Show pims import errors only once (#1266)

* wip show pims import errors only once.

* Avoid wk-libs version warnings on slurm and show pims errors only in from_images.

* update changelog.

* use env vars for restrict number of warnings

* switch order of if statements.

---------

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

Author: markbader

webknossos/Changelog.md

@@ -17,6 +17,7 @@ For upgrade instructions, please check the respective _Breaking Changes_ section
 ### Added
 
 ### Changed
+- Warnings regarding missing pims image readers are only printed once during conversion. Error messages regarding wk-libs version are not displayed in slurm environments. [#1266](https://github.com/scalableminds/webknossos-libs/pull/1266)
 
 ### Fixed
 
@@ -47,7 +48,6 @@ For upgrade instructions, please check the respective _Breaking Changes_ section
 - Fixed the tests for the newest WEBKNOSSOS version. [#1328](https://github.com/scalableminds/webknossos-libs/pull/1328)
 
 
-
 ## [2.4.1](https://github.com/scalableminds/webknossos-libs/releases/tag/v2.4.1) - 2025-07-03
 [Commits](https://github.com/scalableminds/webknossos-libs/compare/v2.4.0...v2.4.1)
 
@@ -94,7 +94,7 @@ For upgrade instructions, please check the respective _Breaking Changes_ section
 ### Added
 - Added `layers_to_ignore` argument to `Dataset.copy_dataset`. [#1321](https://github.com/scalableminds/webknossos-libs/pull/1321)
 
-### Changed
+### Fixed
 - Make number of retries and backoff factor configurable (mainly for tensorstore reads/writes). See `DEFAULT_NUM_RETRIES` and `DEFAULT_BACKOFF_FACTOR` environment variables. [#1323](https://github.com/scalableminds/webknossos-libs/pull/1323)
 
 

webknossos/webknossos/__init__.py

@@ -36,7 +36,12 @@
 
 if not current_version == "0.0.0":
     import multiprocessing
+    import os
 
-    if multiprocessing.parent_process() is None:
+    if (
+        multiprocessing.parent_process() is None
+        and os.getenv("WEBKNOSSOS_SKIP_VERSION_CHECK", "False") != "True"
+    ):
+        os.environ["WEBKNOSSOS_SKIP_VERSION_CHECK"] = "True"
         # Schedule the version check to run non-blocking in a background thread
         check_version_in_background(current_version)

webknossos/webknossos/dataset/_utils/pims_images.py

@@ -2,7 +2,7 @@
 from collections.abc import Iterable, Iterator, Sequence
 from contextlib import AbstractContextManager, contextmanager, nullcontext
 from itertools import chain
-from os import PathLike
+from os import PathLike, environ
 from pathlib import Path
 from typing import TypeVar, Union, cast
 from urllib.error import HTTPError
@@ -22,6 +22,49 @@
 pims.ImageIOReader.frame_shape = pims.FramesSequenceND.frame_shape
 
 
+def _pims_imports() -> str | None:
+    import_exceptions = []
+
+    try:
+        from .pims_czi_reader import PimsCziReader  # noqa: F401 unused-import
+    except ImportError as import_error:
+        import_exceptions.append(f"PimsCziReader: {import_error.msg}")
+
+    try:
+        from .pims_dm_readers import (  # noqa: F401 unused-import
+            PimsDm3Reader,
+            PimsDm4Reader,
+        )
+    except ImportError as import_error:
+        import_exceptions.append(f"PimsDmReaders: {import_error.msg}")
+
+    try:
+        from .pims_tiff_reader import PimsTiffReader  # noqa: F401 unused-import
+    except ImportError as import_error:
+        import_exceptions.append(f"PimsTiffReader: {import_error.msg}")
+
+    if import_exceptions:
+        import_exception_string = "".join(
+            f"\t- {import_exception}\n" for import_exception in import_exceptions
+        )
+
+        return import_exception_string
+    return None
+
+
+if (pims_warnings := _pims_imports()) is not None:
+    if environ.get("WEBKNOSSOS_SHOWED_PIMS_IMPORT_WARNING", "False") == "False":
+        # If the environment variable is not set, we assume that the user has not seen the warning yet.
+        # We set it to True to prevent showing the warning again.
+        environ["WEBKNOSSOS_SHOWED_PIMS_IMPORT_WARNING"] = "True"
+        warnings.warn(
+            f"[WARNING] Not all pims readers could be imported:\n{pims_warnings}Install the readers you need or use 'webknossos[all]' to install all readers.",
+            category=UserWarning,
+            source=None,
+            stacklevel=2,
+        )
+
+
 def _assume_color_channel(dim_size: int, dtype: np.dtype) -> bool:
     return dim_size == 1 or (dim_size == 3 and dtype == np.dtype("uint8"))
 
@@ -306,33 +349,6 @@ def _disable_pil_image_size_limit(self) -> None:
     def _try_open_pims_images(
         self, original_images: str | list[str], exceptions: list[Exception]
     ) -> pims.FramesSequence | None:
-        import_exceptions = []
-
-        try:
-            from .pims_czi_reader import PimsCziReader  # noqa: F401 unused-import
-        except ImportError as import_error:
-            import_exceptions.append(f"PimsCziReader: {import_error.msg}")
-
-        try:
-            from .pims_dm_readers import (  # noqa: F401 unused-import
-                PimsDm3Reader,
-                PimsDm4Reader,
-            )
-        except ImportError as import_error:
-            import_exceptions.append(f"PimsDmReaders: {import_error.msg}")
-
-        try:
-            from .pims_tiff_reader import PimsTiffReader  # noqa: F401 unused-import
-        except ImportError as import_error:
-            import_exceptions.append(f"PimsTiffReader: {import_error.msg}")
-
-        if import_exceptions:
-            import_exception_string = "\n\t" + "\n\t".join(import_exceptions)
-            warnings.warn(
-                f"[WARNING] Not all pims readers could be imported: {import_exception_string}\nInstall the readers you need or use 'webknossos[all]' to install all readers.",
-                category=UserWarning,
-            )
-
         if self._use_bioformats:
             return None