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Simplify and fix land cover demendacy in snakemake #24

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Merged
mdales merged 1 commit into from
Feb 2, 2026
Merged

Simplify and fix land cover demendacy in snakemake #24

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1 change: 1 addition & 0 deletions workflow/rules/aoh.smk
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Original file line number Diff line number Diff line change
Expand Up @@ -58,6 +58,7 @@ def aoh_species_inputs(wildcards):
"habitat_sentinel": ancient(
DATADIR / "habitat_layers" / SCENARIO / ".habitat_complete"
),
"lcc_0": DATADIR / "habitat_layers" / SCENARIO / "lcc_0.tif",
"crosswalk": DATADIR / "crosswalk.csv",
"mask": ancient(DATADIR / "masks" / "CGLS100Inland_withGADMIslands.tif"),
"elevation_max": ancient(DATADIR / config["inputs"]["zenodo_elevation_max"]),
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30 changes: 0 additions & 30 deletions workflow/rules/prepare.smk
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Expand Up @@ -135,33 +135,3 @@ rule copy_islands_layer:
"""
cp {input.islands} {output.lcc_0} 2>&1 | tee {log}
"""


# =============================================================================
# Helper rule to get specific habitat layer
# =============================================================================


def get_habitat_layer(wildcards):
"""
Returns the path to a specific habitat layer.
lcc_0 is special (islands layer), others come from habitat processing.
"""
n = int(wildcards.n)
if n == 0:
return DATADIR / "habitat_layers" / SCENARIO / "lcc_0.tif"
else:
return DATADIR / "habitat_layers" / SCENARIO / f"lcc_{n}.tif"


rule habitat_layer:
"""
Pseudo-rule to request a specific habitat layer.
This triggers either the habitat processing or islands copy as needed.
"""
input:
layer=get_habitat_layer,
output:
# This is a bit of a trick - we declare the output but let the
# upstream rules actually create it
touch(DATADIR / "habitat_layers" / SCENARIO / ".lcc_{n}_exists"),