🎉 Release: merge develop into master

docs/dev/issues/closed/cli-fit-command-never-saves-results-to-disk.md

@@ -1,10 +1,8 @@
 # 137. CLI `fit` Command Never Saves Results to Disk
 
-Closed on re-verification — **not a defect**. `Analysis.fit()`
-auto-saves via `self.project.save()` in `_run_single` / `_run_joint` /
-`_run_sequential` (`analysis.py:2661,2688,2727`) whenever the project
-path is set. The CLI `fit` command's non-`--dry` path leaves
-`project.info.path` set, so results persist; `--dry` nulls the path to
-suppress saving (asserted by `test_cli_fit_dry_clears_path`). The
-original audit finding read the CLI in isolation and missed `fit()`'s
-internal save; no code change is needed.
+Closed after fixing the CLI persistence boundary. `Analysis.fit()`
+updates fit state without saving the project. The CLI `fit` command now
+calls `project.save()` explicitly after a successful non-`--dry` fit, so
+updated results still persist. With `--dry`, the project path is cleared
+for the fit and the explicit save is skipped, preventing project files
+and fit sidecars from being overwritten.

docs/dev/issues/open/lowest_live-notebook-plotly-delivery-loader-vs-native-mimetype.md

@@ -41,7 +41,16 @@ gap. Two ways to fix it:
   (the loader only needs Plotly once it renders), then calls the same
   `renderSpec` entry point. `google.colab.output.pauseOutputUntil` holds
   the output frame until the figure — or a visible error message — is on
-  screen. Concurrent outputs in one cell share frame-global loading
+  screen. Colab pauses outputframe auto-resizing (and the cell's later
+  outputs) while that promise is pending, so the bootstrap asks for a
+  remeasure just after it resolves; otherwise the height taken before
+  the plot replaced its placeholder stays as blank space below the
+  chart. That request is scheduled on the next paint with a timer
+  backstop, because a hidden browser tab never paints. Where that API is
+  absent, the fallback measures Colab's output area — every output of
+  the cell, so siblings are not clipped — rather than the root scroll
+  height, which is clamped to the frame viewport and so can only grow
+  it. Concurrent outputs in one cell share frame-global loading
   promises, so each asset is fetched and parsed only once. An immutable,
   exact-release-tag jsDelivr URL is the fallback while a new
   documentation version is deploying or if that deployment fails. Dev

docs/docs/tutorials/bayesian-dream-lbco-hrpt.ipynb

@@ -769,6 +769,26 @@
    "source": [
     "project.display.posterior.predictive(expt_name='hrpt', x_min=92, x_max=93)"
    ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "63",
+   "metadata": {},
+   "source": [
+    "## 💾 Save Project\n",
+    "\n",
+    "Save the fitted parameters and analysis results."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "64",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "project.save()"
+   ]
   }
  ],
  "metadata": {

docs/docs/tutorials/bayesian-dream-lbco-hrpt.py

@@ -362,3 +362,11 @@
 
 # %%
 project.display.posterior.predictive(expt_name='hrpt', x_min=92, x_max=93)
+
+# %% [markdown]
+# ## 💾 Save Project
+#
+# Save the fitted parameters and analysis results.
+
+# %%
+project.save()

docs/docs/tutorials/bayesian-emcee-lbco-hrpt.ipynb

@@ -755,6 +755,26 @@
    "source": [
     "project.display.posterior.predictive(expt_name='hrpt', x_min=92, x_max=93)"
    ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "62",
+   "metadata": {},
+   "source": [
+    "## 💾 Save Project\n",
+    "\n",
+    "Save the fitted parameters and analysis results."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "63",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "project.save()"
+   ]
   }
  ],
  "metadata": {

docs/docs/tutorials/bayesian-emcee-lbco-hrpt.py

@@ -355,3 +355,11 @@
 
 # %%
 project.display.posterior.predictive(expt_name='hrpt', x_min=92, x_max=93)
+
+# %% [markdown]
+# ## 💾 Save Project
+#
+# Save the fitted parameters and analysis results.
+
+# %%
+project.save()

docs/docs/tutorials/bayesian-emcee-tbti-heidi.ipynb

@@ -621,6 +621,26 @@
    "source": [
     "project.display.posterior.predictive(expt_name='heidi')"
    ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "53",
+   "metadata": {},
+   "source": [
+    "## 💾 Save Project\n",
+    "\n",
+    "Save the fitted parameters and analysis results."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "54",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "project.save()"
+   ]
   }
  ],
  "metadata": {

docs/docs/tutorials/bayesian-emcee-tbti-heidi.py

@@ -276,3 +276,11 @@
 
 # %%
 project.display.posterior.predictive(expt_name='heidi')
+
+# %% [markdown]
+# ## 💾 Save Project
+#
+# Save the fitted parameters and analysis results.
+
+# %%
+project.save()

docs/docs/tutorials/calibrate-beer-ess.ipynb

@@ -785,6 +785,26 @@
     "    x_max=2.13,\n",
     ")"
    ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "67",
+   "metadata": {},
+   "source": [
+    "## 💾 Save Project\n",
+    "\n",
+    "Save the fitted parameters and analysis results."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "68",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "project.save()"
+   ]
   }
  ],
  "metadata": {

docs/docs/tutorials/calibrate-beer-ess.py

@@ -350,3 +350,11 @@
     x_min=2.08,
     x_max=2.13,
 )
+
+# %% [markdown]
+# ## 💾 Save Project
+#
+# Save the fitted parameters and analysis results.
+
+# %%
+project.save()

docs/docs/tutorials/refine-cosio-d20-tscan.ipynb

@@ -870,6 +870,26 @@
     "display.fit.series(struct.atom_sites['O2'].fract_z, versus=temperature)\n",
     "display.fit.series(struct.atom_sites['O3'].fract_z, versus=temperature)"
    ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "75",
+   "metadata": {},
+   "source": [
+    "## 💾 Save Project\n",
+    "\n",
+    "Save the fitted parameters and analysis results."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "76",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "project.save()"
+   ]
   }
  ],
  "metadata": {

docs/docs/tutorials/refine-cosio-d20-tscan.py

@@ -404,3 +404,11 @@
 display.fit.series(struct.atom_sites['O1'].fract_z, versus=temperature)
 display.fit.series(struct.atom_sites['O2'].fract_z, versus=temperature)
 display.fit.series(struct.atom_sites['O3'].fract_z, versus=temperature)
+
+# %% [markdown]
+# ## 💾 Save Project
+#
+# Save the fitted parameters and analysis results.
+
+# %%
+project.save()

docs/docs/tutorials/refine-cosio-d20.ipynb

@@ -665,6 +665,26 @@
     "The HTML report is written automatically when the project is saved;\n",
     "enable `project.report.pdf` as well for a PDF version."
    ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "57",
+   "metadata": {},
+   "source": [
+    "## 💾 Save Project\n",
+    "\n",
+    "Save the fitted parameters and analysis results."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "58",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "project.save()"
+   ]
   }
  ],
  "metadata": {

docs/docs/tutorials/refine-cosio-d20.py

@@ -299,3 +299,11 @@
 #
 # The HTML report is written automatically when the project is saved;
 # enable `project.report.pdf` as well for a PDF version.
+
+# %% [markdown]
+# ## 💾 Save Project
+#
+# Save the fitted parameters and analysis results.
+
+# %%
+project.save()

docs/docs/user-guide/analysis-workflow/analysis.md

@@ -312,12 +312,14 @@ Select a Bayesian minimizer through the same category-owned selector:
 project.analysis.minimizer.type = 'emcee'
 project.save_as(dir_path='lbco_hrpt')  # required before an emcee fit
 project.analysis.fit()
+project.save()
 ```
 
 For a saved `emcee` project, resume the chain with extra steps:
 
 ```python
 project.analysis.fit(resume=True, extra_steps=500)
+project.save()
 ```
 
 After a Bayesian fit, inspect posterior summaries and plots:

src/easydiffraction/__main__.py

@@ -299,6 +299,8 @@ def fit(
     if dry:
         project.metadata._path = None
     project.analysis.fit()
+    if not dry:
+        project.save()
     _display_fit_outputs(project)
 
 

src/easydiffraction/analysis/analysis.py

@@ -2860,9 +2860,6 @@ def _run_single(
         )
         self._stamp_software_provenance()
 
-        if self.project.metadata.path is not None:
-            self.project.save()
-
     def _run_joint(
         self,
         *,
@@ -2887,9 +2884,6 @@ def _run_joint(
         )
         self._stamp_software_provenance()
 
-        if self.project.metadata.path is not None:
-            self.project.save()
-
     def _run_sequential(self) -> None:
         """
         Execute sequential fitting from persisted sequential settings.
@@ -2926,9 +2920,6 @@ def _run_sequential(self) -> None:
 
         self._stamp_software_provenance()
 
-        if self.project.metadata.path is not None:
-            self.project.save()
-
     def _fit_joint(
         self,
         verb: VerbosityEnum,

src/easydiffraction/core/validation.py

@@ -25,7 +25,8 @@
 
 
 def validate_datablock_name(value: str, *, kind: str) -> str:
-    """Return a datablock name that survives backend normalization.
+    """
+    Return a datablock name that survives backend normalization.
 
     Calculator backends such as Cryspy normalize CIF datablock names to
     lowercase. Reject uppercase names at the public model boundary so

src/easydiffraction/datablocks/experiment/item/base.py

@@ -650,7 +650,7 @@ def _get_valid_linked_structures(
             A list of valid linked structures.
         """
         if not self.linked_structures:
-            log.warning('No linked structures defined. Returning empty pattern.')
+            # log.warning('No linked structures defined.')
             return []
 
         valid_linked_structures = []