updated docs with pypi

Added sort_compass_files function

Sort compass filenames and associated tests

Using absolute path for compass_data

Update libra_toolbox/neutron_detection/activation_foils/compass.py

Co-authored-by: Rémi Delaporte-Mathurin <40028739+RemDelaporteMathurin@users.noreply.github.com>

Update libra_toolbox/neutron_detection/activation_foils/compass.py

Co-authored-by: Rémi Delaporte-Mathurin <40028739+RemDelaporteMathurin@users.noreply.github.com>

Added full set of test files

Reduced filesize

Added new test cases to test_compass

Reformatted with black

Deleted old test files

removed large files

Author: RemDelaporteMathurin

.gitignore

@@ -161,4 +161,8 @@ cython_debug/
 #  option (not recommended) you can uncomment the following to ignore the entire idea folder.
 #.idea/
 
-**/_version.py
+**/_version.py
+
+# Compass binary file
+*.DS_Store
+settings.xml

docs/index.rst

@@ -34,7 +34,7 @@ To install libra-toolbox, use pip:
 
 .. code-block:: bash
 
-   pip install git+https://github.com/LIBRA-project/libra-toolbox
+   pip install libra-toolbox
 
 For more details, see the :ref:`installation` page.
 
@@ -45,9 +45,10 @@ Roadmap
 
 - :strike:`Tritium model: 0D model for tritium release`
 - :strike:`Neutron detection: tools and scripts for neutron detection post processing`
-- Neutronics: tools to facilitate building `OpenMC <https://docs.openmc.org/en/stable/>`_ models
+- :strike:`Neutronics: tools to facilitate building OpenMC models`
 - Tritium transport: tools to facilitate building `FESTIM <https://github.com/festim-dev/festim>`_ tritium transport models
 - :strike:`Code coverage with Codecov`
+- Conda package
 
 
 .. toctree::

docs/installation.rst

@@ -3,23 +3,23 @@
 Installation
 ============
 
-``libra-toolbox`` relies on python. You can install it from the official website: https://www.python.org/downloads/
+``libra-toolbox`` relies on Python. You can install it from the official website: https://www.python.org/downloads/
 
-To install ``libra-toolbox``, use pip:
+To install ``libra-toolbox`` from PyPI, use pip:
 
 .. code-block:: bash
 
-   pip install git+https://github.com/LIBRA-project/libra-toolbox
+   pip install libra-toolbox
 
 This will install the latest version of the code along with all the dependencies (``numpy``, ``pint``, ``scipy``...).
 
 To install a specific version of the code:
 
 .. code-block:: bash
 
-   pip install git+https://github.com/LIBRA-project/libra-toolbox@v0.1
+   pip install libra-toolbox==0.6.1
 
-Here, ``v0.1`` is the version number. You can replace it with the version you want to install.
+Here, ``0.6.1`` is the version number. You can replace it with the version you want to install.
 
 To install the code in editable mode (i.e. the code is installed in the current directory and any changes to the code are immediately available to the user):
 
@@ -29,11 +29,17 @@ To install the code in editable mode (i.e. the code is installed in the current
    cd libra-toolbox
    pip install -e .
 
-To install the code alongside with the optional dependencies for the neutronics module, first [install OpenMC](https://docs.openmc.org/en/stable/quickinstall.html) with conda:
+To install the code alongside the optional dependencies for the neutronics module, first install `OpenMC <https://docs.openmc.org/en/stable/quickinstall.html>`_ with conda:
 
-```
-conda install -c conda-forge openmc>=0.14.0
-```
+.. code-block:: bash
+
+   conda install -c conda-forge openmc>=0.14.0
+
+Then install the code with the optional dependencies:
+
+.. code-block:: bash
+
+   pip install libra-toolbox[neutronics]
 
 To uninstall the package:
 

libra_toolbox/neutron_detection/activation_foils/compass.py

@@ -1,3 +1,5 @@
+import numpy as np
+import os
 
 
 def get_channel(filename):
@@ -23,4 +25,33 @@ def get_channel(filename):
     return int(filename.split('@')[0][7:])
 
 
+def sort_compass_files(directory: str) -> dict:
+    """ Gets Compass csv data filenames
+    and sorts them according to channel and ending number.
+    The filenames need to be sorted by ending number because only
+    the first csv file for each channel contains a header.
+    
+    Example of sorted filenames in directory: 
+        1st file: Data_CH4@...22.CSV
+        2nd file: Data_CH4@...22_1.CSV
+        3rd file: Data_CH4@...22_2.CSV """
+
+    filenames = os.listdir(directory)
+    data_filenames = {}
+    for filename in filenames:
+        if filename.lower().endswith('.csv'):
+            ch = get_channel(filename)
+            # initialize filenames for each channel
+            if ch not in data_filenames.keys():
+                data_filenames[ch] = []
+
+            data_filenames[ch].append(filename)
+    # Sort filenames by number at end
+    for ch in data_filenames.keys():
+        data_filenames[ch] = np.sort(data_filenames[ch])
+
+    return data_filenames
+
+
+
 

test/neutron_detection/test_compass.py

@@ -1,12 +1,87 @@
 import pytest
+import numpy as np
+import os
 from libra_toolbox.neutron_detection.activation_foils import compass
 
-@pytest.mark.parametrize("filename, expected_channel", [
-    ("Data_CH14@V1725_292_Background_250322.CSV", 14),
-    ("Data_CH7@V1725_123_Background_250322.CSV", 7),
-    ("Data_CH21@V1725_456_Background_250322.CSV", 21),
-])
+
+@pytest.mark.parametrize(
+    "filename, expected_channel",
+    [
+        ("Data_CH14@V1725_292_Background_250322.CSV", 14),
+        ("Data_CH7@V1725_123_Background_250322.CSV", 7),
+        ("Data_CH21@V1725_456_Background_250322.CSV", 21),
+    ],
+)
 def test_get_channel(filename, expected_channel):
     ch = compass.get_channel(filename)
     assert ch == expected_channel
-   
+
+
+def create_empty_csv_files(directory, base_name, count, channel):
+    """
+    Creates empty CSV files in a specified directory with a specific pattern.
+
+    Args:
+        directory (str): The directory where the files will be created.
+        base_name (str): The base name of the file (e.g., "Data_CH14").
+        count (int): The number of files to generate.
+
+    Returns:
+        list: A list of file paths for the created CSV files.
+    """
+    if not os.path.exists(directory):
+        os.makedirs(directory)
+
+    file_paths = []
+    for i in range(count):
+        if i == 0:
+            filename = f"Data_CH{channel}@{base_name}.csv"
+        else:
+            filename = f"Data_CH{channel}@{base_name}_{i}.csv"
+        file_path = os.path.join(directory, filename)
+        with open(file_path, "w") as f:
+            pass  # Create an empty file
+        file_paths.append(file_path)
+
+    return file_paths
+
+
+@pytest.mark.parametrize(
+    "base_name, expected_filenames",
+    [
+        (
+            "base",
+            {
+                4: [
+                    "Data_CH4@base.csv",
+                    "Data_CH4@base_1.csv",
+                    "Data_CH4@base_2.csv",
+                    "Data_CH4@base_3.csv",
+                ],
+                1: [
+                    "Data_CH1@base.csv",
+                ],
+            },
+        ),
+    ],
+)
+def test_sort_compass_files(tmpdir, base_name: str, expected_filenames: dict):
+    for ch, list_of_filenames in expected_filenames.items():
+        create_empty_csv_files(
+            tmpdir, base_name, count=len(list_of_filenames), channel=ch
+        )
+
+    data_filenames = compass.sort_compass_files(tmpdir)
+
+    assert isinstance(data_filenames, dict)
+
+    # Check if dictionaries have the same keys, length of filenames array, and
+    # the same overall filenames array
+    for key in expected_filenames:
+        assert key in data_filenames
+        assert len(data_filenames[key]) == len(expected_filenames[key])
+        for a, b in zip(data_filenames[key], expected_filenames[key]):
+            if isinstance(a, np.ndarray) and isinstance(b, np.ndarray):
+                assert np.array_equal(a, b)
+            else:
+                assert a == b