Merge pull request #14 from DeepRank/setup_ci

Setup ci

.github/workflows/build.yml

@@ -0,0 +1,40 @@
+name: build
+
+on: [push]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    strategy:
+      fail-fast: false
+      matrix:
+        version: [3.7, 3.8]
+
+    steps:
+    - name: Cancel Previous Runs
+      uses: styfle/cancel-workflow-action@0.4.0
+      with:
+          access_token: ${{ github.token }}
+    - uses: actions/checkout@v2
+    - name: Setup conda
+      uses: s-weigand/setup-conda@v1
+      with:
+        update-conda: true
+        python-version: ${{ matrix.version }}
+        conda-channels: anaconda
+    - run: conda --version
+    - run: which python
+    - run: conda install mpi4py h5py pytorch torchvision cpuonly -c pytorch -c conda-forge
+
+    - name: Install the package
+      run: pip install .[test]
+      env:
+        CONDA_PREFIX: /usr/share/miniconda
+
+    - name: Test with pytest
+      env:
+        CONDA_PREFIX: /usr/share/miniconda
+      run: |
+        pytest --cov-config setup.cfg

.gitignore

@@ -15,3 +15,8 @@ GraphProt.egg-info
 # hdf5
 *.hdf5
 *.tar
+
+# test
+htmlcov
+.coverage
+covergage.xml

README.md

@@ -1,5 +1,7 @@
 # GraphProt
 
+[![Build Status](https://github.com/DeepRank/GraphProt/workflows/build/badge.svg)](https://github.com/DeepRank/GraphProt/actions)
+
 Use Graph CNN to rank conformations.
 
 ![alt-text](./graphprot.png)

setup.cfg

@@ -0,0 +1,21 @@
+[metadata]
+description-file = README.rst
+
+[aliases]
+# Define `python setup.py test`
+test=pytest
+
+[coverage:run]
+branch = True
+source = graphprot
+
+[tool:pytest]
+testpaths = tests
+addopts = --cov --cov-report xml --cov-report term --cov-report html
+
+# Define `python setup.py build_sphinx`
+# [build_sphinx]
+# source-dir = docs
+# build-dir = docs/_build
+# all_files = 1
+# builder = html

setup.py

@@ -21,7 +21,7 @@
     description='Graph Neural network Scoring of protein-protein conformations',
     long_description=readme + '\n\n',
     long_description_content_type='text/markdown',
-    author=["Nicolas Renaud"],
+    author=["Nicolas Renaud", "Manon Reau"],
     author_email='n.renaud@esciencecenter.nl',
     url='https://github.com/DeepRank/GraphProt',
     packages=find_packages(),

tests/test_create_graph.py

@@ -0,0 +1,16 @@
+import unittest
+from graphprot.GraphGenMP import GraphHDF5
+
+
+class TestCreateGraph(unittest.TestCase):
+
+    def setUp(self):
+
+        self.pdb_path = './tests/data/pdb/1ATN/'
+        self.pssm_path = './tests/data/pssm/1ATN/'
+        self.ref = './tests/data/ref/1ATN/'
+
+    def test_create(self):
+        GraphHDF5(pdb_path=self.pdb_path, ref_path=self.ref, pssm_path=self.pssm_path,
+                  graph_type='residue', outfile='1ATN_residue.hdf5',
+                  nproc=1, tmpdir='./tmpdir')

tests/test_nn.py

@@ -0,0 +1,30 @@
+import unittest
+
+from graphprot.NeuralNet import NeuralNet
+from graphprot.ginet import GINet
+from graphprot.foutnet import FoutNet
+
+
+__PLOT__ = False
+
+
+class TestNeuralNet(unittest.TestCase):
+
+    def setUp(self):
+        self.database = 'tests//hdf5/1ATN_residue.hdf5'
+
+    def test_neural_net(self):
+        NN = NeuralNet(self.database, GINet,
+                       node_feature=['type', 'polarity', 'bsa',
+                                     'depth', 'hse', 'ic', 'pssm'],
+                       edge_feature=['dist'],
+                       target='irmsd',
+                       index=None,
+                       task='reg',
+                       batch_size=64,
+                       percent=[0.8, 0.2])
+
+        NN.train(nepoch=25, validate=False)
+
+        if __PLOT__:
+            NN.plot_scatter()

tests/utils.py

@@ -0,0 +1,12 @@
+"""Module containing some utilities for testing."""
+
+from pathlib import Path
+import pkg_resources as pkg
+
+__all__ = ["PATH_GRAPHPROT", "PATH_TEST"]
+
+# Environment data
+PATH_GRAPHPROT = Path(pkg.resource_filename('graphprot', ''))
+ROOT = PATH_GRAPHPROT.parent
+
+PATH_TEST = ROOT / "tests"