chore: refactor how package.json's were getting generated to remove t…

…he deprecate generatePackageJson flag from nx

.eslintrc.json

@@ -1,12 +1,24 @@
 {
   "root": true,
   "plugins": ["@nx"],
-  "extends": ["plugin:@nx/react"],
+  "extends": ["plugin:@nx/react", "plugin:jsonc/base"],
   "parserOptions": {
     "sourceType": "module",
     "allowImportExportEverywhere": true
   },
   "overrides": [
+    {
+      "files": ["**/*.json"],
+      "parser": "jsonc-eslint-parser",
+      "rules": {
+        "@nx/dependency-checks": [
+          "error",
+          {
+            "ignoredDependencies": ["recompose"]
+          }
+        ]
+      }
+    },
     {
       "files": ["*.ts", "*.tsx", "*.js", "*.jsx"],
       "rules": {

CHANGELOG.md

@@ -78,6 +78,6 @@ Generated by [`auto-changelog`](https://github.com/CookPete/auto-changelog).
 - Added menu item to allow user to export DNA as FASTA when looking at a protein sequence to resolve https://github.com/TeselaGen/tg-oss/issues/61 [`#61`](https://github.com/TeselaGen/tg-oss/issues/61)
 - Added fix for clipboard commands when there are multiple editors on a page to resolve https://github.com/TeselaGen/tg-oss/issues/24 [`#24`](https://github.com/TeselaGen/tg-oss/issues/24)
 - closes #35 [`#35`](https://github.com/TeselaGen/tg-oss/issues/35)
+- updating yarn lock [`ff41df0`](https://github.com/TeselaGen/tg-oss/commit/ff41df0b49b8051fcba084f7eaa44cf23284926d)
 - delete bounce-loader [`3135ae0`](https://github.com/TeselaGen/tg-oss/commit/3135ae0e611fb2c54ffb9372be2ac4386e794059)
 - alignment view refactor [`d8bc528`](https://github.com/TeselaGen/tg-oss/commit/d8bc528a6c7a7f30300c8aa06db7b31940bca13b)
-- chore: update yarn lock for example-demos [`0ce2dba`](https://github.com/TeselaGen/tg-oss/commit/0ce2dbac417e7832a3d8ac469830874ba3440372)

output.json

@@ -35,7 +35,10 @@
               "outputs": ["{options.outputFile}"],
               "options": {
                 "maxWarnings": 0,
-                "lintFilePatterns": ["packages/sequence-utils/**/*.js"]
+                "lintFilePatterns": [
+                  "packages/sequence-utils/**/*.js",
+                  "packages/sequence-utils/package.json"
+                ]
               },
               "configurations": {}
             },
@@ -103,7 +106,6 @@
               "outputs": ["{options.outputPath}"],
               "defaultConfiguration": "production",
               "options": {
-                "generatePackageJson": true,
                 "outputPath": "dist/bounce-loader"
               },
               "configurations": {
@@ -123,7 +125,8 @@
               "options": {
                 "maxWarnings": 0,
                 "lintFilePatterns": [
-                  "packages/bounce-loader/**/*.{ts,tsx,js,jsx}"
+                  "packages/bounce-loader/**/*.{ts,tsx,js,jsx}",
+                  "packages/bounce-loader/package.json"
                 ]
               },
               "configurations": {}
@@ -238,7 +241,10 @@
               "outputs": ["{options.outputFile}"],
               "options": {
                 "maxWarnings": 0,
-                "lintFilePatterns": ["packages/bio-parsers/**/*.js"]
+                "lintFilePatterns": [
+                  "packages/bio-parsers/**/*.js",
+                  "packages/bio-parsers/package.json"
+                ]
               },
               "configurations": {}
             },
@@ -320,7 +326,10 @@
               "outputs": ["{options.outputFile}"],
               "options": {
                 "maxWarnings": 0,
-                "lintFilePatterns": ["packages/range-utils/**/*.js"]
+                "lintFilePatterns": [
+                  "packages/range-utils/**/*.js",
+                  "packages/range-utils/package.json"
+                ]
               },
               "configurations": {}
             },
@@ -422,7 +431,10 @@
               "outputs": ["{options.outputFile}"],
               "options": {
                 "maxWarnings": 0,
-                "lintFilePatterns": ["packages/file-utils/**/*.js"]
+                "lintFilePatterns": [
+                  "packages/file-utils/**/*.js",
+                  "packages/file-utils/package.json"
+                ]
               },
               "configurations": {}
             },
@@ -503,7 +515,10 @@
               "outputs": ["{options.outputFile}"],
               "options": {
                 "maxWarnings": 0,
-                "lintFilePatterns": ["packages/uploader/**/*.{ts,tsx,js,jsx}"]
+                "lintFilePatterns": [
+                  "packages/uploader/**/*.{ts,tsx,js,jsx}",
+                  "packages/uploader/package.json"
+                ]
               },
               "configurations": {}
             }
@@ -536,7 +551,6 @@
               "defaultConfiguration": "production",
               "options": {
                 "emptyOutDir": false,
-                "generatePackageJson": true,
                 "outputPath": "dist/ove"
               },
               "configurations": {
@@ -563,7 +577,10 @@
               "outputs": ["{options.outputFile}"],
               "options": {
                 "maxWarnings": 0,
-                "lintFilePatterns": ["packages/ove/**/*.{ts,tsx,js,jsx}"]
+                "lintFilePatterns": [
+                  "packages/ove/**/*.{ts,tsx,js,jsx}",
+                  "packages/ove/package.json"
+                ]
               },
               "configurations": {}
             },
@@ -697,7 +714,6 @@
               "outputs": ["{options.outputPath}"],
               "defaultConfiguration": "production",
               "options": {
-                "generatePackageJson": true,
                 "outputPath": "dist/ui"
               },
               "configurations": {
@@ -721,7 +737,10 @@
               "outputs": ["{options.outputFile}"],
               "options": {
                 "maxWarnings": 0,
-                "lintFilePatterns": ["packages/ui/**/*.{ts,tsx,js,jsx}"]
+                "lintFilePatterns": [
+                  "packages/ui/**/*.{ts,tsx,js,jsx}",
+                  "packages/ui/package.json"
+                ]
               },
               "configurations": {}
             },

package.json

@@ -10,79 +10,7 @@
   },
   "type": "module",
   "private": true,
-  "dependencies": {
-    "@blueprintjs/core": "3.54.0",
-    "@blueprintjs/datetime": "^3.24.1",
-    "@blueprintjs/select": "3.18.11",
-    "@dnd-kit/core": "^6.1.0",
-    "@dnd-kit/modifiers": "^7.0.0",
-    "@dnd-kit/sortable": "^8.0.0",
-    "@hello-pangea/dnd": "16.2.0",
-    "@risingstack/react-easy-state": "^6.3.0",
-    "@teselagen/react-table": "6.10.16",
-    "@types/lodash-es": "^4.17.12",
-    "@use-gesture/react": "^10.2.23",
-    "axios": "^0.21.1",
-    "browser-or-node": "^2.0.0",
-    "classnames": "^2.3.2",
-    "color": "^3.2.1",
-    "combokeys": "^3.0.1",
-    "copy-to-clipboard": "^3.3.1",
-    "dayjs": "^1.10.4",
-    "deep-equal": "^1.1.1",
-    "dom-scroll-into-view": "^2.0.1",
-    "dom-to-image": "^2.6.0",
-    "downloadjs": "^1.4.7",
-    "file-saver": "^2.0.5",
-    "fuse.js": "^6.6.2",
-    "fuzzysearch": "^1.0.3",
-    "html2canvas": "^1.4.1",
-    "immer": "^9.0.15",
-    "is-mobile": "^3.0.0",
-    "jszip": "^3.10.1",
-    "lodash-es": "^4.17.21",
-    "math-expression-evaluator": "^1.3.7",
-    "mobx": "^6.10.2",
-    "mobx-react": "^9.0.1",
-    "nanoid": "^4.0.0",
-    "node-interval-tree": "^1.3.3",
-    "papaparse": "5.3.2",
-    "paths-js": "^0.4.11",
-    "pluralize": "^7.0.0",
-    "popper.js": "^1.16.1",
-    "prop-types": "^15.6.2",
-    "qs": "^6.9.6",
-    "react": "^18.3.1",
-    "react-color": "^2.19.3",
-    "react-dom": "^18.3.1",
-    "react-draggable": "4.4.5",
-    "react-dropzone": "^11.4.2",
-    "react-markdown": "9.0.1",
-    "react-measure": "^2.5.2",
-    "react-redux": "^8.0.5",
-    "react-rnd": "^10.2.4",
-    "react-router-dom": "5",
-    "react-sizeme": "^2.6.12",
-    "react-transition-group": "^2.4.0",
-    "recompose": "npm:react-recompose@0.31.1",
-    "redux": "^4.1.2",
-    "redux-act": "^1.8.0",
-    "redux-form": "^8.3.10",
-    "redux-ignore": "^1.2.5",
-    "redux-thunk": "2.4.1",
-    "remark-gfm": "^4.0.0",
-    "reselect": "^4.1.7",
-    "shortid": "^2.2.16",
-    "tg-use-local-storage-state": "^16.0.3",
-    "tippy.js": "^6.3.7",
-    "url-join": "^4.0.1",
-    "use-debounce": "^8.0.4",
-    "use-deep-compare-effect": "^1.6.1",
-    "use-local-storage-state": "^13.0.0",
-    "validate.io-nonnegative-integer-array": "^1.0.1",
-    "wait-on": "^7.0.1",
-    "write-excel-file": "^1.4.25"
-  },
+  "dependencies": {},
   "devDependencies": {
     "@babel/preset-react": "^7.24.6",
     "@cypress/code-coverage": "^3.12.39",
@@ -93,8 +21,8 @@
     "@nx/eslint-plugin": "19.1.0",
     "@nx/jest": "19.1.0",
     "@nx/js": "19.1.0",
-    "@nx/linter": "19.1.0",
-    "@nx/react": "19.1.0",
+    "@nx/linter": "19.8.4",
+    "@nx/react": "20.4.6",
     "@nx/vite": "19.1.0",
     "@nx/web": "19.1.0",
     "@nx/workspace": "19.1.0",
@@ -104,6 +32,7 @@
     "@types/bluebird": "^3.5.42",
     "@types/jest": "^29.5.8",
     "@types/jszip": "^3.4.1",
+    "@types/lodash-es": "^4.17.12",
     "@types/node": "20.9.0",
     "@types/papaparse": "^5.3.11",
     "@types/react": "18.2.37",
@@ -130,6 +59,7 @@
     "eslint-config-prettier": "9.0.0",
     "eslint-plugin-cypress": "^2.15.1",
     "eslint-plugin-import": "2.29.0",
+    "eslint-plugin-jsonc": "^2.19.1",
     "eslint-plugin-jsx-a11y": "6.8.0",
     "eslint-plugin-no-only-tests": "^3.1.0",
     "eslint-plugin-react": "7.33.2",
@@ -139,6 +69,7 @@
     "jest": "^29.7.0",
     "jest-environment-jsdom": "^29.7.0",
     "jsdom": "~24.0.0",
+    "jsonc-eslint-parser": "^2.4.0",
     "lint-staged": "^15.2.4",
     "million": "^3.1.5",
     "nx": "19.1.0",

packages/bio-parsers/package.json

@@ -1,17 +1,19 @@
 {
   "name": "@teselagen/bio-parsers",
-  "version": "0.4.24",
+  "version": "0.4.27",
   "type": "module",
   "dependencies": {
     "@gmod/gff": "^1.2.1",
-    "buffer": "^6.0.3",
+    "buffer": "5.7.1",
     "bufferpack": "^0.0.6",
-    "color": "^4.2.3",
+    "color": "3.2.1",
     "fast-xml-parser": "^4.2.5",
     "fflate": "^0.8.0",
     "lodash-es": "^4.17.21",
     "string_decoder": "^1.3.0",
-    "validate.io-nonnegative-integer-array": "^1.0.1"
+    "validate.io-nonnegative-integer-array": "^1.0.1",
+    "@teselagen/sequence-utils": "file:../sequence-utils",
+    "@teselagen/range-utils": "file:../range-utils"
   },
   "exports": {
     ".": {

packages/bio-parsers/project.json

@@ -33,7 +33,10 @@
       "executor": "@nx/linter:eslint",
       "outputs": ["{options.outputFile}"],
       "options": {
-        "lintFilePatterns": ["packages/bio-parsers/**/*.js"]
+        "lintFilePatterns": [
+          "packages/bio-parsers/**/*.js",
+          "packages/bio-parsers/package.json"
+        ]
       }
     }
   },

packages/bounce-loader/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@teselagen/bounce-loader",
-  "version": "0.3.11",
+  "version": "0.3.15",
   "main": "./src/index.js",
   "type": "module",
   "exports": {
@@ -9,5 +9,9 @@
       "require": "./index.cjs.js"
     },
     "./style.css": "./style.css"
+  },
+  "dependencies": {
+    "classnames": "^2.3.2",
+    "react": "^18.3.1"
   }
 }

packages/bounce-loader/project.json

@@ -9,15 +9,17 @@
       "executor": "@nx/linter:eslint",
       "outputs": ["{options.outputFile}"],
       "options": {
-        "lintFilePatterns": ["packages/bounce-loader/**/*.{ts,tsx,js,jsx}"]
+        "lintFilePatterns": [
+          "packages/bounce-loader/**/*.{ts,tsx,js,jsx}",
+          "packages/bounce-loader/package.json"
+        ]
       }
     },
     "build": {
       "executor": "@nx/vite:build",
       "outputs": ["{options.outputPath}"],
       "defaultConfiguration": "production",
       "options": {
-        "generatePackageJson": true,
         "outputPath": "dist/bounce-loader"
       },
       "configurations": {

packages/file-utils/package.json

@@ -1,12 +1,13 @@
 {
   "name": "@teselagen/file-utils",
-  "version": "0.3.18",
+  "version": "0.3.20",
   "type": "module",
   "dependencies": {
     "bluebird": "^3.7.2",
     "jszip": "^3.10.1",
     "lodash-es": "^4.17.21",
-    "papaparse": "5.3.2"
+    "papaparse": "5.3.2",
+    "buffer": "5.7.1"
   },
   "devDependencies": {
     "mock-fs": "^5.2.0"

packages/file-utils/project.json

@@ -33,7 +33,10 @@
       "executor": "@nx/linter:eslint",
       "outputs": ["{options.outputFile}"],
       "options": {
-        "lintFilePatterns": ["packages/file-utils/**/*.js"]
+        "lintFilePatterns": [
+          "packages/file-utils/**/*.js",
+          "packages/file-utils/package.json"
+        ]
       }
     }
   },