Merge pull request #42 from cfe-lab/small-improvements-0001

Small improvements

Author: Donaim

.github/workflows/main.yml

@@ -0,0 +1,46 @@
+name: main tests
+
+on:
+  push:
+  workflow_dispatch:
+
+jobs:
+  build-and-test:
+    runs-on: ubuntu-latest
+    
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+        with:
+          submodules: recursive
+          fetch-depth: 0
+      
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+      
+      - name: Build Docker image
+        uses: docker/build-push-action@v5
+        with:
+          context: .
+          file: ./bblab.dockerfile
+          target: bblab-site
+          push: false
+          tags: cfe-lab/bblab-site
+          load: true
+          cache-from: type=gha
+          cache-to: type=gha,mode=max
+
+      - name: Run pytest tests
+        run: |
+          docker run --rm \
+            -w /alldata/bblab_site \
+            cfe-lab/bblab-site \
+            uv run pytest -v
+
+      - name: Run Django tests
+        run: |
+          docker run --rm \
+            --env-file ./compose-template.env \
+            -w /alldata/bblab_site \
+            cfe-lab/bblab-site \
+            uv run python manage.py test --noinput

alldata/bblab_site/pyproject.toml

@@ -93,3 +93,29 @@ include = [
 
 [tool.hatch.metadata]
 allow-direct-references = true
+
+[tool.pytest.ini_options]
+testpaths = [
+    ".",
+]
+# Exclude vendor/dependency directories and submodule repos that have their own test suites
+norecursedirs = [
+    "depend",
+    ".venv",
+    "build",
+    "dist",
+    "*.egg",
+    ".git",
+    "git",
+    ".tox",
+    "repo",  # Excludes submodule repos like tools/phage_i_expanded/repo/
+    "blind_dating",
+    "phylodating",
+    "translate_DNA",
+    "tests/phylodating",  # Exclude the test submodule copy
+    "tools",  # Skip the empty Django test stubs
+]
+# Only collect test files from our actual project, not vendored dependencies
+python_files = ["test_*.py"]
+python_classes = ["Test*"]
+python_functions = ["test_*"]

alldata/bblab_site/test_smoke.py

@@ -0,0 +1,37 @@
+"""
+Smoke tests to verify the Docker container build is working correctly.
+"""
+
+
+def test_imports():
+    """Test that core dependencies can be imported."""
+    import django
+    import numpy
+    import scipy
+    import yaml
+    assert django.VERSION is not None
+    assert numpy.__version__ is not None
+
+
+def test_django_setup():
+    """Test that Django can be set up (even without database)."""
+    import os
+    import django
+    
+    # Set minimal Django settings for testing
+    os.environ.setdefault('DJANGO_SETTINGS_MODULE', 'bblab_site.settings')
+    
+    # We expect this to fail without proper environment variables,
+    # but it should fail gracefully, not with import errors
+    try:
+        django.setup()
+    except KeyError:
+        # Expected - missing environment variables like BBLAB_WEB_ADDRESS
+        pass
+
+
+def test_python_version():
+    """Test that we're running the expected Python version."""
+    import sys
+    assert sys.version_info >= (3, 12)
+    assert sys.version_info < (3, 13)

bblab.dockerfile

@@ -114,6 +114,23 @@ RUN wget https://github.com/cfe-lab/bblab-server/releases/download/v0.1.0-alpha/
     tar -xzf blast-2.2.16-x64-linux.tar.gz && \
     tar -xzf tcrdist_extras_v2.tgz
 
+# load configuration for Apache server
+COPY conf/apache2.conf /etc/apache2/
+COPY conf/tools-*.conf /etc/apache2/mods-available/
+COPY conf/php.conf /etc/apache2/mods-available
+RUN ln -sf /etc/apache2/mods-available/tools-gld.conf /etc/apache2/mods-enabled/tools-gld.conf && \
+    ln -sf /etc/apache2/mods-available/tools-pld.conf /etc/apache2/mods-enabled/tools-pld.conf && \
+    ln -sf /etc/apache2/mods-available/tools-hla.conf /etc/apache2/mods-enabled/tools-hla.conf && \
+    ln -sf /etc/apache2/mods-available/php.conf /etc/apache2/mods-enabled/php.conf && \
+    ln -sf /var/log/apache2/access.log /dev/stdout && \
+    ln -sf /var/log/apache2/error.log /dev/stderr && \
+    chmod 766 -R /var/log/apache2/ && \
+    a2dissite 000-default.conf && a2dissite default-ssl.conf
+
+# Copy shell scripts for Phylodating
+COPY phylodating_setup/clean.sh /var/www/phylodating/clean.sh
+COPY phylodating_setup/logwatcher.sh /var/www/phylodating/logwatcher.sh
+
 # copy source code
 COPY alldata /alldata
 
@@ -148,23 +165,6 @@ RUN mv ./tcrdist_extras_v2/external/ /alldata/bblab_site/depend/apps/tcr-dist/ &
 
 USER root
 
-# load configuration for Apache server
-COPY conf/apache2.conf /etc/apache2/
-COPY conf/tools-*.conf /etc/apache2/mods-available/
-COPY conf/php.conf /etc/apache2/mods-available
-RUN ln -sf /etc/apache2/mods-available/tools-gld.conf /etc/apache2/mods-enabled/tools-gld.conf && \
-    ln -sf /etc/apache2/mods-available/tools-pld.conf /etc/apache2/mods-enabled/tools-pld.conf && \
-    ln -sf /etc/apache2/mods-available/tools-hla.conf /etc/apache2/mods-enabled/tools-hla.conf && \
-    ln -sf /etc/apache2/mods-available/php.conf /etc/apache2/mods-enabled/php.conf && \
-    ln -sf /var/log/apache2/access.log /dev/stdout && \
-    ln -sf /var/log/apache2/error.log /dev/stderr && \
-    chmod 766 -R /var/log/apache2/ && \
-    a2dissite 000-default.conf && a2dissite default-ssl.conf
-
-# Copy shell scripts for Phylodating
-COPY phylodating_setup/clean.sh /var/www/phylodating/clean.sh
-COPY phylodating_setup/logwatcher.sh /var/www/phylodating/logwatcher.sh
-
 # Set permissions and ownership for WSGI user/group (www-data:varwwwusers)
 RUN mkdir -p /alldata/bblab_site/tools/sequencing_layout/output && \
     mkdir /alldata/bblab_site/tools/sequencing_layout/output/archived_layouts && \