Updates following GP's review.

docs_rst/api/modules.rst

@@ -4,4 +4,3 @@ turbomoleio
 .. toctree::
    :maxdepth: 4
 
-   turbomoleio

src/turbomoleio/testing/__init__.py

@@ -94,6 +94,15 @@ def get_test_data_dir(module=None):
     p = Path(module)
     parts = p.parts
     found_paths = []
+    # Depending on where we call this function (in which case module should be
+    # provided), we want to find the test_data directory. We do that by recursively
+    # looking for a path that "ends" with "/tests/test_data".
+    # For example if we apply it in a directory "/abc/def/ghi", it will see if it can
+    # find:
+    # 1/ /abc/def/ghi/tests/test_data, then
+    # 2/ /abc/def/tests/test_data, then
+    # 3/ /abc/tests/test_data, then
+    # 4/ /tests/test_data
     for ii in range(len(parts), 0, -1):
         test_path = Path(*parts[:ii]) / "tests" / "test_data"
         if test_path.exists():
@@ -109,8 +118,6 @@ def get_tests_configs_tm_versions(test_data_dir):
     """Get the test configs for all supported tm versions."""
     from monty.serialization import loadfn
 
-    from turbomoleio.testing import TM_VERSIONS
-
     return {
         tmv: loadfn(os.path.join(test_data_dir, "outputs", tmv, "tests_config.yaml"))
         for tmv in TM_VERSIONS

tests/integration_tests/test_aoforce.py

@@ -32,7 +32,7 @@
 @pytest.mark.integration
 class TestAoforce:
     @pytest.mark.parametrize("structure", structures)
-    def test_run_ridft_aoforce_nosym(self, structure):
+    def test_run_ridft_aoforce_nosym(self, structure, test_data):
         dp = get_define_template("ridft")
         dp["desy"] = False
 
@@ -42,10 +42,11 @@ def test_run_ridft_aoforce_nosym(self, structure):
             structure,
             "ridft_aoforce_{}_nosym".format(structure),
             [ScfOutput, AoforceOutput],
+            test_data=test_data,
         )
 
     @pytest.mark.parametrize("structure", structures)
-    def test_run_dscf_aoforce_sym(self, structure):
+    def test_run_dscf_aoforce_sym(self, structure, test_data):
         dp = get_define_template("dscf")
         dp["desy"] = True
 
@@ -55,4 +56,5 @@ def test_run_dscf_aoforce_sym(self, structure):
             structure,
             "dscf_aoforce_{}_sym".format(structure),
             [ScfOutput, AoforceOutput],
+            test_data=test_data,
         )

tests/integration_tests/test_dscf.py

@@ -44,27 +44,33 @@
 @pytest.mark.integration
 class TestDscf:
     @pytest.mark.parametrize("structure", structures)
-    def test_run_dscf(self, structure):
+    def test_run_dscf(self, structure, test_data):
 
         assert run_itest(
             "dscf",
             get_define_template("dscf"),
             structure,
             "dscf_{}_std".format(structure),
             ScfOutput,
+            test_data=test_data,
         )
 
     @pytest.mark.parametrize("structure", structures)
-    def test_run_dscf_ired(self, structure):
+    def test_run_dscf_ired(self, structure, test_data):
         define_opt = get_define_template("dscf")
         define_opt["ired"] = True
 
         assert run_itest(
-            "dscf", define_opt, structure, "dscf_{}_ired".format(structure), ScfOutput
+            "dscf",
+            define_opt,
+            structure,
+            "dscf_{}_ired".format(structure),
+            ScfOutput,
+            test_data=test_data,
         )
 
     @pytest.mark.parametrize("structure", structures)
-    def test_run_dscf_hf(self, structure):
+    def test_run_dscf_hf(self, structure, test_data):
 
         define_opt = get_define_template("dscf")
         define_opt["method"] = "hf"
@@ -76,7 +82,12 @@ def test_run_dscf_hf(self, structure):
         define_opt["title"] = None
 
         assert run_itest(
-            "dscf", define_opt, structure, "dscf_{}_hf".format(structure), ScfOutput
+            "dscf",
+            define_opt,
+            structure,
+            "dscf_{}_hf".format(structure),
+            ScfOutput,
+            test_data=test_data,
         )
 
     def test_run_dscf_usemo(self, test_data):
@@ -89,9 +100,11 @@ def test_run_dscf_usemo(self, test_data):
         define_opt["basis"] = "def2-SV(P)"
         define_opt["usemo"] = test_data / "mo" / "mos_nh3_nosym"
 
-        assert run_itest("dscf", define_opt, "nh3", "dscf_nh3_usemo", ScfOutput)
+        assert run_itest(
+            "dscf", define_opt, "nh3", "dscf_nh3_usemo", ScfOutput, test_data=test_data
+        )
 
-    def test_run_dscf_ecp_atom(self):
+    def test_run_dscf_ecp_atom(self, test_data):
         """
         Tests the usemo functionalities with mos file
         """
@@ -101,10 +114,17 @@ def test_run_dscf_ecp_atom(self):
         define_opt["basis"] = "def2-SV(P)"
         define_opt["ecp_atom"] = {"N": "ecp-2-sdf"}
 
-        assert run_itest("dscf", define_opt, "nh3", "dscf_nh3_ecp_atom", ScfOutput)
+        assert run_itest(
+            "dscf",
+            define_opt,
+            "nh3",
+            "dscf_nh3_ecp_atom",
+            ScfOutput,
+            test_data=test_data,
+        )
 
     # TODO check if alpha/beta for usemo are needed
-    # def test_run_dscf_usemo_alpha(self):
+    # def test_run_dscf_usemo_alpha(self, test_data):
     #     """
     #     Tests the usemo functionalities with alpha and
     #     beta files in the case of unpaired electrons
@@ -117,7 +137,14 @@ def test_run_dscf_ecp_atom(self):
     #     define_opt["unpaired_electrons"] = 1
     #     define_opt["usemo"] = os.path.join(get_tfp(), "mo", "alpha_beta_nh3")
     #
-    #     assert run_itest("dscf", define_opt, "nh3", "dscf_nh3_usemo_alpha", {})
+    #     assert run_itest(
+    #         "dscf",
+    #         define_opt,
+    #         "nh3",
+    #         "dscf_nh3_usemo_alpha",
+    #         {},
+    #         test_data=test_data
+    #     )
 
     def test_run_dscf_copymo(self, test_data):
         """
@@ -129,7 +156,14 @@ def test_run_dscf_copymo(self, test_data):
         define_opt["basis"] = "def2-SV(P)"
         define_opt["copymo"] = test_data / "mo" / "mos_nh3"
 
-        assert run_itest("dscf", define_opt, "nh3", "dscf_nh3_copymo_mos", ScfOutput)
+        assert run_itest(
+            "dscf",
+            define_opt,
+            "nh3",
+            "dscf_nh3_copymo_mos",
+            ScfOutput,
+            test_data=test_data,
+        )
 
     def test_run_dscf_copymo_mos_unpaired(self, test_data):
         """
@@ -144,7 +178,12 @@ def test_run_dscf_copymo_mos_unpaired(self, test_data):
         define_opt["copymo"] = test_data / "mo" / "mos_nh3"
 
         assert run_itest(
-            "dscf", define_opt, "nh3", "dscf_nh3_copymo_mos_unpaired", ScfOutput
+            "dscf",
+            define_opt,
+            "nh3",
+            "dscf_nh3_copymo_mos_unpaired",
+            ScfOutput,
+            test_data=test_data,
         )
 
     def test_run_dscf_copymo_alpha_unpaired(self, test_data):
@@ -160,11 +199,16 @@ def test_run_dscf_copymo_alpha_unpaired(self, test_data):
         define_opt["copymo"] = test_data / "mo" / "alpha_beta_nh3"
 
         assert run_itest(
-            "dscf", define_opt, "nh3", "dscf_nh3_copymo_alpha_unpaired", ScfOutput
+            "dscf",
+            define_opt,
+            "nh3",
+            "dscf_nh3_copymo_alpha_unpaired",
+            ScfOutput,
+            test_data=test_data,
         )
 
     @pytest.mark.parametrize("structure", structures)
-    def test_run_dscf_cosmo(self, structure):
+    def test_run_dscf_cosmo(self, structure, test_data):
 
         define_opt = get_define_template("dscf")
         define_opt["use_cosmo"] = True
@@ -180,13 +224,20 @@ def test_run_dscf_cosmo(self, structure):
             }
         )
         assert run_itest(
-            "dscf", define_opt, structure, "dscf_{}_cosmo".format(structure), ScfOutput
+            "dscf",
+            define_opt,
+            structure,
+            "dscf_{}_cosmo".format(structure),
+            ScfOutput,
+            test_data=test_data,
         )
 
     @pytest.mark.parametrize("disp", disp_corrections)
-    def test_run_dscf_disp(self, disp):
+    def test_run_dscf_disp(self, disp, test_data):
 
         define_opt = get_define_template("dscf")
         define_opt["disp"] = disp
         disp_fn = "dscf_nh3_disp_{}".format("_".join(disp.split()))
-        assert run_itest("dscf", define_opt, "nh3", disp_fn, ScfOutput)
+        assert run_itest(
+            "dscf", define_opt, "nh3", disp_fn, ScfOutput, test_data=test_data
+        )

tests/integration_tests/test_escf.py

@@ -34,7 +34,7 @@
 @pytest.mark.integration
 class TestEscf:
     @pytest.mark.parametrize("structure", structures)
-    def test_run_ridft_escf(self, structure):
+    def test_run_ridft_escf(self, structure, test_data):
         dp = get_define_template("ridft_escf")
         dp["desy"] = True
         dp["ex_all_states"] = 12
@@ -45,10 +45,11 @@ def test_run_ridft_escf(self, structure):
             structure,
             "ridft_escf_{}_std".format(structure),
             [ScfOutput, EscfOutput],
+            test_data=test_data,
         )
 
     @pytest.mark.parametrize("structure", structures)
-    def test_run_dscf_escf(self, structure):
+    def test_run_dscf_escf(self, structure, test_data):
         dp = get_define_template("dscf_escf")
         dp["desy"] = False
         dp["ex_all_states"] = None
@@ -60,10 +61,11 @@ def test_run_dscf_escf(self, structure):
             structure,
             "dscf_escf_{}_std".format(structure),
             [ScfOutput, EscfOutput],
+            test_data=test_data,
         )
 
     @pytest.mark.parametrize("structure", structures)
-    def test_run_dscf_escf_triplet(self, structure):
+    def test_run_dscf_escf_triplet(self, structure, test_data):
         dp = get_define_template("dscf_escf")
         dp["desy"] = True
         dp["ex_all_states"] = 10
@@ -75,10 +77,11 @@ def test_run_dscf_escf_triplet(self, structure):
             structure,
             "dscf_escf_{}_triplet".format(structure),
             [ScfOutput, EscfOutput],
+            test_data=test_data,
         )
 
     @pytest.mark.parametrize("structure", structures)
-    def test_run_dscf_escf_charged(self, structure):
+    def test_run_dscf_escf_charged(self, structure, test_data):
         dp = get_define_template("dscf_escf")
         dp["desy"] = True
         dp["ex_all_states"] = 10
@@ -90,9 +93,10 @@ def test_run_dscf_escf_charged(self, structure):
             structure,
             "dscf_escf_{}_charged".format(structure),
             [ScfOutput, EscfOutput],
+            test_data=test_data,
         )
 
-    def test_run_dscf_escf_set_dict(self):
+    def test_run_dscf_escf_set_dict(self, test_data):
         """
         Tests some properties that are set with a dictionary.
 
@@ -119,4 +123,5 @@ def test_run_dscf_escf_set_dict(self):
             "nh3_wrong_internal",
             "dscf_escf_nh3_set_dict",
             [ScfOutput, EscfOutput],
+            test_data=test_data,
         )

tests/integration_tests/test_jobex.py

@@ -35,7 +35,7 @@
 @pytest.mark.integration
 class TestJobex:
     @pytest.mark.parametrize("structure", structures)
-    def test_run_jobex_dscf(self, structure):
+    def test_run_jobex_dscf(self, structure, test_data):
         dp = get_define_template("dscf")
         dp["desy"] = True
         dp["ired"] = True
@@ -47,10 +47,11 @@ def test_run_jobex_dscf(self, structure):
             "jobex_dscf_{}_sym".format(structure),
             JobexOutput,
             arguments="-c 2",
+            test_data=test_data,
         )
 
     @pytest.mark.parametrize("structure_filename", ["graphene"])
-    def test_run_jobex_riper(self, structure_filepath):
+    def test_run_jobex_riper(self, structure_filepath, test_data):
         structure_filename = os.path.basename(structure_filepath)
         dp = get_define_template("ridft")
         periodic = sdg("periodic", structure_filepath)
@@ -63,4 +64,5 @@ def test_run_jobex_riper(self, structure_filepath):
             JobexOutput,
             arguments="-c 2",
             datagroups_options={"periodic": periodic, "cell": cell, "optcell": ""},
+            test_data=test_data,
         )

tests/integration_tests/test_relax.py

@@ -38,7 +38,7 @@
 @pytest.mark.integration
 class TestRelax:
     @pytest.mark.parametrize("structure", structures)
-    def test_run_dscf_grad_statpt(self, structure):
+    def test_run_dscf_grad_statpt(self, structure, test_data):
         dp = get_define_template("dscf")
         dp["desy"] = True
         dp["ired"] = True
@@ -49,10 +49,11 @@ def test_run_dscf_grad_statpt(self, structure):
             structure,
             "dscf_grad_statpt_{}_sym".format(structure),
             [ScfOutput, GradOutput, StatptOutput],
+            test_data=test_data,
         )
 
     @pytest.mark.parametrize("structure", structures)
-    def test_run_ridft_rdgrad_relax(self, structure):
+    def test_run_ridft_rdgrad_relax(self, structure, test_data):
         dp = get_define_template("ridft")
         dp["desy"] = True
         dp["ired"] = True
@@ -63,10 +64,11 @@ def test_run_ridft_rdgrad_relax(self, structure):
             structure,
             "ridft_rdgrad_relax_{}_sym".format(structure),
             [ScfOutput, GradOutput, RelaxOutput],
+            test_data=test_data,
         )
 
     @pytest.mark.parametrize("structure", structures)
-    def test_run_dscf_egrad_relax(self, structure):
+    def test_run_dscf_egrad_relax(self, structure, test_data):
         dp = get_define_template("dscf_escf")
         dp["desy"] = False
         dp["ired"] = False
@@ -77,10 +79,11 @@ def test_run_dscf_egrad_relax(self, structure):
             structure,
             "dscf_escf_relax_{}_nosym".format(structure),
             [ScfOutput, EgradOutput, RelaxOutput],
+            test_data=test_data,
         )
 
     @pytest.mark.parametrize("structure", structures)
-    def test_run_ridft_egrad_statpt_ex_irrep(self, structure):
+    def test_run_ridft_egrad_statpt_ex_irrep(self, structure, test_data):
         dp = get_define_template("ridft_escf")
         dp["desy"] = True
         dp["ired"] = True
@@ -93,4 +96,5 @@ def test_run_ridft_egrad_statpt_ex_irrep(self, structure):
             structure,
             "ridft_egrad_statpt_{}_ex_irrep".format(structure),
             [ScfOutput, EgradOutput, StatptOutput],
+            test_data=test_data,
         )