Merge pull request #38 from chrisjonesBSU/unit-tests

Refactor Unit Tests

.github/workflows/pytest.yml

@@ -4,15 +4,15 @@ on:
   push:
     branches: [ master ]
     paths:
-      - '.github/workflows/pytest.yml'
-      - 'environment-cpu.yml'
-      - 'msibi/**'
+      - msibi/**
+      - environment-dev.yml
+      - .github/workflows/pytest.yml
   pull_request:
     branches: [ master ]
     paths:
-      - 'msibi/**'
-      - 'environment-cpu.yml'
-      - '.github/workflows/pytest.yml'
+      - msibi/**
+      - environment-dev.yml
+      - .github/workflows/pytest.yml
   # Allows workflow to be manually triggered
   workflow_dispatch:
 
@@ -27,9 +27,9 @@ jobs:
     - name: Build environment
       uses: conda-incubator/setup-miniconda@v2
       with:
-        environment-file: environment-cpu.yml
+        environment-file: environment-dev.yml
         miniforge-variant: Mambaforge
-        miniforge-version: 4.9.2-4
+        miniforge-version: 23.11.0-0 
         use-mamba: true
 
     - name: Install package
@@ -38,10 +38,10 @@ jobs:
 
     - name: Run pytest with coverage report
       shell: bash -l {0}
-      run: python -m pytest --cov=./ --cov-report=xml -v
+      run: python -m pytest -rs -v --cov=./ --cov-report=xml
 
     - name: Upload coverage to Codecov
-      uses: codecov/codecov-action@v1
+      uses: codecov/codecov-action@v3
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
         file: ./coverage.xml

.gitignore

@@ -10,7 +10,7 @@ msibi/tutorials/lj/state*/run.py
 *.dcd
 .DS_Store
 *.egg-info
-
+*.idea/
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]

README.md

@@ -2,8 +2,6 @@
 
 # MultiState Iterative Boltzmann Inversion (MS-IBI)
 ----------------------------------------
-[![build_cpu](https://github.com/cmelab/msibi/actions/workflows/build_cpu.yml/badge.svg)](https://github.com/cmelab/msibi/actions/workflows/build_cpu.yml)
-[![build_gpu](https://github.com/cmelab/msibi/actions/workflows/build_gpu.yml/badge.svg)](https://github.com/cmelab/msibi/actions/workflows/build_gpu.yml)
 [![pytest](https://github.com/cmelab/msibi/actions/workflows/pytest.yml/badge.svg)](https://github.com/cmelab/msibi/actions/workflows/pytest.yml)
 [![codecov](https://codecov.io/gh/cmelab/msibi/branch/master/graph/badge.svg?token=7NFPBMBN0I)](https://codecov.io/gh/cmelab/msibi)
 
@@ -20,10 +18,6 @@ pip install .
 ```
 
 
-### Tutorials
-[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/cmelab/msibi/master?urlpath=tree/msibi/tutorials/lj/LJ_Tutorial.ipynb) - Tutorial showing how to recreate the Lennard Jones potential using MS-IBI
-
-
 ### Citation [![Citing MSIBI](https://img.shields.io/badge/DOI-10.1063%2F1.4880555-blue.svg)](http://dx.doi.org/10.1063/1.4880555)
 Details of the underlying method and its validation can be found [here](http://dx.doi.org/10.1063/1.4880555).