Merge pull request #271 from JADE-V-V/pre-release_dev

Release of v3.0.0

README.md

@@ -1,4 +1,4 @@
-[![Testing](https://github.com/dodu94/JADE/actions/workflows/TestPy38.yml/badge.svg?branch=master)](https://github.com/dodu94/JADE/actions/workflows/TestPy38.yml)
+[![Testing](https://github.com/JADE-V-V/JADE/actions/workflows/pytest.yml/badge.svg?branch=master)](https://github.com/JADE-V-V/JADE/actions/workflows/pytest.yml)
 [![Documentation Status](https://readthedocs.org/projects/jade-a-nuclear-data-libraries-vv-tool/badge/?version=latest)](https://jade-a-nuclear-data-libraries-vv-tool.readthedocs.io/en/latest/?badge=latest)
 
 <img src="https://user-images.githubusercontent.com/25747626/118662537-5f124900-b7f0-11eb-8d69-282305f795c4.png" width="300" />

docs/source/contributors.rst

@@ -8,7 +8,7 @@ JADE project was originally started as a joint effort between between `NIER inge
 `Università di Bologna (UNIBO) <https://ingegneriaindustriale.unibo.it/it>`_
 and `Fusion For Energy (F4E) <https://fusionforenergy.europa.eu/>`_.
 
-Nowadays new development is mostly carried on by F4E and the
+Currently, new development is largely undertaken by `Fusion For Energy (F4E) <https://fusionforenergy.europa.eu/>`_ and the
 `United Kingdom Atomic Energy Authority (UKAEA) <https://ccfe.ukaea.uk/>`_.
 
 This activity was partially funded by Fusion For Energy under F4E-OPE-1128 contract.

docs/source/futuredev.rst

@@ -1,3 +1,5 @@
+.. _futuredev:
+
 ###################
 Future developments
 ###################

docs/source/nutshell.rst

@@ -5,14 +5,14 @@ JADE in a nutshell
 .. image:: img/JADE_scheme.jpg
     :width: 600
 
-JADE is a tool for nuclear libraries V&V.
+JADE is a tool for validation and verification (V&V) of nuclear data libraries.
 Development was initially started by NIER, University of Bologna (UNIBO) and Fusion For Energy (F4E),
 and it is today carried out mainly by F4E and the United Kingdom Atomic Energy Authority (UKAEA).
 You can find an up to date and detailed list of contributors in the :ref:`contributor_list` section.
 
 JADE is an open source, Python 3 based software able to:
 
-* Automatically build a series of MCNP input file using different nuclear
+* Automatically build a series of MCNP input files using different nuclear
   data libraries;
 * Run simulations on such inputs;
 * Automatically parse and post-process all the generated transport codes outputs.
@@ -23,11 +23,11 @@ and experimental benchmarks. The post-processing output includes:
 * Raw data in *.csv* files containing the entire tallied output from the
   simulations;
 * Formatted Excel recap files;
-* Word and PDF atlas files collecting the plots generated during the post-processing.
+* Word files collecting the plots generated during the post-processing.
 
 Additional JADE features are:
 
-* Run JADE with the transport codes OpenMC and Serpent.
+* Run JADE with the transport codes OpenMC and Serpent for the sphere leakage benchmark.
 * The possibility to implement user-defined benchmarks;
 * Operate on the material definitions (e.g. create material mixtures, 
   translate it to a different nuclear data library or switch between atom and
@@ -47,7 +47,7 @@ When using JADE for scientific publications you are kindly encouraged to cite th
 For additional information contact: [email protected]
 
 For additional information on future developments please check the issues list on the
-`JADE GitHub repository <https://github.com/dodu94/JADE/>`_.
+`JADE GitHub repository <https://github.com/dodu94/JADE/>`_ and :ref:`futuredev`.
 
 .. seealso:: 
   * **MCNP**, Werner C.J., 2017, "MCNP User’S Manual Code", Los Alamos: LAUR-17-29981 (version 6.2).

docs/source/usage/folders.rst

@@ -97,10 +97,10 @@ Hereafter, a general overview of the different JADE tree branches is presented.
 
 Benchmark inputs
 ================
-``<JADE_root>\Benchmark_Inputs`` contains all the inputs of the default benchmarks avaialble in the JADE suite.
+``<JADE_root>\Benchmark_Inputs`` contains all the inputs of the default benchmarks available in the JADE suite.
 This is the folder where eventual user defined benchmark inputs should be positioned.
 In case of benchmarks that are composed by more than one run, all the inputs are reunited in a sub-folder
-(e.g. ``<JADE_root>\Benchmark_Inputs\Oktavian\Oktavian_Al\``.
+(e.g. ``<JADE_root>\Benchmark_Inputs\Oktavian\Oktavian_Al\mcnp``).
 
 If weight windows are available, they should be placed in same folder as the input. 
 
@@ -125,7 +125,7 @@ jade
         Contains files to be used during the first JADE run. They do have not any appeal to the general user.
 
     resources
-        Miscelaneous resources, currently information on natural isotope abundances and atomic masses.
+        Miscellaneous resources, currently information on natural isotope abundances and atomic masses.
 
 
 tests
@@ -135,7 +135,7 @@ Configuration
 =============
 ``<JADE_root>\Configuration`` stores the main JADE configuration file ``Config.xlsx`` and all benchmark-specific configuration
 files that are stored in ``<JADE_root>\Code\Benchmarks_Configuration``. For users running on UNIX systems, this folder also 
-contains templates for several common job submission systems (Slurm, LoadLeveler), and config shell scripts for configuring 
+contains templates for several common job submission systems such as *slurm*, and code specific shell scripts for configuring 
 modules and environment variables at runtime.
 
 .. seealso::
@@ -145,7 +145,7 @@ Experimental results
 ====================
 ``<JADE_root>\Experimental_Results`` stores all the experimental results needed for the post-processing of
 experimental benchmarks. In case of benchmarks that are composed by more than one run, all the inputs are reunited in a sub-folder
-(e.g. ``<JADE_root>\Experimental_Results\Oktavian``.
+(e.g. ``<JADE_root>\Experimental_Results\Oktavian\Al``).
 
 Quality
 =======
@@ -157,7 +157,7 @@ Tests
 ``<JADE_root>\Tests`` reunites all the outputs of the benchmarks assessments. 
 
 Simulations
-    contains the results of the transport simulations.
+    location transport simulations are performed.
 
 Post-Processing
     contains all the results coming from the post-processing of results. These are divided between

docs/source/usage/installation.rst

@@ -13,7 +13,7 @@ Installation on Linux
 
 Firstly, create a virtual environment and activate it:
 
-  | ``python -m venv jade``
+  | ``python -m venv jade_venv``
   | ``source jade/bin/activate``
 
 Visit the `JADE repository <https://github.com/JADE-V-V/jade>`_ and if you have `git <https://git-scm.com/>`_

docs/source/usage/menu.rst

@@ -12,7 +12,7 @@ Once JADE is correctly configured
 
 The main menu is loaded at this point:
 
-.. image:: ../img/main_menu.png
+.. image:: ../img/main_menu.jpg
     :width: 400
 
 This menu allows users to interact with the tool directly from the

jade/excelsupport.py

@@ -1646,7 +1646,9 @@ def sphere_single_excel_writer(self, outpath, lib, values, errors, stats=None):
     wb.close()
 
 
-def sphere_comp_excel_writer(self, outpath, name, final, absdiff, std_dev, summary):
+def sphere_comp_excel_writer(
+    self, outpath, name, final, absdiff, std_dev, summary, single_pp_files
+):
     """
     Produces library comparison excel file for Sphere leakage using XLSXwriter
 
@@ -1666,6 +1668,9 @@ def sphere_comp_excel_writer(self, outpath, name, final, absdiff, std_dev, summa
     summary: Dataframe
        Contains total number of percentage difference in the column
        within certain bounds
+    single_pp_files: list
+       Path to the single library Excel files that should be copied
+       as additional tabs
 
     Returns
     -------
@@ -2335,6 +2340,18 @@ def sphere_comp_excel_writer(self, outpath, name, final, absdiff, std_dev, summa
 
     wb.close()
 
+    # Copy the single post processed results into the comparison workbook
+    target_file = outpath  # Target workbook filename
+    target_sheet_names = [
+        "Values",
+        "Errors",
+        "Statistical Checks",
+    ]  # Target sheet names
+
+    # Loop over the library source files
+    for source_file in single_pp_files:
+        copy_sheets_to_target(source_file, target_file, target_sheet_names)
+
 
 def sphere_sddr_single_excel_writer(outpath, lib, results, errors, stat_checks):
     """
@@ -2508,7 +2525,7 @@ def sphere_sddr_single_excel_writer(outpath, lib, results, errors, stat_checks):
     tal_sheet.set_column(max_width + 1, max_width + 20, 18, oob_format)
     for i in range(9):
         tal_sheet.set_row(i, None, oob_format)
-    for i in range(10 + max_len, max_len + 200):
+    for i in range(10 + max_len, max_len + 1000):
         tal_sheet.set_row(i, None, oob_format)
 
     # Column widths
@@ -2592,7 +2609,7 @@ def sphere_sddr_single_excel_writer(outpath, lib, results, errors, stat_checks):
     err_sheet.set_column(max_width, max_width + 50, 18, oob_format)
     for i in range(9):
         err_sheet.set_row(i, None, oob_format)
-    for i in range(8 + max_len, max_len + 50):
+    for i in range(10 + max_len, max_len + 1000):
         err_sheet.set_row(i, None, oob_format)
 
     # Column widths for errors, set up to 15th col by default to ensure title format correct
@@ -2847,6 +2864,9 @@ def sphere_sddr_comp_excel_writer(
     std_dev: Dataframe
        Difference between reference and target library in terms of
        standard deviations from the mean of the reference library
+    single_pp_files: list
+       Path to the single library Excel files that should be copied
+       as additional tabs
 
 
     Returns