From fb6fedce908cd50a77e1b9ddba9a1a5cadb60401 Mon Sep 17 00:00:00 2001
From: Edan Bainglass <45081142+edan-bainglass@users.noreply.github.com>
Date: Tue, 14 Jan 2025 09:17:20 +0100
Subject: [PATCH 1/2] Unpin pymatgen (#1086)

---
 setup.cfg | 1 -
 1 file changed, 1 deletion(-)

diff --git a/setup.cfg b/setup.cfg
index d7716144c..c88f0e60a 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -32,7 +32,6 @@ install_requires =
     filelock~=3.8
     importlib-resources~=5.2
     aiida-wannier90-workflows==2.3.0
-    pymatgen==2024.5.1
     anywidget==0.9.13
     table_widget~=0.0.2
 

From 37a230fb3873484039d915cfefa67e53f7f27d1c Mon Sep 17 00:00:00 2001
From: Edan Bainglass <45081142+edan-bainglass@users.noreply.github.com>
Date: Tue, 14 Jan 2025 09:20:21 +0100
Subject: [PATCH 2/2] Fix process tree issues (#1087)

- Remove "vc-" from calculation type
- Add link to restart feature
- Fix style
---
 .../app/result/components/status/status.py    |  4 ++-
 .../app/result/components/status/tree.py      | 34 ++++++++++++++++---
 src/aiidalab_qe/app/static/styles/status.css  | 13 ++++---
 src/aiidalab_qe/common/widgets.py             |  1 +
 4 files changed, 42 insertions(+), 10 deletions(-)

diff --git a/src/aiidalab_qe/app/result/components/status/status.py b/src/aiidalab_qe/app/result/components/status/status.py
index 7f38c8b57..49d27c897 100644
--- a/src/aiidalab_qe/app/result/components/status/status.py
+++ b/src/aiidalab_qe/app/result/components/status/status.py
@@ -66,7 +66,9 @@ def _render(self):
         self.to_advanced_view_button.on_click(self._switch_to_advanced_view)
 
         simplified_tree_container = ipw.VBox(
-            children=[self.simplified_process_tree],
+            children=[
+                self.simplified_process_tree,
+            ],
         )
 
         simplified_tree_node_view_container = ipw.VBox(
diff --git a/src/aiidalab_qe/app/result/components/status/tree.py b/src/aiidalab_qe/app/result/components/status/tree.py
index 799020cab..d7be654a4 100644
--- a/src/aiidalab_qe/app/result/components/status/tree.py
+++ b/src/aiidalab_qe/app/result/components/status/tree.py
@@ -77,11 +77,32 @@ def _render(self):
         self.children = [
             self.collapse_button,
             self.trunk,
-            ipw.HTML("""
-                <div style="margin-top: 5px; font-style: italic;">
-                    *workflow will re-submit failed calculations
-                </div>
-            """),
+            ipw.HBox(
+                children=[
+                    ipw.HTML(
+                        value="*",
+                        layout=ipw.Layout(margin="0"),
+                    ),
+                    ipw.HTML(
+                        value="""
+                            <div style="font-style: italic;">
+                                workflow will automatically re-submit failed calculations
+                                <br>
+                                <b>(advanced users)</b> click
+                                <a
+                                    href="https://aiida.readthedocs.io/projects/aiida-core/en/stable/howto/workchains_restart.html"
+                                    target="_blank"
+                                >here</a> to learn how AiiDA handles errors
+                            </div>
+                        """,
+                        layout=ipw.Layout(margin="0"),
+                    ),
+                ],
+                layout=ipw.Layout(
+                    align_items="flex-start",
+                    margin="5px 0 0 0",
+                ),
+            ),
         ]
 
     def _update(self):
@@ -108,12 +129,14 @@ class ProcessTreeNode(ipw.VBox, t.Generic[ProcessNodeType]):
             "nscf": "NSCF workflow",
             "bands": "Bands workflow",
             "relax": "Structure relaxation workflow",
+            "md": "Molecular dynamics workflow",
         },
         "PwCalculation": {
             "scf": "Run SCF cycle",
             "nscf": "Run NSCF cycle",
             "bands": "Compute bands",
             "relax": "Optimize structure geometry",
+            "md": "Run molecular dynamics simulation",
         },
         "DosCalculation": "Compute density of states",
         "ProjwfcCalculation": "Compute projections",
@@ -186,6 +209,7 @@ def _get_human_readable_title(self):
         if label in ("PwBaseWorkChain", "PwCalculation"):
             inputs = node.inputs.pw if label == "PwBaseWorkChain" else node.inputs
             calculation: str = inputs.parameters.get_dict()["CONTROL"]["calculation"]
+            calculation = calculation.replace("vc-", "")
             return self._TITLE_MAPPING.get(label, {}).get(calculation, label)
         return self._TITLE_MAPPING.get(label, label)
 
diff --git a/src/aiidalab_qe/app/static/styles/status.css b/src/aiidalab_qe/app/static/styles/status.css
index e94d78b24..2dc17cc51 100644
--- a/src/aiidalab_qe/app/static/styles/status.css
+++ b/src/aiidalab_qe/app/static/styles/status.css
@@ -21,6 +21,14 @@
   }
 }
 
+.simplified-view .widget-button {
+  min-height: 28px;
+}
+
+.filename-display {
+  min-height: 32px;
+}
+
 /* Process tree */
 
 .rolling-output {
@@ -50,10 +58,6 @@
   line-height: 1.5;
 }
 
-.simplified-process-tree .widget-button {
-  height: fit-content;
-}
-
 .simplified-process-tree .tree-node-toggle:focus:enabled,
 .simplified-process-tree .tree-node-toggle:hover:enabled,
 .simplified-process-tree .tree-node-toggle:active:enabled,
@@ -96,6 +100,7 @@
 
 .simplified-process-tree .calculation-link {
   color: var(--color-link);
+  margin: 0 2px;
 }
 
 .simplified-process-tree .calculation-link:hover:enabled,
diff --git a/src/aiidalab_qe/common/widgets.py b/src/aiidalab_qe/common/widgets.py
index 4bbe8e613..bb2273131 100644
--- a/src/aiidalab_qe/common/widgets.py
+++ b/src/aiidalab_qe/common/widgets.py
@@ -159,6 +159,7 @@ def __init__(self, max_width=None, **kwargs):
         self.max_width = max_width
         self._html = ipw.HTML()
         super().__init__([self._html], **kwargs)
+        self.add_class("filename-display")
 
     @traitlets.observe("value")
     def _observe_filename(self, change):