Add basic snakemake script (test)

.gitignore

@@ -84,3 +84,6 @@ venv/
 
 # custom scripts
 examples/*.sh
+
+# snakemake
+.snakemake/*

MANIFEST.in

@@ -1,5 +1,6 @@
 include LICENSE
 include README.md
+include Snakefile
 exclude .pre-commit-config.yaml
 
 recursive-include calcium_imaging_automation *.py

Snakefile

@@ -0,0 +1,6 @@
+rule setup:
+    input:
+        datasets_path="/nfs/winstor/margrie/SimonWeiler/RawData/Invivo_imaging/3photon_rotation/shared/",
+        writing_path="/ceph/margrie/laura/cimaut/",
+    output: "setup_output.txt"
+    shell: "python calcium_imaging_automation/core/rules/setup.py {input.datasets_path} {input.writing_path} --folder_read_pattern '2*' --file_read_pattern 'rotation_00001.tif' --file_read_pattern '*.bin' > {output}"

calcium_imaging_automation/core/rules/setup.py

@@ -0,0 +1,70 @@
+import argparse
+import shutil
+from pathlib import Path
+
+from calcium_imaging_automation.core.reader import ReadAquiredData
+from calcium_imaging_automation.core.writer import DatashuttleWrapper
+
+
+def setup(raw_data_path, folder_read_pattern, file_read_pattern, output_path):
+    try:
+        shutil.rmtree("/ceph/margrie/laura/cimaut/derivatives/")
+        shutil.rmtree("/ceph/margrie/laura/cimaut/submitit/")
+    except FileNotFoundError:
+        print("No derivatives folder found")
+
+    print(f"Reading data from {raw_data_path}")
+    reader = ReadAquiredData(
+        raw_data_path,
+        folder_read_pattern,
+        file_read_pattern,
+    )
+    print(f"Found {len(reader.datasets_paths)} datasets.")
+
+    number_of_tiffs = reader.max_session_number(filetype="tif")
+    print(f"Max of tiffs found: {number_of_tiffs}")
+
+    writer = DatashuttleWrapper(output_path)
+    print(f"Dataset names: {reader.dataset_names}")
+    writer.create_folders(reader.dataset_names, session_number=number_of_tiffs)
+    print("Folders created")
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(
+        description="Example usage of the pipeline manager."
+    )
+
+    parser.add_argument(
+        "raw_data_path", type=Path, help="Path to the raw data."
+    )
+    parser.add_argument(
+        "output_path", type=Path, help="Path to the output data."
+    )
+    parser.add_argument(
+        "--folder_read_pattern",
+        type=str,
+        help="Glob pattern for reading folder.",
+        default="*",
+    )
+    parser.add_argument(
+        "--file_read_pattern",
+        type=str,
+        help="List of glob patterns for reading files.",
+        action="append",
+    )
+
+    args = parser.parse_args()
+
+    try:
+        setup(
+            args.raw_data_path,
+            args.folder_read_pattern,
+            args.file_read_pattern,
+            args.output_path,
+        )
+
+        print("Success")
+    except Exception as e:
+        print(f"Error: {e.args}")
+        print(e.with_traceback(e.__traceback__))