[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

@@ -11,10 +11,6 @@ with open(workflow.source_path("../../config/config.yaml"), "r") as f:
 # `config`: specifies the module configuration.
 # `pathvars:` helps you re-wire where the module places files.
 module module_co2stop_cdr:
-    snakefile:
-        "../../workflow/Snakefile"
-    config:
-        module_config["module_co2stop_cdr"]
     pathvars:
         # Redirect specific user resources (inputs)
         user_shapes="resources/inputs/{shapes}/shapes.parquet",
@@ -25,6 +21,10 @@ module module_co2stop_cdr:
         logs="resources/co2stop_cdr/logs",
         resources="resources/co2stop_cdr/resources",
         results="resources/co2stop_cdr/results",
+    snakefile:
+        "../../workflow/Snakefile"
+    config:
+        module_config["module_co2stop_cdr"]
 
 
 # rename all module rules with a prefix, to avoid naming conflicts.
@@ -36,8 +36,8 @@ FILES = ["aquifer"]
 
 # Request something from the module
 rule all:
-    message:
-        "A generic test case for your module."
     default_target: True
     input:
         expand("results/outputs/BALK/medium/{cdr}.parquet", cdr=FILES),
+    message:
+        "A generic test case for your module."

workflow/Snakefile

@@ -43,14 +43,14 @@ workflow.source_path("scripts/_utils.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/aggregate.smk

@@ -2,13 +2,6 @@
 
 
 rule aggregate_co2stop:
-    message:
-        "Aggregating '{wildcards.shapes}-{wildcards.scenario}-{wildcards.cdr_group}'."
-    params:
-        bounds_mtco2=lambda wc: config["imputation"]["aggregated"][wc.cdr_group][
-            "bounds_mtco2"
-        ],
-        proj_crs=config["crs"]["projected"],
     input:
         shapes="<user_shapes>",
         storage_units=rules.prepare_co2stop_storage_units.output.mtco2,
@@ -28,15 +21,18 @@ rule aggregate_co2stop:
         cdr_group="|".join(CDR_GROUP),
     conda:
         "../envs/co2stop.yaml"
+    params:
+        bounds_mtco2=lambda wc: config["imputation"]["aggregated"][wc.cdr_group][
+            "bounds_mtco2"
+        ],
+        proj_crs=config["crs"]["projected"],
+    message:
+        "Aggregating '{wildcards.shapes}-{wildcards.scenario}-{wildcards.cdr_group}'."
     script:
         "../scripts/aggregate_co2stop.py"
 
 
 rule aggregate_totals:
-    message:
-        "Aggregating totals for '{wildcards.shapes}-{wildcards.scenario}'."
-    params:
-        proj_crs=config["crs"]["projected"],
     input:
         shapes="<user_shapes>",
         aggregates=lambda wc: expand(
@@ -59,5 +55,9 @@ rule aggregate_totals:
         scenario="|".join(["low", "medium", "high"]),
     conda:
         "../envs/co2stop.yaml"
+    params:
+        proj_crs=config["crs"]["projected"],
+    message:
+        "Aggregating totals for '{wildcards.shapes}-{wildcards.scenario}'."
     script:
         "../scripts/aggregate_totals.py"

workflow/rules/automatic.smk

@@ -2,29 +2,21 @@
 
 
 rule download_co2stop:
-    message:
-        "Downloading the open CO2Stop dataset."
-    params:
-        url=internal["resources"]["automatic"]["co2stop"],
     output:
         zipfile="<resources>/automatic/co2stop.zip",
     log:
         "<logs>/download_co2stop.log",
     conda:
         "../envs/shell.yaml"
+    params:
+        url=internal["resources"]["automatic"]["co2stop"],
+    message:
+        "Downloading the open CO2Stop dataset."
     shell:
         "curl -sSLo {output.zipfile:q} {params.url:q}"
 
 
 rule unzip_co2stop:
-    message:
-        "Unzipping necessary data from the CO2Stop file."
-    params:
-        storage_data="CO2Stop_DataInterrogationSystem/Hydrocarbon_Storage_Units.csv",
-        storage_map="CO2Stop_Polygons Data/StorageUnits_March13.kml",
-        traps_data="CO2Stop_DataInterrogationSystem/Hydrocarbon_Traps.csv",
-        traps_map="CO2Stop_Polygons Data/DaughterUnits_March13.kml",
-        country_map="CO2Stop_Polygons Data/Basemap.kml",
     input:
         zipfile=rules.download_co2stop.output.zipfile,
     output:
@@ -37,5 +29,13 @@ rule unzip_co2stop:
         "<logs>/automatic/unzip_co2stop.log",
     conda:
         "../envs/co2stop.yaml"
+    params:
+        storage_data="CO2Stop_DataInterrogationSystem/Hydrocarbon_Storage_Units.csv",
+        storage_map="CO2Stop_Polygons Data/StorageUnits_March13.kml",
+        traps_data="CO2Stop_DataInterrogationSystem/Hydrocarbon_Traps.csv",
+        traps_map="CO2Stop_Polygons Data/DaughterUnits_March13.kml",
+        country_map="CO2Stop_Polygons Data/Basemap.kml",
+    message:
+        "Unzipping necessary data from the CO2Stop file."
     script:
         "../scripts/unzip_co2stop.py"

workflow/rules/prepare.smk

@@ -4,13 +4,6 @@ CDR_GROUP = ["aquifer", "gas", "oil"]
 
 
 rule prepare_co2stop_storage_units:
-    message:
-        "Harmonising CO2Stop storage units: aquifer."
-    params:
-        cdr_group="aquifer",
-        cdr_group_config=lambda wc: config["imputation"]["co2stop"]["aquifer"],
-        dataset="storage_units",
-        geo_crs=config["crs"]["geographic"],
     input:
         table=rules.unzip_co2stop.output.storage_data,
         polygons=rules.unzip_co2stop.output.storage_map,
@@ -33,18 +26,18 @@ rule prepare_co2stop_storage_units:
         "<logs>/storage_units/aquifer/prepare_co2stop.log",
     conda:
         "../envs/co2stop.yaml"
+    params:
+        cdr_group="aquifer",
+        cdr_group_config=lambda wc: config["imputation"]["co2stop"]["aquifer"],
+        dataset="storage_units",
+        geo_crs=config["crs"]["geographic"],
+    message:
+        "Harmonising CO2Stop storage units: aquifer."
     script:
         "../scripts/prepare_co2stop.py"
 
 
 rule prepare_co2stop_traps:
-    message:
-        "Harmonising CO2Stop traps: {wildcards.cdr_group}."
-    params:
-        cdr_group=lambda wc: wc.cdr_group,
-        cdr_group_config=lambda wc: config["imputation"]["co2stop"][wc.cdr_group],
-        dataset="traps",
-        geo_crs=config["crs"]["geographic"],
     input:
         table=rules.unzip_co2stop.output.traps_data,
         polygons=rules.unzip_co2stop.output.traps_map,
@@ -69,5 +62,12 @@ rule prepare_co2stop_traps:
         cdr_group="|".join(CDR_GROUP),
     conda:
         "../envs/co2stop.yaml"
+    params:
+        cdr_group=lambda wc: wc.cdr_group,
+        cdr_group_config=lambda wc: config["imputation"]["co2stop"][wc.cdr_group],
+        dataset="traps",
+        geo_crs=config["crs"]["geographic"],
+    message:
+        "Harmonising CO2Stop traps: {wildcards.cdr_group}."
     script:
         "../scripts/prepare_co2stop.py"