Update imports and error messages of import errors. (#1104)

* Update imports and error messages of import errors.

* Update poetry lock file.

* Update changelog.

* Display error message, not all pims readers imported only once.

* Update changelog.

Author: markbader

docs/poetry.lock

@@ -1,2 +1,2 @@
 dunamai==1.18.1
-poetry==1.6.1
+poetry==1.8.2

requirements.txt

@@ -21,6 +21,7 @@ For upgrade instructions, please check the respective _Breaking Changes_ section
 
 ### Fixed
 - Fixed an issue where cube jobs upsampling, downsampling and compress failed when performed on more than 3 dimensions. [#1095](https://github.com/scalableminds/webknossos-libs/pull/1095)
+- Fixed an issue where webknossos libs crash when installed with minimal dependencies. [#1104](https://github.com/scalableminds/webknossos-libs/pull/1104)
 
 
 ## [0.14.23](https://github.com/scalableminds/webknossos-libs/releases/tag/v0.14.23) - 2024-06-28

webknossos/Changelog.md

@@ -41,6 +41,7 @@ natsort = "^6.2.0"
 networkx = "^2.6.2"
 numcodecs = "^0.11"
 numpy = "^1.21.0"  # see https://numpy.org/neps/nep-0029-deprecation_policy.html#support-table
+pims = "^0.6.0"
 psutil = "^5.6.7"
 python-dateutil = "^2.8.0"
 python-dotenv = "^0.19.0"
@@ -58,17 +59,15 @@ zipp = "^3.5.0"
 # below `extras`. They can be opted into by apps.
 imagecodecs = { version = ">=2021.11.20", optional = true }
 JPype1 = { version = "^1.3.0", optional = true }
-pims = { version = "^0.6.0", optional = true }
 tifffile = { version = ">=2021.11.2", optional = true }
 pylibCZIrw = { version = "3.5.2", source = "scm", optional = true }
 
 [tool.poetry.extras]
-pims = ["pims"]
-tifffile = ["pims", "tifffile"]
-imagecodecs = ["pims", "imagecodecs"]
-bioformats = ["pims","JPype1"]
-czi = ["pims", "pylibCZIrw"]
-all = ["pims","tifffile","imagecodecs","JPype1","pylibCZIrw"]
+tifffile = ["tifffile"]
+imagecodecs = ["imagecodecs"]
+bioformats = ["JPype1"]
+czi = ["pylibCZIrw"]
+all = ["tifffile","imagecodecs","JPype1","pylibCZIrw"]
 
 [tool.poetry.group.dev]
 optional = true

webknossos/poetry.lock

@@ -4,18 +4,12 @@
 from typing import Dict, Iterator, List, Set
 
 import numpy as np
-
-try:
-    from pims import FramesSequenceND
-except ImportError as e:
-    raise RuntimeError(
-        "Cannot import pims, please install it e.g. using 'webknossos[all]'"
-    ) from e
+from pims import FramesSequenceND
 
 try:
     from pylibCZIrw import czi as pyczi
 except ImportError as e:
-    raise RuntimeError(
+    raise ImportError(
         "Cannot import pylibCZIrw, please install it e.g. using 'webknossos[czi]'"
     ) from e
 

webknossos/pyproject.toml

@@ -4,18 +4,12 @@
 from typing import Iterator, Set
 
 import numpy as np
+from pims import FramesSequenceND
 
 from .vendor.dm3 import DM3  # type: ignore[attr-defined]
 from .vendor.dm3 import dT_str as DM3_DTYPE_MAPPING  # type: ignore[attr-defined]
 from .vendor.dm4 import DM4File  # type: ignore[attr-defined]
 
-try:
-    from pims import FramesSequenceND
-except ImportError as e:
-    raise RuntimeError(
-        "Cannot import pims, please install it e.g. using 'webknossos[all]'"
-    ) from e
-
 
 class PimsDm3Reader(FramesSequenceND):
     @classmethod

webknossos/webknossos/dataset/_utils/pims_czi_reader.py

@@ -3,18 +3,12 @@
 from typing import Set
 
 import numpy as np
-
-try:
-    from pims import FramesSequenceND
-except ImportError as e:
-    raise RuntimeError(
-        "Cannot import pims, please install it e.g. using 'webknossos[all]'"
-    ) from e
+from pims import FramesSequenceND
 
 try:
     import tifffile
 except ImportError as e:
-    raise RuntimeError(
+    raise ImportError(
         "Cannot import tifffile, please install it e.g. using 'webknossos[tifffile]'"
     ) from e