From 470571434cb4566e8c403b282dc30f200ddddd90 Mon Sep 17 00:00:00 2001 From: Johanna Bayer Date: Sun, 22 Mar 2026 16:29:37 -0400 Subject: [PATCH 01/14] add simple button to create a PR against the main repository to add new content --- CLAUDE.md | 82 + frontend/dist/assets/index-Bq7rTnOb.css | 1 + frontend/dist/assets/index-CRvjnaR5.js | 190 ++ frontend/dist/data/reproinventory_data.json | 2080 +++++++++++++++++ frontend/dist/index.html | 13 + frontend/src/components/AddMaterialDialog.tsx | 424 ++++ frontend/src/main.tsx | 1 + frontend/src/training-materials-browser.tsx | 8 + 8 files changed, 2799 insertions(+) create mode 100644 CLAUDE.md create mode 100644 frontend/dist/assets/index-Bq7rTnOb.css create mode 100644 frontend/dist/assets/index-CRvjnaR5.js create mode 100644 frontend/dist/data/reproinventory_data.json create mode 100644 frontend/dist/index.html create mode 100644 frontend/src/components/AddMaterialDialog.tsx diff --git a/CLAUDE.md b/CLAUDE.md new file mode 100644 index 0000000..b729136 --- /dev/null +++ b/CLAUDE.md @@ -0,0 +1,82 @@ +# ReproInventory - Claude Instructions + +## Project Overview + +ReproInventory is a web application for browsing neuroimaging and reproducibility training materials. It is part of the ReproNim project. Users can search and filter a catalog of training resources by level, platform, format, programming language, neuroimaging software, and more. + +## Tech Stack + +- **Frontend:** React 19 + TypeScript + Vite +- **Styling:** Tailwind CSS v4 +- **UI Components:** shadcn/ui (built on Radix UI primitives) +- **Icons:** lucide-react +- **Data:** Static JSON file served from `frontend/public/data/reproinventory_data.json` +- **Model/Schema:** YAML-based schema in `model/`, with Python scripts to generate JSON +- **Deploy:** GitHub Pages via GitHub Actions (pushes to `main` auto-deploy) + +## Directory Structure + +``` +frontend/ # Main React app + src/ + components/ # Custom components (e.g. Footer, EditMaterialDialog, AddMaterialDialog) + components/ui/ # shadcn/ui primitives (accordion, badge, button, card, etc.) + types/ # TypeScript types generated from the YAML schema + training-materials-browser.tsx # Main browser/filter UI + App.tsx # Root component + public/ + data/ + reproinventory_data.json # The training materials dataset + +model/ # Schema and data source of truth + model.yaml # LinkML schema definition + reproinventory_data.yaml # Raw training data + reproinventory_schema.yaml # Schema + generate_reproinventory_data.py # Generates JSON from YAML + convert_yaml_to_json.py + +SimpleViewer/ # Legacy Python/Flask viewer (archived, do not modify) +``` + +## Development Commands + +All commands run from the `frontend/` directory: + +```bash +npm run dev # Start local dev server +npm run build # TypeScript check + Vite build +npm run lint # ESLint +npm run preview # Preview production build locally +``` + +## Data Model + +The data schema is defined in `model/model.yaml` (LinkML). TypeScript types in `frontend/src/types/reproinventory.ts` are generated from this schema. Key fields on `ReproInventoryEntry`: + +- `id`, `course_name`, `url`, `review`, `notes`, `keywords` +- `level`, `platform`, `course_length`, `instruction_medium`, `delivery` +- `language`, `programming_language`, `neuroimaging_software`, `imaging_modality` +- `open_dataset`, `assessment`, `quadrants`, `tag_team` + +Enum values are strict — always use values that match the schema. + +## Code Conventions + +- Use the types from `frontend/src/types/reproinventory.ts` for all data model types; do not redefine them locally (note: `AddMaterialDialog.tsx` currently duplicates types — prefer importing from the shared types file in new code). +- Use `@/` path alias for imports (e.g. `@/components/ui/button`). +- UI primitives live in `frontend/src/components/ui/` — use these rather than raw HTML elements. +- Custom components go in `frontend/src/components/`. +- The dataset is fetched at runtime from `/ReproInventory/data/reproinventory_data.json` (the GitHub Pages base path). + +## Deployment + +- Pushing to `main` triggers GitHub Actions which builds the frontend and deploys to GitHub Pages. +- The Vite base path is set for GitHub Pages — keep this in mind when referencing public assets. +- Do not push broken builds to `main`. + +## What to Avoid + +- Do not modify files in `SimpleViewer/` — it is a legacy viewer and not actively used. +- Do not change enum values without also updating `model/model.yaml` and regenerating types. +- Do not hardcode data that belongs in `reproinventory_data.json` or the YAML source. +- Do not add dependencies without good reason — the stack is intentionally minimal. diff --git a/frontend/dist/assets/index-Bq7rTnOb.css b/frontend/dist/assets/index-Bq7rTnOb.css new file mode 100644 index 0000000..049cea5 --- /dev/null +++ b/frontend/dist/assets/index-Bq7rTnOb.css @@ -0,0 +1 @@ +/*! tailwindcss v4.1.10 | MIT License | https://tailwindcss.com */@layer properties{@supports (((-webkit-hyphens:none)) and (not (margin-trim:inline))) or 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+ + diff --git a/frontend/src/components/AddMaterialDialog.tsx b/frontend/src/components/AddMaterialDialog.tsx new file mode 100644 index 0000000..1befdd7 --- /dev/null +++ b/frontend/src/components/AddMaterialDialog.tsx @@ -0,0 +1,424 @@ +import React, { useState } from "react"; +import { DialogContent, DialogHeader, DialogTitle, DialogDescription } from "@/components/ui/dialog"; +import { Button } from "@/components/ui/button"; +import { Input } from "@/components/ui/input"; +import { Label } from "@/components/ui/label"; +import { Checkbox } from "@/components/ui/checkbox"; +import { Select, SelectContent, SelectItem, SelectTrigger, SelectValue } from "@/components/ui/select"; +import { Plus, Minus } from "lucide-react"; +import type { + ReproInventoryEntry, + LevelEnum, + PlatformEnum, + CourseLengthEnum, + ContentFormatEnum, + DeliveryEnum, + LanguageEnum, + ProgrammingLanguageEnum, + NeuroimagingSoftwareEnum, + ImagingModalityEnum, + OpenDatasetEnum, + QuadrantsEnum, +} from "@/types/reproinventory"; + +const GITHUB_REPO = "https://github.com/likeajumprope/ReproInventory"; + +const levelOptions: LevelEnum[] = ["Beginner", "Intermediate", "Advanced", "NA"]; +const platformOptions: PlatformEnum[] = ["Mac", "Windows", "Linux", "Docker", "Jupyter", "NA"]; +const courseLengthOptions: CourseLengthEnum[] = ["<1 hr", "1-4 hrs", "1 day", "1-3 days", "1 week", "1+ weeks", "NA"]; +const instructionMediumOptions: ContentFormatEnum[] = ["Hands-on tutorial / notebooks", "lecture", "video", "notes", "blog post", "reference", "slides", "website", "outline", "meta-resource", "NA"]; +const deliveryOptions: DeliveryEnum[] = ["self-paced", "instructor", "Hybrid", "Discussion needed"]; +const languageOptions: LanguageEnum[] = ["English", "French", "Spanish", "Chinese", "German", "English, French", "English, German", "Other", "NA"]; +const programmingLanguageOptions: ProgrammingLanguageEnum[] = ["Python", "R", "shell scripting", "Matlab", "Git", "NA"]; +const neuroimagingSoftwareOptions: NeuroimagingSoftwareEnum[] = ["AFNI", "SPM", "FSL", "Freesurfer", "Python", "Multiple", "NA"]; +const imagingModalityOptions: ImagingModalityEnum[] = ["DWI", "Structural", "Functional", "Task-based", "Resting-State", "EEG", "Behavioral", "MEG", "MRI", "NA"]; +const openDatasetOptions: OpenDatasetEnum[] = ["True", "False", "NA"]; +const quadrantsOptions: QuadrantsEnum[] = ["information-oriented (reference)", "understanding-oriented (explanation)", "learning-oriented (tutorials)", "problem-oriented (how to guides)", "NA"]; + +function formatAsYaml(material: ReproInventoryEntry): string { + const lines: string[] = []; + + const addScalar = (key: string, value: string | number | boolean | undefined | null) => { + if (value !== undefined && value !== null && value !== "") { + lines.push(`${key}: ${value}`); + } + }; + + const addList = (key: string, values: string[] | undefined | null) => { + if (values && values.length > 0) { + lines.push(`${key}:`); + values.forEach((v) => lines.push(` - ${v}`)); + } + }; + + lines.push("id: TBD"); + addScalar("course_name", material.course_name); + addScalar("url", material.url); + addList("level", material.level); + addList("platform", material.platform); + addList("keywords", material.keywords); + addScalar("course_length", material.course_length); + addList("instruction_medium", material.instruction_medium); + addList("delivery", material.delivery); + addList("language", material.language); + addList("programming_language", material.programming_language); + addList("neuroimaging_software", material.neuroimaging_software); + addList("imaging_modality", material.imaging_modality); + addScalar("open_dataset", material.open_dataset); + addScalar("review", material.review); + addScalar("notes", material.notes); + addList("quadrants", material.quadrants); + + return lines.join("\n"); +} + +function openGitHubIssue(material: ReproInventoryEntry) { + const yaml = formatAsYaml(material); + const title = `Add material: ${material.course_name || "New training material"}`; + const body = + `## New Training Material Submission\n\n` + + `Please review the following training material for addition to ReproInventory.\n\n` + + `\`\`\`yaml\n${yaml}\n\`\`\``; + const url = `${GITHUB_REPO}/issues/new?title=${encodeURIComponent(title)}&body=${encodeURIComponent(body)}`; + window.open(url, "_blank"); +} + +interface AddMaterialDialogProps { + onClose: () => void; +} + +const AddMaterialDialog: React.FC = ({ onClose }) => { + const [material, setMaterial] = useState({ + id: "", + course_name: "", + url: "", + level: [], + platform: [], + keywords: [], + course_length: undefined, + instruction_medium: [], + delivery: [], + language: [], + programming_language: [], + neuroimaging_software: [], + imaging_modality: [], + open_dataset: undefined, + review: "", + notes: "", + quadrants: [], + }); + + const handleChange = (field: keyof ReproInventoryEntry, value: any) => { + setMaterial((prev) => ({ ...prev, [field]: value })); + }; + + const handleMultiSelectChange = (field: keyof ReproInventoryEntry, option: string, checked: boolean) => { + const current = (material[field] || []) as string[]; + handleChange(field, checked ? [...current, option] : current.filter((v) => v !== option)); + }; + + const handleArrayItemChange = (field: keyof ReproInventoryEntry, index: number, value: string) => { + const arr = [...((material[field] || []) as string[])]; + arr[index] = value; + handleChange(field, arr); + }; + + const handleAddArrayItem = (field: keyof ReproInventoryEntry) => { + handleChange(field, [...((material[field] || []) as string[]), ""]); + }; + + const handleRemoveArrayItem = (field: keyof ReproInventoryEntry, index: number) => { + handleChange(field, ((material[field] || []) as string[]).filter((_, i) => i !== index)); + }; + + const handleSubmit = () => { + if (!material.course_name?.trim()) { + alert("Please provide a course name."); + return; + } + openGitHubIssue(material); + onClose(); + }; + + return ( + + + Add New Training Material + + Fill in the details below. Submitting will open a pre-filled GitHub issue for maintainer review. + Only course name is required. + + + +
+ {/* Essential fields */} +
+ + handleChange("course_name", e.target.value)} + className="col-span-3" + placeholder="Enter course name" + /> +
+ +
+ + handleChange("url", e.target.value)} + className="col-span-3" + placeholder="https://example.com" + /> +
+ +
+ + handleChange("review", e.target.value)} + className="col-span-3" + placeholder="Brief description of the material" + /> +
+ + {/* Keywords */} +
+ +
+ {(material.keywords || []).map((keyword, index) => ( +
+ handleArrayItemChange("keywords", index, e.target.value)} + className="flex-grow" + placeholder="Enter keyword" + /> + +
+ ))} + +
+
+ + {/* Course Length */} +
+ + +
+ + {/* Multi-select grid */} +
+ {/* Level */} +
+ +
+ {levelOptions.map((option) => ( +
+ handleMultiSelectChange("level", option, checked as boolean)} + /> + +
+ ))} +
+
+ + {/* Platform */} +
+ +
+ {platformOptions.map((option) => ( +
+ handleMultiSelectChange("platform", option, checked as boolean)} + /> + +
+ ))} +
+
+ + {/* Instruction Medium */} +
+ +
+ {instructionMediumOptions.map((option) => ( +
+ handleMultiSelectChange("instruction_medium", option, checked as boolean)} + /> + +
+ ))} +
+
+ + {/* Delivery */} +
+ +
+ {deliveryOptions.map((option) => ( +
+ handleMultiSelectChange("delivery", option, checked as boolean)} + /> + +
+ ))} +
+
+ + {/* Language */} +
+ +
+ {languageOptions.map((option) => ( +
+ handleMultiSelectChange("language", option, checked as boolean)} + /> + +
+ ))} +
+
+ + {/* Programming Language */} +
+ +
+ {programmingLanguageOptions.map((option) => ( +
+ handleMultiSelectChange("programming_language", option, checked as boolean)} + /> + +
+ ))} +
+
+ + {/* Neuroimaging Software */} +
+ +
+ {neuroimagingSoftwareOptions.map((option) => ( +
+ handleMultiSelectChange("neuroimaging_software", option, checked as boolean)} + /> + +
+ ))} +
+
+ + {/* Imaging Modality */} +
+ +
+ {imagingModalityOptions.map((option) => ( +
+ handleMultiSelectChange("imaging_modality", option, checked as boolean)} + /> + +
+ ))} +
+
+
+ + {/* Open Dataset */} +
+ + +
+ + {/* Quadrants */} +
+ +
+ {quadrantsOptions.map((option) => ( +
+ handleMultiSelectChange("quadrants", option, checked as boolean)} + /> + +
+ ))} +
+
+ + {/* Notes */} +
+ + handleChange("notes", e.target.value)} + className="col-span-3" + placeholder="Additional notes" + /> +
+
+ +
+ + +
+ + ); +}; + +export default AddMaterialDialog; diff --git a/frontend/src/main.tsx b/frontend/src/main.tsx index bef5202..360a3c3 100644 --- a/frontend/src/main.tsx +++ b/frontend/src/main.tsx @@ -8,3 +8,4 @@ createRoot(document.getElementById('root')!).render( , ) + diff --git a/frontend/src/training-materials-browser.tsx b/frontend/src/training-materials-browser.tsx index ec23847..ab1a211 100644 --- a/frontend/src/training-materials-browser.tsx +++ b/frontend/src/training-materials-browser.tsx @@ -13,6 +13,7 @@ import { Tabs, TabsContent, TabsList, TabsTrigger } from "@/components/ui/tabs" import { Accordion, AccordionContent, AccordionItem, AccordionTrigger } from "@/components/ui/accordion" import { Dialog, DialogTrigger, DialogContent, DialogHeader, DialogTitle, DialogDescription } from "@/components/ui/dialog" // Adjusted import import EditMaterialDialog from "@/components/EditMaterialDialog"; // Import the new component +import AddMaterialDialog from "@/components/AddMaterialDialog"; import { type ReproInventoryEntry, type LevelEnum, @@ -34,6 +35,7 @@ export default function TrainingMaterialsBrowser() { const [error, setError] = useState(null) const [selectedRawMaterial, setSelectedRawMaterial] = useState(null) const [editingMaterial, setEditingMaterial] = useState(null) + const [showAddMaterial, setShowAddMaterial] = useState(false) useEffect(() => { const fetchData = async () => { @@ -590,6 +592,12 @@ export default function TrainingMaterialsBrowser() {

Results for "{searchQuery}"

)} + + + + + setShowAddMaterial(false)} /> +
From d8ef4931b12b70f9150aca014d5b2ff2ee747c8f Mon Sep 17 00:00:00 2001 From: Johanna Bayer Date: Sun, 22 Mar 2026 17:43:11 -0400 Subject: [PATCH 02/14] Add the edit and delete button --- frontend/dist/assets/index-Bq7rTnOb.css | 1 - .../{index-CRvjnaR5.js => index-COgKbmi3.js} | 79 +++++++++++-------- frontend/dist/assets/index-Cw0xPReC.css | 1 + frontend/dist/data/reproinventory_data.json | 4 +- frontend/dist/index.html | 4 +- .../src/components/EditMaterialDialog.tsx | 65 ++++++++++++++- frontend/src/training-materials-browser.tsx | 24 +++--- 7 files changed, 125 insertions(+), 53 deletions(-) delete mode 100644 frontend/dist/assets/index-Bq7rTnOb.css rename frontend/dist/assets/{index-CRvjnaR5.js => index-COgKbmi3.js} (53%) create mode 100644 frontend/dist/assets/index-Cw0xPReC.css diff --git a/frontend/dist/assets/index-Bq7rTnOb.css b/frontend/dist/assets/index-Bq7rTnOb.css deleted file mode 100644 index 049cea5..0000000 --- a/frontend/dist/assets/index-Bq7rTnOb.css +++ /dev/null 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(hover:hover){a.\[a\&\]\:hover\:bg-accent:hover{background-color:var(--accent)}a.\[a\&\]\:hover\:bg-destructive\/90:hover{background-color:var(--destructive)}@supports (color:color-mix(in lab,red,red)){a.\[a\&\]\:hover\:bg-destructive\/90:hover{background-color:color-mix(in oklab,var(--destructive)90%,transparent)}}a.\[a\&\]\:hover\:bg-primary\/90:hover{background-color:var(--primary)}@supports (color:color-mix(in lab,red,red)){a.\[a\&\]\:hover\:bg-primary\/90:hover{background-color:color-mix(in oklab,var(--primary)90%,transparent)}}a.\[a\&\]\:hover\:bg-secondary\/90:hover{background-color:var(--secondary)}@supports (color:color-mix(in lab,red,red)){a.\[a\&\]\:hover\:bg-secondary\/90:hover{background-color:color-mix(in oklab,var(--secondary)90%,transparent)}}a.\[a\&\]\:hover\:text-accent-foreground:hover{color:var(--accent-foreground)}}}@property --tw-animation-delay{syntax:"*";inherits:false;initial-value:0s}@property 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--tw-exit-translate-y{syntax:"*";inherits:false;initial-value:0}:root{--radius:.625rem;--background:oklch(100% 0 0);--foreground:oklch(14.5% 0 0);--card:oklch(100% 0 0);--card-foreground:oklch(14.5% 0 0);--popover:oklch(100% 0 0);--popover-foreground:oklch(14.5% 0 0);--primary:oklch(20.5% 0 0);--primary-foreground:oklch(98.5% 0 0);--secondary:oklch(97% 0 0);--secondary-foreground:oklch(20.5% 0 0);--muted:oklch(97% 0 0);--muted-foreground:oklch(55.6% 0 0);--accent:oklch(97% 0 0);--accent-foreground:oklch(20.5% 0 0);--destructive:oklch(57.7% .245 27.325);--border:oklch(92.2% 0 0);--input:oklch(92.2% 0 0);--ring:oklch(70.8% 0 0);--chart-1:oklch(64.6% .222 41.116);--chart-2:oklch(60% .118 184.704);--chart-3:oklch(39.8% .07 227.392);--chart-4:oklch(82.8% .189 84.429);--chart-5:oklch(76.9% .188 70.08);--sidebar:oklch(98.5% 0 0);--sidebar-foreground:oklch(14.5% 0 0);--sidebar-primary:oklch(20.5% 0 0);--sidebar-primary-foreground:oklch(98.5% 0 0);--sidebar-accent:oklch(97% 0 0);--sidebar-accent-foreground:oklch(20.5% 0 0);--sidebar-border:oklch(92.2% 0 0);--sidebar-ring:oklch(70.8% 0 0)}.dark{--background:oklch(14.5% 0 0);--foreground:oklch(98.5% 0 0);--card:oklch(20.5% 0 0);--card-foreground:oklch(98.5% 0 0);--popover:oklch(20.5% 0 0);--popover-foreground:oklch(98.5% 0 0);--primary:oklch(92.2% 0 0);--primary-foreground:oklch(20.5% 0 0);--secondary:oklch(26.9% 0 0);--secondary-foreground:oklch(98.5% 0 0);--muted:oklch(26.9% 0 0);--muted-foreground:oklch(70.8% 0 0);--accent:oklch(26.9% 0 0);--accent-foreground:oklch(98.5% 0 0);--destructive:oklch(70.4% .191 22.216);--border:oklch(100% 0 0/.1);--input:oklch(100% 0 0/.15);--ring:oklch(55.6% 0 0);--chart-1:oklch(48.8% .243 264.376);--chart-2:oklch(69.6% .17 162.48);--chart-3:oklch(76.9% .188 70.08);--chart-4:oklch(62.7% .265 303.9);--chart-5:oklch(64.5% .246 16.439);--sidebar:oklch(20.5% 0 0);--sidebar-foreground:oklch(98.5% 0 0);--sidebar-primary:oklch(48.8% .243 264.376);--sidebar-primary-foreground:oklch(98.5% 0 0);--sidebar-accent:oklch(26.9% 0 0);--sidebar-accent-foreground:oklch(98.5% 0 0);--sidebar-border:oklch(100% 0 0/.1);--sidebar-ring:oklch(55.6% 0 0)}@property --tw-translate-x{syntax:"*";inherits:false;initial-value:0}@property --tw-translate-y{syntax:"*";inherits:false;initial-value:0}@property --tw-translate-z{syntax:"*";inherits:false;initial-value:0}@property --tw-space-y-reverse{syntax:"*";inherits:false;initial-value:0}@property --tw-space-x-reverse{syntax:"*";inherits:false;initial-value:0}@property --tw-border-style{syntax:"*";inherits:false;initial-value:solid}@property --tw-leading{syntax:"*";inherits:false}@property --tw-font-weight{syntax:"*";inherits:false}@property --tw-tracking{syntax:"*";inherits:false}@property --tw-shadow{syntax:"*";inherits:false;initial-value:0 0 #0000}@property --tw-shadow-color{syntax:"*";inherits:false}@property --tw-shadow-alpha{syntax:"";inherits:false;initial-value:100%}@property --tw-inset-shadow{syntax:"*";inherits:false;initial-value:0 0 #0000}@property --tw-inset-shadow-color{syntax:"*";inherits:false}@property --tw-inset-shadow-alpha{syntax:"";inherits:false;initial-value:100%}@property --tw-ring-color{syntax:"*";inherits:false}@property --tw-ring-shadow{syntax:"*";inherits:false;initial-value:0 0 #0000}@property --tw-inset-ring-color{syntax:"*";inherits:false}@property --tw-inset-ring-shadow{syntax:"*";inherits:false;initial-value:0 0 #0000}@property --tw-ring-inset{syntax:"*";inherits:false}@property --tw-ring-offset-width{syntax:"";inherits:false;initial-value:0}@property --tw-ring-offset-color{syntax:"*";inherits:false;initial-value:#fff}@property --tw-ring-offset-shadow{syntax:"*";inherits:false;initial-value:0 0 #0000}@property --tw-outline-style{syntax:"*";inherits:false;initial-value:solid}@property --tw-blur{syntax:"*";inherits:false}@property --tw-brightness{syntax:"*";inherits:false}@property --tw-contrast{syntax:"*";inherits:false}@property --tw-grayscale{syntax:"*";inherits:false}@property --tw-hue-rotate{syntax:"*";inherits:false}@property --tw-invert{syntax:"*";inherits:false}@property --tw-opacity{syntax:"*";inherits:false}@property --tw-saturate{syntax:"*";inherits:false}@property --tw-sepia{syntax:"*";inherits:false}@property --tw-drop-shadow{syntax:"*";inherits:false}@property --tw-drop-shadow-color{syntax:"*";inherits:false}@property --tw-drop-shadow-alpha{syntax:"";inherits:false;initial-value:100%}@property --tw-drop-shadow-size{syntax:"*";inherits:false}@property --tw-backdrop-blur{syntax:"*";inherits:false}@property --tw-backdrop-brightness{syntax:"*";inherits:false}@property --tw-backdrop-contrast{syntax:"*";inherits:false}@property --tw-backdrop-grayscale{syntax:"*";inherits:false}@property --tw-backdrop-hue-rotate{syntax:"*";inherits:false}@property --tw-backdrop-invert{syntax:"*";inherits:false}@property --tw-backdrop-opacity{syntax:"*";inherits:false}@property --tw-backdrop-saturate{syntax:"*";inherits:false}@property --tw-backdrop-sepia{syntax:"*";inherits:false}@property --tw-duration{syntax:"*";inherits:false}@keyframes enter{0%{opacity:var(--tw-enter-opacity,1);transform:translate3d(var(--tw-enter-translate-x,0),var(--tw-enter-translate-y,0),0)scale3d(var(--tw-enter-scale,1),var(--tw-enter-scale,1),var(--tw-enter-scale,1))rotate(var(--tw-enter-rotate,0))}}@keyframes exit{to{opacity:var(--tw-exit-opacity,1);transform:translate3d(var(--tw-exit-translate-x,0),var(--tw-exit-translate-y,0),0)scale3d(var(--tw-exit-scale,1),var(--tw-exit-scale,1),var(--tw-exit-scale,1))rotate(var(--tw-exit-rotate,0))}}@keyframes accordion-down{0%{height:0}to{height:var(--radix-accordion-content-height,var(--bits-accordion-content-height,var(--reka-accordion-content-height,var(--kb-accordion-content-height,auto))))}}@keyframes accordion-up{0%{height:var(--radix-accordion-content-height,var(--bits-accordion-content-height,var(--reka-accordion-content-height,var(--kb-accordion-content-height,auto))))}to{height:0}} diff --git a/frontend/dist/assets/index-CRvjnaR5.js b/frontend/dist/assets/index-COgKbmi3.js similarity index 53% rename from frontend/dist/assets/index-CRvjnaR5.js rename to frontend/dist/assets/index-COgKbmi3.js index a1fd1e2..93f1fc4 100644 --- a/frontend/dist/assets/index-CRvjnaR5.js +++ b/frontend/dist/assets/index-COgKbmi3.js @@ -1,4 +1,4 @@ -function f0(a,r){for(var o=0;oc[f]})}}}return Object.freeze(Object.defineProperty(a,Symbol.toStringTag,{value:"Module"}))}(function(){const r=document.createElement("link").relList;if(r&&r.supports&&r.supports("modulepreload"))return;for(const f of document.querySelectorAll('link[rel="modulepreload"]'))c(f);new MutationObserver(f=>{for(const d of f)if(d.type==="childList")for(const g of 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diff --git a/frontend/src/components/EditMaterialDialog.tsx b/frontend/src/components/EditMaterialDialog.tsx index 3428921..bde32f5 100644 --- a/frontend/src/components/EditMaterialDialog.tsx +++ b/frontend/src/components/EditMaterialDialog.tsx @@ -21,9 +21,66 @@ import type { QuadrantsEnum, } from "@/types/reproinventory"; +const GITHUB_REPO = "https://github.com/likeajumprope/ReproInventory"; + +function formatAsYaml(material: ReproInventoryEntry): string { + const lines: string[] = []; + + const addScalar = (key: string, value: string | number | boolean | undefined | null) => { + if (value !== undefined && value !== null && value !== "") { + lines.push(`${key}: ${value}`); + } + }; + + const addList = (key: string, values: string[] | undefined | null) => { + if (values && values.length > 0) { + lines.push(`${key}:`); + values.forEach((v) => lines.push(` - ${v}`)); + } + }; + + addScalar("id", material.id); + addList("tag_team", material.tag_team); + addScalar("course_name", material.course_name); + addScalar("url", material.url); + addList("level", material.level); + addList("platform", material.platform); + addList("keywords", material.keywords); + addScalar("course_length", material.course_length); + addList("instruction_medium", material.instruction_medium); + addList("delivery", material.delivery); + addList("language", material.language); + addList("programming_language", material.programming_language); + addList("neuroimaging_software", material.neuroimaging_software); + addList("imaging_modality", material.imaging_modality); + addScalar("open_dataset", material.open_dataset); + addScalar("last_updated", material.last_updated); + addScalar("functionality", material.functionality); + addScalar("assessment", material.assessment); + addList("prerequisite", material.prerequisite); + addList("source", material.source); + addScalar("review", material.review); + addScalar("exclude_from_repro_inventory", material.exclude_from_repro_inventory); + addScalar("alias_links", material.alias_links); + addScalar("notes", material.notes); + addList("quadrants", material.quadrants); + + return lines.join("\n"); +} + +function openGitHubIssue(material: ReproInventoryEntry) { + const yaml = formatAsYaml(material); + const title = `Edit material: ${material.course_name || "Unknown"} (ID: ${material.id})`; + const body = + `## Edit Training Material Request\n\n` + + `Please update entry **ID: ${material.id}** in \`model/reproinventory_data.yaml\` with the following:\n\n` + + `\`\`\`yaml\n${yaml}\n\`\`\``; + const url = `${GITHUB_REPO}/issues/new?title=${encodeURIComponent(title)}&body=${encodeURIComponent(body)}`; + window.open(url, "_blank"); +} + interface EditMaterialDialogProps { material: ReproInventoryEntry; - onSave: (updatedMaterial: ReproInventoryEntry) => void; onClose: () => void; } @@ -39,7 +96,7 @@ const imagingModalityOptions: ImagingModalityEnum[] = ["DWI", "Structural", "Fun const openDatasetOptions: OpenDatasetEnum[] = ["True", "False", "NA"]; const quadrantsOptions: QuadrantsEnum[] = ["information-oriented (reference)", "understanding-oriented (explanation)", "learning-oriented (tutorials)", "problem-oriented (how to guides)", "NA"]; -const EditMaterialDialog: React.FC = ({ material, onSave, onClose }) => { +const EditMaterialDialog: React.FC = ({ material, onClose }) => { const [editedMaterial, setEditedMaterial] = useState(material); useEffect(() => { @@ -77,7 +134,7 @@ const EditMaterialDialog: React.FC = ({ material, onSav }; const handleSave = () => { - onSave(editedMaterial); + openGitHubIssue(editedMaterial); onClose(); }; @@ -439,7 +496,7 @@ const EditMaterialDialog: React.FC = ({ material, onSav
- +
); diff --git a/frontend/src/training-materials-browser.tsx b/frontend/src/training-materials-browser.tsx index ab1a211..dce90fd 100644 --- a/frontend/src/training-materials-browser.tsx +++ b/frontend/src/training-materials-browser.tsx @@ -664,7 +664,7 @@ export default function TrainingMaterialsBrowser() { )} -
+
+
From db5318d0dc0bb1c9aedbadea918e0dadcd8a562d Mon Sep 17 00:00:00 2001 From: Johanna Bayer Date: Wed, 25 Mar 2026 10:34:43 -0400 Subject: [PATCH 03/14] add github actions --- .github/scripts/process_issue.py | 99 +++++++++++++++++++ .github/workflows/create-pr-from-issue.yml | 66 +++++++++++++ .../{index-COgKbmi3.js => index-BN5M8IzP.js} | 6 +- frontend/dist/index.html | 2 +- frontend/src/components/AddMaterialDialog.tsx | 2 +- .../src/components/EditMaterialDialog.tsx | 2 +- frontend/src/training-materials-browser.tsx | 2 +- 7 files changed, 172 insertions(+), 7 deletions(-) create mode 100644 .github/scripts/process_issue.py create mode 100644 .github/workflows/create-pr-from-issue.yml rename frontend/dist/assets/{index-COgKbmi3.js => index-BN5M8IzP.js} (90%) diff --git a/.github/scripts/process_issue.py b/.github/scripts/process_issue.py new file mode 100644 index 0000000..0f4af66 --- /dev/null +++ b/.github/scripts/process_issue.py @@ -0,0 +1,99 @@ +""" +Processes a GitHub issue and updates reproinventory_data.yaml and +frontend/public/data/reproinventory_data.json accordingly. + +Reads: + /tmp/issue_body.txt - full issue body + /tmp/issue_title.txt - issue title + +Environment variables: + ISSUE_LABEL - one of: new-material, edit-material, delete-material + ISSUE_NUMBER - issue number (for logging) +""" + +import os +import re +import json +import yaml + +YAML_PATH = "model/reproinventory_data.yaml" +JSON_PATH = "frontend/public/data/reproinventory_data.json" + +label = os.environ["ISSUE_LABEL"] +issue_number = os.environ["ISSUE_NUMBER"] + +with open("/tmp/issue_body.txt", "r", encoding="utf-8") as f: + issue_body = f.read() + +with open("/tmp/issue_title.txt", "r", encoding="utf-8") as f: + issue_title = f.read().strip() + +# Load current data +with open(YAML_PATH, "r", encoding="utf-8") as f: + data = yaml.safe_load(f) or [] + + +def extract_yaml_block(body): + """Extract the first ```yaml ... ``` block from the issue body.""" + match = re.search(r"```yaml\s*\n(.*?)\n```", body, re.DOTALL) + if not match: + raise ValueError("No YAML block found in issue body.") + return yaml.safe_load(match.group(1)) + + +if label == "new-material": + entry = extract_yaml_block(issue_body) + + # Assign a new numeric ID + numeric_ids = [e["id"] for e in data if isinstance(e.get("id"), int)] + entry["id"] = max(numeric_ids, default=0) + 1 + + data.append(entry) + print(f"Added new entry with ID {entry['id']}: {entry.get('course_name')}") + +elif label == "edit-material": + entry = extract_yaml_block(issue_body) + entry_id = entry.get("id") + + replaced = False + for i, e in enumerate(data): + if str(e.get("id")) == str(entry_id): + data[i] = entry + replaced = True + break + + if not replaced: + raise ValueError(f"Entry with ID '{entry_id}' not found in data.") + print(f"Updated entry ID {entry_id}: {entry.get('course_name')}") + +elif label == "delete-material": + # Extract ID from issue title: "Delete material: Name (ID: 123)" + match = re.search(r"ID:\s*(\S+?)\)", issue_title) + if not match: + raise ValueError(f"Could not extract ID from issue title: {issue_title!r}") + + raw_id = match.group(1) + try: + entry_id = int(raw_id) + except ValueError: + entry_id = raw_id + + original_len = len(data) + data = [e for e in data if str(e.get("id")) != str(entry_id)] + + if len(data) == original_len: + raise ValueError(f"Entry with ID '{entry_id}' not found in data.") + print(f"Deleted entry with ID {entry_id}") + +else: + raise ValueError(f"Unknown label: {label!r}") + +# Write updated YAML +with open(YAML_PATH, "w", encoding="utf-8") as f: + yaml.dump(data, f, sort_keys=False, default_flow_style=False, allow_unicode=True) + +# Write updated JSON +with open(JSON_PATH, "w", encoding="utf-8") as f: + json.dump(data, f, indent=2, ensure_ascii=False) + +print(f"Successfully processed '{label}' for issue #{issue_number}.") diff --git a/.github/workflows/create-pr-from-issue.yml b/.github/workflows/create-pr-from-issue.yml new file mode 100644 index 0000000..09298b3 --- /dev/null +++ b/.github/workflows/create-pr-from-issue.yml @@ -0,0 +1,66 @@ +name: Create PR from Issue + +on: + issues: + types: [labeled] + +jobs: + create-pr: + runs-on: ubuntu-latest + if: contains(fromJSON('["new-material", "edit-material", "delete-material"]'), github.event.label.name) + + permissions: + contents: write + pull-requests: write + + steps: + - name: Checkout + uses: actions/checkout@v4 + + - name: Set up Python + uses: actions/setup-python@v5 + with: + python-version: '3.11' + + - name: Install dependencies + run: pip install pyyaml + + - name: Write issue data to files + env: + ISSUE_BODY: ${{ github.event.issue.body }} + ISSUE_TITLE: ${{ github.event.issue.title }} + run: | + printf '%s' "$ISSUE_BODY" > /tmp/issue_body.txt + printf '%s' "$ISSUE_TITLE" > /tmp/issue_title.txt + + - name: Process issue and update files + env: + ISSUE_LABEL: ${{ github.event.label.name }} + ISSUE_NUMBER: ${{ github.event.issue.number }} + run: python .github/scripts/process_issue.py + + - name: Create branch and open PR + env: + GH_TOKEN: ${{ secrets.GITHUB_TOKEN }} + ISSUE_NUMBER: ${{ github.event.issue.number }} + ISSUE_LABEL: ${{ github.event.label.name }} + ISSUE_TITLE: ${{ github.event.issue.title }} + run: | + BRANCH="auto/${ISSUE_LABEL}-issue-${ISSUE_NUMBER}" + git config user.name "github-actions[bot]" + git config user.email "github-actions[bot]@users.noreply.github.com" + git checkout -b "$BRANCH" + git add model/reproinventory_data.yaml frontend/public/data/reproinventory_data.json + if git diff --cached --quiet; then + echo "No changes detected — nothing to commit." + exit 1 + fi + git commit -m "${ISSUE_TITLE}" + git push origin "$BRANCH" + gh pr create \ + --title "${ISSUE_TITLE}" \ + --body "Closes #${ISSUE_NUMBER} + +Automatically generated from issue #${ISSUE_NUMBER}." \ + --base main \ + --head "$BRANCH" diff --git a/frontend/dist/assets/index-COgKbmi3.js b/frontend/dist/assets/index-BN5M8IzP.js similarity index 90% rename from frontend/dist/assets/index-COgKbmi3.js rename to frontend/dist/assets/index-BN5M8IzP.js index 93f1fc4..e2a81e2 100644 --- a/frontend/dist/assets/index-COgKbmi3.js +++ b/frontend/dist/assets/index-BN5M8IzP.js @@ -187,13 +187,13 @@ Please update entry **ID: ${a.id}** in \`model/reproinventory_data.yaml\` with t \`\`\`yaml ${r} -\`\`\``,f=`${FE}/issues/new?title=${encodeURIComponent(s)}&body=${encodeURIComponent(c)}`;window.open(f,"_blank")}const JE=["Beginner","Intermediate","Advanced","NA"],WE=["Mac","Windows","Linux","Docker","Jupyter","NA"],eA=["<1 hr","1-4 hrs","1 day","1-3 days","1 week","1+ weeks","NA"],tA=["Hands-on tutorial / notebooks","lecture","video","notes","blog post","reference","slides","website","outline","meta-resource","NA"],nA=["self-paced","instructor","Hybrid","Discussion needed"],lA=["English","French","Spanish","Chinese","German","English, French","English, German","Other","NA"],aA=["Python","R","shell scripting","Matlab","Git","NA"],iA=["AFNI","SPM","FSL","Freesurfer","Python","Multiple","NA"],rA=["DWI","Structural","Functional","Task-based","Resting-State","EEG","Behavioral","MEG","MRI","NA"],cA=["True","False","NA"],sA=["information-oriented (reference)","understanding-oriented (explanation)","learning-oriented (tutorials)","problem-oriented (how to guides)","NA"],oA=({material:a,onClose:r})=>{const[s,c]=S.useState(a);S.useEffect(()=>{c(a)},[a]);const f=(g,b)=>{c(w=>({...w,[g]:b}))},d=(g,b,w)=>{const _=s[g]||[],M=w?[..._,b]:_.filter(N=>N!==b);f(g,M)},v=(g,b,w)=>{const M=[...s[g]||[]];M[b]=w,f(g,M)},p=g=>{const b=s[g]||[];f(g,[...b,""])},x=(g,b)=>{const _=(s[g]||[]).filter((M,N)=>N!==b);f(g,_)},m=()=>{IE(s),r()};return u.jsxs(Qc,{className:"sm:max-w-[800px] overflow-y-auto max-h-[90vh]",children:[u.jsxs(Zc,{children:[u.jsxs(Kc,{children:["Edit ",s.course_name||"Material"]}),u.jsx($c,{children:"Update the details of this training material."})]}),u.jsxs("div",{className:"grid gap-4 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u.jsx(AA,{})}b0.createRoot(document.getElementById("root")).render(u.jsx(S.StrictMode,{children:u.jsx(CA,{})})); +Please remove entry **ID: ${Q.id}** ("${Q.course_name}") from \`model/reproinventory_data.yaml\`.`,ot=`https://github.com/likeajumprope/ReproInventory/issues/new?labels=delete-material&title=${encodeURIComponent(ht)}&body=${encodeURIComponent(dn)}`;window.open(ot,"_blank")},children:"Delete"})]})]})]},Q.id)})}),Pt.length===0&&u.jsxs("div",{className:"text-center py-12",children:[u.jsx("div",{className:"mx-auto w-24 h-24 bg-muted rounded-full flex items-center justify-center mb-4",children:u.jsx(jg,{className:"w-8 h-8 text-muted-foreground"})}),u.jsx("h3",{className:"text-lg font-semibold mb-2",children:"No materials found"}),u.jsx("p",{className:"text-muted-foreground mb-4",children:"Try adjusting your search criteria or clearing some filters"}),u.jsx(nt,{onClick:at,children:"Clear All Filters"})]})]})]})]})]}),u.jsx($0,{})]})}function CA(){return u.jsx(AA,{})}b0.createRoot(document.getElementById("root")).render(u.jsx(S.StrictMode,{children:u.jsx(CA,{})})); diff --git a/frontend/dist/index.html b/frontend/dist/index.html index b71ab89..e310748 100644 --- a/frontend/dist/index.html +++ b/frontend/dist/index.html @@ -4,7 +4,7 @@ ReproInventory - + diff --git a/frontend/src/components/AddMaterialDialog.tsx b/frontend/src/components/AddMaterialDialog.tsx index 1befdd7..d3a8ec8 100644 --- a/frontend/src/components/AddMaterialDialog.tsx +++ b/frontend/src/components/AddMaterialDialog.tsx @@ -79,7 +79,7 @@ function openGitHubIssue(material: ReproInventoryEntry) { `## New Training Material Submission\n\n` + `Please review the following training material for addition to ReproInventory.\n\n` + `\`\`\`yaml\n${yaml}\n\`\`\``; - const url = `${GITHUB_REPO}/issues/new?title=${encodeURIComponent(title)}&body=${encodeURIComponent(body)}`; + const url = `${GITHUB_REPO}/issues/new?labels=new-material&title=${encodeURIComponent(title)}&body=${encodeURIComponent(body)}`; window.open(url, "_blank"); } diff --git a/frontend/src/components/EditMaterialDialog.tsx b/frontend/src/components/EditMaterialDialog.tsx index bde32f5..0d62879 100644 --- a/frontend/src/components/EditMaterialDialog.tsx +++ b/frontend/src/components/EditMaterialDialog.tsx @@ -75,7 +75,7 @@ function openGitHubIssue(material: ReproInventoryEntry) { `## Edit Training Material Request\n\n` + `Please update entry **ID: ${material.id}** in \`model/reproinventory_data.yaml\` with the following:\n\n` + `\`\`\`yaml\n${yaml}\n\`\`\``; - const url = `${GITHUB_REPO}/issues/new?title=${encodeURIComponent(title)}&body=${encodeURIComponent(body)}`; + const url = `${GITHUB_REPO}/issues/new?labels=edit-material&title=${encodeURIComponent(title)}&body=${encodeURIComponent(body)}`; window.open(url, "_blank"); } diff --git a/frontend/src/training-materials-browser.tsx b/frontend/src/training-materials-browser.tsx index dce90fd..25e6060 100644 --- a/frontend/src/training-materials-browser.tsx +++ b/frontend/src/training-materials-browser.tsx @@ -716,7 +716,7 @@ export default function TrainingMaterialsBrowser() { const body = `## Delete Training Material Request\n\n` + `Please remove entry **ID: ${material.id}** ("${material.course_name}") from \`model/reproinventory_data.yaml\`.`; - const url = `https://github.com/likeajumprope/ReproInventory/issues/new?title=${encodeURIComponent(title)}&body=${encodeURIComponent(body)}`; + const url = `https://github.com/likeajumprope/ReproInventory/issues/new?labels=delete-material&title=${encodeURIComponent(title)}&body=${encodeURIComponent(body)}`; window.open(url, "_blank"); }} > From 1e83b6df74044871979bcfb408d084b9d14b6828 Mon Sep 17 00:00:00 2001 From: Johanna Bayer Date: Wed, 25 Mar 2026 10:45:31 -0400 Subject: [PATCH 04/14] create-pr-from-issue.yml update --- .github/workflows/create-pr-from-issue.yml | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/.github/workflows/create-pr-from-issue.yml b/.github/workflows/create-pr-from-issue.yml index 09298b3..076c030 100644 --- a/.github/workflows/create-pr-from-issue.yml +++ b/.github/workflows/create-pr-from-issue.yml @@ -57,10 +57,11 @@ jobs: fi git commit -m "${ISSUE_TITLE}" git push origin "$BRANCH" + PR_BODY="Closes #${ISSUE_NUMBER} + +Automatically generated from issue #${ISSUE_NUMBER}." gh pr create \ --title "${ISSUE_TITLE}" \ - --body "Closes #${ISSUE_NUMBER} - -Automatically generated from issue #${ISSUE_NUMBER}." \ + --body "$PR_BODY" \ --base main \ --head "$BRANCH" From 24845e688b9bf5b5da96c0e533582a1889f1717f Mon Sep 17 00:00:00 2001 From: Johanna Bayer Date: Wed, 25 Mar 2026 10:47:41 -0400 Subject: [PATCH 05/14] update --- .github/workflows/create-pr-from-issue.yml | 2 -- 1 file changed, 2 deletions(-) diff --git a/.github/workflows/create-pr-from-issue.yml b/.github/workflows/create-pr-from-issue.yml index 076c030..f327012 100644 --- a/.github/workflows/create-pr-from-issue.yml +++ b/.github/workflows/create-pr-from-issue.yml @@ -58,8 +58,6 @@ jobs: git commit -m "${ISSUE_TITLE}" git push origin "$BRANCH" PR_BODY="Closes #${ISSUE_NUMBER} - -Automatically generated from issue #${ISSUE_NUMBER}." gh pr create \ --title "${ISSUE_TITLE}" \ --body "$PR_BODY" \ From 6a8252c318b5efcb65b1a7569a3db5198c5c2afa Mon Sep 17 00:00:00 2001 From: Johanna Bayer Date: Wed, 25 Mar 2026 10:53:46 -0400 Subject: [PATCH 06/14] update --- .github/workflows/create-pr-from-issue.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/create-pr-from-issue.yml b/.github/workflows/create-pr-from-issue.yml index f327012..a2e7451 100644 --- a/.github/workflows/create-pr-from-issue.yml +++ b/.github/workflows/create-pr-from-issue.yml @@ -57,9 +57,9 @@ jobs: fi git commit -m "${ISSUE_TITLE}" git push origin "$BRANCH" - PR_BODY="Closes #${ISSUE_NUMBER} + PR_BODY=$(printf "Closes #%s\n\nAutomatically generated from issue #%s." "${ISSUE_NUMBER}" "${ISSUE_NUMBER}") gh pr create \ --title "${ISSUE_TITLE}" \ - --body "$PR_BODY" \ + --body "${PR_BODY}" \ --base main \ - --head "$BRANCH" + --head "${BRANCH}" From 39d29c8968fcc4d8e74948c1fd26e9d60e318a97 Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" Date: Wed, 25 Mar 2026 14:56:30 +0000 Subject: [PATCH 07/14] Add material: test course --- frontend/public/data/reproinventory_data.json | 34 +++++++++++-------- model/reproinventory_data.yaml | 6 ++-- 2 files changed, 23 insertions(+), 17 deletions(-) diff --git a/frontend/public/data/reproinventory_data.json b/frontend/public/data/reproinventory_data.json index 699bb27..f204d4d 100644 --- a/frontend/public/data/reproinventory_data.json +++ b/frontend/public/data/reproinventory_data.json @@ -1502,7 +1502,7 @@ "SS", "JB" ], - "course_name": "The Princeton Handbook for Reproducible Neuroimaging\u00b6", + "course_name": "The Princeton Handbook for Reproducible Neuroimaging¶", "url": "https://brainhack-princeton.github.io/handbook/", "level": [ "Beginner" @@ -1601,7 +1601,7 @@ ] }, { - "id": 51, + "id": 50, "tag_team": [ "CF", "SS", @@ -2027,10 +2027,10 @@ "JB" ], "course_name": "ABCD Repronim ML course", - "url": null, - "level": null, + "url": "https://www.abcd-repronim.org/ml.html", + "level": "intermediate", "platform": null, - "keywords": null, + "keywords": "Machine Learning", "course_length": "NA", "instruction_medium": null, "delivery": null, @@ -2039,18 +2039,18 @@ "neuroimaging_software": null, "imaging_modality": null, "open_dataset": "NA", - "last_updated": null, + "last_updated": 2025, "functionality": null, - "assessment": null, + "assessment": true, "prerequisite": null, "source": null, - "review": null, + "review": "3 week machone learning course", "alias_links": null, "notes": null, "quadrants": null }, { - "id": null, + "id": 61, "tag_team": [ "JB" ], @@ -2058,23 +2058,27 @@ "url": "https://sina-mansour.github.io/ohbm2025-reproducible-research/intro.html", "level": null, "platform": null, - "keywords": null, - "course_length": "NA", + "keywords": "Reproducible Pipelines, Best Practices, Data Visualization", + "course_length": null, "instruction_medium": null, "delivery": null, "language": "English", - "programming_language": null, + "programming_language": "Python", "neuroimaging_software": null, "imaging_modality": null, "open_dataset": "NA", - "last_updated": null, + "last_updated": 2025, "functionality": null, "assessment": null, "prerequisite": null, "source": null, - "review": null, + "review": "Comprehensive website describing the necessity of reproducible research and how to achieve it (notebooks, visualisation)", "alias_links": null, "notes": null, "quadrants": null + }, + { + "id": 62, + "course_name": "test course" } -] +] \ No newline at end of file diff --git a/model/reproinventory_data.yaml b/model/reproinventory_data.yaml index 70cd334..2b3c83b 100644 --- a/model/reproinventory_data.yaml +++ b/model/reproinventory_data.yaml @@ -1152,7 +1152,7 @@ - CF - SS - JB - course_name: "The Princeton Handbook for Reproducible Neuroimaging\xB6" + course_name: The Princeton Handbook for Reproducible Neuroimaging¶ url: https://brainhack-princeton.github.io/handbook/ level: - Beginner @@ -1602,7 +1602,7 @@ level: null platform: null keywords: Reproducible Pipelines, Best Practices, Data Visualization - course_length: + course_length: null instruction_medium: null delivery: null language: English @@ -1620,3 +1620,5 @@ alias_links: null notes: null quadrants: null +- id: 62 + course_name: test course From 194e7b6f146b440a4e6ea7f12e4bf87971d20d35 Mon Sep 17 00:00:00 2001 From: Johanna Bayer Date: Wed, 25 Mar 2026 11:11:59 -0400 Subject: [PATCH 08/14] add normalizing step before recreating the json --- .github/scripts/process_issue.py | 20 +++++++++++--- frontend/public/data/reproinventory_data.json | 26 ++++++++++++------- model/reproinventory_data.yaml | 19 +++++++++----- 3 files changed, 46 insertions(+), 19 deletions(-) diff --git a/.github/scripts/process_issue.py b/.github/scripts/process_issue.py index 0f4af66..c44f832 100644 --- a/.github/scripts/process_issue.py +++ b/.github/scripts/process_issue.py @@ -19,6 +19,20 @@ YAML_PATH = "model/reproinventory_data.yaml" JSON_PATH = "frontend/public/data/reproinventory_data.json" +ARRAY_FIELDS = [ + "tag_team", "level", "platform", "keywords", "instruction_medium", + "delivery", "language", "programming_language", "neuroimaging_software", + "imaging_modality", "quadrants", "source", +] + +def normalize_entry(entry): + """Ensure all array fields are lists, not scalars.""" + for field in ARRAY_FIELDS: + val = entry.get(field) + if val is not None and not isinstance(val, list): + entry[field] = [val] + return entry + label = os.environ["ISSUE_LABEL"] issue_number = os.environ["ISSUE_NUMBER"] @@ -30,7 +44,7 @@ # Load current data with open(YAML_PATH, "r", encoding="utf-8") as f: - data = yaml.safe_load(f) or [] + data = [normalize_entry(e) for e in (yaml.safe_load(f) or [])] def extract_yaml_block(body): @@ -42,7 +56,7 @@ def extract_yaml_block(body): if label == "new-material": - entry = extract_yaml_block(issue_body) + entry = normalize_entry(extract_yaml_block(issue_body)) # Assign a new numeric ID numeric_ids = [e["id"] for e in data if isinstance(e.get("id"), int)] @@ -52,7 +66,7 @@ def extract_yaml_block(body): print(f"Added new entry with ID {entry['id']}: {entry.get('course_name')}") elif label == "edit-material": - entry = extract_yaml_block(issue_body) + entry = normalize_entry(extract_yaml_block(issue_body)) entry_id = entry.get("id") replaced = False diff --git a/frontend/public/data/reproinventory_data.json b/frontend/public/data/reproinventory_data.json index f204d4d..939a633 100644 --- a/frontend/public/data/reproinventory_data.json +++ b/frontend/public/data/reproinventory_data.json @@ -2028,9 +2028,13 @@ ], "course_name": "ABCD Repronim ML course", "url": "https://www.abcd-repronim.org/ml.html", - "level": "intermediate", + "level": [ + "Intermediate" + ], "platform": null, - "keywords": "Machine Learning", + "keywords": [ + "Machine Learning" + ], "course_length": "NA", "instruction_medium": null, "delivery": null, @@ -2058,12 +2062,20 @@ "url": "https://sina-mansour.github.io/ohbm2025-reproducible-research/intro.html", "level": null, "platform": null, - "keywords": "Reproducible Pipelines, Best Practices, Data Visualization", + "keywords": [ + "Reproducible Pipelines", + "Best Practices", + "Data Visualization" + ], "course_length": null, "instruction_medium": null, "delivery": null, - "language": "English", - "programming_language": "Python", + "language": [ + "English" + ], + "programming_language": [ + "Python" + ], "neuroimaging_software": null, "imaging_modality": null, "open_dataset": "NA", @@ -2076,9 +2088,5 @@ "alias_links": null, "notes": null, "quadrants": null - }, - { - "id": 62, - "course_name": "test course" } ] \ No newline at end of file diff --git a/model/reproinventory_data.yaml b/model/reproinventory_data.yaml index 2b3c83b..10423a8 100644 --- a/model/reproinventory_data.yaml +++ b/model/reproinventory_data.yaml @@ -1574,9 +1574,11 @@ - JB course_name: ABCD Repronim ML course url: https://www.abcd-repronim.org/ml.html - level: intermediate + level: + - Intermediate platform: null - keywords: Machine Learning + keywords: + - Machine Learning course_length: NA instruction_medium: null delivery: null @@ -1601,12 +1603,17 @@ url: https://sina-mansour.github.io/ohbm2025-reproducible-research/intro.html level: null platform: null - keywords: Reproducible Pipelines, Best Practices, Data Visualization + keywords: + - Reproducible Pipelines + - Best Practices + - Data Visualization course_length: null instruction_medium: null delivery: null - language: English - programming_language: Python + language: + - English + programming_language: + - Python neuroimaging_software: null imaging_modality: null open_dataset: NA @@ -1620,5 +1627,3 @@ alias_links: null notes: null quadrants: null -- id: 62 - course_name: test course From 54e93766d537e24c9f972479008c64a70051127c Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" Date: Wed, 25 Mar 2026 15:12:35 +0000 Subject: [PATCH 09/14] Add material: test course --- frontend/public/data/reproinventory_data.json | 16 ++++++++++++++++ model/reproinventory_data.yaml | 10 ++++++++++ 2 files changed, 26 insertions(+) diff --git a/frontend/public/data/reproinventory_data.json b/frontend/public/data/reproinventory_data.json index 939a633..3803ac5 100644 --- a/frontend/public/data/reproinventory_data.json +++ b/frontend/public/data/reproinventory_data.json @@ -2088,5 +2088,21 @@ "alias_links": null, "notes": null, "quadrants": null + }, + { + "id": 62, + "course_name": "test course", + "platform": [ + "Mac" + ], + "instruction_medium": [ + "blog post" + ], + "delivery": [ + "instructor" + ], + "imaging_modality": [ + "Behavioral" + ] } ] \ No newline at end of file diff --git a/model/reproinventory_data.yaml b/model/reproinventory_data.yaml index 10423a8..122cfcc 100644 --- a/model/reproinventory_data.yaml +++ b/model/reproinventory_data.yaml @@ -1627,3 +1627,13 @@ alias_links: null notes: null quadrants: null +- id: 62 + course_name: test course + platform: + - Mac + instruction_medium: + - blog post + delivery: + - instructor + imaging_modality: + - Behavioral From 477f0caa94fe8699cab8ec0495bfc0d61d5784f1 Mon Sep 17 00:00:00 2001 From: Johanna Bayer Date: Wed, 25 Mar 2026 11:31:59 -0400 Subject: [PATCH 10/14] changes for edit --- .../src/components/EditMaterialDialog.tsx | 21 +++++++++++++++++-- 1 file changed, 19 insertions(+), 2 deletions(-) diff --git a/frontend/src/components/EditMaterialDialog.tsx b/frontend/src/components/EditMaterialDialog.tsx index 0d62879..8f31795 100644 --- a/frontend/src/components/EditMaterialDialog.tsx +++ b/frontend/src/components/EditMaterialDialog.tsx @@ -96,11 +96,28 @@ const imagingModalityOptions: ImagingModalityEnum[] = ["DWI", "Structural", "Fun const openDatasetOptions: OpenDatasetEnum[] = ["True", "False", "NA"]; const quadrantsOptions: QuadrantsEnum[] = ["information-oriented (reference)", "understanding-oriented (explanation)", "learning-oriented (tutorials)", "problem-oriented (how to guides)", "NA"]; +const ARRAY_FIELDS: (keyof ReproInventoryEntry)[] = [ + "tag_team", "level", "platform", "keywords", "instruction_medium", + "delivery", "language", "programming_language", "neuroimaging_software", + "imaging_modality", "quadrants", "source", "prerequisite", +]; + +function normalizeMaterial(m: ReproInventoryEntry): ReproInventoryEntry { + const normalized = { ...m }; + for (const field of ARRAY_FIELDS) { + const val = normalized[field]; + if (val !== null && val !== undefined && !Array.isArray(val)) { + (normalized as any)[field] = [val]; + } + } + return normalized; +} + const EditMaterialDialog: React.FC = ({ material, onClose }) => { - const [editedMaterial, setEditedMaterial] = useState(material); + const [editedMaterial, setEditedMaterial] = useState(() => normalizeMaterial(material)); useEffect(() => { - setEditedMaterial(material); + setEditedMaterial(normalizeMaterial(material)); }, [material]); const handleChange = (field: keyof ReproInventoryEntry, value: any) => { From 1c8f170844e3dd79559be4b1a048e7066606f031 Mon Sep 17 00:00:00 2001 From: Johanna Bayer Date: Wed, 25 Mar 2026 11:42:38 -0400 Subject: [PATCH 11/14] update layout and edit --- frontend/src/training-materials-browser.tsx | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/frontend/src/training-materials-browser.tsx b/frontend/src/training-materials-browser.tsx index 25e6060..842c3b9 100644 --- a/frontend/src/training-materials-browser.tsx +++ b/frontend/src/training-materials-browser.tsx @@ -604,17 +604,17 @@ export default function TrainingMaterialsBrowser() { {filteredMaterials.map((material) => ( -
+
{getFormatIcon(material.instruction_medium?.[0] || "")} {material.instruction_medium?.[0] || "N/A"}
- {material.assessment && Assessment} + {material.assessment && Assessment}
- {material.course_name} - {material.review} + {material.course_name} + {material.review}
@@ -659,8 +659,8 @@ export default function TrainingMaterialsBrowser() {
{material.url && ( - - Access Material + + Access Material )}
From d1252a3277b583a1c9fa665de00a3894b99cef7f Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" Date: Wed, 25 Mar 2026 15:49:24 +0000 Subject: [PATCH 12/14] Edit material: Andy's brain book (ID: 58) --- frontend/public/data/reproinventory_data.json | 23 ++++--------------- model/reproinventory_data.yaml | 22 ++++-------------- 2 files changed, 9 insertions(+), 36 deletions(-) diff --git a/frontend/public/data/reproinventory_data.json b/frontend/public/data/reproinventory_data.json index 3803ac5..8544292 100644 --- a/frontend/public/data/reproinventory_data.json +++ b/frontend/public/data/reproinventory_data.json @@ -1972,26 +1972,13 @@ ], "course_name": "Andy's brain book", "url": "https://andysbrainbook.readthedocs.io/en/latest/", - "level": null, - "platform": null, - "keywords": null, "course_length": "NA", - "instruction_medium": null, - "delivery": null, - "language": null, - "programming_language": null, - "neuroimaging_software": null, - "imaging_modality": null, + "instruction_medium": [ + "blog post", + "Hands-on tutorial / notebooks" + ], "open_dataset": "NA", - "last_updated": null, - "functionality": null, - "assessment": null, - "prerequisite": null, - "source": null, - "review": null, - "alias_links": null, - "notes": null, - "quadrants": null + "last_updated": 2026 }, { "id": 59, diff --git a/model/reproinventory_data.yaml b/model/reproinventory_data.yaml index 122cfcc..86b7b96 100644 --- a/model/reproinventory_data.yaml +++ b/model/reproinventory_data.yaml @@ -1524,26 +1524,12 @@ - JB course_name: Andy's brain book url: https://andysbrainbook.readthedocs.io/en/latest/ - level: null - platform: null - keywords: null course_length: NA - instruction_medium: null - delivery: null - language: null - programming_language: null - neuroimaging_software: null - imaging_modality: null + instruction_medium: + - blog post + - Hands-on tutorial / notebooks open_dataset: NA - last_updated: null - functionality: null - assessment: null - prerequisite: null - source: null - review: null - alias_links: null - notes: null - quadrants: null + last_updated: 2026 - id: 59 tag_team: - JB From 45c9a1c644cc0bbd8c9f445ff437f1c7f717beb5 Mon Sep 17 00:00:00 2001 From: Johanna Bayer Date: Wed, 1 Apr 2026 10:24:51 -0400 Subject: [PATCH 13/14] change constant links to point to the upstream repository --- frontend/src/components/AddMaterialDialog.tsx | 2 +- frontend/src/components/EditMaterialDialog.tsx | 2 +- frontend/src/training-materials-browser.tsx | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/frontend/src/components/AddMaterialDialog.tsx b/frontend/src/components/AddMaterialDialog.tsx index d3a8ec8..1e252ff 100644 --- a/frontend/src/components/AddMaterialDialog.tsx +++ b/frontend/src/components/AddMaterialDialog.tsx @@ -21,7 +21,7 @@ import type { QuadrantsEnum, } from "@/types/reproinventory"; -const GITHUB_REPO = "https://github.com/likeajumprope/ReproInventory"; +const GITHUB_REPO = "https://github.com/ReproNim/ReproInventory"; const levelOptions: LevelEnum[] = ["Beginner", "Intermediate", "Advanced", "NA"]; const platformOptions: PlatformEnum[] = ["Mac", "Windows", "Linux", "Docker", "Jupyter", "NA"]; diff --git a/frontend/src/components/EditMaterialDialog.tsx b/frontend/src/components/EditMaterialDialog.tsx index 8f31795..c0a5f54 100644 --- a/frontend/src/components/EditMaterialDialog.tsx +++ b/frontend/src/components/EditMaterialDialog.tsx @@ -21,7 +21,7 @@ import type { QuadrantsEnum, } from "@/types/reproinventory"; -const GITHUB_REPO = "https://github.com/likeajumprope/ReproInventory"; +const GITHUB_REPO = "https://github.com/ReproNim/ReproInventory"; function formatAsYaml(material: ReproInventoryEntry): string { const lines: string[] = []; diff --git a/frontend/src/training-materials-browser.tsx b/frontend/src/training-materials-browser.tsx index 842c3b9..fba7826 100644 --- a/frontend/src/training-materials-browser.tsx +++ b/frontend/src/training-materials-browser.tsx @@ -716,7 +716,7 @@ export default function TrainingMaterialsBrowser() { const body = `## Delete Training Material Request\n\n` + `Please remove entry **ID: ${material.id}** ("${material.course_name}") from \`model/reproinventory_data.yaml\`.`; - const url = `https://github.com/likeajumprope/ReproInventory/issues/new?labels=delete-material&title=${encodeURIComponent(title)}&body=${encodeURIComponent(body)}`; + const url = `https://github.com/ReproNim/ReproInventory/issues/new?labels=delete-material&title=${encodeURIComponent(title)}&body=${encodeURIComponent(body)}`; window.open(url, "_blank"); }} > From d5c41e7f63e92c9e297e9cfb230ecd2b91438022 Mon Sep 17 00:00:00 2001 From: Johanna Bayer Date: Wed, 1 Apr 2026 10:45:38 -0400 Subject: [PATCH 14/14] Update .github/scripts/process_issue.py Co-authored-by: gemini-code-assist[bot] <176961590+gemini-code-assist[bot]@users.noreply.github.com> --- .github/scripts/process_issue.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/scripts/process_issue.py b/.github/scripts/process_issue.py index c44f832..0328e04 100644 --- a/.github/scripts/process_issue.py +++ b/.github/scripts/process_issue.py @@ -22,7 +22,7 @@ ARRAY_FIELDS = [ "tag_team", "level", "platform", "keywords", "instruction_medium", "delivery", "language", "programming_language", "neuroimaging_software", - "imaging_modality", "quadrants", "source", + "imaging_modality", "quadrants", "source", "prerequisite", ] def normalize_entry(entry):