easylink 0.1.5__tar.gz → 0.1.6__tar.gz

{easylink-0.1.5 → easylink-0.1.6}/CHANGELOG.rst

@@ -1,3 +1,7 @@
+**0.1.6 - 2/21/25**
+
+ - Move test dictionaries to yaml files
+
 **0.1.5 - 2/20/25**
 
  - Fix handling of templated steps when no looping or parallelism is requested

{easylink-0.1.5 → easylink-0.1.6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: easylink
-Version: 0.1.5
+Version: 0.1.6
 Summary: Research repository for the EasyLink ER ecosystem project.
 Home-page: https://github.com/ihmeuw/easylink
 Author: The EasyLink developers

easylink-0.1.6/src/easylink/_version.py

@@ -0,0 +1 @@
+__version__ = "0.1.6"

{easylink-0.1.5 → easylink-0.1.6}/src/easylink/pipeline_schema_constants/__init__.py

@@ -6,7 +6,7 @@ ALLOWED_SCHEMA_PARAMS = {
 
 TESTING_SCHEMA_PARAMS = {
     "integration": testing.SINGLE_STEP_SCHEMA_PARAMS,
-    "combined_bad_topology": testing.BAD_COMBINED_TOPOLOGY_SCHEMA_PARAMS,
-    "combined_bad_implementation_names": testing.BAD_COMBINED_TOPOLOGY_SCHEMA_PARAMS,
+    "combine_bad_topology": testing.BAD_COMBINED_TOPOLOGY_SCHEMA_PARAMS,
+    "combine_bad_implementation_names": testing.BAD_COMBINED_TOPOLOGY_SCHEMA_PARAMS,
     "nested_templated_steps": testing.NESTED_TEMPLATED_STEPS_SCHEMA_PARAMS,
 }

{easylink-0.1.5 → easylink-0.1.6}/src/easylink/step.py

@@ -822,7 +822,7 @@ class TemplatedStep(Step, ABC):
 
         Notes
         -----
-        A ``TemplatedStep`` is always assigned a :class:`NonLeafConfigurationState`
+        A ``TemplatedStep`` is *always* assigned a :class:`NonLeafConfigurationState`
         even if it has no multiplicity since (despite having no copies to make) we
         still need to traverse the sub-``Steps`` to get to the one with a single
         :class:`~easylink.implementation.Implementation`, i.e. the one with a
@@ -851,9 +851,8 @@ class TemplatedStep(Step, ABC):
             self.slot_mappings = self._update_slot_mappings(num_repeats)
         # Manually set the configuration state to non-leaf instead of relying
         # on super().get_configuration_state() because that method will erroneously
-        # set to leaf state when we have no multiplicity (because in that case the
-        # user didn't actually include the config_key in the pipeline specification
-        # file, hence num_repeats == 1)
+        # set to leaf state in the event the user didn't include the config_key
+        # in the pipeline specification.
         self._configuration_state = NonLeafConfigurationState(
             self, expanded_config, combined_implementations, input_data_config
         )

{easylink-0.1.5 → easylink-0.1.6}/src/easylink.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: easylink
-Version: 0.1.5
+Version: 0.1.6
 Summary: Research repository for the EasyLink ER ecosystem project.
 Home-page: https://github.com/ihmeuw/easylink
 Author: The EasyLink developers

{easylink-0.1.5 → easylink-0.1.6}/src/easylink.egg-info/SOURCES.txt

@@ -112,6 +112,33 @@ tests/specifications/e2e/pipeline_expanded.yaml
 tests/specifications/integration/environment_spark_slurm.yaml
 tests/specifications/integration/pipeline.yaml
 tests/specifications/integration/pipeline_spark.yaml
+tests/specifications/unit/environment_minimum.yaml
+tests/specifications/unit/environment_spark_slurm.yaml
+tests/specifications/unit/pipeline.yaml
+tests/specifications/unit/pipeline_bad_combined_implementations.yaml
+tests/specifications/unit/pipeline_bad_implementation.yaml
+tests/specifications/unit/pipeline_bad_loop_formatting.yaml
+tests/specifications/unit/pipeline_bad_step.yaml
+tests/specifications/unit/pipeline_bad_type_key.yaml
+tests/specifications/unit/pipeline_combine_bad_implementation_names.yaml
+tests/specifications/unit/pipeline_combine_bad_topology.yaml
+tests/specifications/unit/pipeline_combine_two_steps.yaml
+tests/specifications/unit/pipeline_combine_with_extra_node.yaml
+tests/specifications/unit/pipeline_combine_with_iteration.yaml
+tests/specifications/unit/pipeline_combine_with_iteration_cycle.yaml
+tests/specifications/unit/pipeline_combine_with_missing_node.yaml
+tests/specifications/unit/pipeline_combine_with_parallel.yaml
+tests/specifications/unit/pipeline_missing_implementation_name.yaml
+tests/specifications/unit/pipeline_missing_implementations.yaml
+tests/specifications/unit/pipeline_missing_loop_nodes.yaml
+tests/specifications/unit/pipeline_missing_step.yaml
+tests/specifications/unit/pipeline_missing_substeps.yaml
+tests/specifications/unit/pipeline_missing_type_key.yaml
+tests/specifications/unit/pipeline_nested_templated_steps.yaml
+tests/specifications/unit/pipeline_out_of_order.yaml
+tests/specifications/unit/pipeline_spark.yaml
+tests/specifications/unit/pipeline_type_config_mismatch.yaml
+tests/specifications/unit/pipeline_wrong_parallel_split_keys.yaml
 tests/unit/__init__.py
 tests/unit/conftest.py
 tests/unit/test_cli.py

easylink-0.1.6/tests/specifications/unit/environment_minimum.yaml

@@ -0,0 +1,2 @@
+computing_environment: local
+container_engine: undefined

easylink-0.1.6/tests/specifications/unit/environment_spark_slurm.yaml

@@ -0,0 +1,15 @@
+computing_environment: slurm
+container_engine: singularity
+slurm:
+  account: some-account
+  partition: some-partition
+implementation_resources:
+  memory: 42
+  cpus: 42
+  time_limit: 42
+spark:
+  workers:
+    num_workers: 42
+    cpus_per_node: 42
+    mem_per_node: 42
+    time_limit: 42

easylink-0.1.6/tests/specifications/unit/pipeline.yaml

@@ -0,0 +1,15 @@
+steps:
+  step_1:
+    implementation:
+      name: step_1_python_pandas
+  step_2:
+    implementation:
+      name: step_2_python_pandas
+  step_3:
+    implementation:
+      name: step_3_python_pandas
+  choice_section:
+    type: simple
+    step_4:
+      implementation:
+        name: step_4_python_pandas

easylink-0.1.6/tests/specifications/unit/pipeline_bad_combined_implementations.yaml

@@ -0,0 +1,14 @@
+steps:
+  step_1:
+    implementation:
+      name: step_1_python_pandas
+  step_2:
+    implementation:
+      name: step_2_python_pandas
+  step_3:
+    combined_implementation_key: foo
+  choice_section:
+    type: simple
+    step_4:
+      implementation:
+        name: step_4_python_pandas

easylink-0.1.6/tests/specifications/unit/pipeline_bad_implementation.yaml

@@ -0,0 +1,15 @@
+steps:
+  step_1:
+    implementation:
+      name: foo  # not a valid/supported implementation
+  step_2:
+    implementation:
+      name: step_2_python_pandas
+  step_3:
+    implementation:
+      name: step_3_python_pandas
+  choice_section:
+    type: simple
+    step_4:
+      implementation:
+        name: step_4_python_pandas

easylink-0.1.6/tests/specifications/unit/pipeline_bad_loop_formatting.yaml

@@ -0,0 +1,15 @@
+steps:
+  step_1:
+    implementation:
+      name: step_1_python_pandas
+  step_2:
+    implementation:
+      name: step_2_python_pandas
+  step_3:
+    iterate:
+      implementation: step_3_python_pandas
+  choice_section:
+    type: simple
+    step_4:
+      implementation:
+        name: step_4_python_pandas

easylink-0.1.6/tests/specifications/unit/pipeline_bad_step.yaml

@@ -0,0 +1,18 @@
+steps:
+  foo:
+    implementation:
+      name: step_1_python_pandas
+  step_1:
+    implementation:
+      name: step_1_python_pandas
+  step_2:
+    implementation:
+      name: step_2_python_pandas
+  step_3:
+    implementation:
+      name: step_3_python_pandas
+  choice_section:
+    type: simple
+    step_4:
+      implementation:
+        name: step_4_python_pandas

easylink-0.1.6/tests/specifications/unit/pipeline_bad_type_key.yaml

@@ -0,0 +1,15 @@
+steps:
+  step_1:
+    implementation:
+      name: step_1_python_pandas
+  step_2:
+    implementation:
+      name: step_2_python_pandas
+  step_3:
+    implementation:
+      name: step_3_python_pandas
+  choice_section:
+    type: foo  # not a supported type
+    step_4:
+      implementation:
+        name: step_4_python_pandas

easylink-0.1.6/tests/specifications/unit/pipeline_combine_bad_implementation_names.yaml

@@ -0,0 +1,18 @@
+steps:
+  step_1:
+    implementation:
+      name: step_1_python_pandas
+  step_2:
+    implementation:
+      name: step_2_python_pandas
+    combined_implementation_key: step_3_4  # incorrect key
+  step_3:
+    implementation:
+      name: step_3_python_pandas
+  choice_section:
+    type: simple
+    step_4:
+      combined_implementation_key: step_3_4
+combined_implementations:
+  step_3_4:
+    name: step_3_and_step_4_combined_python_pandas

easylink-0.1.6/tests/specifications/unit/pipeline_combine_bad_topology.yaml

@@ -0,0 +1,18 @@
+steps:
+  step_1:
+    iterate:
+    - substeps:
+        step_1a:
+          implementation:
+            name: step_1a_python_pandas
+        step_1b:
+          combined_implementation_key: step_1a_1b
+    - substeps:
+        step_1a:
+          combined_implementation_key: step_1a_1b
+        step_1b:
+          implementation:
+            name: step_1b_python_pandas
+combined_implementations:
+  step_1a_1b:
+    name: step_1a_and_step_1b_combined_python_pandas

easylink-0.1.6/tests/specifications/unit/pipeline_combine_two_steps.yaml

@@ -0,0 +1,16 @@
+steps:
+  step_1:
+    implementation:
+      name: step_1_python_pandas
+  step_2:
+    implementation:
+      name: step_2_python_pandas
+  step_3:
+    combined_implementation_key: step_3_4
+  choice_section:
+    type: simple
+    step_4:
+      combined_implementation_key: step_3_4
+combined_implementations:
+  step_3_4:
+    name: step_3_and_step_4_combined_python_pandas

easylink-0.1.6/tests/specifications/unit/pipeline_combine_with_extra_node.yaml

@@ -0,0 +1,15 @@
+steps:
+  step_1:
+    implementation:
+      name: step_1_python_pandas
+  step_2:
+    combined_implementation_key: step_3_4
+  step_3:
+    combined_implementation_key: step_3_4
+  choice_section:
+    type: simple
+    step_4:
+      combined_implementation_key: step_3_4
+combined_implementations:
+  step_3_4:
+    name: step_3_and_step_4_combined_python_pandas

easylink-0.1.6/tests/specifications/unit/pipeline_combine_with_iteration.yaml

@@ -0,0 +1,19 @@
+steps:
+  step_1:
+    implementation:
+      name: step_1_python_pandas
+  step_2:
+    implementation:
+      name: step_2_python_pandas
+  step_3:
+    iterate:
+    - implementation:
+        name: step_3_python_pandas
+    - combined_implementation_key: step_3_4
+  choice_section:
+    type: simple
+    step_4:
+      combined_implementation_key: step_3_4
+combined_implementations:
+  step_3_4:
+    name: step_3_and_step_4_combined_python_pandas

easylink-0.1.6/tests/specifications/unit/pipeline_combine_with_iteration_cycle.yaml

@@ -0,0 +1,19 @@
+steps:
+  step_1:
+    implementation:
+      name: step_1_python_pandas
+  step_2:
+    implementation:
+      name: step_2_python_pandas
+  step_3:
+    iterate:
+    - combined_implementation_key: step_3_4
+    - implementation:
+        name: step_3_python_pandas
+  choice_section:
+    type: simple
+    step_4:
+      combined_implementation_key: step_3_4
+combined_implementations:
+  step_3_4:
+    name: step_3_and_step_4_combined_python_pandas

easylink-0.1.6/tests/specifications/unit/pipeline_combine_with_missing_node.yaml

@@ -0,0 +1,17 @@
+steps:
+  step_1:
+    implementation:
+      name: step_1_python_pandas
+  step_2:
+    implementation:
+      name: step_2_python_pandas
+  step_3:
+    implementation:
+      name: step_3_python_pandas
+  choice_section:
+    type: simple
+    step_4:
+      combined_implementation_key: step_3_4
+combined_implementations:
+  step_3_4:
+    name: step_3_and_step_4_combined_python_pandas

easylink-0.1.6/tests/specifications/unit/pipeline_combine_with_parallel.yaml

@@ -0,0 +1,24 @@
+steps:
+  step_1:
+    parallel:
+    - input_data_file: file1
+      implementation:
+        name: step_1_python_pandas
+    - input_data_file: file2
+      implementation:
+        name: step_1_python_pandas
+    - input_data_file: file2
+      combined_implementation_key: steps_1_and_2_combined
+  step_2:
+    combined_implementation_key: steps_1_and_2_combined
+  step_3:
+    implementation:
+      name: step_3_python_pandas
+  choice_section:
+    type: simple
+    step_4:
+      implementation:
+        name: step_4_python_pandas
+combined_implementations:
+  steps_1_and_2_combined:
+    name: step_1_and_step_2_combined_python_pandas

easylink-0.1.6/tests/specifications/unit/pipeline_missing_implementation_name.yaml

@@ -0,0 +1,15 @@
+steps:
+  step_1:
+    implementation:
+      foo: bar  # missing name key
+  step_2:
+    implementation:
+      name: step_2_python_pandas
+  step_3:
+    implementation:
+      name: step_3_python_pandas
+  choice_section:
+    type: simple
+    step_4:
+      implementation:
+        name: step_4_python_pandas

easylink-0.1.6/tests/specifications/unit/pipeline_missing_implementations.yaml

@@ -0,0 +1,14 @@
+steps:
+  step_1:
+    foo: bar  # missing implementation key
+  step_2:
+    implementation:
+      name: step_2_python_pandas
+  step_3:
+    implementation:
+      name: step_3_python_pandas
+  choice_section:
+    type: simple
+    step_4:
+      implementation:
+        name: step_4_python_pandas

easylink-0.1.6/tests/specifications/unit/pipeline_missing_loop_nodes.yaml

@@ -0,0 +1,14 @@
+steps:
+  step_1:
+    implementation:
+      name: step_1_python_pandas
+  step_2:
+    implementation:
+      name: step_2_python_pandas
+  step_3:
+    iterate: []
+  choice_section:
+    type: simple
+    step_4:
+      implementation:
+        name: step_4_python_pandas

easylink-0.1.6/tests/specifications/unit/pipeline_missing_step.yaml

@@ -0,0 +1,4 @@
+steps:
+  step_2:
+    implementation:
+      name: step_2_python_pandas

easylink-0.1.6/tests/specifications/unit/pipeline_missing_substeps.yaml

@@ -0,0 +1,17 @@
+steps:
+  step_1:
+    implementation:
+      name: step_1_python_pandas
+  step_2:
+    implementation:
+      name: step_2_python_pandas
+  step_3:
+    implementation:
+      name: step_3_python_pandas
+  choice_section:
+    type: simple
+    step_4:
+      substeps:
+        step_4a:
+          implementation: foo  # missing name key
+        # missing step_4b

easylink-0.1.6/tests/specifications/unit/pipeline_missing_type_key.yaml

@@ -0,0 +1,15 @@
+steps:
+  step_1:
+    implementation:
+      name: step_1_python_pandas
+  step_2:
+    implementation:
+      name: step_2_python_pandas
+  step_3:
+    implementation:
+      name: step_3_python_pandas
+  choice_section:
+    # missing 'type' key
+    step_4:
+      implementation:
+        name: step_4_python_pandas

easylink-0.1.6/tests/specifications/unit/pipeline_nested_templated_steps.yaml

@@ -0,0 +1,21 @@
+steps:
+  step_1:
+    iterate:
+    - parallel:  # loop 1: parallel with multiplicity
+      - implementation:
+          name: step_1_python_pandas
+        input_data_file: file1
+      - implementation:
+          name: step_1_python_pandas
+        input_data_file: file2
+    - parallel:  # loop 2: parallel with no multiplicity
+      - implementation:
+          name: step_1_python_pandas
+        input_data_file: file1
+    - substeps:  # loop 3: missing 'parallel' key, uses hierarchical step
+        step_1a:
+          implementation:
+            name: step_1a_python_pandas
+        step_1b:
+          implementation:
+            name: step_1b_python_pandas

easylink-0.1.6/tests/specifications/unit/pipeline_out_of_order.yaml

@@ -0,0 +1,15 @@
+steps:
+  step_2:
+    implementation:
+      name: step_2_python_pandas
+  step_1:
+    implementation:
+      name: step_1_python_pandas
+  step_3:
+    implementation:
+      name: step_3_python_pandas
+  choice_section:
+    type: simple
+    step_4:
+      implementation:
+        name: step_4_python_pandas

easylink-0.1.6/tests/specifications/unit/pipeline_spark.yaml

@@ -0,0 +1,7 @@
+steps:
+  step_1:
+    implementation:
+      name: step_1_python_pyspark
+  step_2:
+    implementation:
+      name: step_2_python_pyspark

easylink-0.1.6/tests/specifications/unit/pipeline_type_config_mismatch.yaml

@@ -0,0 +1,18 @@
+steps:
+  step_1:
+    implementation:
+      name: step_1_python_pandas
+  step_2:
+    implementation:
+      name: step_2_python_pandas
+  step_3:
+    implementation:
+      name: step_3_python_pandas
+  choice_section:
+    type: simple
+    step_5:
+      implementation:
+        name: step_5_python_pandas
+    step_6:
+      implementation:
+        name: step_6_python_pandas

easylink-0.1.6/tests/specifications/unit/pipeline_wrong_parallel_split_keys.yaml

@@ -0,0 +1,19 @@
+steps:
+  step_1:
+    parallel:
+      - implementation:
+          name: step_1_python_pandas
+        input_data_file: foo
+    implementation:
+      name: step_1_python_pandas
+  step_2:
+    implementation:
+      name: step_2_python_pandas
+  step_3:
+    implementation:
+      name: step_3_python_pandas
+  choice_section:
+    type: simple
+    step_4:
+      implementation:
+        name: step_4_python_pandas