From a20b7ec9cbaa65eef8d5aee44ddb7317b2b42217 Mon Sep 17 00:00:00 2001
From: jimnel <janelson@tcd.ie>
Date: Mon, 7 Apr 2025 14:16:35 +0100
Subject: [PATCH 1/9] refactor

---
 qse/calc/__init__.py   | 109 +----------------------------------------
 qse/calc/abc.py        |  65 ------------------------
 qse/calc/calculator.py |  41 ++--------------
 qse/calc/signal.py     |  94 +++++++++++++++++++++++++++++++++++
 4 files changed, 98 insertions(+), 211 deletions(-)
 delete mode 100644 qse/calc/abc.py
 create mode 100644 qse/calc/signal.py

diff --git a/qse/calc/__init__.py b/qse/calc/__init__.py
index 29cd5c5..28c247b 100644
--- a/qse/calc/__init__.py
+++ b/qse/calc/__init__.py
@@ -1,116 +1,9 @@
 """Interface to different QSE calculators."""
 
 __all__ = ["abc", "calculator", "signal"]
-from typing import Union
 
-import qse.calc.abc
 import qse.calc.calculator
-
-np = qse.np
-
-
-class signal(object):
-    """
-    signal class to represent a a signal with a duration.
-    It has two components: values, and duration.
-    Instantiation of this class supports '+' in two ways.
-    If w1, w2 are instantiation of signal, then
-    - w1 + 3 gives a signal with values, w1.values + 3 and
-    same duration.
-    - w = w1 + w2 gives signal with concatenated values, i.e.,
-    w.values = [w1.values, w2.values], and added duration.
-    w.duration = w1.duration + w2.duration
-
-    Note: Currently, the object gets created for multi-dim
-    arrays as well. However, it should be used for 1D only,
-    we haven't made it useful or consistent for multi-dim usage.
-    """
-
-    #
-    # __slots__ = ('duration', 'values')
-    def __init__(self, values, duration=None) -> None:
-        self.values = np.asarray(values)
-        self._duration = len(self.values) if duration is None else int(duration)
-
-    #
-    @property
-    def duration(self):
-        """time duration of signal"""
-        return self._duration
-
-    @duration.setter
-    def duration(self, value):
-        self._duration = value
-
-    def __iter__(self):
-        return iter(self.values)
-
-    #
-    def __getitem__(self, i):
-        return self.values[i]
-
-    #
-    def __eq__(self, other) -> bool:
-        return (self.duration == other.duration) and (self.values == other.values).all()
-
-    #
-    def __add__(self, other):
-        if isinstance(other, signal):
-            res = signal(
-                values=np.append(self.values, other.values),
-                duration=self.duration + other.duration,
-            )
-        else:
-            if isinstance(other, Union[float, int]):
-                res = signal(values=self.values + other, duration=self.duration)
-            else:
-                raise TypeError(f"wrong type for operand {type(other)}")
-        return res
-
-    #
-    def __radd__(self, other):
-        return self.__add__(other)
-
-    #
-    def __iadd__(self, other):
-        if isinstance(other, signal):
-            self.values = np.append(self.values, other.values)
-            self.duration += other.duration
-        else:
-            if isinstance(other, Union[float, int]):
-                self.values += other
-            else:
-                raise TypeError(f"wrong type for operand {type(other)}")
-        return self
-
-    #
-    def __mul__(self, other):
-        if isinstance(other, Union[float, int]):
-            res = signal(values=self.values * other, duration=self.duration)
-        else:
-            raise TypeError(f"wrong type for operand {type(other)}")
-        return res
-
-    #
-    def __rmul__(self, other):
-        return self.__mul__(other)
-
-    #
-    def __imul__(self, other):
-        if isinstance(other, Union[float, int]):
-            self.values *= other
-        else:
-            raise TypeError(f"wrong type for operand {type(other)}")
-        return self
-
-    #
-    def __repr__(self) -> str:
-        return f"signal(duration={self.duration}, values={self.values})"
-
-    # we need to define interpolating scheme to resample points if duration is changed externally.
-
-
-#
+from qse.calc.signal import Signal
 
 from .myqlm import Myqlm
 from .pulser import Pulser
diff --git a/qse/calc/abc.py b/qse/calc/abc.py
deleted file mode 100644
index 0341438..0000000
--- a/qse/calc/abc.py
+++ /dev/null
@@ -1,65 +0,0 @@
-"""
-This module defines abstract helper classes with the objective of reducing
-boilerplace method definitions (i.e. duplication) in calculators.
-"""
-
-from abc import ABC, abstractmethod
-from typing import Any, Mapping
-
-
-class GetPropertiesMixin(ABC):
-    """Mixin class which provides get_forces(), get_stress() and so on.
-
-    Inheriting class must implement get_property()."""
-
-    @abstractmethod
-    def get_property(self, name, qbits=None, allow_calculation=True):
-        """Get the named property."""
-
-    # def get_energies(self, qbits=None):
-    #    return self.get_property('energies', qbits)
-
-    # def get_moment(self, qbits=None):
-    #    return self.get_property('magmom', qbits)
-
-
-""" class GetOutputsMixin(ABC):
-    #Mixin class for providing get_fermi_level() and others.
-    #
-    #Effectively this class expresses data in calc.results as
-    #methods such as get_fermi_level().
-    #
-    #Inheriting class must implement _outputmixin_get_results(),
-    #typically returning self.results, which must be a mapping
-    #using the naming defined in ase.outputs.Properties.
-    
-    @abstractmethod
-    def _outputmixin_get_results(self) -> Mapping[str, Any]:
-        #Return Mapping of names to result value.
-        #This may be called many times and should hence not be
-        #expensive (except possibly the first time).
-
-    def _get(self, name):
-        # Cyclic import, should restructure.
-        from ase.calculators.calculator import PropertyNotPresent
-        dct = self._outputmixin_get_results()
-        try:
-            return dct[name]
-        except KeyError:
-            raise PropertyNotPresent(name)
-
-    def get_fermi_level(self):
-        return self._get('fermi_level')
-
-    def get_eigenvalues(self, kpt=0, spin=0):
-        eigs = self._get('eigenvalues')
-        return eigs[kpt, spin]
-
-    def _eigshape(self):
-        # We don't need this if we already have a Properties object.
-        return self._get('eigenvalues').shape
-
-    def get_occupation_numbers(self, kpt=0, spin=0):
-        occs = self._get('occupations')
-        return occs[kpt, spin]
- """
diff --git a/qse/calc/calculator.py b/qse/calc/calculator.py
index bf0aac3..d70c8ef 100644
--- a/qse/calc/calculator.py
+++ b/qse/calc/calculator.py
@@ -3,15 +3,10 @@
 import pathlib
 import subprocess
 import warnings
-from math import pi, sqrt
 from typing import Any, Dict, List, Optional, Set, Union
 
 import numpy as np
-from ase.cell import Cell
 from ase.outputs import Properties, all_outputs
-from ase.utils import jsonable
-
-from qse.calc.abc import GetPropertiesMixin
 
 
 class CalculatorError(RuntimeError):
@@ -192,37 +187,6 @@ def equal(a, b, tol=None, rtol=None, atol=None):
     return np.allclose(a, b, rtol=rtol, atol=atol)
 
 
-# def kptdensity2monkhorstpack(atoms, kptdensity=3.5, even=True):  """Convert k-point density to Monkhorst-Pack grid size.
-
-"""
-class EigenvalOccupationMixin:
-    #Define 'eigenvalues' and 'occupations' properties on class.
-    #
-    #eigenvalues and occupations will be arrays of shape (spin, kpts, nbands).
-    #
-    #Classes must implement the old-fashioned get_eigenvalues and
-    #get_occupations methods.
-
-    @property
-    def eigenvalues(self):
-        return self.build_eig_occ_array(self.get_eigenvalues)
-
-    @property
-    def occupations(self):
-        return self.build_eig_occ_array(self.get_occupation_numbers)
-
-    def build_eig_occ_array(self, getter):
-        nspins = self.get_number_of_spins()
-        nkpts = len(self.get_ibz_k_points())
-        nbands = self.get_number_of_bands()
-        arr = np.zeros((nspins, nkpts, nbands))
-        for s in range(nspins):
-            for k in range(nkpts):
-                arr[s, k, :] = getter(spin=s, kpt=k)
-        return arr
-"""
-
-
 class Parameters(dict):
     """Dictionary for parameters.
 
@@ -278,8 +242,9 @@ def write(self, filename):
         pathlib.Path(filename).write_text(self.tostring())
 
 
-class Calculator(GetPropertiesMixin):
-    """Base-class for all QSE calculators, adapted from ASE calculators.
+class Calculator:
+    """
+    Base-class for all QSE calculators, adapted from ASE calculators.
 
     A calculator must raise PropertyNotImplementedError if asked for a
     property that it can't calculate.  So, if calculation of the
diff --git a/qse/calc/signal.py b/qse/calc/signal.py
new file mode 100644
index 0000000..57b9943
--- /dev/null
+++ b/qse/calc/signal.py
@@ -0,0 +1,94 @@
+"""The Signal class."""
+
+from typing import Union
+
+import numpy as np
+
+
+class Signal(object):
+    """
+    Signal class to represent a a signal with a duration.
+    It has two components: values, and duration.
+    Instantiation of this class supports '+' in two ways.
+    If w1, w2 are instantiation of signal, then
+    - w1 + 3 gives a signal with values, w1.values + 3 and
+    same duration.
+    - w = w1 + w2 gives signal with concatenated values, i.e.,
+    w.values = [w1.values, w2.values], and added duration.
+    w.duration = w1.duration + w2.duration
+
+    Note: Currently, the object gets created for multi-dim
+    arrays as well. However, it should be used for 1D only,
+    we haven't made it useful or consistent for multi-dim usage.
+    """
+
+    def __init__(self, values, duration=None) -> None:
+        self.values = np.asarray(values)
+        self._duration = len(self.values) if duration is None else int(duration)
+
+    @property
+    def duration(self):
+        """time duration of signal"""
+        return self._duration
+
+    @duration.setter
+    def duration(self, value):
+        self._duration = value
+
+    def __iter__(self):
+        return iter(self.values)
+
+    def __getitem__(self, i):
+        return self.values[i]
+
+    def __eq__(self, other) -> bool:
+        return (self.duration == other.duration) and (self.values == other.values).all()
+
+    def __add__(self, other):
+        if isinstance(other, Signal):
+            res = Signal(
+                values=np.append(self.values, other.values),
+                duration=self.duration + other.duration,
+            )
+        else:
+            if isinstance(other, Union[float, int]):
+                res = Signal(values=self.values + other, duration=self.duration)
+            else:
+                raise TypeError(f"wrong type for operand {type(other)}")
+        return res
+
+    def __radd__(self, other):
+        return self.__add__(other)
+
+    def __iadd__(self, other):
+        if isinstance(other, Signal):
+            self.values = np.append(self.values, other.values)
+            self.duration += other.duration
+        else:
+            if isinstance(other, Union[float, int]):
+                self.values += other
+            else:
+                raise TypeError(f"wrong type for operand {type(other)}")
+        return self
+
+    def __mul__(self, other):
+        if isinstance(other, Union[float, int]):
+            res = Signal(values=self.values * other, duration=self.duration)
+        else:
+            raise TypeError(f"wrong type for operand {type(other)}")
+        return res
+
+    def __rmul__(self, other):
+        return self.__mul__(other)
+
+    def __imul__(self, other):
+        if isinstance(other, Union[float, int]):
+            self.values *= other
+        else:
+            raise TypeError(f"wrong type for operand {type(other)}")
+        return self
+
+    def __repr__(self) -> str:
+        return f"signal(duration={self.duration}, values={self.values})"
+
+    # we need to define interpolating scheme to resample points if duration is changed externally.

From d977d75472879746056c73f60ae1d14bc132e75f Mon Sep 17 00:00:00 2001
From: James Nelson <james.nelson@ichec.ie>
Date: Mon, 7 Apr 2025 15:00:33 +0100
Subject: [PATCH 2/9] Update qse/calc/signal.py

---
 qse/calc/signal.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/qse/calc/signal.py b/qse/calc/signal.py
index 57b9943..b51679d 100644
--- a/qse/calc/signal.py
+++ b/qse/calc/signal.py
@@ -1,4 +1,4 @@
-"""The Signal class."""
+"""Definition of the Signal class."""
 
 from typing import Union
 

From 0c47e78d167743b6dbf419392c06da09c15a71d9 Mon Sep 17 00:00:00 2001
From: jimnel <janelson@tcd.ie>
Date: Mon, 7 Apr 2025 16:39:09 +0100
Subject: [PATCH 3/9] create messages.py

---
 qse/calc/calculator.py | 59 ++------------------------------------
 qse/calc/messages.py   | 65 ++++++++++++++++++++++++++++++++++++++++++
 qse/calc/myqlm.py      |  2 +-
 qse/calc/pulser.py     | 14 ++-------
 4 files changed, 71 insertions(+), 69 deletions(-)
 create mode 100644 qse/calc/messages.py

diff --git a/qse/calc/calculator.py b/qse/calc/calculator.py
index d70c8ef..4adfbb6 100644
--- a/qse/calc/calculator.py
+++ b/qse/calc/calculator.py
@@ -3,66 +3,11 @@
 import pathlib
 import subprocess
 import warnings
-from typing import Any, Dict, List, Optional, Set, Union
+from typing import Any, Dict, List, Optional, Set
 
 import numpy as np
 from ase.outputs import Properties, all_outputs
-
-
-class CalculatorError(RuntimeError):
-    """Base class of error types related to ASE calculators."""
-
-
-class CalculatorSetupError(CalculatorError):
-    """Calculation cannot be performed with the given parameters.
-
-    Reasons to raise this errors are:
-      * The calculator is not properly configured
-        (missing executable, environment variables, ...)
-      * The given qbits object is not supported
-      * Calculator parameters are unsupported
-
-    Typically raised before a calculation."""
-
-
-class EnvironmentError(CalculatorSetupError):
-    """Raised if calculator is not properly set up with ASE.
-    May be missing an executable or environment variables."""
-
-
-class InputError(CalculatorSetupError):
-    """Raised if inputs given to the calculator were incorrect.
-    Bad input keywords or values, or missing pseudopotentials.
-    This may be raised before or during calculation, depending on
-    when the problem is detected."""
-
-
-class CalculationFailed(CalculatorError):
-    """Calculation failed unexpectedly.
-
-    Reasons to raise this error are:
-      * Calculation did not converge
-      * Calculation ran out of memory
-      * Segmentation fault or other abnormal termination
-      * Arithmetic trouble (singular matrices, NaN, ...)
-
-    Typically raised during calculation."""
-
-
-class ReadError(CalculatorError):
-    """Unexpected irrecoverable error while reading calculation results."""
-
-
-class PropertyNotImplementedError(NotImplementedError):
-    """Raised if a calculator does not implement the requested property."""
-
-
-class PropertyNotPresent(CalculatorError):
-    """Requested property is missing.
-
-    Maybe it was never calculated, or for some reason was not extracted
-    with the rest of the results, without being a fatal ReadError."""
-
+from qse.calc.messages import PropertyNotImplementedError, PropertyNotPresent, CalculatorSetupError, CalculationFailed
 
 def compare_qbits(qbits1, qbits2, tol=1e-15, excluded_properties=None):
     """Check for system changes since last calculation.  Properties in
diff --git a/qse/calc/messages.py b/qse/calc/messages.py
new file mode 100644
index 0000000..8dd5861
--- /dev/null
+++ b/qse/calc/messages.py
@@ -0,0 +1,65 @@
+"""Messages that are thrown when using the calculator."""
+
+class CalculatorError(RuntimeError):
+    """Base class of error types related to QSE calculators."""
+
+
+class CalculatorSetupError(CalculatorError):
+    """
+    Calculation cannot be performed with the given parameters.
+
+    Reasons to raise this errors are:
+      * The calculator is not properly configured
+        (missing executable, environment variables, ...)
+      * The given qbits object is not supported
+      * Calculator parameters are unsupported
+
+    Typically raised before a calculation.
+    """
+
+
+class EnvironmentError(CalculatorSetupError):
+    """
+    Raised if calculator is not properly set up with QSE.
+    May be missing an executable or environment variables.
+    """
+
+
+class InputError(CalculatorSetupError):
+    """
+    Raised if inputs given to the calculator were incorrect.
+    Bad input keywords or values, or missing pseudopotentials.
+    This may be raised before or during calculation, depending on
+    when the problem is detected.
+    """
+
+
+class CalculationFailed(CalculatorError):
+    """
+    Calculation failed unexpectedly.
+
+    Reasons to raise this error are:
+      * Calculation did not converge
+      * Calculation ran out of memory
+      * Segmentation fault or other abnormal termination
+      * Arithmetic trouble (singular matrices, NaN, ...)
+
+    Typically raised during calculation.
+    """
+
+
+class ReadError(CalculatorError):
+    """Unexpected irrecoverable error while reading calculation results."""
+
+
+class PropertyNotImplementedError(NotImplementedError):
+    """Raised if a calculator does not implement the requested property."""
+
+
+class PropertyNotPresent(CalculatorError):
+    """
+    Requested property is missing.
+
+    Maybe it was never calculated, or for some reason was not extracted
+    with the rest of the results, without being a fatal ReadError.
+    """
diff --git a/qse/calc/myqlm.py b/qse/calc/myqlm.py
index 61855ed..c3d72cd 100644
--- a/qse/calc/myqlm.py
+++ b/qse/calc/myqlm.py
@@ -7,7 +7,7 @@
 
 import numpy as np
 
-from qse.calc.calculator import Calculator, all_changes
+from qse.calc.calculator import Calculator
 
 qat_available = False
 qlmaas_available = False
diff --git a/qse/calc/pulser.py b/qse/calc/pulser.py
index bba6580..41464df 100644
--- a/qse/calc/pulser.py
+++ b/qse/calc/pulser.py
@@ -4,17 +4,8 @@
 ASE calculator.
 https://pulser.readthedocs.io/en/stable/
 """
-
-import os
-import os.path
-from abc import ABCMeta
-from subprocess import PIPE, Popen
-from warnings import warn
-
-import ase.io
 import numpy as np
 import pulser
-import pulser.pulse
 import pulser.waveforms
 
 # from pulser_simulation import Simulation, SimConfig, QutipEmulator
@@ -24,8 +15,9 @@
 from qse.calc.calculator import (
     Calculator,
     CalculatorSetupError,
-    Parameters,
-    all_changes,
+)
+from qse.calc.messages import (
+    CalculatorSetupError,
 )
 
 # from ase.calculators.calculator import (Calculator, all_changes, Parameters, CalculatorSetupError)

From 7b5a82b0ee5788c1e56b8bffbce665fe1e4220fb Mon Sep 17 00:00:00 2001
From: jimnel <janelson@tcd.ie>
Date: Mon, 7 Apr 2025 16:40:35 +0100
Subject: [PATCH 4/9] update __init__

---
 qse/calc/__init__.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/qse/calc/__init__.py b/qse/calc/__init__.py
index 28c247b..34bd7ba 100644
--- a/qse/calc/__init__.py
+++ b/qse/calc/__init__.py
@@ -1,9 +1,10 @@
 """Interface to different QSE calculators."""
 
-__all__ = ["abc", "calculator", "signal"]
+__all__ = ["abc", "calculator", "Signal", "PropertyNotImplementedError", "PropertyNotPresent", "CalculatorSetupError", "CalculationFailed"]
 
 import qse.calc.calculator
 from qse.calc.signal import Signal
+from qse.calc.messages import PropertyNotImplementedError, PropertyNotPresent, CalculatorSetupError, CalculationFailed
 
 from .myqlm import Myqlm
 from .pulser import Pulser

From 1b3ad4615d550ae0807449c868bb25b67323f646 Mon Sep 17 00:00:00 2001
From: jimnel <janelson@tcd.ie>
Date: Mon, 7 Apr 2025 16:42:23 +0100
Subject: [PATCH 5/9] isort + black

---
 qse/calc/__init__.py   | 17 +++++++++++++++--
 qse/calc/calculator.py |  9 ++++++++-
 qse/calc/messages.py   |  1 +
 qse/calc/pulser.py     | 10 +++-------
 4 files changed, 27 insertions(+), 10 deletions(-)

diff --git a/qse/calc/__init__.py b/qse/calc/__init__.py
index 34bd7ba..78399e4 100644
--- a/qse/calc/__init__.py
+++ b/qse/calc/__init__.py
@@ -1,10 +1,23 @@
 """Interface to different QSE calculators."""
 
-__all__ = ["abc", "calculator", "Signal", "PropertyNotImplementedError", "PropertyNotPresent", "CalculatorSetupError", "CalculationFailed"]
+__all__ = [
+    "abc",
+    "calculator",
+    "Signal",
+    "PropertyNotImplementedError",
+    "PropertyNotPresent",
+    "CalculatorSetupError",
+    "CalculationFailed",
+]
 
 import qse.calc.calculator
+from qse.calc.messages import (
+    CalculationFailed,
+    CalculatorSetupError,
+    PropertyNotImplementedError,
+    PropertyNotPresent,
+)
 from qse.calc.signal import Signal
-from qse.calc.messages import PropertyNotImplementedError, PropertyNotPresent, CalculatorSetupError, CalculationFailed
 
 from .myqlm import Myqlm
 from .pulser import Pulser
diff --git a/qse/calc/calculator.py b/qse/calc/calculator.py
index 4adfbb6..ac81c90 100644
--- a/qse/calc/calculator.py
+++ b/qse/calc/calculator.py
@@ -7,7 +7,14 @@
 
 import numpy as np
 from ase.outputs import Properties, all_outputs
-from qse.calc.messages import PropertyNotImplementedError, PropertyNotPresent, CalculatorSetupError, CalculationFailed
+
+from qse.calc.messages import (
+    CalculationFailed,
+    CalculatorSetupError,
+    PropertyNotImplementedError,
+    PropertyNotPresent,
+)
+
 
 def compare_qbits(qbits1, qbits2, tol=1e-15, excluded_properties=None):
     """Check for system changes since last calculation.  Properties in
diff --git a/qse/calc/messages.py b/qse/calc/messages.py
index 8dd5861..2c663f5 100644
--- a/qse/calc/messages.py
+++ b/qse/calc/messages.py
@@ -1,5 +1,6 @@
 """Messages that are thrown when using the calculator."""
 
+
 class CalculatorError(RuntimeError):
     """Base class of error types related to QSE calculators."""
 
diff --git a/qse/calc/pulser.py b/qse/calc/pulser.py
index 41464df..e901808 100644
--- a/qse/calc/pulser.py
+++ b/qse/calc/pulser.py
@@ -4,6 +4,7 @@
 ASE calculator.
 https://pulser.readthedocs.io/en/stable/
 """
+
 import numpy as np
 import pulser
 import pulser.waveforms
@@ -12,13 +13,8 @@
 from pulser_simulation import QutipEmulator
 
 from qse.calc import signal
-from qse.calc.calculator import (
-    Calculator,
-    CalculatorSetupError,
-)
-from qse.calc.messages import (
-    CalculatorSetupError,
-)
+from qse.calc.calculator import Calculator, CalculatorSetupError
+from qse.calc.messages import CalculatorSetupError
 
 # from ase.calculators.calculator import (Calculator, all_changes, Parameters, CalculatorSetupError)
 

From ecf31b4070de0c334bb7e8218fbb841791cb4683 Mon Sep 17 00:00:00 2001
From: jimnel <janelson@tcd.ie>
Date: Mon, 7 Apr 2025 16:46:33 +0100
Subject: [PATCH 6/9] remove abc

---
 qse/calc/__init__.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/qse/calc/__init__.py b/qse/calc/__init__.py
index 78399e4..6ca6135 100644
--- a/qse/calc/__init__.py
+++ b/qse/calc/__init__.py
@@ -1,7 +1,6 @@
 """Interface to different QSE calculators."""
 
 __all__ = [
-    "abc",
     "calculator",
     "Signal",
     "PropertyNotImplementedError",

From ed4acc9a9835fd597e7d9bc508e28e3f24083ae7 Mon Sep 17 00:00:00 2001
From: jimnel <janelson@tcd.ie>
Date: Wed, 9 Apr 2025 14:36:27 +0100
Subject: [PATCH 7/9] move signal

---
 qse/__init__.py      |  1 +
 qse/calc/__init__.py |  1 -
 qse/calc/pulser.py   |  2 +-
 qse/calc/signal.py   | 94 --------------------------------------------
 4 files changed, 2 insertions(+), 96 deletions(-)
 delete mode 100644 qse/calc/signal.py

diff --git a/qse/__init__.py b/qse/__init__.py
index f1dba64..7f2bf66 100644
--- a/qse/__init__.py
+++ b/qse/__init__.py
@@ -15,4 +15,5 @@
 from qse import utils
 from qse.qbit import Qbit
 from qse.qbits import Qbits
+from qse.signal import Signal
 from qse.visualise import draw
diff --git a/qse/calc/__init__.py b/qse/calc/__init__.py
index 6ca6135..8ae421c 100644
--- a/qse/calc/__init__.py
+++ b/qse/calc/__init__.py
@@ -16,7 +16,6 @@
     PropertyNotImplementedError,
     PropertyNotPresent,
 )
-from qse.calc.signal import Signal
 
 from .myqlm import Myqlm
 from .pulser import Pulser
diff --git a/qse/calc/pulser.py b/qse/calc/pulser.py
index e901808..ad82538 100644
--- a/qse/calc/pulser.py
+++ b/qse/calc/pulser.py
@@ -12,7 +12,7 @@
 # from pulser_simulation import Simulation, SimConfig, QutipEmulator
 from pulser_simulation import QutipEmulator
 
-from qse.calc import signal
+from qse import signal
 from qse.calc.calculator import Calculator, CalculatorSetupError
 from qse.calc.messages import CalculatorSetupError
 
diff --git a/qse/calc/signal.py b/qse/calc/signal.py
deleted file mode 100644
index b51679d..0000000
--- a/qse/calc/signal.py
+++ /dev/null
@@ -1,94 +0,0 @@
-"""Definition of the Signal class."""
-
-from typing import Union
-
-import numpy as np
-
-
-class Signal(object):
-    """
-    Signal class to represent a a signal with a duration.
-    It has two components: values, and duration.
-    Instantiation of this class supports '+' in two ways.
-    If w1, w2 are instantiation of signal, then
-    - w1 + 3 gives a signal with values, w1.values + 3 and
-    same duration.
-    - w = w1 + w2 gives signal with concatenated values, i.e.,
-    w.values = [w1.values, w2.values], and added duration.
-    w.duration = w1.duration + w2.duration
-
-    Note: Currently, the object gets created for multi-dim
-    arrays as well. However, it should be used for 1D only,
-    we haven't made it useful or consistent for multi-dim usage.
-    """
-
-    def __init__(self, values, duration=None) -> None:
-        self.values = np.asarray(values)
-        self._duration = len(self.values) if duration is None else int(duration)
-
-    @property
-    def duration(self):
-        """time duration of signal"""
-        return self._duration
-
-    @duration.setter
-    def duration(self, value):
-        self._duration = value
-
-    def __iter__(self):
-        return iter(self.values)
-
-    def __getitem__(self, i):
-        return self.values[i]
-
-    def __eq__(self, other) -> bool:
-        return (self.duration == other.duration) and (self.values == other.values).all()
-
-    def __add__(self, other):
-        if isinstance(other, Signal):
-            res = Signal(
-                values=np.append(self.values, other.values),
-                duration=self.duration + other.duration,
-            )
-        else:
-            if isinstance(other, Union[float, int]):
-                res = Signal(values=self.values + other, duration=self.duration)
-            else:
-                raise TypeError(f"wrong type for operand {type(other)}")
-        return res
-
-    def __radd__(self, other):
-        return self.__add__(other)
-
-    def __iadd__(self, other):
-        if isinstance(other, Signal):
-            self.values = np.append(self.values, other.values)
-            self.duration += other.duration
-        else:
-            if isinstance(other, Union[float, int]):
-                self.values += other
-            else:
-                raise TypeError(f"wrong type for operand {type(other)}")
-        return self
-
-    def __mul__(self, other):
-        if isinstance(other, Union[float, int]):
-            res = Signal(values=self.values * other, duration=self.duration)
-        else:
-            raise TypeError(f"wrong type for operand {type(other)}")
-        return res
-
-    def __rmul__(self, other):
-        return self.__mul__(other)
-
-    def __imul__(self, other):
-        if isinstance(other, Union[float, int]):
-            self.values *= other
-        else:
-            raise TypeError(f"wrong type for operand {type(other)}")
-        return self
-
-    def __repr__(self) -> str:
-        return f"signal(duration={self.duration}, values={self.values})"
-
-    # we need to define interpolating scheme to resample points if duration is changed externally.

From 61dc316eaaf7cec27816bf966d060b821253915f Mon Sep 17 00:00:00 2001
From: jimnel <janelson@tcd.ie>
Date: Wed, 9 Apr 2025 14:39:16 +0100
Subject: [PATCH 8/9] init

---
 qse/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/qse/__init__.py b/qse/__init__.py
index 7f2bf66..1f1b506 100644
--- a/qse/__init__.py
+++ b/qse/__init__.py
@@ -5,7 +5,7 @@
 This package is adapted from Atomic Simulation Environment (ASE).
 """
 
-__all__ = ["Qbits", "Qbit"]
+__all__ = ["Qbits", "Qbit", "Signal"]
 __version__ = "0.1.1"
 
 # from qse.calc.pulser import Pulser

From 870c4188f916923b58a18c43e1ef2d2f9736b265 Mon Sep 17 00:00:00 2001
From: jimnel <janelson@tcd.ie>
Date: Wed, 9 Apr 2025 14:40:21 +0100
Subject: [PATCH 9/9] signal

---
 qse/signal.py | 94 +++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 94 insertions(+)
 create mode 100644 qse/signal.py

diff --git a/qse/signal.py b/qse/signal.py
new file mode 100644
index 0000000..17b576d
--- /dev/null
+++ b/qse/signal.py
@@ -0,0 +1,94 @@
+"""Definition of the Signal class."""
+
+from typing import Union
+
+import numpy as np
+
+
+class Signal:
+    """
+    Signal class to represent a a signal with a duration.
+    It has two components: values, and duration.
+    Instantiation of this class supports '+' in two ways.
+    If w1, w2 are instantiation of signal, then
+    - w1 + 3 gives a signal with values, w1.values + 3 and
+    same duration.
+    - w = w1 + w2 gives signal with concatenated values, i.e.,
+    w.values = [w1.values, w2.values], and added duration.
+    w.duration = w1.duration + w2.duration
+
+    Note: Currently, the object gets created for multi-dim
+    arrays as well. However, it should be used for 1D only,
+    we haven't made it useful or consistent for multi-dim usage.
+    """
+
+    def __init__(self, values, duration=None) -> None:
+        self.values = np.asarray(values)
+        self._duration = len(self.values) if duration is None else int(duration)
+
+    @property
+    def duration(self):
+        """time duration of signal"""
+        return self._duration
+
+    @duration.setter
+    def duration(self, value):
+        self._duration = value
+
+    def __iter__(self):
+        return iter(self.values)
+
+    def __getitem__(self, i):
+        return self.values[i]
+
+    def __eq__(self, other) -> bool:
+        return (self.duration == other.duration) and (self.values == other.values).all()
+
+    def __add__(self, other):
+        if isinstance(other, Signal):
+            res = Signal(
+                values=np.append(self.values, other.values),
+                duration=self.duration + other.duration,
+            )
+        else:
+            if isinstance(other, Union[float, int]):
+                res = Signal(values=self.values + other, duration=self.duration)
+            else:
+                raise TypeError(f"wrong type for operand {type(other)}")
+        return res
+
+    def __radd__(self, other):
+        return self.__add__(other)
+
+    def __iadd__(self, other):
+        if isinstance(other, Signal):
+            self.values = np.append(self.values, other.values)
+            self.duration += other.duration
+        else:
+            if isinstance(other, Union[float, int]):
+                self.values += other
+            else:
+                raise TypeError(f"wrong type for operand {type(other)}")
+        return self
+
+    def __mul__(self, other):
+        if isinstance(other, Union[float, int]):
+            res = Signal(values=self.values * other, duration=self.duration)
+        else:
+            raise TypeError(f"wrong type for operand {type(other)}")
+        return res
+
+    def __rmul__(self, other):
+        return self.__mul__(other)
+
+    def __imul__(self, other):
+        if isinstance(other, Union[float, int]):
+            self.values *= other
+        else:
+            raise TypeError(f"wrong type for operand {type(other)}")
+        return self
+
+    def __repr__(self) -> str:
+        return f"signal(duration={self.duration}, values={self.values})"
+
+    # we need to define interpolating scheme to resample points if duration is changed externally.