update for pycopanlpjml

[jnnsbrr]

This MR introduces new features for the compatibility with the latest pycopanlpjml version:

• default model name set to copan, instead of copan:CORE - if provided via CoupledConfig it can be set
• functionality to kill remaining processes on coupled port to avoid blocked port in the next simulation
• debug historic years reading for coupling
• adjust slurm.jcf file creation for older LPJmL versions to avoid slurm ending the job before coupled program has finished
• deprecation warning for old objects names, attributes

[codecov]

Codecov Report

❌ Patch coverage is 82.87037% with 74 lines in your changes missing coverage. Please review.
✅ Project coverage is 81.43%. Comparing base (9490c5e) to head (bbf7b67).

Files with missing lines	Patch %	Lines
pycoupler/coupler.py	70.65%	27 Missing ⚠️
pycoupler/data.py	87.36%	24 Missing ⚠️
pycoupler/run.py	85.71%	16 Missing ⚠️
pycoupler/config.py	65.00%	7 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #17      +/-   ##
==========================================
+ Coverage   78.47%   81.43%   +2.96%     
==========================================
  Files           7        7              
  Lines        1640     1988     +348     
==========================================
+ Hits         1287     1619     +332     
- Misses        353      369      +16     

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

🚀 New features to boost your workflow:

• ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

[Copilot]

Pull request overview

This PR updates pycoupler for compatibility with newer pycopanlpjml/LPJmL coupling expectations, including a new default coupled model name, improved Slurm coupled-job handling, additional port/process cleanup, and expanded test coverage for utilities, run submission, and NetCDF export helpers.

Changes:

• Default coupled model name updated to copan, with support for overriding via a coupled config.
• Slurm coupled-job submission now patches slurm.jcf to ensure the coupler process is waited on (and submits via sbatch when needed).
• Adds NetCDF writing + grid transform utilities for LPJmLData/LPJmLDataSet, plus substantial new tests.

Reviewed changes

Copilot reviewed 16 out of 17 changed files in this pull request and generated 10 comments.

Show a summary per file

File	Description
pycoupler/config.py	Adjusts coupled config defaults/behavior (model default + coupled config support).
pycoupler/coupler.py	Adds port cleanup utilities; fixes historic years handling; improves input sending conversion logic.
pycoupler/run.py	Introduces start_lpjml and deprecated alias; patches Slurm submission flow for coupled runs.
pycoupler/utils.py	Adds standardized deprecation warning helper.
pycoupler/data.py	Implements transform() and NetCDF export helpers for LPJmL data structures.
tests/test_config.py	Updates expectations for new default coupled model.
tests/test_couple.py	Adjusts time assignment and historic years expectation in coupling test.
tests/test_run.py	Extends Slurm submission tests to cover slurm.jcf patching and sbatch flow.
tests/test_run_additional.py	Adds additional run-related tests incl. deprecated alias warning behavior.
tests/test_utils.py	Extends detect_io_type test coverage for invalid UTF-8 bytes.
tests/test_utils_additional.py	Adds coverage for create_subdirs and read_json.
tests/test_data.py	Adds comprehensive coverage for grid transforms and NetCDF writing.
tests/test_coupler_utils.py	Adds coverage for new port cleanup utilities.
tests/data/invalid_utf8.bin	Adds a sample binary file (currently appears redundant with the updated test).
pycoupler/release.py	Clarifies release script instructions.
pycoupler/__init__.py	Minor formatting cleanup.
CITATION.cff	Bumps version to 1.7.0.

Comments suppressed due to low confidence (1)

pycoupler/run.py:265

• slurm_jcf_dir is documented/used as the directory where slurm.jcf should be written, but the lpjsubmit subprocess is still executed without cwd=.... If lpjsubmit writes slurm.jcf to its working directory (typical), _patch_slurm_and_submit() will look in slurm_jcf_dir/slurm.jcf and fail even though the file exists elsewhere. Consider ensuring the directory exists and running lpjsubmit with cwd=slurm_jcf_dir (or otherwise directing lpjsubmit output) so slurm_jcf_path matches where the file is actually created.

    # run in coupled mode and pass coupling program/model
    needs_coupler_wait = bool(couple_to)
    if slurm_jcf_dir is None:
        slurm_jcf_dir = os.getcwd()
    slurm_jcf_path = Path(slurm_jcf_dir) / "slurm.jcf"

    couple_file = None

    if couple_to:
        python_path = "python3"
        if venv_path:
            python_path = os.path.join(venv_path, "bin/python")
            if not os.path.isfile(python_path):
                raise FileNotFoundError(
                    f"venv path contains no python binary at '{python_path}'."
                )

        bash_script = f"""#!/bin/bash

# Define the path to the config file
config_file="{config_file}"

# Call the Python script with the config file as an argument
{python_path} {couple_to} $config_file
"""

        couple_file = f"{output_path}/copan_lpjml.sh"

        with open(couple_file, "w") as file:
            file.write(bash_script)

        # Change the permissions of the file to make it executable
        run(["chmod", "+x", couple_file])

        cmd.extend(["-couple", couple_file])

    if needs_coupler_wait:
        cmd.append("-norun")

    cmd.extend([str(ntasks), config_file])

    # Intialize submit_status in higher scope
    submit_status = None
    # set LPJROOT to model_path to be able to call lpjsubmit
    try:
        os.environ["LPJROOT"] = config.model_path
        # call lpjsubmit via subprocess and return status if successfull
        submit_status = run(cmd, capture_output=True)
    except Exception as e:

---

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.