refactoring for zipstore and ome zarr outputs

- fixes a bug (was writing to zarr to .snakemake_touch)
- hopefully cleans things up and makes more readable

config/config.yml

@@ -7,6 +7,8 @@ remote_creds: '~/.config/gcloud/application_default_credentials.json' #this is n
 
 write_ome_zarr_direct: True #use this to skip writing the final zarr output to work first and copying afterwards -- useful when work is not a fast local disk
 
+use_zipstore: False #if True, produce SPIM.ome.zarr.zip instead of SPIM.ome.zarr
+
 #total resources available, used to set rule resources
 total_cores: 32 
 total_mem_mb: 128000 
@@ -100,7 +102,6 @@ ome_zarr:
       id: 0
       name: spim
       version: "0.4"  
-  use_zipstore: False #if True, produce SPIM.ome.zarr.zip instead of SPIM.ome.zarr
 
 nifti:
   levels: #cannot be higher than max_downsampling_layers in ome_zarr

pyproject.toml

@@ -20,13 +20,22 @@ universal-pathlib = "^0.2.2"
 snakefmt = "^0.10.0"
 mkdocs-material = "^9.5.20"
 mkdocs-include-markdown-plugin = "^6.0.6"
+poethepoet = "^0.29.0"
 
 
 [tool.poetry.group.dataset_creation.dependencies]
 typer = "^0.12.3"
 xmltodict = "^0.13.0"
 tifffile = "^2024.5.10"
 
+[tool.poe.tasks]
+test_localin_gcsout = "snakemake --dry-run --config datasets=testing/dryrun_tests/datasets_local.tsv root='gcs://khanlab-lightsheet/data/test_bids'"
+test_localin_localout = "snakemake --dry-run --config datasets=testing/dryrun_tests/datasets_gcs.tsv root=bids"
+test_gcsin_gcsout = "snakemake --dry-run --config datasets=testing/dryrun_tests/datasets_gcs.tsv root='gcs://khanlab-lightsheet/data/test_bids'"
+test_gcsin_localout = "snakemake --dry-run --config datasets=testing/dryrun_tests/datasets_gcs.tsv root=bids"
+test_localin_localout_zipstore = "snakemake --dry-run --config datasets=testing/dryrun_tests/datasets_gcs.tsv root=bids use_zipstore=True"
+test_localin_gcsout_zipstore = "snakemake --dry-run --config datasets=testing/dryrun_tests/datasets_gcs.tsv root='gcs://khanlab-lightsheet/data/test_bids' use_zipstore=True"
+
 [build-system]
 requires = ["poetry-core"]
 build-backend = "poetry.core.masonry.api"