feat: add error handling to FitCalculator.fit()

Author: choutkaj

architecture.md

@@ -331,7 +331,7 @@ Optional behavior:
 FitSettings(errors="collect")
 ```
 
-In collect mode, failed fits are returned as `FitResult` objects with `success = False` and a failure message.
+In collect mode, failed fits are returned as `FitResult` objects with `success = False`.
 
 ## Quality control
 

bindcurve/fitting/calculator.py

@@ -40,7 +40,20 @@ def fit(
         for compound_id in compound_ids:
             try:
                 compound = data.select_compound(compound_id)
-                for experiment_id in compound.experiments:
+            except Exception:
+                if self.settings.errors == "raise":
+                    raise
+                fits.append(
+                    FitResult.failed(
+                        compound_id=str(compound_id),
+                        model_name=self.model.name,
+                        experiment_id=None,
+                    )
+                )
+                continue
+
+            for experiment_id in compound.experiments:
+                try:
                     fit_data = compound.select_experiment(experiment_id)
                     fits.append(
                         self._fit_one(
@@ -50,17 +63,16 @@ def fit(
                             bounds=bounds,
                         )
                     )
-            except Exception as exc:
-                if self.settings.errors == "raise":
-                    raise
-                fits.append(
-                    FitResult.failed(
-                        compound_id=str(compound_id),
-                        model_name=self.model.name,
-                        experiment_id=None,
-                        message=str(exc),
+                except Exception:
+                    if self.settings.errors == "raise":
+                        raise
+                    fits.append(
+                        FitResult.failed(
+                            compound_id=str(compound_id),
+                            model_name=self.model.name,
+                            experiment_id=experiment_id,
+                        )
                     )
-                )
 
         summaries = summarize_fit_parameters(
             fits,
@@ -126,7 +138,6 @@ def _fit_one(
             experiment_id=experiment_id,
             model_name=self.model.name,
             success=bool(lmfit_result.success),
-            message=lmfit_result.message,
             parameters=estimates,
             metrics=metrics,
             lmfit_result=lmfit_result,

bindcurve/results/core.py

@@ -51,7 +51,6 @@ class FitResult:
     model_name: str
     experiment_id: str | None = None
     success: bool = True
-    message: str | None = None
     parameters: dict[str, ParameterEstimate] = field(default_factory=dict)
     metrics: FitMetrics | None = None
     lmfit_result: Any | None = None
@@ -63,15 +62,13 @@ def failed(
         compound_id: str,
         model_name: str,
         experiment_id: str | None,
-        message: str,
     ) -> FitResult:
         """Create a failed result container."""
         return cls(
             compound_id=compound_id,
             model_name=model_name,
             experiment_id=experiment_id,
             success=False,
-            message=message,
         )
 
     def parameter(self, name: str) -> ParameterEstimate:
@@ -176,7 +173,6 @@ def fit_summary(self) -> pd.DataFrame:
                 "experiment_id": fit.experiment_id,
                 "model": fit.model_name,
                 "success": fit.success,
-                "message": fit.message,
             }
             if fit.metrics is not None:
                 row.update(

pyproject.toml

@@ -19,6 +19,7 @@ dependencies = [
   "pandas",
   "matplotlib",
   "lmfit",
+  "scipy",
 ]
 classifiers = [
   "Development Status :: 4 - Beta",
@@ -41,7 +42,6 @@ Documentation = "https://choutkaj.github.io/bindcurve/"
 [dependency-groups]
 test = [
   "pytest",
-  "scipy",
 ]
 lint = [
   "ruff",

tests/test_ic50_skeleton.py

@@ -156,3 +156,29 @@ def test_collect_errors_returns_failed_result():
 
     assert len(results.failed()) == 1
     assert results.failed()[0].success is False
+
+
+def test_collect_errors_continues_after_experiment_failure():
+    class FailsForExp2Model(bc.IC50Model):
+        name = "fails_for_exp2"
+
+        def guess(self, compound: bc.CompoundData) -> dict[str, float]:
+            experiment_id = str(compound.table["experiment_id"].iloc[0])
+            if experiment_id == "exp2":
+                raise RuntimeError("synthetic experiment failure")
+            return super().guess(compound)
+
+    data = make_synthetic_data().keep_only("cmpd_a")
+    results = bc.fit(
+        data,
+        model=FailsForExp2Model(),
+        settings=bc.FitSettings(errors="collect"),
+        fixed={"ymin": 0.0, "ymax": 100.0},
+    )
+
+    successful_experiments = {fit.experiment_id for fit in results.successful()}
+    failed_experiments = {fit.experiment_id for fit in results.failed()}
+
+    assert successful_experiments == {"exp1", "exp3"}
+    assert failed_experiments == {"exp2"}
+    assert len(results.fit_results) == 3

tests/test_quality_dashboards.py

@@ -103,7 +103,6 @@ def test_results_quality_dashboard_handles_failed_fit_and_preserves_order():
             compound_id="cmpd_a",
             model_name="ic50",
             experiment_id="exp4",
-            message="failed",
         )
     )
     merged = bc.FitResults(

tests/test_quality_reports.py

@@ -174,7 +174,6 @@ def test_results_quality_report_orange_for_partial_fit_failure():
             compound_id="cmpd_a",
             model_name="ic50",
             experiment_id="exp4",
-            message="failed",
         )
     )
 
@@ -192,13 +191,11 @@ def test_results_quality_report_red_for_all_failed_fits():
                 compound_id="cmpd_a",
                 model_name="ic50",
                 experiment_id="exp1",
-                message="failed",
             ),
             bc.FitResult.failed(
                 compound_id="cmpd_a",
                 model_name="ic50",
                 experiment_id="exp2",
-                message="failed",
             ),
         ],
         summaries=[],

tests/test_results_reporting.py

@@ -84,6 +84,13 @@ def test_report_omits_missing_uncertainty_for_single_experiment():
     assert "±" not in report.loc[0, "report"]
 
 
+def test_fit_summary_omits_message_column():
+    data = make_single_experiment_data()
+    results = bc.fit(data, model="ic50", fixed={"ymin": 0.0, "ymax": 100.0})
+
+    assert "message" not in results.fit_summary().columns
+
+
 def test_report_auto_raises_for_multiple_reportable_quantities():
     fit = bc.FitResult(compound_id="cmpd_a", model_name="mock", success=True)
     summaries = [

tutorials/00_basics.ipynb

@@ -144,7 +144,7 @@
     "    format=\"wide\",\n",
     ")\n",
     "\n",
-    "data.summary()\n"
+    "data.summary()"
    ]
   },
   {
@@ -892,7 +892,6 @@
        "      <th>experiment_id</th>\n",
        "      <th>model</th>\n",
        "      <th>success</th>\n",
-       "      <th>message</th>\n",
        "      <th>n_data</th>\n",
        "      <th>n_varying_parameters</th>\n",
        "      <th>chisqr</th>\n",
@@ -917,7 +916,6 @@
        "      <td>exp_1</td>\n",
        "      <td>ic50</td>\n",
        "      <td>True</td>\n",
-       "      <td>Fit succeeded.</td>\n",
        "      <td>11</td>\n",
        "      <td>2</td>\n",
        "      <td>4.98</td>\n",
@@ -940,7 +938,6 @@
        "      <td>exp_2</td>\n",
        "      <td>ic50</td>\n",
        "      <td>True</td>\n",
-       "      <td>Fit succeeded.</td>\n",
        "      <td>11</td>\n",
        "      <td>2</td>\n",
        "      <td>15.27</td>\n",
@@ -963,7 +960,6 @@
        "      <td>exp_3</td>\n",
        "      <td>ic50</td>\n",
        "      <td>True</td>\n",
-       "      <td>Fit succeeded.</td>\n",
        "      <td>11</td>\n",
        "      <td>2</td>\n",
        "      <td>12.66</td>\n",
@@ -986,7 +982,6 @@
        "      <td>exp_1</td>\n",
        "      <td>ic50</td>\n",
        "      <td>True</td>\n",
-       "      <td>Fit succeeded.</td>\n",
        "      <td>11</td>\n",
        "      <td>2</td>\n",
        "      <td>5.69</td>\n",
@@ -1009,7 +1004,6 @@
        "      <td>exp_2</td>\n",
        "      <td>ic50</td>\n",
        "      <td>True</td>\n",
-       "      <td>Fit succeeded.</td>\n",
        "      <td>11</td>\n",
        "      <td>2</td>\n",
        "      <td>16.06</td>\n",
@@ -1032,7 +1026,6 @@
        "      <td>exp_3</td>\n",
        "      <td>ic50</td>\n",
        "      <td>True</td>\n",
-       "      <td>Fit succeeded.</td>\n",
        "      <td>11</td>\n",
        "      <td>2</td>\n",
        "      <td>7.35</td>\n",
@@ -1055,7 +1048,6 @@
        "      <td>exp_1</td>\n",
        "      <td>ic50</td>\n",
        "      <td>True</td>\n",
-       "      <td>Fit succeeded.</td>\n",
        "      <td>11</td>\n",
        "      <td>2</td>\n",
        "      <td>8.78</td>\n",
@@ -1078,7 +1070,6 @@
        "      <td>exp_2</td>\n",
        "      <td>ic50</td>\n",
        "      <td>True</td>\n",
-       "      <td>Fit succeeded.</td>\n",
        "      <td>11</td>\n",
        "      <td>2</td>\n",
        "      <td>10.57</td>\n",
@@ -1101,7 +1092,6 @@
        "      <td>exp_3</td>\n",
        "      <td>ic50</td>\n",
        "      <td>True</td>\n",
-       "      <td>Fit succeeded.</td>\n",
        "      <td>11</td>\n",
        "      <td>2</td>\n",
        "      <td>14.00</td>\n",
@@ -1123,16 +1113,16 @@
        "</div>"
       ],
       "text/plain": [
-       "  compound_id experiment_id model  success         message  n_data  n_varying_parameters  chisqr  redchi   aic   bic  r_squared  ymin  ymin_stderr   ymax  ymax_stderr  IC50  IC50_stderr  hill_slope  \\\n",
-       "0      cmpd_1         exp_1  ic50     True  Fit succeeded.      11                     2    4.98    0.55 -4.72 -3.92        1.0   0.0          0.0  100.0          0.0  0.02     3.42e-04       -1.00   \n",
-       "1      cmpd_1         exp_2  ic50     True  Fit succeeded.      11                     2   15.27    1.70  7.61  8.40        1.0   0.0          0.0  100.0          0.0  0.02     7.15e-04       -0.99   \n",
-       "2      cmpd_1         exp_3  ic50     True  Fit succeeded.      11                     2   12.66    1.41  5.55  6.34        1.0   0.0          0.0  100.0          0.0  0.02     6.24e-04       -0.98   \n",
-       "3      cmpd_2         exp_1  ic50     True  Fit succeeded.      11                     2    5.69    0.63 -3.26 -2.46        1.0   0.0          0.0  100.0          0.0  0.19     3.92e-03       -1.01   \n",
-       "4      cmpd_2         exp_2  ic50     True  Fit succeeded.      11                     2   16.06    1.78  8.16  8.96        1.0   0.0          0.0  100.0          0.0  0.20     6.98e-03       -0.97   \n",
-       "5      cmpd_2         exp_3  ic50     True  Fit succeeded.      11                     2    7.35    0.82 -0.43  0.37        1.0   0.0          0.0  100.0          0.0  0.22     5.17e-03       -1.02   \n",
-       "6      cmpd_3         exp_1  ic50     True  Fit succeeded.      11                     2    8.78    0.98  1.52  2.31        1.0   0.0          0.0  100.0          0.0  2.09     5.54e-02       -0.99   \n",
-       "7      cmpd_3         exp_2  ic50     True  Fit succeeded.      11                     2   10.57    1.17  3.57  4.36        1.0   0.0          0.0  100.0          0.0  1.95     5.74e-02       -0.97   \n",
-       "8      cmpd_3         exp_3  ic50     True  Fit succeeded.      11                     2   14.00    1.56  6.65  7.45        1.0   0.0          0.0  100.0          0.0  1.81     6.13e-02       -0.97   \n",
+       "  compound_id experiment_id model  success  n_data  n_varying_parameters  chisqr  redchi   aic   bic  r_squared  ymin  ymin_stderr   ymax  ymax_stderr  IC50  IC50_stderr  hill_slope  \\\n",
+       "0      cmpd_1         exp_1  ic50     True      11                     2    4.98    0.55 -4.72 -3.92        1.0   0.0          0.0  100.0          0.0  0.02     3.42e-04       -1.00   \n",
+       "1      cmpd_1         exp_2  ic50     True      11                     2   15.27    1.70  7.61  8.40        1.0   0.0          0.0  100.0          0.0  0.02     7.15e-04       -0.99   \n",
+       "2      cmpd_1         exp_3  ic50     True      11                     2   12.66    1.41  5.55  6.34        1.0   0.0          0.0  100.0          0.0  0.02     6.24e-04       -0.98   \n",
+       "3      cmpd_2         exp_1  ic50     True      11                     2    5.69    0.63 -3.26 -2.46        1.0   0.0          0.0  100.0          0.0  0.19     3.92e-03       -1.01   \n",
+       "4      cmpd_2         exp_2  ic50     True      11                     2   16.06    1.78  8.16  8.96        1.0   0.0          0.0  100.0          0.0  0.20     6.98e-03       -0.97   \n",
+       "5      cmpd_2         exp_3  ic50     True      11                     2    7.35    0.82 -0.43  0.37        1.0   0.0          0.0  100.0          0.0  0.22     5.17e-03       -1.02   \n",
+       "6      cmpd_3         exp_1  ic50     True      11                     2    8.78    0.98  1.52  2.31        1.0   0.0          0.0  100.0          0.0  2.09     5.54e-02       -0.99   \n",
+       "7      cmpd_3         exp_2  ic50     True      11                     2   10.57    1.17  3.57  4.36        1.0   0.0          0.0  100.0          0.0  1.95     5.74e-02       -0.97   \n",
+       "8      cmpd_3         exp_3  ic50     True      11                     2   14.00    1.56  6.65  7.45        1.0   0.0          0.0  100.0          0.0  1.81     6.13e-02       -0.97   \n",
        "\n",
        "   hill_slope_stderr  \n",
        "0               0.02  \n",
@@ -1530,4 +1520,4 @@
  },
  "nbformat": 4,
  "nbformat_minor": 5
-}
+}