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Remove libblas, mkl and m2w64-toolchain dependencies (#4932)
* Remove libblas, mkl and m2w64-toolchain dependencies. As PyMC3 itself does not compile anything, it should not have these dependencies. Instead, it is aesaras job to specify its compile-chain dependencies. Closes #4715. Add custom envs for testing. Remove patsy dependency. * Regenerate rerquirements.
1 parent f184912 commit b54c8af

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+157
-37
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‎.github/workflows/pytest.yml

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@@ -107,12 +107,12 @@ jobs:
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- name: Cache conda
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uses: actions/cache@v1
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env:
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# Increase this value to reset cache if environment-dev-py37.yml has not changed
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# Increase this value to reset cache if environment-test-py37.yml has not changed
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CACHE_NUMBER: 0
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with:
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path: ~/conda_pkgs_dir
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key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{
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hashFiles('conda-envs/environment-dev-py37.yml') }}
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hashFiles('conda-envs/environment-test-py37.yml') }}
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- name: Cache multiple paths
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uses: actions/cache@v2
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env:
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hashFiles('requirements.txt') }}
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- uses: conda-incubator/setup-miniconda@v2
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with:
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activate-environment: pymc-dev-py37
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activate-environment: pymc-test-py37
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channel-priority: strict
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environment-file: conda-envs/environment-dev-py37.yml
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environment-file: conda-envs/environment-test-py37.yml
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use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly!
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- name: Install-pymc
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run: |
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conda activate pymc-dev-py37
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conda activate pymc-test-py37
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pip install -e .
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pip install --pre -U polyagamma
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python --version
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- name: Run tests
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run: |
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conda activate pymc-dev-py37
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conda activate pymc-test-py37
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python -m pytest -vv --cov=pymc --cov-append --cov-report=xml --cov-report term --durations=50 $TEST_SUBSET
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- name: Upload coverage to Codecov
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uses: codecov/codecov-action@v1
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- name: Cache conda
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uses: actions/cache@v1
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env:
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# Increase this value to reset cache if conda-envs/environment-dev-py38.yml has not changed
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# Increase this value to reset cache if conda-envs/environment-test-py38.yml has not changed
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CACHE_NUMBER: 0
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with:
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path: ~/conda_pkgs_dir
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key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{
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hashFiles('conda-envs/windows-environment-dev-py38.yml') }}
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hashFiles('conda-envs/windows-environment-test-py38.yml') }}
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- name: Cache multiple paths
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uses: actions/cache@v2
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env:
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hashFiles('requirements.txt') }}
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- uses: conda-incubator/setup-miniconda@v2
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with:
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activate-environment: pymc-dev-py38
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activate-environment: pymc-test-py38
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channel-priority: strict
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environment-file: conda-envs/windows-environment-dev-py38.yml
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environment-file: conda-envs/windows-environment-test-py38.yml
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use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly!
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- name: Install-pymc
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run: |
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conda activate pymc-dev-py38
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conda activate pymc-test-py38
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pip install -e .
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pip install --pre -U polyagamma
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python --version
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- name: Run tests
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# This job uses a cmd shell, therefore the environment variable syntax is different!
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# The ">-" in the next line replaces newlines with spaces (see https://stackoverflow.com/a/66809682).
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run: >-
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conda activate pymc-dev-py38 &&
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conda activate pymc-test-py38 &&
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python -m pytest -vv --cov=pymc --cov-append --cov-report=xml --cov-report term --durations=50 %TEST_SUBSET%

‎conda-envs/environment-dev-py37.yml

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@@ -8,10 +8,8 @@ dependencies:
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- cachetools>=4.2.1
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- cloudpickle
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- fastprogress>=0.2.0
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- h5py>=2.7
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- ipython>=7.16
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- libblas=*=*mkl
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- mkl-service
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- h5py
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- ipython
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- myst-nb
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- numpy>=1.15
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- numpydoc>=0.9

‎conda-envs/environment-dev-py38.yml

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@@ -8,10 +8,8 @@ dependencies:
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- cachetools>=4.2.1
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- cloudpickle
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- fastprogress>=0.2.0
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- h5py>=2.7
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- ipython>=7.16
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- libblas=*=*mkl
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- mkl-service
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- h5py
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- ipython
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- myst-nb
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- numpy>=1.15.0
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- numpydoc>=0.9

‎conda-envs/environment-dev-py39.yml

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@@ -9,13 +9,11 @@ dependencies:
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- cloudpickle
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- fastprogress>=0.2.0
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- h5py>=2.7
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- ipython>=7.16
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- libblas=*=*mkl
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- mkl-service
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- ipython
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- myst-nb
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- numpy>=1.15.0
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- numpydoc>=0.9
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- pandas>=0.24.0
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- pandas
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- pre-commit>=2.8.0
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- pydata-sphinx-theme
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- pytest-cov>=2.5

‎conda-envs/environment-test-py37.yml

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@@ -0,0 +1,31 @@
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name: pymc3-test-py37
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channels:
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- conda-forge
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- defaults
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dependencies:
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- aesara>=2.1.0
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- arviz>=0.11.2
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- cachetools>=4.2.1
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- cloudpickle
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- fastprogress>=0.2.0
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- h5py>=2.7
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- ipython
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- libblas=*=*mkl
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- mkl-service
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- myst-nb
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- numpy>=1.15.0
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- numpydoc>=0.9
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- pandas=0.24
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- pre-commit>=2.8.0
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- pydata-sphinx-theme
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- pytest-cov>=2.5
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- pytest>=3.0
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- python-graphviz
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- python=3.7
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- recommonmark>=0.4
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- scipy>1.4.1
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- sphinx-autobuild>=0.7
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- sphinx-panels
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- sphinx>=1.5
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- typing-extensions
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- watermark

‎conda-envs/environment-test-py38.yml

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name: pymc3-test-py38
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channels:
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- conda-forge
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- defaults
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dependencies:
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- aesara>=2.1.0
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- arviz>=0.11.2
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- cachetools>=4.2.1
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- cloudpickle
10+
- fastprogress>=0.2.0
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- h5py>=2.7
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- ipython
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- libblas=*=*mkl
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- mkl-service
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- myst-nb
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- nbsphinx>=0.4
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- numpy>=1.15.0
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- numpydoc>=0.9
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- pandas
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- pre-commit>=2.8.0
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- pydata-sphinx-theme
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- pytest-cov>=2.5
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- pytest>=3.0
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- python-graphviz
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- python=3.8
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- recommonmark>=0.4
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- scipy>1.4.1
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- sphinx-autobuild>=0.7
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- sphinx-panels
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- sphinx>=1.5
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- typing-extensions>=3.7.4
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- watermark

‎conda-envs/environment-test-py39.yml

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name: pymc3-test-py39
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channels:
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- conda-forge
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- defaults
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dependencies:
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- aesara>=2.1.0
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- arviz>=0.11.2
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- cachetools
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- cloudpickle
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- fastprogress>=0.2.0
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- h5py
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- ipython>=7.16
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- libblas=*=*mkl
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- mkl-service
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- myst-nb
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- nbsphinx>=0.4
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- numpy>=1.15.0
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- numpydoc>=0.9
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- pandas
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- pre-commit>=2.8.0
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- pydata-sphinx-theme
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- pytest-cov>=2.5
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- pytest>=3.0
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- python-graphviz
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- python=3.9
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- recommonmark>=0.4
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- scipy>1.4.1
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- sphinx-autobuild>=0.7
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- sphinx-panels
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- sphinx>=1.5
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- typing-extensions>=3.7.4
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- watermark

‎conda-envs/windows-environment-dev-py38.yml

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@@ -9,20 +9,16 @@ dependencies:
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- cachetools>=4.2.1
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- cloudpickle
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- fastprogress>=0.2.0
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- h5py>=2.7
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- libpython
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- mkl-service
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- m2w64-toolchain
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- numba
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- h5py
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- numpy>=1.15.0
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- pandas>=0.24.0
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- pandas
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- pip
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- python=3.8
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- python-graphviz
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- scipy>1.4.1
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- typing-extensions>=3.7.4
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# Extra stuff for dev, testing and docs build
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- ipython>=7.16
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- ipython
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- myst-nb
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- numpydoc>=0.9
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- pre-commit>=2.8.0

‎conda-envs/windows-environment-test-py38.yml

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name: pymc3-test-py38
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channels:
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- conda-forge
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- defaults
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dependencies:
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# base dependencies (see install guide for Windows)
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- aesara>=2.1.0
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- arviz>=0.11.2
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- cachetools
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- cloudpickle
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- fastprogress>=0.2.0
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- h5py>=2.7
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- libpython
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- mkl-service
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- m2w64-toolchain
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- numpy>=1.15.0
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- pandas
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- pip
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- python=3.8
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- python-graphviz
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- scipy>1.4.1
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- typing-extensions>=3.7.4
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# Extra stuff for dev, testing and docs build
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- ipython>=7.16
25+
- myst-nb
26+
- nbsphinx>=0.4
27+
- numpydoc>=0.9
28+
- pre-commit>=2.8.0
29+
- pydata-sphinx-theme
30+
- pytest-cov>=2.5
31+
- pytest>=3.0
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- recommonmark>=0.4
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- sphinx-autobuild>=0.7
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- sphinx-panels
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- sphinx>=1.5
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- watermark

‎requirements-dev.txt

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# See that file for comments about the need/usage of each dependency.
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aesara>=2.1.0
5-
arviz>=0.11.4
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cachetools>=4.2.1
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arviz>=0.11.2
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cachetools
77
cloudpickle
88
fastprogress>=0.2.0
99
h5py>=2.7
1010
ipython>=7.16
1111
myst-nb
12+
nbsphinx>=0.4
1213
numpy>=1.15.0
1314
numpydoc>=0.9
14-
pandas>=0.24.0
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pandas
1516
pre-commit>=2.8.0
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pydata-sphinx-theme
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pytest-cov>=2.5
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pytest>=3.0
1920
recommonmark>=0.4
2021
scipy>1.4.1
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sphinx-autobuild>=0.7
22-
sphinx-design
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sphinx-notfound-page
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sphinx-panels
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sphinx>=1.5
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typing-extensions>=3.7.4

‎requirements.txt

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fastprogress>=0.2.0
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numpy>=1.15.0
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pandas>=0.24.0
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patsy>=0.5.1
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scipy>=1.4.1
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typing-extensions>=3.7.4

‎scripts/generate_pip_deps_from_conda.py

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"pip",
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"python",
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"libblas",
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"libblas=*=*mkl",
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"libpython",
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"m2w64-toolchain",
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"mkl-service",

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