Merge pull request #45 from neurostuff/enh/bump_nimare_0.11.1

bump nimare and simplify run.py

Author: jdkent

compose_runner/run.py

@@ -80,8 +80,8 @@ def __init__(
         self.cached_studyset = None
         self.cached_annotation = None
         self.cached_specification = None
-        self.first_dataset = None
-        self.second_dataset = None
+        self.first_studyset = None
+        self.second_studyset = None
         self.estimator = None
         self.corrector = None
 
@@ -292,13 +292,9 @@ def process_bundle(self, n_cores=None):
         studyset = Studyset(self.cached_studyset)
         annotation = Annotation(self.cached_annotation, studyset)
         first_studyset, second_studyset = self.apply_filter(studyset, annotation)
-        first_dataset = first_studyset.to_dataset()
-        second_dataset = (
-            second_studyset.to_dataset() if second_studyset is not None else None
-        )
         estimator, corrector = self.load_specification(n_cores=n_cores)
-        self.first_dataset = first_dataset
-        self.second_dataset = second_dataset
+        self.first_studyset = first_studyset
+        self.second_studyset = second_studyset
         self.estimator = estimator
         self.corrector = corrector
 
@@ -323,25 +319,28 @@ def create_result_object(self):
             raise ValueError(f"Could not create result for {self.meta_analysis_id}")
 
     def run_meta_analysis(self):
-        if self.second_dataset and isinstance(self.estimator, PairwiseCBMAEstimator):
+        if self.second_studyset and isinstance(self.estimator, PairwiseCBMAEstimator):
             workflow = PairwiseCBMAWorkflow(
                 estimator=self.estimator,
                 corrector=self.corrector,
                 diagnostics="focuscounter",
                 output_dir=self.result_dir,
             )
-            self.meta_results = workflow.fit(self.first_dataset, self.second_dataset)
-        elif self.second_dataset is None and isinstance(self.estimator, CBMAEstimator):
+            self.meta_results = workflow.fit(
+                self.first_studyset,
+                self.second_studyset,
+            )
+        elif self.second_studyset is None and isinstance(self.estimator, CBMAEstimator):
             workflow = CBMAWorkflow(
                 estimator=self.estimator,
                 corrector=self.corrector,
                 diagnostics="focuscounter",
                 output_dir=self.result_dir,
             )
-            self.meta_results = workflow.fit(self.first_dataset, self.second_dataset)
+            self.meta_results = workflow.fit(self.first_studyset)
         else:
             raise ValueError(
-                f"Estimator {self.estimator} and datasets {self.first_dataset} and {self.second_dataset} are not compatible."
+                f"Estimator {self.estimator} and studysets {self.first_studyset} and {self.second_studyset} are not compatible."
             )
         self._persist_meta_results()
 

compose_runner/tests/test_cli.py

@@ -1,13 +1,47 @@
 from click.testing import CliRunner
 
+from compose_runner import cli as cli_module
 from compose_runner.cli import cli
 
 
-def test_cli():
+def test_cli(monkeypatch):
+    calls = {}
+
+    def fake_run(meta_analysis_id, environment, result_dir, nsc_key, nv_key, no_upload, n_cores):
+        calls["args"] = {
+            "meta_analysis_id": meta_analysis_id,
+            "environment": environment,
+            "result_dir": result_dir,
+            "nsc_key": nsc_key,
+            "nv_key": nv_key,
+            "no_upload": no_upload,
+            "n_cores": n_cores,
+        }
+        return "https://example.org/result", None
+
+    monkeypatch.setattr(cli_module, "run", fake_run)
+
     runner = CliRunner()
-    result = runner.invoke(cli, [
-        "4nBwrGsqVWtt",
-        '--environment', "staging",
-        "--n-cores", 1,
-        "--no-upload"])
+    result = runner.invoke(
+        cli,
+        [
+            "3opENJpHxRsH",
+            "--environment",
+            "staging",
+            "--n-cores",
+            1,
+            "--no-upload",
+        ],
+    )
+
     assert result.exit_code == 0
+    assert calls["args"] == {
+        "meta_analysis_id": "3opENJpHxRsH",
+        "environment": "staging",
+        "result_dir": None,
+        "nsc_key": None,
+        "nv_key": None,
+        "no_upload": True,
+        "n_cores": 1,
+    }
+    assert "https://example.org/result" in result.output

compose_runner/tests/test_run.py

@@ -1,9 +1,9 @@
 import pytest
 from requests.exceptions import HTTPError
 
+from compose_runner import run as run_module
 from compose_runner.run import Runner
 
-
 @pytest.mark.vcr(record_mode="once")
 def test_incorrect_id():
     runner = Runner(
@@ -62,6 +62,120 @@ def test_run_string_group_comparison_workflow():
     )
     runner.run_workflow()
 
+
+def test_process_bundle_keeps_studysets(monkeypatch):
+    first_studyset = object()
+    second_studyset = object()
+    estimator = object()
+    corrector = object()
+
+    class FakeStudyset:
+        def __init__(self, source):
+            self.source = source
+
+    class FakeAnnotation:
+        def __init__(self, source, studyset):
+            self.source = source
+            self.studyset = studyset
+
+    def fake_apply_filter(self, studyset, annotation):
+        assert isinstance(studyset, FakeStudyset)
+        assert isinstance(annotation, FakeAnnotation)
+        return first_studyset, second_studyset
+
+    def fake_load_specification(self, n_cores=None):
+        assert n_cores == 3
+        return estimator, corrector
+
+    monkeypatch.setattr(run_module, "Studyset", FakeStudyset)
+    monkeypatch.setattr(run_module, "Annotation", FakeAnnotation)
+    monkeypatch.setattr(Runner, "apply_filter", fake_apply_filter)
+    monkeypatch.setattr(Runner, "load_specification", fake_load_specification)
+
+    runner = Runner(meta_analysis_id="made_up_id", environment="staging")
+    runner.cached_studyset = {"id": "studyset", "studies": []}
+    runner.cached_annotation = {"note_keys": {}}
+
+    runner.process_bundle(n_cores=3)
+
+    assert runner.first_studyset is first_studyset
+    assert runner.second_studyset is second_studyset
+    assert runner.estimator is estimator
+    assert runner.corrector is corrector
+
+
+def test_run_meta_analysis_single_studyset_uses_cbma_workflow(monkeypatch, tmp_path):
+    calls = {}
+
+    class FakeCBMAEstimator:
+        pass
+
+    class FakeWorkflow:
+        def __init__(self, estimator, corrector, diagnostics, output_dir):
+            calls["init"] = {
+                "estimator": estimator,
+                "corrector": corrector,
+                "diagnostics": diagnostics,
+                "output_dir": output_dir,
+            }
+
+        def fit(self, dataset):
+            calls["fit"] = {"dataset": dataset}
+            return "meta-results"
+
+    monkeypatch.setattr(run_module, "CBMAEstimator", FakeCBMAEstimator)
+    monkeypatch.setattr(run_module, "CBMAWorkflow", FakeWorkflow)
+
+    runner = Runner(meta_analysis_id="made_up_id", environment="staging", result_dir=tmp_path)
+    runner.first_studyset = object()
+    runner.second_studyset = None
+    runner.estimator = FakeCBMAEstimator()
+    runner.corrector = object()
+    runner._persist_meta_results = lambda: None
+
+    runner.run_meta_analysis()
+
+    assert calls["fit"] == {"dataset": runner.first_studyset}
+    assert runner.meta_results == "meta-results"
+
+
+def test_run_meta_analysis_pairwise_uses_pairwise_workflow(monkeypatch, tmp_path):
+    calls = {}
+
+    class FakePairwiseEstimator:
+        pass
+
+    class FakeWorkflow:
+        def __init__(self, estimator, corrector, diagnostics, output_dir):
+            calls["init"] = {
+                "estimator": estimator,
+                "corrector": corrector,
+                "diagnostics": diagnostics,
+                "output_dir": output_dir,
+            }
+
+        def fit(self, dataset1, dataset2):
+            calls["fit"] = {"dataset1": dataset1, "dataset2": dataset2}
+            return "pairwise-results"
+
+    monkeypatch.setattr(run_module, "PairwiseCBMAEstimator", FakePairwiseEstimator)
+    monkeypatch.setattr(run_module, "PairwiseCBMAWorkflow", FakeWorkflow)
+
+    runner = Runner(meta_analysis_id="made_up_id", environment="staging", result_dir=tmp_path)
+    runner.first_studyset = object()
+    runner.second_studyset = object()
+    runner.estimator = FakePairwiseEstimator()
+    runner.corrector = object()
+    runner._persist_meta_results = lambda: None
+
+    runner.run_meta_analysis()
+
+    assert calls["fit"] == {
+        "dataset1": runner.first_studyset,
+        "dataset2": runner.second_studyset,
+    }
+    assert runner.meta_results == "pairwise-results"
+
 # def test_yifan_workflow():
 #     runner = Runner(
 #         meta_analysis_id="4WELjap2yCJm",

pyproject.toml

@@ -14,7 +14,7 @@ classifiers = [
     "Programming Language :: Python :: 3",
 ]
 dynamic = ["version"]
-dependencies = ["nimare>=0.11.0", "click", "sentry-sdk", "numpy"]
+dependencies = ["nimare>=0.11.1", "click", "sentry-sdk", "numpy"]
 
 [project.urls]
 Repository = "https://github.com/neurostuff/compose-runner"