add limited python2 compatibility (#13)

codefresh.yml

@@ -11,4 +11,5 @@ steps:
     image: '${{build-torchani}}'
     commands:
       - flake8
-      - python setup.py test
+      - python setup.py test
\ No newline at end of file
+      - python2 setup.py test
\ No newline at end of file

tests/test_data.py

-import torchani
-import unittest
-import tempfile
-import os
-import torch
-import torchani.pyanitools as pyanitools
-import torchani.data
-from math import ceil
-from bisect import bisect
-from pickle import dump, load
-
-
-path = os.path.dirname(os.path.realpath(__file__))
-dataset_dir = os.path.join(path, 'dataset')
-
-
-class TestDataset(unittest.TestCase):
-
-    def setUp(self, data_path=dataset_dir):
-        self.data_path = data_path
-        self.ds = torchani.data.load_dataset(data_path)
-
-    def testLen(self):
-        # compute data length using Dataset
-        l1 = len(self.ds)
-        # compute data lenght using pyanitools
-        l2 = 0
-        for f in os.listdir(self.data_path):
-            f = os.path.join(self.data_path, f)
-            if os.path.isfile(f) and \
-               (f.endswith('.h5') or f.endswith('.hdf5')):
-                for j in pyanitools.anidataloader(f):
-                    l2 += j['energies'].shape[0]
-        # compute data length using iterator
-        l3 = len(list(self.ds))
-        # these lengths should match
-        self.assertEqual(l1, l2)
-        self.assertEqual(l1, l3)
-
-    def testNumChunks(self):
-        chunksize = 64
-        # compute number of chunks using batch sampler
-        bs = torchani.data.BatchSampler(self.ds, chunksize, 1)
-        l1 = len(bs)
-        # compute number of chunks using pyanitools
-        l2 = 0
-        for f in os.listdir(self.data_path):
-            f = os.path.join(self.data_path, f)
-            if os.path.isfile(f) and \
-               (f.endswith('.h5') or f.endswith('.hdf5')):
-                for j in pyanitools.anidataloader(f):
-                    conformations = j['energies'].shape[0]
-                    l2 += ceil(conformations / chunksize)
-        # compute number of chunks using iterator
-        l3 = len(list(bs))
-        # these lengths should match
-        self.assertEqual(l1, l2)
-        self.assertEqual(l1, l3)
-
-    def testNumBatches(self):
-        chunksize = 64
-        batch_chunks = 4
-        # compute number of batches using batch sampler
-        bs = torchani.data.BatchSampler(self.ds, chunksize, batch_chunks)
-        l1 = len(bs)
-        # compute number of batches by simple math
-        bs2 = torchani.data.BatchSampler(self.ds, chunksize, 1)
-        l2 = ceil(len(bs2) / batch_chunks)
-        # compute number of batches using iterator
-        l3 = len(list(bs))
-        # these lengths should match
-        self.assertEqual(l1, l2)
-        self.assertEqual(l1, l3)
-
-    def testBatchSize1(self):
-        bs = torchani.data.BatchSampler(self.ds, 1, 1)
-        self.assertEqual(len(bs), len(self.ds))
-
-    def testSplitSize(self):
-        chunksize = 64
-        bs = torchani.data.BatchSampler(self.ds, chunksize, 1)
-        chunks = len(bs)
-        ds1, ds2 = torchani.data.random_split(
-            self.ds, [200, chunks-200], chunksize)
-        bs1 = torchani.data.BatchSampler(ds1, chunksize, 1)
-        bs2 = torchani.data.BatchSampler(ds2, chunksize, 1)
-        self.assertEqual(len(bs1), 200)
-        self.assertEqual(len(bs2), chunks-200)
-
-    def testSplitNoOverlap(self):
-        chunksize = 64
-        bs = torchani.data.BatchSampler(self.ds, chunksize, 1)
-        chunks = len(bs)
-        ds1, ds2 = torchani.data.random_split(
-            self.ds, [200, chunks-200], chunksize)
-        indices1 = ds1.dataset.indices
-        indices2 = ds2.dataset.indices
-        self.assertEqual(len(indices1), len(ds1))
-        self.assertEqual(len(indices2), len(ds2))
-        self.assertEqual(len(indices1), len(set(indices1)))
-        self.assertEqual(len(indices2), len(set(indices2)))
-        self.assertEqual(len(self.ds), len(set(indices1+indices2)))
-
-    def _testMolSizes(self, ds):
-        for i in range(len(ds)):
-            left = bisect(ds.cumulative_sizes, i)
-            moli = ds[i][0].item()
-            for j in range(len(ds)):
-                left2 = bisect(ds.cumulative_sizes, j)
-                molj = ds[j][0].item()
-                if left == left2:
-                    self.assertEqual(moli, molj)
-                else:
-                    if moli == molj:
-                        print(i, j)
-                    self.assertNotEqual(moli, molj)
-
-    def testMolSizes(self):
-        chunksize = 8
-        bs = torchani.data.BatchSampler(self.ds, chunksize, 1)
-        chunks = len(bs)
-        ds1, ds2 = torchani.data.random_split(
-            self.ds, [50, chunks-50], chunksize)
-        self._testMolSizes(ds1)
-
-    def testSaveLoad(self):
-        chunksize = 8
-        bs = torchani.data.BatchSampler(self.ds, chunksize, 1)
-        chunks = len(bs)
-        ds1, ds2 = torchani.data.random_split(
-            self.ds, [50, chunks-50], chunksize)
-
-        tmpdir = tempfile.TemporaryDirectory()
-        tmpdirname = tmpdir.name
-        filename = os.path.join(tmpdirname, 'test.obj')
-
-        with open(filename, 'wb') as f:
-            dump(ds1, f)
-
-        with open(filename, 'rb') as f:
-            ds1_loaded = load(f)
-
-        self.assertEqual(len(ds1), len(ds1_loaded))
-        self.assertListEqual(ds1.sizes, ds1_loaded.sizes)
-        self.assertIsInstance(ds1_loaded, torchani.data.ANIDataset)
-
-        for i in range(len(ds1)):
-            i1 = ds1[i]
-            i2 = ds1_loaded[i]
-            molid1 = i1[0].item()
-            molid2 = i2[0].item()
-            self.assertEqual(molid1, molid2)
-            xyz1 = i1[1]
-            xyz2 = i2[1]
-            maxdiff = torch.max(torch.abs(xyz1-xyz2)).item()
-            self.assertEqual(maxdiff, 0)
-            e1 = i1[2].item()
-            e2 = i2[2].item()
-            self.assertEqual(e1, e2)
-
-
-if __name__ == '__main__':
-    unittest.main()
+import sys
+
+if sys.version_info.major >= 3:
+    import torchani
+    import unittest
+    import tempfile
+    import os
+    import torch
+    import torchani.pyanitools as pyanitools
+    import torchani.data
+    from math import ceil
+    from bisect import bisect
+    from pickle import dump, load
+
+    path = os.path.dirname(os.path.realpath(__file__))
+    dataset_dir = os.path.join(path, 'dataset')
+
+    class TestDataset(unittest.TestCase):
+
+        def setUp(self, data_path=dataset_dir):
+            self.data_path = data_path
+            self.ds = torchani.data.load_dataset(data_path)
+
+        def testLen(self):
+            # compute data length using Dataset
+            l1 = len(self.ds)
+            # compute data lenght using pyanitools
+            l2 = 0
+            for f in os.listdir(self.data_path):
+                f = os.path.join(self.data_path, f)
+                if os.path.isfile(f) and \
+                   (f.endswith('.h5') or f.endswith('.hdf5')):
+                    for j in pyanitools.anidataloader(f):
+                        l2 += j['energies'].shape[0]
+            # compute data length using iterator
+            l3 = len(list(self.ds))
+            # these lengths should match
+            self.assertEqual(l1, l2)
+            self.assertEqual(l1, l3)
+
+        def testNumChunks(self):
+            chunksize = 64
+            # compute number of chunks using batch sampler
+            bs = torchani.data.BatchSampler(self.ds, chunksize, 1)
+            l1 = len(bs)
+            # compute number of chunks using pyanitools
+            l2 = 0
+            for f in os.listdir(self.data_path):
+                f = os.path.join(self.data_path, f)
+                if os.path.isfile(f) and \
+                   (f.endswith('.h5') or f.endswith('.hdf5')):
+                    for j in pyanitools.anidataloader(f):
+                        conformations = j['energies'].shape[0]
+                        l2 += ceil(conformations / chunksize)
+            # compute number of chunks using iterator
+            l3 = len(list(bs))
+            # these lengths should match
+            self.assertEqual(l1, l2)
+            self.assertEqual(l1, l3)
+
+        def testNumBatches(self):
+            chunksize = 64
+            batch_chunks = 4
+            # compute number of batches using batch sampler
+            bs = torchani.data.BatchSampler(self.ds, chunksize, batch_chunks)
+            l1 = len(bs)
+            # compute number of batches by simple math
+            bs2 = torchani.data.BatchSampler(self.ds, chunksize, 1)
+            l2 = ceil(len(bs2) / batch_chunks)
+            # compute number of batches using iterator
+            l3 = len(list(bs))
+            # these lengths should match
+            self.assertEqual(l1, l2)
+            self.assertEqual(l1, l3)
+
+        def testBatchSize1(self):
+            bs = torchani.data.BatchSampler(self.ds, 1, 1)
+            self.assertEqual(len(bs), len(self.ds))
+
+        def testSplitSize(self):
+            chunksize = 64
+            bs = torchani.data.BatchSampler(self.ds, chunksize, 1)
+            chunks = len(bs)
+            ds1, ds2 = torchani.data.random_split(
+                self.ds, [200, chunks-200], chunksize)
+            bs1 = torchani.data.BatchSampler(ds1, chunksize, 1)
+            bs2 = torchani.data.BatchSampler(ds2, chunksize, 1)
+            self.assertEqual(len(bs1), 200)
+            self.assertEqual(len(bs2), chunks-200)
+
+        def testSplitNoOverlap(self):
+            chunksize = 64
+            bs = torchani.data.BatchSampler(self.ds, chunksize, 1)
+            chunks = len(bs)
+            ds1, ds2 = torchani.data.random_split(
+                self.ds, [200, chunks-200], chunksize)
+            indices1 = ds1.dataset.indices
+            indices2 = ds2.dataset.indices
+            self.assertEqual(len(indices1), len(ds1))
+            self.assertEqual(len(indices2), len(ds2))
+            self.assertEqual(len(indices1), len(set(indices1)))
+            self.assertEqual(len(indices2), len(set(indices2)))
+            self.assertEqual(len(self.ds), len(set(indices1+indices2)))
+
+        def _testMolSizes(self, ds):
+            for i in range(len(ds)):
+                left = bisect(ds.cumulative_sizes, i)
+                moli = ds[i][0].item()
+                for j in range(len(ds)):
+                    left2 = bisect(ds.cumulative_sizes, j)
+                    molj = ds[j][0].item()
+                    if left == left2:
+                        self.assertEqual(moli, molj)
+                    else:
+                        if moli == molj:
+                            print(i, j)
+                        self.assertNotEqual(moli, molj)
+
+        def testMolSizes(self):
+            chunksize = 8
+            bs = torchani.data.BatchSampler(self.ds, chunksize, 1)
+            chunks = len(bs)
+            ds1, ds2 = torchani.data.random_split(
+                self.ds, [50, chunks-50], chunksize)
+            self._testMolSizes(ds1)
+
+        def testSaveLoad(self):
+            chunksize = 8
+            bs = torchani.data.BatchSampler(self.ds, chunksize, 1)
+            chunks = len(bs)
+            ds1, ds2 = torchani.data.random_split(
+                self.ds, [50, chunks-50], chunksize)
+
+            tmpdir = tempfile.TemporaryDirectory()
+            tmpdirname = tmpdir.name
+            filename = os.path.join(tmpdirname, 'test.obj')
+
+            with open(filename, 'wb') as f:
+                dump(ds1, f)
+
+            with open(filename, 'rb') as f:
+                ds1_loaded = load(f)
+
+            self.assertEqual(len(ds1), len(ds1_loaded))
+            self.assertListEqual(ds1.sizes, ds1_loaded.sizes)
+            self.assertIsInstance(ds1_loaded, torchani.data.ANIDataset)
+
+            for i in range(len(ds1)):
+                i1 = ds1[i]
+                i2 = ds1_loaded[i]
+                molid1 = i1[0].item()
+                molid2 = i2[0].item()
+                self.assertEqual(molid1, molid2)
+                xyz1 = i1[1]
+                xyz2 = i2[1]
+                maxdiff = torch.max(torch.abs(xyz1-xyz2)).item()
+                self.assertEqual(maxdiff, 0)
+                e1 = i1[2].item()
+                e2 = i2[2].item()
+                self.assertEqual(e1, e2)
+
+    if __name__ == '__main__':
+        unittest.main()