diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 8d26380..6e6a423 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -39,14 +39,7 @@ jobs: - name: Install conda packages shell: bash -l {0} - run: mamba install -c conda-forge biom-format patsy pytest xarray scikit-bio flake8 arviz - - # Temp req before CmdStanPy cuts a new release - - name: Install develop branch of CmdStanPy - shell: bash -l {0} - run: > - pip install git+https://github.com/stan-dev/cmdstanpy.git@develop; - install_cmdstan + run: mamba install -c conda-forge biom-format patsy pytest xarray scikit-bio flake8 arviz cmdstanpy pytest-cov - name: Install BIRDMAn shell: bash -l {0} @@ -54,8 +47,8 @@ jobs: - name: Check style shell: bash -l {0} - run: flake8 birdman/*.py tests/*.py setup.py + run: make stylecheck - name: Run tests shell: bash -l {0} - run: pytest --disable-pytest-warnings + run: make pytest diff --git a/.gitignore b/.gitignore index 3d1a5c4..787f8d3 100644 --- a/.gitignore +++ b/.gitignore @@ -17,3 +17,4 @@ tests/custom_model /build docs/_build tags +.coverage* diff --git a/Makefile b/Makefile index 7aca32a..108f801 100644 --- a/Makefile +++ b/Makefile @@ -6,7 +6,7 @@ stylecheck: flake8 birdman/*.py tests/*.py setup.py pytest: - pytest tests -W ignore::FutureWarning + pytest --cov-report term-missing --cov=birdman --cov-branch tests documentation: cd docs && make html diff --git a/README.md b/README.md index f146ea1..0ce171b 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,6 @@ # BIRDMAn -[![GitHub Actions CI](https://github.com/gibsramen/birdman/workflows/BIRDMAn%20CI/badge.svg)](https://github.com/gibsramen/BIRDMAn/actions) +[![GitHub Actions CI](https://github.com/biocore/birdman/workflows/BIRDMAn%20CI/badge.svg)](https://github.com/biocore/BIRDMAn/actions) [![Documentation Status](https://readthedocs.org/projects/birdman/badge/?version=stable)](https://birdman.readthedocs.io/en/stable/?badge=stable) [![PyPI](https://img.shields.io/pypi/v/birdman.svg)](https://pypi.org/project/birdman) [![DOI](https://zenodo.org/badge/312046610.svg)](https://zenodo.org/badge/latestdoi/312046610) @@ -11,7 +11,9 @@ See the [documentation](https://birdman.readthedocs.io/en/stable/?badge=stable) ## Installation -Currently BIRDMAn requires Python 3.7 or higher. +Currently BIRDMAn requires Python 3.8 or higher. + +We recommend using [mamba](https://github.com/mamba-org/mamba) for installation of dependencies. ```bash conda install -c conda-forge biom-format patsy xarray arviz cmdstanpy diff --git a/pytest.ini b/pytest.ini index c24fe5b..7538d7f 100644 --- a/pytest.ini +++ b/pytest.ini @@ -1,3 +1,4 @@ [pytest] filterwarnings = ignore::DeprecationWarning + ignore::FutureWarning