Add .pre-commit-config.yaml with snakefmt

.pre-commit-config.yaml

@@ -0,0 +1,5 @@
+repos:
+  - repo: https://github.com/snakemake/snakefmt
+    rev: v0.10.2
+    hooks:
+      - id: snakefmt

Snakefile

@@ -1,5 +1,6 @@
 configfile: "snakemake.yml"
 
+
 include: "benchmarks/backgrounds/Snakefile"
 include: "benchmarks/backwards_ecal/Snakefile"
 include: "benchmarks/barrel_ecal/Snakefile"
@@ -19,6 +20,7 @@ include: "benchmarks/femc_electron/Snakefile"
 include: "benchmarks/femc_photon/Snakefile"
 include: "benchmarks/femc_pi0/Snakefile"
 
+
 use_s3 = config["remote_provider"].lower() == "s3"
 use_xrootd = config["remote_provider"].lower() == "xrootd"
 
@@ -29,32 +31,45 @@ def get_remote_path(path):
     elif use_xrootd:
         return f"root://dtn-eic.jlab.org//work/eic2/{path}"
     else:
-        raise runtime_exception('Unexpected value for config["remote_provider"]: {config["remote_provider"]}')
+        raise runtime_exception(
+            'Unexpected value for config["remote_provider"]: {config["remote_provider"]}'
+        )
 
 
 rule fetch_epic:
     output:
-        filepath="EPIC/{PATH}"
+        filepath="EPIC/{PATH}",
     params:
         # wildcards are not included in hash for caching, we need to add them as params
-        PATH=lambda wildcards: wildcards.PATH
+        PATH=lambda wildcards: wildcards.PATH,
     cache: True
     retries: 3
-    shell: """
+    shell:
+        (
+            """
 xrdcp --debug 2 root://dtn-eic.jlab.org//work/eic2/{output.filepath} {output.filepath}
-""" if use_xrootd else """
+"""
+            if use_xrootd
+            else (
+                """
 mc cp S3/eictest/{output.filepath} {output.filepath}
-""" if use_s3 else f"""
-echo 'Unexpected value for config["remote_provider"]: {config["remote_provider"]}'
-exit 1
 """
+                if use_s3
+                else f"""
+                        echo 'Unexpected value for config["remote_provider"]: {config["remote_provider"]}'
+                        exit 1
+                        """
+            )
+        )
 
 
 rule warmup_run:
     output:
         "warmup/{DETECTOR_CONFIG}.edm4hep.root",
-    message: "Ensuring that calibrations/fieldmaps are available for {wildcards.DETECTOR_CONFIG}"
-    shell: """
+    message:
+        "Ensuring that calibrations/fieldmaps are available for {wildcards.DETECTOR_CONFIG}"
+    shell:
+        """
 set -m # monitor mode to prevent lingering processes
 exec ddsim \
   --runType batch \
@@ -80,7 +95,7 @@ rule org2py:
         notebook=workflow.basedir + "/{NOTEBOOK}.org",
         converter=workflow.source_path("benchmarks/common/org2py.awk"),
     output:
-        "{NOTEBOOK}.py"
+        "{NOTEBOOK}.py",
     shell:
         """
 awk -f {input.converter} {input.notebook} > {output}

benchmarks/backgrounds/Snakefile

@@ -27,17 +27,24 @@ exec ddsim \
 """
 
 
-DETECTOR_CONFIG=os.environ["DETECTOR_CONFIG"]
+DETECTOR_CONFIG = os.environ["DETECTOR_CONFIG"]
+
 
 rule backgrounds_ecal_backwards:
     input:
         matplotlibrc=".matplotlibrc",
         script="benchmarks/backgrounds/ecal_backwards.py",
-        electron_beam_gas_sim="sim_output/" + DETECTOR_CONFIG + "/backgrounds/EPIC/EVGEN/BACKGROUNDS/BEAMGAS/electron/GETaLM1.0.0-1.0/10GeV/GETaLM1.0.0-1.0_ElectronBeamGas_10GeV_foam_emin10keV_run001.edm4hep.root",
-        physics_signal_sim="sim_output/" + DETECTOR_CONFIG + "/backgrounds/EPIC/EVGEN/DIS/NC/10x100/minQ2=1/pythia8NCDIS_10x100_minQ2=1_beamEffects_xAngle=-0.025_hiDiv_1.edm4hep.root",
-        proton_beam_gas_sim="sim_output/" + DETECTOR_CONFIG + "/backgrounds/EPIC/EVGEN/BACKGROUNDS/BEAMGAS/proton/pythia8.306-1.0/100GeV/pythia8.306-1.0_ProtonBeamGas_100GeV_run001.edm4hep.root",
+        electron_beam_gas_sim="sim_output/"
+        + DETECTOR_CONFIG
+        + "/backgrounds/EPIC/EVGEN/BACKGROUNDS/BEAMGAS/electron/GETaLM1.0.0-1.0/10GeV/GETaLM1.0.0-1.0_ElectronBeamGas_10GeV_foam_emin10keV_run001.edm4hep.root",
+        physics_signal_sim="sim_output/"
+        + DETECTOR_CONFIG
+        + "/backgrounds/EPIC/EVGEN/DIS/NC/10x100/minQ2=1/pythia8NCDIS_10x100_minQ2=1_beamEffects_xAngle=-0.025_hiDiv_1.edm4hep.root",
+        proton_beam_gas_sim="sim_output/"
+        + DETECTOR_CONFIG
+        + "/backgrounds/EPIC/EVGEN/BACKGROUNDS/BEAMGAS/proton/pythia8.306-1.0/100GeV/pythia8.306-1.0_ProtonBeamGas_100GeV_run001.edm4hep.root",
     output:
-        directory("results/backgrounds/backwards_ecal")
+        directory("results/backgrounds/backwards_ecal"),
     threads: workflow.cores
     shell:
         """

benchmarks/backwards_ecal/Snakefile

@@ -1,13 +1,15 @@
 def get_n_events(wildcards):
     energy = float(wildcards.ENERGY.replace("GeV", "").replace("MeV", "e-3"))
     n_events = 1000 if wildcards.PARTICLE == "e-" else 2000
-    n_events = int(n_events // (energy ** 0.5))
+    n_events = int(n_events // (energy**0.5))
     return n_events
 
 
 rule backwards_ecal_sim:
     input:
-        steering_file=ancient("EPIC/EVGEN/SINGLE/{PARTICLE}/{ENERGY}/{PHASE_SPACE}/{PARTICLE}_{ENERGY}_{PHASE_SPACE}.steer"),
+        steering_file=ancient(
+            "EPIC/EVGEN/SINGLE/{PARTICLE}/{ENERGY}/{PHASE_SPACE}/{PARTICLE}_{ENERGY}_{PHASE_SPACE}.steer"
+        ),
         warmup="warmup/{DETECTOR_CONFIG}.edm4hep.root",
     output:
         "sim_output/backwards_ecal/{DETECTOR_CONFIG}/{PARTICLE}/{ENERGY}/{PHASE_SPACE}/{PARTICLE}_{ENERGY}_{PHASE_SPACE}.{INDEX}.edm4hep.root",
@@ -19,7 +21,7 @@ rule backwards_ecal_sim:
         PHASE_SPACE="(3to50|45to135|130to177)deg",
         INDEX="\d{4}",
     params:
-        N_EVENTS=get_n_events
+        N_EVENTS=get_n_events,
     shell:
         """
 set -m # monitor mode to prevent lingering processes
@@ -45,7 +47,8 @@ rule backwards_ecal_recon:
         "sim_output/backwards_ecal/{DETECTOR_CONFIG}/{PARTICLE}/{ENERGY}/{PHASE_SPACE}/{PARTICLE}_{ENERGY}_{PHASE_SPACE}.{INDEX}.eicrecon.tree.edm4eic.root.log",
     wildcard_constraints:
         INDEX="\d{4}",
-    shell: """
+    shell:
+        """
 set -m # monitor mode to prevent lingering processes
 exec env DETECTOR_CONFIG={wildcards.DETECTOR_CONFIG} \
   eicrecon {input} -Ppodio:output_file={output} \
@@ -60,15 +63,20 @@ rule backwards_ecal_recon_many:
             INDEX=range(20),
         ),
     output:
-        touch("sim_output/backwards_ecal/{DETECTOR_CONFIG}/{PARTICLE}/{ENERGY}/{PHASE_SPACE}/flag"),
+        touch(
+            "sim_output/backwards_ecal/{DETECTOR_CONFIG}/{PARTICLE}/{ENERGY}/{PHASE_SPACE}/flag"
+        ),
 
 
-DETECTOR_CONFIG=os.environ["DETECTOR_CONFIG"]
+DETECTOR_CONFIG = os.environ["DETECTOR_CONFIG"]
+
 
 rule backwards_ecal:
     input:
         expand(
-            "sim_output/backwards_ecal/" + DETECTOR_CONFIG + "/{PARTICLE}/{ENERGY}/{PHASE_SPACE}/flag",
+            "sim_output/backwards_ecal/"
+            + DETECTOR_CONFIG
+            + "/{PARTICLE}/{ENERGY}/{PHASE_SPACE}/flag",
             PARTICLE=["pi-", "e-"],
             ENERGY=[
                 "100MeV",
@@ -85,14 +93,22 @@ rule backwards_ecal:
         matplotlibrc=".matplotlibrc",
         script="benchmarks/backwards_ecal/backwards_ecal.py",
     output:
-        directory("results/backwards_ecal")
+        directory("results/backwards_ecal"),
     shell:
-        """
+        (
+            """
 env \
 MATPLOTLIBRC={input.matplotlibrc} \
-DETECTOR_CONFIG=""" + DETECTOR_CONFIG + """ \
-PLOT_TITLE=""" + DETECTOR_CONFIG + """ \
-INPUT_PATH_FORMAT=sim_output/backwards_ecal/""" + DETECTOR_CONFIG + """/{{particle}}/{{energy}}/130to177deg/{{particle}}_{{energy}}_130to177deg.{{ix:04d}}.eicrecon.tree.edm4eic.root \
-OUTPUT_DIR={output} \
-python {input.script}
-"""
+DETECTOR_CONFIG="""
+            + DETECTOR_CONFIG
+            + """ \
+                        PLOT_TITLE="""
+            + DETECTOR_CONFIG
+            + """ \
+                        INPUT_PATH_FORMAT=sim_output/backwards_ecal/"""
+            + DETECTOR_CONFIG
+            + """/{{particle}}/{{energy}}/130to177deg/{{particle}}_{{energy}}_130to177deg.{{ix:04d}}.eicrecon.tree.edm4eic.root \
+                        OUTPUT_DIR={output} \
+                        python {input.script}
+                        """
+        )

benchmarks/barrel_ecal/Snakefile

@@ -6,7 +6,7 @@ rule emcal_barrel_particles_gen:
         workflow.source_path("scripts/emcal_barrel_common_functions.h"),
         script=workflow.source_path("scripts/emcal_barrel_particles_gen.cxx"),
     params:
-        JUGGLER_N_EVENTS = 100,
+        JUGGLER_N_EVENTS=100,
     output:
         "data/emcal_barrel_{PARTICLE}_energies{E_MIN}_{E_MAX}.hepmc",
     shell:
@@ -19,24 +19,28 @@ env \
 
 rule emcal_barrel_particles:
     input:
-        "data/emcal_barrel_{PARTICLE}_energies{E_MIN}_{E_MAX}.hepmc"
+        "data/emcal_barrel_{PARTICLE}_energies{E_MIN}_{E_MAX}.hepmc",
     params:
-        JUGGLER_N_EVENTS = 100,
+        JUGGLER_N_EVENTS=100,
     output:
-        "{DETECTOR_CONFIG}/sim_output/sim_emcal_barrel_{PARTICLE}_energies{E_MIN}_{E_MAX}.edm4hep.root"
+        "{DETECTOR_CONFIG}/sim_output/sim_emcal_barrel_{PARTICLE}_energies{E_MIN}_{E_MAX}.edm4hep.root",
     shell:
-        """
+        (
+            """
 set -m # monitor mode to prevent lingering processes
 exec ddsim \
    --runType batch \
    -v WARNING \
    --part.minimalKineticEnergy 0.5*GeV  \
    --filter.tracker edep0 \
    --numberOfEvents {params.JUGGLER_N_EVENTS} \
-   --compactFile """ + DETECTOR_PATH + """/{wildcards.DETECTOR_CONFIG}.xml \
-   --inputFiles {input} \
-   --outputFile {output}
-"""
+   --compactFile """
+            + DETECTOR_PATH
+            + """/{wildcards.DETECTOR_CONFIG}.xml \
+                                   --inputFiles {input} \
+                                   --outputFile {output}
+                                """
+        )
 
 
 # This is needed to bridge snakemake rule files to "normal" benchmarks
@@ -73,7 +77,7 @@ rule emcal_barrel_particles_analysis:
         script=workflow.source_path("scripts/emcal_barrel_particles_analysis.cxx"),
         sim="{DETECTOR_CONFIG}/sim_output/sim_emcal_barrel_{PARTICLE}.edm4hep.root",
     wildcard_constraints:
-        PARTICLE="(electron|photon|piplus|piminus)", # avoid clash with "pions"
+        PARTICLE="(electron|photon|piplus|piminus)",  # avoid clash with "pions"
     output:
         "{DETECTOR_CONFIG}/results/emcal_barrel_{PARTICLE}_calibration.json",
         "{DETECTOR_CONFIG}/results/emcal_barrel_{PARTICLE}_Ethr.png",
@@ -123,19 +127,24 @@ rule emcal_barrel_pi0_analysis:
             var_name=["Ethr", "nhits", "Esim", "dE_rel"],
             extension=["pdf", "png"],
         ),
-        "{DETECTOR_CONFIG}/results/Barrel_emcal_pi0.json"
+        "{DETECTOR_CONFIG}/results/Barrel_emcal_pi0.json",
     shell:
         """
 cd {wildcards.DETECTOR_CONFIG}
 root -l -b -q '{input.script}+("../{input.sim}")'
 """
 
 
-ENERGY_SCAN_ENERGIES = [0.5, 1., 2., 5., 10.]
+ENERGY_SCAN_ENERGIES = [0.5, 1.0, 2.0, 5.0, 10.0]
+
+
 rule emcal_energy_scan:
     input:
         # Require all simulations produced for this rule
-        expand("{{DETECTOR_CONFIG}}/sim_output/energy_scan/{energy}/sim_emcal_barrel_{{PARTICLE}}.edm4hep.root", energy=ENERGY_SCAN_ENERGIES),
+        expand(
+            "{{DETECTOR_CONFIG}}/sim_output/energy_scan/{energy}/sim_emcal_barrel_{{PARTICLE}}.edm4hep.root",
+            energy=ENERGY_SCAN_ENERGIES,
+        ),
     output:
         "{DETECTOR_CONFIG}/sim_output/emcal_barrel_energy_scan_points_{PARTICLE}.txt",
     run:
@@ -154,7 +163,15 @@ rule emcal_barrel_particles_energy_scan_analysis:
         expand(
             "{{DETECTOR_CONFIG}}/results/energy_scan/{energy}/emcal_barrel_{{PARTICLE}}_{plot}.png",
             energy=ENERGY_SCAN_ENERGIES,
-            plot=["Esim_layer", "Layer_nodep", "Layer_Esim_mean", "Ethr", "nhits", "Esim", "fsam"],
+            plot=[
+                "Esim_layer",
+                "Layer_nodep",
+                "Layer_Esim_mean",
+                "Ethr",
+                "nhits",
+                "Esim",
+                "fsam",
+            ],
         ),
     shell:
         """
@@ -174,7 +191,16 @@ rule emcal_barrel_pion_rejection_analysis:
         "{DETECTOR_CONFIG}/results/Barrel_emcal_pion_rej.json",
         expand(
             "{{DETECTOR_CONFIG}}/results/emcal_barrel_pion_rej_uncut_comb_{var_save}.png",
-            var_save=["Esim", "EsimTot", "EDep6", "EDep6OverP", "pT", "eta", "EsimScFi", "EsimScFiOverP"],
+            var_save=[
+                "Esim",
+                "EsimTot",
+                "EDep6",
+                "EDep6OverP",
+                "pT",
+                "eta",
+                "EsimScFi",
+                "EsimScFiOverP",
+            ],
         ),
         expand(
             "{{DETECTOR_CONFIG}}/results/emcal_barrel_pion_rej_uncut_comb_E{i}Eta{j}.png",
@@ -187,7 +213,13 @@ rule emcal_barrel_pion_rejection_analysis:
             eta_bin=range(2, 4),
             tag=(
                 ["cut_mom_ele", "cut_mom_pim", "cut_ratio_pim"]
-                + sum([[f"cut_{var}_ele", f"cut_{var}_pim", f"cut_{var}_comb"] for var in ["pT", "EDep6OverP"]], [])
+                + sum(
+                    [
+                        [f"cut_{var}_ele", f"cut_{var}_pim", f"cut_{var}_comb"]
+                        for var in ["pT", "EDep6OverP"]
+                    ],
+                    [],
+                )
             ),
             extension=["pdf", "png"],
         ),

benchmarks/ecal_gaps/Snakefile

@@ -3,7 +3,9 @@ import os
 
 rule ecal_gaps_sim:
     input:
-        steering_file=ancient("EPIC/EVGEN/SINGLE/{PARTICLE}/{ENERGY}/{PHASE_SPACE}/{PARTICLE}_{ENERGY}_{PHASE_SPACE}.steer"),
+        steering_file=ancient(
+            "EPIC/EVGEN/SINGLE/{PARTICLE}/{ENERGY}/{PHASE_SPACE}/{PARTICLE}_{ENERGY}_{PHASE_SPACE}.steer"
+        ),
         warmup="warmup/{DETECTOR_CONFIG}.edm4hep.root",
     output:
         "sim_output/ecal_gaps/{DETECTOR_CONFIG}/{PARTICLE}/{ENERGY}/{PHASE_SPACE}/{PARTICLE}_{ENERGY}_{PHASE_SPACE}.{INDEX}.edm4hep.root",
@@ -15,7 +17,7 @@ rule ecal_gaps_sim:
         PHASE_SPACE="(3to50|45to135|130to177)deg",
         INDEX="\d{4}",
     params:
-        N_EVENTS=1000
+        N_EVENTS=1000,
     shell:
         """
 set -m # monitor mode to prevent lingering processes
@@ -41,15 +43,17 @@ rule ecal_gaps_recon:
         "sim_output/ecal_gaps/{DETECTOR_CONFIG}/{PARTICLE}/{ENERGY}/{PHASE_SPACE}/{PARTICLE}_{ENERGY}_{PHASE_SPACE}.{INDEX}.eicrecon.tree.edm4eic.root.log",
     wildcard_constraints:
         INDEX="\d{4}",
-    shell: """
+    shell:
+        """
 set -m # monitor mode to prevent lingering processes
 exec env DETECTOR_CONFIG={wildcards.DETECTOR_CONFIG} \
   eicrecon {input} -Ppodio:output_file={output} \
   -Ppodio:output_collections=EcalEndcapNRecHits,EcalBarrelScFiRecHits,EcalBarrelImagingRecHits,EcalEndcapPRecHits,MCParticles
 """
 
 
-DETECTOR_CONFIG=os.environ["DETECTOR_CONFIG"]
+DETECTOR_CONFIG = os.environ["DETECTOR_CONFIG"]
+
 
 rule ecal_gaps:
     input: