diff --git a/.github/workflows/quality.yml b/.github/workflows/quality.yml index ffe18b2..a0c0321 100644 --- a/.github/workflows/quality.yml +++ b/.github/workflows/quality.yml @@ -31,7 +31,7 @@ jobs: - name: Install Poetry uses: snok/install-poetry@v1 with: - version: 1.2.0 + version: 1.4.2 virtualenvs-create: true virtualenvs-in-project: true diff --git a/labelmerge/workflow/Snakefile b/labelmerge/workflow/Snakefile index 4f83663..af44ce9 100644 --- a/labelmerge/workflow/Snakefile +++ b/labelmerge/workflow/Snakefile @@ -38,7 +38,6 @@ base_inputs = generate_inputs( derivatives=config["derivatives"], pybids_inputs=base_config, participant_label=config["participant_label"], - use_bids_inputs=True, ) overlay_inputs = generate_inputs( bids_dir=config.get("overlay_bids_dir", config["bids_dir"]), @@ -46,7 +45,6 @@ overlay_inputs = generate_inputs( derivatives=config["derivatives"], pybids_inputs=overlay_config, participant_label=config["participant_label"], - use_bids_inputs=True, ) @@ -64,14 +62,10 @@ include: "rules/label_harmonization.smk" rule all: input: - expand( + base_inputs["labelmap"].expand( rules.merge_labels.output["merged_map"], - zip, - **base_inputs["labelmap"].input_zip_lists ), - expand( + base_inputs["labelmap"].expand( rules.merge_labels.output["merged_metadata"], - zip, - **base_inputs["labelmap"].input_zip_lists ), default_target: True diff --git a/labelmerge/workflow/rules/label_harmonization.smk b/labelmerge/workflow/rules/label_harmonization.smk index fa7e2ff..f173b14 100644 --- a/labelmerge/workflow/rules/label_harmonization.smk +++ b/labelmerge/workflow/rules/label_harmonization.smk @@ -45,11 +45,11 @@ def load_metadata(atlas_path, bids_dir): def build_metadata_path(wildcards): base_metadata = load_metadata( - Path(expand(base_inputs["labelmap"].input_path, **wildcards)[0]), + Path(expand(base_inputs["labelmap"].path, **wildcards)[0]), config["bids_dir"], ) overlay_metadata = load_metadata( - Path(expand(overlay_inputs["labelmap"].input_path, **wildcards)[0]), + Path(expand(overlay_inputs["labelmap"].path, **wildcards)[0]), config["overlay_bids_dir"], ) return { @@ -61,20 +61,20 @@ def build_metadata_path(wildcards): rule merge_labels: input: unpack(build_metadata_path), - base_map=base_inputs["labelmap"].input_path, - overlay_map=overlay_inputs["labelmap"].input_path, + base_map=base_inputs["labelmap"].path, + overlay_map=overlay_inputs["labelmap"].path, output: merged_map=bids( root=str(Path(config["output_dir"]) / "combined"), suffix="dseg.nii.gz", desc="combined", - **base_inputs["labelmap"].input_wildcards, + **base_inputs["labelmap"].wildcards, ), merged_metadata=bids( root=str(Path(config["output_dir"]) / "combined"), suffix="dseg.tsv", desc="combined", - **base_inputs["labelmap"].input_wildcards, + **base_inputs["labelmap"].wildcards, ), params: base_exceptions=f"--base_exceptions {' '.join(config['base_exceptions'])}" diff --git a/poetry.lock b/poetry.lock index d95a222..9532325 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,3 +1,5 @@ +# This file is automatically @generated by Poetry 1.4.2 and should not be changed by hand. + [[package]] name = "appdirs" version = "1.4.4" @@ -5,6 +7,10 @@ description = "A small Python module for determining appropriate platform-specif category = "main" optional = false python-versions = "*" +files = [ + {file = "appdirs-1.4.4-py2.py3-none-any.whl", hash = "sha256:a841dacd6b99318a741b166adb07e19ee71a274450e68237b4650ca1055ab128"}, + {file = "appdirs-1.4.4.tar.gz", hash = "sha256:7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41"}, +] [[package]] name = "arrow" @@ -13,6 +19,10 @@ description = "Better dates & times for Python" category = "main" optional = false python-versions = ">=3.6" +files = [ + {file = "arrow-1.2.3-py3-none-any.whl", hash = "sha256:5a49ab92e3b7b71d96cd6bfcc4df14efefc9dfa96ea19045815914a6ab6b1fe2"}, + {file = "arrow-1.2.3.tar.gz", hash = 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