Switch from nose to pytest (#54)

* Use pytest everywhere

* Set pytest as test requirement

* Update outdated build-system information

* Update install docs

* Add pytest config file

* Run CI with pytest

* Switch to codecov

* Update docs section about CI

* Point to correct directory

* Drop plus from doctest flag

* Increase fetch-depth

* Increment version number

.github/workflows/ci.yml

@@ -15,6 +15,8 @@ jobs:
       fail-fast: false
     steps:
       - uses: actions/checkout@v2
+        with:
+          fetch-depth: 2
       - name: Cache conda packages
         uses: actions/cache@v1
         env:
@@ -43,24 +45,9 @@ jobs:
       - name: Run tests
         shell: bash -l {0}
         run: |
-            conda install -c conda-forge nose mock coverage coveralls
-            nosetests --with-coverage --with-doctest --doctest-options=+ELLIPSIS e3fp
-      - name: Upload to coveralls
-        shell: bash -l {0}
-        run: |
-          coveralls
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-          COVERALLS_REPO_TOKEN: hTn1CWmaoGxWHc3Kpnv3f1ctfGLL2S01K
-          COVERALLS_FLAG_NAME: Python ${{ matrix.python-version }} - ${{ matrix.os }})
-          COVERALLS_PARALLEL: true
-  finish:
-    name: Coveralls Finished
-    needs: test
-    runs-on: ubuntu-latest
-    steps:
-      - run: |
-          $CONDA/bin/conda install -c conda-forge coveralls
-          $CONDA/bin/coveralls --finish
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+            conda install -c conda-forge pytest pytest-cov mock
+            pytest --cov=e3fp --cov-report=xml e3fp/test
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v1
+        with:
+          fail_ci_if_error: false

README.rst

@@ -1,7 +1,7 @@
 E3FP: Extended 3-Dimensional FingerPrint
 ========================================
 
-|Docs Status| |CI Status| |Coveralls Status| |PyPi Version| |Conda Version| |License|
+|Docs Status| |CI Status| |Codecov Status| |PyPi Version| |Conda Version| |License|
 
 E3FP [1]_ is a 3D molecular fingerprinting method inspired by Extended
 Connectivity FingerPrints (ECFP) [2]_, integrating tightly with the RDKit_.
@@ -52,8 +52,8 @@ References
 .. |Docs Status| image:: http://readthedocs.org/projects/e3fp/badge/?version=latest
    :target: http://e3fp.readthedocs.io/en/latest/?badge=latest
    :alt: Documentation Status
-.. |Coveralls Status| image:: https://coveralls.io/repos/github/keiserlab/e3fp/badge.svg?branch=master
-   :target: https://coveralls.io/github/keiserlab/e3fp?branch=master
+.. |Codecov Status| image:: https://codecov.io/github/keiserlab/e3fp/coverage.svg?branch=master
+   :target: https://codecov.io/github/keiserlab/e3fp?branch=master
    :alt: Code Coverage
 .. |PyPi Version| image:: https://img.shields.io/pypi/v/e3fp.svg
    :target: https://pypi.python.org/pypi/e3fp

doc/source/dev/index.rst

@@ -117,10 +117,10 @@ produce a specific output. For examples, see the `fingeprinting tests
 Continuous Integration
 ~~~~~~~~~~~~~~~~~~~~~~
 
-E3FP uses `Travis CI`_ for continuous integration. This ensures that each commit
+E3FP uses `GitHub Actions`_ for continuous integration. This ensures that each commit
 and pull request passes all tests on a variety of a systems and for all
-supported versions of Python. Additionally, Travis CI updates code coverage on
-Coveralls_ and tests all usage examples in the documentation using `doctest`.
+supported versions of Python. Additionally, GitHub Actions updates code coverage on
+Codecov_ and tests all usage examples in the documentation using `doctest`.
 
 Documentation
 -------------
@@ -169,7 +169,7 @@ Releasing Code
 .. _Sphinx: http://www.sphinx-doc.org/en/stable/index.html
 .. _doctest: https://docs.python.org/3/library/doctest.html
 .. _pull request: https://help.github.com/articles/creating-a-pull-request/
-.. _Travis CI: https://travis-ci.org/keiserlab/e3fp
-.. _Coveralls: https://coveralls.io/github/keiserlab/e3fp
+.. _GitHub Actions: https://github.com/keiserlab/e3fp/actions
+.. _Codecov: https://codecov.io/github/keiserlab/e3fp
 
 .. include:: ../substitutions.rst

doc/source/install.rst

@@ -116,12 +116,12 @@ Option 3: Clone the Repository
 Testing
 -------
 
-After installation, it is recommended to run all tests with ``nose``.
-After running :code:`pip install nose` or :code:`conda install -c conda-forge nose`, run
+After installation, it is recommended to run all tests with ``pytest``.
+After running :code:`pip install pytest` or :code:`conda install -c conda-forge pytest`, run
 
 .. code:: bash
 
-    $ nosetests e3fp
+    $ pytest e3fp
 
 
 .. include:: substitutions.rst

e3fp/__init__.py

@@ -1,5 +1,5 @@
 from .util import E3FPWarning, E3FPDeprecationWarning
 
-version_info = (1, 2, 2)
+version_info = (1, 2, 3)
 version = ".".join(str(c) for c in version_info)
 __version__ = version

e3fp/test/test_config.py

@@ -4,15 +4,10 @@
 E-mail: [email protected]
 """
 import os
-import unittest
 
 
-class ConfigTestCases(unittest.TestCase):
+class TestConfig:
     def test_config_file_exists(self):
         from e3fp.config.params import DEF_PARAM_FILE
 
-        self.assertTrue(os.path.isfile(DEF_PARAM_FILE))
-
-
-if __name__ == "__main__":
-    unittest.main()
+        assert os.path.isfile(DEF_PARAM_FILE)

e3fp/test/test_conformer.py

@@ -3,10 +3,9 @@
 Author: Seth Axen
 E-mail: [email protected]
 """
-import unittest
 
 
-class ConformerTestCases(unittest.TestCase):
+class TestConformer:
     def test_standardisation(self):
         import rdkit.Chem
         from e3fp.conformer.util import (
@@ -16,10 +15,10 @@ def test_standardisation(self):
 
         smiles = "C[N-]c1cccc[n+]1C"
         mol = mol_from_smiles(smiles, "tmp")
-        self.assertEqual(rdkit.Chem.MolToSmiles(mol), smiles)
+        assert rdkit.Chem.MolToSmiles(mol) == smiles
 
         mol = mol_to_standardised_mol(mol)
-        self.assertEqual(rdkit.Chem.MolToSmiles(mol), "CN=c1ccccn1C")
+        assert rdkit.Chem.MolToSmiles(mol) == "CN=c1ccccn1C"
 
     def test_default_is_unseeded(self):
         import rdkit.Chem
@@ -46,7 +45,7 @@ def test_default_is_unseeded(self):
                 if rms > 1e-2:
                     fail = False
                     break
-        self.assertFalse(fail)
+        assert not fail
 
     def test_seed_produces_same_conformers(self):
         import rdkit.Chem
@@ -73,8 +72,4 @@ def test_seed_produces_same_conformers(self):
                 if rms > 1e-2:
                     fail = True
                     break
-        self.assertFalse(fail)
-
-
-if __name__ == "__main__":
-    unittest.main()
+        assert not fail

e3fp/test/test_dependencies.py

@@ -3,10 +3,9 @@
 Author: Seth Axen
 E-mail: [email protected]
 """
-import unittest
 
 
-class RequiredDependenciesTestCase(unittest.TestCase):
+class TestRequiredDependencies:
     def test_rdkit(self):
         import rdkit
 
@@ -23,15 +22,15 @@ def test_python_utilities(self):
         import python_utilities
 
 
-class OptionalFeatureDependenciesTestCase(unittest.TestCase):
+class TestOptionalFeatureDependencies:
     def test_h5py(self):
         import h5py
 
     def test_standardiser(self):
         import standardiser
 
 
-class OptionalParallelDependenciesTestCase(unittest.TestCase):
+class TestOptionalParallelDependencies:
     def test_mpi4py(self):
         import mpi4py
 
@@ -40,7 +39,3 @@ def test_concurrent(self):
 
     def test_python_utilities(self):
         import python_utilities.parallel
-
-
-if __name__ == "__main__":
-    unittest.main()

e3fp/test/test_fingerprint.py

@@ -3,10 +3,9 @@
 Author: Seth Axen
 E-mail: [email protected]
 """
-import unittest
+import pytest
 
-
-class FingerprintIOTestCases(unittest.TestCase):
+class TestFingerprintIO:
     def test_fprint_from_indices(self):
         from e3fp.fingerprint.fprint import (
             Fingerprint,
@@ -18,7 +17,7 @@ def test_fprint_from_indices(self):
             in_indices = [3, 1, 4, 5]
             bits = 32
             fprint = fp_type.from_indices(in_indices, bits=bits)
-            self.assertEqual(sorted(in_indices), sorted(fprint.indices))
+            assert sorted(in_indices) == sorted(fprint.indices)
 
     def test_fprint_from_fprint(self):
         from e3fp.fingerprint.fprint import (
@@ -32,7 +31,7 @@ def test_fprint_from_fprint(self):
             bits = 32
             fprint1 = fp_type.from_indices(in_indices, bits=bits)
             fprint2 = fp_type.from_fingerprint(fprint1)
-            self.assertEqual(fprint1, fprint2)
+            assert fprint1 == fprint2
 
     def test_countfprint_from_counts(self):
         from e3fp.fingerprint.fprint import CountFingerprint
@@ -41,7 +40,7 @@ def test_countfprint_from_counts(self):
         bits = 32
         fprint = CountFingerprint.from_counts(in_counts, bits=bits)
         out_counts = fprint.counts
-        self.assertEqual(in_counts, out_counts)
+        assert in_counts == out_counts
 
     def test_floatfprint_from_counts(self):
         from e3fp.fingerprint.fprint import FloatFingerprint
@@ -50,7 +49,7 @@ def test_floatfprint_from_counts(self):
         bits = 32
         fprint = FloatFingerprint.from_counts(in_counts, bits=bits)
         out_counts = fprint.counts
-        self.assertEqual(in_counts, out_counts)
+        assert in_counts == out_counts
 
     def test_unique_indices(self):
         from e3fp.fingerprint.fprint import (
@@ -63,7 +62,7 @@ def test_unique_indices(self):
             in_indices = [3, 1, 4, 5, 1, 5, 9]
             bits = 32
             fprint = fp_type.from_indices(in_indices, bits=bits)
-            self.assertEqual(sorted(set(in_indices)), sorted(fprint.indices))
+            assert sorted(set(in_indices)) == sorted(fprint.indices)
 
     def test_bitstring_io(self):
         from e3fp.fingerprint.fprint import (
@@ -76,7 +75,7 @@ def test_bitstring_io(self):
             in_bitstring = "1001001111011000"
             fprint = fp_type.from_bitstring(in_bitstring)
             out_bitstring = fprint.to_bitstring()
-            self.assertEqual(in_bitstring, out_bitstring)
+            assert in_bitstring == out_bitstring
 
     def test_vector_io(self):
         from e3fp.fingerprint.fprint import (
@@ -106,7 +105,7 @@ def test_rdkit_io(self):
             rdkit_fprint1 = fprint1.to_rdkit()
             fprint2 = fp_type.from_rdkit(rdkit_fprint1)
             rdkit_fprint2 = fprint2.to_rdkit()
-            self.assertEqual(rdkit_fprint1, rdkit_fprint2)
+            assert rdkit_fprint1 == rdkit_fprint2
 
     def test_basic_properties(self):
         from e3fp.fingerprint.fprint import (
@@ -123,21 +122,15 @@ def test_basic_properties(self):
             level = int(np.random.randint(0, 10))
             for fp_type in (Fingerprint, CountFingerprint, FloatFingerprint):
                 fp = fp_type.from_indices(indices, bits=bits, level=level)
-                self.assertEqual(fp.bits, bits)
-                self.assertEqual(len(fp), bits)
-                self.assertEqual(fp.bit_count, unique_inds.size)
-                self.assertAlmostEqual(
-                    fp.density, float(unique_inds.size) / bits
-                )
+                assert fp.bits == bits
+                assert len(fp) == bits
+                assert fp.bit_count == unique_inds.size
+                assert fp.density == pytest.approx(float(unique_inds.size) / bits)
 
 
-class FingerprintAlgebraTestCases(unittest.TestCase):
+class TestFingerprintAlgebra:
     pass
 
 
-class FingerprintComparisonTestCases(unittest.TestCase):
+class TestFingerprintComparison:
     pass
-
-
-if __name__ == "__main__":
-    unittest.main()