Use click

custom_analyses/src/a00/requirements.in

@@ -0,0 +1 @@
+click

custom_analyses/src/a00/requirements.txt

@@ -0,0 +1 @@
+click==8.1.7

custom_analyses/src/a01/requirements.in

@@ -1,2 +1,3 @@
-bluepysnap>=2.0.0
 blueetl>=0.4.0
+bluepysnap>=2.0.0
+click

custom_analyses/src/a01/requirements.txt

@@ -1,43 +1,43 @@
 annotated-types==0.6.0
-attrs==23.1.0
-blueetl==0.4.3
+attrs==23.2.0
+blueetl==0.7.1
 blueetl-core==0.1.7
-bluepysnap==2.0.2
+bluepysnap==3.0.1
 cached-property==1.5.2
 click==8.1.7
 contourpy==1.2.0
 cycler==0.12.1
 deprecation==2.1.0
-fonttools==4.46.0
+fonttools==4.49.0
 h5py==3.10.0
-importlib-resources==6.1.1
+importlib_resources==6.1.3
 joblib==1.3.2
-jsonschema==4.20.0
-jsonschema-specifications==2023.11.2
+jsonschema==4.21.1
+jsonschema-specifications==2023.12.1
 kiwisolver==1.4.5
 libsonata==0.1.24
-matplotlib==3.8.2
-more-itertools==10.1.0
-morph-tool==2.9.1
+matplotlib==3.8.3
+more-itertools==10.2.0
+morph-tool==2.10.2
 MorphIO==3.3.7
-neurom==3.2.5
-numpy==1.26.2
+neurom==3.2.8
+numpy==1.26.4
 packaging==23.2
-pandas==2.1.4
-Pillow==10.1.0
-pyarrow==14.0.1
-pydantic==2.5.2
-pydantic_core==2.14.5
-pyparsing==3.1.1
-python-dateutil==2.8.2
-pytz==2023.3.post1
+pandas==2.2.1
+pillow==10.2.0
+pyarrow==15.0.1
+pydantic==2.6.3
+pydantic_core==2.16.3
+pyparsing==3.1.2
+python-dateutil==2.9.0.post0
+pytz==2024.1
 PyYAML==6.0.1
-referencing==0.32.0
-rpds-py==0.13.2
-scipy==1.11.4
+referencing==0.33.0
+rpds-py==0.18.0
+scipy==1.12.0
 six==1.16.0
-tqdm==4.66.1
-typing_extensions==4.9.0
-tzdata==2023.3
-xarray==2023.12.0
+tqdm==4.66.2
+typing_extensions==4.10.0
+tzdata==2024.1
+xarray==2024.2.0
 xmltodict==0.13.0

custom_analyses/src/a02/requirements.in

@@ -1,3 +1,4 @@
+blueetl>=0.4.0
 bluepysnap>=2.0.0
 blueetl>=0.4.0
 submitit>=1.5.1

custom_analyses/src/a02/requirements.txt

@@ -1,45 +1,45 @@
 annotated-types==0.6.0
-attrs==23.1.0
-blueetl==0.4.3
+attrs==23.2.0
+blueetl==0.7.1
 blueetl-core==0.1.7
-bluepysnap==2.0.2
+bluepysnap==3.0.1
 cached-property==1.5.2
 click==8.1.7
 cloudpickle==3.0.0
 contourpy==1.2.0
 cycler==0.12.1
 deprecation==2.1.0
-fonttools==4.46.0
+fonttools==4.49.0
 h5py==3.10.0
-importlib-resources==6.1.1
+importlib_resources==6.1.3
 joblib==1.3.2
-jsonschema==4.20.0
-jsonschema-specifications==2023.11.2
+jsonschema==4.21.1
+jsonschema-specifications==2023.12.1
 kiwisolver==1.4.5
 libsonata==0.1.24
-matplotlib==3.8.2
-more-itertools==10.1.0
-morph-tool==2.9.1
+matplotlib==3.8.3
+more-itertools==10.2.0
+morph-tool==2.10.2
 MorphIO==3.3.7
-neurom==3.2.5
-numpy==1.26.2
+neurom==3.2.8
+numpy==1.26.4
 packaging==23.2
-pandas==2.1.4
-Pillow==10.1.0
-pyarrow==14.0.1
-pydantic==2.5.2
-pydantic_core==2.14.5
-pyparsing==3.1.1
-python-dateutil==2.8.2
-pytz==2023.3.post1
+pandas==2.2.1
+pillow==10.2.0
+pyarrow==15.0.1
+pydantic==2.6.3
+pydantic_core==2.16.3
+pyparsing==3.1.2
+python-dateutil==2.9.0.post0
+pytz==2024.1
 PyYAML==6.0.1
-referencing==0.32.0
-rpds-py==0.13.2
-scipy==1.11.4
+referencing==0.33.0
+rpds-py==0.18.0
+scipy==1.12.0
 six==1.16.0
 submitit==1.5.1
-tqdm==4.66.1
-typing_extensions==4.9.0
-tzdata==2023.3
-xarray==2023.12.0
+tqdm==4.66.2
+typing_extensions==4.10.0
+tzdata==2024.1
+xarray==2024.2.0
 xmltodict==0.13.0

custom_analyses/src/common/utils.py

@@ -3,11 +3,12 @@
 import logging
 import multiprocessing
 import os
-import sys
 import time
 from collections.abc import Callable
 from pathlib import Path
 
+import click
+
 L = logging.getLogger("analysis")
 
 
@@ -58,11 +59,28 @@ def wrapper(
         return result
 
     if func.__module__ == "__main__":
-        # if the script is called directly, automatically execute the function
-        wrapper(
-            analysis_config=load_json(Path(sys.argv[1])),
-            analysis_output=Path(sys.argv[2]),
+        # if the script is called directly, automatically wrap and execute the function
+        @click.command()
+        @click.option(
+            "--log-level",
+            default="INFO",
+            help="Log level",
+            type=click.Choice(
+                choices=["DEBUG", "INFO", "WARNING", "ERROR", "CRITICAL"],
+                case_sensitive=False,
+            ),
+            show_default=True,
         )
+        @click.argument("analysis_config_file", type=click.Path(exists=True))
+        @click.argument("analysis_output_file", type=click.Path(exists=False))
+        def cli_wrapper(analysis_config_file, analysis_output_file, log_level):
+            wrapper(
+                analysis_config=load_json(Path(analysis_config_file)),
+                analysis_output=Path(analysis_output_file),
+                log_level=log_level,
+            )
+
+        cli_wrapper()
 
     return wrapper
 

custom_analyses/src/emodel_00/requirements.in

@@ -1,4 +1,5 @@
 bluecellulab<2.3.2
+click
 joblib
 matplotlib
 neuron

custom_analyses/src/emodel_01/requirements.in

@@ -1,2 +1,3 @@
 bluepyemodel
+click
 neuron