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Make changes to work with snakemake version >8.0
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Benjamin Gros authored and Benjamin Gros committed Aug 23, 2024
1 parent 7245ef2 commit c8bd7b9
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Showing 16 changed files with 35 additions and 19 deletions.
3 changes: 2 additions & 1 deletion testing/testing_scripts/test_apply_basic_flatfield_corr.py
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Expand Up @@ -32,7 +32,8 @@ def test_apply_basic_flatfield_corr():
"work/sub-mouse1/micr/sub-mouse1_sample-brain_acq-blaze1x_desc-flatcorr_SPIM.zarr",
"-f",
"-j1",
"--keep-target-files",
"--target-files-omit-workdir-adjustment",
"--use-singularity",

"--directory",
workdir,
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5 changes: 3 additions & 2 deletions testing/testing_scripts/test_bids_readme.py
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Expand Up @@ -23,6 +23,7 @@ def test_bids_readme():

# dbg
print("bids/README.md", file=sys.stderr)
#Hello

# Run the test job.
sp.check_output([
Expand All @@ -32,12 +33,12 @@ def test_bids_readme():
"bids/README.md",
"-f",
"-j1",
"--keep-target-files",
"--target-files-omit-workdir-adjustment",
"--use-singularity",

"--directory",
workdir,
])

# Check the output byte by byte using cmp.
# To modify this behavior, you can inherit from common.OutputChecker in here
# and overwrite the method `compare_files(generated_file, expected_file),
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3 changes: 2 additions & 1 deletion testing/testing_scripts/test_bids_samples_json.py
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Expand Up @@ -32,7 +32,8 @@ def test_bids_samples_json():
"bids/samples.json",
"-f",
"-j1",
"--keep-target-files",
"--target-files-omit-workdir-adjustment",
"--use-singularity",

"--directory",
workdir,
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3 changes: 2 additions & 1 deletion testing/testing_scripts/test_blaze_to_metadata.py
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Expand Up @@ -32,7 +32,8 @@ def test_blaze_to_metadata():
"bids/sub-mouse1/micr/sub-mouse1_sample-brain_acq-blaze1x_SPIM.json",
"-f",
"-j1",
"--keep-target-files",
"--target-files-omit-workdir-adjustment",
"--use-singularity",

"--directory",
workdir,
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3 changes: 2 additions & 1 deletion testing/testing_scripts/test_create_samples_tsv.py
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Expand Up @@ -32,7 +32,8 @@ def test_create_samples_tsv():
"bids/samples.tsv",
"-f",
"-j1",
"--keep-target-files",
"--target-files-omit-workdir-adjustment",
"--use-singularity",

"--directory",
workdir,
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3 changes: 2 additions & 1 deletion testing/testing_scripts/test_extract_dataset.py
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Expand Up @@ -32,7 +32,8 @@ def test_extract_dataset():
"work/sub-mouse1/micr/sub-mouse1_sample-brain_acq-blaze1x_desc-raw_SPIM",
"-f",
"-j1",
"--keep-target-files",
"--target-files-omit-workdir-adjustment",
"--use-singularity",

"--directory",
workdir,
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5 changes: 3 additions & 2 deletions testing/testing_scripts/test_fit_basic_flatfield_corr.py
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Expand Up @@ -32,7 +32,8 @@ def test_fit_basic_flatfield_corr():
"work/sub-mouse1/micr/sub-mouse1_sample-brain_acq-blaze1x_stain-abeta_basicmodel",
"-f",
"-j1",
"--keep-target-files",
"--target-files-omit-workdir-adjustment",
"--use-singularity",

"--directory",
workdir,
Expand All @@ -42,4 +43,4 @@ def test_fit_basic_flatfield_corr():
# To modify this behavior, you can inherit from common.OutputChecker in here
# and overwrite the method `compare_files(generated_file, expected_file),
# also see common.py.
common.OutputChecker(data_path, expected_path, workdir).check()
common.ImperfectOutputChecker(data_path, expected_path, workdir).check()
3 changes: 2 additions & 1 deletion testing/testing_scripts/test_generate_flatfield_qc.py
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Expand Up @@ -36,7 +36,8 @@ def test_generate_flatfield_qc():
"qc/sub-mouse1_sample-brain_acq-blaze1x/images/uncorr",
"-f",
"-j1",
"--keep-target-files",
"--target-files-omit-workdir-adjustment",
"--use-singularity",

"--directory",
workdir,
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3 changes: 2 additions & 1 deletion testing/testing_scripts/test_generate_subject_qc.py
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Expand Up @@ -34,7 +34,8 @@ def test_generate_subject_qc():
"qc/sub-mouse1_sample-brain_acq-blaze1x/subject.html",
"-f",
"-j1",
"--keep-target-files",
"--target-files-omit-workdir-adjustment",
"--use-singularity",

"--directory",
workdir,
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3 changes: 2 additions & 1 deletion testing/testing_scripts/test_generate_volume_qc.py
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Expand Up @@ -34,7 +34,8 @@ def test_generate_volume_qc():
"qc/sub-mouse1_sample-brain_acq-blaze1x/volume_qc.html",
"-f",
"-j1",
"--keep-target-files",
"--target-files-omit-workdir-adjustment",
"--use-singularity",

"--directory",
workdir,
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3 changes: 2 additions & 1 deletion testing/testing_scripts/test_generate_whole_slice_qc.py
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Original file line number Diff line number Diff line change
Expand Up @@ -35,7 +35,8 @@ def test_generate_whole_slice_qc():
"qc/sub-mouse1_sample-brain_acq-blaze1x/images/whole",
"-f",
"-j1",
"--keep-target-files",
"--target-files-omit-workdir-adjustment",
"--use-singularity",

"--directory",
workdir,
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3 changes: 2 additions & 1 deletion testing/testing_scripts/test_ome_zarr_to_nii.py
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Expand Up @@ -32,7 +32,8 @@ def test_ome_zarr_to_nii():
"bids/derivatives/resampled/sub-mouse1/micr/sub-mouse1_sample-brain_acq-blaze1x_stain-abeta_res-3x_SPIM.nii",
"-f",
"-j1",
"--keep-target-files",
"--target-files-omit-workdir-adjustment",
"--use-singularity",

"--directory",
workdir,
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3 changes: 2 additions & 1 deletion testing/testing_scripts/test_raw_dataset_desc.py
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Original file line number Diff line number Diff line change
Expand Up @@ -32,7 +32,8 @@ def test_raw_dataset_desc():
"bids/dataset_description.json",
"-f",
"-j1",
"--keep-target-files",
"--target-files-omit-workdir-adjustment",
"--use-singularity",

"--directory",
workdir,
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3 changes: 2 additions & 1 deletion testing/testing_scripts/test_resampled_dataset_desc.py
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Original file line number Diff line number Diff line change
Expand Up @@ -32,7 +32,8 @@ def test_resampled_dataset_desc():
"bids/derivatives/resampled/dataset_description.json",
"-f",
"-j1",
"--keep-target-files",
"--target-files-omit-workdir-adjustment",
"--use-singularity",

"--directory",
workdir,
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3 changes: 2 additions & 1 deletion testing/testing_scripts/test_tif_to_zarr.py
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Original file line number Diff line number Diff line change
Expand Up @@ -32,7 +32,8 @@ def test_tif_to_zarr():
"work/sub-mouse1/micr/sub-mouse1_sample-brain_acq-blaze1x_desc-raw_SPIM.zarr",
"-f",
"-j1",
"--keep-target-files",
"--target-files-omit-workdir-adjustment",
"--use-singularity",

"--directory",
workdir,
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5 changes: 3 additions & 2 deletions testing/testing_scripts/test_zarr_to_bdv.py
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Original file line number Diff line number Diff line change
Expand Up @@ -33,7 +33,8 @@ def test_zarr_to_bdv():
"work/sub-mouse1/micr/sub-mouse1_sample-brain_acq-blaze1x_desc-flatcorr_bdv.xml",
"-f",
"-j1",
"--keep-target-files",
"--target-files-omit-workdir-adjustment",
"--use-singularity",

"--directory",
workdir,
Expand All @@ -43,4 +44,4 @@ def test_zarr_to_bdv():
# To modify this behavior, you can inherit from common.OutputChecker in here
# and overwrite the method `compare_files(generated_file, expected_file),
# also see common.py.
common.OutputChecker(data_path, expected_path, workdir).check()
common.ImperfectOutputChecker(data_path, expected_path, workdir).check()

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