Diagram notation: update stored notebook outputs and prose to the shipped brand notation

- Stored dj.Diagram SVG outputs in 16 notebooks recolored from the
  interim #1534 hues to the shipped #1544 tier palette (deterministic
  hex mapping, light and dark values).
- Stored make_mermaid text output updated to the palette the library
  now emits.
- Legends and notation prose corrected (calcium-imaging, both ephys
  tutorials, relational-workflow-model, diagram spec): orange computed
  tier, rounded boxes, entity clusters for master-part, underline =
  new dimension; the spec's tier table now carries the exact palette.
- rwm-pipeline.svg recolored; rwm-legend.svg already current.

Author: dimitri-yatsenko

src/explanation/relational-workflow-model.md

@@ -13,10 +13,10 @@ the lineage of relational modeling follows.
 ## A worked example
 
 Diagrams in this documentation use the same notation as `dj.Diagram` in
-`datajoint-python`: **Manual** tables are green rectangles, **Lookup**
-tables are gray rectangles, **Imported** tables are blue ovals, and
-**Computed** tables are red ovals. A **Part** table is a plain rectangle
-grouped with its master inside a light box. Tier is conveyed by shape and
+`datajoint-python`: **Manual** tables are green rounded boxes, **Lookup**
+tables are gray rounded boxes, **Imported** tables are blue ellipses, and
+**Computed** tables are orange ellipses. A **Part** table is a small plain box
+grouped with its master inside a light box (the *entity cluster*). Tier is conveyed by shape and
 color, and **edge thickness** shows how a child relates to its parent — a
 thick line means the child **extends** the parent (one per parent); a thin
 line means the child is **contained within** the parent (many per parent).
@@ -41,7 +41,7 @@ dimension. The legend below the figure keys the full notation.
 
 ![Worked-example imaging pipeline diagram spanning two schemas: experiment (Mouse → Session → Scan) and analysis (AverageFrame → Segmentation → Fluorescence, with Lookup SegmentationParam feeding Segmentation, and the Part tables Roi on Segmentation and Trace on Fluorescence).](../images/rwm-pipeline.svg)
 
-![Legend: table tiers — Manual (green rectangle), Lookup (gray rectangle), Imported (blue oval), Computed (red oval), Part (smaller plain rectangle); an underlined name is a new entity type (a new schema dimension, many rows per parent) while a plain name is composed from existing entities (one row per parent); edge thickness — thick means the child extends the parent, thin means the child is contained within the parent; a dashed rounded box is a schema module (labeled in the corner); a gray box encloses a master with its parts; edges have no arrowheads, so direction follows the layout.](../images/rwm-legend.svg)
+![Legend: table tiers — Manual (green rounded box), Lookup (gray rounded box), Imported (blue ellipse), Computed (orange ellipse), Part (smaller plain box); an underlined name is a new entity type (a new schema dimension, many rows per parent) while a plain name is composed from existing entities (one row per parent); edge thickness — thick means the child extends the parent, thin means the child is contained within the parent; a dashed rounded box is a schema module (labeled in the corner); a gray box encloses a master with its parts; edges have no arrowheads, so direction follows the layout.](../images/rwm-legend.svg)
 
 The notation is specified in full in the [Diagram specification](../reference/specs/diagram.md). The concepts it depicts are explained in depth elsewhere: [entity integrity](entity-integrity.md) (keys, entity types, and schema dimensions), [master–part tables](../reference/specs/master-part.md) (the entity group and its all-or-nothing populate), the [computation model](computation-model.md) (how `make()` produces Imported and Computed tables), and [semantic matching](semantic-matching.md) (why a name means the same thing everywhere it appears).
 

src/how-to/master-part.ipynb

@@ -102,30 +102,30 @@
        "  [fill="#fffde7"] { fill: #3A3620; }\n",
        "  [stroke="#c9bc5b"] { stroke: #C9BC5B; }\n",
        "  [fill="#6b6420"] { fill: #EBE3A0; }\n",
-       "  [fill="#e7f3ec"] { fill: #16281F; }\n",
-       "  [stroke="#2f7d5b"] { stroke: #4FA97F; }\n",
-       "  [fill="#1b5138"] { fill: #BCE6CF; }\n",
-       "  [fill="#f2f4f7"] { fill: #242832; }\n",
-       "  [stroke="#a9b1bd"] { stroke: #8A93A1; }\n",
-       "  [fill="#495261"] { fill: #C9CFD9; }\n",
-       "  [fill="#fbeaec"] { fill: #331A1F; }\n",
-       "  [stroke="#b23a48"] { stroke: #D0687A; }\n",
-       "  [fill="#7c2430"] { fill: #F3C2CB; }\n",
-       "  [fill="#e2ecfa"] { fill: #152538; }\n",
-       "  [stroke="#2a5fa5"] { stroke: #5E92D6; }\n",
-       "  [fill="#123a6d"] { fill: #C3DAF6; }\n",
+       "  [fill="#E8F0E9"] { fill: #16281F; }\n",
+       "  [stroke="#3E7A52"] { stroke: #6BBF94; }\n",
+       "  [fill="#28513A"] { fill: #BCE6CF; }\n",
+       "  [fill="#F0F0F1"] { fill: #242832; }\n",
+       "  [stroke="#808285"] { stroke: #9DA0A4; }\n",
+       "  [fill="#5A5C5F"] { fill: #C9CFD9; }\n",
+       "  [fill="#FFEDE5"] { fill: #331B12; }\n",
+       "  [stroke="#FF5113"] { stroke: #FF7A47; }\n",
+       "  [fill="#B23200"] { fill: #FFC7AE; }\n",
+       "  [fill="#E0F4FC"] { fill: #0F2433; }\n",
+       "  [stroke="#00A0DF"] { stroke: #33B8E8; }\n",
+       "  [fill="#00537A"] { fill: #BEE7F9; }\n",
        "  [fill="#ffffff"] { fill: #1E232C; }\n",
-       "  [stroke="#9aa6b8"] { stroke: #7B879B; }\n",
-       "  [fill="#46536b"] { fill: #C4CCDB; }\n",
+       "  [stroke="#B9BBBE"] { stroke: #8F959D; }\n",
+       "  [fill="#55585C"] { fill: #C8CED8; }\n",
        "  [fill="#edeef0"] { fill: #242730; }\n",
        "  [stroke="#808890"] { stroke: #8890A0; }\n",
        "  [fill="#404040"] { fill: #C7CDD6; }\n",
-       "  [stroke="#3a424f"] { stroke: #AEB6C2; stroke-opacity: 0.753; }\n",
+       "  [stroke="#171C39"] { stroke: #AEB6C2; stroke-opacity: 0.753; }\n",
        "  [stroke="#c77d3a"] { stroke: #D68C4A; stroke-opacity: 0.753; }\n",
        "  [fill="#f3f5f8"] { fill: #2A313D; }\n",
        "  [stroke="#f3f5f8"] { stroke: #2A313D; }\n",
        "  [stroke="gray"] { stroke: #606875; }\n",
-       "  [fill="gray"] { fill: #8A93A1; }\n",
+       "  [fill="gray"] { fill: #9DA0A4; }\n",
        "}\n",
        "</style>\n",
        "<g id=\"graph0\" class=\"graph\" transform=\"scale(1 1) rotate(0) translate(4 152)\">\n",
@@ -147,8 +147,8 @@
        "------------------------------\r",
        "session_date         \r",
        "\">\n",
-       "<path fill=\"#e7f3ec\" stroke=\"#2f7d5b\" d=\"M150.91,-58.28C150.91,-58.28 118.36,-58.28 118.36,-58.28 112.6,-58.28 106.84,-52.52 106.84,-46.76 106.84,-46.76 106.84,-35.24 106.84,-35.24 106.84,-29.48 112.6,-23.72 118.36,-23.72 118.36,-23.72 150.91,-23.72 150.91,-23.72 156.67,-23.72 162.43,-29.48 162.43,-35.24 162.43,-35.24 162.43,-46.76 162.43,-46.76 162.43,-52.52 156.67,-58.28 150.91,-58.28\"/>\n",
-       "<text text-anchor=\"start\" x=\"114.76\" y=\"-38.1\" font-family=\"Helvetica,sans-Serif\" text-decoration=\"underline\" font-size=\"12.00\" fill=\"#1b5138\">Session</text>\n",
+       "<path fill=\"#E8F0E9\" stroke=\"#3E7A52\" d=\"M150.91,-58.28C150.91,-58.28 118.36,-58.28 118.36,-58.28 112.6,-58.28 106.84,-52.52 106.84,-46.76 106.84,-46.76 106.84,-35.24 106.84,-35.24 106.84,-29.48 112.6,-23.72 118.36,-23.72 118.36,-23.72 150.91,-23.72 150.91,-23.72 156.67,-23.72 162.43,-29.48 162.43,-35.24 162.43,-35.24 162.43,-46.76 162.43,-46.76 162.43,-52.52 156.67,-58.28 150.91,-58.28\"/>\n",
+       "<text text-anchor=\"start\" x=\"114.76\" y=\"-38.1\" font-family=\"Helvetica,sans-Serif\" text-decoration=\"underline\" font-size=\"12.00\" fill=\"#28513A\">Session</text>\n",
        "</a>\n",
        "</g>\n",
        "</g>\n",
@@ -162,15 +162,15 @@
        "response             \r",
        "reaction_time        \r",
        "\">\n",
-       "<path fill=\"#ffffff\" stroke=\"#9aa6b8\" d=\"M145.55,-97.69C145.55,-97.69 123.72,-97.69 123.72,-97.69 120.15,-97.69 116.59,-94.13 116.59,-90.56 116.59,-90.56 116.59,-83.44 116.59,-83.44 116.59,-79.87 120.15,-76.31 123.72,-76.31 123.72,-76.31 145.55,-76.31 145.55,-76.31 149.12,-76.31 152.68,-79.87 152.68,-83.44 152.68,-83.44 152.68,-90.56 152.68,-90.56 152.68,-94.13 149.12,-97.69 145.55,-97.69\"/>\n",
-       "<text text-anchor=\"start\" x=\"124.51\" y=\"-84.88\" font-family=\"Helvetica,sans-Serif\" text-decoration=\"underline\" font-size=\"10.00\" fill=\"#46536b\">Trial</text>\n",
+       "<path fill=\"#ffffff\" stroke=\"#B9BBBE\" d=\"M145.55,-97.69C145.55,-97.69 123.72,-97.69 123.72,-97.69 120.15,-97.69 116.59,-94.13 116.59,-90.56 116.59,-90.56 116.59,-83.44 116.59,-83.44 116.59,-79.87 120.15,-76.31 123.72,-76.31 123.72,-76.31 145.55,-76.31 145.55,-76.31 149.12,-76.31 152.68,-79.87 152.68,-83.44 152.68,-83.44 152.68,-90.56 152.68,-90.56 152.68,-94.13 149.12,-97.69 145.55,-97.69\"/>\n",
+       "<text text-anchor=\"start\" x=\"124.51\" y=\"-84.88\" font-family=\"Helvetica,sans-Serif\" text-decoration=\"underline\" font-size=\"10.00\" fill=\"#55585C\">Trial</text>\n",
        "</a>\n",
        "</g>\n",
        "</g>\n",
        "<!-- Session&#45;&gt;Session.Trial -->\n",
        "<g id=\"edge2\" class=\"edge\">\n",
        "<title>Session-&gt;Session.Trial</title>\n",
-       "<path fill=\"none\" stroke=\"#3a424f\" stroke-width=\"0.75\" stroke-opacity=\"0.619608\" d=\"M134.63,-58.61C134.63,-64.38 134.63,-70.14 134.63,-75.91\"/>\n",
+       "<path fill=\"none\" stroke=\"#171C39\" stroke-width=\"0.75\" stroke-opacity=\"0.619608\" d=\"M134.63,-58.61C134.63,-64.38 134.63,-70.14 134.63,-75.91\"/>\n",
        "</g>\n",
        "<!-- Subject -->\n",
        "<g id=\"node2\" class=\"node\">\n",
@@ -179,15 +179,15 @@
        "------------------------------\r",
        "species              \r",
        "\">\n",
-       "<path fill=\"#e7f3ec\" stroke=\"#2f7d5b\" d=\"M59.32,-58.28C59.32,-58.28 27.52,-58.28 27.52,-58.28 21.76,-58.28 16,-52.52 16,-46.76 16,-46.76 16,-35.24 16,-35.24 16,-29.48 21.76,-23.72 27.52,-23.72 27.52,-23.72 59.32,-23.72 59.32,-23.72 65.08,-23.72 70.84,-29.48 70.84,-35.24 70.84,-35.24 70.84,-46.76 70.84,-46.76 70.84,-52.52 65.08,-58.28 59.32,-58.28\"/>\n",
-       "<text text-anchor=\"start\" x=\"23.92\" y=\"-38.1\" font-family=\"Helvetica,sans-Serif\" text-decoration=\"underline\" font-size=\"12.00\" fill=\"#1b5138\">Subject</text>\n",
+       "<path fill=\"#E8F0E9\" stroke=\"#3E7A52\" d=\"M59.32,-58.28C59.32,-58.28 27.52,-58.28 27.52,-58.28 21.76,-58.28 16,-52.52 16,-46.76 16,-46.76 16,-35.24 16,-35.24 16,-29.48 21.76,-23.72 27.52,-23.72 27.52,-23.72 59.32,-23.72 59.32,-23.72 65.08,-23.72 70.84,-29.48 70.84,-35.24 70.84,-35.24 70.84,-46.76 70.84,-46.76 70.84,-52.52 65.08,-58.28 59.32,-58.28\"/>\n",
+       "<text text-anchor=\"start\" x=\"23.92\" y=\"-38.1\" font-family=\"Helvetica,sans-Serif\" text-decoration=\"underline\" font-size=\"12.00\" fill=\"#28513A\">Subject</text>\n",
        "</a>\n",
        "</g>\n",
        "</g>\n",
        "<!-- Subject&#45;&gt;Session -->\n",
        "<g id=\"edge1\" class=\"edge\">\n",
        "<title>Subject-&gt;Session</title>\n",
-       "<path fill=\"none\" stroke=\"#3a424f\" stroke-width=\"0.75\" stroke-opacity=\"0.619608\" d=\"M71.19,-41C82.38,-41 95.36,-41 106.58,-41\"/>\n",
+       "<path fill=\"none\" stroke=\"#171C39\" stroke-width=\"0.75\" stroke-opacity=\"0.619608\" d=\"M71.19,-41C82.38,-41 95.36,-41 106.58,-41\"/>\n",
        "</g>\n",
        "</g>\n",
        "</svg>"