Using consistent code_root in expoutput taken from Session.

jade/expoutput.py

@@ -172,8 +172,7 @@ def build_atlas(self):
         globalname = globalname[:-4]
         globalname = self.testname + '_' + globalname
         # Initialize the atlas
-        template = os.path.join(self.code_path, 'Code', 'jade', 'templates',
-                                'AtlasTemplate.docx')
+        template = os.path.join(self.code_path, 'templates', 'AtlasTemplate.docx')
         atlas = at.Atlas(template, globalname)
 
         # Fill the atlas

jade/main.py

@@ -78,32 +78,32 @@ def initialize(self) -> None:
 
         """
 
-        code_root = os.path.join(os.path.dirname(os.path.abspath(__file__)))
-        jade_root = os.getcwd()
+        self.code_root = os.path.join(os.path.dirname(os.path.abspath(__file__)))
+        self.jade_root = os.getcwd()
 
-        if os.path.dirname(code_root) in jade_root:
+        if os.path.dirname(self.code_root) in self.jade_root:
             fatal_exception("Cannot initialise JADE in Code directory")
 
-        self.path_default_settings = os.path.join(code_root, "default_settings")
-        self.path_templates = os.path.join(code_root, "templates")
+        self.path_default_settings = os.path.join(self.code_root, "default_settings")
+        self.path_templates = os.path.join(self.code_root, "templates")
 
         # --- INITIALIZATION ---
         # --- Create/memorize JADE folder structure ---
         # Future implementation
-        self.path_quality = os.path.join(jade_root, "Quality")
+        self.path_quality = os.path.join(self.jade_root, "Quality")
         # Test level 1
-        self.path_test = os.path.join(jade_root, "Tests")
+        self.path_test = os.path.join(self.jade_root, "Tests")
         # Test level 2
         self.path_run = os.path.join(self.path_test, "Simulations")
         self.path_pp = os.path.join(self.path_test, "Post-Processing")
         # Test level 3
         self.path_single = os.path.join(self.path_pp, "Single_Libraries")
         self.path_comparison = os.path.join(self.path_pp, "Comparisons")
         # Utilities
-        self.path_uti = os.path.join(jade_root, "Utilities")
-        self.path_logs = os.path.join(jade_root, "Utilities", "Log_Files")
+        self.path_uti = os.path.join(self.jade_root, "Utilities")
+        self.path_logs = os.path.join(self.jade_root, "Utilities", "Log_Files")
         self.path_test_install = os.path.join(
-            jade_root, "Utilities", "Installation_Test"
+            self.jade_root, "Utilities", "Installation_Test"
         )
 
         keypaths = [
@@ -124,12 +124,12 @@ def initialize(self) -> None:
         # --This paths must exist or are created at the first initialization--
         # Configuration
         self.path_cnf = os.path.join(
-            jade_root, "Configuration", "Benchmarks_Configuration"
+            self.jade_root, "Configuration", "Benchmarks_Configuration"
         )
         # Experimental results
-        self.path_exp_res = os.path.join(jade_root, "Experimental_Results")
+        self.path_exp_res = os.path.join(self.jade_root, "Experimental_Results")
         # Benchmark inputs
-        self.path_inputs = os.path.join(jade_root, "Benchmarks_Inputs")
+        self.path_inputs = os.path.join(self.jade_root, "Benchmarks_Inputs")
 
         # Copy default settings if it is the first initialization
         if not os.path.exists(self.path_cnf):
@@ -138,19 +138,19 @@ def initialize(self) -> None:
             shutil.copytree(files, os.path.dirname(self.path_cnf))
 
             # Copy files into benchmark inputs folder
-            files = os.path.join(code_root, "install_files", "Benchmarks_Inputs")
+            files = os.path.join(self.code_root, "install_files", "Benchmarks_Inputs")
             shutil.copytree(files, self.path_inputs)
 
             # Copy experimental results folder
-            files = os.path.join(code_root, "install_files", "Experimental_Results")
+            files = os.path.join(self.code_root, "install_files", "Experimental_Results")
             shutil.copytree(files, self.path_exp_res)
 
             # the application needs to be closed
             sys.exit()
 
         # Read global configuration file. All vital variables are stored here
         self.conf = cnf.Configuration(
-            os.path.join(jade_root, "Configuration", "Config.xlsx")
+            os.path.join(self.jade_root, "Configuration", "Config.xlsx")
         )
 
         # --- Create the session LOG ---
@@ -161,8 +161,8 @@ def initialize(self) -> None:
 
         # --- Create the library manager ---
         # dl = self.conf.default_lib
-        activationfile = os.path.join(jade_root, "Configuration", "Activation.xlsx")
-        isotopes_file = os.path.join(code_root, "resources", "Isotopes.txt")
+        activationfile = os.path.join(self.jade_root, "Configuration", "Activation.xlsx")
+        isotopes_file = os.path.join(self.code_root, "resources", "Isotopes.txt")
         self.lib_manager = libmanager.LibManager(
             self.conf.lib, activationfile=activationfile, isotopes_file=isotopes_file
         )

jade/output.py

@@ -21,24 +21,28 @@
 # You should have received a copy of the GNU General Public License
 # along with JADE.  If not, see <http://www.gnu.org/licenses/>.
 
-
-import jade.MCTAL_READER2 as mtal
-
 # import xlwings as xw
+from __future__ import annotations
 import pandas as pd
 import os
 import shutil
-import jade.plotter as plotter
-import jade.excelsupport as exsupp
 from tqdm import tqdm
-import jade.atlas as at
 import numpy as np
 import string
-from jade.outputFile import OutputFile
-from jade.meshtal import Meshtal
 import pickle
 import sys
 import abc
+from typing import TYPE_CHECKING
+
+import jade.atlas as at
+from jade.outputFile import OutputFile
+from jade.meshtal import Meshtal
+import jade.plotter as plotter
+import jade.excelsupport as exsupp
+import jade.MCTAL_READER2 as mtal
+
+if TYPE_CHECKING:
+    from jade.main import Session
 
 # RED color
 CRED = "\033[91m"
@@ -108,7 +112,7 @@ def _get_output_files(results_path):
 
 
 class BenchmarkOutput(AbstractOutput):
-    def __init__(self, lib, config, session):
+    def __init__(self, lib, config, session:Session):
         """
         General class for a Benchmark output
 
@@ -131,7 +135,7 @@ def __init__(self, lib, config, session):
         self.raw_data = {}  # Raw data
         self.outputs = {}  # outputs linked to the benchmark
         self.testname = config["Folder Name"]  # test name
-        self.code_path = os.getcwd()  # path to code
+        self.code_path = session.code_root  # path to code
         self.state = session.state
         self.session = session
         self.path_templates = session.path_templates