Merge branch 'master' into python-315-sampling-profiler

Author: bzaczynski

python-mixins-course/README.md

@@ -0,0 +1,3 @@
+# Understanding Mixin Classes in Python
+
+This folder contains sample code for the Real Python video course [Understanding Mixin Classes in Python](https://realpython.com/courses/understanding-mixin-classes-in-python/).

python-mixins-course/as_dict_mixin.py

@@ -0,0 +1,22 @@
+class Person:
+    def __init__(self, name, age):
+        self.name = name
+        self.age = age
+
+    def as_dict(self):
+        return {
+            "name": self.name,
+            "age": self.age,
+        }
+
+
+class Car:
+    def __init__(self, make, model):
+        self.make = make
+        self.model = model
+
+    def as_dict(self):
+        return {
+            "make": self.make,
+            "model": self.model,
+        }

python-mixins-course/as_dict_mixin_final.py

@@ -0,0 +1,23 @@
+class AsDictMixin:
+    def as_dict(self):
+        return vars(self)
+
+
+class Person(AsDictMixin):
+    def __init__(self, name, age):
+        self.name = name
+        self.age = age
+
+
+john = Person("John", 42)
+print(john.as_dict())
+
+
+class Car(AsDictMixin):
+    def __init__(self, make, model):
+        self.make = make
+        self.model = model
+
+
+toyota = Car("Toyota", "Prius")
+print(toyota.as_dict())

python-mixins-course/sequence.py

@@ -0,0 +1,11 @@
+from abc import ABC, abstractmethod
+
+
+class Sequence(ABC):
+    @abstractmethod
+    def __getitem__(self, index):
+        pass
+
+    @abstractmethod
+    def __len__(self):
+        pass

python-mixins-course/sequence_abc.py

@@ -0,0 +1,35 @@
+from abc import ABC, abstractmethod
+
+
+class Sequence(ABC):
+    @abstractmethod
+    def __getitem__(self, index):
+        pass
+
+    @abstractmethod
+    def __len__(self):
+        pass
+
+    def __iter__(self):
+        index = 0
+        while index < len(self):
+            yield self[index]
+            index += 1
+
+
+class MyRange(Sequence):
+    def __init__(self, stop):
+        self.stop = stop  # Assume that `stop` is >= 0.
+
+    def __getitem__(self, index):
+        if 0 <= index < self.stop:
+            return index
+        raise IndexError
+
+    def __len__(self):
+        return self.stop
+
+
+r = MyRange(10)
+for number in r:
+    print(number)

python-mixins-course/sequence_final.py

@@ -0,0 +1,35 @@
+from abc import ABC, abstractmethod
+
+
+class Sequence(ABC):
+    @abstractmethod
+    def __getitem__(self, index):
+        pass
+
+    @abstractmethod
+    def __len__(self):
+        pass
+
+    def __iter__(self):
+        index = 0
+        while index < len(self):
+            yield self[index]
+            index += 1
+
+
+class MyRange(Sequence):
+    def __init__(self, stop):
+        self.stop = stop  # Assume that `stop` is >= 0.
+
+    def __getitem__(self, index):
+        if 0 <= index < self.stop:
+            return index
+        raise IndexError
+
+    def __len__(self):
+        return self.stop
+
+
+r = MyRange(10)
+for number in r:
+    print(number)

python-mixins-course/sequence_mixin.py

@@ -0,0 +1,40 @@
+from abc import ABC, abstractmethod
+
+
+class IterMixin:
+    # __iter__ works IF the class inheriting the mixin
+    # already provides __getitem__ and __len__.
+    def __iter__(self):
+        print("Hey from inside IterMixin.__iter__.")
+        index = 0
+        while index < len(self):
+            yield self[index]
+            index += 1
+
+
+class Sequence(IterMixin, ABC):
+    @abstractmethod
+    def __getitem__(self, index):
+        pass
+
+    @abstractmethod
+    def __len__(self):
+        pass
+
+
+class MyRange(Sequence):
+    def __init__(self, stop):
+        self.stop = stop  # Assume that `stop` is >= 0.
+
+    def __getitem__(self, index):
+        if 0 <= index < self.stop:
+            return index
+        raise IndexError
+
+    def __len__(self):
+        return self.stop
+
+
+r = MyRange(10)
+for number in r:
+    print(number)

python-pointblank/README.md

@@ -0,0 +1,21 @@
+# Validating Data With Pointblank in Python
+
+Supporting code and sample data for the Real Python tutorial [Validating Data With Pointblank in Python](https://realpython.com/python-pointblank/).
+
+## Requirements
+
+The Python scripts use PEP 723 dependency metadata and run with [uv](https://docs.astral.sh/uv/):
+
+```console
+$ uv run pointblank_quickstart.py
+$ uv run pointblank_thresholds.py
+$ uv run pointblank_atoms.py
+```
+
+The command-line examples can run without a project environment:
+
+```console
+$ uv run --no-project --with 'pointblank[pl]' -- pb scan pointblank_atoms.csv
+$ uv run --no-project --with 'pointblank[pl]' -- pb missing pointblank_atoms.csv
+$ uvx --from 'pointblank[pl]' pb run pointblank_atoms.yaml --output-html pointblank_report.html
+```

python-pointblank/pointblank_atoms.csv

@@ -0,0 +1,14 @@
+atom_id,symbol,x,y,z,fx,fy,fz
+0,Cu,1.0,0.5,0.1,0.1,0.0,0.0
+1,Pt,2.1,1.5,0.2,-0.2,0.1,-0.1
+2,Cu,3.2,2.5,0.3,0.3,-0.1,0.1
+3,Pt,4.3,3.5,0.4,-0.1,0.0,0.0
+4,Cu,5.4,4.5,0.5,0.2,0.1,-0.1
+5,Pt,6.5,5.5,0.6,-0.3,-0.1,0.1
+6,Cu,7.6,6.5,0.7,0.1,0.0,0.0
+7,Pt,8.7,7.5,0.8,-0.2,0.1,-0.1
+8,Cu,9.8,8.5,0.9,0.3,-0.1,0.1
+9,Pt,10.9,9.5,1.0,-0.1,0.0,0.0
+10,Zz,0.5,0.5,0.1,0.0,0.0,0.0
+11,Cu,,1.5,0.2,0.0,0.0,0.0
+12,Pt,12.1,2.5,0.3,1500.0,0.0,0.0

python-pointblank/pointblank_atoms.py

@@ -0,0 +1,41 @@
+# /// script
+# requires-python = ">=3.10"
+# dependencies = [
+#   "pointblank[pl]",
+# ]
+# ///
+
+import polars as pl
+import pointblank as pb
+
+VALID_ELEMENTS = ["Cu", "Pt"]
+
+
+def main() -> None:
+    atoms = pl.read_csv("pointblank_atoms.csv")
+
+    validation = (
+        pb.Validate(
+            data=atoms,
+            tbl_name="atoms",
+            label="Atom data validation",
+            thresholds=pb.Thresholds(warning=0.02, error=0.05, critical=0.07),
+        )
+        .col_vals_in_set(columns="symbol", set=VALID_ELEMENTS)
+        .col_vals_not_null(columns=["x", "y", "z"])
+        .col_vals_between(columns=["x", "y", "z"], left=0, right=20)
+        .col_vals_between(columns=["fx", "fy", "fz"], left=-1000, right=1000)
+        .interrogate()
+    )
+
+    clean = validation.get_sundered_data(type="pass")
+    dirty = validation.get_sundered_data(type="fail")
+
+    print(f"Clean rows: {len(clean)}")
+    print(clean.select(["atom_id", "symbol", "x", "fx"]))
+    print(f"\nDirty rows: {len(dirty)}")
+    print(dirty.select(["atom_id", "symbol", "x", "fx"]))
+
+
+if __name__ == "__main__":
+    main()