digichem-core 6.10.1__py3-none-any.whl → 6.10.3__py3-none-any.whl

digichem/test/test_image.py

@@ -8,8 +8,10 @@ from digichem.image.orbitals import Orbital_diagram_maker
 from digichem.image.spectroscopy import Absorption_graph_maker, Emission_graph_maker, \
     Frequency_graph_maker, NMR_graph_maker, NMR_graph_zoom_maker
 from digichem.image.structure import Skeletal_image_maker
-from digichem.image.vmd import Structure_image_maker, Orbital_image_maker, Density_image_maker, \
-    Combined_orbital_image_maker, Permanent_dipole_image_maker, Transition_dipole_image_maker
+import digichem.image.vmd
+import digichem.image.render
+
+
 from digichem.parse.util import open_for_parsing, parse_calculation
 
 from digichem.test.util import digichem_options, data_directory
@@ -17,7 +19,9 @@ from digichem.test.test_result import gaussian_ES_result, turbomole_ES_result, o
     gaussian_opt_result, turbomole_opt_result, orca_opt_result, orca_opt_freq_result, \
     orca_nmr_result
 
-HAS_VMD = shutil.which("vmd")
+HAS_VMD = shutil.which(digichem.config.get_config()['render']['vmd']['executable'])
+HAS_BLENDER = shutil.which(digichem.config.get_config()['render']['batoms']['blender'])
+
 
 @pytest.mark.parametrize("result_set", [
     pytest.lazy_fixture("gaussian_ES_result"),
@@ -176,14 +180,14 @@ def test_2d_diagram(result_set, tmp_path, digichem_options):
     assert Path(tmp_path, "tmp.png").exists()
 
 
-@pytest.mark.skipif(not HAS_VMD,
-                    reason="No VMD available")
 @pytest.mark.parametrize("cube_file", [
     Path(data_directory(), "Cubes/Pyridine.HOMO.cube")
 ], ids = ["Gaussian"])
 @pytest.mark.parametrize("maker_cls", [
-    Structure_image_maker,
-    Orbital_image_maker,
+    pytest.param(digichem.image.vmd.Structure_image_maker, marks = pytest.mark.skipif(not HAS_VMD, reason = "VMD is not available")),
+    pytest.param(digichem.image.vmd.Orbital_image_maker, marks = pytest.mark.skipif(not HAS_VMD, reason = "VMD is not available")),
+    pytest.param(digichem.image.render.Structure_image_maker, marks = pytest.mark.skipif(not HAS_BLENDER, reason = "Blender is not available")),
+    pytest.param(digichem.image.render.Orbital_image_maker, marks = pytest.mark.skipif(not HAS_BLENDER, reason = "Blender is not available")),
 ])
 def test_3d_image(cube_file, maker_cls, tmp_path, digichem_options):
     """Can we make a 3D structure image?"""
@@ -197,21 +201,17 @@ def test_3d_image(cube_file, maker_cls, tmp_path, digichem_options):
     assert Path(tmp_path, "tmp.x0y0z0.png").exists()
 
 
-# @pytest.mark.parametrize("result_path", [
-#     Path(data_directory(), "Pyridine/Gaussian 16 Optimisation Frequencies PBE1PBE (GD3BJ) Toluene 6-31G(d,p).tar.gz")
-# ], ids = ["Gaussian"])
-# @pytest.mark.parametrize("density", [
-#     "SCF"
-# ])
-
-@pytest.mark.skipif(not HAS_VMD,
-                    reason="No VMD available")
 @pytest.mark.parametrize("cube_file", [
     Path(data_directory(), "Cubes/Pyridine.SCF.cube")
 ], ids = ["Gaussian"])
-def test_density_image(cube_file, tmp_path, digichem_options):
+@pytest.mark.parametrize("maker_cls", [
+    pytest.param(digichem.image.vmd.Density_image_maker, marks = pytest.mark.skipif(not HAS_VMD, reason = "VMD is not available")),
+    pytest.param(digichem.image.render.Density_image_maker, marks = pytest.mark.skipif(not HAS_BLENDER, reason = "Blender is not available")),
+], ids = ["vmd", "batoms"])
+def test_density_image(cube_file, maker_cls, tmp_path, digichem_options):
     """Can we make a 3D structure image?"""
-    maker = Density_image_maker.from_options(
+
+    maker = maker_cls.from_options(
         tmp_path / "tmp.png",
         cube_file = cube_file,
         options = digichem_options
@@ -221,14 +221,16 @@ def test_density_image(cube_file, tmp_path, digichem_options):
     assert Path(tmp_path, "tmp.x0y0z0.png").exists()
 
 
-@pytest.mark.skipif(not HAS_VMD,
-                    reason="No VMD available")
 @pytest.mark.parametrize("cube_file", [
     Path(data_directory(), "Cubes/Benzene.anion.spin.cube")
 ], ids = ["Gaussian"])
-def test_spin_density_image(cube_file, tmp_path, digichem_options):
+@pytest.mark.parametrize("maker_cls", [
+    pytest.param(digichem.image.vmd.Spin_density_image_maker, marks = pytest.mark.skipif(not HAS_VMD, reason = "VMD is not available")),
+    pytest.param(digichem.image.render.Spin_density_image_maker, marks = pytest.mark.skipif(not HAS_BLENDER, reason = "Blender is not available")),
+], ids = ["vmd", "batoms"])
+def test_spin_density_image(cube_file, maker_cls, tmp_path, digichem_options):
     """Can we make a 3D structure image?"""
-    maker = Density_image_maker.from_options(
+    maker = maker_cls.from_options(
         tmp_path / "tmp.png",
         cube_file = cube_file,
         options = digichem_options
@@ -238,14 +240,16 @@ def test_spin_density_image(cube_file, tmp_path, digichem_options):
     assert Path(tmp_path, "tmp.x0y0z0.png").exists()
 
 
-@pytest.mark.skipif(not HAS_VMD,
-                    reason="No VMD available")
 @pytest.mark.parametrize("homo_cube, lumo_cube", [
     [Path(data_directory(), "Cubes/Pyridine.HOMO.cube"), Path(data_directory(), "Cubes/Pyridine.LUMO.cube")]
 ], ids = ["Gaussian"])
-def test_combined_orbital_image(homo_cube, lumo_cube, tmp_path, digichem_options):
+@pytest.mark.parametrize("maker_cls", [
+    pytest.param(digichem.image.vmd.Combined_orbital_image_maker, marks = pytest.mark.skipif(not HAS_VMD, reason = "VMD is not available")),
+    pytest.param(digichem.image.render.Combined_orbital_image_maker, marks = pytest.mark.skipif(not HAS_BLENDER, reason = "Blender is not available")),
+], ids = ["vmd", "batoms"])
+def test_combined_orbital_image(homo_cube, maker_cls, lumo_cube, tmp_path, digichem_options):
     """Can we make a 3D structure image?"""
-    maker = Combined_orbital_image_maker.from_options(
+    maker = maker_cls.from_options(
         tmp_path / "tmp.png",
         HOMO_cube_file = homo_cube,
         LUMO_cube_file = lumo_cube,
@@ -256,14 +260,16 @@ def test_combined_orbital_image(homo_cube, lumo_cube, tmp_path, digichem_options
     assert Path(tmp_path, "tmp.x0y0z0.png").exists()
 
 
-@pytest.mark.skipif(not HAS_VMD,
-                    reason="No VMD available")
 @pytest.mark.parametrize("cube_file", [
     Path(data_directory(), "Cubes/Benzene.anion.AHOMO.cube")
 ], ids = ["Gaussian"])
-def test_unrestricted_orbital_image(cube_file, tmp_path, digichem_options):
+@pytest.mark.parametrize("maker_cls", [
+    pytest.param(digichem.image.vmd.Alpha_orbital_image_maker, marks = pytest.mark.skipif(not HAS_VMD, reason = "VMD is not available")),
+    pytest.param(digichem.image.render.Alpha_orbital_image_maker, marks = pytest.mark.skipif(not HAS_BLENDER, reason = "Blender is not available")),
+], ids = ["vmd", "batoms"])
+def test_unrestricted_orbital_image(cube_file, maker_cls, tmp_path, digichem_options):
     """Can we make a 3D structure image?"""
-    maker = Orbital_image_maker.from_options(
+    maker = maker_cls.from_options(
         tmp_path / "tmp.png",
         cube_file = cube_file,
         options = digichem_options
@@ -273,19 +279,21 @@ def test_unrestricted_orbital_image(cube_file, tmp_path, digichem_options):
     assert Path(tmp_path, "tmp.x0y0z0.png").exists()
 
 
-@pytest.mark.skipif(not HAS_VMD,
-                    reason="No VMD available")
 @pytest.mark.parametrize("result_path, cube_file", [
     [  
         Path(data_directory(), "Pyridine/Gaussian 16 Optimisation Frequencies PBE1PBE (GD3BJ) Toluene 6-31G(d,p).tar.gz"),
         Path(data_directory(), "Cubes/Pyridine.HOMO.cube"),
     ]
 ])
-def test_pdm_image(result_path, cube_file, tmp_path, digichem_options):
+@pytest.mark.parametrize("maker_cls", [
+    pytest.param(digichem.image.vmd.Permanent_dipole_image_maker, marks = pytest.mark.skipif(not HAS_VMD, reason = "VMD is not available")),
+    pytest.param(digichem.image.render.Permanent_dipole_image_maker, marks = pytest.mark.skipif(not HAS_BLENDER, reason = "Blender is not available")),
+], ids = ["vmd", "batoms"])
+def test_pdm_image(result_path, cube_file, maker_cls, tmp_path, digichem_options):
     """Can we make a 3D structure image?"""
     with open_for_parsing(result_path) as open_files:
         result_set = parse_calculation(*open_files, options = digichem_options)
-        maker = Permanent_dipole_image_maker.from_options(
+        maker = maker_cls.from_options(
             tmp_path / "tmp.png",
             cube_file = cube_file,
             dipole_moment = result_set.dipole_moment,
@@ -296,19 +304,21 @@ def test_pdm_image(result_path, cube_file, tmp_path, digichem_options):
         assert Path(tmp_path, "tmp.x0y0z0.png").exists()
 
 
-@pytest.mark.skipif(not HAS_VMD,
-                    reason="No VMD available")
 @pytest.mark.parametrize("result_path, cube_file", [
     [
         Path(data_directory(), "Pyridine/Gaussian 16 Excited States TDA Optimised S(1) PBE1PBE (GD3BJ) Toluene 6-31G(d,p).tar.gz"),
         Path(data_directory(), "Cubes/Pyridine.HOMO.cube"),
     ]
 ])
-def test_tdm_image(result_path, cube_file, tmp_path, digichem_options):
+@pytest.mark.parametrize("maker_cls", [
+    pytest.param(digichem.image.vmd.Transition_dipole_image_maker, marks = pytest.mark.skipif(not HAS_VMD, reason = "VMD is not available")),
+    pytest.param(digichem.image.render.Transition_dipole_image_maker, marks = pytest.mark.skipif(not HAS_BLENDER, reason = "Blender is not available")),
+], ids = ["vmd", "batoms"])
+def test_tdm_image(result_path, cube_file, maker_cls, tmp_path, digichem_options):
     """Can we make a 3D structure image?"""
     with open_for_parsing(result_path) as open_files:
         result_set = parse_calculation(*open_files, options = digichem_options)
-        maker = Transition_dipole_image_maker.from_options(
+        maker = maker_cls.from_options(
             tmp_path / "tmp.png",
             cube_file = cube_file,
             dipole_moment = result_set.excited_states.find("S(1)").transition_dipole_moment.electric,
@@ -320,14 +330,16 @@ def test_tdm_image(result_path, cube_file, tmp_path, digichem_options):
         assert Path(tmp_path, "tmp.x0y0z0.png").exists()
 
 
-@pytest.mark.skipif(not HAS_VMD,
-                    reason="No VMD available")
 @pytest.mark.parametrize("cube_file", [
     Path(data_directory(), "Cubes/Pyridine.HOMO.cube"),
 ])
-def test_nto_image(cube_file, tmp_path, digichem_options):
+@pytest.mark.parametrize("maker_cls", [
+    pytest.param(digichem.image.vmd.Orbital_image_maker, marks = pytest.mark.skipif(not HAS_VMD, reason = "VMD is not available")),
+    pytest.param(digichem.image.render.Orbital_image_maker, marks = pytest.mark.skipif(not HAS_BLENDER, reason = "Blender is not available")),
+], ids = ["vmd", "batoms"])
+def test_nto_image(cube_file, maker_cls, tmp_path, digichem_options):
     """Can we make a 3D structure image?"""
-    maker = Orbital_image_maker.from_options(
+    maker = maker_cls.from_options(
         tmp_path / "tmp.png",
         cube_file = cube_file,
         options = digichem_options

digichem/test/util.py

@@ -65,6 +65,8 @@ def digichem_options(tmpdir_factory):
         ),
     ]
     config.logging['render_logging'] = True
+    # Set blender quality as low as feasible to shorten test time.
+    config.render['batoms']['render_samples'] = 1
     config.validate()
     return config
 

{digichem_core-6.10.1.dist-info → digichem_core-6.10.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: digichem-core
-Version: 6.10.1
+Version: 6.10.3
 Summary: Open-source library for Digichem core components
 Project-URL: Homepage, https://github.com/Digichem-Project/digichem-core
 Project-URL: Documentation, https://doc.digi-chem.co.uk

{digichem_core-6.10.1.dist-info → digichem_core-6.10.3.dist-info}/RECORD

@@ -1,4 +1,4 @@
-digichem/__init__.py,sha256=zVk9sd1_7i7oSr7Dg9Gw-ODrlnXXHYuzyGWjGDvB6Zw,2288
+digichem/__init__.py,sha256=luFQpfEPAH0YvnW2PNBB7mdfr8BOYNsDXzN8gSn5Yg4,2288
 digichem/basis.py,sha256=khzIS9A_w8QH2vsXctWr16Bw5TA84_9_Fo-vuveP_5w,4875
 digichem/datas.py,sha256=t2PuQFvPb55WO_qVF3Xz67XNodQDimqYD26VkRPEWLA,433
 digichem/log.py,sha256=tjl8Er16HUsAibBZGZMu8KyT0w53YM3u0Neh_l2jD9Q,6166
@@ -6,7 +6,7 @@ digichem/memory.py,sha256=_HJMwiElr0534lr3h17WwvXOi-DxCN-bAD1Ij8Lwg6U,5638
 digichem/translate.py,sha256=YKm7wko13A17zQJW8qOT52rzp9wDmR0GDzOepuzr75I,21326
 digichem/config/README,sha256=0y5sxYPAmpD3XNzgJrr-U8xmiQbheC8bz8lvnNmsNtc,180
 digichem/config/__init__.py,sha256=wXnmk1fuNZeHOKz06wBfTUkM8-XuW08F2H8QiHyS8Xs,227
-digichem/config/base.py,sha256=Wlve8CSKNYB1STVPAkfHREDRUd0Xog8HmzYX1q6dMC8,25005
+digichem/config/base.py,sha256=6K0iQYhxwQEcMdZX_lqxTJ1rrrGLRHU-uugj5D878Jw,25005
 digichem/config/locations.py,sha256=Jlvql0KJrJEIO_2U6BRS5bjHelKjGGIETR9hOuNe0K0,584
 digichem/config/parse.py,sha256=amJx89JXkkEyMMSYr5GvLFnLZO3hWahuZtNlx0F0PhA,2667
 digichem/config/util.py,sha256=i5NgxLPcLx1RM4bArog77hsHxkQmwlqyzJbDtrozBG0,4613
@@ -44,7 +44,7 @@ digichem/image/base.py,sha256=6LGIYK2zB7lQxFhV5t2ZJPcpNMOqRv-JzrBJEeTF9Wg,5193
 digichem/image/excited_states.py,sha256=1YUa8KYXTvh_Vwl2DSaRwpIh15FtW18KpjLlnD8VTOk,14103
 digichem/image/graph.py,sha256=3wcembS3gcI5Ejq1lv4Sw1g_7s-fubDpiho_85kzkks,10880
 digichem/image/orbitals.py,sha256=UcPnOm3tQOdTegsVm_a7AizVe7OpBCz_4sve6u7jAvA,9705
-digichem/image/render.py,sha256=jeZDZoaOtvFfTjeEJA_prrXZqCFr72V6H4DD5kUBrUU,30409
+digichem/image/render.py,sha256=fQu9QcuIolzoeMoaQPQo27Z-JEXUCQCWiSVWQgv2iG4,30470
 digichem/image/spectroscopy.py,sha256=wwguBYBwL8VNTJK5rBZbUiwaFHFLIaqBWYR3qbwDpAs,33567
 digichem/image/structure.py,sha256=gxgX5cXA3BaqBh5K7UPcVGWX-yG5kc6Robf5sWT1IYM,4900
 digichem/image/vmd.py,sha256=GGE35qypgBbpadHo1M929czuxM0U4NRICPkltKWEojE,39305
@@ -55,17 +55,17 @@ digichem/input/gaussian.py,sha256=ZwfCA0jgHcY8JVcyyKmnchU-OyQ26-8ynQJdeYtNT7A,56
 digichem/misc/__init__.py,sha256=gRlflbkXYyKvqeQ2KTnNAdJ00S6Vhmk-tzSVCBSiWgk,162
 digichem/misc/argparse.py,sha256=AG33L7MCi-ftb4XnvndQb4hKcorzJxESAVB0HIZRlcw,1371
 digichem/misc/base.py,sha256=ZaeeLJrRZnF66bhkGdPvhsVGgxzcV_pneESQ1ReDedc,1884
-digichem/misc/io.py,sha256=9ZX4GminIBQnl6ZlOyrBe5U2o0NdmGzlfYtN3k7X0mw,10732
+digichem/misc/io.py,sha256=7Oqi7UQLwhCsVHdEN0n7Vubsbzk14fLSkAYXe4obPbQ,11007
 digichem/misc/layered_dict.py,sha256=Psf30UmHVHAE95RnFYiR2f7oaW05CsUhT4FtXhUtQcw,15561
 digichem/misc/text.py,sha256=FVcxf8ctt3D2yGFYgrZk3dpO48f_0aDhHiry_xGirD8,3673
 digichem/misc/time.py,sha256=Z7FWpkb8gqBHVMXdhFiBWn2VwmXuU9uaMxEKsfAH5Kw,2214
 digichem/parse/__init__.py,sha256=SIAj7do6mXRNuOEkN691Nh-je2YlZ3qL6fxnjsTE6QY,867
 digichem/parse/base.py,sha256=RZOuGCmXk3CyVdK6-lev-DyYWe215JYRVA-SiiXS72E,8757
-digichem/parse/cclib.py,sha256=QngzWGlOtfxa4JoqhSAUdK91AJUR5v-BqxDflCBFVwA,8370
+digichem/parse/cclib.py,sha256=4j1RCMvEb31Lh9DncYgCbcs-u9gFq_z7RkfYLv9EW4w,9897
 digichem/parse/dump.py,sha256=wd1hW7xjjXNPmmf2t3DgtU8FkcTAqYkKbJYVt2NjPIQ,9567
 digichem/parse/gaussian.py,sha256=8Vs07MnlboZiJDJ41dtfRwE2UBHOiVixY3-mQrcoioc,5251
 digichem/parse/orca.py,sha256=QahMQh-rZphDzyM8Kn6xEbEB9imCWpKUhUmlOxpDio0,4680
-digichem/parse/pyscf.py,sha256=LsxqdDIC9KvPmbXHuKAB7t0Lg80qtWPVnfnNoc3INh0,760
+digichem/parse/pyscf.py,sha256=Io13LOxnkSZ1lKFu1tSFzkDZKmFRqDyOVMBesiQIb7o,1197
 digichem/parse/turbomole.py,sha256=WJIjayh0LnuYlJUjDrCkzGcGW1IGUbRgWuKfcVN5LeQ,9249
 digichem/parse/util.py,sha256=z_BS6z0KcecKfv6SBuYKpoCBuVwtsK5EkqGbfJn9fxk,28935
 digichem/result/__init__.py,sha256=FUNL2pc2bP3XNVFRrlyrTppVWEsPRHcThLiVytpsH84,222
@@ -77,7 +77,7 @@ digichem/result/emission.py,sha256=0OPXNR1ZX9ALpjD0Ie5OkrOHNDDz6FsK3pK_0GyqqLI,1
 digichem/result/energy.py,sha256=53Dm2kHA-x8KtDY3Wq52cPbpE5E01W1lQTNaLe0goZE,10851
 digichem/result/excited_state.py,sha256=N41Dm6r4C_C08jmcqiXZZdRoHGE2u9CfjTLNzLo8TAQ,34254
 digichem/result/ground_state.py,sha256=JMRBQ-MC2Ak8Ur-TXGzNkJtSVykkhswHPTOnttZFujE,3790
-digichem/result/metadata.py,sha256=sG1iRRnSsVsCc4eKEqDqiU3gr8QulnU531YN-1dWs6g,37167
+digichem/result/metadata.py,sha256=iHyJ0HGtdM-BodVTtE-Iy3_cOk5sYX5j0VufkWSmunA,39225
 digichem/result/multi.py,sha256=IzupKHMcXTf6AReeUCjY9Szy2b4TdOHVtC2Tlb9xg0o,4330
 digichem/result/nmr.py,sha256=u3qXZRrTBvUnfJexrtEHZLIyQ4dq_zFDXwcC2PoEGqQ,47263
 digichem/result/orbital.py,sha256=6BX4GfnLJRj_AZs75FWPLFX6r0z9OL0OSh1v8EOHqws,28271
@@ -92,23 +92,25 @@ digichem/result/alignment/FAP.py,sha256=so_eTIqdFIBVHinG_17tc4n-CS4A622r4RXndVkO
 digichem/result/alignment/__init__.py,sha256=9OLZUCENNfsPb-_BWpRKY1y0YwPTE-Lh2Au30RrExoU,88
 digichem/result/alignment/base.py,sha256=KY_uQxP5NYgU7hOW028FR63xqskf2I4-wnFC_YAVYJM,11811
 digichem/test/__init__.py,sha256=5rcWC-jYpwJf9DZD3RUzsrZtQXGre0oFnaE3xKiZYlY,116
-digichem/test/conftest.py,sha256=5_KcDWY_ZaSYgib-xlA4mvefTqjbAveipcm6ePtwQcw,124
+digichem/test/conftest.py,sha256=hy9geS4NwXOTrHGO-HnDP3hp_eoPGIToODBXBF3Kcuw,282
 digichem/test/test_basis.py,sha256=is1GdrWhmWJdA18fw1lagmbg8VGlX6_-LKOhjTcjHaQ,1720
 digichem/test/test_calculate.py,sha256=Zvon7TlmVLwIvtaXXMmWJrkvljJ9zWZge6zIyjbx_N0,1486
 digichem/test/test_config.py,sha256=JZGOpSAGQ70n4gGW4sCPCLycygtECOKejB9742nmnj0,2323
 digichem/test/test_cube.py,sha256=y1Cr0cz00pwSWT-z-PgUQAzp41Ttsk_Ti_eQXagzO1Q,14110
 digichem/test/test_exception.py,sha256=f-8XVQqq9gfJFpURjOoEfcC4pxieye8ZxvmguoN9QyY,530
 digichem/test/test_file.py,sha256=n2BJ55_AjNY7IGEjHjJJ-OhE4Lgn3pGyyyfnPIduges,3682
-digichem/test/test_image.py,sha256=x7ybEIeZg0E8ZQdkSzdy1cNWymYie6gWoTR8Q3ebcEQ,11516
+digichem/test/test_image.py,sha256=bGb6xdn4k2VxZlVef0HI2HPrQdxx5XUTMyl97iYzzT8,13598
 digichem/test/test_input.py,sha256=TLGFxsSYGKTUSO5fxjZN2VqzDZFP3AHlbrE2JGmnq8g,1787
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