Merge pull request #195 from AlexVCaron/test/data

[IMPROV] Test data introspection extension for VSCode

.devcontainer/Dockerfile

@@ -1,9 +1,11 @@
 FROM scilus/scilus:2.0.2
 
 ARG NFTEST_VERSION
+ARG POETRY_VERSION
 
 ENV NODE_MAJOR=18
 ENV NFTEST_VERSION=${NFTEST_VERSION:-0.9.0-rc1}
+ENV POETRY_VERSION=${POETRY_VERSION:-1.8.*}
 
 RUN apt update && apt install -y \
         curl \
@@ -14,7 +16,13 @@ RUN apt update && apt install -y \
 
 RUN python3 -m pip install pipx && \
     python3 -m pipx ensurepath && \
-    pipx install poetry
+    pipx install poetry==${POETRY_VERSION}
 
 RUN curl -fsSL https://deb.nodesource.com/setup_${NODE_MAJOR}.x | bash - &&\
-    apt-get install -y nodejs
+    apt-get install -y nodejs && \
+    groupadd --gid 501 yeoman && \
+    useradd --uid 501 --gid yeoman --shell /bin/bash --create-home yeoman && \
+    echo "yeoman ALL=(ALL) NOPASSWD:ALL" >> /etc/sudoers
+
+RUN mkdir /generated && chown yeoman:yeoman /generated
+WORKDIR /generated

.devcontainer/devcontainer.json

@@ -3,13 +3,17 @@
     "build": {
         "dockerfile": "Dockerfile",
         "args": {
-            "NFTEST_VERSION": "0.9.0-rc1"
+            "NFTEST_VERSION": "0.9.0-rc1",
+            "POETRY_VERSION": "1.8.*"
         }
     },
     "forwardPorts": [3000],
     "onCreateCommand": "bash .devcontainer/onCreateCommand.sh",
     "updateContentCommand": "bash .devcontainer/updateContentCommand.sh",
     "postStartCommand": "git config --global --add safe.directory ${containerWorkspaceFolder}",
+    "containerEnv": {
+        "WORKSPACE": "${containerWorkspaceFolder}"
+    },
     "features": {
         "ghcr.io/devcontainers/features/git:1": {},
         "ghcr.io/devcontainers/features/git-lfs:1": {},

.devcontainer/onCreateCommand.sh

@@ -1,5 +1,7 @@
 #!/usr/bin/env bash
 
+# Setup for NF-CORE
+
 npm install -g --save-dev --save-exact prettier
 npm install -g editorconfig
 npm install -g --save-dev editorconfig-checker
@@ -12,3 +14,10 @@ mkdir -p /nf-test/bin
 cd /nf-test/bin/
 curl -fsSL https://code.askimed.com/install/nf-test | bash -s ${NFTEST_VERSION}
 echo "PATH=$PATH:/nf-test/bin" >> ~/.bashrc
+
+
+# Setup for VSCODE Extensions Development
+
+npm install -g typescript
+npm install -g tslint
+npm install -g yo generator-code

.github/workflows/checks.yml

@@ -1,6 +1,22 @@
 name: nf-scil checks
 on:
   workflow_call:
+    inputs:
+      nextflow_version:
+        description: "Nextflow version to use"
+        required: false
+        type: string
+        default: "24.04.4"
+      nf_core_version:
+        description: "nf-core version to use"
+        required: false
+        type: string
+        default: "2.14.*"
+      nf_test_version:
+        description: "nf-test version to use"
+        required: false
+        type: string
+        default: "0.9.0-rc1"
 
 env:
   GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
@@ -11,6 +27,8 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v5
+        with:
+          cache: 'pip'
       - uses: pre-commit/[email protected]
         # FIXME Flip this off once we get to less than a couple hundred. Adding
         # this so it will only run against changed files. It'll make it much
@@ -21,34 +39,32 @@ jobs:
   prettier:
     runs-on: ubuntu-latest
     steps:
-      - name: Check out repository
-        uses: actions/checkout@v4
-
-      - name: Install NodeJS
-        uses: actions/setup-node@v4
+      - uses: actions/checkout@v4
+      - uses: actions/setup-node@v4
         with:
           node-version: "20"
+          cache: 'npm'
 
       - name: Install Prettier
-        run: npm install -g [email protected]
+        run: npm ci
 
       - name: Run Prettier --check
-        run: prettier --check .
+        run: npx prettier --check .
 
   editorconfig:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-
       - uses: actions/setup-node@v4
         with:
           node-version: "20"
+          cache: 'npm'
 
       - name: Install editorconfig-checker
-        run: npm install -g editorconfig-checker
+        run: npm ci
 
       - name: Run ECLint check
-        run: editorconfig-checker -exclude README.md $(git ls-files | grep -v test)
+        run: npx editorconfig-checker -exclude README.md $(git ls-files | grep -v test)
 
   nf-test-changes:
     name: compute - changes
@@ -95,6 +111,7 @@ jobs:
     with:
       type: "module"
       component: ${{ matrix.module }}
+      nextflow_version: ${{ inputs.nextflow_version }}
     secrets: inherit
 
   lint-subworkflows:
@@ -111,6 +128,7 @@ jobs:
     with:
       type: "subworkflow"
       component: ${{ matrix.subworkflow }}
+      nextflow_version: ${{ inputs.nextflow_version }}
     secrets: inherit
 
   nf-test:
@@ -133,12 +151,29 @@ jobs:
       profile: ${{ matrix.profile }}
       paths: ${{ matrix.path }}
       runner: ${{ matrix.runner }}
+      nextflow_version: ${{ inputs.nextflow_version }}
+      nf_test_version: ${{ inputs.nf_test_version }}
     secrets: inherit
 
+  upload-reports:
+    name: upload reports
+    needs: [nf-test-changes, nf-test]
+    if: ${{ ( needs.nf-test-changes.outputs.paths != '[]' ) }}
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/upload-artifact/merge@v4
+        with:
+          name: nf-test-reports
+          pattern: reports-*
+          delete-merged: true
+          retention-days: 10
+          compression-level: 9
+
   confirm-pass:
     name: status
     runs-on: ubuntu-latest
-    needs: [prettier, editorconfig, nf-test-changes, lint-modules, lint-subworkflows, nf-test]
+    needs: [prettier, editorconfig, nf-test-changes, lint-modules, lint-subworkflows, nf-test, upload-reports]
     if: ${{ !cancelled() }}
     steps:
       - name: All tests ok

.github/workflows/lint_module.yml

@@ -14,6 +14,11 @@ on:
         options:
           - module
           - subworkflow
+      nextflow_version:
+        description: "Nextflow version to use"
+        required: false
+        type: string
+        default: "24.04.4"
   workflow_call:
     inputs:
       component:
@@ -24,6 +29,11 @@ on:
         description: "Type of component"
         required: true
         type: string
+      nextflow_version:
+        description: "Nextflow version to use"
+        required: false
+        type: string
+        default: "24.04.4"
 
 run-name: Lint ${{ inputs.component }}
 jobs:
@@ -33,36 +43,30 @@ jobs:
 
     steps:
       - uses: actions/checkout@v4
-
-      - name: Set up Python
-        uses: actions/setup-python@v5
+      - uses: abatilo/actions-poetry@v2
         with:
-          python-version: "3.11"
-
-      - uses: actions/cache@v4
+          poetry-version: "1.8.*"
+      - uses: actions/setup-python@v5
         with:
-          path: ~/.cache/pip
-          key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
-          restore-keys: |
-            ${{ runner.os }}-pip
-            ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
-
-      - name: Install pip
-        run: python -m pip install --upgrade pip
-
+          python-version: "3.11"
+          cache: 'poetry'
       - uses: actions/setup-java@v4
         with:
           distribution: "temurin"
           java-version: "17"
-
-      - name: Setup Nextflow
-        uses: nf-core/setup-nextflow@v2
+      - uses: nf-core/setup-nextflow@v2
+        with:
+          version: ${{ inputs.nextflow_version }}
 
       - name: Install nf-core tools
         run: |
-          python -m pip install --upgrade --force-reinstall nf-core==2.14.*
+          poetry install --no-root
 
       - name: Lint ${{ inputs.type }} ${{ inputs.component }}
         env:
           GIT_CLONE_PROTECTION_ACTIVE: false
-        run: nf-core --verbose ${{ inputs.type }}s --git-remote https://github.com/scilus/nf-scil.git lint ${{ inputs.component }}
+        run: |
+          poetry run nf-core --verbose ${{ inputs.type }}s \
+            --git-remote https://github.com/${{ github.repository }}.git \
+            --branch ${GITHUB_HEAD_REF:-${GITHUB_REF#refs/heads/}} \
+            lint ${{ inputs.component }}