biapy 3.7.0__tar.gz → 3.7.2__tar.gz

{biapy-3.7.0 → biapy-3.7.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: biapy
-Version: 3.7.0
+Version: 3.7.2
 Summary: BiaPy: Bioimage analysis pipelines in Python
 Author-email: Daniel Franco-Barranco <daniel.franco@dipc.org>
 Maintainer-email: Daniel Franco-Barranco <daniel.franco@dipc.org>
@@ -52,7 +52,8 @@ Requires-Dist: torchinfo>=1.8.0
 Requires-Dist: tensorboardX>=2.6.2.2
 Requires-Dist: h5py>=3.9.0
 Requires-Dist: zarr>=3.1.5
-Requires-Dist: bioimageio.core==0.9.6
+Requires-Dist: bioimageio.core==0.11.0
+Requires-Dist: pydantic<2.14
 Requires-Dist: imagecodecs>=2024.1.1
 Requires-Dist: pooch>=1.8.1
 Requires-Dist: xarray==2025.1.*
@@ -60,9 +61,11 @@ Requires-Dist: timm==1.0.14
 Requires-Dist: pytorch-msssim
 Requires-Dist: torchmetrics[image]==1.4.*
 Requires-Dist: safetensors
-Requires-Dist: torch<2.13,>=2.12
-Requires-Dist: torchvision<0.28,>=0.27
+Requires-Dist: torch<3.0,>=2.9
+Requires-Dist: torchvision<1.0,>=0.24
 Requires-Dist: nibabel>=5.4.2
+Requires-Dist: PyWavelets>=1.4.1
+Requires-Dist: einops>=0.7.0
 Dynamic: license-file
 
 ![BiaPy logo](https://raw.githubusercontent.com/BiaPyX/BiaPy/master/img/biapy_logo.png)

{biapy-3.7.0 → biapy-3.7.2}/biapy/__init__.py

@@ -11,16 +11,86 @@ This `__init__.py` file serves as the entry point for the BiaPy package,
 exposing the `BiaPy` class and defining the `main` function for command-line
 execution.
 
-Version: 3.7.0
+Version: 3.7.2
 """
 
-__version__ = "3.7.0"
+__version__ = "3.7.2"
 
 import argparse
 import os
 import sys
-from ._biapy import BiaPy, build_config
 
+# The engine (BiaPy, build_config, validate_config) is imported on first use: importing it loads PyTorch and every workflow,
+# which takes several seconds, and lightweight parts such as biapy.wizard don't need it.
+_LAZY = {"BiaPy": "._biapy", "build_config": "._biapy", "validate_config": "._biapy"}
+__all__ = ["BiaPy", "build_config", "validate_config", "main", "__version__"]
+
+
+def __getattr__(name):
+    if name in _LAZY:
+        import importlib
+
+        value = getattr(importlib.import_module(_LAZY[name], __name__), name)
+        globals()[name] = value  # later accesses don't go through __getattr__
+        return value
+    raise AttributeError(f"module {__name__!r} has no attribute {name!r}")
+
+
+def __dir__():
+    return sorted(list(globals()) + list(_LAZY))
+
+def _validate_config_cli(argv):
+    """
+    Validate a configuration file from the command line.
+
+    This function is intended to be used as a command-line utility to validate
+    a BiaPy configuration file without running anything: no data is loaded, no
+    model is built and nothing is written to disk. It prints ``OK`` if the
+    configuration is valid, or the first error found (naming the wrong key) otherwise.
+
+    Usage::
+
+        biapy validate-config <path_to_config_file>
+        biapy validate-config <path_to_config_file> --no-data-check
+
+    ``--no-data-check`` skips the check that the data paths exist, so a configuration
+    can be validated before the data is available.
+
+    Parameters
+    ----------
+    argv : list of str
+        Command-line arguments after ``validate-config``.
+
+    Exit codes
+    ----------
+    0
+        The configuration is valid.
+    1
+        The configuration is not valid (the error is printed to stderr).
+    2
+        Wrong command-line arguments (raised by ``argparse``).
+    """
+    from ._biapy import validate_config
+    parser = argparse.ArgumentParser(
+        prog="biapy validate-config",
+        description="Check a BiaPy YAML configuration without running anything.",
+    )
+    parser.add_argument("config", help="Path to the YAML configuration file")
+    parser.add_argument(
+        "--no-data-check",
+        action="store_true",
+        help="Skip the check that the data paths exist",
+    )
+    args = parser.parse_args(argv)
+
+    try:
+        cfg = validate_config(args.config, check_data_paths=not args.no_data_check)
+    except (ValueError, AssertionError, FileNotFoundError, KeyError) as e:
+        print(f"ERROR: {e}", file=sys.stderr)
+        sys.exit(1)
+
+    print(f"OK: {args.config} is a valid {cfg.PROBLEM.TYPE} {cfg.PROBLEM.NDIM} configuration")
+    sys.exit(0)      
 
 def main():
     r"""
@@ -81,6 +151,10 @@ def main():
     and calls its `run_job` method to start the workflow. The program exits
     with status 0 upon successful completion.
     """
+    # Subcommand: 'biapy validate-config ...' only checks a config; any other call runs a job
+    if len(sys.argv) > 1 and sys.argv[1] == "validate-config":
+        _validate_config_cli(sys.argv[2:])
+
     ##########################
     #   ARGS COMPROBATION    #
     ##########################
@@ -102,7 +176,10 @@ def main():
     #     --run_id $job_counter \
     #     --gpu 0,1
 
-    parser = argparse.ArgumentParser()
+    parser = argparse.ArgumentParser(
+        epilog="To check a configuration without running anything: biapy validate-config <config> [--no-data-check]",
+    )
+
     parser.add_argument("--config", required=True, help="Path to the configuration file")
     parser.add_argument(
         "--result_dir",
@@ -137,6 +214,8 @@ def main():
     )
     args = parser.parse_args()
 
+    from ._biapy import BiaPy
+
     _biapy = BiaPy(**vars(args), verbose=True)
     _biapy.run_job()
     sys.exit(0)