Merge pull request #221 from easyscience/develop

🎉 Release: merge develop into master

Author: AndrewSazonov

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()