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11 changes: 9 additions & 2 deletions .github/workflows/arviz_compat.yml
Original file line number Diff line number Diff line change
Expand Up @@ -38,8 +38,15 @@ jobs:
channel-priority: strict
environment-file: environment-dev.yml
use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly!
- run: |
- name: Install pymc3
run: |
conda activate testenv
conda remove arviz -y
pip install -e .
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it's probably good to check this works, in case there are any errors in setup.py - it only takes about 5 seconds during CI anyway

- name: Install latest arviz
run: |
conda activate testenv
pip uninstall 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
7 changes: 6 additions & 1 deletion .github/workflows/pytest.yml
Original file line number Diff line number Diff line change
Expand Up @@ -78,7 +78,12 @@ jobs:
channel-priority: strict
environment-file: environment-dev.yml
use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly!
- run: |
- name: Install-pymc3
run: |
conda activate testenv
pip install -e .
- name: Run tests
run: |
conda activate testenv
python -m pytest -vv --cov=pymc3 --cov-report=xml --cov-report term --durations=50 $TEST_SUBSET
- name: Upload coverage to Codecov
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37 changes: 13 additions & 24 deletions CONTRIBUTING.md
Original file line number Diff line number Diff line change
Expand Up @@ -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
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git's new way of switching branches - git checkout still works, but this is meant to be more intuitive to beginners

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and this creates a new branch too?

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yup, -c for "create"

```

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
$ conda env create -f environment-dev.yml
$ conda activate testenv
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I think we can use a more explicit name for the virtual env, maybe pymc-dev-env instead of testenv?

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or just pymc3-dev - sure!

$ pip install -e .
```

_Alternatively_ you may (probably in a [virtual environment](https://docs.python-guide.org/dev/virtualenvs/)) run:

```bash
$ pip install -r requirements.txt
$ pip install -e .
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this includes all the requirements.txt already + gives a local editable install

$ 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:

Expand Down Expand Up @@ -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

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15 changes: 0 additions & 15 deletions environment-dev.yml
Original file line number Diff line number Diff line change
Expand Up @@ -13,24 +13,9 @@ dependencies:
- 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
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@MarcoGorelli MarcoGorelli Nov 30, 2020

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is there a reason to have all these documentation-related dependencies in here or can they be removed? I don't know how the docs are built, but maybe these could live in a separate environment-docs.yml environment

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Yeah, we can move these to a separate env file, but shouldn't just drop them here.

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OK - ended up putting them back an, as they don't take up much extra time anyway, all I've removed now are some nose/unittest-related ones (which shouldn't be necessary any more, given that pytest is used?), and some (bokeh and seaborn) which are only used in a handful of notebooks

- watermark
- parameterized
- ipywidgets
- dataclasses # python_version < 3.7
- contextvars # python_version < 3.7
- mkl-service
Expand Down