Staging (#288)

.github/ISSUE_TEMPLATE/bug-report.yaml

@@ -0,0 +1,85 @@
+name: Bug Report
+description: Report a bug.
+labels: ["bug"]
+body:
+  - type: textarea
+    attributes:
+      label: Describe the bug
+      description: Provide a clear and concise description of what the bug is.
+    validations:
+      required: true
+  - type: textarea
+    attributes:
+      label: Steps to reproduce
+      description: Provide detailed steps to replicate the bug.
+      placeholder: |
+        1. In this environment...
+        2. With this config...
+        3. Run '...'
+        4. See error...
+    validations:
+      required: true
+  - type: textarea
+    attributes:
+      label: Expected behavior
+      description: What did you expect to happen?
+    validations:
+      required: true
+  - type: textarea
+    attributes:
+      label: Current behavior
+      description: |
+        What actually happened?
+
+        Include full errors, stack traces, and/or relevant logs.
+    validations:
+      required: true
+  - type: textarea
+    attributes:
+      label: Possible reason(s)
+      description: Provide any insights into what might be causing the issue.
+    validations:
+      required: false
+  - type: textarea
+    attributes:
+      label: Suggested fix
+      description: Provide any suggestions on how to resolve the bug.
+    validations:
+      required: false
+  - type: textarea
+    attributes:
+      label: Branch, commit, and/or version
+      description: Provide the branch, commit, and/or version you're using.
+      placeholder: |
+        branch: issue-1
+        commit: abc123d
+    validations:
+      required: true
+  - type: textarea
+    attributes:
+      label: Screenshots
+      description: If applicable, add screenshots with descriptions to help explain your problem.
+    validations:
+      required: false
+  - type: textarea
+    attributes:
+      label: Environment details
+      description: Provide environment details (OS name and version, etc).
+    validations:
+      required: true
+  - type: textarea
+    attributes:
+      label: Additional details
+      description: Provide any other additional details about the problem.
+    validations:
+      required: false
+  - type: dropdown
+    attributes:
+      label: Contribution
+      description: Can you contribute to the development of this feature?
+      options:
+        - "Yes, I can create a PR for this fix."
+        - "Yes, but I can only provide ideas and feedback."
+        - "No, I cannot contribute."
+    validations:
+      required: false

.github/ISSUE_TEMPLATE/feature-request.yaml

@@ -0,0 +1,60 @@
+name: Feature Request
+description: Suggest an idea for this project.
+labels: ["enhancement"]
+body:
+  - type: textarea
+    attributes:
+      label: Feature description
+      description: Provide a clear and concise description of what you want to happen.
+    validations:
+      required: true
+  - type: textarea
+    attributes:
+      label: Use case
+      description: |
+        Why do you need this feature? For example: "I'm always frustrated when..."
+    validations:
+      required: true
+  - type: textarea
+    attributes:
+      label: Proposed solution
+      description: Provide proposed solution.
+    validations:
+      required: false
+  - type: textarea
+    attributes:
+      label: Alternatives considered
+      description: Describe any alternative solutions you've considered.
+    validations:
+      required: false
+  - type: textarea
+    attributes:
+      label: Implementation details
+      description: Provide any technical details on how the feature might be implemented.
+    validations:
+      required: false
+  - type: textarea
+    attributes:
+      label: Potential Impact
+      description: |
+        Discuss any potential impacts of this feature on existing functionality or performance, if known.
+        Will this feature cause breaking changes?
+        What challenges might arise?
+    validations:
+      required: false
+  - type: textarea
+    attributes:
+      label: Additional context
+      description: Provide any other context or screenshots about the feature.
+    validations:
+      required: false
+  - type: dropdown
+    attributes:
+      label: Contribution
+      description: Can you contribute to the development of this feature?
+      options:
+        - "Yes, I can create a PR for this feature."
+        - "Yes, but I can only provide ideas and feedback."
+        - "No, I cannot contribute."
+    validations:
+      required: false

.github/workflows/backend_checks.yml

@@ -0,0 +1,31 @@
+name: backend_checks
+on: [push, pull_request]
+jobs:
+  build:
+    name: build
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: 3.11
+
+      - name: Install dependencies
+        run: pip install server/
+  lint:
+    name: lint
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: black
+        uses: psf/black@stable
+        with:
+          src: "./server"
+
+      - name: ruff
+        uses: chartboost/ruff-action@v1
+        with:
+          src: "./server"

.github/workflows/pr-priority-label.yaml

@@ -0,0 +1,23 @@
+name: Pull Request Has Priority Label
+on:
+  pull_request:
+    types: [opened, labeled, unlabeled, synchronize]
+jobs:
+  pr-priority-label:
+    runs-on: ubuntu-latest
+    permissions:
+      issues: write
+      pull-requests: write
+    outputs:
+      status: ${{ steps.check-labels.outputs.status }}
+    steps:
+      - id: check-labels
+        uses: mheap/github-action-required-labels@v5
+        with:
+          mode: exactly
+          count: 1
+          labels: "priority:*"
+          use_regex: true
+          add_comment: true
+          message: "PRs require a priority label. Please add one."
+          exit_type: failure

.github/workflows/stale.yaml

@@ -0,0 +1,27 @@
+name: "Stalebot for issues and PRs"
+
+on:
+  schedule:
+    - cron: "30 13 * * 1-5"
+
+jobs:
+  stale-high-priority:
+    uses: genomicmedlab/software-templates/.github/workflows/reusable-stale.yaml@main
+    with:
+      days-before-issue-stale: 90
+      days-before-pr-stale: 1
+      labels: priority:high
+
+  stale-medium-priority:
+    uses: genomicmedlab/software-templates/.github/workflows/reusable-stale.yaml@main
+    with:
+      days-before-issue-stale: 135
+      days-before-pr-stale: 3
+      labels: priority:medium
+
+  stale-low-priority:
+    uses: genomicmedlab/software-templates/.github/workflows/reusable-stale.yaml@main
+    with:
+      days-before-issue-stale: 180
+      days-before-pr-stale: 7
+      labels: priority:low

.gitignore

@@ -91,7 +91,7 @@ ipython_config.py
 # pyenv
 #   For a library or package, you might want to ignore these files since the code is
 #   intended to run in multiple environments; otherwise, check them in:
-# .python-version
+**/.python-version
 
 # pipenv
 #   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
@@ -160,7 +160,6 @@ dynamodb_local_latest/*
 
 # Build files
 Pipfile.lock
-pyproject.toml
 
 # client-side things
 curation/client/node_modules
@@ -177,8 +176,8 @@ yarn-debug.log*
 yarn-error.log*
 frontend/public/
 frontend/node_modules
-node_modules/
+**/node_modules/
+**/.yarn
 
 # Data
-server/curfu/data
-client/node_modules
+server/src/curfu/data

.pre-commit-config.yaml

@@ -1,18 +1,23 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v1.4.0
+    rev: v4.6.0 # pre-commit-hooks version
     hooks:
-      - id: flake8
-        additional_dependencies: [flake8-docstrings]
-        args: ["--config=server/.flake8"]
       - id: check-added-large-files
-        args: ["--maxkb=2000"]
       - id: detect-private-key
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-merge-conflict
+      - id: detect-aws-credentials
   - repo: https://github.com/psf/black
-    rev: 22.6.0
+    rev: 23.7.0
     hooks:
       - id: black
-        args: [--diff, --check]
+        language_version: python3.11
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.0.286
+    hooks:
+      - id: ruff
+        args: [--fix, --exit-non-zero-on-fix]
   - repo: https://github.com/pre-commit/mirrors-eslint
     rev: "v8.20.0"
     hooks:
@@ -30,3 +35,4 @@ repos:
     rev: "v2.7.1"
     hooks:
       - id: prettier
+minimum_pre_commit_version: 3.7.1

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2021-2022 Alex H. Wagner
+Copyright (c) 2021-2024 Genomic Medicine Lab
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

Procfile

@@ -1 +1 @@
-web: sh -c 'cd ./server/ && gunicorn -k uvicorn.workers.UvicornWorker curfu.main:app --timeout 1000 --log-level debug'
+web: sh -c 'cd ./server/src/ && gunicorn -k uvicorn.workers.UvicornWorker curfu.main:app --timeout 1000 --log-level debug'

client/src/components/Pages/CausativeEvent/CausativeEvent.tsx

@@ -102,32 +102,23 @@ export const CausativeEvent: React.FC<Props> = () => {
               </Box>
             </HelpPopover>
           </Typography>
-          <HelpTooltip
-            placement="bottom"
-            title={
-              <Typography>
-                The type of event that generated the fusion.
-              </Typography>
-            }
+          <RadioGroup
+            aria-label="Causative event?"
+            name="controlled-radio-buttons-group"
+            value={eventType}
+            onChange={handleEventTypeChange}
           >
-            <RadioGroup
-              aria-label="Causative event?"
-              name="controlled-radio-buttons-group"
-              value={eventType}
-              onChange={handleEventTypeChange}
-            >
-              {["rearrangement", "trans-splicing", "read-through"].map(
-                (value, index) => (
-                  <FormControlLabel
-                    value={value}
-                    control={<Radio />}
-                    label={eventDisplayMap[value]}
-                    key={index}
-                  />
-                )
-              )}
-            </RadioGroup>
-          </HelpTooltip>
+            {["rearrangement", "trans-splicing", "read-through"].map(
+              (value, index) => (
+                <FormControlLabel
+                  value={value}
+                  control={<Radio />}
+                  label={eventDisplayMap[value]}
+                  key={index}
+                />
+              )
+            )}
+          </RadioGroup>
         </Box>
       </FormControl>
       <Box className="right column">