Misc fixes

.github/workflows/main.yml

@@ -39,23 +39,16 @@ 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}
         run: pip install -e .[dev]
 
       - 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

.gitignore

@@ -17,3 +17,4 @@ tests/custom_model
 /build
 docs/_build
 tags
+.coverage*

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

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

pytest.ini

@@ -1,3 +1,4 @@
 [pytest]
 filterwarnings =
     ignore::DeprecationWarning
+    ignore::FutureWarning