
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MKL_NUM_THREADS: 1
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OMP_NUM_THREADS: 1
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PART: ${{ matrix.part }}
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FAST_COMPILE: ${{ matrix.fast-compile }}
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FLOAT32: ${{ matrix.float32 }}
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- name: Upload coverage file
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uses: actions/upload-artifact@v2
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with:
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name: coverage
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path: coverage/coverage-${{ steps.matrix-id.outputs.id }}.xml
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all-checks:
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if: ${{ always() }}
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runs-on: ubuntu-latest
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name: "All tests"
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needs: [changes, style, test]
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steps:
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- name: Check build matrix status
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if: ${{ needs.changes.outputs.changes == 'true' && (needs.style.result != 'success' || needs.test.result != 'success') }}
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run: exit 1
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upload-coverage:
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runs-on: ubuntu-latest
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name: "Upload coverage"
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needs: [changes, all-checks]
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if: ${{ needs.changes.outputs.changes == 'true' && needs.all-checks.result == 'success' }}
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steps:
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- uses: actions/checkout@v2
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- name: Set up Python
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uses: actions/setup-python@v1
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with:
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python-version: 3.7
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- name: Install dependencies
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run: |
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python -m pip install -U coverage>=5.1 coveralls
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- name: Download coverage file
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uses: actions/download-artifact@v2
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with:
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name: coverage
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path: coverage
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- name: Upload coverage to Codecov
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uses: codecov/codecov-action@v1
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with:
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directory: ./coverage/
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fail_ci_if_error: true

‎.pre-commit-config.yaml

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exclude: |
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(?x)^(
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versioneer\.py|
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aesara_hmc/_version\.py|
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aehmc/_version\.py|
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doc/.*|
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bin/.*
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)$

‎LICENSE

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MIT License
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Copyright (c) 2021 Ampersand
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Copyright (c) 2021 Aesara Developers
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal

‎MANIFEST.in

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include versioneer.py
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include aesara_hmc/_version.py
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include aehmc/_version.py

‎Makefile

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.PHONY: help venv conda docker docstyle format style black test lint check coverage pypi
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.DEFAULT_GOAL = help
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PROJECT_NAME = aesara-hmc
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PROJECT_DIR = aesara_hmc/
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PROJECT_NAME = aehmc
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PROJECT_DIR = aehmc/
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PYTHON = python
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PIP = pip
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CONDA = conda

‎aesara_hmc/__init__.py renamed to ‎aehmc/__init__.py

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‎aesara_hmc/_version.py renamed to ‎aehmc/_version.py

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cfg.VCS = "git"
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cfg.style = "pep440"
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cfg.tag_prefix = "v"
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cfg.parentdir_prefix = "aesara_hmc-"
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cfg.versionfile_source = "aesara_hmc/_version.py"
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cfg.parentdir_prefix = "aehmc-"
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cfg.versionfile_source = "aehmc/_version.py"
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cfg.verbose = False
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return cfg
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‎aesara_hmc/integrators.py renamed to ‎aehmc/integrators.py

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‎aesara_hmc/metrics.py renamed to ‎aehmc/metrics.py

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‎aesara_hmc/trajectory.py renamed to ‎aehmc/trajectory.py

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‎setup.cfg

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[versioneer]
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VCS = git
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style = pep440
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versionfile_source = aesara_hmc/_version.py
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versionfile_build = aesara_hmc/_version.py
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versionfile_source = aehmc/_version.py
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versionfile_build = aehmc/_version.py
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tag_prefix = v
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parentdir_prefix = aesara_hmc-
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parentdir_prefix = aehmc-
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[pydocstyle]
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[coverage:run]
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omit =
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aesara_hmc/_version.py
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aehmc/_version.py
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tests/*
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branch = True
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ignore_errors = True
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check_untyped_defs = False
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[mypy-aesara_hmc._version]
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[mypy-aehmc._version]
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ignore_errors = True
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check_untyped_defs = False

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