From e204b6212f1a9b1a5cf9c3245a9cea48010383ad Mon Sep 17 00:00:00 2001
From: Cunliang Geng <c.geng@esciencecenter.nl>
Date: Mon, 18 Mar 2024 10:45:34 +0100
Subject: [PATCH 1/4] run building and type check actions for PRs on all
 branches

---
 .github/workflows/build.yml        | 3 ---
 .github/workflows/typing-check.yml | 3 ---
 2 files changed, 6 deletions(-)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index 1533b2f9..e95bcade 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -12,9 +12,6 @@ on:
       - setup.py
       - .github/workflows/build.yml
   pull_request:
-    branches:
-      - main
-      - dev
     paths:
       - bin/**
       - src/**
diff --git a/.github/workflows/typing-check.yml b/.github/workflows/typing-check.yml
index 1993530b..fdfbb657 100644
--- a/.github/workflows/typing-check.yml
+++ b/.github/workflows/typing-check.yml
@@ -9,9 +9,6 @@ on:
       - src/**
       - tests/**
   pull_request:
-    branches:
-      - main
-      - dev
     paths:
       - src/**
       - tests/**

From d6bf0d4beeff77c59542a93966480e1dd6f85a7f Mon Sep 17 00:00:00 2001
From: Cunliang Geng <c.geng@esciencecenter.nl>
Date: Mon, 18 Mar 2024 10:46:56 +0100
Subject: [PATCH 2/4] Delete documentation.yml

---
 .github/workflows/documentation.yml | 40 -----------------------------
 1 file changed, 40 deletions(-)
 delete mode 100644 .github/workflows/documentation.yml

diff --git a/.github/workflows/documentation.yml b/.github/workflows/documentation.yml
deleted file mode 100644
index 5e9999f0..00000000
--- a/.github/workflows/documentation.yml
+++ /dev/null
@@ -1,40 +0,0 @@
-name: documentation
-
-on:
-  push:
-    branches:
-      - main
-      - dev
-    paths:
-      - docs/**
-  pull_request:
-    branches:
-      - main
-      - dev
-    paths:
-      - docs/**
-
-jobs:
-  build-documentation:
-    name: Build documentation
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v2
-      - name: Set up Python 3.10
-        uses: actions/setup-python@v2
-        with:
-          python-version: 3.10
-      - name: Python info
-        shell: bash -l {0}
-        run: |
-          which python3
-          python3 --version
-      - name: Upgrade pip and install dependencies
-        run: |
-          python3 -m pip install --upgrade pip setuptools
-          python3 -m pip install .[dev,publishing]
-      - name: Install pandoc using apt
-        run: sudo apt install pandoc
-      - name: Build documentation
-        run: make coverage doctest html
-        working-directory: docs

From 1e18d78d186d157f86d68271ef27e54600fcbf3b Mon Sep 17 00:00:00 2001
From: Cunliang Geng <c.geng@esciencecenter.nl>
Date: Mon, 18 Mar 2024 11:33:31 +0100
Subject: [PATCH 3/4] separate building and sonarcloud actions

---
 .github/workflows/build.yml       | 34 -----------------
 .github/workflows/sonar-cloud.yml | 63 +++++++++++++++++++++++++++++++
 2 files changed, 63 insertions(+), 34 deletions(-)
 create mode 100644 .github/workflows/sonar-cloud.yml

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index e95bcade..3226cf5a 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -86,37 +86,3 @@ jobs:
           install-nplinker-deps --run-on-github
       - name: Run unit tests
         run: pytest -v
-
-  sonarcloud:
-    name: SonarCloud
-    needs: smoke_test
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-      - name: Set up Python
-        uses: actions/setup-python@v3
-        with:
-          python-version: '3.10'
-      - name: Python info
-        shell: bash -l {0}
-        run: |
-          which python3
-          python3 --version
-      - name: Upgrade pip and setuptools
-        run: |
-          python3 -m pip install --upgrade pip setuptools wheel
-      - name: Install nplinker and its dependencies
-        run: |
-          python3 -m pip install .[dev]
-          install-nplinker-deps --run-on-github
-      - name: Check style against standards using ruff
-        run: ruff .
-      - name: Run unit tests with coverage
-        run: pytest --cov --cov-report term --cov-report xml --junitxml=xunit-result.xml tests/
-      - name: Correct coverage paths
-        run: sed -i "s+$PWD/++g" coverage.xml
-      - name: SonarCloud Scan
-        uses: SonarSource/sonarcloud-github-action@master
-        env:
-          GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN }}
-          SONAR_TOKEN: ${{secrets.SONAR_TOKEN }}
diff --git a/.github/workflows/sonar-cloud.yml b/.github/workflows/sonar-cloud.yml
new file mode 100644
index 00000000..656c0ea7
--- /dev/null
+++ b/.github/workflows/sonar-cloud.yml
@@ -0,0 +1,63 @@
+name: Check format and coverage, then upload to SonarCloud
+
+on:
+  push:
+    branches:
+      - main
+      - dev
+    paths:
+      - bin/**
+      - src/**
+      - tests/**
+      - setup.py
+      - .github/workflows/build.yml
+  pull_request:
+    branches:
+      - main
+      - dev
+    paths:
+      - bin/**
+      - src/**
+      - tests/**
+      - setup.py
+      - .github/workflows/build.yml
+    types:
+      - opened
+      - reopened
+      - synchronize
+      - ready_for_review
+
+jobs:
+
+  sonarcloud:
+    name: SonarCloud
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v3
+        with:
+          python-version: '3.10'
+      - name: Python info
+        shell: bash -l {0}
+        run: |
+          which python3
+          python3 --version
+      - name: Upgrade pip and setuptools
+        run: |
+          python3 -m pip install --upgrade pip setuptools wheel
+      - name: Install nplinker and its dependencies
+        run: |
+          python3 -m pip install .[dev]
+          install-nplinker-deps --run-on-github
+      - name: Check style against standards using ruff
+        run: ruff check .
+      - name: Run unit tests with coverage
+        run: pytest --cov --cov-report term --cov-report xml --junitxml=xunit-result.xml tests/unit
+      - name: Correct coverage paths
+        run: sed -i "s+$PWD/++g" coverage.xml
+      - name: SonarCloud Scan
+        uses: SonarSource/sonarcloud-github-action@master
+        env:
+          GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN }}
+          SONAR_TOKEN: ${{secrets.SONAR_TOKEN }}

From 80c3aea29f50f98ce6538392a4a60ecfbe9f9874 Mon Sep 17 00:00:00 2001
From: Cunliang Geng <c.geng@esciencecenter.nl>
Date: Mon, 18 Mar 2024 11:33:59 +0100
Subject: [PATCH 4/4] Update pyproject.toml

Update ruff settings to be aligned with the latest usage.
---
 pyproject.toml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 3673a9fb..acf50b91 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -67,6 +67,8 @@ ignore_missing_imports = true
 [tool.ruff]
 target-version = "py310"
 line-length = 100
+
+[tool.ruff.lint]
 select = [
     "D", # pydocstyle
     "E", # pycodestyle (error)
@@ -100,7 +102,7 @@ fixable = ["A", "B", "C", "D", "E", "F", "I"]
 ignore-init-module-imports = true
 
 
-[tool.ruff.isort]
+[tool.ruff.lint.isort]
 known-first-party = ["nplinker"]
 force-single-line = true
 lines-after-imports = 2