From d787e943df481b871e098ee8da569a3700c40a13 Mon Sep 17 00:00:00 2001
From: "Josef M. Gallmetzer" <gallmetzer.josef@gmail.com>
Date: Mon, 5 Aug 2024 21:13:40 +0200
Subject: [PATCH 1/4] Refactor: Add __len__ method to AtomicSystem class

---
 PQAnalysis/atomic_system/atomic_system.py | 11 +++++++++++
 tests/atomicSystem/test_atomic_system.py  | 14 ++++++++++++++
 2 files changed, 25 insertions(+)

diff --git a/PQAnalysis/atomic_system/atomic_system.py b/PQAnalysis/atomic_system/atomic_system.py
index cca73fa..7729a4e 100644
--- a/PQAnalysis/atomic_system/atomic_system.py
+++ b/PQAnalysis/atomic_system/atomic_system.py
@@ -680,6 +680,17 @@ def __getitem__(
             topology=self.topology[keys]
         )
 
+    def __len__(self) -> int:
+        """
+        Returns the number of atoms in the AtomicSystem.
+
+        Returns
+        -------
+        int
+            The number of atoms in the AtomicSystem.
+        """
+        return self.n_atoms
+
     def __str__(self) -> str:
         """
         Returns the string representation of the AtomicSystem.
diff --git a/tests/atomicSystem/test_atomic_system.py b/tests/atomicSystem/test_atomic_system.py
index 9bcc15d..4e73580 100644
--- a/tests/atomicSystem/test_atomic_system.py
+++ b/tests/atomicSystem/test_atomic_system.py
@@ -356,6 +356,20 @@ def test_n_atoms(self, caplog):
             system
         )
 
+    def test__len__(self):
+        system = AtomicSystem()
+        assert len(system) == 0
+
+        system = AtomicSystem(pos=np.array([[0, 0, 0], [1, 1, 1]]))
+        assert len(system) == 2
+
+        system = AtomicSystem(
+            pos=np.array([[0, 0, 0], [1, 1, 1]]),
+            atoms=[Atom('C'), Atom('H')],
+            cell=Cell(0.75, 0.75, 0.75)
+        )
+        assert len(system) == 2
+
     def test__str__(self):
         """
         Test the __str__ method of the AtomicSystem class.

From f43393d657915992903be93864c2ed492c9d7f8a Mon Sep 17 00:00:00 2001
From: "Josef M. Gallmetzer" <gallmetzer.josef@gmail.com>
Date: Mon, 5 Aug 2024 21:33:24 +0200
Subject: [PATCH 2/4] chore: Update setup.py with compiler directive for Python
 3 compatibility

---
 setup.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/setup.py b/setup.py
index c9a87ad..e02fd11 100644
--- a/setup.py
+++ b/setup.py
@@ -12,6 +12,7 @@
         sources=['PQAnalysis/io/traj_file/process_lines.pyx'],
         include_dirs=[np.get_include()]
     )
+    compiler_directives={'language_level': 3}
 )
 
 setup(

From b2a96002dfb9df97a3a1e40df4403b198a4ccb90 Mon Sep 17 00:00:00 2001
From: "Josef M. Gallmetzer" <gallmetzer.josef@gmail.com>
Date: Mon, 5 Aug 2024 21:40:36 +0200
Subject: [PATCH 3/4] bug: Missing comma in setup.py

---
 setup.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index e02fd11..978e8d0 100644
--- a/setup.py
+++ b/setup.py
@@ -11,7 +11,7 @@
         'PQAnalysis.io.traj_file.process_lines',
         sources=['PQAnalysis/io/traj_file/process_lines.pyx'],
         include_dirs=[np.get_include()]
-    )
+    ),
     compiler_directives={'language_level': 3}
 )
 

From 7048666713c287af16772ea2b1c1c22b041241c0 Mon Sep 17 00:00:00 2001
From: "Josef M. Gallmetzer" <gallmetzer.josef@gmail.com>
Date: Tue, 6 Aug 2024 09:06:01 +0200
Subject: [PATCH 4/4] chore: Update setup.py, compiler directive for Python 3
 compatibility is not needed

---
 setup.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/setup.py b/setup.py
index 978e8d0..c9a87ad 100644
--- a/setup.py
+++ b/setup.py
@@ -11,8 +11,7 @@
         'PQAnalysis.io.traj_file.process_lines',
         sources=['PQAnalysis/io/traj_file/process_lines.pyx'],
         include_dirs=[np.get_include()]
-    ),
-    compiler_directives={'language_level': 3}
+    )
 )
 
 setup(