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MarcoGorelliMarcoGorelli
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Update contributing guide, fail fast (#4280)
* update contributing * rename * put watermark back in (minimal impact anyway) * keep graphviz in * failfast * add failing test * fail fast * don't fail a test on purpose * indent * indent * remove -x * remove arviz with conda * dont remove patsy * try using python version correctly * move non-theano non-optional dependencies out of environment-dev.yml * keep python in environment-dev.yml, that's a separate issue * typo * put patsy back; final commit? * make separate env files * show python version * update env name in contributing.md * redistribute tests
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‎.github/workflows/arviz_compat.yml‎

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@@ -9,11 +9,11 @@ jobs:
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pytest:
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strategy:
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matrix:
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python-version: ["3.8"]
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os: [ubuntu-18.04]
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floatx: [float64]
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test-subset:
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- pymc3/tests/test_sampling.py
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fail-fast: false
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runs-on: ${{ matrix.os }}
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env:
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TEST_SUBSET: ${{ matrix.test-subset }}
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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.yml has not changed
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# Increase this value to reset cache if environment-dev-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('environment-dev.yml') }}
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hashFiles('conda-envs/environment-dev-py38.yml') }}
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- uses: conda-incubator/setup-miniconda@v2
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with:
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activate-environment: testenv
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activate-environment: pymc3-dev-py38
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channel-priority: strict
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environment-file: environment-dev.yml
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environment-file: conda-envs/environment-dev-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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- run: |
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conda activate testenv
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- name: Install pymc3
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run: |
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conda activate pymc3-dev-py38
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pip install -e .
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python --version
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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 install git+git://github.com/arviz-devs/arviz.git
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- name: Run tests
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run: |
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python -m pytest -vv --cov=pymc3 --cov-report=xml --cov-report term --durations=50 $TEST_SUBSET

‎.github/workflows/pytest.yml‎

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pytest:
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strategy:
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matrix:
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python-version: ["3.6"]
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os: [ubuntu-18.04]
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floatx: [float32, float64]
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test-subset:
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pymc3/tests/test_dist_math.py
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pymc3/tests/test_distribution_defaults.py
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pymc3/tests/test_distributions_random.py
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pymc3/tests/test_distributions_timeseries.py
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pymc3/tests/test_parallel_sampling.py
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pymc3/tests/test_random.py
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pymc3/tests/test_shared.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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pymc3/tests/test_distributions_timeseries.py
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pymc3/tests/test_shape_handling.py
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pymc3/tests/test_updates.py
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pymc3/tests/test_variational_inference.py
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- |
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pymc3/tests/test_distributions.py
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pymc3/tests/test_gp.py
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pymc3/tests/test_sampling.py
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fail-fast: false
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runs-on: ${{ matrix.os }}
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env:
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TEST_SUBSET: ${{ matrix.test-subset }}
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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.yml has not changed
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# Increase this value to reset cache if environment-dev-py36.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('environment-dev.yml') }}
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hashFiles('conda-envs/environment-dev-py36.yml') }}
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- uses: conda-incubator/setup-miniconda@v2
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with:
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activate-environment: testenv
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activate-environment: pymc3-dev-py36
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channel-priority: strict
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environment-file: environment-dev.yml
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environment-file: conda-envs/environment-dev-py36.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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- run: |
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conda activate testenv
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- name: Install-pymc3
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run: |
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conda activate pymc3-dev-py36
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pip install -e .
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python --version
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- name: Run tests
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run: |
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conda activate pymc3-dev-py36
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python -m pytest -vv --cov=pymc3 --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

‎CONTRIBUTING.md‎

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3. Create a ``feature`` branch to hold your development changes:
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```bash
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$ git checkout -b my-feature
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$ git switch -c 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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4. Project requirements are in ``requirements.txt``, and libraries used for development are in ``requirements-dev.txt``. To set up a development environment, you may (probably in a [virtual environment](https://docs.python-guide.org/dev/virtualenvs/)) run:
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4. Project requirements are in ``requirements.txt``, and libraries used for development are in ``requirements-dev.txt``. The easiest (and recommended) way to set up a development environment is via [miniconda](https://docs.conda.io/en/latest/miniconda.html):
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```bash
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$ pip install -r requirements.txt
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$ conda env create -f conda-envs/environment-dev-py36.yml # or py37 or py38
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$ conda activate pymc3-dev-py36
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$ pip install -e .
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```
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_Alternatively_ you may (probably in a [virtual environment](https://docs.python-guide.org/dev/virtualenvs/)) run:
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```bash
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$ pip install -e .
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$ pip install -r requirements-dev.txt
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```
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Alternatively, there is a script to create a docker environment for development. See: [Developing in Docker](#Developing-in-Docker).
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Yet another alternative is to create a docker environment for development. See: [Developing in Docker](#Developing-in-Docker).
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5. Develop the feature on your feature branch. Add changed files using ``git add`` and then ``git commit`` files:
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$ pytest --cov=pymc3 pymc3/tests/<name of test>.py
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```
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* No `pyflakes` warnings, check with:
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```bash
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$ pip install pyflakes
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$ pyflakes path/to/module.py
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```
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* No PEP8 warnings, check with:
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```bash
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$ pip install pycodestyle
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$ pycodestyle path/to/module.py
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```
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* AutoPEP8 can help you fix some of the easy redundant errors:
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```bash
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$ pip install autopep8
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$ autopep8 path/to/pep8.py
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```
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* No `pre-commit` errors: see the [Python code style](https://github.com/pymc-devs/pymc3/wiki/PyMC3-Python-Code-Style) and [Jupyter Notebook style](https://github.com/pymc-devs/pymc3/wiki/PyMC's-Jupyter-Notebook-Style) page from our Wiki on how to install and run it.
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## Developing in Docker
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environment-dev.yml renamed to conda-envs/environment-dev-py36.yml

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name: testenv
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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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dependencies:
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- python>=3.6
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- python=3.6
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- arviz>=0.9
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- theano-pymc==1.0.11
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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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- 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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- bokeh>=0.12
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- coverage>=5.1
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- python-graphviz
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- ipython>=7.16
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- nbsphinx>=0.4
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- nose>=1.3
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- nose-parameterized>=0.6
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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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- seaborn>=0.8
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- sphinx-autobuild>=0.7
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- sphinx>=1.5
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- watermark
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- parameterized
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- ipywidgets
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- dataclasses # python_version < 3.7
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- contextvars # python_version < 3.7
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- mkl-service

‎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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dependencies:
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- python=3.7
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- arviz>=0.9
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- theano-pymc==1.0.11
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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

‎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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dependencies:
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- python=3.8
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- arviz>=0.9
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- theano-pymc==1.0.11
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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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