Merge branch 'main' into python-3.10.11

Author: danielhollas

.github/workflows/main.yml

@@ -55,16 +55,11 @@ jobs:
             runsOn: ubuntu-22.04
             platforms: linux/amd64,linux/arm64
 
-    # To save arm64 runner resources, we run the tests only on main
-    # and only for full-stack image (same for integration tests below).
     test-arm64:
-        #if: >-
-        #    github.repository == 'aiidalab/aiidalab-docker-stack'
-        #    && (github.ref_type == 'tag' || github.ref_name == 'main')
         needs: build
         uses: ./.github/workflows/test.yml
         with:
-            runsOn: buildjet-4vcpu-ubuntu-2204-arm
+            runsOn: ubuntu-22.04-arm
             images: ${{ needs.build.outputs.images }}
             target: full-stack
             integration: false
@@ -74,16 +69,8 @@ jobs:
         needs: build
         strategy:
             fail-fast: false
-            # Trick to exclude arm64 tests from PRs
-            # https://github.com/orgs/community/discussions/26253
             matrix:
-                runner: [ubuntu-22.04, buildjet-4vcpu-ubuntu-2204-arm]
-                isPR:
-                    - ${{ github.event_name == 'pull_request' }}
-                #exclude:
-                    #    - isPR: true
-                    #  runner: buildjet-4vcpu-ubuntu-2204-arm
-
+                runner: [ubuntu-22.04, ubuntu-22.04-arm]
         uses: ./.github/workflows/test.yml
         with:
             runsOn: ${{ matrix.runner }}

.github/workflows/test.yml

@@ -51,9 +51,7 @@ jobs:
                   cache: pip
 
             - name: Install dependencies 📦
-              run: |
-                  pip install -r requirements.txt
-                  pip freeze
+              run: pip install -r requirements.txt
 
             - name: Run tests
               run: pytest -s -m "${{ inputs.integration && 'integration' || 'not integration' }}" --target ${{inputs.target}}

.pre-commit-config.yaml

@@ -18,14 +18,14 @@ repos:
             args: [--preserve-quotes]
 
     - repo: https://github.com/astral-sh/ruff-pre-commit
-      rev: v0.6.9
+      rev: v0.9.2
       hooks:
           - id: ruff-format
           - id: ruff
             args: [--fix, --exit-non-zero-on-fix, --show-fixes]
 
     - repo: https://github.com/python-jsonschema/check-jsonschema
-      rev: "0.29.3"
+      rev: "0.31.0"
       hooks:
           - id: check-dependabot
           - id: check-github-workflows

build.json

@@ -10,13 +10,13 @@
       "default": "3.9.13"
     },
     "AIIDA_VERSION": {
-      "default": "2.6.2"
+      "default": "2.6.3"
     },
     "AIIDALAB_VERSION": {
       "default": "24.09.0"
     },
     "AIIDALAB_HOME_VERSION": {
-      "default": "24.09.0"
+      "default": "25.01.0"
     }
   }
 }

bumpver.toml

@@ -1,5 +1,5 @@
 [bumpver]
-current_version = "v2024.1023"
+current_version = "v2025.1025"
 version_pattern = "vYYYY.BUILD[-TAG]"
 commit_message = "Bump version {old_version} -> {new_version}."
 commit = true

requirements.in

@@ -0,0 +1,7 @@
+docker
+requests
+pre-commit
+pytest~=7.0
+pytest-docker
+doit
+dunamai

requirements.txt

@@ -1,7 +1,32 @@
-docker
-requests
-pre-commit
-pytest~=7.0
-pytest-docker
-doit
-dunamai
+# This file was autogenerated by uv via the following command:
+#    uv pip compile --universal --python 3.9 requirements.in --annotation-style=line -o requirements.txt
+attrs==24.3.0             # via pytest-docker
+certifi==2024.12.14       # via requests
+cfgv==3.4.0               # via pre-commit
+charset-normalizer==3.4.1  # via requests
+cloudpickle==3.1.1        # via doit
+colorama==0.4.6 ; sys_platform == 'win32'  # via pytest
+distlib==0.3.9            # via virtualenv
+docker==7.1.0             # via -r requirements.in
+doit==0.36.0              # via -r requirements.in
+dunamai==1.23.0           # via -r requirements.in
+exceptiongroup==1.2.2 ; python_full_version < '3.11'  # via pytest
+filelock==3.17.0          # via virtualenv
+identify==2.6.6           # via pre-commit
+idna==3.10                # via requests
+importlib-metadata==8.6.1  # via doit
+iniconfig==2.0.0          # via pytest
+nodeenv==1.9.1            # via pre-commit
+packaging==24.2           # via dunamai, pytest
+platformdirs==4.3.6       # via virtualenv
+pluggy==1.5.0             # via pytest
+pre-commit==4.1.0         # via -r requirements.in
+pytest==7.4.4             # via pytest-docker, -r requirements.in
+pytest-docker==3.1.1      # via -r requirements.in
+pywin32==308 ; sys_platform == 'win32'  # via docker
+pyyaml==6.0.2             # via pre-commit
+requests==2.32.3          # via docker, -r requirements.in
+tomli==2.2.1 ; python_full_version < '3.11'  # via pytest
+urllib3==2.3.0            # via docker, requests
+virtualenv==20.29.1       # via pre-commit
+zipp==3.21.0              # via importlib-metadata

stack/base/Dockerfile

@@ -42,8 +42,19 @@ RUN cat /opt/requirements.txt | xargs -I{} conda config --system --add pinned_pa
 
 # Configure pip to use the same requirements file as constraints file.
 ENV PIP_CONSTRAINT /opt/requirements.txt
-# Ensure that pip installs packages to ~/.local by default
-COPY pip.conf /etc/pip.conf
+# Ensure that pip installs packages to '~/.local/lib/python3.X/site-packages/' by default
+# by implicitly passing the '--user' option to 'pip install'
+# Otherwise, pip would install into /opt/conda and such packages would be lost
+# when the container exits.
+# NOTE: We specifically chose the location '/opt/conda/pip.conf'
+# which represents the 'site' config file when VIRTUAL_ENV is not set, per:
+# https://pip.pypa.io/en/stable/topics/configuration/#configuration-files
+# Other locations such as '~/.config/pip/pip.conf' or '/etc/pip.conf' would interfere with virtual environments,
+# for example those used by pre-commit.
+# We can't use the PIP_USER env variable for the same reason.
+# To better understand this, try running `pip config debug` and see
+# https://github.com/aiidalab/aiidalab-docker-stack/issues/501
+COPY pip.conf "${CONDA_DIR}/pip.conf"
 
 # Upgrade pip and mamba to latest
 # Update async_generator, certipy to satisfy `pip check`

tests/conftest.py

@@ -3,7 +3,7 @@
 
 import pytest
 import requests
-from requests.exceptions import ConnectionError
+from requests.exceptions import ConnectionError  # noqa: A004
 
 TARGETS = ("base", "lab", "base-with-services", "full-stack")
 
@@ -112,11 +112,11 @@ def pip_install(aiidalab_exec, nb_user):
     def _pip_install(pkg, **args):
         nonlocal package
         package = pkg
-        return aiidalab_exec(f"pip install {pkg}", **args)
+        return aiidalab_exec(f"pip install {pkg}", user=nb_user, **args)
 
     yield _pip_install
     if package:
-        aiidalab_exec(f"pip uninstall --yes {package}")
+        aiidalab_exec(f"pip uninstall --yes {package}", user=nb_user)
 
 
 @pytest.fixture(scope="session")

tests/test_base.py

@@ -1,11 +1,19 @@
 """This module contains tests for the base image, which are AiiDA and package management related tests."""
 
+import email
 import json
 
 import pytest
 from packaging.version import parse
 
 
+@pytest.fixture
+def venv(tmp_path, aiidalab_exec):
+    venv_path = tmp_path / ".venv"
+    aiidalab_exec(f"python -m venv {venv_path}")
+    return venv_path
+
+
 @pytest.mark.parametrize("pkg_manager", ["pip", "mamba"])
 def test_prevent_installation_of_aiida(
     aiidalab_exec, nb_user, aiida_version, pkg_manager
@@ -76,8 +84,6 @@ def test_path_local_pip(aiidalab_exec, nb_user):
 
 def test_pip_user_install(aiidalab_exec, pip_install, nb_user):
     """Test that pip installs packages to ~/.local/ by default"""
-    import email
-
     # We use 'tuna' as an example of python-only package without dependencies
     pkg = "tuna"
     pip_install(pkg)
@@ -86,3 +92,16 @@ def test_pip_user_install(aiidalab_exec, pip_install, nb_user):
     # `pip show` output is in the RFC-compliant email header format
     msg = email.message_from_string(output)
     assert msg.get("Location").startswith(f"/home/{nb_user}/.local/")
+
+
+def test_pip_install_in_venv(aiidalab_exec, venv, nb_user):
+    """Test that pip installs packages to an activated venv"""
+
+    pkg = "tuna"
+    pip = venv / "bin/pip"
+
+    aiidalab_exec(f"{pip} install {pkg}")
+
+    output = aiidalab_exec(f"{pip} show {pkg}")
+    msg = email.message_from_string(output)
+    assert msg.get("Location").startswith(f"{venv}/lib")