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MarcoGorellitwiecki
MarcoGorelli
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twiecki
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Only pin theano-pymc in requirements.txt (#4322)
* 🔨 add scripts to check theano-pymc pins, to generate requirements-dev from conda, to sort conda deps * 🔧 update conda envs and requirements-dev.txt * 📝 fix typo * 📝 add docstrings * 📝 update pip-to-conda docstring * noop * 🔥 remove pin theano checks, just use requirements.txt * local install in arviz compat * 📝 switch -> checkout, note beginner friendly label * 📝 link to beginner friendly issues * run generate pip deps from conda on all conda env files * 🔧 make sure all conda-envs files generate requirements-dev * 🔀 reorder some tests * 🎨 remove trailing comma * Update scripts/generate_pip_deps_from_conda.py Co-authored-by: Thomas Wiecki <[email protected]>
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‎.github/workflows/arviz_compat.yml

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@@ -33,6 +33,18 @@ jobs:
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path: ~/conda_pkgs_dir
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key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{
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hashFiles('conda-envs/environment-dev-py38.yml') }}
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- name: Cache multiple paths
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uses: actions/cache@v2
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env:
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# Increase this value to reset cache if requirements.txt has not changed
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CACHE_NUMBER: 0
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with:
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path: |
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~/.cache/pip
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$RUNNER_TOOL_CACHE/Python/*
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~\AppData\Local\pip\Cache
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key: ${{ runner.os }}-build-${{ matrix.python-version }}-${{
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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: pymc3-dev-py38
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- name: Install latest arviz
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run: |
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conda activate pymc3-dev-py38
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conda remove arviz -y
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pip uninstall arviz -y
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pip install git+git://github.com/arviz-devs/arviz.git
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- name: Run tests
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run: |

‎.github/workflows/pytest.yml

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--ignore=pymc3/tests/test_examples.py
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--ignore=pymc3/tests/test_gp.py
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--ignore=pymc3/tests/test_mixture.py
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--ignore=pymc3/tests/test_ode.py
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--ignore=pymc3/tests/test_parallel_sampling.py
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--ignore=pymc3/tests/test_posteriors.py
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--ignore=pymc3/tests/test_quadpotential.py
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- |
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pymc3/tests/test_examples.py
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pymc3/tests/test_mixture.py
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pymc3/tests/test_ode.py
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pymc3/tests/test_posteriors.py
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pymc3/tests/test_quadpotential.py
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- |
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path: ~/conda_pkgs_dir
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key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{
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hashFiles('conda-envs/environment-dev-py36.yml') }}
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- name: Cache multiple paths
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uses: actions/cache@v2
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env:
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# Increase this value to reset cache if requirements.txt has not changed
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CACHE_NUMBER: 0
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with:
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path: |
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~/.cache/pip
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$RUNNER_TOOL_CACHE/Python/*
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~\AppData\Local\pip\Cache
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key: ${{ runner.os }}-build-${{ matrix.python-version }}-${{
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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: pymc3-dev-py36

‎.github/workflows/windows.yml

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path: ~/conda_pkgs_dir
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key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{
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hashFiles('conda-envs/environment-dev-py37.yml') }}
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- name: Cache multiple paths
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uses: actions/cache@v2
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env:
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# Increase this value to reset cache if requirements.txt has not changed
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CACHE_NUMBER: 0
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with:
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path: |
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~/.cache/pip
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$RUNNER_TOOL_CACHE/Python/*
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~\AppData\Local\pip\Cache
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key: ${{ runner.os }}-build-${{ matrix.python-version }}-${{
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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: pymc3-dev-py37
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channel-priority: strict
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environment-file: conda-envs/environment-dev-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-pymc3
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run: |
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conda activate pymc3-dev-py37
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pip install -e .
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python --version
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- run: |
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conda activate pymc3-dev-py37
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python -m pytest -vv --cov=pymc3 --cov-report=xml --cov-report term --durations=50 $TEST_SUBSET

‎.pre-commit-config.yaml

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- id: no-commit-to-branch
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args: [--branch, master]
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- id: requirements-txt-fixer
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exclude: ^requirements-dev\.txt$
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- id: trailing-whitespace
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- repo: https://github.com/nbQA-dev/nbQA
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rev: 0.5.4
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language: python
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name: Check no tests are ignored
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pass_filenames: false
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- id: conda-env-sort
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additional_dependencies: [pyyaml]
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entry: python scripts/sort_conda_envs.py
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files: ^conda-envs/
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language: python
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name: Sort dependencies in conda envs
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types: [yaml]
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- id: pip-from-conda
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additional_dependencies: [pyyaml]
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entry: python scripts/generate_pip_deps_from_conda.py
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files: ^conda-envs/
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language: python
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name: Generate pip dependency from conda
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- id: no-relative-imports
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name: No relative imports
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entry: from \.[\.\w]* import

‎CONTRIBUTING.md

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Please verify that your issue is not being currently addressed by other issues or pull requests by using the GitHub search tool to look for key words in the project issue tracker.
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Filter on the ["beginner friendly"](https://github.com/pymc-devs/pymc3/issues?q=is%3Aopen+is%3Aissue+label%3A%22beginner+friendly%22) label for issues which are good for new contributors.
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# Contributing code via pull requests
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While issue reporting is valuable, we strongly encourage users who are inclined to do so to submit patches for new or existing issues via pull requests. This is particularly the case for simple fixes, such as typos or tweaks to documentation, which do not require a heavy investment of time and attention.
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3. Create a ``feature`` branch to hold your development changes:
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```bash
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$ git switch -c my-feature
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$ git checkout -b my-feature
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```
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Always use a ``feature`` branch. It's good practice to never routinely work on the ``master`` branch of any repository.
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For documentation strings, we *prefer* [numpy style](https://numpydoc.readthedocs.io/en/latest/format.html) to comply with the style that predominates in our upstream dependencies.
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Finally, see the [PyMC3 Python Code Style](https://github.com/pymc-devs/pymc3/wiki/PyMC3-Python-Code-Style) and the [PyMC's Jupyter Notebook Style](https://github.com/pymc-devs/pymc3/wiki/PyMC's-Jupyter-Notebook-Style) guides.
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#### This guide was derived from the [scikit-learn guide to contributing](https://github.com/scikit-learn/scikit-learn/blob/master/CONTRIBUTING.md)

‎conda-envs/environment-dev-py36.yml

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name: pymc3-dev-py36
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channels:
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- conda-forge
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- defaults
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- conda-forge
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- defaults
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dependencies:
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- python=3.6
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- arviz>=0.9
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- theano-pymc==1.0.12
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- numpy>=1.13
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- scipy>=0.18
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- pandas>=0.18
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- patsy>=0.5
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- fastprogress>=0.2
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- h5py>=2.7
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- typing-extensions>=3.7
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- python-graphviz
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- ipython>=7.16
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- nbsphinx>=0.4
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- numpydoc>=0.9
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- pre-commit>=2.8.0
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- pytest-cov>=2.5
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- pytest>=3.0
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- recommonmark>=0.4
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- sphinx-autobuild>=0.7
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- sphinx>=1.5
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- watermark
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- dataclasses # python_version < 3.7
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- contextvars # python_version < 3.7
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- mkl-service
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- dill
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- libblas=*=*mkl
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- contextvars
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- dataclasses
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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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- nbsphinx>=0.4
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- numpydoc>=0.9
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- pre-commit>=2.8.0
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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=3.6
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- recommonmark>=0.4
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- sphinx-autobuild>=0.7
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- sphinx>=1.5
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- watermark

‎conda-envs/environment-dev-py37.yml

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name: pymc3-dev-py37
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channels:
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- conda-forge
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- defaults
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- conda-forge
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- defaults
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dependencies:
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- python=3.7
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- arviz>=0.9
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- theano-pymc==1.0.12
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- numpy>=1.13
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- scipy>=0.18
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- pandas>=0.18
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- patsy>=0.5
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- fastprogress>=0.2
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- h5py>=2.7
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- typing-extensions>=3.7
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- python-graphviz
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- ipython>=7.16
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- nbsphinx>=0.4
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- numpydoc>=0.9
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- pre-commit>=2.8.0
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- pytest-cov>=2.5
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- pytest>=3.0
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- recommonmark>=0.4
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- sphinx-autobuild>=0.7
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- sphinx>=1.5
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- watermark
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- mkl-service
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- dill
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- libblas=*=*mkl
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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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- nbsphinx>=0.4
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- numpydoc>=0.9
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- pre-commit>=2.8.0
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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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- sphinx-autobuild>=0.7
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- sphinx>=1.5
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- watermark

‎conda-envs/environment-dev-py38.yml

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name: pymc3-dev-py38
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channels:
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- conda-forge
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- defaults
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- conda-forge
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- defaults
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dependencies:
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- python=3.8
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- arviz>=0.9
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- theano-pymc==1.0.12
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- numpy>=1.13
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- scipy>=0.18
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- pandas>=0.18
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- patsy>=0.5
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- fastprogress>=0.2
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- h5py>=2.7
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- typing-extensions>=3.7
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- python-graphviz
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- ipython>=7.16
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- nbsphinx>=0.4
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- numpydoc>=0.9
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- pre-commit>=2.8.0
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- pytest-cov>=2.5
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- pytest>=3.0
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- recommonmark>=0.4
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- sphinx-autobuild>=0.7
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- sphinx>=1.5
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- watermark
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- mkl-service
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- dill
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- libblas=*=*mkl
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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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- nbsphinx>=0.4
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- numpydoc>=0.9
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- pre-commit>=2.8.0
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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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- sphinx-autobuild>=0.7
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- sphinx>=1.5
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- watermark

‎requirements-dev.txt

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bokeh>=0.12.13
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coverage>=5.1
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dill
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graphviz>=0.8.3
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ipython
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nbsphinx>=0.4.2
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nose>=1.3.7
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nose-parameterized==0.6.0
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numpydoc>=0.9.1
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parameterized
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# This file is auto-generated from by scripts/generate_pip_deps_from_conda.py, do not modify.
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# See that file for comments about the need/usage of each dependency.
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h5py>=2.7
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ipython>=7.16
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nbsphinx>=0.4
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numpydoc>=0.9
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pre-commit>=2.8.0
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pycodestyle>=2.3.1
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pyflakes>=1.5.0
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pylint>=1.7.4
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pytest>=3.0.7
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pytest-cov>=2.5.1
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pytest-xdist
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recommonmark>=0.4.0
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seaborn>=0.8.1
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sphinx>=1.5.5
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sphinx-autobuild==0.7.1
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pytest-cov>=2.5
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pytest>=3.0
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recommonmark>=0.4
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sphinx-autobuild>=0.7
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sphinx>=1.5
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watermark

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