[pre-commit.ci] pre-commit autoupdate

.pre-commit-config.yaml

@@ -4,7 +4,7 @@ default_language_version:
 repos:
   # Generic 'file quality' testing
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v5.0.0
+    rev: v6.0.0
     hooks:
       # Machine-friendliness
       - id: trailing-whitespace
@@ -24,21 +24,21 @@ repos:
 
   # Python file formatting
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.9.6
+    rev: v0.15.9
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]
       - id: ruff-format
 
   # Snakemake file formatting
   - repo: https://github.com/snakemake/snakefmt
-    rev: v0.10.2
+    rev: v1.0.0
     hooks:
       - id: snakefmt
 
   # Spelling
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.4.1
+    rev: v2.4.2
     hooks:
       - id: codespell
         files: .*\.(py|smk|md)$|^Snakefile$

tests/integration/Snakefile

@@ -3,38 +3,36 @@ configfile: workflow.source_path("./test_config.yaml")
 
 
 rule download_netherlands_shapes:
-    message:
-        "Download and unzip the Netherlands shapes."
     output:
         "results/integration_test/resources/user/shapes/NLD.parquet",
     log:
         "results/integration_test/logs/download_netherlands_shapes.log",
     conda:
         "../../workflow/envs/shell.yaml"
+    message:
+        "Download and unzip the Netherlands shapes."
     shell:
         """
         curl -sSLo {output:q} "https://zenodo.org/records/16684683/files/NLD.parquet"
         """
 
 
 rule download_netherlands_protected_areas:
-    message:
-        "Download a dummy drop-in dataset for Netherlands protected areas (not based on WDPA)."
     output:
         "results/integration_test/resources/user/wdpa.gdb.zip",
     log:
         "results/integration_test/logs/download_netherlands_protected_areas.log",
     conda:
         "../../workflow/envs/shell.yaml"
+    message:
+        "Download a dummy drop-in dataset for Netherlands protected areas (not based on WDPA)."
     shell:
         """
         curl -sSLo {output:q} "https://zenodo.org/records/16684513/files/wdpa-nl-dropin.gdb.zip"
         """
 
 
 rule unzip_netherlands_protected_areas:
-    message:
-        "Download protected areas data."
     input:
         script=workflow.source_path("../../workflow/scripts/unzip_like.py"),
         zipfile=rules.download_netherlands_protected_areas.output,
@@ -44,6 +42,8 @@ rule unzip_netherlands_protected_areas:
         "results/integration_test/logs/unzip_netherlands_protected_areas.log",
     conda:
         "../../workflow/envs/shell.yaml"
+    message:
+        "Download protected areas data."
     shell:
         """
         python {input.script:q} {input.zipfile:q} -t "results/integration_test/resources/user/" 2> {log:q}
@@ -68,10 +68,10 @@ use rule * from module_area_potentials as module_area_potentials_*
 
 # Request something from the module
 rule all:
-    message:
-        "Run the module for the Netherlands shapes."
     default_target: True
     input:
         "results/integration_test/resources/user/shapes/NLD.parquet",
         "results/integration_test/resources/user/wdpa.gdb",
         "results/integration_test/results/NLD/area_potential_report.html",
+    message:
+        "Run the module for the Netherlands shapes."

workflow/Snakefile

@@ -35,14 +35,14 @@ include: "rules/process.smk"
 
 
 rule all:
-    message:
-        "ERROR: Invalid `rule all:` call"
     default_target: True
     output:
         "INVALID",
     log:
         stderr="logs/all.stderr",
     conda:
         "envs/shell.yaml"
+    message:
+        "ERROR: Invalid `rule all:` call"
     shell:
         'echo "This workflow must be called as a snakemake module." > {log.stderr}'

workflow/rules/automatic.smk

@@ -7,30 +7,30 @@ if config.get("tiny_files", False):
     ##
 
     rule clip_slope:
-        message:
-            "Download slope data covering the bounds of the input shapefile."
-        params:
-            cog_url=internal["resources"]["automatic"]["slope"],
         input:
             vector="resources/user/shapes/{shape}.parquet",
         output:
             path="resources/automatic/cutout/{shape}/slope.tif",
         log:
             "logs/{shape}/clip_slope.log",
+        params:
+            cog_url=internal["resources"]["automatic"]["slope"],
+        message:
+            "Download slope data covering the bounds of the input shapefile."
         wrapper:
             "v7.2.0/geo/rasterio/clip-geotiff"
 
     rule clip_bathymetry:
-        message:
-            "Download bathymetry data covering the bounds of the input shapefile."
-        params:
-            cog_url=internal["resources"]["automatic"]["bathymetry"],
         input:
             vector="resources/user/shapes/{shape}.parquet",
         output:
             path="resources/automatic/cutout/{shape}/bathymetry.tif",
         log:
             "logs/{shape}/clip_bathymetry.log",
+        params:
+            cog_url=internal["resources"]["automatic"]["bathymetry"],
+        message:
+            "Download bathymetry data covering the bounds of the input shapefile."
         wrapper:
             "v7.2.0/geo/rasterio/clip-geotiff"
 
@@ -41,40 +41,38 @@ else:
     ##
 
     rule download_slope:
-        message:
-            "Download global slope data."
-        params:
-            url=internal["resources"]["automatic"]["slope"],
         output:
             path="resources/automatic/global/slope.tif",
         log:
             "logs/download_slope.log",
         conda:
             "../envs/shell.yaml"
+        params:
+            url=internal["resources"]["automatic"]["slope"],
+        message:
+            "Download global slope data."
         shell:
             """
             curl -sSLo {output:q} {params.url:q}
             """
 
     rule download_bathymetry:
-        message:
-            "Download global bathymetry data."
-        params:
-            url=internal["resources"]["automatic"]["bathymetry"],
         output:
             path="resources/automatic/global/bathymetry.tif",
         log:
             "logs/download_bathymetry.log",
         conda:
             "../envs/shell.yaml"
+        params:
+            url=internal["resources"]["automatic"]["bathymetry"],
+        message:
+            "Download global bathymetry data."
         shell:
             """
             curl -sSLo {output:q} {params.url:q}
             """
 
     rule clip_slope:
-        message:
-            "Cut slope data to the bounds of the input shapefile."
         input:
             script=workflow.source_path("../scripts/clip_raster.py"),
             shapes="resources/user/shapes/{shape}.parquet",
@@ -85,14 +83,14 @@ else:
             "logs/{shape}/clip_slope.log",
         conda:
             "../envs/default.yaml"
+        message:
+            "Cut slope data to the bounds of the input shapefile."
         shell:
             """
             python {input.script:q} {input.slope:q} {input.shapes:q} {output:q} 2> {log:q}
             """
 
     rule clip_bathymetry:
-        message:
-            "Cut bathymetry data to the bounds of the input shapefile."
         input:
             script=workflow.source_path("../scripts/clip_raster.py"),
             shapes="resources/user/shapes/{shape}.parquet",
@@ -103,6 +101,8 @@ else:
             "logs/{shape}/clip_bathymetry.log",
         conda:
             "../envs/default.yaml"
+        message:
+            "Cut bathymetry data to the bounds of the input shapefile."
         shell:
             """
             python {input.script:q} {input.bathymetry:q} {input.shapes:q} {output:q} 2> {log:q}
@@ -115,27 +115,23 @@ else:
 
 
 rule download_globcover:
-    message:
-        "Download the GlobCover land cover data (~380 MB)."
-    params:
-        url=internal["resources"]["automatic"]["globcover"],
     output:
         "resources/automatic/global/globcover.zip",
     log:
         "logs/download_globcover.log",
     conda:
         "../envs/shell.yaml"
+    params:
+        url=internal["resources"]["automatic"]["globcover"],
+    message:
+        "Download the GlobCover land cover data (~380 MB)."
     shell:
         """
         curl -sSLo {output:q} {params.url:q}
         """
 
 
 rule unzip_globcover:
-    message:
-        "Unzip the relevant TIF files from the GlobCover zip file."
-    params:
-        target_file=internal["resources"]["automatic"]["globcover_landcover_tif"],
     input:
         script=workflow.source_path("../scripts/unzip_like.py"),
         zipfile=rules.download_globcover.output,
@@ -145,15 +141,17 @@ rule unzip_globcover:
         "logs/unzip_globcover.log",
     conda:
         "../envs/shell.yaml"
+    params:
+        target_file=internal["resources"]["automatic"]["globcover_landcover_tif"],
+    message:
+        "Unzip the relevant TIF files from the GlobCover zip file."
     shell:
         """
         python {input.script:q} {input.zipfile:q} -f {params.target_file:q} -o {output:q} 2> {log:q}
         """
 
 
 rule clip_landcover:
-    message:
-        "Cut land cover data to the bounds of the input shapefile."
     input:
         script=workflow.source_path("../scripts/clip_raster.py"),
         shapes="resources/user/shapes/{shape}.parquet",
@@ -164,6 +162,8 @@ rule clip_landcover:
         "logs/{shape}/clip_landcover.log",
     conda:
         "../envs/default.yaml"
+    message:
+        "Cut land cover data to the bounds of the input shapefile."
     shell:
         """
         python {input.script:q} {input.landcover:q} {input.shapes:q} {output:q} 2> {log:q}
@@ -176,27 +176,23 @@ rule clip_landcover:
 
 
 rule download_ghsl:
-    message:
-        "Download the GHSL (Global Human Settlement Layer) built-up surface data."
-    params:
-        url=internal["resources"]["automatic"]["ghsl"],
     output:
         "resources/automatic/global/ghsl_built_s.zip",
     log:
         "logs/download_ghsl.log",
     conda:
         "../envs/shell.yaml"
+    params:
+        url=internal["resources"]["automatic"]["ghsl"],
+    message:
+        "Download the GHSL (Global Human Settlement Layer) built-up surface data."
     shell:
         """
         curl -sSLo {output:q} {params.url:q}
         """
 
 
 rule unzip_ghsl:
-    message:
-        "Unzip the relevant TIF file from the GHSL data."
-    params:
-        target_file=internal["resources"]["automatic"]["ghsl_tif"],
     input:
         script=workflow.source_path("../scripts/unzip_like.py"),
         zipfile=rules.download_ghsl.output,
@@ -206,15 +202,17 @@ rule unzip_ghsl:
         "logs/unzip_ghsl.log",
     conda:
         "../envs/shell.yaml"
+    params:
+        target_file=internal["resources"]["automatic"]["ghsl_tif"],
+    message:
+        "Unzip the relevant TIF file from the GHSL data."
     shell:
         """
         python {input.script:q} {input.zipfile:q} -f {params.target_file:q} -o {output:q} 2> {log:q}
         """
 
 
 rule clip_settlement:
-    message:
-        "Cut settlement data to the bounds of the input shapefile."
     input:
         script=workflow.source_path("../scripts/clip_raster.py"),
         shapes="resources/user/shapes/{shape}.parquet",
@@ -225,6 +223,8 @@ rule clip_settlement:
         "logs/{shape}/clip_settlement.log",
     conda:
         "../envs/default.yaml"
+    message:
+        "Cut settlement data to the bounds of the input shapefile."
     shell:
         """
         python {input.script:q} {input.settlement:q} {input.shapes:q} {output:q} 2> {log:q}
@@ -237,8 +237,6 @@ rule clip_settlement:
 
 
 rule rasterise_clip_wdpa:
-    message:
-        "Rasterise and cut WDPA data to the bounds of the input shapefile, using the landcover raster as reference for the rasterisation."
     input:
         script=workflow.source_path("../scripts/clip_and_rasterise_polys.py"),
         shapes="resources/user/shapes/{shape}.parquet",
@@ -250,6 +248,8 @@ rule rasterise_clip_wdpa:
         "logs/{shape}/clip_wdpa.log",
     conda:
         "../envs/default.yaml"
+    message:
+        "Rasterise and cut WDPA data to the bounds of the input shapefile, using the landcover raster as reference for the rasterisation."
     shell:
         """
         python {input.script:q} {input.shapes:q} {input.reference_raster:q} {input.protected_areas:q} {output:q} 2> {log:q}