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

Author: MarcoGorelli

.github/workflows/arviz_compat.yml

@@ -9,11 +9,11 @@ jobs:
   pytest:
     strategy:
       matrix:
-        python-version: ["3.8"]
         os: [ubuntu-18.04]
         floatx: [float64]
         test-subset:
           - pymc3/tests/test_sampling.py
+      fail-fast: false
     runs-on: ${{ matrix.os }}
     env:
       TEST_SUBSET: ${{ matrix.test-subset }}
@@ -26,20 +26,28 @@ jobs:
       - name: Cache conda
         uses: actions/cache@v1
         env:
-          # Increase this value to reset cache if environment-dev.yml has not changed
+          # Increase this value to reset cache if environment-dev-py38.yml has not changed
           CACHE_NUMBER: 0
         with:
           path: ~/conda_pkgs_dir
           key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{
-            hashFiles('environment-dev.yml') }}
+            hashFiles('conda-envs/environment-dev-py38.yml') }}
       - uses: conda-incubator/setup-miniconda@v2
         with:
-          activate-environment: testenv
+          activate-environment: pymc3-dev-py38
           channel-priority: strict
-          environment-file: environment-dev.yml
+          environment-file: conda-envs/environment-dev-py38.yml
           use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly!
-      - run: |
-          conda activate testenv
+      - name: Install pymc3
+        run: |
+          conda activate pymc3-dev-py38
+          pip install -e .
+          python --version
+      - name: Install latest arviz
+        run: |
+          conda activate pymc3-dev-py38
           conda remove arviz -y
           pip install git+git://github.com/arviz-devs/arviz.git
+      - name: Run tests
+        run: |
           python -m pytest -vv --cov=pymc3 --cov-report=xml --cov-report term --durations=50 $TEST_SUBSET

.github/workflows/pytest.yml

@@ -9,7 +9,6 @@ jobs:
   pytest:
     strategy:
       matrix:
-        python-version: ["3.6"]
         os: [ubuntu-18.04]
         floatx: [float32, float64]
         test-subset:
@@ -36,7 +35,6 @@ jobs:
             pymc3/tests/test_dist_math.py
             pymc3/tests/test_distribution_defaults.py
             pymc3/tests/test_distributions_random.py
-            pymc3/tests/test_distributions_timeseries.py
             pymc3/tests/test_parallel_sampling.py
             pymc3/tests/test_random.py
             pymc3/tests/test_shared.py
@@ -47,13 +45,15 @@ jobs:
             pymc3/tests/test_posteriors.py
             pymc3/tests/test_quadpotential.py
           - |
+            pymc3/tests/test_distributions_timeseries.py
             pymc3/tests/test_shape_handling.py
             pymc3/tests/test_updates.py
             pymc3/tests/test_variational_inference.py
           - |
             pymc3/tests/test_distributions.py
             pymc3/tests/test_gp.py
             pymc3/tests/test_sampling.py
+      fail-fast: false
     runs-on: ${{ matrix.os }}
     env:
       TEST_SUBSET: ${{ matrix.test-subset }}
@@ -66,20 +66,26 @@ jobs:
       - name: Cache conda
         uses: actions/cache@v1
         env:
-          # Increase this value to reset cache if environment-dev.yml has not changed
+          # Increase this value to reset cache if environment-dev-py36.yml has not changed
           CACHE_NUMBER: 0
         with:
           path: ~/conda_pkgs_dir
           key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{
-            hashFiles('environment-dev.yml') }}
+            hashFiles('conda-envs/environment-dev-py36.yml') }}
       - uses: conda-incubator/setup-miniconda@v2
         with:
-          activate-environment: testenv
+          activate-environment: pymc3-dev-py36
           channel-priority: strict
-          environment-file: environment-dev.yml
+          environment-file: conda-envs/environment-dev-py36.yml
           use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly!
-      - run: |
-          conda activate testenv
+      - name: Install-pymc3
+        run: |
+          conda activate pymc3-dev-py36
+          pip install -e .
+          python --version
+      - name: Run tests
+        run: |
+          conda activate pymc3-dev-py36
           python -m pytest -vv --cov=pymc3 --cov-report=xml --cov-report term --durations=50 $TEST_SUBSET
       - name: Upload coverage to Codecov
         uses: codecov/codecov-action@v1

CONTRIBUTING.md

@@ -38,19 +38,27 @@ The preferred workflow for contributing to PyMC3 is to fork the [GitHub reposito
 3. Create a ``feature`` branch to hold your development changes:
 
    ```bash
-   $ git checkout -b my-feature
+   $ git switch -c my-feature
    ```
 
    Always use a ``feature`` branch. It's good practice to never routinely work on the ``master`` branch of any repository.
 
-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:
+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):
 
    ```bash
-   $ pip install -r requirements.txt
+   $ conda env create -f conda-envs/environment-dev-py36.yml  # or py37 or py38
+   $ conda activate pymc3-dev-py36
+   $ pip install -e .
+   ```
+
+   _Alternatively_ you may (probably in a [virtual environment](https://docs.python-guide.org/dev/virtualenvs/)) run:
+
+   ```bash
+   $ pip install -e .
    $ pip install -r requirements-dev.txt
    ```
 
-Alternatively, there is a script to create a docker environment for development.  See: [Developing in Docker](#Developing-in-Docker).
+   Yet another alternative is to create a docker environment for development. See: [Developing in Docker](#Developing-in-Docker).
 
 5. Develop the feature on your feature branch. Add changed files using ``git add`` and then ``git commit`` files:
 
@@ -103,26 +111,7 @@ tools:
   $ pytest --cov=pymc3 pymc3/tests/<name of test>.py
   ```
 
-* No `pyflakes` warnings, check with:
-
-  ```bash
-  $ pip install pyflakes
-  $ pyflakes path/to/module.py
-  ```
-
-* No PEP8 warnings, check with:
-
-  ```bash
-  $ pip install pycodestyle
-  $ pycodestyle path/to/module.py
-  ```
-
-* AutoPEP8 can help you fix some of the easy redundant errors:
-
-  ```bash
-  $ pip install autopep8
-  $ autopep8 path/to/pep8.py
-  ```
+* 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.
 
 ## Developing in Docker
 

environment-dev.yml renamed to conda-envs/environment-dev-py36.yml

@@ -1,36 +1,29 @@
-name: testenv
+name: pymc3-dev-py36
 channels:
   - conda-forge
   - defaults
 dependencies:
-  - python>=3.6
+  - python=3.6
   - arviz>=0.9
   - theano-pymc==1.0.11
   - numpy>=1.13
   - scipy>=0.18
-  - pandas >=0.18
+  - pandas>=0.18
   - patsy>=0.5
   - fastprogress>=0.2
   - h5py>=2.7
   - typing-extensions>=3.7
-  - bokeh>=0.12
-  - coverage>=5.1
   - python-graphviz
   - ipython>=7.16
   - nbsphinx>=0.4
-  - nose>=1.3
-  - nose-parameterized>=0.6
   - numpydoc>=0.9
   - pre-commit>=2.8.0
   - pytest-cov>=2.5
   - pytest>=3.0
   - recommonmark>=0.4
-  - seaborn>=0.8
   - sphinx-autobuild>=0.7
   - sphinx>=1.5
   - watermark
-  - parameterized
-  - ipywidgets
   - dataclasses  # python_version < 3.7
   - contextvars  # python_version < 3.7
   - mkl-service

conda-envs/environment-dev-py37.yml

@@ -0,0 +1,29 @@
+name: pymc3-dev-py37
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - python=3.7
+  - arviz>=0.9
+  - theano-pymc==1.0.11
+  - numpy>=1.13
+  - scipy>=0.18
+  - pandas>=0.18
+  - patsy>=0.5
+  - fastprogress>=0.2
+  - h5py>=2.7
+  - typing-extensions>=3.7
+  - python-graphviz
+  - ipython>=7.16
+  - nbsphinx>=0.4
+  - numpydoc>=0.9
+  - pre-commit>=2.8.0
+  - pytest-cov>=2.5
+  - pytest>=3.0
+  - recommonmark>=0.4
+  - sphinx-autobuild>=0.7
+  - sphinx>=1.5
+  - watermark
+  - mkl-service
+  - dill
+  - libblas=*=*mkl

conda-envs/environment-dev-py38.yml

@@ -0,0 +1,29 @@
+name: pymc3-dev-py38
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - python=3.8
+  - arviz>=0.9
+  - theano-pymc==1.0.11
+  - numpy>=1.13
+  - scipy>=0.18
+  - pandas>=0.18
+  - patsy>=0.5
+  - fastprogress>=0.2
+  - h5py>=2.7
+  - typing-extensions>=3.7
+  - python-graphviz
+  - ipython>=7.16
+  - nbsphinx>=0.4
+  - numpydoc>=0.9
+  - pre-commit>=2.8.0
+  - pytest-cov>=2.5
+  - pytest>=3.0
+  - recommonmark>=0.4
+  - sphinx-autobuild>=0.7
+  - sphinx>=1.5
+  - watermark
+  - mkl-service
+  - dill
+  - libblas=*=*mkl