Release v0.0.12

README.md

@@ -2,7 +2,7 @@
 <img src="genimtools/docs/logo.svg" alt="genimtools logo" height="100px">
 </h1>
 
-`genimtools` is a rust crate that provides a set of tools for working with genomic interval data. Its primary goal is to provide processors for our python package, [`geniml`](https:github.com/databio/geniml), a libary for machine learning on genomic intervals. However, it can be used as a standalone library for working with genomic intervals as well.
+`genimtools` is a rust crate that provides a set of tools for working with genomic interval data. Its primary goal is to provide processors for our python package, [`geniml`](https:github.com/databio/geniml), a library for machine learning on genomic intervals. However, it can be used as a standalone library for working with genomic intervals as well.
 
 `genimtools` provides three things:
 

bindings/Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "genimtools-py"
-version = "0.0.11"
+version = "0.0.12"
 edition = "2021"
 
 # See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
@@ -9,5 +9,9 @@ name = "genimtools"
 crate-type = ["cdylib"]
 
 [dependencies]
+anyhow = "1.0.82"
 genimtools = { path = "../genimtools" }
-pyo3 = "0.20.0"
+pyo3 = { version = "0.21", features=["anyhow", "extension-module"] }
+numpy = "0.21"
+# pyo3-tch = { git = "https://github.com/LaurentMazare/tch-rs" }
+# torch-sys = { git = "https://github.com/LaurentMazare/tch-rs" }

bindings/genimtools/__init__.py

@@ -1 +1 @@
-from .genimtools import *
+from .genimtools import *  # noqa: F403

bindings/genimtools/__init__.pyi

@@ -1,11 +1 @@
-PAD_CHR: str
-PAD_START: int
-PAD_END: int
-
-MASK_CHR: str
-MASK_START: int
-MASK_END: int
-
-UNKNOWN_CHR: str
-UNKNOWN_START: int
-UNKNOWN_END: int
+__version__: str

bindings/genimtools/ailist/__init__.py

@@ -1 +1 @@
-from .genimtools.ailist import *
+from .genimtools.ailist import *  # noqa: F403

bindings/genimtools/ailist/__init__.pyi

@@ -1,25 +1,50 @@
 from typing import List
 
 class Interval:
-    start: int
-    end: int
-    def __init__(self, start: int, end: int):
+    """
+    Represents a range of values.
+    """
+
+    def __new__(cls, start: int, end: int) -> Interval:
+        """
+        Create a new Interval object.
+
+        :param start: The start of the interval.
+        :param end: The end of the interval.
+        """
+
+    @property
+    def start(self) -> int:
+        """
+        The start of the interval.
         """
-        Create a new Interval.
+
+    @property
+    def end(self) -> int:
         """
+        The end of the interval.
+        """
+
+    def __repr__(self) -> str: ...
 
 class AIList:
-    def __init__(self, intervals: List[Interval], minimum_coverage_length: int) -> AIList:
-        """
-        Create a new AIList.
+    """
+    The augmented interval list (AILIST) object.
+
+    This object will compute region overlaps very efficiently.
+    """
 
-        :param intervals: The list of intervals to use.
-        :param minimum_coverage_length: The minimum number of intervals that are covered before being decomposed into another list.
+    def __new__(cls, intervals: List[Interval], minimum_coverage_length: int = None) -> AIList:
         """
+        Create a new AIList object.
 
+        :param intervals: A list of intervals.
+        :param minimum_coverage_length: The minimum length of the coverage.
+        """
+
     def query(self, interval: Interval) -> List[Interval]:
         """
-        Query the AIList for the intervals that overlap with the given interval.
+        Query the AIList object for overlapping intervals.
 
         :param interval: The interval to query.
-        """
+        """

bindings/genimtools/tokenizers/__init__.py

@@ -1 +1 @@
-from .genimtools.tokenizers import *
+from .genimtools.tokenizers import *  # noqa: F403