refactor: move tests and fix pytest

.github/workflows/tests-on-pr.yml

@@ -36,8 +36,8 @@ jobs:
       - name: Install diffpy.srreal and requirements
         run: |
           conda install --file requirements/test.txt
-          conda install --file requirements/conda.txt
+          conda install boost numpy libdiffpy setuptools diffpy.structure periodictable gsl
           python -m pip install . --no-deps
 
       - name: Validate diffpy.pdfgui
-        run: python -m diffpy.srreal.tests.run
+        run: pytest tests

tests/conftest.py

@@ -0,0 +1,75 @@
+import json
+import logging
+from pathlib import Path
+
+import pytest
+
+from diffpy.srreal.structureconverters import convertObjCrystCrystal
+
+
+@pytest.fixture
+def user_filesystem(tmp_path):
+    base_dir = Path(tmp_path)
+    home_dir = base_dir / "home_dir"
+    home_dir.mkdir(parents=True, exist_ok=True)
+    cwd_dir = base_dir / "cwd_dir"
+    cwd_dir.mkdir(parents=True, exist_ok=True)
+
+    home_config_data = {"username": "home_username", "email": "[email protected]"}
+    with open(home_dir / "diffpyconfig.json", "w") as f:
+        json.dump(home_config_data, f)
+
+    yield tmp_path
+
+
+# Resolve availability of optional packages.
+
+# pyobjcryst
+
+
+@pytest.fixture(scope="session")
+def _msg_nopyobjcryst():
+    return "No module named 'pyobjcryst'"
+
+
+@pytest.fixture(scope="session")
+def has_pyobjcryst():
+    try:
+        import pyobjcryst.crystal
+
+        convertObjCrystCrystal(pyobjcryst.crystal.Crystal())
+        has_pyobjcryst = True
+    except ImportError:
+        has_pyobjcryst = False
+        logging.warning("Cannot import pyobjcryst, pyobjcryst tests skipped.")
+        print("Cannot import pyobjcryst, pyobjcryst tests skipped.")
+    except TypeError:
+        has_pyobjcryst = False
+        logging.warning("Compiled without ObjCryst, pyobjcryst tests skipped.")
+        print("Compiled without ObjCryst, pyobjcryst tests skipped.")
+
+    return has_pyobjcryst
+
+
+# periodictable
+
+
+@pytest.fixture(scope="session")
+def _msg_noperiodictable():
+    return "No module named 'periodictable'"
+
+
+@pytest.fixture(scope="session")
+def has_periodictable():
+    try:
+        import periodictable
+
+        has_periodictable = True
+
+        # silence the pyflakes syntax checker
+        del periodictable
+    except ImportError:
+        has_periodictable = False
+        logging.warning("Cannot import periodictable, periodictable tests skipped.")
+
+    return has_periodictable

src/diffpy/srreal/tests/testatomradiitable.py → tests/test_atomradiitable.py

@@ -6,14 +6,14 @@
 import pickle
 import unittest
 
+import pytest
+
 from diffpy.srreal.atomradiitable import AtomRadiiTable, ConstantRadiiTable, CovalentRadiiTable
-from diffpy.srreal.tests.testutils import _msg_noperiodictable, has_periodictable
 
 # ----------------------------------------------------------------------------
 
 
 class TestAtomRadiiTable(unittest.TestCase):
-
     def setUp(self):
         self.rtb = AtomRadiiTable()
         self.ctb = ConstantRadiiTable()
@@ -103,9 +103,13 @@ def test_toString(self):
 # ----------------------------------------------------------------------------
 
 
-@unittest.skipUnless(has_periodictable, _msg_noperiodictable)
 class TestCovalentRadiiTable(unittest.TestCase):
 
+    @pytest.fixture(autouse=True)
+    def _check_periodictable(self, has_periodictable, _msg_noperiodictable):
+        if not has_periodictable:
+            pytest.skip(_msg_noperiodictable)
+
     def setUp(self):
         self.rtb = CovalentRadiiTable()
         return

src/diffpy/srreal/tests/testbondcalculator.py → tests/test_bondcalculator.py

@@ -7,15 +7,10 @@
 import unittest
 
 import numpy
+import pytest
+from testutils import loadDiffPyStructure, loadObjCrystCrystal, pickle_with_attr
 
 from diffpy.srreal.bondcalculator import BondCalculator
-from diffpy.srreal.tests.testutils import (
-    _msg_nopyobjcryst,
-    has_pyobjcryst,
-    loadDiffPyStructure,
-    loadObjCrystCrystal,
-    pickle_with_attr,
-)
 
 # ----------------------------------------------------------------------------
 
@@ -81,7 +76,7 @@ def test_pickling(self):
 
     def test_pickling_derived_structure(self):
         """Check pickling of BondCalculator with DerivedStructureAdapter."""
-        from diffpy.srreal.tests.testutils import DerivedStructureAdapter
+        from testutils import DerivedStructureAdapter
 
         bdc = self.bdc
         stru0 = DerivedStructureAdapter()
@@ -249,9 +244,13 @@ def test_setTypeMask(self):
 # ----------------------------------------------------------------------------
 
 
-@unittest.skipUnless(has_pyobjcryst, _msg_nopyobjcryst)
 class TestBondCalculatorObjCryst(unittest.TestCase):
 
+    @pytest.fixture(autouse=True)
+    def _check_periodictable(self, has_pyobjcryst, _msg_nopyobjcryst):
+        if not has_pyobjcryst:
+            pytest.skip(_msg_nopyobjcryst)
+
     def setUp(self):
         self.bdc = BondCalculator()
         if not hasattr(self, "rutile"):

src/diffpy/srreal/tests/testbvscalculator.py → tests/test_bvscalculator.py

@@ -6,8 +6,9 @@
 import pickle
 import unittest
 
+from testutils import loadDiffPyStructure, pickle_with_attr
+
 from diffpy.srreal.bvscalculator import BVSCalculator
-from diffpy.srreal.tests.testutils import loadDiffPyStructure, pickle_with_attr
 
 
 ##############################################################################
@@ -139,7 +140,7 @@ def test_table_pickling(self):
 
     def test_pickling_derived_structure(self):
         """Check pickling of BVSCalculator with DerivedStructureAdapter."""
-        from diffpy.srreal.tests.testutils import DerivedStructureAdapter
+        from testutils import DerivedStructureAdapter
 
         bvc = self.bvc
         stru0 = DerivedStructureAdapter()

src/diffpy/srreal/tests/testdebyepdfcalculator.py → tests/test_debyepdfcalculator.py

@@ -7,10 +7,9 @@
 import unittest
 
 import numpy
+from testutils import _maxNormDiff, loadDiffPyStructure, pickle_with_attr
 
 from diffpy.srreal.pdfcalculator import DebyePDFCalculator, PDFCalculator
-from diffpy.srreal.tests.testpdfcalculator import _maxNormDiff
-from diffpy.srreal.tests.testutils import loadDiffPyStructure, pickle_with_attr
 
 
 ##############################################################################
@@ -189,7 +188,7 @@ def test_mask_pickling(self):
     def test_pickling_derived_structure(self):
         """Check pickling of DebyePDFCalculator with
         DerivedStructureAdapter."""
-        from diffpy.srreal.tests.testutils import DerivedStructureAdapter
+        from testutils import DerivedStructureAdapter
 
         dpdfc = self.dpdfc
         stru0 = DerivedStructureAdapter()