merge with upstream and merge with conflicts

.devcontainer/Dockerfile

@@ -1,11 +1,11 @@
-FROM scilus/scilus:1.6.0
-
-RUN apt update && apt install -y \
-        git \
-        python3-venv \
-        wget \
-    && rm -rf /var/lib/apt/lists/*
-
-RUN python3 -m pip install pipx && \
-    python3 -m pipx ensurepath && \
-    pipx install poetry
+FROM scilus/scilus:1.6.0
+
+RUN apt update && apt install -y \
+        git \
+        python3-venv \
+        wget \
+    && rm -rf /var/lib/apt/lists/*
+
+RUN python3 -m pip install pipx && \
+    python3 -m pipx ensurepath && \
+    pipx install poetry

.devcontainer/devcontainer.json

@@ -1,26 +1,65 @@
-{
-    "name": "NF-SCIL development container",
-    "build": { "dockerfile": "Dockerfile" },
-    "forwardPorts": [3000],
-    "onCreateCommand": "bash .devcontainer/setup_container.sh",
-    "features": {
-        "ghcr.io/devcontainers/features/git:1": {},
-        "ghcr.io/devcontainers/features/git-lfs: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": {}
-    },
-    "customizations": {
-        "vscode": {
-            "extensions": [
-                "AlexVCaron.nf-scil-extensions"
-            ]
-        }
-    },
-    "init": true,
-    "privileged": true
-}
+{
+    "name": "NF-SCIL development container",
+    "build": { "dockerfile": "Dockerfile" },
+    "forwardPorts": [3000],
+    "onCreateCommand": "bash .devcontainer/setup_container.sh",
+    "features": {
+        "ghcr.io/devcontainers/features/git:1": {},
+        "ghcr.io/devcontainers/features/git-lfs: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-scil-venv",
+            "target": "/workspaces/nf-scil/.venv",
+            "type": "volume"
+        },
+        {
+            "source": "nf-scil-tmp",
+            "target": "/tmp",
+            "type": "volume"
+        }
+    ],
+    "customizations": {
+        "vscode": {
+            "settings": {
+                "pythonIndent.keepHangingBracketOnLine": true,
+                "pythonIndent.trimLinesWithOnlyWhitespace": true,
+                "python.createEnvironment.trigger": "off",
+                "python.terminal.activateEnvironment": true,
+                "python.poetryPath": "/root/.local/bin/poetry",
+                "python.defaultInterpreterPath": "${workspaceFolder}/.venv",
+                "python.analysis.exclude": [
+                    "${workspaceFolder}/.dvc",
+                    "${workspaceFolder}/.pytest_cache",
+                    "${workspaceFolder}/.test_data",
+                    "${workspaceFolder}/.vscode",
+                    "${workspaceFolder}/nf-scil-extensions",
+                    "**/__pycache__",
+                    "${workspaceFolder}/.git"
+                ],
+                "python.analysis.ignore": [
+                    "${workspaceFolder}/.dvc",
+                    "${workspaceFolder}/.pytest_cache",
+                    "${workspaceFolder}/.test_data",
+                    "${workspaceFolder}/.vscode",
+                    "${workspaceFolder}/nf-scil-extensions",
+                    "**/__pycache__",
+                    "${workspaceFolder}/.git"
+                ]
+            },
+            "extensions": [
+                "AlexVCaron.nf-scil-extensions",
+                "ms-python.autopep8"
+            ]
+        }
+    },
+    "init": true,
+    "privileged": true
+}

.devcontainer/setup_container.sh

@@ -1,6 +1,5 @@
 #!/usr/bin/env bash
 
-poetry install
-
-echo "poetry shell" >> ~/.bashrc
+poetry install --no-root
 echo "export PROFILE=docker" >> ~/.bashrc
+

.editorconfig

@@ -0,0 +1,15 @@
+root = true
+
+[*]
+charset = utf-8
+end_of_line = lf
+insert_final_newline = true
+trim_trailing_whitespace = true
+indent_size = 4
+indent_style = space
+
+[*.{md,yml,yaml,html,css,scss,js,cff}]
+indent_size = 2
+
+[LICENSE]
+indent_size = 1

.github/ISSUE_TEMPLATE/bug_report.md

@@ -8,9 +8,9 @@ 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-scil` 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-scil` 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.

.github/workflows/code_linting.yml

@@ -0,0 +1,70 @@
+name: Code Linting
+run-name: Code Linting (automated)
+on:
+  issue_comment:
+    types: [created]
+
+jobs:
+  fix-linting:
+    # Only run if comment is on a PR with the main repo, and if it contains the magic keywords
+    if: >
+      contains(github.event.comment.html_url, '/pull/') &&
+      contains(github.event.comment.body, '@nf-scil-bot fix linting') &&
+      github.repository == 'scilus/nf-scil'
+    runs-on: ubuntu-latest
+    steps:
+      # Use the @nf-scil-bot token to check out so we can push later
+      - uses: actions/checkout@v4
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+
+      # indication that the linting is being fixed
+      - name: React on comment
+        uses: peter-evans/create-or-update-comment@v3
+        with:
+          comment-id: ${{ github.event.comment.id }}
+          reactions: eyes
+
+      # Action runs on the issue comment, so we don't get the PR by default
+      # Use the gh cli to check out the PR
+      - name: Checkout Pull Request
+        run: gh pr checkout ${{ github.event.issue.number }}
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+      - uses: actions/setup-node@v4
+
+      - name: Install Prettier
+        run: npm install -g prettier @prettier/plugin-php
+
+      # Check that we actually need to fix something
+      - name: Run 'prettier --check'
+        id: prettier_status
+        run: |
+          if prettier --check ${GITHUB_WORKSPACE}; then
+            echo "::set-output name=result::pass"
+          else
+            echo "::set-output name=result::fail"
+          fi
+      - name: Run 'prettier --write'
+        if: steps.prettier_status.outputs.result == 'fail'
+        run: prettier --write ${GITHUB_WORKSPACE}
+
+      - name: Post nothing-to-do comment
+        if: steps.prettier_status.outputs.result == 'pass'
+        uses: peter-evans/create-or-update-comment@v3
+        with:
+          issue-number: ${{ github.event.issue.number }}
+          body: |
+            Nothing for me to do here! :shrug:
+            This is probably because the linting errors come from `nf-core lint` and have to be fixed manually (or with `nf-core lint --fix`).
+      - name: Commit & push changes
+        if: steps.prettier_status.outputs.result == 'fail'
+        run: |
+          git config user.email "[email protected]"
+          git config user.name "nf-scil-bot"
+          git config push.default upstream
+          git add .
+          git status
+          git commit -m "[automated] Fix linting with Prettier"
+          git push