From 63ae074f35559eef2f82c83a938e605c47b23884 Mon Sep 17 00:00:00 2001
From: Mark Polk <mark.polk@choderalab.org>
Date: Sat, 5 Oct 2024 21:41:19 -0400
Subject: [PATCH 01/20] updated pyproject.toml to include packages

---
 missense_kinase_toolkit/experiments/pyproject.toml | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/missense_kinase_toolkit/experiments/pyproject.toml b/missense_kinase_toolkit/experiments/pyproject.toml
index a4c1d70..e26c083 100644
--- a/missense_kinase_toolkit/experiments/pyproject.toml
+++ b/missense_kinase_toolkit/experiments/pyproject.toml
@@ -5,6 +5,11 @@ description = "Tools to facilitate experimental analyses for missense_kinase_too
 authors = ["Jess White <jess.white@choderalab.org>"]
 license = "MIT"
 readme = "README.md"
+#https://safjan.com/the-importance-of-adding-py-typed-file-to-your-typed-package/
+packages = [
+    {include = "missense_kinase_toolkit"},
+    {include = "missense_kinase_toolkit/py.typed"}
+]
 
 [tool.poetry.dependencies]
 python = "^3.9"

From 34004bfaf405b1063b58dee056a9dfe80a3ec1e1 Mon Sep 17 00:00:00 2001
From: Mark Polk <mark.polk@choderalab.org>
Date: Sat, 5 Oct 2024 22:04:40 -0400
Subject: [PATCH 02/20] instantiate Experiment Class

---
 .../experiments/plate_reader.py                   | 15 +++++++++++++++
 1 file changed, 15 insertions(+)
 create mode 100644 missense_kinase_toolkit/experiments/missense_kinase_toolkit/experiments/plate_reader.py

diff --git a/missense_kinase_toolkit/experiments/missense_kinase_toolkit/experiments/plate_reader.py b/missense_kinase_toolkit/experiments/missense_kinase_toolkit/experiments/plate_reader.py
new file mode 100644
index 0000000..2964e3b
--- /dev/null
+++ b/missense_kinase_toolkit/experiments/missense_kinase_toolkit/experiments/plate_reader.py
@@ -0,0 +1,15 @@
+class Experiment:
+    """Class to process Tecan i-control .XML output."""
+
+    def __init__(
+        self,
+    ) -> None:
+        """Initialize Experiment Class object.
+
+        Parameters
+        ----------
+
+        Attributes
+        ----------
+
+        """
\ No newline at end of file

From b8dce349f529813b0614555af33d11472484f85a Mon Sep 17 00:00:00 2001
From: Mark Polk <mark.polk@choderalab.org>
Date: Sat, 5 Oct 2024 23:30:45 -0400
Subject: [PATCH 03/20] added labels attribute to Experiment Class

---
 .../experiments/plate_reader.py               | 21 ++++++++++++++++++-
 1 file changed, 20 insertions(+), 1 deletion(-)

diff --git a/missense_kinase_toolkit/experiments/missense_kinase_toolkit/experiments/plate_reader.py b/missense_kinase_toolkit/experiments/missense_kinase_toolkit/experiments/plate_reader.py
index 2964e3b..ec1daa7 100644
--- a/missense_kinase_toolkit/experiments/missense_kinase_toolkit/experiments/plate_reader.py
+++ b/missense_kinase_toolkit/experiments/missense_kinase_toolkit/experiments/plate_reader.py
@@ -1,15 +1,34 @@
+import xml.etree.ElementTree as ET
+
+
 class Experiment:
     """Class to process Tecan i-control .XML output."""
 
     def __init__(
         self,
+        filepath
     ) -> None:
         """Initialize Experiment Class object.
 
         Parameters
         ----------
+        filepath : str
+            Filepath to Tecan i-control .XML output.
 
         Attributes
         ----------
+        filepath : str
+            Filepath to Tecan i-control .XML output.
+
+        """
+        self.filepath = filepath
+        self.labels = []
 
-        """
\ No newline at end of file
+        if filepath.lower()[-4:] != '.xml':
+            raise TypeError('Filepath does not point to .xml file')
+        
+        tree = ET.parse(filepath)
+        root = tree.getroot()
+        
+        for section in root.iter('Section'):
+            self.labels.append(section.attrib['Name'])
\ No newline at end of file

From c99e9d44a53252bd6c8ca34027b6ff84c221012b Mon Sep 17 00:00:00 2001
From: Mark Polk <mark.polk@choderalab.org>
Date: Sat, 5 Oct 2024 23:32:28 -0400
Subject: [PATCH 04/20] instantiate automatically generated poetry.lock file

---
 missense_kinase_toolkit/experiments/poetry.lock | 7 +++++++
 1 file changed, 7 insertions(+)
 create mode 100644 missense_kinase_toolkit/experiments/poetry.lock

diff --git a/missense_kinase_toolkit/experiments/poetry.lock b/missense_kinase_toolkit/experiments/poetry.lock
new file mode 100644
index 0000000..ac1e080
--- /dev/null
+++ b/missense_kinase_toolkit/experiments/poetry.lock
@@ -0,0 +1,7 @@
+# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand.
+package = []
+
+[metadata]
+lock-version = "2.0"
+python-versions = "^3.9"
+content-hash = "c595a0588c25d58f3e3834ad7169126836d262b925fe6ca9b5d540dcf301d254"

From 63489216c5a055c36cc69030f5cbb12b560a4161 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Sun, 6 Oct 2024 03:44:51 +0000
Subject: [PATCH 05/20] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 .../experiments/plate_reader.py                 | 17 +++++++----------
 1 file changed, 7 insertions(+), 10 deletions(-)

diff --git a/missense_kinase_toolkit/experiments/missense_kinase_toolkit/experiments/plate_reader.py b/missense_kinase_toolkit/experiments/missense_kinase_toolkit/experiments/plate_reader.py
index ec1daa7..ca0c763 100644
--- a/missense_kinase_toolkit/experiments/missense_kinase_toolkit/experiments/plate_reader.py
+++ b/missense_kinase_toolkit/experiments/missense_kinase_toolkit/experiments/plate_reader.py
@@ -4,10 +4,7 @@
 class Experiment:
     """Class to process Tecan i-control .XML output."""
 
-    def __init__(
-        self,
-        filepath
-    ) -> None:
+    def __init__(self, filepath) -> None:
         """Initialize Experiment Class object.
 
         Parameters
@@ -24,11 +21,11 @@ def __init__(
         self.filepath = filepath
         self.labels = []
 
-        if filepath.lower()[-4:] != '.xml':
-            raise TypeError('Filepath does not point to .xml file')
-        
+        if filepath.lower()[-4:] != ".xml":
+            raise TypeError("Filepath does not point to .xml file")
+
         tree = ET.parse(filepath)
         root = tree.getroot()
-        
-        for section in root.iter('Section'):
-            self.labels.append(section.attrib['Name'])
\ No newline at end of file
+
+        for section in root.iter("Section"):
+            self.labels.append(section.attrib["Name"])

From b8d25b3afa5081eaf2b3a990519d9e363695f0d4 Mon Sep 17 00:00:00 2001
From: Mark Polk <mark.polk@choderalab.org>
Date: Sun, 6 Oct 2024 00:05:58 -0400
Subject: [PATCH 06/20] instantiate Measurement and Parameters classes

---
 .../experiments/plate_reader.py               | 33 +++++++++++++++++++
 1 file changed, 33 insertions(+)

diff --git a/missense_kinase_toolkit/experiments/missense_kinase_toolkit/experiments/plate_reader.py b/missense_kinase_toolkit/experiments/missense_kinase_toolkit/experiments/plate_reader.py
index ca0c763..b75e36f 100644
--- a/missense_kinase_toolkit/experiments/missense_kinase_toolkit/experiments/plate_reader.py
+++ b/missense_kinase_toolkit/experiments/missense_kinase_toolkit/experiments/plate_reader.py
@@ -16,6 +16,8 @@ def __init__(self, filepath) -> None:
         ----------
         filepath : str
             Filepath to Tecan i-control .XML output.
+        labels: list
+            List of labels.
 
         """
         self.filepath = filepath
@@ -29,3 +31,34 @@ def __init__(self, filepath) -> None:
 
         for section in root.iter("Section"):
             self.labels.append(section.attrib["Name"])
+
+class Measurement:
+    """Class to store measurement data."""
+
+    def __init__(self) -> None:
+        """Initialize Measurement Class object.
+        
+        Parameters
+        ----------
+
+        Attributes
+        ----------
+        
+        """
+        pass
+
+class Parameters(Measurement):
+    """Class to store measurement parameters."""
+
+    def __init__(self) -> None:
+        """Initialize Parameters Class object.
+        
+        Parameters
+        ----------
+
+        Attributes
+        ----------
+
+        """
+        pass
+    pass

From b17f44a52cfdcc5b32c5e3deaa31e507434248d4 Mon Sep 17 00:00:00 2001
From: Mark Polk <mark.polk@choderalab.org>
Date: Sun, 6 Oct 2024 01:18:39 -0400
Subject: [PATCH 07/20] removed parameters from separate class to Measurement
 attribute

---
 .../experiments/plate_reader.py               | 46 ++++++++-----------
 1 file changed, 20 insertions(+), 26 deletions(-)

diff --git a/missense_kinase_toolkit/experiments/missense_kinase_toolkit/experiments/plate_reader.py b/missense_kinase_toolkit/experiments/missense_kinase_toolkit/experiments/plate_reader.py
index b75e36f..3172cfd 100644
--- a/missense_kinase_toolkit/experiments/missense_kinase_toolkit/experiments/plate_reader.py
+++ b/missense_kinase_toolkit/experiments/missense_kinase_toolkit/experiments/plate_reader.py
@@ -1,5 +1,7 @@
 import xml.etree.ElementTree as ET
 
+# i-control manual: https://bif.wisc.edu/wp-content/uploads/sites/389/2017/11/i-control_Manual.pdf
+
 
 class Experiment:
     """Class to process Tecan i-control .XML output."""
@@ -9,19 +11,13 @@ def __init__(self, filepath) -> None:
 
         Parameters
         ----------
-        filepath : str
-            Filepath to Tecan i-control .XML output.
 
         Attributes
         ----------
-        filepath : str
-            Filepath to Tecan i-control .XML output.
-        labels: list
-            List of labels.
 
         """
         self.filepath = filepath
-        self.labels = []
+        self.measurements = []
 
         if filepath.lower()[-4:] != ".xml":
             raise TypeError("Filepath does not point to .xml file")
@@ -29,13 +25,22 @@ def __init__(self, filepath) -> None:
         tree = ET.parse(filepath)
         root = tree.getroot()
 
+        # TODO: check if i-control allows duplicate labels
+
         for section in root.iter("Section"):
-            self.labels.append(section.attrib["Name"])
+            self.measurements.append(Measurement(section))
+
+    def get_measurement_by_label(self, label):
+
+        for i in range(len(self.measurements)):
+            if self.measurements[i].label == label:
+                return self.measurements[i]
+
 
 class Measurement:
-    """Class to store measurement data."""
+    """Class to store measurement."""
 
-    def __init__(self) -> None:
+    def __init__(self, section) -> None:
         """Initialize Measurement Class object.
         
         Parameters
@@ -45,20 +50,9 @@ def __init__(self) -> None:
         ----------
         
         """
-        pass
-
-class Parameters(Measurement):
-    """Class to store measurement parameters."""
-
-    def __init__(self) -> None:
-        """Initialize Parameters Class object.
-        
-        Parameters
-        ----------
+        self.label = section.attrib['Name']
+        self.parameters = {}
 
-        Attributes
-        ----------
-
-        """
-        pass
-    pass
+        for parameters in section.iter("Parameters"):
+            for parameter in parameters:
+                self.parameters[parameter.attrib['Name']] = parameter.attrib['Value']
\ No newline at end of file

From 7f5e44bef14438b9ec1708e6185a4b903a0db5d9 Mon Sep 17 00:00:00 2001
From: Mark Polk <mark.polk@choderalab.org>
Date: Sun, 6 Oct 2024 01:37:59 -0400
Subject: [PATCH 08/20] added start time, end time, and duration to Measurement
 class

---
 .../missense_kinase_toolkit/experiments/plate_reader.py  | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/missense_kinase_toolkit/experiments/missense_kinase_toolkit/experiments/plate_reader.py b/missense_kinase_toolkit/experiments/missense_kinase_toolkit/experiments/plate_reader.py
index 3172cfd..936cefb 100644
--- a/missense_kinase_toolkit/experiments/missense_kinase_toolkit/experiments/plate_reader.py
+++ b/missense_kinase_toolkit/experiments/missense_kinase_toolkit/experiments/plate_reader.py
@@ -1,4 +1,5 @@
 import xml.etree.ElementTree as ET
+from datetime import datetime
 
 # i-control manual: https://bif.wisc.edu/wp-content/uploads/sites/389/2017/11/i-control_Manual.pdf
 
@@ -52,7 +53,13 @@ def __init__(self, section) -> None:
         """
         self.label = section.attrib['Name']
         self.parameters = {}
+        self.time_start = datetime.fromisoformat(section[0].text)
+        self.time_end = datetime.fromisoformat(section[-1].text)
 
         for parameters in section.iter("Parameters"):
             for parameter in parameters:
-                self.parameters[parameter.attrib['Name']] = parameter.attrib['Value']
\ No newline at end of file
+                self.parameters[parameter.attrib['Name']] = parameter.attrib['Value']
+
+    def get_duration(self):
+        duration = self.time_end - self.time_start
+        return duration
\ No newline at end of file

From 3ef25ce29a4c889ecaaa6b2623b1d2a9e9f526fb Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Sun, 6 Oct 2024 05:52:09 +0000
Subject: [PATCH 09/20] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 .../experiments/plate_reader.py                        | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/missense_kinase_toolkit/experiments/missense_kinase_toolkit/experiments/plate_reader.py b/missense_kinase_toolkit/experiments/missense_kinase_toolkit/experiments/plate_reader.py
index 936cefb..8403359 100644
--- a/missense_kinase_toolkit/experiments/missense_kinase_toolkit/experiments/plate_reader.py
+++ b/missense_kinase_toolkit/experiments/missense_kinase_toolkit/experiments/plate_reader.py
@@ -43,23 +43,23 @@ class Measurement:
 
     def __init__(self, section) -> None:
         """Initialize Measurement Class object.
-        
+
         Parameters
         ----------
 
         Attributes
         ----------
-        
+
         """
-        self.label = section.attrib['Name']
+        self.label = section.attrib["Name"]
         self.parameters = {}
         self.time_start = datetime.fromisoformat(section[0].text)
         self.time_end = datetime.fromisoformat(section[-1].text)
 
         for parameters in section.iter("Parameters"):
             for parameter in parameters:
-                self.parameters[parameter.attrib['Name']] = parameter.attrib['Value']
+                self.parameters[parameter.attrib["Name"]] = parameter.attrib["Value"]
 
     def get_duration(self):
         duration = self.time_end - self.time_start
-        return duration
\ No newline at end of file
+        return duration

From fa1754f445d4e280a974a793e60b00c357b5fa89 Mon Sep 17 00:00:00 2001
From: Mark Polk <mark.polk@choderalab.org>
Date: Sun, 6 Oct 2024 02:10:42 -0400
Subject: [PATCH 10/20] added Luminescence_Scan_Data class

---
 .../experiments/plate_reader.py               | 36 +++++++++++++++----
 1 file changed, 29 insertions(+), 7 deletions(-)

diff --git a/missense_kinase_toolkit/experiments/missense_kinase_toolkit/experiments/plate_reader.py b/missense_kinase_toolkit/experiments/missense_kinase_toolkit/experiments/plate_reader.py
index 936cefb..e2d9c0e 100644
--- a/missense_kinase_toolkit/experiments/missense_kinase_toolkit/experiments/plate_reader.py
+++ b/missense_kinase_toolkit/experiments/missense_kinase_toolkit/experiments/plate_reader.py
@@ -7,7 +7,7 @@
 class Experiment:
     """Class to process Tecan i-control .XML output."""
 
-    def __init__(self, filepath) -> None:
+    def __init__(self, filepath: str) -> None:
         """Initialize Experiment Class object.
 
         Parameters
@@ -20,18 +20,18 @@ def __init__(self, filepath) -> None:
         self.filepath = filepath
         self.measurements = []
 
-        if filepath.lower()[-4:] != ".xml":
-            raise TypeError("Filepath does not point to .xml file")
+        if filepath.lower()[-4:] != '.xml':
+            raise TypeError('Filepath does not point to .xml file')
 
         tree = ET.parse(filepath)
         root = tree.getroot()
 
         # TODO: check if i-control allows duplicate labels
 
-        for section in root.iter("Section"):
+        for section in root.iter('Section'):
             self.measurements.append(Measurement(section))
 
-    def get_measurement_by_label(self, label):
+    def get_measurement_by_label(self, label: str):
 
         for i in range(len(self.measurements)):
             if self.measurements[i].label == label:
@@ -51,15 +51,37 @@ def __init__(self, section) -> None:
         ----------
         
         """
+        self.section = section
         self.label = section.attrib['Name']
         self.parameters = {}
         self.time_start = datetime.fromisoformat(section[0].text)
         self.time_end = datetime.fromisoformat(section[-1].text)
 
-        for parameters in section.iter("Parameters"):
+        # TODO: add units and other info. as applicable
+
+        for parameters in section.iter('Parameters'):
             for parameter in parameters:
                 self.parameters[parameter.attrib['Name']] = parameter.attrib['Value']
 
     def get_duration(self):
         duration = self.time_end - self.time_start
-        return duration
\ No newline at end of file
+        return duration
+    
+    def get_data(self, cycle=1):
+        for data in self.section.iter('Data'):
+            if int(data.attrib['Cycle']) == cycle:
+                return data
+    
+class Luminescence_Scan_Data:
+    """Class to process Luminescence Scan data."""
+
+    def __init__(self, data) -> None:
+        """Initialize Luminescence_Scan_Data Class object.
+        
+        Parameters
+        ----------
+
+        Attributes
+        ----------
+        
+        """
\ No newline at end of file

From c703457ca7706f7eeedd992fbb2600654a5e905d Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Sun, 6 Oct 2024 06:22:11 +0000
Subject: [PATCH 11/20] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 .../experiments/plate_reader.py                        | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/missense_kinase_toolkit/experiments/missense_kinase_toolkit/experiments/plate_reader.py b/missense_kinase_toolkit/experiments/missense_kinase_toolkit/experiments/plate_reader.py
index 1b1a022..4badd4d 100644
--- a/missense_kinase_toolkit/experiments/missense_kinase_toolkit/experiments/plate_reader.py
+++ b/missense_kinase_toolkit/experiments/missense_kinase_toolkit/experiments/plate_reader.py
@@ -20,15 +20,15 @@ def __init__(self, filepath: str) -> None:
         self.filepath = filepath
         self.measurements = []
 
-        if filepath.lower()[-4:] != '.xml':
-            raise TypeError('Filepath does not point to .xml file')
+        if filepath.lower()[-4:] != ".xml":
+            raise TypeError("Filepath does not point to .xml file")
 
         tree = ET.parse(filepath)
         root = tree.getroot()
 
         # TODO: check if i-control allows duplicate labels
 
-        for section in root.iter('Section'):
+        for section in root.iter("Section"):
             self.measurements.append(Measurement(section))
 
     def get_measurement_by_label(self, label: str):
@@ -59,10 +59,10 @@ def __init__(self, section) -> None:
 
         # TODO: add units and other info. as applicable
 
-        for parameters in section.iter('Parameters'):
+        for parameters in section.iter("Parameters"):
             for parameter in parameters:
                 self.parameters[parameter.attrib["Name"]] = parameter.attrib["Value"]
 
     def get_duration(self):
         duration = self.time_end - self.time_start
-        return duration
\ No newline at end of file
+        return duration

From d8764c0fe35f60e4671185b501034ca0b3c70e21 Mon Sep 17 00:00:00 2001
From: Mark Polk <mark.polk@choderalab.org>
Date: Mon, 7 Oct 2024 23:26:47 -0400
Subject: [PATCH 12/20] changes made during review

---
 .../missense_kinase_toolkit/experiments/plate_reader.py         | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/missense_kinase_toolkit/experiments/missense_kinase_toolkit/experiments/plate_reader.py b/missense_kinase_toolkit/experiments/missense_kinase_toolkit/experiments/plate_reader.py
index 1b1a022..2f90b6f 100644
--- a/missense_kinase_toolkit/experiments/missense_kinase_toolkit/experiments/plate_reader.py
+++ b/missense_kinase_toolkit/experiments/missense_kinase_toolkit/experiments/plate_reader.py
@@ -20,6 +20,8 @@ def __init__(self, filepath: str) -> None:
         self.filepath = filepath
         self.measurements = []
 
+        # try except parsing an xml file
+
         if filepath.lower()[-4:] != '.xml':
             raise TypeError('Filepath does not point to .xml file')
 

From 21e1954f8fcb36836784ae001a8e93a2e9609835 Mon Sep 17 00:00:00 2001
From: Mark Polk <mark.polk@choderalab.org>
Date: Tue, 8 Oct 2024 00:59:51 -0400
Subject: [PATCH 13/20] reworked module to use dataclasses and abstract base
 classes

---
 .../experiments/plate_reader.py               | 116 ++++++++----------
 1 file changed, 51 insertions(+), 65 deletions(-)

diff --git a/missense_kinase_toolkit/experiments/missense_kinase_toolkit/experiments/plate_reader.py b/missense_kinase_toolkit/experiments/missense_kinase_toolkit/experiments/plate_reader.py
index db848e7..aee7893 100644
--- a/missense_kinase_toolkit/experiments/missense_kinase_toolkit/experiments/plate_reader.py
+++ b/missense_kinase_toolkit/experiments/missense_kinase_toolkit/experiments/plate_reader.py
@@ -1,70 +1,56 @@
+import logging
 import xml.etree.ElementTree as ET
 from datetime import datetime
+from abc import ABC, abstractmethod
+from dataclasses import dataclass
 
 # i-control manual: https://bif.wisc.edu/wp-content/uploads/sites/389/2017/11/i-control_Manual.pdf
 
-
-class Experiment:
-    """Class to process Tecan i-control .XML output."""
-
-    def __init__(self, filepath: str) -> None:
-        """Initialize Experiment Class object.
-
-        Parameters
-        ----------
-
-        Attributes
-        ----------
-
-        """
-        self.filepath = filepath
-        self.measurements = []
-
-        # try except parsing an xml file
-
-        if filepath.lower()[-4:] != ".xml":
-            raise TypeError("Filepath does not point to .xml file")
-
-        tree = ET.parse(filepath)
-        root = tree.getroot()
-
-        # TODO: check if i-control allows duplicate labels
-
-        for section in root.iter("Section"):
-            self.measurements.append(Measurement(section))
-
-    def get_measurement_by_label(self, label: str):
-
-        for i in range(len(self.measurements)):
-            if self.measurements[i].label == label:
-                return self.measurements[i]
-
-
-class Measurement:
-    """Class to store measurement."""
-
-    def __init__(self, section) -> None:
-        """Initialize Measurement Class object.
-
-        Parameters
-        ----------
-
-        Attributes
-        ----------
-
-        """
-        self.section = section
-        self.label = section.attrib["Name"]
-        self.parameters = {}
-        self.time_start = datetime.fromisoformat(section[0].text)
-        self.time_end = datetime.fromisoformat(section[-1].text)
-
-        # TODO: add units and other info. as applicable
-
-        for parameters in section.iter("Parameters"):
-            for parameter in parameters:
-                self.parameters[parameter.attrib["Name"]] = parameter.attrib["Value"]
-
-    def get_duration(self):
-        duration = self.time_end - self.time_start
-        return duration
+logger = logging.getLogger(__name__)
+
+@dataclass
+class Measurement(ABC):
+    """Abstract class for measurements."""
+
+    filepath: str
+    """str: Filepath to i-control output .XML."""
+    label: str
+    """str: Label parameter in i-control."""
+
+    def __post_init__(self):
+        self.parse_xml()
+
+    def parse_xml(self):
+        try:
+            tree = ET.parse(self.filepath)
+            root = tree.getroot()
+            # TODO: check that i-control does not allow duplicate labels
+            self.section_element = root.find(f".//Section[@Name='{self.label}']")
+            if self.section_element is None:
+                logger.error("Label not found.")
+        except ET.ParseError as e:
+            logging.error("Could not parse input file", exc_info=e)
+
+    def get_parameter(self, parameter):
+        ...
+
+    @abstractmethod
+    def get_data(self) -> int:
+        ...
+
+@dataclass
+class Luminescence_Scan(Measurement):
+    """Class to parse Luminescence Scan measurement."""
+
+    def get_parameter(self, parameter):
+        # TODO
+        pass
+
+    def get_data(self, cycle, temperature, well, wavelength):
+        data_element = self.section_element.find(f".//Data[@Cycle='{str(cycle)}'][@Temperature='{str(temperature)}']")
+        if data_element is None:
+            logger.error("Data not found.")
+        else:
+            well_element = data_element.find(f".//Well[@Pos='{well}']")
+            scan_element = well_element.find(f".//Scan[@WL='{str(wavelength)}']")
+            return int(scan_element.text)
\ No newline at end of file

From 94f1b311b61d4cbc95c5bbb2f1d2e50685417dce Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 8 Oct 2024 05:00:03 +0000
Subject: [PATCH 14/20] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 .../experiments/plate_reader.py                  | 16 +++++++++-------
 1 file changed, 9 insertions(+), 7 deletions(-)

diff --git a/missense_kinase_toolkit/experiments/missense_kinase_toolkit/experiments/plate_reader.py b/missense_kinase_toolkit/experiments/missense_kinase_toolkit/experiments/plate_reader.py
index aee7893..511c717 100644
--- a/missense_kinase_toolkit/experiments/missense_kinase_toolkit/experiments/plate_reader.py
+++ b/missense_kinase_toolkit/experiments/missense_kinase_toolkit/experiments/plate_reader.py
@@ -1,13 +1,14 @@
 import logging
 import xml.etree.ElementTree as ET
-from datetime import datetime
 from abc import ABC, abstractmethod
 from dataclasses import dataclass
+from datetime import datetime
 
 # i-control manual: https://bif.wisc.edu/wp-content/uploads/sites/389/2017/11/i-control_Manual.pdf
 
 logger = logging.getLogger(__name__)
 
+
 @dataclass
 class Measurement(ABC):
     """Abstract class for measurements."""
@@ -31,12 +32,11 @@ def parse_xml(self):
         except ET.ParseError as e:
             logging.error("Could not parse input file", exc_info=e)
 
-    def get_parameter(self, parameter):
-        ...
+    def get_parameter(self, parameter): ...
 
     @abstractmethod
-    def get_data(self) -> int:
-        ...
+    def get_data(self) -> int: ...
+
 
 @dataclass
 class Luminescence_Scan(Measurement):
@@ -47,10 +47,12 @@ def get_parameter(self, parameter):
         pass
 
     def get_data(self, cycle, temperature, well, wavelength):
-        data_element = self.section_element.find(f".//Data[@Cycle='{str(cycle)}'][@Temperature='{str(temperature)}']")
+        data_element = self.section_element.find(
+            f".//Data[@Cycle='{str(cycle)}'][@Temperature='{str(temperature)}']"
+        )
         if data_element is None:
             logger.error("Data not found.")
         else:
             well_element = data_element.find(f".//Well[@Pos='{well}']")
             scan_element = well_element.find(f".//Scan[@WL='{str(wavelength)}']")
-            return int(scan_element.text)
\ No newline at end of file
+            return int(scan_element.text)

From 6043b63c0e77609954a0ea4da3ab5d15589bb1ab Mon Sep 17 00:00:00 2001
From: Mark Polk <mark.polk@choderalab.org>
Date: Tue, 8 Oct 2024 01:20:57 -0400
Subject: [PATCH 15/20] added basic get parameter

---
 .../experiments/plate_reader.py                       | 11 +++++------
 1 file changed, 5 insertions(+), 6 deletions(-)

diff --git a/missense_kinase_toolkit/experiments/missense_kinase_toolkit/experiments/plate_reader.py b/missense_kinase_toolkit/experiments/missense_kinase_toolkit/experiments/plate_reader.py
index 511c717..bb064e2 100644
--- a/missense_kinase_toolkit/experiments/missense_kinase_toolkit/experiments/plate_reader.py
+++ b/missense_kinase_toolkit/experiments/missense_kinase_toolkit/experiments/plate_reader.py
@@ -32,7 +32,10 @@ def parse_xml(self):
         except ET.ParseError as e:
             logging.error("Could not parse input file", exc_info=e)
 
-    def get_parameter(self, parameter): ...
+    def get_parameter(self, parameter: str) -> str:
+        # TODO: Add units handling
+        parameter_attribute = self.section_element.find(f".//Parameter[@Name='{parameter}']").attrib["Value"]
+        return parameter_attribute
 
     @abstractmethod
     def get_data(self) -> int: ...
@@ -42,11 +45,7 @@ def get_data(self) -> int: ...
 class Luminescence_Scan(Measurement):
     """Class to parse Luminescence Scan measurement."""
 
-    def get_parameter(self, parameter):
-        # TODO
-        pass
-
-    def get_data(self, cycle, temperature, well, wavelength):
+    def get_data(self, cycle: int, temperature: int, well: str, wavelength: int):
         data_element = self.section_element.find(
             f".//Data[@Cycle='{str(cycle)}'][@Temperature='{str(temperature)}']"
         )

From 741c257001f67363b40d199bb669501ed2816b1b Mon Sep 17 00:00:00 2001
From: Mark Polk <mark.polk@choderalab.org>
Date: Tue, 8 Oct 2024 01:26:03 -0400
Subject: [PATCH 16/20] added start, end time tracking

---
 .../missense_kinase_toolkit/experiments/plate_reader.py  | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/missense_kinase_toolkit/experiments/missense_kinase_toolkit/experiments/plate_reader.py b/missense_kinase_toolkit/experiments/missense_kinase_toolkit/experiments/plate_reader.py
index bb064e2..f468dbb 100644
--- a/missense_kinase_toolkit/experiments/missense_kinase_toolkit/experiments/plate_reader.py
+++ b/missense_kinase_toolkit/experiments/missense_kinase_toolkit/experiments/plate_reader.py
@@ -19,9 +19,10 @@ class Measurement(ABC):
     """str: Label parameter in i-control."""
 
     def __post_init__(self):
-        self.parse_xml()
+        self.parse_for_section()
+        self.parse_for_time()
 
-    def parse_xml(self):
+    def parse_for_section(self):
         try:
             tree = ET.parse(self.filepath)
             root = tree.getroot()
@@ -32,6 +33,10 @@ def parse_xml(self):
         except ET.ParseError as e:
             logging.error("Could not parse input file", exc_info=e)
 
+    def parse_for_time(self):
+        self.time_start = datetime.fromisoformat(self.section_element.find(f".//Time_Start").text)
+        self.time_end = datetime.fromisoformat(self.section_element.find(f".//Time_End").text)
+
     def get_parameter(self, parameter: str) -> str:
         # TODO: Add units handling
         parameter_attribute = self.section_element.find(f".//Parameter[@Name='{parameter}']").attrib["Value"]

From db8aef1dc16e3646ceee04b786e3ea194de4e9b1 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 8 Oct 2024 05:26:31 +0000
Subject: [PATCH 17/20] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 .../experiments/plate_reader.py                      | 12 +++++++++---
 1 file changed, 9 insertions(+), 3 deletions(-)

diff --git a/missense_kinase_toolkit/experiments/missense_kinase_toolkit/experiments/plate_reader.py b/missense_kinase_toolkit/experiments/missense_kinase_toolkit/experiments/plate_reader.py
index f468dbb..666525b 100644
--- a/missense_kinase_toolkit/experiments/missense_kinase_toolkit/experiments/plate_reader.py
+++ b/missense_kinase_toolkit/experiments/missense_kinase_toolkit/experiments/plate_reader.py
@@ -34,12 +34,18 @@ def parse_for_section(self):
             logging.error("Could not parse input file", exc_info=e)
 
     def parse_for_time(self):
-        self.time_start = datetime.fromisoformat(self.section_element.find(f".//Time_Start").text)
-        self.time_end = datetime.fromisoformat(self.section_element.find(f".//Time_End").text)
+        self.time_start = datetime.fromisoformat(
+            self.section_element.find(f".//Time_Start").text
+        )
+        self.time_end = datetime.fromisoformat(
+            self.section_element.find(f".//Time_End").text
+        )
 
     def get_parameter(self, parameter: str) -> str:
         # TODO: Add units handling
-        parameter_attribute = self.section_element.find(f".//Parameter[@Name='{parameter}']").attrib["Value"]
+        parameter_attribute = self.section_element.find(
+            f".//Parameter[@Name='{parameter}']"
+        ).attrib["Value"]
         return parameter_attribute
 
     @abstractmethod

From 38ed2ddae849cc6b3fa2daf7d9e9394c68fcd3e0 Mon Sep 17 00:00:00 2001
From: Mark Polk <mark.polk@choderalab.org>
Date: Tue, 8 Oct 2024 01:29:09 -0400
Subject: [PATCH 18/20] fixed use of f strings

---
 .../missense_kinase_toolkit/experiments/plate_reader.py       | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/missense_kinase_toolkit/experiments/missense_kinase_toolkit/experiments/plate_reader.py b/missense_kinase_toolkit/experiments/missense_kinase_toolkit/experiments/plate_reader.py
index 666525b..f0708a3 100644
--- a/missense_kinase_toolkit/experiments/missense_kinase_toolkit/experiments/plate_reader.py
+++ b/missense_kinase_toolkit/experiments/missense_kinase_toolkit/experiments/plate_reader.py
@@ -35,10 +35,10 @@ def parse_for_section(self):
 
     def parse_for_time(self):
         self.time_start = datetime.fromisoformat(
-            self.section_element.find(f".//Time_Start").text
+            self.section_element.find(".//Time_Start").text
         )
         self.time_end = datetime.fromisoformat(
-            self.section_element.find(f".//Time_End").text
+            self.section_element.find(".//Time_End").text
         )
 
     def get_parameter(self, parameter: str) -> str:

From c677a2229243c41ff95be48cd39a2343ac46bac3 Mon Sep 17 00:00:00 2001
From: Jess White <50890758+jessicaw9910@users.noreply.github.com>
Date: Tue, 8 Oct 2024 15:57:17 +0000
Subject: [PATCH 19/20] added initial scatterplotting function to
 Luminescence_Scan

---
 .../experiments/plate_reader.py               | 51 ++++++++++++++++++-
 1 file changed, 50 insertions(+), 1 deletion(-)

diff --git a/missense_kinase_toolkit/experiments/missense_kinase_toolkit/experiments/plate_reader.py b/missense_kinase_toolkit/experiments/missense_kinase_toolkit/experiments/plate_reader.py
index f0708a3..a26c23f 100644
--- a/missense_kinase_toolkit/experiments/missense_kinase_toolkit/experiments/plate_reader.py
+++ b/missense_kinase_toolkit/experiments/missense_kinase_toolkit/experiments/plate_reader.py
@@ -31,7 +31,7 @@ def parse_for_section(self):
             if self.section_element is None:
                 logger.error("Label not found.")
         except ET.ParseError as e:
-            logging.error("Could not parse input file", exc_info=e)
+            logging.error(f"Could not parse input {self.filepath}", exc_info=e)
 
     def parse_for_time(self):
         self.time_start = datetime.fromisoformat(
@@ -51,6 +51,12 @@ def get_parameter(self, parameter: str) -> str:
     @abstractmethod
     def get_data(self) -> int: ...
 
+    @abstractmethod
+    def plot_data(
+        self
+    ) -> Tuple[matplotlib.figure.Figure, plt.Axes] | None:
+    ...
+
 
 @dataclass
 class Luminescence_Scan(Measurement):
@@ -66,3 +72,46 @@ def get_data(self, cycle: int, temperature: int, well: str, wavelength: int):
             well_element = data_element.find(f".//Well[@Pos='{well}']")
             scan_element = well_element.find(f".//Scan[@WL='{str(wavelength)}']")
             return int(scan_element.text)
+
+    def plot_data(
+        cycle: int
+        temperature: int,
+        well: str,
+        header: str,
+        plot_type: str | None = None,
+    ):    
+    if plot_type is None:
+        plot_type = "scatter"
+
+    list_plot_type = ["scatter"]
+    if plot_type not in list_plot_type:
+        logging.error(f"Plot type {plot_type} not yet supported...")
+        return None
+    
+    if plot_type == "scatter":
+        lmin = int(self.get_parameter("Wavelength Start"))
+        lmax = int(self.get_parameter("Wavelength End"))
+        lstep = int(self.get_parameter("Wavelength Step Size"))
+        ll = np.arange(lmin, lmax+lstep, lstep)
+
+        fig, ax = plt.subplots()
+
+        try:
+            counter = 0
+            for l in ll:
+                ax.plot(l, self.get_data(cycle, temperature, well, l), "b.", alpha=0.5)
+                counter += 1
+            assert counter == int(self.get_parameter("Scan Number"))
+            print(f"All {counter} points accounted for")
+        except AssertionError as e:
+            logging.error(f"{counter} / {int(self.get_parameter('Scan Number'))} points accounted for...")
+            return None
+
+        ax.set_box_aspect(1)
+        ax.set_title("Water") # make this a parameter?
+        ax.set_xlabel("Wavelength (nm)")
+        ax.set_ylabel("Luminescence (RLU)")
+        ax.set_xlim([lmin, lmax])
+        ax.set_xticks(np.arange(lmin, lmax+50, 50)) # make this a parameter?
+
+        return (fig, ax)
\ No newline at end of file

From a5565f1407e24385f7813088092b352f7eaed4e3 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 8 Oct 2024 15:58:23 +0000
Subject: [PATCH 20/20] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 .../missense_kinase_toolkit/experiments/plate_reader.py     | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/missense_kinase_toolkit/experiments/missense_kinase_toolkit/experiments/plate_reader.py b/missense_kinase_toolkit/experiments/missense_kinase_toolkit/experiments/plate_reader.py
index a26c23f..55b6b68 100644
--- a/missense_kinase_toolkit/experiments/missense_kinase_toolkit/experiments/plate_reader.py
+++ b/missense_kinase_toolkit/experiments/missense_kinase_toolkit/experiments/plate_reader.py
@@ -79,7 +79,7 @@ def plot_data(
         well: str,
         header: str,
         plot_type: str | None = None,
-    ):    
+    ):
     if plot_type is None:
         plot_type = "scatter"
 
@@ -87,7 +87,7 @@ def plot_data(
     if plot_type not in list_plot_type:
         logging.error(f"Plot type {plot_type} not yet supported...")
         return None
-    
+
     if plot_type == "scatter":
         lmin = int(self.get_parameter("Wavelength Start"))
         lmax = int(self.get_parameter("Wavelength End"))
@@ -114,4 +114,4 @@ def plot_data(
         ax.set_xlim([lmin, lmax])
         ax.set_xticks(np.arange(lmin, lmax+50, 50)) # make this a parameter?
 
-        return (fig, ax)
\ No newline at end of file
+        return (fig, ax)