Update user interface (#211)

* Add mui; facelift settings screen

* Parameter map (#203)

* Enable parameter-mapping support in workflows (no interface yet)

* Disable alphabetical sorting on config.yaml dump

* Pre-commit

* Enable parameter maps and parameter dropdown selection lists

* Tidy-up

* [fix] Close info pane on node delete and deselect

* Bump cryptography from 41.0.4 to 41.0.6 in /electron-app

Bumps [cryptography](https://github.com/pyca/cryptography) from 41.0.4 to 41.0.6.
- [Changelog](https://github.com/pyca/cryptography/blob/main/CHANGELOG.rst)
- [Commits](pyca/cryptography@41.0.4...41.0.6)

---
updated-dependencies:
- dependency-name: cryptography
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>

* Bump @adobe/css-tools from 4.3.1 to 4.3.2 in /nodemapper

Bumps [@adobe/css-tools](https://github.com/adobe/css-tools) from 4.3.1 to 4.3.2.
- [Changelog](https://github.com/adobe/css-tools/blob/main/History.md)
- [Commits](https://github.com/adobe/css-tools/commits)

---
updated-dependencies:
- dependency-name: "@adobe/css-tools"
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <support@github.com>

* Bump pyinstaller from 5.13.0 to 5.13.1 in /electron-app

Bumps [pyinstaller](https://github.com/pyinstaller/pyinstaller) from 5.13.0 to 5.13.1.
- [Release notes](https://github.com/pyinstaller/pyinstaller/releases)
- [Changelog](https://github.com/pyinstaller/pyinstaller/blob/develop/doc/CHANGES.rst)
- [Commits](pyinstaller/pyinstaller@v5.13.0...v5.13.1)

---
updated-dependencies:
- dependency-name: pyinstaller
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>

* Bump paramiko from 3.3.1 to 3.4.0 in /electron-app

Bumps [paramiko](https://github.com/paramiko/paramiko) from 3.3.1 to 3.4.0.
- [Commits](paramiko/paramiko@3.3.1...3.4.0)

---
updated-dependencies:
- dependency-name: paramiko
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>

* Bump follow-redirects from 1.15.3 to 1.15.4 in /nodemapper

Bumps [follow-redirects](https://github.com/follow-redirects/follow-redirects) from 1.15.3 to 1.15.4.
- [Release notes](https://github.com/follow-redirects/follow-redirects/releases)
- [Commits](follow-redirects/follow-redirects@v1.15.3...v1.15.4)

---
updated-dependencies:
- dependency-name: follow-redirects
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <support@github.com>

* Bump gitpython from 3.1.37 to 3.1.41 in /electron-app

Bumps [gitpython](https://github.com/gitpython-developers/GitPython) from 3.1.37 to 3.1.41.
- [Release notes](https://github.com/gitpython-developers/GitPython/releases)
- [Changelog](https://github.com/gitpython-developers/GitPython/blob/main/CHANGES)
- [Commits](gitpython-developers/GitPython@3.1.37...3.1.41)

---
updated-dependencies:
- dependency-name: gitpython
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>

* Bump gitpython from 3.1.37 to 3.1.41 in /runner

Bumps [gitpython](https://github.com/gitpython-developers/GitPython) from 3.1.37 to 3.1.41.
- [Release notes](https://github.com/gitpython-developers/GitPython/releases)
- [Changelog](https://github.com/gitpython-developers/GitPython/blob/main/CHANGES)
- [Commits](gitpython-developers/GitPython@3.1.37...3.1.41)

---
updated-dependencies:
- dependency-name: gitpython
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>

* Pin PuLP to allow snakemake to install [fix] (#185)

* Pin PuLP to allow snakemake to install [fix]

* Wait for module expansion to compete in e2e tests

* Add count check when expanding modules in e2e tests (#187)

* Add count check when expanding modules in e2e tests

* Persistent local settings and master list reload (#186)

* Implement persistent settings (local state) and master list reloading

* [fix] Close info pane on node delete and deselect

* First pass parameter_maps implemented

* Introduce custom Node type for reactflow to formalise Node/Module config and params structures

* Fix HighlightedJSON link error

* (wip) Remove parameter_maps and replace with parameter metadata

* Refactor of parameter mapping from modal dialog

* TreeView interface for parameter mapping

* Refactor Node-info pane to use TreeView; format Parameter-list view

* Pre-commit

* Implement linkage mechanism in builder; add unit and e2e tests

* Pre-commit

* Fix payload_shell test-repo module

* Highlight linked parameters; permit removal; add link removal tests

* Remove parameter links when nodes are deleted

* Pre-commit

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Add 'results' to linkage e2e test paths

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Update nodemapper/src/gui/Builder/components/ParameterList.tsx

Co-authored-by: Stanisław Zakrzewski <41862803+stanislaw-zakrzewski@users.noreply.github.com>

* Update nodemapper/src/gui/Builder/components/Flow.tsx

Co-authored-by: Stanisław Zakrzewski <41862803+stanislaw-zakrzewski@users.noreply.github.com>

* Update nodemapper/src/gui/Builder/components/Flow.tsx

Co-authored-by: Stanisław Zakrzewski <41862803+stanislaw-zakrzewski@users.noreply.github.com>

* Update nodemapper/src/gui/Builder/components/Flow.tsx

Co-authored-by: Stanisław Zakrzewski <41862803+stanislaw-zakrzewski@users.noreply.github.com>

* Update nodemapper/src/gui/Builder/components/Flow.tsx

Co-authored-by: Stanisław Zakrzewski <41862803+stanislaw-zakrzewski@users.noreply.github.com>

* Update nodemapper/src/gui/Builder/components/HighlightedJSON.tsx

Co-authored-by: Stanisław Zakrzewski <41862803+stanislaw-zakrzewski@users.noreply.github.com>

* Update nodemapper/src/gui/Builder/components/HighlightedJSON.tsx

Co-authored-by: Stanisław Zakrzewski <41862803+stanislaw-zakrzewski@users.noreply.github.com>

* Tidy-up

* Merge conflict

* Replace ternary-null with &&

* Remove redundant messages

* Use Icon for key symbol

* Prettier

* yarn update

* Update nodemapper/src/gui/Builder/components/ParameterList.tsx

Co-authored-by: Stanisław Zakrzewski <41862803+stanislaw-zakrzewski@users.noreply.github.com>

* Fix tests after removing examples folder

* Rename code to nodeparams throughout

* Remove redundant json assignment

* Pre-commit

---------

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Stanisław Zakrzewski <41862803+stanislaw-zakrzewski@users.noreply.github.com>

* Merge main

* Move Sidenav.module.css

* Fix yarn.lock conflicts

* (wip) Facelift

* (wip) Facelift

* Facelift

* Deselect nodes after import

* Refactor repo list and search

* Refactor header menus

* Scene save and load; Fix logger sizing; styling

* Prettier

* Refactors of Logger, Modules list, Parameter map

* Tidy-up tests; permit skipping of container tests; add wait cursor during module loading

* Update tests

* Add global.health colour scheme

* Split NodeInfo in a component folder; hide params in nodeinfo

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Project list now only lists projects in selected repos list

* Refactor NodeInfo separate display components

* Refactor NodeInfo editables with mui

* Add editable list types to NodeInfo

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

---------

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Stanisław Zakrzewski <41862803+stanislaw-zakrzewski@users.noreply.github.com>

.github/workflows/GRAPEVNE.yml

@@ -15,17 +15,13 @@ on:
       - "docs/**"
 
 jobs:
-  es-lint-nodemapper:
-    uses: ./.github/workflows/eslint-nodemapper.yml
-  jest-nodemapper:
-    uses: ./.github/workflows/jest-nodemapper.yml
-  es-lint-electron-app:
-    uses: ./.github/workflows/eslint-electron-app.yml
-  jest-electron-app:
-    uses: ./.github/workflows/jest-electron-app.yml
-  pytest-backend:
-    uses: ./.github/workflows/pytest-backend.yml
-  pytest-builder:
-    uses: ./.github/workflows/pytest-builder.yml
-  pytest-runner:
-    uses: ./.github/workflows/pytest-runner.yml
+  nodemapper:
+    uses: ./.github/workflows/nodemapper.yml
+  electron-app:
+    uses: ./.github/workflows/electron-app.yml
+  backend:
+    uses: ./.github/workflows/backend.yml
+  builder:
+    uses: ./.github/workflows/builder.yml
+  runner:
+    uses: ./.github/workflows/runner.yml

.github/workflows/pytest-backend.yml → .github/workflows/backend.yml

@@ -1,13 +1,7 @@
-name: Pytest-backend
+name: Backend
 
 on:
   workflow_call:
-#  push:
-#    branches: [main]
-#    paths:
-#      - ".github/workflows/pytest-backend.yml"
-#      - "backend/**"
-#      - "!backend/README.md"
 
 jobs:
   ci:
@@ -17,7 +11,7 @@ jobs:
         working-directory: backend
     strategy:
       matrix:
-        python-version: ["3.9", "3.10", "3.11"]
+        python-version: ["3.11"]
     steps:
       - uses: actions/checkout@v3
       - name: Set up Python ${{ matrix.python-version }}

.github/workflows/pytest-builder.yml → .github/workflows/builder.yml

@@ -1,13 +1,7 @@
-name: Pytest-builder
+name: Builder
 
 on:
   workflow_call:
-#  push:
-#    branches: [main]
-#    paths:
-#      - ".github/workflows/pytest-builder.yml"
-#      - "builder/**"
-#      - "!builder/README.md"
 
 jobs:
   ci:
@@ -17,7 +11,7 @@ jobs:
         working-directory: builder
     strategy:
       matrix:
-        python-version: ["3.9", "3.10", "3.11"]
+        python-version: ["3.11"]
     steps:
       - uses: actions/checkout@v3
       - name: Set up Python ${{ matrix.python-version }}

.github/workflows/electron-app.yml

@@ -0,0 +1,18 @@
+name: electron-app
+
+on:
+  workflow_call:
+
+jobs:
+  eslint:
+    name: Run eslint scanning
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        working-directory: electron-app
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v3
+
+      - name: Run tests
+        run: ./run_tests.sh

.github/workflows/nodemapper.yml

@@ -0,0 +1,18 @@
+name: nodemapper
+
+on:
+  workflow_call:
+
+jobs:
+  eslint:
+    name: Run eslint scanning
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        working-directory: nodemapper
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v3
+
+      - name: Run tests
+        run: ./run_tests.sh

.github/workflows/pytest-runner.yml → .github/workflows/runner.yml

@@ -17,7 +17,7 @@ jobs:
         working-directory: runner
     strategy:
       matrix:
-        python-version: ["3.9", "3.10", "3.11"]
+        python-version: ["3.11"]
     steps:
       - uses: actions/checkout@v3
       - name: Set up Python ${{ matrix.python-version }}

builder/builder/builder.py

@@ -797,7 +797,7 @@ def ExpandModule(self, rulename: str):
         elif isinstance(node.input_namespace, dict):
             raise ValueError("Input dictionary namespaces not supported yet")
         elif node.input_namespace is None:
-            # Module is a Source and (no incoming connections)
+            # Module is a Source (no incoming connections)
             pass
         else:
             raise ValueError("Namespace type not recognised")

electron-app/.eslintrc.json

@@ -1,15 +1,22 @@
 {
-  "env": {
-    "browser": true,
-    "es2021": true
-  },
-  "extends": ["eslint:recommended", "plugin:@typescript-eslint/recommended"],
-  "overrides": [],
-  "parser": "@typescript-eslint/parser",
-  "parserOptions": {
-    "ecmaVersion": "latest",
-    "sourceType": "module"
-  },
-  "plugins": ["@typescript-eslint"],
-  "rules": {}
+    "env": {
+        "browser": true,
+        "es2021": true
+    },
+    "extends": [
+        "eslint:recommended",
+        "plugin:@typescript-eslint/recommended"
+    ],
+    "overrides": [
+    ],
+    "parser": "@typescript-eslint/parser",
+    "parserOptions": {
+        "ecmaVersion": "latest",
+        "sourceType": "module"
+    },
+    "plugins": [
+        "@typescript-eslint"
+    ],
+    "rules": {
+    }
 }

electron-app/jest.config.ts

@@ -23,4 +23,5 @@ export default {
   transform: {
     "^.+\\.(ts|tsx)$": "ts-jest",
   },
+  "testTimeout": 30000,
 };

electron-app/package.json

@@ -5,10 +5,11 @@
   "main": "dist/main.js",
   "scripts": {
     "start": "electron-forge start",
-    "lint": "eslint src/ --ext .ts",
+    "lint": "eslint src/**/*.{ts,tsx}",
     "build": "tsc",
     "test": "jest ./src",
     "postbuild-tests": "jest --runInBand ./postbuild_tests",
+    "postbuild-tests-no-containers": "jest --runInBand ./postbuild_tests --no-containers",
     "package": "electron-forge package",
     "make": "electron-forge make",
     "publish": "electron-forge publish"
@@ -29,12 +30,13 @@
     "@types/node": "^20.3.1",
     "@types/selenium-webdriver": "^4.1.16",
     "@types/shelljs": "^0.8.13",
-    "@typescript-eslint/eslint-plugin": "^5.60.0",
-    "@typescript-eslint/parser": "^5.60.0",
+    "@typescript-eslint/eslint-plugin": "^7.0.2",
+    "@typescript-eslint/parser": "^7.0.2",
     "babel-jest": "^29.5.0",
     "decompress": "^4.2.1",
     "electron": "27",
     "eslint": "^8.43.0",
+    "eslint-plugin-react": "^7.33.2",
     "fork-ts-checker-webpack-plugin": "^8.0.0",
     "jest": "^29.6.4",
     "jest-environment-jsdom": "^29.5.0",