Merge pull request #3 from AlexVCaron/fix/devcontainer_extensions

[FIX] Update buggy extension package
scilus · Sep 17, 2024 · 4a905d1 · 4a905d1
2 parents 1caf80a + 3c2e25a
commit 4a905d1
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Showing 17 changed files with 794 additions and 152 deletions.
diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
@@ -52,10 +52,8 @@
     "customizations": {
         "vscode": {
             "settings": {
-                "[prettier]": {
-                    "prettierPath": "/usr/lib/node_modules/prettier"
-                },
-                "[python]": {
+                "prettier.prettierPath": "/usr/lib/node_modules/prettier",
+                "python": {
                     "analysis.exclude": [
                         "${containerWorkspaceFolder}/.dvc",
                         "${containerWorkspaceFolder}/.pytest_cache",
@@ -83,13 +81,7 @@
                     "terminal.focusAfterLaunch": true
                 }
             },
-            "extensions": [
-                "nf-neuro.nf-neuro-extensions",
-                "ms-python.autopep8",
-                "ms-python.vscode-pylance",
-                "mutantdino.resourcemonitor",
-                "KorbinianEckstein.niivue"
-            ]
+            "extensions": ["nf-neuro.nf-neuro-extensionpack"]
         }
     },
     "init": true,

diff --git a/.devcontainer/onCreateCommand.sh b/.devcontainer/onCreateCommand.sh
@@ -3,7 +3,7 @@
 # Setup for NF-CORE
 
 npm install -g --save-dev --save-exact prettier
-npm install -g editorconfig
+npm install -g --save-dev editorconfig
 npm install -g --save-dev editorconfig-checker
 
 mkdir -p $XDG_CONFIG_HOME/nf-neuro
@@ -14,10 +14,3 @@ 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
diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md
@@ -1,23 +1,24 @@
 ---
 name: Bug report
 about: Create a report to help us improve
-title: ''
+title: ""
 labels: bug
 assignees: AlexVCaron
-
 ---
 
 **System (complete the following information, else the issue will be closed):**
-  - OS: [e.g. Ubuntu, CentOS, other Linux distributions, MacOS, WSL, Windows, ...]
-  - Python version [e.g. 3.10, PyPa 3.7, CPython 3.9, ...]
-  - `nf-core` version [e.g. 1.0.0, 1.2.post3, 0.1.dev0, main, feat/awesome_module, ...]
-  - `nf-neuro` version [e.g. 1.0.0, 1.2.post3, 0.1.dev0, main, feat/awesome_module, ...]
+
+- OS: [e.g. Ubuntu, CentOS, other Linux distributions, MacOS, WSL, Windows, ...]
+- Python version [e.g. 3.10, PyPa 3.7, CPython 3.9, ...]
+- `nf-core` version [e.g. 1.0.0, 1.2.post3, 0.1.dev0, main, feat/awesome_module, ...]
+- `nf-neuro` version [e.g. 1.0.0, 1.2.post3, 0.1.dev0, main, feat/awesome_module, ...]
 
 **Describe the bug**
 A clear and concise description of what the bug is.
 
 **To Reproduce**
 Steps to reproduce the behavior:
+
 1. Go to '...'
 2. Click on '....'
 3. Scroll down to '....'

diff --git a/.github/ISSUE_TEMPLATE/feature_request.md b/.github/ISSUE_TEMPLATE/feature_request.md
@@ -1,10 +1,9 @@
 ---
 name: Feature request
 about: Suggest an idea for this project
-title: ''
-labels: ''
-assignees: ''
-
+title: ""
+labels: ""
+assignees: ""
 ---
 
 **Is your feature request related to a problem?**

diff --git a/.github/ISSUE_TEMPLATE/usage_issue.md b/.github/ISSUE_TEMPLATE/usage_issue.md
@@ -1,10 +1,9 @@
 ---
 name: Usage issue
 about: I have a problem using nf-neuro
-title: ''
-labels: ''
-assignees: ''
-
+title: ""
+labels: ""
+assignees: ""
 ---
 
 For now, `nf-neuro` is a closed community. Once we open to outside users and contributors, go to [Neurostars](https://neurostars.org/tag/nf-neuro) and post your common issue there. not here !
diff --git a/.github/reviewers.yml b/.github/reviewers.yml
@@ -38,36 +38,36 @@ reviewers:
       - gagnonanthony
 
 files:
-  '**':
+  "**":
     - infrastructure-leads
     - repository-owners
-  'docs/**':
+  "docs/**":
     - documentation-leads
-  'LICENSE':
+  "LICENSE":
     - repository-owners
-  'CONTRIBUTING.md':
+  "CONTRIBUTING.md":
     - repository-owners
     - documentation-leads
-  '.devcontainer/**':
+  ".devcontainer/**":
     - infrastructure-leads
-  '.github/**':
+  ".github/**":
     - infrastructure-leads
-  '.github/ISSUE_TEMPLATE/**':
+  ".github/ISSUE_TEMPLATE/**":
     - infrastructure-leads
     - documentation-leads
-  '.github/PULL_REQUEST_TEMPLATE/**':
+  ".github/PULL_REQUEST_TEMPLATE/**":
     - infrastructure-leads
     - documentation-leads
-  '.github/pull_request_template.md':
+  ".github/pull_request_template.md":
     - infrastructure-leads
     - documentation-leads
-  '.vscode/**':
+  ".vscode/**":
     - infrastructure-leads
-  'tests/**':
+  "tests/**":
     - infrastructure-leads
-  'modules/nf-neuro/**':
+  "modules/nf-neuro/**":
     - guidelines-leads
-  'subworkflows/nf-neuro/**':
+  "subworkflows/nf-neuro/**":
     - guidelines-leads
 
 options:

diff --git a/.github/workflows/lint_component.yml b/.github/workflows/lint_component.yml
@@ -49,7 +49,7 @@ jobs:
       - uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5.2.0
         with:
           python-version: "3.11"
-          cache: 'poetry'
+          cache: "poetry"
       - uses: actions/setup-java@2dfa2011c5b2a0f1489bf9e433881c92c1631f88 # v4.3.0
         with:
           distribution: "temurin"

diff --git a/.github/workflows/run_checks_suite.yml b/.github/workflows/run_checks_suite.yml
@@ -25,7 +25,7 @@ jobs:
       - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
       - uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5.2.0
         with:
-          cache: 'pip'
+          cache: "pip"
       - uses: pre-commit/action@2c7b3805fd2a0fd8c1884dcaebf91fc102a13ecd # v3.0.1
         # 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
@@ -40,7 +40,7 @@ jobs:
       - uses: actions/setup-node@1e60f620b9541d16bece96c5465dc8ee9832be0b # v4.0.3
         with:
           node-version: "20"
-          cache: 'npm'
+          cache: "npm"
 
       - name: Install Prettier
         run: npm ci
@@ -55,7 +55,7 @@ jobs:
       - uses: actions/setup-node@1e60f620b9541d16bece96c5465dc8ee9832be0b # v4.0.3
         with:
           node-version: "20"
-          cache: 'npm'
+          cache: "npm"
 
       - name: Install editorconfig-checker
         run: npm ci
@@ -101,9 +101,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        module: [
-          "${{ fromJson(needs.nf-test-changes.outputs.modules) }}"
-        ]
+        module: ["${{ fromJson(needs.nf-test-changes.outputs.modules) }}"]
     uses: ./.github/workflows/lint_component.yml
     with:
       type: "module"
@@ -118,9 +116,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        subworkflow: [
-          "${{ fromJson(needs.nf-test-changes.outputs.subworkflows) }}"
-        ]
+        subworkflow: ["${{ fromJson(needs.nf-test-changes.outputs.subworkflows) }}"]
     uses: ./.github/workflows/lint_component.yml
     with:
       type: "subworkflow"
@@ -135,7 +131,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        path: [ "${{ fromJson(needs.nf-test-changes.outputs.paths) }}" ]
+        path: ["${{ fromJson(needs.nf-test-changes.outputs.paths) }}"]
         include:
           - profile: docker
           - runner: scilus-nf-neuro-runners

diff --git a/.github/workflows/test_component.yml b/.github/workflows/test_component.yml
@@ -9,14 +9,14 @@ on:
         type: string
       profile:
         description: "Which profile to use to run the component's tests"
-        default: 'docker'
+        default: "docker"
         type: choice
         options:
           - docker
           - singularity
       runner:
         description: "Runner label to use for the test run"
-        default: 'ubuntu-latest'
+        default: "ubuntu-latest"
         type: string
       nextflow_version:
         description: "Nextflow version to use"
@@ -39,11 +39,11 @@ on:
           Which profile to use to run the component's tests, either :
             - docker
             - singularity
-        default: 'docker'
+        default: "docker"
         type: string
       runner:
         description: "Runner label to use for the test run"
-        default: 'ubuntu-latest'
+        default: "ubuntu-latest"
         type: string
       nextflow_version:
         description: "Nextflow version to use"
@@ -78,7 +78,7 @@ jobs:
       - uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5.2.0
         with:
           python-version: "3.11"
-          cache: 'pip'
+          cache: "pip"
       - uses: actions/setup-java@2dfa2011c5b2a0f1489bf9e433881c92c1631f88 # v4.3.0
         with:
           distribution: "temurin"

diff --git a/.github/workflows/update_pr.yml b/.github/workflows/update_pr.yml
@@ -6,8 +6,7 @@ on:
   merge_group:
     types:
       - checks_requested
-    branches:
-      -main
+    branches: -main
 
 # Cancel if a newer run is started
 concurrency:

diff --git a/.prettierignore b/.prettierignore
@@ -1,7 +1,5 @@
 **/package-lock.json
 **/poetry.lock
-.devcontainer/
-.github/
 .nextflow/
 .nf-test/
 .pytest_cache/

diff --git a/.vscode/extension-package/CHANGELOG.md b/.vscode/extension-package/CHANGELOG.md
@@ -1,17 +1,21 @@
 # Change Log
 
-## [Unreleased]
+## [1.0.1] - 2024-09-16
 
-## [0.0.1] - 2023-11-10
+- Upgrade extension list
 
-- Initial release
+## [1.0.0] - 2024-09-13
+
+- Add `Test Data TreeView` to the package
+- Move package under the `nf-neuro` namespace
+- Uniformize branding
 
 ## [0.0.2] - 2023-11-14
 
 - Add `Git Graph` to the package
 
-## [1.0.0] - 2024-09-13
+## [0.0.1] - 2023-11-10
 
-- Add `Test Data TreeView` to the package
-- Move package under the `nf-neuro` namespace
-- Uniformize branding
+- Initial release
+
+## [Unreleased]