CI fixes and improvements (#331)

Put back uploading screenshots as artifacts. Screenshots were previously generated in the `screenshots/` directory inside the Git repo.  However, we now change ownership of the Git repo that is mounted into the testing container to user jovyan. 

Therefore, the Git repo directory is no longer writable from outside the container, which means pytest cannot write to it and screenshot files are not saved. It is workaround by giving the package folder the write access of all user inside the container.

Other fixes:

1. Do not test with multiple Python versions, tests themselves run inside the container so this was meaningles.
2. Fix the `setup.cfg`. See comment below. I needed to remove the `setupcfg-fmt` pre-commit hook, but since we plan to move to `pyproject.toml` anyway I think this is fine. 
3. Version bumps of various testing dependencies.
4. Updated `pre-commit` plugins by running `pre-commit autoupdate` manually. This PR supersecedes #323

.github/workflows/ci.yml

@@ -1,5 +1,5 @@
 ---
-# Run basic tests for this app on the latest aiidalab-docker image.
+# Run basic tests for this app
 
 name: continuous-integration
 
@@ -13,16 +13,21 @@ jobs:
         runs-on: ubuntu-latest
 
         steps:
-            - uses: actions/checkout@v2
+            - uses: actions/checkout@v3
 
             - name: Setup Python
-              uses: actions/setup-python@v2
+              uses: actions/setup-python@v4
               with:
-                  python-version: 3.8
+                  python-version: '3.10'
+                  cache: pip
+                  cache-dependency-path: |
+                      .pre-commit-config.yaml
+                      **/setup.cfg
+                      **/pyproject.toml
+                      **/requirements*.txt
 
             - name: Install dependencies
-              run: |
-                  python -m pip install pre-commit==2.11.1
+              run: python -m pip install pre-commit~=2.20
 
             - name: Run pre-commit
               run: pre-commit run --all-files || ( git status --short ; git diff ; exit 1 )

.github/workflows/di.yml

@@ -16,33 +16,29 @@ jobs:
         strategy:
             matrix:
                 tag: [latest]
+                image: [aiidalab/full-stack]
                 browser: [Chrome, Firefox]
-                python-version: ['3.8', '3.10']
-                firefox: ['96.0']
             fail-fast: false
 
         runs-on: ubuntu-latest
         timeout-minutes: 60
 
         steps:
             - name: Check out app
-              uses: actions/checkout@v2
+              uses: actions/checkout@v3
 
-            - name: Cache Python dependencies
-              uses: actions/cache@v1
+            - name: Set up Python
+              uses: actions/setup-python@v4
               with:
-                  path: ~/.cache/pip
-                  key: pip-${{ matrix.python-version }}-tests-${{ hashFiles('**/setup.json') }}
-                  restore-keys: pip-${{ matrix.python-version }}-tests
-
-            - name: Set up Python ${{ matrix.python-version }}
-              uses: actions/setup-python@v2
-              with:
-                  python-version: ${{ matrix.python-version }}
+                  python-version: '3.10'
+                  cache: pip
+                  cache-dependency-path: |
+                      **/setup.cfg
+                      **/pyproject.toml
+                      **/requirements*.txt
 
             - name: Install dependencies for test
-              run: |
-                  pip install -U -r requirements_test.txt
+              run: pip install -U -r requirements_test.txt
 
             - name: Set jupyter token env
               run: echo "JUPYTER_TOKEN=$(openssl rand -hex 32)" >> $GITHUB_ENV
@@ -52,7 +48,7 @@ jobs:
             - name: Install Firefox
               uses: browser-actions/setup-firefox@latest
               with:
-                  firefox-version: ${{ matrix.firefox }}
+                  firefox-version: '96.0'
               if: matrix.browser == 'Firefox'
 
             - name: Install geckodriver
@@ -65,3 +61,12 @@ jobs:
               run: pytest --driver ${{ matrix.browser }}
               env:
                   TAG: ${{ matrix.tag }}
+                  AIIDALAB_IMAGE: ${{ matrix.image }}
+
+            - name: Upload screenshots as artifacts
+              if: always()
+              uses: actions/upload-artifact@v3
+              with:
+                  name: Screenshots-${{ matrix.tag }}-${{ matrix.browser }}
+                  path: screenshots/
+                  if-no-files-found: error

.pre-commit-config.yaml

@@ -2,7 +2,7 @@
 repos:
 
     - repo: https://github.com/pre-commit/pre-commit-hooks
-      rev: v4.3.0
+      rev: v4.4.0
       hooks:
           - id: check-json
           - id: check-yaml
@@ -22,7 +22,7 @@ repos:
             language_version: python3 # Should be a command that runs python3.6+
 
     - repo: https://github.com/PyCQA/flake8
-      rev: 5.0.4
+      rev: 6.0.0
       hooks:
           - id: flake8
             args: [--count, --show-source, --statistics]
@@ -35,17 +35,12 @@ repos:
           - id: isort
             args: [--profile, black, --filter-files]
 
-    - repo: https://github.com/asottile/setup-cfg-fmt
-      rev: v2.2.0
-      hooks:
-          - id: setup-cfg-fmt
-
     - repo: https://github.com/sirosen/check-jsonschema
       rev: 0.19.2
       hooks:
           - id: check-github-workflows
 
     - repo: https://github.com/kynan/nbstripout
-      rev: 0.5.0
+      rev: 0.6.1
       hooks:
           - id: nbstripout

pyproject.toml

@@ -1,6 +1,6 @@
 [build-system]
 requires = [
-    "setuptools>=42",
+    "setuptools>=62.6",
     "wheel"
 ]
 build-backend = "setuptools.build_meta"

requirements_test.txt

@@ -1,5 +1,5 @@
-pytest~=6.0
+pytest~=6.2
 pytest-docker~=1.0
 pytest-selenium~=4.0
 webdriver-manager~=3.8
-selenium==4.1.0
+selenium~=4.7.0

setup.cfg

@@ -36,9 +36,8 @@ python_requires = >=3.8
 [options.extras_require]
 dev =
     bumpver==2022.1119
-    pre-commit==2.11.1
-test =
-    requirements-test.txt
+    pre-commit~=2.20
+test = file: requirements_test.txt
 
 [options.package_data]
 aiidalab_qe.parameters = qeapp.yaml
@@ -51,9 +50,9 @@ categories =
 
 [flake8]
 ignore =
-    E501  # Line length handled by black.
-    W503  # Line break before binary operator, preferred formatting for black.
-    E203  # Whitespace before ':', preferred formatting for black.
+    E501
+    W503
+    E203
 
 [bumpver]
 current_version = "v22.12.0"

tests/conftest.py

@@ -1,4 +1,5 @@
 import os
+from pathlib import Path
 from urllib.parse import urljoin
 
 import pytest
@@ -17,24 +18,45 @@ def is_responsive(url):
 
 
 @pytest.fixture(scope="session")
-def notebook_service(docker_ip, docker_services):
-    """Ensure that HTTP service is up and responsive."""
+def docker_compose(docker_services):
+    return docker_services._docker_compose
 
-    docker_compose = docker_services._docker_compose
 
-    # assurance for host user UID other that 1000
-    chown_command = "exec -T -u root aiidalab bash -c 'chown -R jovyan:users /home/jovyan/apps/aiidalab-qe'"
-    docker_compose.execute(chown_command)
+@pytest.fixture(scope="session")
+def aiidalab_exec(docker_compose):
+    def execute(command, user=None, workdir=None, **kwargs):
+        opts = "-T"
+        if user:
+            opts = f"{opts} --user={user}"
+        if workdir:
+            opts = f"{opts} --workdir={workdir}"
+        command = f"exec {opts} aiidalab {command}"
 
-    install_command = "bash -c 'pip install -U .'"
-    command = f"exec --workdir /home/jovyan/apps/aiidalab-qe/src -T aiidalab {install_command}"
-    docker_compose.execute(command)
+        return docker_compose.execute(command, **kwargs)
 
-    install_command = "bash -c 'python tests/helper_dep_requirements.py && pip install -U -r /tmp/requirements.txt'"
-    command = (
-        f"exec --workdir /home/jovyan/apps/aiidalab-qe -T aiidalab {install_command}"
-    )
-    docker_compose.execute(command)
+    return execute
+
+
+@pytest.fixture(scope="session")
+def nb_user(aiidalab_exec):
+    return aiidalab_exec("bash -c 'echo \"${NB_USER}\"'").decode().strip()
+
+
+@pytest.fixture(scope="session")
+def notebook_service(docker_ip, docker_services, aiidalab_exec, nb_user):
+    """Ensure that HTTP service is up and responsive."""
+
+    # Directory ~/apps/aiidalab-qe/ is mounted by docker,
+    # make it writeable for jovyan user, needed for `pip install`
+    appdir = f"/home/{nb_user}/apps/aiidalab-qe"
+    aiidalab_exec(f"chmod -R a+rw {appdir}", user="root")
+
+    # Install workchains
+    aiidalab_exec("pip install .", workdir=f"{appdir}/src", user=nb_user)
+
+    # Install App
+    install_command = "bash -c 'python tests/helper_dep_requirements.py && pip install -r /tmp/requirements.txt'"
+    aiidalab_exec(install_command, workdir=appdir, user=nb_user)
 
     # `port_for` takes a container port and returns the corresponding host port
     port = docker_services.port_for("aiidalab", 8888)
@@ -62,6 +84,16 @@ def _selenium_driver(nb_path, wait_time=5.0):
     return _selenium_driver
 
 
+@pytest.fixture(scope="session")
+def screenshot_dir():
+    sdir = Path.joinpath(Path.cwd(), "screenshots")
+    try:
+        os.mkdir(sdir)
+    except FileExistsError:
+        pass
+    return sdir
+
+
 @pytest.fixture
 def firefox_options(firefox_options):
     firefox_options.add_argument("--headless")

tests/docker-compose.yml

@@ -4,7 +4,7 @@ version: '3.4'
 services:
 
     aiidalab:
-        image: aiidalab/full-stack:${TAG:-latest}
+        image: ${AIIDALAB_IMAGE:-aiidalab/full-stack}:${TAG:-latest}
         environment:
             RMQHOST: messaging
             TZ: Europe/Zurich

tests/helper_dep_requirements.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python3
 
-"""This helper script is for temporarily remove the
-`aiidalab-qe-workchain` package from dependencies list so that
+"""This helper script removes the `aiidalab-qe-workchain` package
+from dependencies list so that
 in the test it will not use the remote released source.
 """
 

tests/test_qe_app.py

@@ -1,3 +1,6 @@
+import time
+from pathlib import Path
+
 import requests
 from selenium.webdriver.common.by import By
 
@@ -8,21 +11,29 @@ def test_notebook_service_available(notebook_service):
     assert response.status_code == 200
 
 
-def test_qe_app_take_screenshot(selenium_driver):
+def test_qe_app_take_screenshot(selenium_driver, screenshot_dir):
     driver = selenium_driver("qe.ipynb", wait_time=30.0)
-    driver.set_window_size(1920, 985)
-    driver.get_screenshot_as_file("screenshots/qe-app.png")
+    driver.set_window_size(1920, 1485)
+    time.sleep(15)
+    driver.get_screenshot_as_file(str(Path.joinpath(screenshot_dir, "qe-app.png")))
 
 
-def test_qe_app_select_silicon(selenium_driver):
+def test_qe_app_select_silicon(selenium_driver, screenshot_dir):
     driver = selenium_driver("qe.ipynb", wait_time=30.0)
-    driver.set_window_size(1920, 985)
+    driver.set_window_size(1920, 1485)
     driver.find_element(
         By.XPATH, "//*[text()='From Examples']"
     ).click()  # click `From Examples` tab for input structure
     driver.find_element(By.XPATH, "//option[@value='Diamond']").click()
-    driver.get_screenshot_as_file("screenshots/qe-app-select-diamond-selected.png")
+    time.sleep(2)
+    driver.get_screenshot_as_file(
+        str(Path.joinpath(screenshot_dir, "qe-app-select-diamond-selected.png"))
+    )
     confirm_button = driver.find_element(By.XPATH, "//button[text()='Confirm']")
     confirm_button.location_once_scrolled_into_view  # scroll into view
     confirm_button.click()
-    driver.get_screenshot_as_file("screenshots/qe-app-select-diamond-confirmed.png")
+    # Test that we have indeed proceeded to the next step
+    driver.find_element(By.XPATH, "//span[contains(.,'✓ Step 1')]")
+    driver.get_screenshot_as_file(
+        str(Path.joinpath(screenshot_dir, "qe-app-select-diamond-confirmed.png"))
+    )