Merge pull request #1 from UCL-ARC/paul/setup-repo

Setup workflows and issue templates

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -0,0 +1,32 @@
+name: Bug Report
+description: Have you got a bug? Please report it here!
+labels: ["bug"]
+projects: [""]
+body:
+  - type: markdown
+    attributes:
+      value: |
+        A clear and concise description of what the bug is. Please use a short, concise title for the bug and elaborate here
+  - type: textarea
+    id: actual_behaviour
+    attributes:
+      label: What did you get?
+      description: A clear and concise description of what actually happens.
+      placeholder: "If you have a code sample, error messages, stack traces, please provide it here as well"
+    validations:
+      required: false
+  - type: textarea
+    id: logs
+    attributes:
+      label: Relevant log output (optional)
+      description: Please copy and paste any relevant log output. This will be automatically formatted into code, so no need for backticks.
+      render: Shell
+    validations:
+      required: false
+  - type: textarea
+    id: expected_behaviour
+    attributes:
+      label: What did you expect? (optional)
+      description: A clear and concise description of what you expected to happen.
+    validations:
+      required: false

.github/ISSUE_TEMPLATE/feature_request.yaml

@@ -0,0 +1,38 @@
+name: Feature Request
+description: Submit a proposal/request for a new feature
+labels: ["feature"]
+projects: [""]
+body:
+  - type: markdown
+    attributes:
+      value: |
+        A clear and concise description of the feature proposal
+  - type: textarea
+    id: motivation
+    attributes:
+      label: Motivation
+      description: Please outline the motivation for the proposal.
+      placeholder: "Is your feature request related to a problem? e.g., I'm always frustrated when [...]. If this is related to another GitHub issue, please link here too"
+    validations:
+      required: true
+  - type: textarea
+    id: pitch
+    attributes:
+      label: Pitch
+      description: A clear and concise description of what you want to happen.
+    validations:
+      required: false
+  - type: textarea
+    id: alternatives
+    attributes:
+      label: Alternatives
+      description: A clear and concise description of any alternative solutions or features you've considered, if any.
+    validations:
+      required: false
+  - type: textarea
+    id: additional_context
+    attributes:
+      label: Additional context
+      description: Add any other context or screenshots about the feature request here.
+    validations:
+      required: false

.github/workflows/linting.yml

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+name: Linting
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+
+jobs:
+  linting:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout source
+        uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4
+
+      - name: Cache pre-commit
+        uses: actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 # v4
+        with:
+          path: ~/.cache/pre-commit
+          key: pre-commit-${{ hashFiles('.pre-commit-config.yaml') }}
+
+      - name: Set up python
+        uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f # v5
+        with:
+          python-version: "3.x"
+
+      - name: Install pre-commit
+        run: python -m pip install pre-commit
+
+      - name: Run pre-commit
+        run: pre-commit run --all-files --verbose

.markdownlint.yaml

@@ -0,0 +1,7 @@
+---
+default: true
+
+MD013:
+  line_length: 120
+  code_blocks: false
+  tables: false

.pre-commit-config.yaml

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+repos:
+  - repo: https://github.com/Lucas-C/pre-commit-hooks
+    rev: v1.5.5
+    hooks:
+      - id: forbid-tabs
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.6.0
+    hooks:
+      - id: check-case-conflict
+      - id: check-docstring-first
+      - id: check-merge-conflict
+      - id: end-of-file-fixer
+      - id: mixed-line-ending
+        args:
+          - --fix=lf
+      - id: trailing-whitespace
+  - repo: https://github.com/AleksaC/hadolint-py
+    rev: v2.12.1b3
+    hooks:
+      - id: hadolint
+        args:
+          - --ignore=DL3008
+  - repo: https://github.com/crate-ci/typos
+    rev: v1.24.1
+    hooks:
+      - id: typos
+        args:
+          - --force-exclude
+          - --hidden
+          - --locale=en-gb
+  - repo: https://github.com/igorshubovych/markdownlint-cli
+    rev: v0.41.0
+    hooks:
+      - id: markdownlint-fix
+        args:
+          - --dot
+  - repo: https://github.com/shellcheck-py/shellcheck-py
+    rev: v0.10.0.1
+    hooks:
+      - id: shellcheck
+        args:
+          - --external-sources
+          - --shell=bash

.renovaterc.json5

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+{
+  $schema: "https://docs.renovatebot.com/renovate-schema.json",
+  extends: [
+    "github>UCL-ARC/.github//renovate/default-config.json",
+    "schedule:monthly",
+  ],
+}

README.md

@@ -1,2 +1,3 @@
 # Enigma-PD-WML
+
 Segment White Mater Lesions (WML) in T1-weighted and FLAIR MR images using FSL and U-Net