digichem-core 6.10.1__py3-none-any.whl → 7.0.0__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/test_input.py

@@ -4,14 +4,14 @@ import pytest
 from pathlib import Path
 
 from digichem.test.util import pyridine_si_v2, pyridine_si_v1, pyridine_cml,\
-    result_files
+    result_files, ethane_xyz, benzene_cdx, cyclopentane_com
 from digichem.input.digichem_input import si_from_file
 
 @pytest.mark.parametrize("file_path", [
         pyridine_si_v2,
         pyridine_si_v1
      ])
-def test_input_reading(file_path):
+def test_si_reading(file_path):
     """
     Test whether we can correctly read from an existing si file.
     """
@@ -51,7 +51,7 @@ def test_si_writing(tmp_path):
         [result_files['turbomole'][0], "60a8ebd9e701b849cfccd9cbb41684519a7fdf0b"],
         [result_files['orca'][0], "e48e7f653f4e67c1bd4c5c4bb76405fad2d441d0"],
      ])
-def test_input_history(file_path, sha):
+def test_si_history(file_path, sha):
     """
     Test whether the history attribute is set properly.
     """
@@ -62,3 +62,17 @@ def test_input_history(file_path, sha):
     dump = si_file.dict
     
     assert dump['history'] == sha
+
+
+@pytest.mark.parametrize("file_path, format", [
+    (cyclopentane_com, "mol"),
+    (ethane_xyz, "cml"),
+    (benzene_cdx, "xyz"),
+    (result_files['gaussian'][0], "com")
+])
+def test_si_file_convert(file_path, format, tmp_path):
+    """
+    Test whether we can convert from arbitrary formats to another format.
+    """
+    si_file = si_from_file(file_path)
+    si_file.to_format(format, (tmp_path / "file").with_suffix("." + format))

digichem/test/test_parsing.py

@@ -144,3 +144,12 @@ def test_turbomole_archives(result_files, num_archives, digichem_options):
 
     finally:
         archive.cleanup()
+
+def test_profile_parsing(digichem_options):
+    """Can we parse profile data from profile.csv?"""
+    src = Path(data_directory(), 'Pyridine/Gaussian 16 Excited States TDA Optimised S(1) PBE1PBE (GD3BJ) Toluene 6-31G(d,p).tar.gz')
+
+    res = parse_calculation(src, options = digichem_options)
+
+    assert res.metadata.performance is not None
+

digichem/test/test_prattle.py

@@ -1,9 +1,9 @@
 """Tests for functioning of oprattle"""
+from pathlib import Path
 
 import pytest
 
 from digichem.file.prattle import Oprattle_formats, Openprattle_converter
-
 from digichem.test.util import ethane_xyz, benzene_cdx
 
 @pytest.mark.parametrize("readwrite", ["read", "write"])
@@ -14,14 +14,43 @@ def test_formats(readwrite):
     else:
         assert len(Oprattle_formats().write()) > 0
 
+
 @pytest.mark.parametrize("file_path", [
     ethane_xyz,
     benzene_cdx
 ])
-def test_convert(file_path):
+def test_from_path(file_path):
+    """
+    Can we convert a file found on the filesystem?
+    """
     Openprattle_converter(input_file_path = file_path).convert("com")
 
 
+@pytest.mark.parametrize("file_path, mode", [
+    (ethane_xyz, "r"),
+    (benzene_cdx, "rb")
+])
+def test_from_file(file_path, mode):
+    """
+    Can we convert from an open file?
+    """
+    with open(file_path, mode) as input_file:
+        Openprattle_converter(input_file = input_file, input_file_type = Path(file_path).suffix[1:]).convert("com")
+
+
+@pytest.mark.parametrize("file_path, mode", [
+    (ethane_xyz, "r"),
+    (benzene_cdx, "rb")
+])
+def test_from_buffer(file_path, mode):
+    """
+    Can we convert from an open file?
+    """
+    with open(file_path, mode) as input_file:
+        data = input_file.read()
+        Openprattle_converter(input_file_buffer = data, input_file_type = Path(file_path).suffix[1:]).convert("com")
+
+
 @pytest.mark.parametrize("file_path", [
     ethane_xyz,
     benzene_cdx

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-7.0.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: digichem-core
-Version: 6.10.1
+Version: 7.0.0
 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-7.0.0.dist-info}/RECORD

@@ -1,4 +1,4 @@
-digichem/__init__.py,sha256=zVk9sd1_7i7oSr7Dg9Gw-ODrlnXXHYuzyGWjGDvB6Zw,2288
+digichem/__init__.py,sha256=xXiF18dE2K2qQCknOTMhJtbqi2ZYNp6nGJtkWydiXvQ,2287
 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
@@ -6,10 +6,10 @@ 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=H1hHx8zh3J7PvfOpk9FAwDN_mvxPDNH_bb_1lbsmpuE,26017
 digichem/config/locations.py,sha256=Jlvql0KJrJEIO_2U6BRS5bjHelKjGGIETR9hOuNe0K0,584
 digichem/config/parse.py,sha256=amJx89JXkkEyMMSYr5GvLFnLZO3hWahuZtNlx0F0PhA,2667
-digichem/config/util.py,sha256=i5NgxLPcLx1RM4bArog77hsHxkQmwlqyzJbDtrozBG0,4613
+digichem/config/util.py,sha256=E-5He3AbrwHNHFbBdfNMOimaDPXqtAi96l-4Acmn08o,4611
 digichem/data/README,sha256=0e46Uh0FmsWRlzx-F18cbBQXy-Lo8iJfD6Hye0c9EIU,207
 digichem/data/functionals.csv,sha256=fIuNpFLT64B3PTqmNsj5IP6RSRw8PB5y_L9MpgoBo0w,281
 digichem/data/solvents.csv,sha256=O1-Sv3KCayPvnuD9lviDK-YIolome0JxoBfjD784Kqs,4640
@@ -37,78 +37,80 @@ digichem/file/__init__.py,sha256=vcDfoYlL0YbFcCyw-3D4SiGtA-hxkFKUtP30DO-JvqE,62
 digichem/file/base.py,sha256=D9vnQpzVq7459VhH7AwkhIqN2gYQprFC7WkgKZGT0Pc,18025
 digichem/file/cube.py,sha256=C9wKnWkCnE6phI3X9xsWQr8209YgjEXGWGf_Bj_p3BY,20256
 digichem/file/fchk.py,sha256=tWhp0daZPMlYmqkGkidUFwVHTA-8wCUf6Py6CNeT7tk,4035
-digichem/file/prattle.py,sha256=LDayqA7TZVMJKekyl4laHePOCesfBcQ36ul0516OEfo,9927
+digichem/file/prattle.py,sha256=T30754MjF56FFOrKseBRvxYnqILZ5-Emv9SNMZC1EBU,9947
 digichem/file/types.py,sha256=rLz88eFIv8uwK1jNEkQ9t9LTLTS38TbIhZ1rWC2SbvQ,3612
 digichem/image/__init__.py,sha256=T9fN41dV0oZ7dT_MES7iYaFdPgzZM5R5hhIvvhlY8U4,133
 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/spectroscopy.py,sha256=wwguBYBwL8VNTJK5rBZbUiwaFHFLIaqBWYR3qbwDpAs,33567
+digichem/image/render.py,sha256=fQu9QcuIolzoeMoaQPQo27Z-JEXUCQCWiSVWQgv2iG4,30470
+digichem/image/spectroscopy.py,sha256=fgrLGL1BSUHUmYMWpSSgAbNTu6uzmYxj5a9U94QL0fQ,33892
 digichem/image/structure.py,sha256=gxgX5cXA3BaqBh5K7UPcVGWX-yG5kc6Robf5sWT1IYM,4900
 digichem/image/vmd.py,sha256=GGE35qypgBbpadHo1M929czuxM0U4NRICPkltKWEojE,39305
-digichem/input/__init__.py,sha256=SxCeQkUNOalYu9oxhPGHQHX6s5CqBlSVuMUt7n-ywFw,165
+digichem/input/__init__.py,sha256=DJMFLt-p2DZaTdvk2zIR6gdUepsa1n0e2_mk-BB45Sk,179
 digichem/input/base.py,sha256=9nxut3IlvKSYCjRUzpi7SdlaO_4MU8KWAecV-z3T1jo,3082
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