From f2e186fc00ccbb93bb6477f5621d4049e5aba405 Mon Sep 17 00:00:00 2001
From: Michael Dales <mwd24@cam.ac.uk>
Date: Mon, 2 Feb 2026 14:41:00 +0000
Subject: [PATCH] Simplify and fix land cover demendacy in snakemake

---
 workflow/rules/aoh.smk     |  1 +
 workflow/rules/prepare.smk | 30 ------------------------------
 2 files changed, 1 insertion(+), 30 deletions(-)

diff --git a/workflow/rules/aoh.smk b/workflow/rules/aoh.smk
index e29294a..160a70a 100644
--- a/workflow/rules/aoh.smk
+++ b/workflow/rules/aoh.smk
@@ -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"]),
diff --git a/workflow/rules/prepare.smk b/workflow/rules/prepare.smk
index 00bafe9..ba068a1 100644
--- a/workflow/rules/prepare.smk
+++ b/workflow/rules/prepare.smk
@@ -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"),