From 4f6ee159414e94e36f231fc6b62685e7c3ef6ad7 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Tue, 22 Oct 2024 12:12:10 +0100
Subject: [PATCH] Prefer the ``venv`` module over virtualenv

virtualenv 20.27.0 dropped support to create Python 3.7 virtual
environments.

Also:
- Drop unused `release` Make target
- Use new `build` tox target in GitHub workflow
- Clean also `.mypy_cache` directories
---
 .github/workflows/deploy.yaml |  9 +++------
 .github/workflows/test.yaml   |  2 +-
 .gitignore                    |  2 +-
 Makefile                      | 19 +++++--------------
 run_bioblend_tests.sh         | 10 +++++++---
 tox.ini                       | 12 ++++++++++++
 6 files changed, 29 insertions(+), 25 deletions(-)

diff --git a/.github/workflows/deploy.yaml b/.github/workflows/deploy.yaml
index b4ec25eb9..f44313766 100644
--- a/.github/workflows/deploy.yaml
+++ b/.github/workflows/deploy.yaml
@@ -8,14 +8,11 @@ jobs:
       - uses: actions/setup-python@v5
         with:
           python-version: '3.13'
-      - name: Install dependencies
+      - name: Install tox
         run: |
-          python3 -m pip install --upgrade pip setuptools
-          python3 -m pip install --upgrade build twine
+          python3 -m pip install 'tox>=1.8.0'
       - name: Create and check sdist and wheel packages
-        run: |
-          python3 -m build
-          twine check dist/*
+        run: tox -e build
       - name: Publish to PyPI
         if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/') && github.repository_owner == 'galaxyproject'
         uses: pypa/gh-action-pypi-publish@release/v1
diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml
index c6d344f4a..8df6d5e7f 100644
--- a/.github/workflows/test.yaml
+++ b/.github/workflows/test.yaml
@@ -128,7 +128,7 @@ jobs:
       - name: Install tox
         run: |
           python3 -m pip install --upgrade pip setuptools
-          python3 -m pip install 'tox>=1.8.0' 'virtualenv>=20.0.14'
+          python3 -m pip install 'tox>=1.8.0'
       - name: Set up Python for Galaxy
         uses: actions/setup-python@v5
         with:
diff --git a/.gitignore b/.gitignore
index 06981d39d..9ecd06b44 100644
--- a/.gitignore
+++ b/.gitignore
@@ -41,5 +41,5 @@ cover
 # compiled docs
 docs/_build
 
-# Python virtualenv
+# Python virtual environment
 .venv
diff --git a/Makefile b/Makefile
index 47d90f9d9..695dd3364 100644
--- a/Makefile
+++ b/Makefile
@@ -7,22 +7,13 @@ all:
 
 clean:
 	rm -rf bioblend.egg-info/ build/ dist/
+	find . -type d -name '.mypy_cache' -exec rm -rf {} +
 	make -C docs/ clean
 
 venv:
 	# Create and activate a virtual environment
-	[ -f .venv/bin/activate ] || virtualenv -p python3 .venv
-	( $(IN_VENV) && \
-	  # Install latest versions of pip and setuptools \
-	  python3 -m pip install --upgrade pip setuptools && \
-	  # Install latest versions of other needed packages in the virtualenv \
-	  python3 -m pip install --upgrade twine wheel \
-	)
-
-release: clean venv
-	( $(IN_VENV) && \
-	  # Create files in dist/ \
-	  python3 setup.py sdist bdist_wheel && \
-	  twine check dist/* && \
-	  twine upload dist/*
+	[ -f .venv/bin/activate ] || python3 -m venv .venv || virtualenv -p python3 .venv
+	# Install latest versions of pip and setuptools
+	( $(IN_VENV) \
+	  && python3 -m pip install --upgrade pip setuptools \
 	)
diff --git a/run_bioblend_tests.sh b/run_bioblend_tests.sh
index 89cc4a11a..0862664c9 100755
--- a/run_bioblend_tests.sh
+++ b/run_bioblend_tests.sh
@@ -62,7 +62,7 @@ BIOBLEND_DIR=$(get_abs_dirname "$(dirname "$0")")
 if ! command -v tox >/dev/null; then
     cd "${BIOBLEND_DIR}"
     if [ ! -d .venv ]; then
-        virtualenv -p python3 .venv
+        python3 -m venv .venv
     fi
     . .venv/bin/activate
     python3 -m pip install --upgrade "tox>=1.8.0"
@@ -88,10 +88,14 @@ else
     esac
 fi
 
-# Setup Galaxy virtualenv
+# Setup Galaxy virtual environment
 if [ -n "${GALAXY_PYTHON}" ]; then
     if [ ! -d .venv ]; then
-        virtualenv -p "${GALAXY_PYTHON}" .venv
+        if ! "${GALAXY_PYTHON}" -m venv .venv; then
+            echo "Creating the Python virtual environment for Galaxy using the venv standard library module failed."
+            echo "Trying with virtualenv now."
+            virtualenv -p "$GALAXY_PYTHON"  .venv
+        fi
     fi
     export GALAXY_PYTHON
 fi
diff --git a/tox.ini b/tox.ini
index 0eb7b0508..adb58ceb4 100644
--- a/tox.ini
+++ b/tox.ini
@@ -15,6 +15,18 @@ passenv =
     GALAXY_VERSION
     BIOBLEND_TOOLSHED_URL
 
+[testenv:build]
+commands =
+    make clean
+    python3 -m build
+    twine check dist/*
+deps =
+    build
+    twine
+allowlist_externals =
+    make
+skip_install = true
+
 [testenv:lint]
 commands =
     ruff check .