NickAkhmetov/HMP-233 Switch to PNPM

.github/workflows/node-ci.yml

@@ -12,21 +12,22 @@ jobs:
     runs-on: ubuntu-20.04
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
         with:
           submodules: "recursive"
-
+      - uses: pnpm/action-setup@v2
+        with:
+          version: 8.8.0
       - name: Set up Node
         uses: actions/setup-node@v3
         with:
           node-version-file: ".nvmrc"
-          cache: "npm"
-          cache-dependency-path: context/package-lock.json
-
-      - run: npm --version
+          cache: "pnpm"
+          cache-dependency-path: context/pnpm-lock.yaml
+      - run: pnpm --version
 
       - name: Install node dependencies
-        run: npm ci --prefix context
+        run: pnpm i --frozen-lockfile --dir context
 
       - name: Run test script
         run: etc/test/test-node.sh

.vscode/default.settings.json

@@ -11,6 +11,7 @@
     "editor.defaultFormatter": "ms-python.autopep8"
   },
   "python.formatting.provider": "autopep8",
+  "npm.packageManager": "pnpm",
   "optional": {
     "editor.formatOnSave": true,
     "editor.codeActionsOnSave": {

.vscode/tasks.json

@@ -43,7 +43,7 @@
       }
     },
     {
-      "label": "npm install",
+      "label": "Install JS Dependencies",
       "type": "npm",
       "script": "install",
       "group": {
@@ -66,7 +66,7 @@
       "dependsOn": [
         "Init submodules",
         "pip install",
-        "npm install"
+        "Install JS Dependencies"
       ],
       "dependsOrder": "parallel"
     },
@@ -108,7 +108,7 @@
       "dependsOrder": "sequence"
     },
     {
-      "label": "npm run lint",
+      "label": "Lint JS",
       "type": "npm",
       "script": "lint",
       "problemMatcher": [
@@ -150,7 +150,7 @@
     {
       "label": "React Dev Server (+ lint)",
       "dependsOn": [
-        "npm run lint",
+        "Lint JS",
         "React Dev Server"
       ],
       "dependsOrder": "sequence"
@@ -244,7 +244,7 @@
       "options": {
         "cwd": "${workspaceFolder}/context"
       },
-      "command": "npx --yes kill-port 5000 5001 6006"
+      "command": "pnpm dlx --silent kill-port 5000 5001 6006"
     }
   ]
 }

CHANGELOG-HMP-233.md

@@ -0,0 +1 @@
+- Migrate to `pnpm` package manager.

README.md

@@ -115,9 +115,10 @@ All designs are in [Figma](https://www.figma.com/files/team/834568130405102661/H
     - `` pyenv install `cat .python-version`  ``
     - `` pyenv virtualenv `cat .python-version` portal ``
     - `pyenv activate portal`
-- `nodejs/npm`: Suggest [installing nvm](https://github.com/nvm-sh/nvm#installing-and-updating) and then using it to install the appropriate node version: `nvm install`.
+- `nodejs`: Suggest [installing nvm](https://github.com/nvm-sh/nvm#installing-and-updating) and then using it to install the appropriate node version: `nvm install`.
   - `` nvm install `cat .nvmrc`  ``
   - `` nvm use `cat .nvmrc`  ``
+- `pnpm`: Suggest [install pnpm via npm](https://pnpm.io/installation#using-npm) after installing the proper `nodejs` version.
 
 Optional:
 
@@ -200,8 +201,8 @@ Load tests [are available](end-to-end/artillery/), but they are not run as part
 
 ### Running tests locally without docker
 
-- **Jest**: `cd context; npm run test`
-- **Cypress**: With the application running, `cd end-to-end; npm run cypress:open`
+- **Jest**: `cd context; pnpm run test`
+- **Cypress**: With the application running, `cd end-to-end; pnpm run cypress:open`
   - If using WSL2, see the WSL2-specific steps in the [end to end readme](./end-to-end/README.md).
   - Note that the cypress tests (particularly for the publication page) are expected to be run with the `test` environment enabled in app.conf
 - **Pytest**: `cd context; pytest app --ignore app/api/vitessce_conf_builder`
@@ -215,15 +216,15 @@ You can also lint and auto-correct from the command-line:
 
 ```
 cd context
-npm run lint
-npm run lint:fix
+pnpm run lint
+pnpm run lint:fix
 EXCLUDE=node_modules,ingest-validation-tools,etc/dev/organ-utils
 autopep8 --in-place --aggressive -r . --exclude $EXCLUDE
 ```
 
 ### Storybook
 
-To start storybook locally you can either run `etc/dev/dev-start.sh`, or just `npm run storybook`,
+To start storybook locally you can either run `etc/dev/dev-start.sh`, or just `pnpm run storybook`,
 and after it has started, visit [localhost:6006](http://localhost:6006).
 
 ## Build, tag, and deploy
@@ -234,7 +235,7 @@ The build, tag, deploy, and QA procedures are [detailed here](https://hms-dbmi.a
 
 <details><summary>Webpack</summary>
 
-To view visualizations of the production webpack bundle run `npm run build:analyze`.
+To view visualizations of the production webpack bundle run `pnpm run build:analyze`.
 The script will generate two files, report.html and stats.html, inside the public directory each showing a different visual representation of the bundle.
 
 </details>

context/Dockerfile

@@ -3,15 +3,18 @@ ARG PYTHON_MINOR_V
 
 FROM node:${NODE_V}-alpine as builder
 
+# Run corepack to get `pnpm`
+RUN corepack enable
+
 WORKDIR /work
 RUN apk add --no-cache git
 
 # COPY only what is needed so layers can be cached.
 COPY package.json .
-COPY package-lock.json .
+COPY pnpm-lock.yaml . 
 COPY .npmrc .
 
-RUN npm ci
+RUN pnpm ci
 
 COPY tsconfig.json tsconfig.json
 COPY .swcrc .swcrc
@@ -21,7 +24,7 @@ COPY ingest-validation-tools ingest-validation-tools
 # portal-visualization is python-only, and not needed for the npm build.
 
 ENV NODE_OPTIONS="--max-old-space-size=4096"
-RUN npm run build
+RUN pnpm run build
 
 FROM tiangolo/uwsgi-nginx-flask:python${PYTHON_MINOR_V}