Merge pull request #213 from UW-Macrostrat/obsidian-docs

Obsidian-based documentation system

CONTRIBUTING.md

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+content/Contributing/Contributor guide.md

content/.obsidian/app.json

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+{}

content/.obsidian/appearance.json

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+{
+  "accentColor": ""
+}

content/.obsidian/core-plugins-migration.json

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+{
+  "file-explorer": true,
+  "global-search": true,
+  "switcher": true,
+  "graph": true,
+  "backlink": true,
+  "canvas": true,
+  "outgoing-link": true,
+  "tag-pane": true,
+  "properties": false,
+  "page-preview": true,
+  "daily-notes": true,
+  "templates": true,
+  "note-composer": true,
+  "command-palette": true,
+  "slash-command": false,
+  "editor-status": true,
+  "bookmarks": true,
+  "markdown-importer": false,
+  "zk-prefixer": false,
+  "random-note": false,
+  "outline": true,
+  "word-count": true,
+  "slides": false,
+  "audio-recorder": false,
+  "workspaces": false,
+  "file-recovery": true,
+  "publish": false,
+  "sync": false
+}

content/.obsidian/core-plugins.json

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+[
+  "file-explorer",
+  "global-search",
+  "switcher",
+  "graph",
+  "backlink",
+  "canvas",
+  "outgoing-link",
+  "tag-pane",
+  "page-preview",
+  "daily-notes",
+  "templates",
+  "note-composer",
+  "command-palette",
+  "editor-status",
+  "bookmarks",
+  "outline",
+  "word-count",
+  "file-recovery"
+]

content/.obsidian/workspace.json

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+{
+  "main": {
+    "id": "54bd71a4296930db",
+    "type": "split",
+    "children": [
+      {
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+        "type": "tabs",
+        "children": [
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+            "type": "leaf",
+            "state": {
+              "type": "markdown",
+              "state": {
+                "file": "Macrostrat.md",
+                "mode": "source",
+                "source": false
+              }
+            }
+          },
+          {
+            "id": "dede0fad4051b323",
+            "type": "leaf",
+            "state": {
+              "type": "markdown",
+              "state": {
+                "file": "Macrostrat.md",
+                "mode": "source",
+                "source": false
+              }
+            }
+          }
+        ],
+        "currentTab": 1
+      }
+    ],
+    "direction": "vertical"
+  },
+  "left": {
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+    "type": "split",
+    "children": [
+      {
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+        "type": "tabs",
+        "children": [
+          {
+            "id": "ea16a5b64a96d3fe",
+            "type": "leaf",
+            "state": {
+              "type": "file-explorer",
+              "state": {
+                "sortOrder": "alphabetical"
+              }
+            }
+          },
+          {
+            "id": "aefc63aeb87bc73c",
+            "type": "leaf",
+            "state": {
+              "type": "search",
+              "state": {
+                "query": "",
+                "matchingCase": false,
+                "explainSearch": false,
+                "collapseAll": false,
+                "extraContext": false,
+                "sortOrder": "alphabetical"
+              }
+            }
+          },
+          {
+            "id": "df790a7090ccb6bd",
+            "type": "leaf",
+            "state": {
+              "type": "bookmarks",
+              "state": {}
+            }
+          }
+        ]
+      }
+    ],
+    "direction": "horizontal",
+    "width": 300
+  },
+  "right": {
+    "id": "a60526d3595b51d4",
+    "type": "split",
+    "children": [
+      {
+        "id": "673fc4209c079446",
+        "type": "tabs",
+        "children": [
+          {
+            "id": "23ccb1734eaf33d6",
+            "type": "leaf",
+            "state": {
+              "type": "backlink",
+              "state": {
+                "file": "Macrostrat.md",
+                "collapseAll": false,
+                "extraContext": false,
+                "sortOrder": "alphabetical",
+                "showSearch": false,
+                "searchQuery": "",
+                "backlinkCollapsed": false,
+                "unlinkedCollapsed": true
+              }
+            }
+          },
+          {
+            "id": "e90ef1ec860287d2",
+            "type": "leaf",
+            "state": {
+              "type": "outgoing-link",
+              "state": {
+                "file": "Macrostrat.md",
+                "linksCollapsed": false,
+                "unlinkedCollapsed": true
+              }
+            }
+          },
+          {
+            "id": "75b5ba0c40b2c900",
+            "type": "leaf",
+            "state": {
+              "type": "tag",
+              "state": {
+                "sortOrder": "frequency",
+                "useHierarchy": true
+              }
+            }
+          },
+          {
+            "id": "5404a44c5aae78a4",
+            "type": "leaf",
+            "state": {
+              "type": "outline",
+              "state": {
+                "file": "Macrostrat.md"
+              }
+            }
+          }
+        ]
+      }
+    ],
+    "direction": "horizontal",
+    "width": 300,
+    "collapsed": true
+  },
+  "left-ribbon": {
+    "hiddenItems": {
+      "switcher:Open quick switcher": false,
+      "graph:Open graph view": false,
+      "canvas:Create new canvas": false,
+      "daily-notes:Open today's daily note": false,
+      "templates:Insert template": false,
+      "command-palette:Open command palette": false
+    }
+  },
+  "active": "dede0fad4051b323",
+  "lastOpenFiles": [
+    "Community.md",
+    "Frequently asked questions.md",
+    "Macrostrat.md"
+  ]
+}

content/Architecture.md

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+- Macrostrat is centered around a [[PostgreSQL]] database
+		- A "database-centric" application
+
+## Architectural models
+
+- Supabase
+- [[PostgREST]]

content/Community.md

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+Macrostrat is part of a broad geoinformatics ecosystem.

content/Components/Macrostrat data services.md

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+Macrostrat has emerged as the go-to resource for digital geological map and
+geologic column data.
+
+There are two main reasons for this:
+
+1. Macrostrat currently contains voluminous geologic map and column data that cannot be accessed in aggregate anywhere else.
+	- Over 300 different geologic maps, containing more than 2.5 million rock unit polygons covering the world, have been integrated into a single, unified, queryable environment in Macrostrat.
+	- Additionally, more than 35,000 rock units from over 1,500 regional columns covering all of North America and limited other regions are publicly available.
+2. Macrostrat has a public "REST" application programming interface (API) that makes the full complement of data available in Findable, Accessible, Interoperable, and Reusable (FAIR) fashion with a CC-BY license.
+
+Many third-party applications and users take advantage of Macrostrat FAIR data services:
+
+- Mancos
+- StraboSpot
+- Flyover Country
+- MinDat
+- The iNaturalist web and mobile applications
+- A California Academy of Sciences interactive museum kiosk
+- Local geological surveys and individual scientists.
+
+## Usage
+
+Macrostrat’s data services have become impactful community resources for geologic information:
+- Our geologic map server has served more than 2 billion tile requests since logging began in 2018 (~10 per second)
+- Over the last 28 days, our other data APIs have served 3.8 million requests (~2 per second).
+- Conservatively, these amount to 100,000 requests for information each day.

content/Components/Macrostrat lexicon.md

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+Macrostrat maintains a lexicon of geologic information, such as stratigraphic units, etc.
+
+## Concepts
+
+- Lithologies (e.g., sandstone)
+- Lithology attributes (e.g., _hummocky cross-stratified_)
+- Environmental interpretations
+- Stratigraphic names
+
+## Mechanics
+
+- This lexicon integrates curated information from a variety of publishers
+    - Notably the USGS Stratigraphic Names lexicon
+    - Also lexicons from other organizations
+- Linked to from map and column descriptive information (mostly using autogenerated scripts)
+- The capability to manage geologic names and concepts is not unique but the tools on top of it are

content/Components/Macrostrat stratigraphic columns.md

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+- Representation of stratigraphy in chronostratigraphic or lithostratigraphic context
+- Provided by [[Macrostrat data services]]
+- Will soon be viewable in [[Macrostrat user interfaces]]

content/Components/Macrostrat user interfaces.md

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+[[Macrostrat]] user interfaces seek to express the world as geologists are used to seeing it
+
+## Core components
+
+- Maps
+- Stratigraphic columns
+- Summary pages for geologic entities (units, samples, geochemical datasets, etc.)
+
+Based on [[Macrostrat data services]]

content/Contributing/Contributor guide.md

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+# Code style
+
+- Prefer Hyperscript (using the `@macrostrat/hyper` package) over JSX.
+- Prefer functional components over class components.
+- Prefer named exports over default exports (default exports make it more difficult to track names through the codebase).
+- Prefer relative imports (e.g., `import { fetchHelper } from '../helpers'`) over absolute imports (e.g., `import { fetchHelper } from '~/pages/page1/helpers'`). Minimizing the number of up-directory imports or imports from other parts of the codebase is a good way to keep it maintainable.
+- Extract logic into hooks or utility functions to keep components straightforward.
+- Generally, try to make sure folders have an `index.ts` file that exports all the files that might be used from the outside.
+- Put the most important function in the file first, and the least important (ex., utility functions) last.
+- Prefer `function foo() {}` over `const foo = () => {}` for named functions.
+
+# Code format
+
+- Use Prettier to format your code. You can run `yarn format` to format the entire codebase, or set up your editor to format on save.
+- Sort and prune imports periodically to keep them organized.
+
+# Styling and interface design
+
+- Prefer CSS modules where possible, but don't be afraid to use semantically named global classes for straightforward cases.
+- Use sentence case for headings, button text, and other UI elements
+
+# Dumb things to avoid
+
+This codebase has been modernized and kept maintainable
+by avoiding (or belatedly correcting) many anti-patterns:
+
+- Hard-coding specific colors
+- Creating URLs by concatenating strings
+- Deeply nested code blocks (often with confusing [control flow](https://en.wikipedia.org/wiki/Control_flow) or [side effects](<https://en.wikipedia.org/wiki/Side_effect_(computer_science)>) instead of unambiguous returns)
+- Duplicated code of more than a few lines

content/Frequently asked questions.md

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+
+> [!question] I am interested in downloading the data from a search I ran on Macrostrat to import into ArcGIS.
+> For example, if I searched "basalt", how might I be able to download the results as GIS metadata?
+
+We don’t have a great way to bulk-download data in a form suitable for ArcGIS (yet; we are working on it). Part of the problem is that our GIS dataset is huge, so it’s usually easier to stream it from the web. For now, there are a few options:
+
+- There is a way to view our layers directly in QGIS and filter/style them by their attributes (using the QGIS filter functions). Unfortunately this doesn’t work in ArcGIS. But you can pretty easily apply different styles and categories to make the thematic map you desire.
+- [macrostratpy](https://github.com/DARPA-CRITICALMAAS/macrostratpy) is a prototype library to download Macrostrat tiles over large areas into a GIS-ready GeoPackage format. Right now it’s difficult to use but we hope to improve that over time.

content/Get involved.md

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+Macrostrat is improved by thousands of geologists
+
+- Contribute to code
+- Use our web components
+- Contribute maps
+- Add Rockd checkins
+
+## Coming soon
+
+- Contribute columns