easylink 0.1.16__tar.gz → 0.1.17__tar.gz

{easylink-0.1.16 → easylink-0.1.17}/CHANGELOG.rst

@@ -1,3 +1,7 @@
+**0.1.17 - 5/14/25**
+
+ - Support directories as step intermediates
+
 **0.1.16 - 5/13/25**
 
  - Implement new cli command to simplify implementation creation

{easylink-0.1.16 → easylink-0.1.17}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: easylink
-Version: 0.1.16
+Version: 0.1.17
 Summary: Research repository for the EasyLink ER ecosystem project.
 Home-page: https://github.com/ihmeuw/easylink
 Author: The EasyLink developers

easylink-0.1.17/src/easylink/_version.py

@@ -0,0 +1 @@
+__version__ = "0.1.17"

{easylink-0.1.16 → easylink-0.1.17}/src/easylink/implementation.py

@@ -135,8 +135,17 @@ class Implementation:
 
     @property
     def outputs(self) -> dict[str, list[str]]:
-        """The expected output metadata."""
-        return self._metadata["outputs"]
+        """The expected output paths. If output metadata is provided, use it. Otherwise,
+        assume that the output is a sub-directory with the name of the output slot.
+        If there is only one output slot, use '.'."""
+        if len(self.output_slots) == 1:
+            return self._metadata.get("outputs", {list(self.output_slots.keys())[0]: "."})
+        return {
+            output_slot_name: self._metadata.get("outputs", {}).get(
+                output_slot_name, output_slot_name
+            )
+            for output_slot_name in self.output_slots
+        }
 
 
 class NullImplementation:

{easylink-0.1.16 → easylink-0.1.17}/src/easylink/implementation_metadata.yaml

@@ -192,3 +192,25 @@ step_1a_and_step_1b_combined_python_pandas:
   script_cmd: python /dummy_step.py
   outputs:
     step_1_main_output: result.parquet
+dummy_step_1_for_output_dir_example:
+  steps:
+  - step_1_for_output_dir_example
+  image_path: /mnt/team/simulation_science/priv/engineering/er_ecosystem/images/zmbc/dummy_step_1_for_output_dir_example.sif
+  script_cmd: python /dummy_step_1_for_output_dir_example.py
+  outputs:
+    step_1_main_output_directory: output_dir/
+dummy_step_1_for_output_dir_example_default:
+  steps:
+  - step_1_for_output_dir_example
+  image_path: /mnt/team/simulation_science/priv/engineering/er_ecosystem/images/zmbc/dummy_step_1_for_output_dir_example.sif
+  script_cmd: python /dummy_step_1_for_output_dir_example.py
+  # leave outputs out for testing purposes
+  # outputs:
+  #   step_1_main_output_directory: output_dir/
+dummy_step_2_for_output_dir_example:
+  steps:
+  - step_2_for_output_dir_example
+  image_path: /mnt/team/simulation_science/priv/engineering/er_ecosystem/images/zmbc/dummy_step_2_for_output_dir_example.sif
+  script_cmd: python /dummy_step_2_for_output_dir_example.py
+  outputs:
+    step_2_main_output: result.parquet

{easylink-0.1.16 → easylink-0.1.17}/src/easylink/pipeline_schema_constants/__init__.py

@@ -17,6 +17,7 @@ ALLOWED_SCHEMA_PARAMS = {
 
 TESTING_SCHEMA_PARAMS = {
     "integration": testing.SCHEMA_PARAMS_ONE_STEP,
+    "output_dir": testing.SCHEMA_PARAMS_OUTPUT_DIR,
     "combine_bad_topology": testing.SCHEMA_PARAMS_BAD_COMBINED_TOPOLOGY,
     "combine_bad_implementation_names": testing.SCHEMA_PARAMS_BAD_COMBINED_TOPOLOGY,
     "nested_templated_steps": testing.SCHEMA_PARAMS_NESTED_TEMPLATED_STEPS,

{easylink-0.1.16 → easylink-0.1.17}/src/easylink/pipeline_schema_constants/testing.py

@@ -26,7 +26,7 @@ from easylink.step import (
 )
 from easylink.utilities.aggregator_utils import concatenate_datasets
 from easylink.utilities.splitter_utils import split_data_in_two
-from easylink.utilities.validation_utils import validate_input_file_dummy
+from easylink.utilities.validation_utils import validate_dir, validate_input_file_dummy
 
 NODES_ONE_STEP = [
     InputStep(),
@@ -582,3 +582,55 @@ EDGES_ONE_STEP_TWO_ISLOTS = [
     ),
 ]
 SCHEMA_PARAMS_EP_HIERARCHICAL_STEP = (NODES_EP_HIERARCHICAL_STEP, EDGES_ONE_STEP_TWO_ISLOTS)
+
+NODES_OUTPUT_DIR = [
+    InputStep(),
+    Step(
+        step_name="step_1_for_output_dir_example",
+        input_slots=[
+            InputSlot(
+                name="step_1_main_input",
+                env_var="STEP_1_MAIN_INPUT_FILE_PATHS",
+                validator=validate_input_file_dummy,
+            )
+        ],
+        output_slots=[OutputSlot("step_1_main_output_directory")],
+    ),
+    Step(
+        step_name="step_2_for_output_dir_example",
+        input_slots=[
+            InputSlot(
+                name="step_2_main_input",
+                env_var="DUMMY_CONTAINER_MAIN_INPUT_DIR_PATH",
+                validator=validate_dir,
+            )
+        ],
+        output_slots=[OutputSlot("step_2_main_output")],
+    ),
+    OutputStep(
+        input_slots=[
+            InputSlot(name="result", env_var=None, validator=validate_input_file_dummy)
+        ],
+    ),
+]
+EDGES_OUTPUT_DIR = [
+    EdgeParams(
+        source_node="input_data",
+        target_node="step_1_for_output_dir_example",
+        output_slot="all",
+        input_slot="step_1_main_input",
+    ),
+    EdgeParams(
+        source_node="step_1_for_output_dir_example",
+        target_node="step_2_for_output_dir_example",
+        output_slot="step_1_main_output_directory",
+        input_slot="step_2_main_input",
+    ),
+    EdgeParams(
+        source_node="step_2_for_output_dir_example",
+        target_node="results",
+        output_slot="step_2_main_output",
+        input_slot="result",
+    ),
+]
+SCHEMA_PARAMS_OUTPUT_DIR = (NODES_OUTPUT_DIR, EDGES_OUTPUT_DIR)

{easylink-0.1.16 → easylink-0.1.17}/src/easylink/rule.py

@@ -17,6 +17,7 @@ import os
 from abc import ABC, abstractmethod
 from collections.abc import Callable
 from dataclasses import dataclass
+from pathlib import Path
 
 
 class Rule(ABC):
@@ -125,6 +126,18 @@ class ImplementedRule(Rule):
     def _build_io(self) -> str:
         """Builds the input/output portion of the rule."""
         log_path_chunk_adder = "-{chunk}" if self.is_embarrassingly_parallel else ""
+        # Handle output files vs directories
+        files = [path for path in self.output if Path(path).suffix != ""]
+        if len(files) == len(self.output):
+            output = self.output
+        elif len(files) == 0:
+            if len(self.output) != 1:
+                raise NotImplementedError("Multiple output directories is not supported.")
+            output = f"directory('{self.output[0]}')"
+        else:
+            raise NotImplementedError(
+                "Mixed output types (files and directories) is not supported."
+            )
         io_str = (
             f"""
 rule:
@@ -132,7 +145,7 @@ rule:
     message: "Running {self.step_name} implementation: {self.implementation_name}" """
             + self._build_input()
             + f"""        
-    output: {self.output}
+    output: {output}
     log: "{self.diagnostics_dir}/{self.name}-output{log_path_chunk_adder}.log"
     container: "{self.image_path}" """
         )

easylink-0.1.17/src/easylink/steps/output_dir/dummy_step_1_for_output_dir_example.def

@@ -0,0 +1,22 @@
+
+Bootstrap: docker
+From: python@sha256:1c26c25390307b64e8ff73e7edf34b4fbeac59d41da41c08da28dc316a721899
+
+%files
+    ./dummy_step_1_for_output_dir_example.py /dummy_step_1_for_output_dir_example.py
+
+%post
+    # Create directories
+    mkdir -p /input_data
+    mkdir -p /extra_implementation_specific_input_data
+    mkdir -p /results
+    mkdir -p /diagnostics
+
+    # Install Python packages with specific versions
+    pip install pandas==2.1.2 pyarrow
+
+%environment
+    export LC_ALL=C
+
+%runscript
+    python /dummy_step_1_for_output_dir_example.py '$@'

easylink-0.1.17/src/easylink/steps/output_dir/dummy_step_1_for_output_dir_example.py

@@ -0,0 +1,18 @@
+# PIPELINE_SCHEMA: output_dir
+# STEP_NAME: step_1_for_output_dir_example
+# REQUIREMENTS: pandas==2.1.2 pyarrow
+
+import os
+from pathlib import Path
+
+import pandas as pd
+
+data = pd.read_parquet(os.environ["STEP_1_MAIN_INPUT_FILE_PATHS"])
+
+print(data)
+
+dir_path = Path(os.environ["DUMMY_CONTAINER_OUTPUT_PATHS"])
+dir_path.mkdir(parents=True, exist_ok=True)
+
+for i in range(3):
+    data.to_parquet(dir_path / f"result_{i}.parquet")

easylink-0.1.17/src/easylink/steps/output_dir/dummy_step_2_for_output_dir_example.def

@@ -0,0 +1,22 @@
+
+Bootstrap: docker
+From: python@sha256:1c26c25390307b64e8ff73e7edf34b4fbeac59d41da41c08da28dc316a721899
+
+%files
+    ./dummy_step_2_for_output_dir_example.py /dummy_step_2_for_output_dir_example.py
+
+%post
+    # Create directories
+    mkdir -p /input_data
+    mkdir -p /extra_implementation_specific_input_data
+    mkdir -p /results
+    mkdir -p /diagnostics
+
+    # Install Python packages with specific versions
+    pip install pandas==2.1.2 pyarrow
+
+%environment
+    export LC_ALL=C
+
+%runscript
+    python /dummy_step_2_for_output_dir_example.py '$@'

easylink-0.1.17/src/easylink/steps/output_dir/dummy_step_2_for_output_dir_example.py

@@ -0,0 +1,22 @@
+# PIPELINE_SCHEMA: output_dir
+# STEP_NAME: step_2_for_output_dir_example
+# REQUIREMENTS: pandas==2.1.2 pyarrow
+
+import os
+import shutil
+from pathlib import Path
+
+import pandas as pd
+
+dir_path = Path(os.environ["DUMMY_CONTAINER_MAIN_INPUT_DIR_PATH"])
+saved = False
+
+for i, f in enumerate([f for f in dir_path.iterdir() if f.is_file()]):
+    if "snakemake" in str(f):
+        continue
+
+    if not saved:
+        shutil.copy(f, os.environ["DUMMY_CONTAINER_OUTPUT_PATHS"])
+        saved = True
+
+    print(pd.read_parquet(f))

{easylink-0.1.16 → easylink-0.1.17}/src/easylink/utilities/validation_utils.py

@@ -50,3 +50,9 @@ def validate_input_file_dummy(filepath: str) -> None:
         raise LookupError(
             f"Data file {filepath} is missing required column(s) {missing_columns}"
         )
+
+
+def validate_dir(filepath: str) -> None:
+    input_path = Path(filepath)
+    if not input_path.is_dir():
+        raise NotADirectoryError(f"The path {filepath} is not a directory.")

{easylink-0.1.16 → easylink-0.1.17}/src/easylink.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: easylink
-Version: 0.1.16
+Version: 0.1.17
 Summary: Research repository for the EasyLink ER ecosystem project.
 Home-page: https://github.com/ihmeuw/easylink
 Author: The EasyLink developers

{easylink-0.1.16 → easylink-0.1.17}/src/easylink.egg-info/SOURCES.txt

@@ -128,6 +128,10 @@ src/easylink/steps/dev/python_pyspark/python_pyspark.def
 src/easylink/steps/dev/r/README.md
 src/easylink/steps/dev/r/dummy_step.R
 src/easylink/steps/dev/r/r-image.def
+src/easylink/steps/output_dir/dummy_step_1_for_output_dir_example.def
+src/easylink/steps/output_dir/dummy_step_1_for_output_dir_example.py
+src/easylink/steps/output_dir/dummy_step_2_for_output_dir_example.def
+src/easylink/steps/output_dir/dummy_step_2_for_output_dir_example.py
 src/easylink/utilities/__init__.py
 src/easylink/utilities/aggregator_utils.py
 src/easylink/utilities/data_utils.py
@@ -146,12 +150,15 @@ tests/integration/test_snakemake_slurm.py
 tests/integration/test_snakemake_spark.py
 tests/specifications/common/environment_local.yaml
 tests/specifications/common/input_data.yaml
+tests/specifications/common/input_data_one_file.yaml
 tests/specifications/common/pipeline.yaml
 tests/specifications/e2e/environment_slurm.yaml
 tests/specifications/e2e/pipeline.yaml
 tests/specifications/e2e/pipeline_expanded.yaml
 tests/specifications/integration/environment_spark_slurm.yaml
 tests/specifications/integration/pipeline.yaml
+tests/specifications/integration/pipeline_output_dir.yaml
+tests/specifications/integration/pipeline_output_dir_default.yaml
 tests/specifications/integration/pipeline_spark.yaml
 tests/specifications/integration/embarrassingly_parallel/pipeline_hierarchical_step.yaml
 tests/specifications/integration/embarrassingly_parallel/pipeline_loop_step.yaml

easylink-0.1.17/tests/integration/test_snakemake.py

@@ -0,0 +1,78 @@
+# mypy: ignore-errors
+import pytest
+
+from easylink.pipeline_schema import PipelineSchema
+from easylink.pipeline_schema_constants import TESTING_SCHEMA_PARAMS
+from easylink.runner import main
+from tests.conftest import SPECIFICATIONS_DIR
+
+
+@pytest.mark.slow
+def test_missing_results(test_specific_results_dir, mocker, caplog):
+    """Test that the pipeline fails when a step is missing output files."""
+    nodes, edges = TESTING_SCHEMA_PARAMS["integration"]
+    mocker.patch("easylink.pipeline_schema.ALLOWED_SCHEMA_PARAMS", TESTING_SCHEMA_PARAMS)
+    mocker.patch(
+        "easylink.configuration.Config._get_schema",
+        return_value=PipelineSchema("integration", nodes=nodes, edges=edges),
+    )
+
+    ## Mock implementation script call to wait 1s instead of running something
+    mocker.patch(
+        "easylink.implementation.Implementation.script_cmd",
+        new_callable=mocker.PropertyMock,
+        return_value="sleep 1s",
+    )
+    with pytest.raises(SystemExit) as exit:
+        main(
+            command="run",
+            pipeline_specification=SPECIFICATIONS_DIR / "integration" / "pipeline.yaml",
+            input_data=SPECIFICATIONS_DIR / "common/input_data.yaml",
+            computing_environment=SPECIFICATIONS_DIR / "common/environment_local.yaml",
+            results_dir=test_specific_results_dir,
+        )
+    assert exit.value.code == 1
+    assert "MissingOutputException" in caplog.text
+
+
+@pytest.mark.slow
+@pytest.mark.parametrize("outputs_specified", [True, False])
+def test_outputting_a_directory(outputs_specified: bool, test_specific_results_dir, mocker):
+    """Test that the pipeline fails when a step is missing output files."""
+    nodes, edges = TESTING_SCHEMA_PARAMS["output_dir"]
+    mocker.patch("easylink.pipeline_schema.ALLOWED_SCHEMA_PARAMS", TESTING_SCHEMA_PARAMS)
+    mocker.patch(
+        "easylink.configuration.Config._get_schema",
+        return_value=PipelineSchema("output_dir", nodes=nodes, edges=edges),
+    )
+
+    pipeline_yaml_name = (
+        "pipeline_output_dir.yaml"
+        if outputs_specified
+        else "pipeline_output_dir_default.yaml"
+    )
+    step_1_output_subdir = (
+        "dummy_step_1_for_output_dir_example/output_dir"
+        if outputs_specified
+        else "dummy_step_1_for_output_dir_example_default"
+    )
+
+    with pytest.raises(SystemExit) as exit:
+        main(
+            command="run",
+            pipeline_specification=SPECIFICATIONS_DIR / "integration" / pipeline_yaml_name,
+            input_data=SPECIFICATIONS_DIR / "common/input_data_one_file.yaml",
+            computing_environment=SPECIFICATIONS_DIR / "common/environment_local.yaml",
+            results_dir=test_specific_results_dir,
+        )
+    assert exit.value.code == 0
+    assert (
+        len(
+            list(
+                (test_specific_results_dir / "intermediate" / step_1_output_subdir).rglob(
+                    "*.parquet"
+                )
+            )
+        )
+        == 3
+    )

easylink-0.1.17/tests/specifications/common/input_data_one_file.yaml

@@ -0,0 +1 @@
+input_file_1: /mnt/team/simulation_science/priv/engineering/er_ecosystem/sample_data/dummy/input_file_1.parquet

easylink-0.1.17/tests/specifications/integration/pipeline_output_dir.yaml

@@ -0,0 +1,7 @@
+steps:
+  step_1_for_output_dir_example:
+    implementation:
+      name: dummy_step_1_for_output_dir_example
+  step_2_for_output_dir_example:
+    implementation:
+      name: dummy_step_2_for_output_dir_example

easylink-0.1.17/tests/specifications/integration/pipeline_output_dir_default.yaml

@@ -0,0 +1,7 @@
+steps:
+  step_1_for_output_dir_example:
+    implementation:
+      name: dummy_step_1_for_output_dir_example_default
+  step_2_for_output_dir_example:
+    implementation:
+      name: dummy_step_2_for_output_dir_example

{easylink-0.1.16 → easylink-0.1.17}/tests/unit/rule_strings/implemented_rule_local.txt

@@ -6,12 +6,12 @@ rule:
         dummy_container_main_input_file_paths=['foo'],
         dummy_container_secondary_input_file_paths=['bar'],
         validations=['bar'],
-    output: ['baz']
+    output: ['some/file.txt']
     log: "spam/foo_rule-output.log"
     container: "Multipolarity.sif"
     shell:
         '''
-        export DUMMY_CONTAINER_OUTPUT_PATHS=baz
+        export DUMMY_CONTAINER_OUTPUT_PATHS=some/file.txt
         export DUMMY_CONTAINER_DIAGNOSTICS_DIRECTORY=spam
         export DUMMY_CONTAINER_MAIN_INPUT_FILE_PATHS=foo
         export DUMMY_CONTAINER_SECONDARY_INPUT_FILE_PATHS=bar

{easylink-0.1.16 → easylink-0.1.17}/tests/unit/rule_strings/implemented_rule_slurm.txt

@@ -6,7 +6,7 @@ rule:
         dummy_container_main_input_file_paths=['foo'],
         dummy_container_secondary_input_file_paths=['bar'],
         validations=['bar'],
-    output: ['baz']
+    output: ['some/file.txt']
     log: "spam/foo_rule-output.log"
     container: "Multipolarity.sif"
     resources:
@@ -17,7 +17,7 @@ rule:
         slurm_extra="--output 'spam/foo_rule-slurm-%j.log'"
     shell:
         '''
-        export DUMMY_CONTAINER_OUTPUT_PATHS=baz
+        export DUMMY_CONTAINER_OUTPUT_PATHS=some/file.txt
         export DUMMY_CONTAINER_DIAGNOSTICS_DIRECTORY=spam
         export DUMMY_CONTAINER_MAIN_INPUT_FILE_PATHS=foo
         export DUMMY_CONTAINER_SECONDARY_INPUT_FILE_PATHS=bar

easylink-0.1.17/tests/unit/test_implementation.py

@@ -0,0 +1,92 @@
+# mypy: ignore-errors
+import pytest
+from layered_config_tree import LayeredConfigTree
+from pytest_mock import MockerFixture
+
+from easylink.graph_components import OutputSlot
+from easylink.implementation import Implementation
+
+
+def test__get_env_vars(mocker):
+    mocker.patch(
+        "easylink.implementation.load_yaml",
+        return_value={
+            "test": {"steps": ["this_step"], "env": {"foo": "corge", "spam": "eggs"}}
+        },
+    )
+    implementation = Implementation(
+        schema_steps=["this_step"],
+        implementation_config=LayeredConfigTree(
+            {"name": "test", "configuration": {"foo": "bar", "baz": "qux"}}
+        ),
+        input_slots=[],
+        output_slots=[],
+    )
+    assert implementation.environment_variables == {
+        "foo": "bar",
+        "baz": "qux",
+        "spam": "eggs",
+    }
+
+
+@pytest.mark.parametrize(
+    "output_slots, metadata_outputs, expected_outputs",
+    [
+        # one slot, defined output
+        (
+            ["main_output"],
+            {"main_output": "main/output/filepath"},
+            {"main_output": "main/output/filepath"},
+        ),
+        # one slot, undefined output
+        (["main_output"], None, {"main_output": "."}),
+        # two slots, defined outputs
+        (
+            ["main_output", "secondary_output"],
+            {
+                "main_output": "main/output/filepath",
+                "secondary_output": "secondary/output/filepath",
+            },
+            {
+                "main_output": "main/output/filepath",
+                "secondary_output": "secondary/output/filepath",
+            },
+        ),
+        # two slots, one defined and one undefined output
+        (
+            ["main_output", "secondary_output"],
+            {"secondary_output": "secondary/output/filepath"},
+            {"main_output": "main_output", "secondary_output": "secondary/output/filepath"},
+        ),
+        # two slots, both undefined outputs
+        (
+            ["main_output", "secondary_output"],
+            None,
+            {"main_output": "main_output", "secondary_output": "secondary_output"},
+        ),
+    ],
+)
+def test_outputs(
+    output_slots: list[str],
+    metadata_outputs: dict[str, str],
+    expected_outputs: dict[str, str],
+    mocker: MockerFixture,
+):
+    """Test that the outputs property returns the correct output details."""
+    mocker.patch(
+        "easylink.implementation.Implementation._load_metadata",
+        return_value={
+            "steps": [
+                "this_step",
+            ],
+            "image_path": "/path/to/image.sif",
+            "script_cmd": "python /path/to/script.py",
+            **({"outputs": metadata_outputs} if metadata_outputs else {}),
+        },
+    )
+    implementation = Implementation(
+        schema_steps=["this_step"],
+        implementation_config=LayeredConfigTree({"name": "test"}),
+        output_slots=[OutputSlot(slot) for slot in output_slots],
+    )
+    assert implementation.outputs == expected_outputs

{easylink-0.1.16 → easylink-0.1.17}/tests/unit/test_rule.py

@@ -49,7 +49,19 @@ def test_target_rule_build_rule():
 
 
 @pytest.mark.parametrize("computing_environment", ["local", "slurm"])
-def test_implemented_rule_build_rule(computing_environment):
+@pytest.mark.parametrize(
+    "output",
+    [
+        ["some/file.txt"],
+        ["some/file.txt", "some/other/file.txt"],
+        ["some/directory"],
+        ["some/directory", "some/other/directory"],
+        ["some/file.txt", "some/directory"],
+    ],
+)
+def test_implemented_rule_build_rule(
+    computing_environment: str, output: list[str], tmp_path: Path
+) -> None:
     if computing_environment == "slurm":
         resources = {
             "slurm_partition": "'slurmpart'",
@@ -60,6 +72,46 @@ def test_implemented_rule_build_rule(computing_environment):
     else:
         resources = None
 
+    if output == ["some/directory", "some/other/directory"]:
+        pytest.xfail(
+            reason="NotImplementedError: Multiple output directories is not supported."
+        )
+    if output == ["some/file.txt", "some/directory"]:
+        pytest.xfail(
+            reason="NotImplementedError: Mixed output types (files and directories) is not supported."
+        )
+
+    # The output in the snakefile will depend on whether the output is a file or a directory.
+    file_path = (
+        Path(os.path.dirname(__file__))
+        / RULE_STRINGS[f"implemented_rule_{computing_environment}"]
+    )
+    with open(file_path) as expected_file:
+        expected_str = expected_file.read()
+
+    if output == ["some/file.txt"]:
+        pass  # the epxected file is already correct
+    elif output == ["some/file.txt", "some/other/file.txt"]:
+        expected_str = expected_str.replace("output: ['some/file.txt']", f"output: {output}")
+        expected_str = expected_str.replace(
+            "export DUMMY_CONTAINER_OUTPUT_PATHS=some/file.txt",
+            "export DUMMY_CONTAINER_OUTPUT_PATHS=some/file.txt,some/other/file.txt",
+        )
+    elif output == ["some/directory"]:
+        expected_str = expected_str.replace(
+            "output: ['some/file.txt']", "output: directory('some/directory')"
+        )
+        expected_str = expected_str.replace(
+            "export DUMMY_CONTAINER_OUTPUT_PATHS=some/file.txt",
+            "export DUMMY_CONTAINER_OUTPUT_PATHS=some/directory",
+        )
+    else:
+        raise NotImplementedError
+    # move the modified snakefile to tmpdir
+    expected_filepath = tmp_path / file_path.name
+    with open(expected_filepath, "w") as expected_file:
+        expected_file.write(expected_str)
+
     rule = ImplementedRule(
         name="foo_rule",
         step_name="foo_step",
@@ -77,7 +129,7 @@ def test_implemented_rule_build_rule(computing_environment):
             },
         },
         validations=["bar"],
-        output=["baz"],
+        output=output,
         resources=resources,
         envvars={"eggs": "coconut"},
         diagnostics_dir="spam",
@@ -86,11 +138,7 @@ def test_implemented_rule_build_rule(computing_environment):
         requires_spark=False,
     )
 
-    file_path = (
-        Path(os.path.dirname(__file__))
-        / RULE_STRINGS[f"implemented_rule_{computing_environment}"]
-    )
-    _check_rule(rule, file_path)
+    _check_rule(rule, expected_filepath)
 
 
 def test_embarrassingly_parallel_rule_build_rule():

easylink-0.1.16/src/easylink/_version.py

@@ -1 +0,0 @@
-__version__ = "0.1.16"