Set default data format with enviroment variable (#958)

* Set default data format with enviroment variable

* format

* Add env variable for chunks per shard

* Parse Vec3Int from string

* parse vec3int with regex

* add type annotation

* Update changelog

* fix linting error

---------

Co-authored-by: Norman Rzepka <[email protected]>

Author: sm1lla

webknossos/Changelog.md

@@ -15,6 +15,8 @@ For upgrade instructions, please check the respective _Breaking Changes_ section
 ### Breaking Changes
 
 ### Added
+- The `DEFAULT_DATA_FORMAT` and `DEFAULT_CHUNKS_PER_SHARD` can now be set with the env variables `WK_DEFAULT_DATA_FORMAT` and `WK_DEFAULT_CHUNKS_PER_SHARD`
+- A `Vec3Int` can now be initialized with a string containing an int or a tuple.
 
 ### Changed
 - Upgrades mypy to 1.6. [#956](https://github.com/scalableminds/webknossos-libs/pull/956)

webknossos/webknossos/dataset/defaults.py

@@ -1,13 +1,23 @@
+import os
+
 from ..geometry import Vec3Int
 from .data_format import DataFormat
 
 DEFAULT_WKW_FILE_LEN = 32
 DEFAULT_CHUNK_SHAPE = Vec3Int.full(32)
-DEFAULT_CHUNKS_PER_SHARD = Vec3Int.full(32)
+DEFAULT_DATA_FORMAT = (
+    DataFormat(os.environ["WK_DEFAULT_DATA_FORMAT"])
+    if "WK_DEFAULT_DATA_FORMAT" in os.environ
+    else DataFormat.WKW
+)
+DEFAULT_CHUNKS_PER_SHARD = (
+    Vec3Int.from_str(os.environ["WK_DEFAULT_CHUNKS_PER_SHARD"])
+    if "WK_DEFAULT_CHUNKS_PER_SHARD" in os.environ
+    else Vec3Int.full(32)
+)
 DEFAULT_CHUNKS_PER_SHARD_ZARR = Vec3Int.full(1)
 DEFAULT_CHUNKS_PER_SHARD_FROM_IMAGES = Vec3Int(128, 128, 1)
 DEFAULT_BIT_DEPTH = 8
-DEFAULT_DATA_FORMAT = DataFormat.WKW
 PROPERTIES_FILE_NAME = "datasource-properties.json"
 ZGROUP_FILE_NAME = ".zgroup"
 ZATTRS_FILE_NAME = ".zattrs"

webknossos/webknossos/geometry/vec3_int.py

@@ -1,3 +1,4 @@
+import re
 from operator import add, floordiv, mod, mul, sub
 from typing import Any, Callable, Iterable, List, Optional, Tuple, Union, cast
 
@@ -72,6 +73,13 @@ def from_vec_or_int(vec_or_int: Union["Vec3IntLike", int]) -> "Vec3Int":
         else:
             return Vec3Int(vec_or_int)
 
+    @staticmethod
+    def from_str(string: str) -> "Vec3Int":
+        if re.match(r"\(\d+,\d+,\d+\)", string):
+            return Vec3Int(tuple(map(int, re.findall(r"\d+", string))))
+        else:
+            return Vec3Int.full(int(string))
+
     @property
     def x(self) -> int:
         return self[0]