Merge branch 'dev_next' into main

README.md

@@ -79,5 +79,5 @@ On the other hand the `qpcr.Normaliser` will perform actions on a single Assay u
 
 
 #### Citation
-Kleinschmidt, N. (2023). qpcr - a python package for easy and versatile qPCR data analysis for small-scale datasets and high-throughput (Version 4.1.1) [Computer software]. https://github.com/NoahHenrikKleinschmidt/qpcr.git
+Kleinschmidt, N. (2023). qpcr - a python package for easy and versatile qPCR data analysis for small-scale datasets and high-throughput (Version 4.1.3) [Computer software]. https://github.com/NoahHenrikKleinschmidt/qpcr.git
 

qpcr/_auxiliary/__init__.py

@@ -7,6 +7,7 @@
 import re
 import qpcr.defaults as defaults
 import logging
+from copy import deepcopy
 
 
 def pseudo_isinstance(obj, ref_name: str):
@@ -63,7 +64,6 @@ def log(filename=None, level=None, format=None, name="qpcr"):
         handler = logging.StreamHandler()
     else:
         if filename is None:
-
             # try to use a fileHandler but if we have a jupyter notebook or terminal
             # just use StreamHandler instead...
             try:
@@ -72,7 +72,9 @@ def log(filename=None, level=None, format=None, name="qpcr"):
                 filename = f"{os.path.dirname( __main__.__file__ )}/{name}.log"
             except Exception as e:
                 logger.info(e)
-                logger.info("Could not generate a filename for the log file. Using stdout instead.")
+                logger.info(
+                    "Could not generate a filename for the log file. Using stdout instead."
+                )
                 return log(filename="stdout", level=level, format=format, name=name)
 
         elif not filename.endswith(".log"):
@@ -153,7 +155,14 @@ class _ID:
     A meta_superclass that simply adds an ID getter-setter to itself
     """
 
-    __slots__ = ["_id", "_id_was_set", "_id_label", "_id_label_was_set", "_id_func", "__dict__"]
+    __slots__ = [
+        "_id",
+        "_id_was_set",
+        "_id_label",
+        "_id_label_was_set",
+        "_id_func",
+        "__dict__",
+    ]
 
     def __init__(self):
         self._id = uuid.uuid1()
@@ -274,6 +283,15 @@ def id_reset(self):
         self._id_label_was_set = False
         self._id_was_set = False
 
+    def copy(self):
+        """
+        Returns a deepcopy of itself
+        """
+        new = deepcopy(self)
+        new.id_reset()
+        new._id = str(uuid.uuid1())
+        return new
+
 
 def fileID(filename):
     """
@@ -289,7 +307,6 @@ def fileID(filename):
 logger = default_logger()
 
 if __name__ == "__main__":
-
     obj1 = _ID()
     obj1.id("Hnrnp l_nmd")
     obj1.split_id("_")

qpcr/main/Assay.py

@@ -106,15 +106,31 @@ class Assay(aux._ID):
         group will be inferred automatically. Otherwise, default group names will be set if no `group_names` are provided.
     """
 
-    __slots__ = ["_df", "_id", "_efficiency", "_efficiency", "_replicates", "_group_names", "_groups"]
-
-    def __init__(self, df: pd.DataFrame, id: str = None, replicates: (int or tuple or str) = None, group_names: list = None):
+    __slots__ = [
+        "_df",
+        "_id",
+        "_efficiency",
+        "_efficiency",
+        "_replicates",
+        "_group_names",
+        "_groups",
+    ]
+
+    def __init__(
+        self,
+        df: pd.DataFrame,
+        id: str = None,
+        replicates: (int or tuple or str) = None,
+        group_names: list = None,
+    ):
         super().__init__()
 
         if isinstance(df, pd.DataFrame):
             self._df = df
         else:
-            raise TypeError(f"df argument must be a pandas DataFrame (got {type(df).__name__})")
+            raise TypeError(
+                f"df argument must be a pandas DataFrame (got {type(df).__name__})"
+            )
 
         if id is not None:
             self._id = id
@@ -158,11 +174,15 @@ def efficiency(self, eff: float = None):
         if isinstance(eff, float):
             self._efficiency = eff
             self._eff = 2 * self._efficiency
-            logger.info(f"New efficiency set to {self._efficiency} (computes as binary factor {self._efficiency} * 2 = {self._eff})")
+            logger.info(
+                f"New efficiency set to {self._efficiency} (computes as binary factor {self._efficiency} * 2 = {self._eff})"
+            )
         elif eff is None:
             return self._efficiency
         else:
-            raise TypeError(f"Expected a float efficiency but got type {type(eff).__name__}")
+            raise TypeError(
+                f"Expected a float efficiency but got type {type(eff).__name__}"
+            )
 
     def save(self, filename: str):
         """
@@ -294,6 +314,13 @@ def Ct(self):
         Ct.name = f"{self.id()}_Ct"
         return Ct
 
+    @Ct.setter
+    def Ct(self, Ct):
+        """
+        Sets the Ct values of the Assay.
+        """
+        self._df[raw_col_names[1]] = Ct
+
     @property
     def dCt(self):
         """
@@ -307,6 +334,13 @@ def dCt(self):
         dCt.name = f"{self.id()}_dCt"
         return dCt
 
+    @dCt.setter
+    def dCt(self, dCt):
+        """
+        Sets the Delta-Ct values of the Assay.
+        """
+        self._df["dCt"] = dCt
+
     @property
     def ddCt(self):
         """
@@ -496,8 +530,14 @@ def replicates(self, replicates: (int or tuple or str) = None):
             if self._vet_replicates(replicates):
                 self._replicates = replicates
             else:
-                logger.critical(aw.AssayError("reps_dont_cover", n_samples=self.n(), reps=replicates))
-                raise aw.AssayError("reps_dont_cover", n_samples=self.n(), reps=replicates)
+                logger.critical(
+                    aw.AssayError(
+                        "reps_dont_cover", n_samples=self.n(), reps=replicates
+                    )
+                )
+                raise aw.AssayError(
+                    "reps_dont_cover", n_samples=self.n(), reps=replicates
+                )
         return self._replicates
 
     def group(self, replicates: (int or tuple or str) = None, infer_names=True):
@@ -644,7 +684,9 @@ def _identically_named(self):
             names_set = names.unique()
             # names_set = aux.sorted_set(names)
             first_name = names_set[0]
-            group0 = self._df.query(f"{raw_col_names[0]} == '{first_name}'")[raw_col_names[0]]
+            group0 = self._df.query(f"{raw_col_names[0]} == '{first_name}'")[
+                raw_col_names[0]
+            ]
             entries = len(group0)
             all_identical = entries > 1
         else:
@@ -669,7 +711,11 @@ def _rename_per_key(self, names):
             new_names = new_names.split("$")
             return new_names
         else:
-            e = aw.AssayError("groupnames_dont_colver", current_groups=current_names, new_received=names)
+            e = aw.AssayError(
+                "groupnames_dont_colver",
+                current_groups=current_names,
+                new_received=names,
+            )
             logger.critical(e)
             raise e
 
@@ -691,7 +737,11 @@ def _rename_per_index(self, names):
             new_names = new_names.split("$")
             return new_names
         else:
-            e = aw.AssayError("groupnames_dont_colver", current_groups=current_names, new_received=names)
+            e = aw.AssayError(
+                "groupnames_dont_colver",
+                current_groups=current_names,
+                new_received=names,
+            )
             logger.critical(e)
             raise e
 
@@ -750,7 +800,6 @@ def _vet_replicates(self, replicates: (int or tuple)):
         return verdict
 
     def __str__(self):
-
         _length = len(str(self._df).split("\n")[0])
         s = f"""
 {"-" * _length}

setup.py

@@ -5,7 +5,7 @@
 
 setuptools.setup(
     name="qpcr",
-    version="4.1.2",
+    version="4.1.3",
     author="Noah H. Kleinschmidt",
     author_email="noah.kleinschmidt@students.unibe.ch",
     description="A python package to perform analysis of qPCR data",
@@ -42,5 +42,5 @@
         "Operating System :: OS Independent",
         "Topic :: Scientific/Engineering :: Bio-Informatics",
     ],
-    python_requires='>=3.8',
+    python_requires=">=3.8",
 )