[pre-commit.ci] pre-commit autoupdate

.pre-commit-config.yaml

@@ -25,21 +25,21 @@ repos:
 
   # Python file formatting
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.15.4
+    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: v0.11.4
+    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

@@ -7,17 +7,17 @@ configfile: workflow.source_path("./test_config.yaml")
 # `config`: specifies the module configuration.
 # `pathvars:` helps you re-wire where the module places files.
 module module_geo_boundaries:
-    snakefile:
-        "../../workflow/Snakefile"
-    config:
-        config["module_geo_boundaries"]
     pathvars:
         # Redirect specific module results (outputs)
         shapes="results/outputs/shapes.parquet",
         # Redirect module intermediate files
         logs="resources/geo_boundaries/logs",
         resources="resources/geo_boundaries/resources",
         results="resources/geo_boundaries/results",
+    snakefile:
+        "../../workflow/Snakefile"
+    config:
+        config["module_geo_boundaries"]
 
 
 # Add a prefix to all module rules, to avoid naming conflicts.
@@ -26,8 +26,8 @@ use rule * from module_geo_boundaries as geo_boundaries_module_*
 
 # Request something from the module
 rule all:
-    message:
-        "A generic test case for this module."
     default_target: True
     input:
         "results/outputs/shapes.parquet",
+    message:
+        "A generic test case for this module."

workflow/Snakefile

@@ -35,14 +35,14 @@ workflow.source_path("scripts/_schemas.py")
 
 
 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

@@ -5,23 +5,21 @@ Small transformations might be performed to make the data easier to work with.
 
 
 rule download_country_overture:
-    message:
-        "Download '{wildcards.country}_{wildcards.subtype}' dataset from Overture Maps."
-    params:
-        version=config["overture_release"],
     output:
         path="<resources>/automatic/countries/overture_{country}_{subtype}.parquet",
     log:
         "<logs>/{country}/download_country_overture_{subtype}.log",
     conda:
         "../envs/shape.yaml"
+    params:
+        version=config["overture_release"],
+    message:
+        "Download '{wildcards.country}_{wildcards.subtype}' dataset from Overture Maps."
     script:
         "../scripts/download_country_overture.py"
 
 
 rule download_country_gadm:
-    message:
-        "Download '{wildcards.country}_{wildcards.subtype}' dataset from GADM."
     output:
         path=temp(
             "<resources>/automatic/countries/raw_gadm_{country}_{subtype}.parquet"
@@ -30,16 +28,13 @@ rule download_country_gadm:
         "<logs>/{country}/download_country_gadm_{subtype}.log",
     conda:
         "../envs/shape.yaml"
+    message:
+        "Download '{wildcards.country}_{wildcards.subtype}' dataset from GADM."
     script:
         "../scripts/download_country_gadm.py"
 
 
 rule standardise_country_gadm:
-    message:
-        "Standardise '{wildcards.country}_{wildcards.subtype}' GADM dataset."
-    params:
-        country_id=lambda wc: str(wc.country),
-        subtype=lambda wc: str(wc.subtype),
     input:
         raw="<resources>/automatic/countries/raw_gadm_{country}_{subtype}.parquet",
     output:
@@ -48,30 +43,31 @@ rule standardise_country_gadm:
         "<logs>/{country}/standardise_country_gadm_{subtype}.log",
     conda:
         "../envs/shape.yaml"
+    params:
+        country_id=lambda wc: str(wc.country),
+        subtype=lambda wc: str(wc.subtype),
+    message:
+        "Standardise '{wildcards.country}_{wildcards.subtype}' GADM dataset."
     script:
         "../scripts/standardise_country_gadm.py"
 
 
 rule download_nuts:
-    message:
-        "Download '{wildcards.resolution}_{wildcards.year}_{wildcards.level}' from NUTS."
-    params:
-        epsg=internal["nuts"]["epsg"],
     output:
         path="<resources>/automatic/nuts/nuts_{resolution}_{year}_{level}.parquet",
     log:
         "<logs>/download_nuts_{resolution}_{year}_{level}.log",
     conda:
         "../envs/shape.yaml"
+    params:
+        epsg=internal["nuts"]["epsg"],
+    message:
+        "Download '{wildcards.resolution}_{wildcards.year}_{wildcards.level}' from NUTS."
     script:
         "../scripts/download_nuts.py"
 
 
 rule standardise_country_nuts:
-    message:
-        "Standardise '{wildcards.country}_{wildcards.subtype}' NUTS dataset."
-    params:
-        year=lambda wc: config["countries"][wc.country]["year"],
     input:
         raw=lambda wc: f"<resources>/automatic/nuts/nuts_{config["countries"][wc.country]["resolution"]}_{config["countries"][wc.country]["year"]}_{wc.subtype}.parquet",
     output:
@@ -80,19 +76,23 @@ rule standardise_country_nuts:
         "<logs>/{country}/standardise_country_nuts_{subtype}.log",
     conda:
         "../envs/shape.yaml"
+    params:
+        year=lambda wc: config["countries"][wc.country]["year"],
+    message:
+        "Standardise '{wildcards.country}_{wildcards.subtype}' NUTS dataset."
     script:
         "../scripts/standardise_country_nuts.py"
 
 
 rule download_marine_eez_area:
-    message:
-        "Download and standardise '{wildcards.country}' EEZ dataset."
     output:
         path="<resources>/automatic/eez/{country}.parquet",
         plot="<resources>/automatic/eez/{country}.png",
     log:
         "<logs>/{country}/download_marine_eez_area.log",
     conda:
         "../envs/shape.yaml"
+    message:
+        "Download and standardise '{wildcards.country}' EEZ dataset."
     script:
         "../scripts/download_marine_eez_area.py"

workflow/rules/build.smk

@@ -2,10 +2,6 @@
 
 
 rule build_combined_area:
-    message:
-        "Combine land and marine polygons."
-    params:
-        crs=config["crs"],
     input:
         countries=[
             f"<resources>/automatic/countries/{data['source']}_{country}_{data['subtype']}.parquet"
@@ -26,5 +22,9 @@ rule build_combined_area:
         "<logs>/build_combined_area.log",
     conda:
         "../envs/shape.yaml"
+    params:
+        crs=config["crs"],
+    message:
+        "Combine land and marine polygons."
     script:
         "../scripts/build_combined_area.py"