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FileNotFoundError when running pypsa-eur as a submodule #1762

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Bug
#1768
Closed
FileNotFoundError when running pypsa-eur as a submodule#1762
Bug
#1768
@jonathan-peel

Description

@jonathan-peel
jonathan-peel
opened on Jul 18, 2025

Version Checks (indicate both or one)

  • I have confirmed this bug exists on the lastest release of PyPSA-Eur.

  • I have confirmed this bug exists on the current master branch of PyPSA-Eur.

Issue Description

Summary: running pypsa-eur as a submodule causes FileNotFoundErrors in the retrieve.smk rules wherever the code attempts to write a file to a directory that doesn't exist yet without creating the parents first.

Given the same starting conditions:

  • Same conda environment pypsa-eur (from osx-arm64.lock.yaml)
  • Same tag release (v2025.07.0)
  • Same starting point (cleared repo clean git repo at v2025.07.0)

Case 1

Run from pypsa-eur directory
cd pypsa-eur
snakemake data/eez/World_EEZ_v12_20231025_LR/eez_v12_lowres.gpkg --cores 1

  • Works: produces the file as expected

Case 2

Run from upper-module, from which pypsa-eur is a git submodule, and we are importing pypsa-eur as a snakemake submodule and declaring its rules to be used in the current snakemake.
snakemake pypsa-eur/data/eez/World_EEZ_v12_20231025_LR/eez_v12_lowres.gpkg --cores 1

  • Doesn't work: FileNotFoundError for rule retrieve_eez on creation of pypsa-eur/data/eez/...: when calling from `preferred-energy-systems
  • The problematic line of code is retrieve.smk", line 371, i.e., with open(params["zip"], "wb") as f:. The problem is that the destination folder (i.e., ./pypsa-eur/data/eez/World_EEZ_v12_20231025_LR) does not exist when the file (i.e., pypsa-eur/data/eez/World_EEZ_v12_20231025_LR/eez_v12_lowres.gpkg) is attempted to be created. The open function does not create parent directories and will raise a FileNotFoundError, see this stack overflow question.
Details

(pypsa-eur) jopeel@ied-mac-101 preferred-energy-systems % snakemake pypsa-eur/data/eez/World_EEZ_v12_20231025_LR/eez_v12_lowres.gpkg --cores 1
Set parameter Username
Academic license - for non-commercial use only - expires 2026-02-17
Using workflow specific profile profiles/default for setting default command line arguments.
Set parameter Username
Academic license - for non-commercial use only - expires 2026-02-17
The flag 'directory' used in rule pypsa_all is only valid for outputs, not inputs.
The flag 'directory' used in rule pypsa_all is only valid for outputs, not inputs.
localrules directive specifies rules that are not present in the Snakefile:
prepare_elec_networks
solve_elec_networks
solve_sector_networks
cluster_networks
prepare_sector_networks
purge

Assuming unrestricted shared filesystem usage.
host: ied-mac-101.local
Building DAG of jobs...
Using shell: /bin/bash
Provided cores: 1 (use --cores to define parallelism)
Rules claiming more threads will be scaled down.
Job stats:
job count

pypsa_retrieve_eez 1
total 1

Select jobs to execute...
Execute 1 jobs...

[Fri Jul 18 15:14:49 2025]
localrule pypsa_retrieve_eez:
output: pypsa-eur/data/eez/World_EEZ_v12_20231025_LR/eez_v12_lowres.gpkg
jobid: 0
reason: Missing output files: pypsa-eur/data/eez/World_EEZ_v12_20231025_LR/eez_v12_lowres.gpkg
resources: tmpdir=/var/folders/cd/3symzw7d0833vd8qj4shbrl80000gp/T
Set parameter Username
Academic license - for non-commercial use only - expires 2026-02-17
The flag 'directory' used in rule pypsa_all is only valid for outputs, not inputs.
The flag 'directory' used in rule pypsa_all is only valid for outputs, not inputs.
localrules directive specifies rules that are not present in the Snakefile:
cluster_networks
prepare_sector_networks
prepare_elec_networks
solve_elec_networks
purge
solve_sector_networks

RuleException:
FileNotFoundError in file "/Users/XX/Documents/Code/Development/my-project/pypsa-eur/rules/retrieve.smk", line 371:
[Errno 2] No such file or directory: 'data/eez/World_EEZ_v12_20231025_LR.zip'
File "/Users/jopeel/Documents/Code/Development/preferred-systems/preferred-energy-systems/pypsa-eur/rules/retrieve.smk", line 371, in __rule_retrieve_eez
Exiting because a job execution failed. Look below for error messages
WorkflowError:
At least one job did not complete successfully.
Traceback (most recent call last):

File "/Users/jopeel/miniconda3/envs/pypsa-eur/lib/python3.12/site-packages/snakemake/executors/local.py", line 232, in spawn_job
subprocess.check_call(cmd, shell=True)

File "/Users/jopeel/miniconda3/envs/pypsa-eur/lib/python3.12/subprocess.py", line 413, in check_call
raise CalledProcessError(retcode, cmd)

subprocess.CalledProcessError: Command 'cd /Users/jopeel/Documents/Code/Development/preferred-systems/preferred-energy-systems && /Users/jopeel/miniconda3/envs/pypsa-eur/bin/python3.12 -m snakemake --snakefile '/Users/jopeel/Documents/Code/Development/preferred-systems/preferred-energy-systems/Snakefile' --target-jobs 'pypsa_retrieve_eez:' --allowed-rules pypsa_retrieve_eez --cores 1 --attempt 1 --force-use-threads --force --target-files-omit-workdir-adjustment --max-inventory-time 0 --nocolor --notemp --no-hooks --nolock --ignore-incomplete --rerun-triggers code input mtime software-env params --deployment-method conda --conda-frontend 'conda' --conda-prefix '../envs/snakemake/preferred-energy-systems' --conda-base-path '/Users/jopeel/miniconda3' --shared-fs-usage input-output persistence storage-local-copies sources software-deployment source-cache --wrapper-prefix 'https://github.com/snakemake/snakemake-wrappers/raw/' --latency-wait 5 --scheduler 'ilp' --local-storage-prefix base64//LnNuYWtlbWFrZS9zdG9yYWdl --scheduler-solver-path '/Users/jopeel/miniconda3/envs/pypsa-eur/bin' --storage-http-allow-redirects True --storage-http-supports-head True --default-resources base64//dG1wZGlyPXN5c3RlbV90bXBkaXI= --quiet progress rules host --mode 'subprocess' --local-groupid 'local'' returned non-zero exit status 1.

During handling of the above exception, another exception occurred:

Traceback (most recent call last):

File "/Users/jopeel/miniconda3/envs/pypsa-eur/lib/python3.12/concurrent/futures/thread.py", line 59, in run
result = self.fn(*self.args, **self.kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

File "/Users/jopeel/miniconda3/envs/pypsa-eur/lib/python3.12/site-packages/snakemake/executors/local.py", line 247, in cached_or_run
run_func(*args)

File "/Users/jopeel/miniconda3/envs/pypsa-eur/lib/python3.12/site-packages/snakemake/executors/local.py", line 234, in spawn_job
raise SpawnedJobError()

snakemake.exceptions.SpawnedJobError

[Fri Jul 18 15:15:00 2025]
Error in rule pypsa_retrieve_eez:
message: None
jobid: 0
output: pypsa-eur/data/eez/World_EEZ_v12_20231025_LR/eez_v12_lowres.gpkg
Shutting down, this might take some time.
Exiting because a job execution failed. Look below for error messages
[Fri Jul 18 15:15:00 2025]
Error in rule pypsa_retrieve_eez:
message: None
jobid: 0
output: pypsa-eur/data/eez/World_EEZ_v12_20231025_LR/eez_v12_lowres.gpkg
Complete log(s): /Users/jopeel/Documents/Code/Development/preferred-systems/preferred-energy-systems/.snakemake/log/2025-07-18T151449.418828.snakemake.log
WorkflowError:
At least one job did not complete successfully.

Cause

The cause of the FileNotFoundError in Case 2 is clear - it is a built-in and deliberate behaviour of Python's open function. However, it is not clear to me why this line doesn't fail in Case 1. I presume it is some under-the-hood snakemake wizardry.

Reproducible Example

In terminal:
`(base) jopeel@ied-mac-101 pypsa-bug % git submodule add https://github.com/PyPSA/pypsa-eur.git`
`(base) jopeel@ied-mac-101 pypsa-bug % touch Snakefile`
`(base) jopeel@ied-mac-101 pypsa-bug % touch helpers.py`

In `Snakefile`:

from helpers import inject_module

configfile: "pypsa-eur/config/config.default.yaml"

with inject_module("scripts._helpers", "pypsa-eur/scripts/_helpers.py"):
    module pypsa:
        snakefile: "pypsa-eur/Snakefile"
        prefix: "pypsa-eur"
        config: config

    use rule * from pypsa as pypsa_*


In `helpers.py`:

import importlib.util
import sys
from contextlib import contextmanager


@contextmanager
def inject_module(module_name, file_path):
    """
    Allows a context manager to temporarily inject a module into sys.modules.
    Useful when using rules from a snakemake submodule, whose Snakefile references
    a module that is not in the current sys.path.
    """
    if module_name in sys.modules:
        # Module already exists, don't modify
        yield
        return

    # Load and inject the module
    spec = importlib.util.spec_from_file_location(module_name, file_path)
    if spec is None or spec.loader is None:
        raise ImportError(f"Could not load module {module_name} from {file_path}")

    module = importlib.util.module_from_spec(spec)
    spec.loader.exec_module(module)
    sys.modules[module_name] = module

    try:
        yield
    finally:
        # Clean up - remove the injected module
        if module_name in sys.modules:
            del sys.modules[module_name]


In terminal:
`(base) jopeel@ied-mac-101 pypsa-bug % conda env create -f pypsa-eur/envs/osx-arm64.lock.yaml`
`(base) jopeel@ied-mac-101 pypsa-bug % conda activate pypsa-eur`
`snakemake pypsa-eur/data/eez/World_EEZ_v12_20231025_LR/eez_v12_lowres.gpkg --cores 1`

Expected Behavior

(pypsa-eur) jopeel@ied-mac-101 pypsa-eur % snakemake data/eez/World_EEZ_v12_20231025_LR/eez_v12_lowres.gpkg --cores 1
Set parameter Username
Academic license - for non-commercial use only - expires 2026-02-17
The flag 'directory' used in rule all is only valid for outputs, not inputs.
The flag 'directory' used in rule all is only valid for outputs, not inputs.
Assuming unrestricted shared filesystem usage.
host: ied-mac-101.local
Building DAG of jobs...
Using shell: /bin/bash
Provided cores: 1 (use --cores to define parallelism)
Rules claiming more threads will be scaled down.
Conda environments: ignored
Job stats:
job             count
------------  -------
retrieve_eez        1
total               1

Select jobs to execute...
Execute 1 jobs...

[Fri Jul 18 15:55:55 2025]
localrule retrieve_eez:
    output: data/eez/World_EEZ_v12_20231025_LR/eez_v12_lowres.gpkg
    jobid: 0
    reason: Missing output files: data/eez/World_EEZ_v12_20231025_LR/eez_v12_lowres.gpkg
    resources: tmpdir=/var/folders/cd/3symzw7d0833vd8qj4shbrl80000gp/T
Set parameter Username
Academic license - for non-commercial use only - expires 2026-02-17
The flag 'directory' used in rule all is only valid for outputs, not inputs.
The flag 'directory' used in rule all is only valid for outputs, not inputs.
[Fri Jul 18 15:56:04 2025]
Finished jobid: 0 (Rule: retrieve_eez)
1 of 1 steps (100%) done
Complete log(s): /Users/jopeel/Documents/Code/Cloned/pypsa-eur/.snakemake/log/2025-07-18T155555.456186.snakemake.log

Installed Versions

Details 
# This file may be used to create an environment using:
# $ conda create --name <env> --file <this file>
# platform: osx-arm64
# created-by: conda 25.3.1
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https://conda.anaconda.org/conda-forge/osx-arm64/bzip2-1.0.8-h99b78c6_7.conda
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https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.6.15-hbd8a1cb_0.conda
https://conda.anaconda.org/conda-forge/osx-arm64/epoxy-1.5.10-h1c322ee_1.tar.bz2
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