restore files from main

mantis/cli/option_eat_all.py

@@ -1,5 +1,3 @@
-import warnings
-
 import click
 
 
@@ -14,12 +12,6 @@ def __init__(self, *args, **kwargs):
         self._previous_parser_process = None
         self._eat_all_parser = None
 
-        warnings.warn(
-            "This function is being moved to the biahub library, available at https://github.com/czbiohub-sf/biahub",
-            DeprecationWarning,
-            stacklevel=2,
-        )
-
     def add_to_parser(self, parser, ctx):
         def parser_process(value, state):
             # method to hook to the parser.process

mantis/cli/run_acquisition.py

@@ -1,5 +1,3 @@
-import warnings
-
 from pathlib import Path
 
 import click
@@ -43,12 +41,6 @@ def run_acquisition(
 
     >> mantis run-acquisition -c path/to/config.yaml -o ./YYYY_MM_DD_experiment_name/acquisition_name
     """
-    # Emitting a deprecation warning
-    warnings.warn(
-        "This function is being moved to the biahub library, available at https://github.com/czbiohub-sf/biahub",
-        DeprecationWarning,
-        stacklevel=2,
-    )
 
     # These imports are placed here to accelerate CLI help calls
     from mantis.acquisition.acq_engine import MantisAcquisition

pyproject.toml

@@ -21,7 +21,6 @@ classifiers = [
 # list package dependencies here
 dependencies = [
   "copylot @ git+https://github.com/czbiohub-sf/coPylot",
-  "deprecated",
   "iohub==0.2.0a1",
   "matplotlib",
   "napari; 'arm64' in platform_machine",                 # without Qt5 and skimage