Merge branch 'main' into fixerrorcodes

.devcontainer/devcontainer.json → .devcontainer/devops/devcontainer.json

@@ -1,5 +1,5 @@
 {
-    "name": "NF-NEURO development container",
+    "name": "devops",
     "build": {
         "dockerfile": "Dockerfile",
         "args": {
@@ -8,8 +8,8 @@
         }
     },
     "forwardPorts": [3000],
-    "onCreateCommand": "bash .devcontainer/onCreateCommand.sh",
-    "updateContentCommand": "bash .devcontainer/updateContentCommand.sh",
+    "onCreateCommand": "bash .devcontainer/devops/onCreateCommand.sh",
+    "updateContentCommand": "bash .devcontainer/devops/updateContentCommand.sh",
     "postStartCommand": "git config --global --add safe.directory ${containerWorkspaceFolder}",
     "containerEnv": {
         "WORKSPACE": "${containerWorkspaceFolder}"

.devcontainer/prototyping/Dockerfile

@@ -0,0 +1,17 @@
+FROM scilus/scilus:2.0.2
+
+ARG POETRY_VERSION
+
+ENV POETRY_VERSION=${POETRY_VERSION:-1.8.*}
+
+RUN apt update && apt install -y \
+        curl \
+        git \
+        openjdk-17-jre \
+        python3-venv \
+        wget \
+    && rm -rf /var/lib/apt/lists/*
+
+RUN python3 -m pip install pipx && \
+    python3 -m pipx ensurepath && \
+    pipx install poetry==${POETRY_VERSION}

.devcontainer/prototyping/devcontainer.json

@@ -0,0 +1,77 @@
+{
+    "name": "prototyping",
+    "build": {
+        "dockerfile": "Dockerfile",
+        "args": {
+            "POETRY_VERSION": "1.8.*"
+        }
+    },
+    "forwardPorts": [3000],
+    "initializeCommand": "bash .devcontainer/prototyping/initializeCommand.sh",
+    "onCreateCommand": "bash .devcontainer/prototyping/onCreateCommand.sh",
+    "updateContentCommand": "bash .devcontainer/prototyping/updateContentCommand.sh",
+    "postStartCommand": "git config --global --add safe.directory ${containerWorkspaceFolder}",
+    "containerEnv": {
+        "WORKSPACE": "${containerWorkspaceFolder}"
+    },
+    "features": {
+        "ghcr.io/devcontainers/features/git:1": {},
+        "ghcr.io/devcontainers/features/github-cli:1": {},
+        "ghcr.io/devcontainers/features/docker-in-docker:2": {},
+        "ghcr.io/devcontainers-contrib/features/apt-get-packages:1": {},
+        "ghcr.io/robsyme/features/nextflow:1": {},
+        "ghcr.io/devcontainers-contrib/features/curl-apt-get:1": {},
+        "ghcr.io/devcontainers-contrib/features/tmux-apt-get:1": {},
+        "ghcr.io/devcontainers-contrib/features/wget-apt-get:1": {}
+    },
+    "mounts": [
+        {
+            "source": "nf-proto-${devcontainerId}-venv",
+            "target": "${containerWorkspaceFolder}/.venv",
+            "type": "volume"
+        },
+        {
+            "target": "/tmp",
+            "type": "volume"
+        },
+        {
+            "source": "nf-proto-${devcontainerId}-profile",
+            "target": "/root",
+            "type": "volume"
+        },
+        {
+            "target": "/root/.vscode-server",
+            "type": "volume"
+        }
+    ],
+    "customizations": {
+        "vscode": {
+            "settings": {
+                "python": {
+                    "analysis.exclude": [
+                        "${containerWorkspaceFolder}/.vscode",
+                        "${containerWorkspaceFolder}/.venv",
+                        "**/__pycache__",
+                        "${containerWorkspaceFolder}/.git"
+                    ],
+                    "analysis.ignore": [
+                        "${containerWorkspaceFolder}/.vscode",
+                        "${containerWorkspaceFolder}/.venv",
+                        "**/__pycache__",
+                        "${containerWorkspaceFolder}/.git"
+                    ],
+                    "createEnvironment.trigger": "off",
+                    "interpreter.infoVisibility": "always",
+                    "poetryPath": "/root/.local/bin/poetry",
+                    "defaultInterpreterPath": "${containerWorkspaceFolder}/.venv",
+                    "terminal.activateEnvironment": true,
+                    "terminal.activateEnvInCurrentTerminal": true,
+                    "terminal.focusAfterLaunch": true
+                }
+            },
+            "extensions": ["nf-neuro.nf-neuro-extensionpack"]
+        }
+    },
+    "init": true,
+    "privileged": true
+}

.devcontainer/prototyping/initializeCommand.sh

@@ -0,0 +1,13 @@
+#!/usr/bin/env bash
+
+# The prototyping environment must not be started in the nf-neuro repository.
+
+if [[ $PWD =~ .*/nf-neuro$ ]]
+then
+
+echo "You cannot open a prototyping environment in the nf-neuro repository."
+echo "Please, locate yourself elsewhere, outside the nf-neuro tree if possible."
+
+exit 1
+
+fi

.devcontainer/prototyping/onCreateCommand.sh

@@ -0,0 +1,32 @@
+#!/usr/bin/env bash
+
+# Setup for NF-CORE
+
+mkdir -p $XDG_CONFIG_HOME/nf-neuro
+touch $XDG_CONFIG_HOME/nf-neuro/.env
+echo "source $XDG_CONFIG_HOME/nf-neuro/.env" >> ~/.bashrc
+
+# Try to download nf-neuro setup with poetry. If it fails, we defer to pip
+{
+    NFNEURO_RAW_REPOSITORY=https://raw.githubusercontent.com/scilus/nf-neuro/main
+    NFCORE_VERSION=2.14.1
+    wget -N $NFNEURO_RAW_REPOSITORY/pyproject.toml \
+            $NFNEURO_RAW_REPOSITORY/poetry.toml \
+            $NFNEURO_RAW_REPOSITORY/poetry.lock
+} || {
+    echo "Failed to download nf-neuro base project configuration. Creating requirements.txt for pip"
+    echo "nf-core==$NFCORE_VERSION" > requirements.txt
+}
+
+# Try to download VSCode settings from nf-neuro
+{
+    NFNEURO_RAW_REPOSITORY=https://raw.githubusercontent.com/scilus/nf-neuro/main
+    mkdir -p .vscode
+    wget -N -P .vscode $NFNEURO_RAW_REPOSITORY/.vscode/settings.json
+} || {
+    echo "Could not fetch default extension settings from nf-neuro"
+}
+
+# Initial setup for a pipeline prototyping environment
+#  - nf-core requires a .nf-core.yml file present, else it bugs out (issue nfcore/tools#3340)
+touch .nf-core.yml

.devcontainer/prototyping/updateContentCommand.sh

@@ -0,0 +1,33 @@
+#!/usr/bin/env bash
+
+
+maxmem=$(grep MemTotal /proc/meminfo | awk '{print $2}')
+
+cat <<EOF > $XDG_CONFIG_HOME/nf-neuro/.env
+# This file is used to store environment variables for the project.
+# It is sourced by the shell on startup of every terminals.
+
+export PROFILE=docker
+export NFCORE_MODULES_GIT_REMOTE=https://github.com/scilus/nf-neuro.git
+export NFCORE_MODULES_BRANCH=main
+export NFCORE_SUBWORKFLOWS_GIT_REMOTE=https://github.com/scilus/nf-neuro.git
+export NFCORE_SUBWORKFLOWS_BRANCH=main
+
+export DEVCONTAINER_RAM_LIMIT_GB=$((maxmem / 1024 / 1024))
+export DEVCONTAINER_CPU_LIMIT=$(grep -c ^processor /proc/cpuinfo)
+
+EOF
+
+unset maxmem
+NFCORE_VERSION=2.14.1
+
+if [ -f poetry.lock ] && [ -f pyproject.toml ]
+then
+    poetry install --no-root
+elif [ -f requirements.txt ]
+then
+    python3 -m pip install -r requirements.txt
+else
+    echo "No requirements file found, installing nf-core to version $NFCORE_VERSION using pip"
+    python3 -m pip install nf-core==$NFCORE_VERSION
+fi

.github/workflows/manual_checks.yml

@@ -0,0 +1,16 @@
+name: Trigger checks manually
+on:
+  issue_comment:
+    types:
+      - created
+      - edited
+
+jobs:
+  checks:
+    if: github.event.issue.pull_request && contains(github.event.comment.body, '@rerun-checks')
+    # Cancel if a newer run is started
+    concurrency:
+      group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+      cancel-in-progress: true
+    uses: ./.github/workflows/run_checks_suite.yml
+    secrets: inherit

.github/workflows/update_pr.yml

@@ -6,7 +6,8 @@ on:
   merge_group:
     types:
       - checks_requested
-    branches: -main
+    branches:
+      - main
 
 # Cancel if a newer run is started
 concurrency:

.vscode/extension-package/CHANGELOG.md

@@ -1,5 +1,9 @@
 # Change Log
 
+## [1.0.2] - 2024-12-10
+
+- Add `errorlens` to packages
+
 ## [1.0.1] - 2024-09-16
 
 - Upgrade extension list

.vscode/extension-package/package.json

@@ -7,10 +7,10 @@
         "url": "https://github.com/scilus/nf-neuro.git"
     },
     "icon": "icon.avif",
-    "version": "1.0.1",
+    "version": "1.0.2",
     "publisher": "nf-neuro",
     "engines": {
-        "vscode": "^1.84.0"
+        "vscode": "^1.95.0"
     },
     "categories": [
         "Extension Packs"
@@ -50,6 +50,7 @@
         "ryu1kn.annotator",
         "trond-snekvik.simple-rst",
         "twxs.cmake",
+        "usernamehw.errorlens",
         "yahyabatulu.vscode-markdown-alert",
         "yzhang.markdown-all-in-one"
     ]

.vscode/settings.json

@@ -19,5 +19,24 @@
     "testDataExplorer.dataserver": "scil.usherbrooke.ca",
     "testDataExplorer.serverdatalocation": "scil_test_data/dvc-store/files/md5",
     "testDataExplorer.localListingLocation": "tests/test_data.json",
-    "testDataExplorer.remoteListingLocation": "tests/test_data.json"
+    "testDataExplorer.remoteListingLocation": "tests/test_data.json",
+    "nextflow.files.exclude": [
+        ".git",
+        ".nf-test",
+        "work",
+        ".venv",
+        ".nextflow",
+        "node_modules",
+        ".tests/runs"
+    ],
+    "cSpell.ignorePaths": [
+        "package-lock.json",
+        "node_modules",
+        "vscode-extension",
+        ".git/",
+        ".vscode",
+        ".vscode-insiders",
+        ".venv",
+        "tests/.runs"
+    ]
 }