Add contributors #249

rvandewater · 2025-10-02T07:16:39Z

Taken directly from https://github.com/McDermottHealthAI/MHAL-template/blob/main/CONTRIBUTORS.md#installing-the-project-for-development

codecov · 2025-10-02T07:17:52Z

❌ 1 Tests Failed:

Tests completed	Failed	Passed	Skipped
32	1	31	0

View the top 1 failed test(s) by shortest run time

tests.test_0_datasets::test_datasets_configured[MIMIC-IV]

Stack Traces | 15.7s run time

request = <SubRequest 'demo_dataset' for <Function test_datasets_configured[MIMIC-IV]>>
venv_cache = PosixPath('.../tmp/tmpml1lg3bm/venvs')

    @pytest.fixture(scope="session")
    def demo_dataset(request, venv_cache: Path) -> NAME_AND_DIR:
        dataset_name = request.param
        persistent_cache_dir, (cache_datasets, _, _) = get_and_validate_cache_settings(request)
        reuse_datasets, _, _ = get_and_validate_reuse_settings(request)
    
        do_overwrite = not (dataset_name in reuse_datasets)
    
        with cache_dir(persistent_cache_dir if dataset_name in cache_datasets else None) as root_dir:
            root_dir = Path(root_dir)
    
            check_fp = root_dir / f".{dataset_name}.check"
            output_dir = root_dir / dataset_name
    
            data_exists = (output_dir / "data").is_dir()
            metadata_exists = (output_dir / "metadata").is_dir()
    
            already_tested = check_fp.exists() and data_exists and metadata_exists
            if do_overwrite or not already_tested:
                venv_dir = venv_cache / "datasets" / dataset_name
    
>               run_command(
                    "meds-dev-dataset",
                    test_name=f"Build {dataset_name}",
                    hydra_kwargs={
                        "dataset": dataset_name,
                        "output_dir": str(output_dir.resolve()),
                        "demo": True,
                        "venv_dir": str(venv_dir.resolve()),
                    },
                )

tests/conftest.py:352: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

script = ['meds-dev-dataset', 'dataset=MIMIC-IV output_dir=...................../tmp/tmpujv1c5bl/MIMIC-IV demo=true venv_dir=....../venvs/datasets/MIMIC-IV']
test_name = 'Build MIMIC-IV'
hydra_kwargs = {'dataset': 'MIMIC-IV', 'demo': True, 'output_dir': '...................../tmp/tmpujv1c5bl/MIMIC-IV', 'venv_dir': '....../venvs/datasets/MIMIC-IV'}
config_name = None, should_error = False, want_err_msg = None
do_use_config_yaml = False

    def run_command(
        script: Path | str,
        test_name: str,
        hydra_kwargs: dict[str, str] | None = None,
        config_name: str | None = None,
        should_error: bool = False,
        want_err_msg: str | None = None,
        do_use_config_yaml: bool = False,
    ):
        script = ["python", str(script.resolve())] if isinstance(script, Path) else [script]
        command_parts = script
    
        err_cmd_lines = []
    
        if config_name is not None and not config_name.startswith("_"):
            config_name = f"_{config_name}"
    
        if hydra_kwargs is None:
            hydra_kwargs = {}
    
        if do_use_config_yaml:
            if config_name is None:
                raise ValueError("config_name must be provided if do_use_config_yaml is True.")
    
            conf = OmegaConf.create(
                {
                    "defaults": [config_name],
                    **hydra_kwargs,
                }
            )
    
            conf_dir = tempfile.TemporaryDirectory()
            conf_path = Path(conf_dir.name) / "config.yaml"
            OmegaConf.save(conf, conf_path)
    
            command_parts.extend(
                [
                    f"--config-path={str(conf_path.parent.resolve())}",
                    "--config-name=config",
                    "'hydra.searchpath=[pkg://MEDS_transforms.configs]'",
                ]
            )
            err_cmd_lines.append(f"Using config yaml:\n{OmegaConf.to_yaml(conf)}")
        else:
            if config_name is not None:
                command_parts.append(f"--config-name={config_name}")
            command_parts.append(" ".join(dict_to_hydra_kwargs(hydra_kwargs)))
    
        full_cmd = " ".join(command_parts)
        err_cmd_lines.append(f"Running command: {full_cmd}")
        command_out = subprocess.run(full_cmd, shell=True, capture_output=True)
    
        command_errored = command_out.returncode != 0
    
        stderr = command_out.stderr.decode()
        err_cmd_lines.append(f"stderr:\n{stderr}")
        stdout = command_out.stdout.decode()
        err_cmd_lines.append(f"stdout:\n{stdout}")
    
        if should_error:
            err_cmd_str = "\n".join(err_cmd_lines)
            if not command_errored:
                if do_use_config_yaml:
                    conf_dir.cleanup()
                raise AssertionError(f"{test_name} failed as command did not error when expected!\n{err_cmd_str}")
            if want_err_msg is not None and want_err_msg not in stderr:
                if do_use_config_yaml:
                    conf_dir.cleanup()
                raise AssertionError(
                    f"{test_name} failed as expected error message not found in stderr!\n{err_cmd_str}"
                )
        elif not should_error and command_errored:
            if do_use_config_yaml:
                conf_dir.cleanup()
>           raise AssertionError(
                f"{test_name} failed as command errored when not expected!\n" + "\n".join(err_cmd_lines)
            )
E           AssertionError: Build MIMIC-IV failed as command errored when not expected!
E           Running command: meds-dev-dataset dataset=MIMIC-IV output_dir=...................../tmp/tmpujv1c5bl/MIMIC-IV demo=true venv_dir=....../venvs/datasets/MIMIC-IV
E           stderr:
E           
E           [notice] A new release of pip is available: 24.0 -> 25.2
E           [notice] To update, run: python -m pip install --upgrade pip
E           Error executing job with overrides: ['dataset=MIMIC-IV', 'output_dir=...................../tmp/tmpujv1c5bl/MIMIC-IV', 'demo=true', 'venv_dir=....../venvs/datasets/MIMIC-IV']
E           Traceback (most recent call last):
E             File ".../MEDS_DEV/datasets/__main__.py", line 42, in main
E               run_in_env(build_cmd, cfg.output_dir, env=env, do_overwrite=cfg.do_overwrite, cwd=build_temp_dir)
E             File ".../src/MEDS_DEV/utils.py", line 395, in run_in_env
E               raise RuntimeError(
E           RuntimeError: Command failed with exit code 1:
E           SCRIPT:
E           #!/bin/bash
E           set -e
E           MEDS_extract-MIMIC_IV do_demo=True raw_input_dir="........./tmp/tmp8pzkv5dd/raw" pre_MEDS_dir="........./tmp/tmp8pzkv5dd/pre_MEDS" MEDS_cohort_dir="...................../tmp/tmpujv1c5bl/MIMIC-IV" log_dir="................../tmpujv1c5bl/MIMIC-IV/.pipeline_logs"
E           STDERR:
E           Traceback (most recent call last):
E             File "....../venvs/datasets/MIMIC-IV/bin/MEDS_extract-MIMIC_IV", line 5, in <module>
E               from MIMIC_IV_MEDS.__main__ import main
E             File "....../venvs/datasets/MIMIC-IV/lib/python3.11.../site-packages/MIMIC_IV_MEDS/__main__.py", line 17, in <module>
E               from .pre_MEDS import main as pre_MEDS_transform
E             File "....../venvs/datasets/MIMIC-IV/lib/python3.11.../site-packages/MIMIC_IV_MEDS/pre_MEDS.py", line 9, in <module>
E               from MEDS_transforms.extract.utils import get_supported_fp
E           ModuleNotFoundError: No module named 'MEDS_transforms.extract'
E           
E           STDOUT:
E           
E           
E           Set the environment variable HYDRA_FULL_ERROR=1 for a complete stack trace.
E           
E           stdout:
E           [2025-10-02 07:17:28,301][MEDS_DEV.utils][INFO] - Installing requirements from .../datasets/MIMIC-IV/requirements.txt into virtual environment.
E           Collecting MIMIC-IV-MEDS==0.0.3 (from -r .../datasets/MIMIC-IV/requirements.txt (line 1))
E             Downloading MIMIC_IV_MEDS-0.0.3-py3-none-any.whl.metadata (4.4 kB)
E           Collecting meds-transforms>=0.1 (from MIMIC-IV-MEDS==0.0.3->-r .../datasets/MIMIC-IV/requirements.txt (line 1))
E             Downloading meds_transforms-0.6.0-py3-none-any.whl.metadata (17 kB)
E           Collecting requests (from MIMIC-IV-MEDS==0.0.3->-r .../datasets/MIMIC-IV/requirements.txt (line 1))
E             Downloading requests-2.32.5-py3-none-any.whl.metadata (4.9 kB)
E           Collecting beautifulsoup4 (from MIMIC-IV-MEDS==0.0.3->-r .../datasets/MIMIC-IV/requirements.txt (line 1))
E             Downloading beautifulsoup4-4.14.2-py3-none-any.whl.metadata (3.8 kB)
E           Collecting hydra-core (from MIMIC-IV-MEDS==0.0.3->-r .../datasets/MIMIC-IV/requirements.txt (line 1))
E             Using cached hydra_core-1.3.2-py3-none-any.whl.metadata (5.5 kB)
E           Collecting polars~=1.30.0 (from meds-transforms>=0.1->MIMIC-IV-MEDS==0.0.3->-r .../datasets/MIMIC-IV/requirements.txt (line 1))
E             Downloading polars-1.30.0-cp39-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (14 kB)
E           Collecting pyarrow (from meds-transforms>=0.1->MIMIC-IV-MEDS==0.0.3->-r .../datasets/MIMIC-IV/requirements.txt (line 1))
E             Downloading pyarrow-21.0.0-cp311-cp311-manylinux_2_28_x86_64.whl.metadata (3.3 kB)
E           Collecting numpy (from meds-transforms>=0.1->MIMIC-IV-MEDS==0.0.3->-r .../datasets/MIMIC-IV/requirements.txt (line 1))
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E           Collecting filelock (from meds-transforms>=0.1->MIMIC-IV-MEDS==0.0.3->-r .../datasets/MIMIC-IV/requirements.txt (line 1))
E             Downloading filelock-3.19.1-py3-none-any.whl.metadata (2.1 kB)
E           Collecting pytest (from meds-transforms>=0.1->MIMIC-IV-MEDS==0.0.3->-r .../datasets/MIMIC-IV/requirements.txt (line 1))
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E           Collecting meds_testing_helpers~=0.3.0 (from meds-transforms>=0.1->MIMIC-IV-MEDS==0.0.3->-r .../datasets/MIMIC-IV/requirements.txt (line 1))
E             Using cached meds_testing_helpers-0.3.0-py3-none-any.whl.metadata (7.6 kB)
E           Collecting pretty-print-directory>=0.1.3 (from meds-transforms>=0.1->MIMIC-IV-MEDS==0.0.3->-r .../datasets/MIMIC-IV/requirements.txt (line 1))
E             Downloading pretty_print_directory-0.1.3-py3-none-any.whl.metadata (6.9 kB)
E           Collecting soupsieve>1.2 (from beautifulsoup4->MIMIC-IV-MEDS==0.0.3->-r .../datasets/MIMIC-IV/requirements.txt (line 1))
E             Downloading soupsieve-2.8-py3-none-any.whl.metadata (4.6 kB)
E           Collecting typing-extensions>=4.0.0 (from beautifulsoup4->MIMIC-IV-MEDS==0.0.3->-r .../datasets/MIMIC-IV/requirements.txt (line 1))
E             Using cached typing_extensions-4.15.0-py3-none-any.whl.metadata (3.3 kB)
E           Collecting omegaconf<2.4,>=2.2 (from hydra-core->MIMIC-IV-MEDS==0.0.3->-r .../datasets/MIMIC-IV/requirements.txt (line 1))
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E             Using cached antlr4_python3_runtime-4.9.3-py3-none-any.whl
E           Collecting packaging (from hydra-core->MIMIC-IV-MEDS==0.0.3->-r .../datasets/MIMIC-IV/requirements.txt (line 1))
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E           Collecting certifi>=2017.4.17 (from requests->MIMIC-IV-MEDS==0.0.3->-r .../datasets/MIMIC-IV/requirements.txt (line 1))
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E           Collecting jsonschema>=4.0.0 (from meds~=0.4.0->meds-transforms>=0.1->MIMIC-IV-MEDS==0.0.3->-r .../datasets/MIMIC-IV/requirements.txt (line 1))
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E           Using cached referencing-0.36.2-py3-none-any.whl (26 kB)
E           Using cached rpds_py-0.27.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (384 kB)
E           Installing collected packages: pytimeparse, antlr4-python3-runtime, urllib3, typing-extensions, soupsieve, rpds-py, PyYAML, pygments, pyarrow, polars, pluggy, packaging, numpy, iniconfig, idna, filelock, charset_normalizer, certifi, attrs, annotated-types, requests, referencing, pytest, omegaconf, beautifulsoup4, pretty-print-directory, jsonschema-specifications, hydra-core, jsonschema, flexible_schema, meds, meds_testing_helpers, meds-transforms, MIMIC-IV-MEDS
E           Successfully installed MIMIC-IV-MEDS-0.0.3 PyYAML-6.0.3 annotated-types-0.7.0 antlr4-python3-runtime-4.9.3 attrs-25.3.0 beautifulsoup4-4.14.2 certifi-2025.8.3 charset_normalizer-3.4.3 filelock-3.19.1 flexible_schema-0.1 hydra-core-1.3.2 idna-3.10 iniconfig-2.1.0 jsonschema-4.25.1 jsonschema-specifications-2025.9.1 meds-0.4.0 meds-transforms-0.6.0 meds_testing_helpers-0.3.0 numpy-2.3.3 omegaconf-2.3.0 packaging-25.0 pluggy-1.6.0 polars-1.30.0 pretty-print-directory-0.1.3 pyarrow-21.0.0 pygments-2.19.2 pytest-8.4.2 pytimeparse-1.1.8 referencing-0.36.2 requests-2.32.5 rpds-py-0.27.1 soupsieve-2.8 typing-extensions-4.15.0 urllib3-2.5.0
E           [2025-10-02 07:17:42,806][MEDS_DEV.utils][INFO] - Installed requirements from .../datasets/MIMIC-IV/requirements.txt into virtual environment.
E           [2025-10-02 07:17:42,806][MEDS_DEV.datasets.__main__][INFO] - Considering running build command: MEDS_extract-MIMIC_IV do_demo=True raw_input_dir="........./tmp/tmp8pzkv5dd/raw" pre_MEDS_dir="........./tmp/tmp8pzkv5dd/pre_MEDS" MEDS_cohort_dir="...................../tmp/tmpujv1c5bl/MIMIC-IV" log_dir="................../tmpujv1c5bl/MIMIC-IV/.pipeline_logs"
E           [2025-10-02 07:17:42,806][MEDS_DEV.utils][INFO] - Running command in ...................../tmpujv1c5bl/MIMIC-IV/cmd.sh:
E           #!/bin/bash
E           set -e
E           MEDS_extract-MIMIC_IV do_demo=True raw_input_dir="........./tmp/tmp8pzkv5dd/raw" pre_MEDS_dir="........./tmp/tmp8pzkv5dd/pre_MEDS" MEDS_cohort_dir="...................../tmp/tmpujv1c5bl/MIMIC-IV" log_dir="................../tmpujv1c5bl/MIMIC-IV/.pipeline_logs"

tests/utils.py:146: AssertionError

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rvandewater · 2025-10-02T07:19:43Z

@mmcdermott do we want to use uv for version management? I have no experience with it so far.

mmcdermott · 2025-10-02T15:28:34Z

We should eventually for sure @rvandewater , but it will take a dedicated PR to get it added.

mmcdermott · 2025-10-02T15:29:44Z

I think the test failure is because we need to incorporate commit a233132 to update the MIMIC ETL version.

rvandewater · 2025-10-13T11:17:40Z

@mmcdermott seems to be meds-tab related: https://github.com/Medical-Event-Data-Standard/MEDS-DEV/actions/runs/18461127482/job/52592654691?pr=250

mmcdermott · 2025-10-13T15:56:50Z

CONTRIBUTORS.md

+environment:
+
+```bash
+uv sync


@rvandewater does this actually work for MEDS-DEV? If so, we should commit and merge straight away, if not we need to update.

@mmcdermott, I haven't worked with UV before, but a quick try runs into errors for me. Is there a reason we would require people to work with a certain environment manager? Otherwise, I would just say install pre-commit and run tests in your favorite environment manager.

mmcdermott · 2025-10-14T10:25:20Z

Basically the reason to use UV or poetry or anything is that the version specifier you make for installation may be less precise than the version specifiers for development. But given we don't have it set up for MEDS-DEV yet, we should just tell them to use more standard tools for now.

…

On Tue, Oct 14, 2025, 5:24 AM Robin van de Water ***@***.***> wrote: ***@***.**** commented on this pull request. ------------------------------ In CONTRIBUTORS.md <#249 (comment)> : > + +## Good Practice + +- Discuss large changes with the maintainers before significant work begins. +- Keep commits focused and provide clear commit messages. +- Include tests for new functionality and bug fixes. +- Ensure documentation is updated for user-facing changes. + +## Installing the Project for Development + +This project uses [`uv`](https://docs.astral.sh/uv/) for environment management. To set up the project for +development, simply clone the repository, then sync the uv environment, activate it, and install the pre-commit +environment: + +```bash +uv sync @mmcdermott <https://github.com/mmcdermott>, I haven't worked with UV before, but a quick try runs into errors for me. Is there a reason we would require people to work with a certain environment manager? Otherwise, I would just say install pre-commit and run tests in your favorite environment manager. — Reply to this email directly, view it on GitHub <#249 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AADS5XZCWJHS3HNSJBZFB2L3XS6MDAVCNFSM6AAAAACICQX5LCVHI2DSMVQWIX3LMV43YUDVNRWFEZLROVSXG5CSMV3GSZLXHMZTGMZUGY4DMMBVGU> . You are receiving this because you were mentioned.Message ID: ***@***.*** com>

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Taken directly from https://github.com/McDermottHealthAI/MHAL-template/blob/main/CONTRIBUTORS.md#installing-the-project-for-development

mmcdermott reviewed Oct 13, 2025

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