Set optional dependencies, bump version

Author: rodvrees

im2deep/__init__.py

@@ -1,3 +1,3 @@
 """IM2Deep: Deep learning framework for peptide collisional cross section prediction."""
 
-__version__ = "0.3.1"
+__version__ = "1.0.0"

im2deep/__main__.py

@@ -18,8 +18,6 @@
 from psm_utils.psm_list import PSMList
 from rich.logging import RichHandler
 
-from im2deep._exceptions import IM2DeepError
-from im2deep.im2deep import predict_ccs
 
 # from im2deep.calibrate import linear_calibration
 
@@ -149,6 +147,12 @@ def main(
     """Command line interface to IM2Deep."""
     setup_logging(log_level)
 
+    if multi:
+        check_optional_dependencies()
+
+    from im2deep._exceptions import IM2DeepError
+    from im2deep.im2deep import predict_ccs
+
     with open(psm_file) as f:
         first_line_pred = f.readline().strip()
     if calibration_file:

im2deep/im2deep.py

@@ -6,7 +6,6 @@
 from psm_utils.psm_list import PSMList
 
 from im2deep.calibrate import linear_calibration
-from im2deep.predict_multi import predict_multi
 from im2deep.utils import ccs2im
 
 LOGGER = logging.getLogger(__name__)
@@ -62,6 +61,8 @@ def predict_ccs(
         )
 
     if multi:
+        from im2deep.predict_multi import predict_multi
+
         LOGGER.info("Predicting multiconformer CCS values...")
         pred_df = predict_multi(
             psm_list_pred,

pyproject.toml

@@ -23,7 +23,7 @@ dependencies = [
     "deeplc",
     "psm_utils",
     "pandas",
-    "numpy",
+    "numpy==1.26.0",
     "rich",
 ]