Alex' pull request review

docs/source/api/general.rst

@@ -17,7 +17,7 @@ Paths
     through Session it is possible to recover many paths to the
     different folders that constitutes the JADE tree (see also :ref:`folders`).
 Status
-    the Status object has informations on which libraries have
+    the Status object has information on which libraries have
     been assessed or post-processed.
 Configuration
     the Configuration object is the one that handles the
@@ -50,8 +50,8 @@ module.
 In JADE the object representing a benchmark is the Test object (or MultipleTest object
 in case the benchmark is composed by more than one run). This object is responsible
 for the creation of the MCNP input and for its run. A vital attribute of the benchmark
-is its associated Input object (`<https://f4enix.readthedocs.io/en/latest/_autosummary/f4enix.input.MCNPinput.html>`_) or one of its children. In case the benchmark is run
-with d1s code, an irradiation file and a reaction file (`<https://f4enix.readthedocs.io/en/latest/_autosummary/f4enix.input.d1suned.html>`) are also associated with the
+is its associated Input object (`Input object <https://f4enix.readthedocs.io/en/latest/_autosummary/f4enix.input.MCNPinput.html>`_) or one of its children. In case the benchmark is run
+with d1s code, an irradiation file and a reaction file (`D1S files <https://f4enix.readthedocs.io/en/latest/_autosummary/f4enix.input.d1suned.html>`_) are also associated with the
 test.
 
 Post-processing

docs/source/nutshell.rst

@@ -17,6 +17,9 @@ JADE is an open source, Python 3 based software able to:
 * Run simulations on such inputs;
 * Automatically parse and post-process all the generated transport codes outputs.
 
+MCNP input and output handling is performed by F4Enix (`f4enix documentation <https://f4enix.readthedocs.io/en/latest/>`_).
+This package contains a range of utilities for the creation and post-processing of MCNP files.
+
 The benchmarks implemented by default are divided between computational
 and experimental benchmarks. The post-processing output includes:
 

jade/output.py

@@ -293,7 +293,7 @@ def _read_code_version(self, pathtofile: os.PathLike) -> str | None:
         return None
 
     def _read_mcnp_code_version(self, pathtofile: os.PathLike) -> str | None:
-        if self.testname in ['Sphere', 'SphereSDDR']:
+        if self.testname in ["Sphere", "SphereSDDR"]:
             if not os.path.exists(pathtofile):
                 # this can happen the first time
                 return None
@@ -1093,9 +1093,9 @@ def __init__(self, mctal_file, output_file, meshtal_file=None):
                     self.tallydata[tallynum] = tallydata
                     self.totalbin[tallynum] = None
                     # Create fake tallies to be added to the mctal
-                    faketally = Tally(tallynum)
-                    faketally.tallyComment = [comment]
-                    self.mctal.tallies.append(faketally)
+                    dummyTally = Tally(tallynum)
+                    dummyTally.tallyComment = [comment]
+                    self.mctal.tallies.append(dummyTally)
                 else:
                     continue
 

jade/utilitiesgui.py

@@ -28,7 +28,7 @@
 
 from jade.acepyne import Library
 import jade.resources as pkg_res
-from importlib.resources import files, as_file
+from importlib.resources import files
 
 JADE_RESOURCES = files(pkg_res)
 

tests/computational_test.py

@@ -92,7 +92,7 @@ def test_executeBenchmarksRoutines(session_mock: MockUpSession):
     executeBenchmarksRoutines(session_mock, lib, runoption, exp)
 
 
-def test_select_lib(monkeypatch):
+def test_select_lib_1(monkeypatch):
     # monkeypatch the "input" function
     lm = LibManager(os.path.join(resources, "xsdir"))
     # Good trials
@@ -101,12 +101,16 @@ def test_select_lib(monkeypatch):
         selectedlib = select_lib(lm, ["mcnp"])
         assert selectedlib == lib
 
+
+def test_select_lib_2(monkeypatch):
+    # monkeypatch the "input" function
+    lm = LibManager(os.path.join(resources, "xsdir"))
+    # Good trials
     # Not found
     for lib in ["44c", '{"21c": "44c", "44c": "71c"}', "21c-44c"]:
         monkeypatch.setattr("builtins.input", lambda _: lib)
         try:
-            selectedlib = select_lib(lm, ["mcnp"])
-            print(lib)
+            select_lib(lm, ["mcnp"])
             assert False
         except ValueError:
             assert True

tests/expoutput_test.py

@@ -63,7 +63,7 @@ def lm(self):
             df_lib, activationfile=ACTIVATION_FILE, isotopes_file=ISOTOPES_FILE
         )
 
-    def test_benchmarkoutput(self, session_mock: MockUpSession, lm: LibManager):
+    def test_benchmarkoutput(self, session_mock: MockUpSession):
 
         code = "mcnp"
         testname = "ITER_1D"
@@ -77,9 +77,11 @@ def test_benchmarkoutput(self, session_mock: MockUpSession, lm: LibManager):
             ["32c", "31c"], code, testname, session_mock
         )
         self.benchoutput_comp.compare()
+        assert self.benchoutput_31c.raw_data[24]["Error"].iloc[10] == 0.7602
+        assert self.benchoutput_31c.raw_data[94]["Cells"].iloc[2] == 54
         assert True
 
-    def test_benchmarkoutputmesh(self, session_mock: MockUpSession, lm: LibManager):
+    def test_benchmarkoutputmesh(self, session_mock: MockUpSession):
         code = "mcnp"
         testname = "WCLL_TBM_1D"
         os.makedirs(session_mock.path_comparison)
@@ -92,6 +94,8 @@ def test_benchmarkoutputmesh(self, session_mock: MockUpSession, lm: LibManager):
             ["32c", "31c"], code, testname, session_mock
         )
         self.benchoutput_comp.compare()
+        assert self.benchoutput_31c.raw_data[214]["Error"].iloc[74] == 0.028364
+        assert self.benchoutput_31c.raw_data[244]["Cor A"].iloc[78] == 1084.20
         assert True
 
     def test_spectrumoutput(self, session_mock: MockUpSession):