Merge pull request #1 from Acylation/initial-submit

Initial submit

.editorconfig

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+# top-most EditorConfig file
+root = true
+
+[*]
+charset = utf-8
+end_of_line = lf
+insert_final_newline = true
+indent_style = tab
+indent_size = 4
+tab_width = 4

.eslintignore

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+node_modules/
+
+main.js

.eslintrc.json

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+{
+  "root": true,
+  "parser": "@typescript-eslint/parser",
+  "env": {
+    "node": true
+  },
+  "plugins": [
+    "@typescript-eslint"
+  ],
+  "extends": [
+    "eslint:recommended",
+    "plugin:@typescript-eslint/eslint-recommended",
+    "plugin:@typescript-eslint/recommended"
+  ],
+  "parserOptions": {
+    "sourceType": "module"
+  },
+  "rules": {
+    "no-unused-vars": "off",
+    "@typescript-eslint/no-unused-vars": [
+      "error",
+      {
+        "args": "none"
+      }
+    ],
+    "@typescript-eslint/ban-ts-comment": "off",
+    "no-prototype-builtins": "off",
+    "@typescript-eslint/no-empty-function": "off"
+  }
+}

.github/ISSUE_TEMPLATE/bug-report.yml

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+name: Bug Report
+description: Report a bug encountered while using the Chem plugin
+labels: ['triage']
+body:
+    - type: textarea
+      id: problem
+      attributes:
+          label: What happened?
+          description: |
+              Please provide as much info as possible.
+      validations:
+          required: true
+
+    - type: textarea
+      id: expected
+      attributes:
+          label: What did you expect to happen?
+      validations:
+          required: true
+
+    - type: textarea
+      id: repro
+      attributes:
+          label: How can we reproduce it (as minimally and precisely as possible)?
+      validations:
+          required: true
+
+    - type: textarea
+      id: additional
+      attributes:
+          label: Anything else we need to know?
+
+    - type: input
+      id: pluginVersion
+      attributes:
+          label: Plugin version
+          description: You can find the version under Settings -> Community plugins -> Installed plugins -> Chem.
+      validations:
+          required: true
+
+    - type: input
+      id: obsidianVersion
+      attributes:
+          label: Obsidian version
+          description: You can find the version under Settings -> About -> Current version.
+      validations:
+          required: true

.github/ISSUE_TEMPLATE/feature-request.yml

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+name: Feature Request
+description: Suggest a new feature
+labels: ['triage']
+body:
+    - type: textarea
+      id: feature
+      attributes:
+          label: What would you like to be added?
+      validations:
+          required: true
+
+    - type: textarea
+      id: rationale
+      attributes:
+          label: Why is this needed?
+      validations:
+          required: true

.github/workflows/ci.yml

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+name: Node.js CI
+
+on:
+    push:
+        branches: [main]
+    pull_request:
+        branches: [main]
+
+jobs:
+    build:
+        runs-on: ubuntu-latest
+
+        steps:
+            - uses: actions/checkout@v3
+            - name: Use Node.js
+              uses: actions/setup-node@v3
+              with:
+                  node-version: '18.x'
+
+            - name: Install dependencies
+              run: npm install
+            - name: Build plugin
+              run: npm run build
+            - name: Lint plugin (ESLint)
+              run: npm run lint

.gitignore

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+# vscode
+.vscode 
+
+# Intellij
+*.iml
+.idea
+
+# npm
+node_modules
+
+# Don't include the compiled main.js file in the repo.
+# They should be uploaded to GitHub releases instead.
+main.js
+
+# Exclude sourcemaps
+*.map
+
+# obsidian
+data.json
+
+# Exclude macOS Finder (System Explorer) View States
+.DS_Store

.npmrc

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+tag-version-prefix=""

.prettierignore

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+# vscode
+.vscode 
+
+# Intellij
+*.iml
+.idea
+
+# npm
+node_modules
+
+# Don't include the compiled main.js file in the repo.
+# They should be uploaded to GitHub releases instead.
+main.js
+
+# Exclude sourcemaps
+*.map
+
+# obsidian
+data.json
+
+# Exclude macOS Finder (System Explorer) View States
+.DS_Store

.prettierrc

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+{
+    "semi": true,
+    "singleQuote": true,
+    "trailingComma": "es5",
+    "tabWidth": 4,
+    "printWidth": 80,
+    "jsxBracketSameLine": false,
+    "arrowParens": "always"
+}

README.md

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+# Obsidian Chem
+
+**Chem** is a plugin for [Obsidian.md](https://obsidian.md/) providing chemistry support. It allows you to insert chemical structures into your notes through code blocks containing SMILES strings (powered by [Smiles Drawer](https://github.com/reymond-group/smilesDrawer)).
+
+## Features & Usage
+
+### Render SMILES strings as chemical structures
+
+You can use this plugin to render chemical structures from SMILES strings. Just type the SMILES strings in a code block with `smiles` as the language. Each line should have only one string.
+
+The data is stored as plain text, so you won’t lose it. The renderer will always work, even if the plugin changes its cheminfo core.
+
+![Image](https://user-images.githubusercontent.com/73122375/235232368-614cb591-a19a-4e1e-94df-781a317d25d0.jpg)
+
+You can adjust the image size and configure light themes and dark themes of the molecule pictures in the plugin’s settings page.
+
+![Image](https://user-images.githubusercontent.com/73122375/235232505-08386ce2-bc44-4fd6-96b4-22fa9c8c6fbf.jpg)
+
+> **Notice**  
+> For now, you need to refresh the file containing SMILES blocks, or refresh the blocks themselves by edit & quit the blocks to apply the new settings, as well as adapting the Obsidian light/dark theme changes.
+
+#### What is SMILES?
+
+SMILES stands for Simplified Molecular-Input Line-Entry System. It is a specification to describe chemical structures using linear ASCII strings. You can learn more about SMILES from the [official website](http://opensmiles.org/opensmiles.html) or [Wikipedia](https://en.wikipedia.org/wiki/Simplified_molecular-input_line-entry_system).
+
+#### Why using SMILES?
+
+Using SMILES strings to represent molecules is easier and more widely supported by chemistry drawing tools than using LaTeX packages like mhchem and chemfig.
+
+#### How to generate SMILES strings?
+
+ For simple structures, you can type them in by yourself, but for more complex ones, you may want to use structure editors, such as ChemDraw, [ChemDrawJS](https://chemdrawdirect.perkinelmer.cloud/js/sample/index.html#), [MarvinJS](https://marvinjs-demo.chemaxon.com/latest/index.html) and [Ketcher](https://lifescience.opensource.epam.com/KetcherDemoSA/index.html).
+
+## Installation
+
+The plugin is not available in the official plugin market for now. Please follow the steps below to install it manually.
+
+1. Go to the repo's latest [release page](https://github.com/Acylation/obsidian-chem/releases), and download the `main.js`, `style.css`, and `manifest.json`. Alternatively, you can download the latest zip file and then unzip it to get the three files.
+
+2. Copy these files to your local path `[yourvault]/.obsidian/plugins/obsidian-chem/`. You may need to create the folder `obsidian-chem` by yourself.
+
+3. Launch/restart Obsidian, or refresh the plugin list, you will see this plugin. (Make sure that you are not in restricted mode).
+
+4. In the plugin list, enable `Chem` and enjoy!
+
+## Plugin Scope
+
+I have a lot of ideas for this plugin, but my coding skills and resources are limited. I want to make it useful for anyone who needs to take notes on chemistry (such as research records, organic chemistry anki cards, etc.). As examples, here are some of the features I have in mind.
+
+- Displaying chemical formulas and structures.
+- Importing structures from the clipboard, .cdxml files, etc.
+- Appending chemical info (e.g. exact mass) next to the structures. This can help MS users and beginners in chemistry.
+- Supporting internal coordinates like .mol files. Would be useful in computational chemistry.
+- Shortcuts for physicochemical formulas in LaTeX.
+- ......
+
+I would love to hear your feedback and suggestions. Actually, the first feature of the plugin, to render SMILES strings, was suggested by community users! I’m very grateful for their input. (See the [acknowledgment](https://github.com/Acylation/obsidian-chem#acknowledgment) section for more details)
+
+Before working on a new feature, I will consider the following criteria. The feature should meet at least one of them to be useful.
+
+- It helps with taking notes on chemical research, like experimental records, literature notes, paper writing, etc.
+- It promotes a workflow that integrates well with other chemistry tools.
+- It aids in learning chemistry and related subjects.
+
+## Contributing
+
+Thank you for your interest in contributing to this project! We welcome bug reports, feature requests, and pull requests from anyone.
+
+### How to report a bug or suggest a feature
+
+- Please use the [issue tracker](https://github.com/Acylation/obsidian-chem/issues) to report any problems or suggest new features.
+- Before creating a new issue, please search for existing issues to avoid duplicates.
+- When creating a new issue, please follow the templates to provide necessary information.
+- You can also vote for existing issues by adding a 👍 reaction to show your support.
+
+### How to submit a pull request
+
+- If you want to contribute code, please fork the repository and create a new branch for your work.
+- If you are a beginner in plugin development, you can check the official [developer documentation](https://docs.obsidian.md/Plugins/Getting+started/Build+a+plugin).
+- Please include a clear and concise description of your changes in the pull request title and body.
+- Please reference any related issues in the pull request body using keywords like `fixes #123` or `closes #456`.
+- Please wait for a review before merging your pull request.
+
+### How to get help
+
+- If you have any questions or need help with using or developing this project, please join our [discussions](https://github.com/Acylation/obsidian-chem/discussions) right here in the repo.
+
+Thank you for being a part of this project! 🙌
+
+## Roadmap
+
+Check out the [roadmap](https://github.com/users/Acylation/projects/6) to see what's been working on.
+
+## Acknowledgement
+
+The plugin relies on [Smiles Drawer](https://github.com/reymond-group/smilesDrawer) as the parsing and drawing core, and uses [Mathpix](https://github.com/Mathpix/mathpix-markdown-it) as an example of how to integrate the package.
+
+During the whole process of development, I found the [developer documentation](https://docs.obsidian.md/Plugins/Getting+started/Build+a+plugin) super helpful. Massive thanks to @marcusolssonfor leading this project!
+
+The plugin is motivated by forum requests for including chemical structures in Obsidian. Thank you for the inspiration and great ideas!
+
+- <https://forum.obsidian.md/t/smiles-in-obsidian/35974>
+- <https://forum.obsidian.md/t/structural-formulas-for-chemistry/29366>
+- <https://forum.obsidian.md/t/chemistry-formulas-in-obsidian/25772>
+- <https://forum.obsidian.md/t/obsidian-for-chemistry/33491>

esbuild.config.mjs

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+import esbuild from "esbuild";
+import process from "process";
+import builtins from "builtin-modules";
+
+const banner =
+	`/*
+THIS IS A GENERATED/BUNDLED FILE BY ESBUILD
+if you want to view the source, please visit the github repository of this plugin
+*/
+`;
+
+const prod = (process.argv[2] === "production");
+
+const context = await esbuild.context({
+	banner: {
+		js: banner,
+	},
+	entryPoints: ["./src/main.ts"],
+	bundle: true,
+	external: [
+		"obsidian",
+		"electron",
+		"@codemirror/autocomplete",
+		"@codemirror/collab",
+		"@codemirror/commands",
+		"@codemirror/language",
+		"@codemirror/lint",
+		"@codemirror/search",
+		"@codemirror/state",
+		"@codemirror/view",
+		"@lezer/common",
+		"@lezer/highlight",
+		"@lezer/lr",
+		...builtins],
+	format: "cjs",
+	target: "es2018",
+	logLevel: "info",
+	sourcemap: prod ? false : "inline",
+	treeShaking: true,
+	outfile: "main.js",
+});
+
+if (prod) {
+	await context.rebuild();
+	process.exit(0);
+} else {
+	await context.watch();
+}

manifest.json

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+{
+	"id": "obsidian-chem",
+	"name": "Chem",
+	"version": "0.1.0",
+	"minAppVersion": "1.0.0",
+	"description": "Chemistry support for Obsidian.",
+	"author": "Acylation",
+	"authorUrl": "https://github.com/Acylation",
+	"isDesktopOnly": false
+}