easydiffraction 0.20.0__tar.gz → 0.20.1__tar.gz

{easydiffraction-0.20.0 → easydiffraction-0.20.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.5
 Name: easydiffraction
-Version: 0.20.0
+Version: 0.20.1
 Summary: Diffraction data analysis
 Project-URL: Homepage, https://easydiffraction.org
 Project-URL: Documentation, https://easyscience.github.io/diffraction-lib

easydiffraction-0.20.1/docs/dev/issues/closed/cli-fit-command-never-saves-results-to-disk.md

@@ -0,0 +1,8 @@
+# 137. CLI `fit` Command Never Saves Results to Disk
+
+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.

{easydiffraction-0.20.0 → easydiffraction-0.20.1}/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

{easydiffraction-0.20.0 → easydiffraction-0.20.1}/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": {

{easydiffraction-0.20.0 → easydiffraction-0.20.1}/docs/docs/tutorials/bayesian-dream-lbco-hrpt.py

@@ -362,3 +362,11 @@ project.display.posterior.predictive(expt_name='hrpt')
 
 # %%
 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()

{easydiffraction-0.20.0 → easydiffraction-0.20.1}/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": {

{easydiffraction-0.20.0 → easydiffraction-0.20.1}/docs/docs/tutorials/bayesian-emcee-lbco-hrpt.py

@@ -355,3 +355,11 @@ project.display.posterior.predictive(expt_name='hrpt')
 
 # %%
 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()

{easydiffraction-0.20.0 → easydiffraction-0.20.1}/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": {

{easydiffraction-0.20.0 → easydiffraction-0.20.1}/docs/docs/tutorials/bayesian-emcee-tbti-heidi.py

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

{easydiffraction-0.20.0 → easydiffraction-0.20.1}/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": {

{easydiffraction-0.20.0 → easydiffraction-0.20.1}/docs/docs/tutorials/calibrate-beer-ess.py

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

{easydiffraction-0.20.0 → easydiffraction-0.20.1}/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": {

{easydiffraction-0.20.0 → easydiffraction-0.20.1}/docs/docs/tutorials/refine-cosio-d20-tscan.py

@@ -404,3 +404,11 @@ display.fit.series(struct.atom_sites['Co2'].fract_z, versus=temperature)
 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()

{easydiffraction-0.20.0 → easydiffraction-0.20.1}/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": {

{easydiffraction-0.20.0 → easydiffraction-0.20.1}/docs/docs/tutorials/refine-cosio-d20.py

@@ -299,3 +299,11 @@ project.display.pattern(expt_name='d20', x_min=42, x_max=52)
 #
 # 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()

{easydiffraction-0.20.0 → easydiffraction-0.20.1}/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:

{easydiffraction-0.20.0 → easydiffraction-0.20.1}/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)
 
 

{easydiffraction-0.20.0 → easydiffraction-0.20.1}/src/easydiffraction/analysis/analysis.py

@@ -2860,9 +2860,6 @@ class Analysis(
         )
         self._stamp_software_provenance()
 
-        if self.project.metadata.path is not None:
-            self.project.save()
-
     def _run_joint(
         self,
         *,
@@ -2887,9 +2884,6 @@ class Analysis(
         )
         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 @@ class Analysis(
 
         self._stamp_software_provenance()
 
-        if self.project.metadata.path is not None:
-            self.project.save()
-
     def _fit_joint(
         self,
         verb: VerbosityEnum,

{easydiffraction-0.20.0 → easydiffraction-0.20.1}/src/easydiffraction/core/validation.py

@@ -25,7 +25,8 @@ _MISSING_DEFAULT = object()
 
 
 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

{easydiffraction-0.20.0 → easydiffraction-0.20.1}/src/easydiffraction/datablocks/experiment/item/base.py

@@ -650,7 +650,7 @@ class PdExperimentBase(ExperimentBase):
             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 = []

{easydiffraction-0.20.0 → easydiffraction-0.20.1}/src/easydiffraction/display/plotters/plotly.py

@@ -1406,6 +1406,64 @@ class PlotlyPlotter(PlotterBase):
     return loading;
   }}
 
+  function resizeColabOutput() {{
+    var output =
+      window.google && window.google.colab && window.google.colab.output;
+    if (!output) {{
+      return;
+    }}
+    try {{
+      if (typeof output.resizeIframeToContent === 'function') {{
+        output.resizeIframeToContent();
+      }} else if (typeof output.setIframeHeight === 'function') {{
+        // The root element's scroll height never drops below the
+        // current iframe viewport, so it can only ever grow the frame.
+        // Measure the intrinsic content instead, preferring Colab's own
+        // output area: it holds every output of this cell, so a sibling
+        // figure is never clipped.
+        var area =
+          typeof output.getDefaultOutputArea === 'function'
+            ? output.getDefaultOutputArea()
+            : null;
+        var content = area || document.body;
+        var bounds = content.getBoundingClientRect();
+        var style =
+          typeof window.getComputedStyle === 'function'
+            ? window.getComputedStyle(content)
+            : null;
+        var gap = style ? parseFloat(style.marginBottom) || 0 : 0;
+        output.setIframeHeight(
+          Math.ceil(bounds.bottom + (window.scrollY || 0) + gap),
+          true
+        );
+      }}
+    }} catch (error) {{
+      console.warn('Unable to resize the Colab plot output.', error);
+    }}
+  }}
+
+  function afterLayout(callback) {{
+    var done = false;
+    function once() {{
+      if (done) {{
+        return;
+      }}
+      done = true;
+      callback();
+    }}
+    try {{
+      if (typeof window.requestAnimationFrame === 'function') {{
+        window.requestAnimationFrame(once);
+      }}
+      // requestAnimationFrame never fires while the browser tab is
+      // hidden, so keep a timer as the backstop: first one through
+      // wins, and neither can leave the callback unrun.
+      window.setTimeout(once, 100);
+    }} catch (error) {{
+      once();
+    }}
+  }}
+
   // The loader does not touch Plotly until it renders, so both assets
   // can travel together: one round trip instead of two per frame.
   var rendering = Promise.all([
@@ -1422,7 +1480,7 @@ class PlotlyPlotter(PlotterBase):
     );
   }});
 
-  var settled = rendering.catch(function (error) {{
+  var painted = rendering.catch(function (error) {{
     console.error(error);
     var target = document.getElementById({json.dumps(plot_id)});
     var figure = target && (target.closest('.ed-figure') || target);
@@ -1432,7 +1490,7 @@ class PlotlyPlotter(PlotterBase):
     }}
   }});
 
-  // Hand Colab the settled promise, so the output frame is released
+  // Hand Colab the painted promise, so the output frame is released
   // only once the plot (or its error message) is on screen, and Colab
   // never receives a rejected promise of ours.
   if (
@@ -1441,8 +1499,16 @@ class PlotlyPlotter(PlotterBase):
     window.google.colab.output &&
     typeof window.google.colab.output.pauseOutputUntil === 'function'
   ) {{
-    window.google.colab.output.pauseOutputUntil(settled);
+    window.google.colab.output.pauseOutputUntil(painted);
   }}
+
+  // Colab holds outputframe auto-resizing (and the cell's later
+  // outputs) while that promise is pending, so remeasure once it has
+  // resolved: the frame otherwise keeps the height measured before the
+  // plot replaced its placeholder.
+  painted.then(function () {{
+    afterLayout(resizeColabOutput);
+  }});
 }})();
 </script>
 """.strip()

{easydiffraction-0.20.0 → easydiffraction-0.20.1}/src/easydiffraction/project/project.py

@@ -576,40 +576,41 @@ class Project(GuardedBase):  # noqa: PLR0904
 
         # Ensure project directory exists
         self.metadata.path.mkdir(parents=True, exist_ok=True)
+        tree_lines: list[str] = []
 
         # Save project-level configuration
         with (self.metadata.path / 'project.edi').open('w') as f:
             f.write(section_to_edi(project_config_to_cif(self)))
-            console.print('├── 📄 project.edi')
+            tree_lines.append('├── 📄 project.edi')
 
         # Save structures
         sm_dir = self.metadata.path / 'structures'
         sm_dir.mkdir(parents=True, exist_ok=True)
-        console.print('├── 📁 structures/')
+        tree_lines.append('├── 📁 structures/')
         for structure in self.structures.values():
             file_name: str = f'{structure.name}.edi'
             file_path = sm_dir / file_name
             with file_path.open('w') as f:
                 f.write(section_to_edi(structure.as_cif))
-                console.print(f'│   └── 📄 {file_name}')
+                tree_lines.append(f'│   └── 📄 {file_name}')
 
         # Save experiments
         expt_dir = self.metadata.path / 'experiments'
         expt_dir.mkdir(parents=True, exist_ok=True)
-        console.print('├── 📁 experiments/')
+        tree_lines.append('├── 📁 experiments/')
         for experiment in self.experiments.values():
             file_name: str = f'{experiment.name}.edi'
             file_path = expt_dir / file_name
             with file_path.open('w') as f:
                 f.write(section_to_edi(experiment.as_cif))
-                console.print(f'│   └── 📄 {file_name}')
+                tree_lines.append(f'│   └── 📄 {file_name}')
 
         # Save analysis
         analysis_dir = self.metadata.path / 'analysis'
         analysis_dir.mkdir(parents=True, exist_ok=True)
         with (analysis_dir / 'analysis.edi').open('w') as f:
             f.write(section_to_edi(self.analysis.as_cif))
-            console.print('├── 📁 analysis/')
+            tree_lines.append('├── 📁 analysis/')
         write_analysis_results_sidecar(
             analysis=self.analysis,
             analysis_dir=analysis_dir,
@@ -622,16 +623,20 @@ class Project(GuardedBase):  # noqa: PLR0904
         )
         for index, file_name in enumerate(analysis_file_names):
             branch = '└──' if index == len(analysis_file_names) - 1 else '├──'
-            console.print(f'│   {branch} 📄 {file_name}')
+            tree_lines.append(f'│   {branch} 📄 {file_name}')
 
         report_paths = self.report._save_configured()
         if report_paths:
             reports_dir = self.metadata.path / 'reports'
-            console.print('└── 📁 reports/')
+            tree_lines.append('└── 📁 reports/')
             for index, report_path in enumerate(report_paths):
                 branch = '└──' if index == len(report_paths) - 1 else '├──'
                 relative_path = report_path.relative_to(reports_dir)
-                console.print(f'    {branch} 📄 {relative_path}')
+                tree_lines.append(f'    {branch} 📄 {relative_path}')
+
+        # A single console call keeps the tree in one notebook
+        # output block.
+        console.print('\n'.join(tree_lines))
 
         self.metadata.update_last_modified()
         self._saved = True

{easydiffraction-0.20.0 → easydiffraction-0.20.1}/tests/integration/fitting/test_cli_entrypoints.py

@@ -81,6 +81,10 @@ def test_cli_fit_loads_and_fits(monkeypatch, tmp_path):
         metadata = FakeMetadata()
         experiments = [FakeExperiment()]
 
+        @staticmethod
+        def save() -> None:
+            calls.append('SAVE')
+
         class _analysis:
             @staticmethod
             def fit() -> None:
@@ -123,13 +127,15 @@ def test_cli_fit_loads_and_fits(monkeypatch, tmp_path):
     result = runner.invoke(main_mod.app, ['fit', str(project_dir)])
 
     assert result.exit_code == 0
-    assert calls == ['FIT', 'DISPLAY', 'PLOT_CORR', 'PLOT_exp1_False']
+    assert calls == ['FIT', 'SAVE', 'DISPLAY', 'PLOT_CORR', 'PLOT_exp1_False']
 
 
 def test_cli_fit_dry_clears_path(monkeypatch, tmp_path):
     import easydiffraction.__main__ as main_mod
     from easydiffraction.project.project import Project
 
+    calls: list[str] = []
+
     class FakeMetadata:
         _path = '/some/path'
 
@@ -140,6 +146,10 @@ def test_cli_fit_dry_clears_path(monkeypatch, tmp_path):
         metadata = FakeMetadata()
         experiments = [FakeExperiment()]
 
+        @staticmethod
+        def save() -> None:
+            calls.append('SAVE')
+
         class _analysis:
             @staticmethod
             def fit() -> None:
@@ -182,3 +192,4 @@ def test_cli_fit_dry_clears_path(monkeypatch, tmp_path):
 
     assert result.exit_code == 0
     assert fake_project.metadata._path is None
+    assert calls == []

{easydiffraction-0.20.0 → easydiffraction-0.20.1}/tests/unit/easydiffraction/analysis/test_analysis.py

@@ -852,7 +852,7 @@ def test_fit_single_short_reuses_tracker_display_handle(monkeypatch):
     assert handle.closed is True
 
 
-def test_run_sequential_sets_mode_and_saves_project(monkeypatch, tmp_path):
+def test_run_sequential_sets_mode_without_saving_project(monkeypatch, tmp_path):
     from easydiffraction.analysis.analysis import Analysis
 
     project = SimpleNamespace(
@@ -919,7 +919,7 @@ def test_run_sequential_sets_mode_and_saves_project(monkeypatch, tmp_path):
         ('reverse', True),
         ('update_categories', None),
     ]
-    assert project.save_calls == 1
+    assert project.save_calls == 0
     assert analysis.fit_results is None
     assert analysis.fitter.results is None
 

{easydiffraction-0.20.0 → easydiffraction-0.20.1}/tests/unit/easydiffraction/analysis/test_analysis_coverage.py

@@ -2543,7 +2543,9 @@ class TestRunSingleAndJoint:
         a._run_single()
         assert called == []
 
-    def test_run_single_invokes_fit_and_stamps_provenance(self, monkeypatch, tmp_path):
+    def test_run_single_invokes_fit_and_stamps_provenance_without_saving(
+        self, monkeypatch, tmp_path
+    ):
         from easydiffraction.analysis.analysis import Analysis
         from easydiffraction.utils.enums import VerbosityEnum
 
@@ -2570,7 +2572,7 @@ class TestRunSingleAndJoint:
         a._run_single(resume=True, extra_steps=5)
 
         assert captured == {'resume': True, 'extra_steps': 5, 'stamped': True}
-        assert project.save_calls == 1
+        assert project.save_calls == 0
 
     def test_run_joint_rejects_resume(self):
         import pytest
@@ -2592,6 +2594,37 @@ class TestRunSingleAndJoint:
         a._run_joint()
         assert called == []
 
+    def test_run_joint_invokes_fit_and_stamps_provenance_without_saving(
+        self, monkeypatch, tmp_path
+    ):
+        from easydiffraction.analysis.analysis import Analysis
+        from easydiffraction.utils.enums import VerbosityEnum
+
+        project = _fit_project(structures=['s'], experiments=['e'], path=tmp_path)
+        project.save_calls = 0
+        project.save = lambda: setattr(project, 'save_calls', project.save_calls + 1)
+        a = Analysis(project=project)
+
+        captured = {}
+        monkeypatch.setattr(
+            a,
+            '_prepare_fit_run',
+            lambda *, resume=False: (VerbosityEnum.SILENT, ['s'], ['e']),
+        )
+        monkeypatch.setattr(
+            a,
+            '_fit_joint',
+            lambda verb, structures, experiments, *, fit_options: captured.update(
+                resume=fit_options.resume, extra_steps=fit_options.extra_steps
+            ),
+        )
+        monkeypatch.setattr(a, '_stamp_software_provenance', lambda: captured.update(stamped=True))
+
+        a._run_joint()
+
+        assert captured == {'resume': False, 'extra_steps': None, 'stamped': True}
+        assert project.save_calls == 0
+
 
 # ------------------------------------------------------------------
 # Joint fitting execution

{easydiffraction-0.20.0 → easydiffraction-0.20.1}/tests/unit/easydiffraction/datablocks/experiment/item/test_base_coverage.py

@@ -660,8 +660,8 @@ class TestGetValidLinkedStructures:
 
         result = ex._get_valid_linked_structures(_FakeStructures([]))
 
+        # assert any('No linked structures defined' in w for w in warnings)
         assert result == []
-        assert any('No linked structures defined' in w for w in warnings)
 
     def test_skips_phases_absent_from_structures(self, monkeypatch):
         from easydiffraction.datablocks.experiment.item import base as item_base