From f7da9e16cb8aa5b4a0666b07c3fc7eaa3272a87b Mon Sep 17 00:00:00 2001
From: Bilal Mahmoud <bmahmoud@mpi-cbg.de>
Date: Wed, 11 Dec 2024 15:32:24 +0100
Subject: [PATCH 1/5] feat: replace lockfile-lint

---
 .github/workflows/lint.yml |  13 -----
 package.json               |  21 ++------
 yarn.config.cjs            | 107 ++++++++++++++++++++++++++++---------
 3 files changed, 84 insertions(+), 57 deletions(-)

diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
index 138029c4bb0..2b8585aa04e 100644
--- a/.github/workflows/lint.yml
+++ b/.github/workflows/lint.yml
@@ -228,19 +228,6 @@ jobs:
             exit 1
           fi
 
-      - name: Run yarn lint:lockfile-lint
-        if: ${{ success() || failure() }}
-        run: |
-          if ! yarn lint:lockfile-lint; then
-            echo ''
-            echo ''
-            echo 'ℹ️ ℹ️ ℹ️'
-            echo 'Try resetting yarn.lock to its previous state and then run `yarn install`.'
-            echo 'If your `~/.npmrc` mentions a custom registry, you should remove this setting first.'
-            echo 'ℹ️ ℹ️ ℹ️'
-            exit 1
-          fi
-
       - name: Run yarn lint:license-in-workspaces
         if: ${{ success() || failure() }}
         env:
diff --git a/package.json b/package.json
index 55c46c78361..c0dd9b993f0 100644
--- a/package.json
+++ b/package.json
@@ -47,7 +47,6 @@
     "lint:constraints": "yarn constraints",
     "lint:eslint": "turbo --continue lint:eslint --",
     "lint:license-in-workspaces": "yarn workspace @local/repo-chores exe scripts/check-license-in-workspaces.ts",
-    "lint:lockfile-lint": "lockfile-lint --path yarn.lock --type yarn --allowed-hosts npm yarn",
     "lint:markdownlint": "markdownlint --dot .",
     "lint:prettier": "prettier --check --ignore-unknown .",
     "lint:taplo": "taplo fmt --check",
@@ -56,7 +55,7 @@
     "postinstall": "turbo run postinstall",
     "seed-data:opensearch": "yarn workspace @apps/hash-search-loader clear-opensearch",
     "seed-data:redis": "yarn workspace @apps/hash-realtime clear-redis",
-    "seed-data": "concurrently \"yarn:seed-data:*\"",
+    "seed-data": "npm-run-all --parallel \"seed-data:*\"",
     "test": "npm-run-all --continue-on-error \"test:*\"",
     "test:unit": "turbo run test:unit --env-mode=loose --",
     "test:integration": "turbo run test:integration --env-mode=loose --",
@@ -68,19 +67,9 @@
   },
   "prettier": {
     "plugins": [
-      "prettier-plugin-packagejson",
-      "prettier-plugin-sh"
+      "prettier-plugin-packagejson"
     ],
-    "trailingComma": "all",
-    "overrides": [
-      {
-        "files": "*.sql",
-        "options": {
-          "keywordCase": "upper",
-          "language": "postgresql"
-        }
-      }
-    ]
+    "trailingComma": "all"
   },
   "resolutions": {
     "@artilleryio/int-commons@npm:2.11.0": "patch:@artilleryio/int-commons@npm%3A2.11.0#~/.yarn/patches/@artilleryio-int-commons-npm-2.11.0-5b69c05121.patch",
@@ -116,15 +105,11 @@
     "@sentry/cli": "^2.39.1",
     "@taplo/cli": "0.7.0",
     "@yarnpkg/types": "^4.0.0",
-    "concurrently": "7.6.0",
     "lefthook": "1.9.2",
-    "lockfile-lint": "4.14.0",
     "markdownlint-cli": "0.43.0",
     "npm-run-all2": "7.0.1",
     "prettier": "3.4.2",
     "prettier-plugin-packagejson": "2.5.6",
-    "prettier-plugin-sh": "0.14.0",
-    "suppress-exit-code": "3.2.0",
     "turbo": "2.3.3"
   },
   "packageManager": "yarn@4.5.3+sha512.3003a14012e2987072d244c720506549c1aab73ee728208f1b2580a9fd67b92d61ba6b08fe93f6dce68fd771e3af1e59a0afa28dd242dd0940d73b95fedd4e90"
diff --git a/yarn.config.cjs b/yarn.config.cjs
index 0f921e4553c..513ecbec26f 100644
--- a/yarn.config.cjs
+++ b/yarn.config.cjs
@@ -22,6 +22,8 @@ const ignoredWorkspaces = [
   "@blocks/person",
 ];
 
+const allowedGitDependencies = [];
+
 /**
  *
  * @param {Dependency} dependency
@@ -72,40 +74,94 @@ function enforceNoDualTypeDependencies({ Yarn }) {
 }
 
 /**
- * Enforces the use of the `workspace:` protocol for all workspace dependencies.
- *
- * This rule ensures that all dependencies that are part of the workspace are
- * declared using the `workspace:` protocol.
+ * Enforce that the package protocols are correct.
  *
- * @param {Context} context - The Yarn constraint context.
+ * @param {Context} context
  */
-function enforceWorkspaceDependenciesDeclaredAsSuch({ Yarn }) {
+function enforceProtocols({ Yarn }) {
   const workspaces = Yarn.workspaces();
 
   for (const dependency of Yarn.dependencies()) {
-    if (
-      workspaces.some(
-        (workspace) =>
-          workspace.ident === dependency.ident &&
-          workspace.pkg.version === dependency.range,
-      )
-    ) {
-      dependency.update("workspace:^");
+    if (shouldIgnoreDependency(dependency)) {
+      continue;
+    }
+
+    const workspaceDependency = workspaces.find(
+      (workspace) => workspace.ident === dependency.ident,
+    );
+
+    if (workspaceDependency) {
+      // turbo doesn't support the `workspace:` protocol when rewriting lockfiles, leading to inconsistent lockfiles
+      dependency.update(workspaceDependency.pkg.version);
     }
-  }
-}
 
-/**
- * This rule prohibits the use of the 'file:' protocol in dependency ranges
- * and replaces it with the 'portal:' protocol.
- *
- * @param {Context} context - The Yarn constraint context.
- */
-function enforcePortalProtocolInsteadOfFileProtocol({ Yarn }) {
-  for (const dependency of Yarn.dependencies()) {
     if (dependency.range.startsWith("file:")) {
+      // the file: protocol makes problems when used in conjunction with pnpm mode, portal is the equivalent protocol
       dependency.update(dependency.range.replace("file:", "portal:"));
     }
+
+    if (dependency.range.startsWith("link:")) {
+      dependency.error(
+        `The link protocol allows for non-packages to be linked and is not allowed, dependency: ${dependency.ident}`,
+      );
+    }
+
+    if (dependency.range.startsWith("exec:")) {
+      dependency.error(
+        `The exec protocol allows for arbitrary code execution and is not allowed, dependency: ${dependency.ident}`,
+      );
+    }
+
+    let shouldCheckIfValidGitDependency = false;
+
+    if (
+      dependency.range.startsWith("https://") ||
+      dependency.range.startsWith("http://")
+    ) {
+      // always prefix with the git protocol
+      dependency.update(`git:${dependency.range}`);
+      shouldCheckIfValidGitDependency = true;
+    }
+
+    if (dependency.range.startsWith("ssh://")) {
+      // always prefix with the git protocol
+      dependency.update(`git:${dependency.range.replace(/^ssh:\/\//, "git:")}`);
+      shouldCheckIfValidGitDependency = true;
+    }
+
+    if (
+      (shouldCheckIfValidGitDependency ||
+        dependency.range.startsWith("git:")) &&
+      !allowedGitDependencies.includes(dependency.ident)
+    ) {
+      dependency.error(
+        `arbitrary git dependencies are not allowed, dependency: ${dependency.ident}`,
+      );
+    }
+
+    // patches are only allowed if they are for an `npm:` dpeendenct
+    if (dependency.range.startsWith("patch:")) {
+      const dependencySpecification = dependency.range.match(/^patch:([^#]+)/);
+      if (!dependencySpecification) {
+        dependency.error(
+          `invalid patch protocol, dependency: ${dependency.ident}`,
+        );
+        continue;
+      }
+
+      // locator is on the right side
+      // splitRight at `@`
+      const segments = dependencySpecification[1].split("@");
+      const last = segments.pop();
+      // urldecode the last segment
+      const version = decodeURIComponent(last);
+
+      if (!version.startsWith("npm:")) {
+        dependency.error(
+          `patch protocol is only allowed for npm dependencies, dependency: ${dependency.ident}, patches: ${version}`,
+        );
+      }
+    }
   }
 }
 
@@ -180,10 +236,9 @@ function enforceDevDependenciesAreProperlyDeclared({ Yarn }) {
 
 module.exports = defineConfig({
   async constraints(context) {
-    // enforceWorkspaceDependenciesDeclaredAsSuch(context);
     enforceConsistentDependenciesAcrossTheProject(context);
     enforceNoDualTypeDependencies(context);
-    // enforcePortalProtocolInsteadOfFileProtocol(context);
+    enforceProtocols(context);
     enforceDevDependenciesAreProperlyDeclared(context);
   },
 });

From 83de6120a1b3f9f67ec51348d5b71a2cd3efd9cc Mon Sep 17 00:00:00 2001
From: Bilal Mahmoud <bmahmoud@mpi-cbg.de>
Date: Thu, 12 Dec 2024 13:02:10 +0100
Subject: [PATCH 2/5] fix: prettier

---
 apps/hash/README.md | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/apps/hash/README.md b/apps/hash/README.md
index 3d2b397b50a..169ca5c7a97 100644
--- a/apps/hash/README.md
+++ b/apps/hash/README.md
@@ -54,28 +54,28 @@ To run HASH locally, please follow these steps:
    ```sh
    git --version
    ## ≥ 2.17
-   
+
    node --version
    ## ≥ 20.12
-   
+
    yarn --version
    ## ≥ 1.16
-   
+
    rustup --version
    ## ≥ 1.27.1 (Required to match the toolchain as specified in `rust-toolchain.toml`)
-   
+
    docker --version
    ## ≥ 20.10
-   
+
    docker compose version
    ## ≥ 2.17.2
-   
+
    docker buildx version
    ## ≥ 0.10.4
-   
+
    protoc --version
    ## ≥ 25
-   
+
    java --version
    ## ≥ 8
    ```

From 1cfdcd0085b8421bd73f3fd32ea7f51ba93df1b7 Mon Sep 17 00:00:00 2001
From: Bilal Mahmoud <bmahmoud@mpi-cbg.de>
Date: Thu, 12 Dec 2024 13:03:16 +0100
Subject: [PATCH 3/5] chore: update lockfile

---
 yarn.lock | 571 ++++++++++++++++++++++--------------------------------
 1 file changed, 235 insertions(+), 336 deletions(-)

diff --git a/yarn.lock b/yarn.lock
index 2a31fa76460..6d505681266 100644
--- a/yarn.lock
+++ b/yarn.lock
@@ -434,7 +434,7 @@ __metadata:
     cors: "npm:2.8.5"
     cross-env: "npm:7.0.3"
     dedent: "npm:0.7.0"
-    effect: "npm:3.11.5"
+    effect: "npm:3.11.4"
     eslint: "npm:9.16.0"
     exponential-backoff: "npm:3.1.1"
     express: "npm:4.21.2"
@@ -529,8 +529,8 @@ __metadata:
     "@sentry/react": "npm:7.120.1"
     "@sentry/webpack-plugin": "npm:1.21.0"
     "@sigma/edge-curve": "patch:@sigma/edge-curve@npm%3A3.0.0-beta.16#~/.yarn/patches/@sigma-edge-curve-npm-3.0.0-beta.16-3d8b985284.patch"
-    "@sigma/node-border": "npm:3.0.0"
-    "@sigma/node-image": "npm:3.0.0"
+    "@sigma/node-border": "npm:3.0.0-beta.7"
+    "@sigma/node-image": "npm:3.0.0-beta.16"
     "@svgr/webpack": "npm:8.1.0"
     "@tldraw/editor": "patch:@tldraw/editor@npm%3A2.0.0-alpha.12#~/.yarn/patches/@tldraw-editor-npm-2.0.0-alpha.12-ba59bf001c.patch"
     "@tldraw/primitives": "npm:2.0.0-alpha.12"
@@ -597,7 +597,7 @@ __metadata:
     react-dom: "npm:18.2.0"
     react-dropzone: "npm:14.3.5"
     react-full-screen: "npm:1.1.1"
-    react-hook-form: "npm:7.54.1"
+    react-hook-form: "npm:7.54.0"
     react-markdown: "npm:9.0.1"
     react-pdf: "npm:9.1.1"
     react-responsive-carousel: "npm:3.2.23"
@@ -609,9 +609,9 @@ __metadata:
     rimraf: "npm:6.0.1"
     rooks: "npm:7.14.1"
     safe-stable-stringify: "npm:2.5.0"
-    sass: "npm:1.83.0"
+    sass: "npm:1.82.0"
     setimmediate: "npm:1.0.5"
-    sigma: "npm:3.0.0"
+    sigma: "npm:3.0.0-beta.39"
     signia: "npm:0.1.5"
     signia-react: "npm:0.1.5"
     typescript: "npm:5.6.3"
@@ -862,7 +862,7 @@ __metadata:
     react-refresh: "npm:0.14.0"
     react-refresh-typescript: "npm:2.0.9"
     rimraf: "npm:6.0.1"
-    sass: "npm:1.83.0"
+    sass: "npm:1.82.0"
     sass-loader: "npm:13.3.3"
     source-map-loader: "npm:3.0.2"
     style-loader: "npm:3.3.4"
@@ -4786,7 +4786,7 @@ __metadata:
     "@mui/material": "npm:5.16.11"
     "@types/lodash.debounce": "npm:4.0.9"
     "@types/react-dom": "npm:18.2.25"
-    "@types/react-is": "npm:18.3.1"
+    "@types/react-is": "npm:18.3.0"
     block-scripts: "npm:0.3.4"
     echarts: "npm:5.5.1"
     eslint: "npm:9.16.0"
@@ -4795,7 +4795,7 @@ __metadata:
     prettier: "npm:3.4.2"
     react: "npm:18.2.0"
     react-dom: "npm:18.2.0"
-    react-hook-form: "npm:7.54.1"
+    react-hook-form: "npm:7.54.0"
     typescript: "npm:5.6.3"
   peerDependencies:
     react: ^18.2.0
@@ -5236,7 +5236,7 @@ __metadata:
   languageName: node
   linkType: hard
 
-"@chainsafe/is-ip@npm:^2.0.1, @chainsafe/is-ip@npm:^2.0.2":
+"@chainsafe/is-ip@npm:2.0.2, @chainsafe/is-ip@npm:^2.0.1, @chainsafe/is-ip@npm:^2.0.2":
   version: 2.0.2
   resolution: "@chainsafe/is-ip@npm:2.0.2"
   checksum: 10c0/0bb8b9d0babe583642d31ffafad603ac5e5dc48884266feae57479d81f4e81ef903628527d81b39d5305657a957bf435bd2ef38b98a4526a7aab366febf793ad
@@ -5753,7 +5753,7 @@ __metadata:
   languageName: node
   linkType: hard
 
-"@effect/platform-node-shared@npm:^0.20.7":
+"@effect/platform-node-shared@npm:^0.20.6":
   version: 0.20.7
   resolution: "@effect/platform-node-shared@npm:0.20.7"
   dependencies:
@@ -5766,40 +5766,40 @@ __metadata:
   languageName: node
   linkType: hard
 
-"@effect/platform-node@npm:0.65.7":
-  version: 0.65.7
-  resolution: "@effect/platform-node@npm:0.65.7"
+"@effect/platform-node@npm:0.65.6":
+  version: 0.65.6
+  resolution: "@effect/platform-node@npm:0.65.6"
   dependencies:
-    "@effect/platform-node-shared": "npm:^0.20.7"
+    "@effect/platform-node-shared": "npm:^0.20.6"
     mime: "npm:^3.0.0"
     undici: "npm:^6.19.7"
     ws: "npm:^8.18.0"
   peerDependencies:
-    "@effect/platform": ^0.70.7
-    effect: ^3.11.5
-  checksum: 10c0/bc31367ea54cef8bea00dc437729d5f34dc4cc63f4fca33334c4d5fe3c7da82b92cc00cd2fa15ec21a11fc5b59bb4ad6cc1397d39430392f7370fc6e9f558914
+    "@effect/platform": ^0.70.6
+    effect: ^3.11.4
+  checksum: 10c0/c50bbde0be0b20c9920cce3e7c19f1d7f2d78e68c90e98b0299f0d07a725c96ee9ac4bf0fc29aed90661849fddb499ce8f6cc871ebe92e067f2ba6a1e1b5c6e2
   languageName: node
   linkType: hard
 
-"@effect/platform@npm:0.70.7":
-  version: 0.70.7
-  resolution: "@effect/platform@npm:0.70.7"
+"@effect/platform@npm:0.70.6":
+  version: 0.70.6
+  resolution: "@effect/platform@npm:0.70.6"
   dependencies:
     find-my-way-ts: "npm:^0.1.5"
     multipasta: "npm:^0.2.5"
   peerDependencies:
-    effect: ^3.11.5
-  checksum: 10c0/7e4be2bca8f4ad589dbe6d5739aa9e5c4d16bdbddb9ad42cdf7517bb5f29fb1ea187ecd32de1fa422315a032d3dcca33c1f59585efa820e478f1f32534848b70
+    effect: ^3.11.4
+  checksum: 10c0/1ef1261c578a84021cb3e2616519f86acc96bf2ad2828d43549930a5e2cb6067dc57e022db5de9d359f709aba2c6ba331b35a24da424d85429c44348f5b8d895
   languageName: node
   linkType: hard
 
-"@effect/vitest@npm:0.14.5":
-  version: 0.14.5
-  resolution: "@effect/vitest@npm:0.14.5"
+"@effect/vitest@npm:0.14.3":
+  version: 0.14.3
+  resolution: "@effect/vitest@npm:0.14.3"
   peerDependencies:
-    effect: ^3.11.5
+    effect: ^3.11.3
     vitest: ^2.0.5
-  checksum: 10c0/b9592e1143bf2d52b06302c76ce1b25f1133cab6d95232a578f2f05ed673ac1058ff11a295f37ac578b48e6807a19b27965661a741027bf7d5e6c1c7555547cd
+  checksum: 10c0/06c1630e03b67eab565913090918532cdace2655cf6345accb42db5f60a01cfe1fbd03d6119d9c03554786ad2584520cc06034ebab7d6432355920133a8df53c
   languageName: node
   linkType: hard
 
@@ -7939,14 +7939,14 @@ __metadata:
     eslint-plugin-storybook: "npm:0.11.1"
     react: "npm:18.2.0"
     react-dom: "npm:18.2.0"
-    react-hook-form: "npm:7.54.1"
+    react-hook-form: "npm:7.54.0"
     typescript: "npm:5.6.3"
   peerDependencies:
     "@mui/material": ^5.14.0
     "@mui/system": ^5.14.0
     react: ^18.0.0
     react-dom: ^18.0.0
-    react-hook-form: 7.54.1
+    react-hook-form: 7.54.0
   languageName: unknown
   linkType: soft
 
@@ -7974,7 +7974,7 @@ __metadata:
     material-ui-popup-state: "npm:4.1.0"
     react: "npm:18.2.0"
     react-dom: "npm:18.2.0"
-    react-hook-form: "npm:7.54.1"
+    react-hook-form: "npm:7.54.0"
     rooks: "npm:7.14.1"
     setimmediate: "npm:1.0.5"
     typescript: "npm:5.6.3"
@@ -7983,7 +7983,7 @@ __metadata:
     "@mui/system": ^5.14.0
     react: ^18.0.0
     react-dom: ^18.0.0
-    react-hook-form: 7.54.1
+    react-hook-form: 7.54.0
   languageName: unknown
   linkType: soft
 
@@ -8663,7 +8663,23 @@ __metadata:
   languageName: node
   linkType: hard
 
-"@libp2p/crypto@npm:5.0.8, @libp2p/crypto@npm:^5.0.0, @libp2p/crypto@npm:^5.0.8":
+"@libp2p/crypto@npm:5.0.7":
+  version: 5.0.7
+  resolution: "@libp2p/crypto@npm:5.0.7"
+  dependencies:
+    "@libp2p/interface": "npm:^2.2.1"
+    "@noble/curves": "npm:^1.4.0"
+    "@noble/hashes": "npm:^1.4.0"
+    asn1js: "npm:^3.0.5"
+    multiformats: "npm:^13.1.0"
+    protons-runtime: "npm:^5.4.0"
+    uint8arraylist: "npm:^2.4.8"
+    uint8arrays: "npm:^5.1.0"
+  checksum: 10c0/f55ff2d7203b1c81d306b657407fc2b98069ed17c35ec372ebc98596df0669980b8ced8ca587fac049d5b8ccca837591ed4034c46778520b1cea26bf9c01851a
+  languageName: node
+  linkType: hard
+
+"@libp2p/crypto@npm:^5.0.0, @libp2p/crypto@npm:^5.0.7, @libp2p/crypto@npm:^5.0.8":
   version: 5.0.8
   resolution: "@libp2p/crypto@npm:5.0.8"
   dependencies:
@@ -8679,43 +8695,57 @@ __metadata:
   languageName: node
   linkType: hard
 
-"@libp2p/identify@npm:3.0.14":
-  version: 3.0.14
-  resolution: "@libp2p/identify@npm:3.0.14"
-  dependencies:
-    "@libp2p/crypto": "npm:^5.0.8"
-    "@libp2p/interface": "npm:^2.3.0"
-    "@libp2p/interface-internal": "npm:^2.2.1"
-    "@libp2p/peer-id": "npm:^5.0.9"
-    "@libp2p/peer-record": "npm:^8.0.13"
-    "@libp2p/utils": "npm:^6.3.0"
-    "@multiformats/multiaddr": "npm:^12.3.3"
-    "@multiformats/multiaddr-matcher": "npm:^1.6.0"
+"@libp2p/identify@npm:3.0.12":
+  version: 3.0.12
+  resolution: "@libp2p/identify@npm:3.0.12"
+  dependencies:
+    "@libp2p/crypto": "npm:^5.0.7"
+    "@libp2p/interface": "npm:^2.2.1"
+    "@libp2p/interface-internal": "npm:^2.1.1"
+    "@libp2p/peer-id": "npm:^5.0.8"
+    "@libp2p/peer-record": "npm:^8.0.12"
+    "@libp2p/utils": "npm:^6.2.1"
+    "@multiformats/multiaddr": "npm:^12.2.3"
+    "@multiformats/multiaddr-matcher": "npm:^1.2.1"
     it-drain: "npm:^3.0.7"
-    it-parallel: "npm:^3.0.8"
-    it-protobuf-stream: "npm:^1.1.5"
-    protons-runtime: "npm:^5.5.0"
+    it-parallel: "npm:^3.0.7"
+    it-protobuf-stream: "npm:^1.1.3"
+    protons-runtime: "npm:^5.4.0"
     uint8arraylist: "npm:^2.4.8"
     uint8arrays: "npm:^5.1.0"
     wherearewe: "npm:^2.0.1"
-  checksum: 10c0/83f3dea9e68bc6b62cd1e574a03c2964b5c11f49d752f8c48568aa13986d0634fef21826c4a00a9a059eb11b4a139485edc59c93c22db1b2e77eba941461b622
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+  resolution: "@libp2p/interface@npm:2.2.1"
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-    "@libp2p/interface": "npm:^2.3.0"
-    "@libp2p/interface-internal": "npm:^2.2.1"
-    "@multiformats/multiaddr": "npm:^12.3.3"
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+    "@libp2p/interface": "npm:^2.2.1"
+    "@libp2p/interface-internal": "npm:^2.1.1"
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-  resolution: "@libp2p/tcp@npm:10.0.14"
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+  resolution: "@libp2p/tcp@npm:10.0.13"
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-    "@libp2p/utils": "npm:^6.3.0"
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-    "@multiformats/multiaddr": "npm:^12.3.3"
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     p-event: "npm:^6.0.1"
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-    "@libp2p/ping": "npm:2.0.14"
-    "@libp2p/tcp": "npm:10.0.14"
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+    "@effect/platform-node": "npm:0.65.6"
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     eslint: "npm:9.16.0"
     it-stream-types: "npm:2.0.2"
-    libp2p: "npm:2.4.2"
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     typescript: "npm:5.6.3"
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+    effect: "npm:3.11.4"
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-  resolution: "@sigma/node-image@npm:3.0.0"
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-  resolution: "@types/react-is@npm:18.3.1"
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+  resolution: "@types/react-is@npm:18.3.0"
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-    spawn-command: "npm:^0.0.2-1"
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-    yargs: "npm:^17.3.1"
-  bin:
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-  resolution: "effect@npm:3.11.5"
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-  languageName: node
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   resolution: "execa@npm:8.0.1"
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-    concurrently: "npm:7.6.0"
-    lefthook: "npm:1.9.2"
-    lockfile-lint: "npm:4.14.0"
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     markdownlint-cli: "npm:0.43.0"
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     prettier: "npm:3.4.2"
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-    suppress-exit-code: "npm:3.2.0"
     turbo: "npm:2.3.3"
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@@ -30322,13 +30302,6 @@ __metadata:
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-"it-byte-stream@npm:^1.0.0, it-byte-stream@npm:^1.1.0":
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   resolution: "it-parallel@npm:3.0.8"
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   resolution: "it-protobuf-stream@npm:1.1.5"
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-  resolution: "lefthook-darwin-arm64@npm:1.9.2"
+"lefthook-darwin-arm64@npm:1.9.1":
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+  resolution: "lefthook-darwin-arm64@npm:1.9.1"
   conditions: os=darwin & cpu=arm64
   languageName: node
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-  resolution: "lefthook-darwin-x64@npm:1.9.2"
+"lefthook-darwin-x64@npm:1.9.1":
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+  resolution: "lefthook-darwin-x64@npm:1.9.1"
   conditions: os=darwin & cpu=x64
   languageName: node
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-"lefthook-freebsd-arm64@npm:1.9.2":
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-  resolution: "lefthook-freebsd-arm64@npm:1.9.2"
+"lefthook-freebsd-arm64@npm:1.9.1":
+  version: 1.9.1
+  resolution: "lefthook-freebsd-arm64@npm:1.9.1"
   conditions: os=freebsd & cpu=arm64
   languageName: node
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-  resolution: "lefthook-freebsd-x64@npm:1.9.2"
+"lefthook-freebsd-x64@npm:1.9.1":
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+  resolution: "lefthook-freebsd-x64@npm:1.9.1"
   conditions: os=freebsd & cpu=x64
   languageName: node
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-  version: 1.9.2
-  resolution: "lefthook-linux-arm64@npm:1.9.2"
+"lefthook-linux-arm64@npm:1.9.1":
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+  resolution: "lefthook-linux-arm64@npm:1.9.1"
   conditions: os=linux & cpu=arm64
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-"lefthook-linux-x64@npm:1.9.2":
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-  resolution: "lefthook-linux-x64@npm:1.9.2"
+"lefthook-linux-x64@npm:1.9.1":
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+  resolution: "lefthook-linux-x64@npm:1.9.1"
   conditions: os=linux & cpu=x64
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-  version: 1.9.2
-  resolution: "lefthook-openbsd-arm64@npm:1.9.2"
+"lefthook-openbsd-arm64@npm:1.9.1":
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+  resolution: "lefthook-openbsd-arm64@npm:1.9.1"
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-  resolution: "lefthook-openbsd-x64@npm:1.9.2"
+"lefthook-openbsd-x64@npm:1.9.1":
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+  resolution: "lefthook-openbsd-x64@npm:1.9.1"
   conditions: os=openbsd & cpu=x64
   languageName: node
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-  resolution: "lefthook-windows-arm64@npm:1.9.2"
+"lefthook-windows-arm64@npm:1.9.1":
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+  resolution: "lefthook-windows-arm64@npm:1.9.1"
   conditions: os=win32 & cpu=arm64
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-  resolution: "lefthook-windows-x64@npm:1.9.2"
+"lefthook-windows-x64@npm:1.9.1":
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+  resolution: "lefthook-windows-x64@npm:1.9.1"
   conditions: os=win32 & cpu=x64
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-    lefthook-darwin-x64: "npm:1.9.2"
-    lefthook-freebsd-arm64: "npm:1.9.2"
-    lefthook-freebsd-x64: "npm:1.9.2"
-    lefthook-linux-arm64: "npm:1.9.2"
-    lefthook-linux-x64: "npm:1.9.2"
-    lefthook-openbsd-arm64: "npm:1.9.2"
-    lefthook-openbsd-x64: "npm:1.9.2"
-    lefthook-windows-arm64: "npm:1.9.2"
-    lefthook-windows-x64: "npm:1.9.2"
+"lefthook@npm:1.9.1":
+  version: 1.9.1
+  resolution: "lefthook@npm:1.9.1"
+  dependencies:
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+    lefthook-darwin-x64: "npm:1.9.1"
+    lefthook-freebsd-arm64: "npm:1.9.1"
+    lefthook-freebsd-x64: "npm:1.9.1"
+    lefthook-linux-arm64: "npm:1.9.1"
+    lefthook-linux-x64: "npm:1.9.1"
+    lefthook-openbsd-arm64: "npm:1.9.1"
+    lefthook-openbsd-x64: "npm:1.9.1"
+    lefthook-windows-arm64: "npm:1.9.1"
+    lefthook-windows-x64: "npm:1.9.1"
   dependenciesMeta:
     lefthook-darwin-arm64:
       optional: true
@@ -33073,7 +33046,7 @@ __metadata:
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   bin:
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-    "@libp2p/peer-store": "npm:^11.0.13"
-    "@libp2p/utils": "npm:^6.3.0"
+"libp2p@npm:2.3.1":
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+  resolution: "libp2p@npm:2.3.1"
+  dependencies:
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+    "@libp2p/interface": "npm:^2.2.1"
+    "@libp2p/interface-internal": "npm:^2.1.1"
+    "@libp2p/logger": "npm:^5.1.4"
+    "@libp2p/multistream-select": "npm:^6.0.9"
+    "@libp2p/peer-collections": "npm:^6.0.12"
+    "@libp2p/peer-id": "npm:^5.0.8"
+    "@libp2p/peer-store": "npm:^11.0.12"
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     "@multiformats/dns": "npm:^1.0.6"
-    "@multiformats/multiaddr": "npm:^12.3.3"
-    "@multiformats/multiaddr-matcher": "npm:^1.6.0"
+    "@multiformats/multiaddr": "npm:^12.2.3"
+    "@multiformats/multiaddr-matcher": "npm:^1.2.1"
     any-signal: "npm:^4.1.1"
-    datastore-core: "npm:^10.0.2"
-    interface-datastore: "npm:^8.3.1"
-    it-byte-stream: "npm:^1.1.0"
+    datastore-core: "npm:^10.0.0"
+    interface-datastore: "npm:^8.3.0"
+    it-byte-stream: "npm:^1.0.12"
     it-merge: "npm:^3.0.5"
-    it-parallel: "npm:^3.0.8"
+    it-parallel: "npm:^3.0.7"
     merge-options: "npm:^3.0.4"
-    multiformats: "npm:^13.3.1"
+    multiformats: "npm:^13.1.0"
     p-defer: "npm:^4.0.1"
-    p-retry: "npm:^6.2.1"
-    progress-events: "npm:^1.0.1"
+    p-retry: "npm:^6.2.0"
+    progress-events: "npm:^1.0.0"
     race-event: "npm:^1.3.0"
-    race-signal: "npm:^1.1.0"
+    race-signal: "npm:^1.0.2"
     uint8arrays: "npm:^5.1.0"
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-  resolution: "lockfile-lint-api@npm:5.9.1"
-  dependencies:
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-    object-hash: "npm:^3.0.0"
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-  languageName: node
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-  resolution: "lockfile-lint@npm:4.14.0"
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-    yargs: "npm:^17.7.2"
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-"multiformats@npm:13.3.1, multiformats@npm:^13.0.0, multiformats@npm:^13.3.1":
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@@ -36467,13 +36412,6 @@ __metadata:
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@@ -37363,13 +37301,6 @@ __metadata:
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-  resolution: "prettier-plugin-sh@npm:0.14.0"
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 "prettier@npm:*, prettier@npm:3.4.2":
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   resolution: "prettier@npm:3.4.2"
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-"protons-runtime@npm:^5.5.0":
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   resolution: "protons-runtime@npm:5.5.0"
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@@ -40470,12 +40389,12 @@ __metadata:
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-"react-hook-form@npm:7.54.1":
-  version: 7.54.1
-  resolution: "react-hook-form@npm:7.54.1"
+"react-hook-form@npm:7.54.0":
+  version: 7.54.0
+  resolution: "react-hook-form@npm:7.54.0"
   peerDependencies:
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-  checksum: 10c0/2d960ddf8aa654f34e36f5d995f0ec067a4c01340d650eca44f22aa4421e278dcc449c8522e66c5c66b1c61d62fbdf914b9e0a8de9deb4c6346cc3b37ef4eb82
+  checksum: 10c0/8dbc68e8b82aafda1271bbc291052b5efb091505865cd10e3d7dd618ca3870bd05596d7ba68f128427d47ff11e0d9f03089fd7afb88d2a8865ff81f21af417a0
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@@ -42182,7 +42101,7 @@ __metadata:
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-"rxjs@npm:*, rxjs@npm:7.8.1, rxjs@npm:^7.0.0, rxjs@npm:^7.5.5, rxjs@npm:^7.8.1":
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-"sass@npm:1.83.0, sass@npm:^1.52.3":
-  version: 1.83.0
-  resolution: "sass@npm:1.83.0"
+"sass@npm:1.82.0, sass@npm:^1.52.3":
+  version: 1.82.0
+  resolution: "sass@npm:1.82.0"
   dependencies:
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     chokidar: "npm:^4.0.0"
@@ -42347,7 +42266,7 @@ __metadata:
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@@ -42727,15 +42646,6 @@ __metadata:
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-  resolution: "sh-syntax@npm:0.4.2"
-  dependencies:
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-  languageName: node
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   resolution: "sha.js@npm:2.4.11"
@@ -42993,13 +42903,13 @@ __metadata:
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-"sigma@npm:3.0.0":
-  version: 3.0.0
-  resolution: "sigma@npm:3.0.0"
+"sigma@npm:3.0.0-beta.39":
+  version: 3.0.0-beta.39
+  resolution: "sigma@npm:3.0.0-beta.39"
   dependencies:
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     graphology-utils: "npm:^2.5.2"
-  checksum: 10c0/76c0dac7f800cf876f242cf9dcfadee624ce4a1210ae56cf17408384a6ab2eadbe840c57b23b03d7718d6159f3e727921cb4fa5a52ee54e73ae52151af294052
+  checksum: 10c0/42194a49990c929caa873f6026546351dbf079092e5feaca5b77150c415cfdb50b7a9ce61248b0087881ad267e896389d67227e79651cce842edb00f1a25fce5
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@@ -44476,17 +44386,6 @@ __metadata:
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-  resolution: "suppress-exit-code@npm:3.2.0"
-  dependencies:
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-  bin:
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-  languageName: node
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   resolution: "svg-parser@npm:2.0.4"
@@ -48517,7 +48416,7 @@ __metadata:
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-"yargs@npm:17.7.2, yargs@npm:^17.0.0, yargs@npm:^17.0.1, yargs@npm:^17.1.1, yargs@npm:^17.3.1, yargs@npm:^17.7.1, yargs@npm:^17.7.2":
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   version: 17.7.2
   resolution: "yargs@npm:17.7.2"
   dependencies:

From 2d0431757623c9ba38c5a27bec71534b0af42170 Mon Sep 17 00:00:00 2001
From: Bilal Mahmoud <bmahmoud@mpi-cbg.de>
Date: Fri, 13 Dec 2024 13:28:04 +0100
Subject: [PATCH 4/5] fix: yarn.lock

---
 yarn.lock | 444 ++++++++++++++++++++++++++----------------------------
 1 file changed, 216 insertions(+), 228 deletions(-)

diff --git a/yarn.lock b/yarn.lock
index 6d505681266..447957ca41e 100644
--- a/yarn.lock
+++ b/yarn.lock
@@ -434,7 +434,7 @@ __metadata:
     cors: "npm:2.8.5"
     cross-env: "npm:7.0.3"
     dedent: "npm:0.7.0"
-    effect: "npm:3.11.4"
+    effect: "npm:3.11.5"
     eslint: "npm:9.16.0"
     exponential-backoff: "npm:3.1.1"
     express: "npm:4.21.2"
@@ -529,8 +529,8 @@ __metadata:
     "@sentry/react": "npm:7.120.1"
     "@sentry/webpack-plugin": "npm:1.21.0"
     "@sigma/edge-curve": "patch:@sigma/edge-curve@npm%3A3.0.0-beta.16#~/.yarn/patches/@sigma-edge-curve-npm-3.0.0-beta.16-3d8b985284.patch"
-    "@sigma/node-border": "npm:3.0.0-beta.7"
-    "@sigma/node-image": "npm:3.0.0-beta.16"
+    "@sigma/node-border": "npm:3.0.0"
+    "@sigma/node-image": "npm:3.0.0"
     "@svgr/webpack": "npm:8.1.0"
     "@tldraw/editor": "patch:@tldraw/editor@npm%3A2.0.0-alpha.12#~/.yarn/patches/@tldraw-editor-npm-2.0.0-alpha.12-ba59bf001c.patch"
     "@tldraw/primitives": "npm:2.0.0-alpha.12"
@@ -597,7 +597,7 @@ __metadata:
     react-dom: "npm:18.2.0"
     react-dropzone: "npm:14.3.5"
     react-full-screen: "npm:1.1.1"
-    react-hook-form: "npm:7.54.0"
+    react-hook-form: "npm:7.54.1"
     react-markdown: "npm:9.0.1"
     react-pdf: "npm:9.1.1"
     react-responsive-carousel: "npm:3.2.23"
@@ -609,9 +609,9 @@ __metadata:
     rimraf: "npm:6.0.1"
     rooks: "npm:7.14.1"
     safe-stable-stringify: "npm:2.5.0"
-    sass: "npm:1.82.0"
+    sass: "npm:1.83.0"
     setimmediate: "npm:1.0.5"
-    sigma: "npm:3.0.0-beta.39"
+    sigma: "npm:3.0.0"
     signia: "npm:0.1.5"
     signia-react: "npm:0.1.5"
     typescript: "npm:5.6.3"
@@ -862,7 +862,7 @@ __metadata:
     react-refresh: "npm:0.14.0"
     react-refresh-typescript: "npm:2.0.9"
     rimraf: "npm:6.0.1"
-    sass: "npm:1.82.0"
+    sass: "npm:1.83.0"
     sass-loader: "npm:13.3.3"
     source-map-loader: "npm:3.0.2"
     style-loader: "npm:3.3.4"
@@ -4786,7 +4786,7 @@ __metadata:
     "@mui/material": "npm:5.16.11"
     "@types/lodash.debounce": "npm:4.0.9"
     "@types/react-dom": "npm:18.2.25"
-    "@types/react-is": "npm:18.3.0"
+    "@types/react-is": "npm:18.3.1"
     block-scripts: "npm:0.3.4"
     echarts: "npm:5.5.1"
     eslint: "npm:9.16.0"
@@ -4795,7 +4795,7 @@ __metadata:
     prettier: "npm:3.4.2"
     react: "npm:18.2.0"
     react-dom: "npm:18.2.0"
-    react-hook-form: "npm:7.54.0"
+    react-hook-form: "npm:7.54.1"
     typescript: "npm:5.6.3"
   peerDependencies:
     react: ^18.2.0
@@ -5236,7 +5236,7 @@ __metadata:
   languageName: node
   linkType: hard
 
-"@chainsafe/is-ip@npm:2.0.2, @chainsafe/is-ip@npm:^2.0.1, @chainsafe/is-ip@npm:^2.0.2":
+"@chainsafe/is-ip@npm:^2.0.1, @chainsafe/is-ip@npm:^2.0.2":
   version: 2.0.2
   resolution: "@chainsafe/is-ip@npm:2.0.2"
   checksum: 10c0/0bb8b9d0babe583642d31ffafad603ac5e5dc48884266feae57479d81f4e81ef903628527d81b39d5305657a957bf435bd2ef38b98a4526a7aab366febf793ad
@@ -5753,7 +5753,7 @@ __metadata:
   languageName: node
   linkType: hard
 
-"@effect/platform-node-shared@npm:^0.20.6":
+"@effect/platform-node-shared@npm:^0.20.7":
   version: 0.20.7
   resolution: "@effect/platform-node-shared@npm:0.20.7"
   dependencies:
@@ -5766,40 +5766,40 @@ __metadata:
   languageName: node
   linkType: hard
 
-"@effect/platform-node@npm:0.65.6":
-  version: 0.65.6
-  resolution: "@effect/platform-node@npm:0.65.6"
+"@effect/platform-node@npm:0.65.7":
+  version: 0.65.7
+  resolution: "@effect/platform-node@npm:0.65.7"
   dependencies:
-    "@effect/platform-node-shared": "npm:^0.20.6"
+    "@effect/platform-node-shared": "npm:^0.20.7"
     mime: "npm:^3.0.0"
     undici: "npm:^6.19.7"
     ws: "npm:^8.18.0"
   peerDependencies:
-    "@effect/platform": ^0.70.6
-    effect: ^3.11.4
-  checksum: 10c0/c50bbde0be0b20c9920cce3e7c19f1d7f2d78e68c90e98b0299f0d07a725c96ee9ac4bf0fc29aed90661849fddb499ce8f6cc871ebe92e067f2ba6a1e1b5c6e2
+    "@effect/platform": ^0.70.7
+    effect: ^3.11.5
+  checksum: 10c0/bc31367ea54cef8bea00dc437729d5f34dc4cc63f4fca33334c4d5fe3c7da82b92cc00cd2fa15ec21a11fc5b59bb4ad6cc1397d39430392f7370fc6e9f558914
   languageName: node
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-"@effect/platform@npm:0.70.6":
-  version: 0.70.6
-  resolution: "@effect/platform@npm:0.70.6"
+"@effect/platform@npm:0.70.7":
+  version: 0.70.7
+  resolution: "@effect/platform@npm:0.70.7"
   dependencies:
     find-my-way-ts: "npm:^0.1.5"
     multipasta: "npm:^0.2.5"
   peerDependencies:
-    effect: ^3.11.4
-  checksum: 10c0/1ef1261c578a84021cb3e2616519f86acc96bf2ad2828d43549930a5e2cb6067dc57e022db5de9d359f709aba2c6ba331b35a24da424d85429c44348f5b8d895
+    effect: ^3.11.5
+  checksum: 10c0/7e4be2bca8f4ad589dbe6d5739aa9e5c4d16bdbddb9ad42cdf7517bb5f29fb1ea187ecd32de1fa422315a032d3dcca33c1f59585efa820e478f1f32534848b70
   languageName: node
   linkType: hard
 
-"@effect/vitest@npm:0.14.3":
-  version: 0.14.3
-  resolution: "@effect/vitest@npm:0.14.3"
+"@effect/vitest@npm:0.14.5":
+  version: 0.14.5
+  resolution: "@effect/vitest@npm:0.14.5"
   peerDependencies:
-    effect: ^3.11.3
+    effect: ^3.11.5
     vitest: ^2.0.5
-  checksum: 10c0/06c1630e03b67eab565913090918532cdace2655cf6345accb42db5f60a01cfe1fbd03d6119d9c03554786ad2584520cc06034ebab7d6432355920133a8df53c
+  checksum: 10c0/b9592e1143bf2d52b06302c76ce1b25f1133cab6d95232a578f2f05ed673ac1058ff11a295f37ac578b48e6807a19b27965661a741027bf7d5e6c1c7555547cd
   languageName: node
   linkType: hard
 
@@ -7939,14 +7939,14 @@ __metadata:
     eslint-plugin-storybook: "npm:0.11.1"
     react: "npm:18.2.0"
     react-dom: "npm:18.2.0"
-    react-hook-form: "npm:7.54.0"
+    react-hook-form: "npm:7.54.1"
     typescript: "npm:5.6.3"
   peerDependencies:
     "@mui/material": ^5.14.0
     "@mui/system": ^5.14.0
     react: ^18.0.0
     react-dom: ^18.0.0
-    react-hook-form: 7.54.0
+    react-hook-form: 7.54.1
   languageName: unknown
   linkType: soft
 
@@ -7974,7 +7974,7 @@ __metadata:
     material-ui-popup-state: "npm:4.1.0"
     react: "npm:18.2.0"
     react-dom: "npm:18.2.0"
-    react-hook-form: "npm:7.54.0"
+    react-hook-form: "npm:7.54.1"
     rooks: "npm:7.14.1"
     setimmediate: "npm:1.0.5"
     typescript: "npm:5.6.3"
@@ -7983,7 +7983,7 @@ __metadata:
     "@mui/system": ^5.14.0
     react: ^18.0.0
     react-dom: ^18.0.0
-    react-hook-form: 7.54.0
+    react-hook-form: 7.54.1
   languageName: unknown
   linkType: soft
 
@@ -8663,23 +8663,7 @@ __metadata:
   languageName: node
   linkType: hard
 
-"@libp2p/crypto@npm:5.0.7":
-  version: 5.0.7
-  resolution: "@libp2p/crypto@npm:5.0.7"
-  dependencies:
-    "@libp2p/interface": "npm:^2.2.1"
-    "@noble/curves": "npm:^1.4.0"
-    "@noble/hashes": "npm:^1.4.0"
-    asn1js: "npm:^3.0.5"
-    multiformats: "npm:^13.1.0"
-    protons-runtime: "npm:^5.4.0"
-    uint8arraylist: "npm:^2.4.8"
-    uint8arrays: "npm:^5.1.0"
-  checksum: 10c0/f55ff2d7203b1c81d306b657407fc2b98069ed17c35ec372ebc98596df0669980b8ced8ca587fac049d5b8ccca837591ed4034c46778520b1cea26bf9c01851a
-  languageName: node
-  linkType: hard
-
-"@libp2p/crypto@npm:^5.0.0, @libp2p/crypto@npm:^5.0.7, @libp2p/crypto@npm:^5.0.8":
+"@libp2p/crypto@npm:5.0.8, @libp2p/crypto@npm:^5.0.0, @libp2p/crypto@npm:^5.0.8":
   version: 5.0.8
   resolution: "@libp2p/crypto@npm:5.0.8"
   dependencies:
@@ -8695,57 +8679,43 @@ __metadata:
   languageName: node
   linkType: hard
 
-"@libp2p/identify@npm:3.0.12":
-  version: 3.0.12
-  resolution: "@libp2p/identify@npm:3.0.12"
-  dependencies:
-    "@libp2p/crypto": "npm:^5.0.7"
-    "@libp2p/interface": "npm:^2.2.1"
-    "@libp2p/interface-internal": "npm:^2.1.1"
-    "@libp2p/peer-id": "npm:^5.0.8"
-    "@libp2p/peer-record": "npm:^8.0.12"
-    "@libp2p/utils": "npm:^6.2.1"
-    "@multiformats/multiaddr": "npm:^12.2.3"
-    "@multiformats/multiaddr-matcher": "npm:^1.2.1"
+"@libp2p/identify@npm:3.0.14":
+  version: 3.0.14
+  resolution: "@libp2p/identify@npm:3.0.14"
+  dependencies:
+    "@libp2p/crypto": "npm:^5.0.8"
+    "@libp2p/interface": "npm:^2.3.0"
+    "@libp2p/interface-internal": "npm:^2.2.1"
+    "@libp2p/peer-id": "npm:^5.0.9"
+    "@libp2p/peer-record": "npm:^8.0.13"
+    "@libp2p/utils": "npm:^6.3.0"
+    "@multiformats/multiaddr": "npm:^12.3.3"
+    "@multiformats/multiaddr-matcher": "npm:^1.6.0"
     it-drain: "npm:^3.0.7"
-    it-parallel: "npm:^3.0.7"
-    it-protobuf-stream: "npm:^1.1.3"
-    protons-runtime: "npm:^5.4.0"
+    it-parallel: "npm:^3.0.8"
+    it-protobuf-stream: "npm:^1.1.5"
+    protons-runtime: "npm:^5.5.0"
     uint8arraylist: "npm:^2.4.8"
     uint8arrays: "npm:^5.1.0"
     wherearewe: "npm:^2.0.1"
-  checksum: 10c0/9e1e42760ceb095ce7b717ae53e913ef125b6190443a07220b1e32b3583e6b410d3f17e46d68cd84f329e304f43120d784a770966e3aa4ab647034d7c88e9d0a
+  checksum: 10c0/83f3dea9e68bc6b62cd1e574a03c2964b5c11f49d752f8c48568aa13986d0634fef21826c4a00a9a059eb11b4a139485edc59c93c22db1b2e77eba941461b622
   languageName: node
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-"@libp2p/interface-internal@npm:^2.1.1":
-  version: 2.2.0
-  resolution: "@libp2p/interface-internal@npm:2.2.0"
+"@libp2p/interface-internal@npm:^2.2.1":
+  version: 2.2.1
+  resolution: "@libp2p/interface-internal@npm:2.2.1"
   dependencies:
     "@libp2p/interface": "npm:^2.3.0"
     "@libp2p/peer-collections": "npm:^6.0.13"
     "@multiformats/multiaddr": "npm:^12.3.3"
     progress-events: "npm:^1.0.1"
     uint8arraylist: "npm:^2.4.8"
-  checksum: 10c0/241c5962ab1a11ff3f0b613ad3db82fc4616672e5bf5dcc36023925c815d4382221ad57f4cd5d31d83a825d39d54eb4808acd525d00d8c4a8e916ec950b54aa7
+  checksum: 10c0/9e4b71bdce08ce83bab7a580863ee146861c8ecdacef1dbe58e97bb7f31fc0d5146b572089ac78a21c051dba987ec813a9b29b3dd49fbc3f30bf55ef77169e63
   languageName: node
   linkType: hard
 
-"@libp2p/interface@npm:2.2.1":
-  version: 2.2.1
-  resolution: "@libp2p/interface@npm:2.2.1"
-  dependencies:
-    "@multiformats/multiaddr": "npm:^12.2.3"
-    it-pushable: "npm:^3.2.3"
-    it-stream-types: "npm:^2.0.1"
-    multiformats: "npm:^13.1.0"
-    progress-events: "npm:^1.0.0"
-    uint8arraylist: "npm:^2.4.8"
-  checksum: 10c0/0eeff44808dd3a96effd44fee805efa3ef8db8b70b0cbd3e3c467949d26f0b1fd9887297f487764083b451907262b88a6e14f8b722df139e5feeda9266c21602
-  languageName: node
-  linkType: hard
-
-"@libp2p/interface@npm:^2.0.0, @libp2p/interface@npm:^2.2.1, @libp2p/interface@npm:^2.3.0":
+"@libp2p/interface@npm:2.3.0, @libp2p/interface@npm:^2.0.0, @libp2p/interface@npm:^2.3.0":
   version: 2.3.0
   resolution: "@libp2p/interface@npm:2.3.0"
   dependencies:
@@ -8759,7 +8729,7 @@ __metadata:
   languageName: node
   linkType: hard
 
-"@libp2p/logger@npm:^5.0.1, @libp2p/logger@npm:^5.1.4, @libp2p/logger@npm:^5.1.5":
+"@libp2p/logger@npm:^5.0.1, @libp2p/logger@npm:^5.1.5":
   version: 5.1.5
   resolution: "@libp2p/logger@npm:5.1.5"
   dependencies:
@@ -8772,7 +8742,7 @@ __metadata:
   languageName: node
   linkType: hard
 
-"@libp2p/multistream-select@npm:^6.0.9":
+"@libp2p/multistream-select@npm:^6.0.10":
   version: 6.0.10
   resolution: "@libp2p/multistream-select@npm:6.0.10"
   dependencies:
@@ -8789,7 +8759,7 @@ __metadata:
   languageName: node
   linkType: hard
 
-"@libp2p/peer-collections@npm:^6.0.12, @libp2p/peer-collections@npm:^6.0.13":
+"@libp2p/peer-collections@npm:^6.0.13":
   version: 6.0.13
   resolution: "@libp2p/peer-collections@npm:6.0.13"
   dependencies:
@@ -8801,7 +8771,7 @@ __metadata:
   languageName: node
   linkType: hard
 
-"@libp2p/peer-id@npm:^5.0.0, @libp2p/peer-id@npm:^5.0.8, @libp2p/peer-id@npm:^5.0.9":
+"@libp2p/peer-id@npm:^5.0.0, @libp2p/peer-id@npm:^5.0.9":
   version: 5.0.9
   resolution: "@libp2p/peer-id@npm:5.0.9"
   dependencies:
@@ -8813,7 +8783,7 @@ __metadata:
   languageName: node
   linkType: hard
 
-"@libp2p/peer-record@npm:^8.0.12, @libp2p/peer-record@npm:^8.0.13":
+"@libp2p/peer-record@npm:^8.0.13":
   version: 8.0.13
   resolution: "@libp2p/peer-record@npm:8.0.13"
   dependencies:
@@ -8831,7 +8801,7 @@ __metadata:
   languageName: node
   linkType: hard
 
-"@libp2p/peer-store@npm:^11.0.12":
+"@libp2p/peer-store@npm:^11.0.13":
   version: 11.0.13
   resolution: "@libp2p/peer-store@npm:11.0.13"
   dependencies:
@@ -8851,39 +8821,39 @@ __metadata:
   languageName: node
   linkType: hard
 
-"@libp2p/ping@npm:2.0.12":
-  version: 2.0.12
-  resolution: "@libp2p/ping@npm:2.0.12"
+"@libp2p/ping@npm:2.0.14":
+  version: 2.0.14
+  resolution: "@libp2p/ping@npm:2.0.14"
   dependencies:
-    "@libp2p/crypto": "npm:^5.0.7"
-    "@libp2p/interface": "npm:^2.2.1"
-    "@libp2p/interface-internal": "npm:^2.1.1"
-    "@multiformats/multiaddr": "npm:^12.2.3"
+    "@libp2p/crypto": "npm:^5.0.8"
+    "@libp2p/interface": "npm:^2.3.0"
+    "@libp2p/interface-internal": "npm:^2.2.1"
+    "@multiformats/multiaddr": "npm:^12.3.3"
     it-byte-stream: "npm:^1.1.0"
     uint8arrays: "npm:^5.1.0"
-  checksum: 10c0/84fe8f1c24dd5d8854cab1f37a9f2582abf1039ac7fc0bea8629e7a066a1555843c8bf1a3e19544b22c36b8f4696edb010c082417593ad9ab54e4bb512daf2fd
+  checksum: 10c0/46f6205f743ebe6dfef309fb18cb9d3be55972da6db655f0bd4433e7fd1df1c5cb5e3094ab1f6d8a512b7aa385cdbb551adc992af9aaa2b8d8b9581061a95a5c
   languageName: node
   linkType: hard
 
-"@libp2p/tcp@npm:10.0.13":
-  version: 10.0.13
-  resolution: "@libp2p/tcp@npm:10.0.13"
+"@libp2p/tcp@npm:10.0.14":
+  version: 10.0.14
+  resolution: "@libp2p/tcp@npm:10.0.14"
   dependencies:
-    "@libp2p/interface": "npm:^2.2.1"
-    "@libp2p/utils": "npm:^6.2.1"
+    "@libp2p/interface": "npm:^2.3.0"
+    "@libp2p/utils": "npm:^6.3.0"
     "@multiformats/mafmt": "npm:^12.1.6"
-    "@multiformats/multiaddr": "npm:^12.2.3"
+    "@multiformats/multiaddr": "npm:^12.3.3"
     "@types/sinon": "npm:^17.0.3"
     p-defer: "npm:^4.0.1"
     p-event: "npm:^6.0.1"
-    progress-events: "npm:^1.0.0"
+    progress-events: "npm:^1.0.1"
     race-event: "npm:^1.3.0"
     stream-to-it: "npm:^1.0.1"
-  checksum: 10c0/b67c3a5484124e26b0e620e532d02cd058c454f894774703e1d88f4650df8a55cd1e8ed6c63293a7c94d1c0179fb9d967aafc5ae5936a09d129f34ec75d34a28
+  checksum: 10c0/3e924eea5ae3df35db45ee6b358b02c40290ed6b3219ea98bad50b376ad22b805fe9bf49acd85a6f6cb1802b6b524276201ba24cb489c2d8885ec488e0c7424d
   languageName: node
   linkType: hard
 
-"@libp2p/utils@npm:^6.0.0, @libp2p/utils@npm:^6.2.1, @libp2p/utils@npm:^6.3.0":
+"@libp2p/utils@npm:^6.0.0, @libp2p/utils@npm:^6.3.0":
   version: 6.3.0
   resolution: "@libp2p/utils@npm:6.3.0"
   dependencies:
@@ -9081,7 +9051,7 @@ __metadata:
     "@types/babel__core": "npm:^7"
     "@types/eslint__eslintrc": "npm:2.1.2"
     "@types/node": "npm:22.10.2"
-    effect: "npm:3.11.4"
+    effect: "npm:3.11.5"
     eslint: "npm:9.16.0"
     eslint-config-airbnb: "npm:19.0.4"
     eslint-config-flat-gitignore: "npm:0.3.0"
@@ -9104,17 +9074,16 @@ __metadata:
   version: 0.0.0-use.local
   resolution: "@local/harpc-client@workspace:libs/@local/harpc/client/typescript"
   dependencies:
-    "@chainsafe/is-ip": "npm:2.0.2"
     "@chainsafe/libp2p-noise": "npm:16.0.0"
     "@chainsafe/libp2p-yamux": "npm:7.0.1"
-    "@effect/platform": "npm:0.70.6"
-    "@effect/platform-node": "npm:0.65.6"
-    "@effect/vitest": "npm:0.14.3"
-    "@libp2p/crypto": "npm:5.0.7"
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     prettier: "npm:3.4.2"
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-    lefthook-windows-arm64: "npm:1.9.1"
-    lefthook-windows-x64: "npm:1.9.1"
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+    lefthook-windows-x64: "npm:1.9.2"
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@@ -33046,7 +33015,7 @@ __metadata:
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+    chokidar: "npm:^4.0.0"
+    immutable: "npm:^5.0.2"
+    source-map-js: "npm:>=0.6.2 <2.0.0"
+  dependenciesMeta:
+    "@parcel/watcher":
+      optional: true
+  bin:
+    sass: sass.js
+  checksum: 10c0/4415361229879a9041d77c953da85482e89032aa4321ba13250a9987d39c80fac6c88af3777f2a2d76a4e8b0c8afbd21c1970fdbe84e0b3ec25fb26741f92beb
+  languageName: node
+  linkType: hard
+
+"sass@npm:^1.52.3":
   version: 1.82.0
   resolution: "sass@npm:1.82.0"
   dependencies:
@@ -42903,13 +42891,13 @@ __metadata:
   languageName: node
   linkType: hard
 
-"sigma@npm:3.0.0-beta.39":
-  version: 3.0.0-beta.39
-  resolution: "sigma@npm:3.0.0-beta.39"
+"sigma@npm:3.0.0":
+  version: 3.0.0
+  resolution: "sigma@npm:3.0.0"
   dependencies:
     events: "npm:^3.3.0"
     graphology-utils: "npm:^2.5.2"
-  checksum: 10c0/42194a49990c929caa873f6026546351dbf079092e5feaca5b77150c415cfdb50b7a9ce61248b0087881ad267e896389d67227e79651cce842edb00f1a25fce5
+  checksum: 10c0/76c0dac7f800cf876f242cf9dcfadee624ce4a1210ae56cf17408384a6ab2eadbe840c57b23b03d7718d6159f3e727921cb4fa5a52ee54e73ae52151af294052
   languageName: node
   linkType: hard
 

From 035bd368316a3c27be810951e0e29c0cfa550b9e Mon Sep 17 00:00:00 2001
From: Bilal Mahmoud <bmahmoud@mpi-cbg.de>
Date: Fri, 13 Dec 2024 13:34:13 +0100
Subject: [PATCH 5/5] fix: yarn dedupe

---
 yarn.lock | 19 +------------------
 1 file changed, 1 insertion(+), 18 deletions(-)

diff --git a/yarn.lock b/yarn.lock
index 447957ca41e..d24a40e0581 100644
--- a/yarn.lock
+++ b/yarn.lock
@@ -42224,7 +42224,7 @@ __metadata:
   languageName: node
   linkType: hard
 
-"sass@npm:1.83.0":
+"sass@npm:1.83.0, sass@npm:^1.52.3":
   version: 1.83.0
   resolution: "sass@npm:1.83.0"
   dependencies:
@@ -42241,23 +42241,6 @@ __metadata:
   languageName: node
   linkType: hard
 
-"sass@npm:^1.52.3":
-  version: 1.82.0
-  resolution: "sass@npm:1.82.0"
-  dependencies:
-    "@parcel/watcher": "npm:^2.4.1"
-    chokidar: "npm:^4.0.0"
-    immutable: "npm:^5.0.2"
-    source-map-js: "npm:>=0.6.2 <2.0.0"
-  dependenciesMeta:
-    "@parcel/watcher":
-      optional: true
-  bin:
-    sass: sass.js
-  checksum: 10c0/7f86fe6ade4f6018862c448ed69d5c52f485b0125c9dab24e63f679739a04cc7c56562d588e3cf16b5efb4d2c4d0530e62740e1cfd273e2e3707d04d11011736
-  languageName: node
-  linkType: hard
-
 "sax@npm:1.2.1":
   version: 1.2.1
   resolution: "sax@npm:1.2.1"