Merge pull request #825 from PyPSA/snakemake-8

Compatibility with `snakemake>=8`

Snakefile

@@ -7,13 +7,11 @@ from shutil import copyfile, move, rmtree
 from pathlib import Path
 import yaml
 
-from snakemake.remote.HTTP import RemoteProvider as HTTPRemoteProvider
 from snakemake.utils import min_version
 
-from scripts._helpers import path_provider
+min_version("8.5")
 
-min_version("7.7")
+from scripts._helpers import path_provider
-HTTP = HTTPRemoteProvider()
 
 default_files = {
     "config/config.default.yaml": "config/config.yaml",

config/config.default.yaml

@@ -813,8 +813,8 @@ solving:
     cbc-default: {} # Used in CI
     glpk-default: {} # Used in CI
 
-  mem: 30000 #memory in MB; 20 GB enough for 50+B+I+H2; 100 GB for 181+B+I+H2
+  mem_mb: 30000 #memory in MB; 20 GB enough for 50+B+I+H2; 100 GB for 181+B+I+H2
-  walltime: "12:00:00"
+  runtime: 6h #runtime in humanfriendly style https://humanfriendly.readthedocs.io/en/latest/
 
 # docs in https://pypsa-eur.readthedocs.io/en/latest/configuration.html#plotting
 plotting:

doc/release_notes.rst

@@ -10,6 +10,11 @@ Release Notes
 Upcoming Release
 ================
 
+* Upgrade to Snakemake v8.5+. This version is the new minimum version required.
+  To upgrade an existing environment, run ``conda install -c bioconda
+  snakemake-minimal">=8.5"`` and ``pip install snakemake-storage-plugin-http``
+  (https://github.com/PyPSA/pypsa-eur/pull/825).
+
 * Corrected a bug leading to power plants operating after their DateOut
   (https://github.com/PyPSA/pypsa-eur/pull/958). Added additional grouping years
   before 1980.

envs/environment.yaml

@@ -20,8 +20,7 @@ dependencies:
 - openpyxl!=3.1.1
 - pycountry
 - seaborn
-  # snakemake 8 introduced a number of breaking changes which the workflow has yet to be made compatible with
+- snakemake-minimal>=8.5
-- snakemake-minimal>=7.7.0,<8.0.0
 - memory_profiler
 - yaml
 - pytables
@@ -61,4 +60,7 @@ dependencies:
 
 - pip:
   - tsam>=2.3.1
+  - snakemake-storage-plugin-http
+  - snakemake-executor-plugin-slurm
+  - snakemake-executor-plugin-cluster-generic
   - highspy

envs/retrieve.yaml

@@ -8,6 +8,11 @@ channels:
 - bioconda
 dependencies:
 - python>=3.8
-- snakemake-minimal>=7.7.0,<8.0.0
+- pip
+- snakemake-minimal>=8.5
 - pandas>=2.1
 - tqdm
+- pip:
+  - snakemake-storage-plugin-http
+  - snakemake-executor-plugin-slurm
+  - snakemake-executor-plugin-cluster-generic

rules/build_sector.smk

@@ -93,7 +93,7 @@ rule build_gas_network:
 
 rule build_gas_input_locations:
     input:
-        gem=HTTP.remote(
+        gem=storage(
             "https://globalenergymonitor.org/wp-content/uploads/2023/07/Europe-Gas-Tracker-2023-03-v3.xlsx",
             keep_local=True,
         ),
@@ -293,7 +293,7 @@ rule build_biomass_potentials:
     params:
         biomass=config_provider("biomass"),
     input:
-        enspreso_biomass=HTTP.remote(
+        enspreso_biomass=storage(
             "https://zenodo.org/records/10356004/files/ENSPRESO_BIOMASS.xlsx",
             keep_local=True,
         ),
@@ -325,8 +325,8 @@ rule build_biomass_potentials:
 
 rule build_biomass_transport_costs:
     input:
-        transport_cost_data=HTTP.remote(
+        transport_cost_data=storage(
-            "publications.jrc.ec.europa.eu/repository/bitstream/JRC98626/biomass potentials in europe_web rev.pdf",
+            "https://publications.jrc.ec.europa.eu/repository/bitstream/JRC98626/biomass potentials in europe_web rev.pdf",
             keep_local=True,
         ),
     output:
@@ -350,7 +350,7 @@ rule build_sequestration_potentials:
             "sector", "regional_co2_sequestration_potential"
         ),
     input:
-        sequestration_potential=HTTP.remote(
+        sequestration_potential=storage(
             "https://raw.githubusercontent.com/ericzhou571/Co2Storage/main/resources/complete_map_2020_unit_Mt.geojson",
             keep_local=True,
         ),

rules/retrieve.smk

@@ -64,9 +64,8 @@ if config["enable"]["retrieve"] and config["enable"].get("retrieve_cutout", True
 
     rule retrieve_cutout:
         input:
-            HTTP.remote(
+            storage(
-                "zenodo.org/record/6382570/files/{cutout}.nc",
+                "https://zenodo.org/record/6382570/files/{cutout}.nc",
-                static=True,
             ),
         output:
             protected("cutouts/" + CDIR + "{cutout}.nc"),
@@ -104,10 +103,9 @@ if config["enable"]["retrieve"] and config["enable"].get(
 
     rule retrieve_natura_raster:
         input:
-            HTTP.remote(
+            storage(
-                "zenodo.org/record/4706686/files/natura.tiff",
+                "https://zenodo.org/record/4706686/files/natura.tiff",
                 keep_local=True,
-                static=True,
             ),
         output:
             resources("natura.tiff"),
@@ -200,10 +198,9 @@ if config["enable"]["retrieve"]:
 
     rule retrieve_ship_raster:
         input:
-            HTTP.remote(
+            storage(
                 "https://zenodo.org/record/6953563/files/shipdensity_global.zip",
                 keep_local=True,
-                static=True,
             ),
         output:
             protected("data/shipdensity_global.zip"),
@@ -223,9 +220,8 @@ if config["enable"]["retrieve"]:
     # Website: https://land.copernicus.eu/global/products/lc
     rule download_copernicus_land_cover:
         input:
-            HTTP.remote(
+            storage(
-                "zenodo.org/record/3939050/files/PROBAV_LC100_global_v3.0.1_2019-nrt_Discrete-Classification-map_EPSG-4326.tif",
+                "https://zenodo.org/record/3939050/files/PROBAV_LC100_global_v3.0.1_2019-nrt_Discrete-Classification-map_EPSG-4326.tif",
-                static=True,
             ),
         output:
             "data/Copernicus_LC100_global_v3.0.1_2019-nrt_Discrete-Classification-map_EPSG-4326.tif",
@@ -240,9 +236,8 @@ if config["enable"]["retrieve"]:
     # Website: https://ec.europa.eu/jrc/en/luisa
     rule retrieve_luisa_land_cover:
         input:
-            HTTP.remote(
+            storage(
-                "jeodpp.jrc.ec.europa.eu/ftp/jrc-opendata/LUISA/EUROPE/Basemaps/LandUse/2018/LATEST/LUISA_basemap_020321_50m.tif",
+                "https://jeodpp.jrc.ec.europa.eu/ftp/jrc-opendata/LUISA/EUROPE/Basemaps/LandUse/2018/LATEST/LUISA_basemap_020321_50m.tif",
-                static=True,
             ),
         output:
             "data/LUISA_basemap_020321_50m.tif",
@@ -285,11 +280,7 @@ if config["enable"]["retrieve"]:
     # Website: https://www.protectedplanet.net/en/thematic-areas/wdpa
     rule download_wdpa:
         input:
-            HTTP.remote(
+            storage(url, keep_local=True),
-                url,
-                static=True,
-                keep_local=True,
-            ),
         params:
             zip="data/WDPA_shp.zip",
             folder=directory("data/WDPA"),
@@ -311,9 +302,8 @@ if config["enable"]["retrieve"]:
         # extract the main zip and then merge the contained 3 zipped shapefiles
         # Website: https://www.protectedplanet.net/en/thematic-areas/marine-protected-areas
         input:
-            HTTP.remote(
+            storage(
-                f"d1gam3xoknrgr2.cloudfront.net/current/WDPA_WDOECM_{bYYYY}_Public_marine_shp.zip",
+                f"https://d1gam3xoknrgr2.cloudfront.net/current/WDPA_WDOECM_{bYYYY}_Public_marine_shp.zip",
-                static=True,
                 keep_local=True,
             ),
         params:
@@ -336,10 +326,9 @@ if config["enable"]["retrieve"]:
 
     rule retrieve_monthly_co2_prices:
         input:
-            HTTP.remote(
+            storage(
                 "https://www.eex.com/fileadmin/EEX/Downloads/EUA_Emission_Spot_Primary_Market_Auction_Report/Archive_Reports/emission-spot-primary-market-auction-report-2019-data.xls",
                 keep_local=True,
-                static=True,
             ),
         output:
             "data/validation/emission-spot-primary-market-auction-report-2019-data.xls",

rules/solve_electricity.smk

@@ -29,7 +29,7 @@ rule solve_network:
     threads: solver_threads
     resources:
         mem_mb=memory,
-        walltime=config_provider("solving", "walltime", default="12:00:00"),
+        runtime=config_provider("solving", "runtime", default="6h"),
     shadow:
         "minimal"
     conda:
@@ -60,7 +60,7 @@ rule solve_operations_network:
     threads: 4
     resources:
         mem_mb=(lambda w: 10000 + 372 * int(w.clusters)),
-        walltime=config_provider("solving", "walltime", default="12:00:00"),
+        runtime=config_provider("solving", "runtime", default="6h"),
     shadow:
         "minimal"
     conda:

rules/solve_myopic.smk

@@ -132,8 +132,8 @@ rule solve_sector_network_myopic:
         + "logs/elec_s{simpl}_{clusters}_l{ll}_{opts}_{sector_opts}_{planning_horizons}_python.log",
     threads: solver_threads
     resources:
-        mem_mb=config_provider("solving", "mem"),
+        mem_mb=config_provider("solving", "mem_mb"),
-        walltime=config_provider("solving", "walltime", default="12:00:00"),
+        runtime=config_provider("solving", "runtime", default="6h"),
     benchmark:
         (
             RESULTS

rules/solve_overnight.smk

@@ -30,8 +30,8 @@ rule solve_sector_network:
         + "logs/elec_s{simpl}_{clusters}_l{ll}_{opts}_{sector_opts}_{planning_horizons}_python.log",
     threads: solver_threads
     resources:
-        mem_mb=config_provider("solving", "mem"),
+        mem_mb=config_provider("solving", "mem_mb"),
-        walltime=config_provider("solving", "walltime", default="12:00:00"),
+        runtime=config_provider("solving", "runtime", default="6h"),
     benchmark:
         (
             RESULTS

scripts/_helpers.py

@@ -354,7 +354,16 @@ def mock_snakemake(
 
     import snakemake as sm
     from pypsa.descriptors import Dict
+    from snakemake.api import Workflow
+    from snakemake.common import SNAKEFILE_CHOICES
     from snakemake.script import Snakemake
+    from snakemake.settings import (
+        ConfigSettings,
+        DAGSettings,
+        ResourceSettings,
+        StorageSettings,
+        WorkflowSettings,
+    )
 
     script_dir = Path(__file__).parent.resolve()
     if root_dir is None:
@@ -374,7 +383,7 @@ def mock_snakemake(
             f" {root_dir} or scripts directory {script_dir}"
         )
     try:
-        for p in sm.SNAKEFILE_CHOICES:
+        for p in SNAKEFILE_CHOICES:
             if os.path.exists(p):
                 snakefile = p
                 break
@@ -383,8 +392,18 @@ def mock_snakemake(
         elif isinstance(configfiles, str):
             configfiles = [configfiles]
 
-        workflow = sm.Workflow(
+        resource_settings = ResourceSettings()
-            snakefile, overwrite_configfiles=configfiles, rerun_triggers=[]
+        config_settings = ConfigSettings(configfiles=configfiles)
+        workflow_settings = WorkflowSettings()
+        storage_settings = StorageSettings()
+        dag_settings = DAGSettings(rerun_triggers=[])
+        workflow = Workflow(
+            config_settings,
+            resource_settings,
+            workflow_settings,
+            storage_settings,
+            dag_settings,
+            storage_provider_settings=dict(),
         )
         workflow.include(snakefile)
 

scripts/build_gas_input_locations.py

@@ -25,7 +25,7 @@ def read_scigrid_gas(fn):
 
 
 def build_gem_lng_data(fn):
-    df = pd.read_excel(fn[0], sheet_name="LNG terminals - data")
+    df = pd.read_excel(fn, sheet_name="LNG terminals - data")
     df = df.set_index("ComboID")
 
     remove_country = ["Cyprus", "Turkey"]  # noqa: F841
@@ -46,7 +46,7 @@ def build_gem_lng_data(fn):
 
 
 def build_gem_prod_data(fn):
-    df = pd.read_excel(fn[0], sheet_name="Gas extraction - main")
+    df = pd.read_excel(fn, sheet_name="Gas extraction - main")
     df = df.set_index("GEM Unit ID")
 
     remove_country = ["Cyprus", "Türkiye"]  # noqa: F841
@@ -60,7 +60,7 @@ def build_gem_prod_data(fn):
               & ~Longitude.isna()"
     ).copy()
 
-    p = pd.read_excel(fn[0], sheet_name="Gas extraction - production")
+    p = pd.read_excel(fn, sheet_name="Gas extraction - production")
     p = p.set_index("GEM Unit ID")
     p = p[p["Fuel description"] == "gas"]