delete .editorconfig

.gitattributes

@@ -9,4 +9,3 @@
 *.sh text
 *.bat text
 *.toml text
-*.zip filter=lfs diff=lfs merge=lfs -text

.github/workflows/build.yml

@@ -12,9 +12,6 @@ on:
       - setup.py
       - .github/workflows/build.yml
   pull_request:
-    branches:
-      - main
-      - dev
     paths:
       - bin/**
       - src/**
@@ -34,7 +31,7 @@ jobs:
     runs-on: ubuntu-latest
     if: github.event.pull_request.draft == false
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set up Python 3.10
         uses: actions/setup-python@v3
         with:
@@ -47,7 +44,7 @@ jobs:
       - name: Upgrade pip and install dependencies
         run: |
           python3 -m pip install --upgrade pip setuptools
-          pip install build pytest wheel
+          pip install build pytest wheel pytest-xdist
       - name: Build the package
         run: 	python -m build
       - name: Install nplinker
@@ -67,7 +64,7 @@ jobs:
         os: ['ubuntu-latest']
         python-version: ['3.9', '3.11']
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v3
         with:
@@ -80,7 +77,7 @@ jobs:
       - name: Upgrade pip and install dependencies
         run: |
           python3 -m pip install --upgrade pip setuptools
-          pip install build pytest wheel
+          pip install build pytest wheel pytest-xdist
       - name: Build the package
         run: 	python -m build
       - name: Install nplinker
@@ -89,39 +86,3 @@ jobs:
           install-nplinker-deps --run-on-github
       - name: Run unit tests
         run: pytest -v
-
-  sonarcloud:
-    name: SonarCloud
-    needs: smoke_test
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v3
-        with:
-          fetch-depth: 0
-      - name: Set up Python
-        uses: actions/setup-python@v3
-        with:
-          python-version: '3.10'
-      - name: Python info
-        shell: bash -l {0}
-        run: |
-          which python3
-          python3 --version
-      - name: Upgrade pip and setuptools
-        run: |
-          python3 -m pip install --upgrade pip setuptools wheel
-      - name: Install nplinker and its dependencies
-        run: |
-          python3 -m pip install .[dev]
-          install-nplinker-deps --run-on-github
-      - name: Check style against standards using ruff
-        run: ruff .
-      - name: Run unit tests with coverage
-        run: pytest --cov --cov-report term --cov-report xml --junitxml=xunit-result.xml tests/
-      - name: Correct coverage paths
-        run: sed -i "s+$PWD/++g" coverage.xml
-      - name: SonarCloud Scan
-        uses: SonarSource/sonarcloud-github-action@master
-        env:
-          GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN }}
-          SONAR_TOKEN: ${{secrets.SONAR_TOKEN }}

.github/workflows/publish_gh_release.yml

@@ -33,7 +33,7 @@ jobs:
     runs-on: ubuntu-latest
     if:  ${{ inputs.current_version != inputs.new_version }}
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up Python 3.10
       uses: actions/setup-python@v3
       with:

.github/workflows/publish_to_pypi.yml

@@ -11,7 +11,7 @@ jobs:
   publish:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@master
+    - uses: actions/checkout@v4
     - uses: actions/setup-python@v3
       with:
         python-version: '3.x'

.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 }}

.github/workflows/typing-check.yml

@@ -9,9 +9,6 @@ on:
       - src/**
       - tests/**
   pull_request:
-    branches:
-      - main
-      - dev
     paths:
       - src/**
       - tests/**
@@ -21,7 +18,7 @@ jobs:
   lint:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set up Python 3.10
         uses: actions/setup-python@v3
         with:

.gitignore

@@ -62,3 +62,4 @@ tags
 webapp/npapp/static/css/bokeh*.css
 webapp/npapp/static/js/bokeh*.js
 src/nplinker/scoring/iokr/data/SPEC/
+tests/integration/data/nplinker_local_mode_example.zip

MANIFEST.in

@@ -3,3 +3,4 @@ include LICENSE
 include NOTICE
 include requirements.txt
 include requirements.dev.txt
+prune tests

Makefile

@@ -22,7 +22,7 @@ clean-pyc:
 	find . -name '*.pyc' -exec rm -f {} +
 	find . -name '*.pyo' -exec rm -f {} +
 	find . -name '*~' -exec rm -f {} +
-	find . -name '__pycache__' -exec rm -fr {} +
+	find . -name '*__pycache__' -exec rm -fr {} +
 	find . -name '*_cache' -exec rm -fr {} +
 
 clean-test: