Some cleanups and split the CI

Author: psobolewskiPhD

.github/workflows/ci.yml

@@ -63,34 +63,64 @@ jobs:
           python -m pip install .[test]
           python -m pip install ${{ matrix.backend }}
 
-      - name: Set up OMERO
-        if: runner.os == 'Linux'
+      - name: Test (local)
+        run: pytest ./tests/local --color=yes --cov=napari_omero --cov-report=xml
+
+#      - name: Codecov
+#        uses: codecov/codecov-action@v5
+#        env:
+#          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+
+  # Integration tests against a real, containerized OMERO server.
+  # Kept as a separate job (single OS + Python) so the server stack is only
+  # started once, rather than across the full test matrix.
+  test-server:
+    name: server tests
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
+    steps:
+      - uses: actions/checkout@v6
+      - uses: conda-incubator/setup-miniconda@v3
+        with:
+          miniforge-version: "latest"
+          python-version: "3.12"
+
+      # the server test for the browser widget needs a Qt backend + display
+      - uses: pyvista/setup-headless-display-action@v4
+        with:
+          qt: true
+
+      - name: Install dependencies
+        run: |
+          conda install omero-py
+          python -m pip install --upgrade pip
+          python -m pip install .[test]
+          python -m pip install PyQt5
+
+      - name: Set up OMERO server
         run: |
-          git clone https://github.com/openmicroscopy/omero-test-infra .omero
-          # ensure the ports are bound correctly
+          # omero-test-infra is used only to stand up a server stack (compose up);
+          # Pinned to latest commit: Dec 2025
+          git clone https://github.com/ome/omero-test-infra .omero
+          git -C .omero checkout c8a0015b0ce72ee0a49e6968af33de10ea00bc77
+          # Bind the server/web ports to fixed host ports so the host-side tests
+          # can reach localhost:4064 / :4080 (compose defaults to random ports).
           # see also: https://github.com/ome/omero-test-infra/issues/77
           echo 'OMERO_SERVER_SSL=4064:' >> .omero/.env
           echo 'OMERO_WEB_PORT=4080:' >> .omero/.env
           .omero/compose up -d
           .omero/wait-on-login
 
-      - name: Test with OMERO server
-        if: runner.os == 'Linux'
+      - name: Test (server)
         run: pytest ./tests/server --color=yes --cov=napari_omero --cov-report=xml
 
-      - name: Test local
-        run: pytest ./tests/local --color=yes --cov=napari_omero --cov-report=xml --cov-append
-
-#      - name: Codecov
-#        uses: codecov/codecov-action@v5
-#        env:
-#          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
-
   deploy:
     # this will run when you have tagged a commit, starting with "v*"
     # and requires that you have put your twine API key in your
-    needs: [test]
-    if: success() && startsWith(github.ref, 'refs/tags/') && github.repository == 'tlambert03/napari-omero'
+    needs: [test, test-server]
+    if: success() && startsWith(github.ref, 'refs/tags/') && github.repository == 'ome/napari-omero'
     runs-on: ubuntu-latest
     permissions:
       id-token: write

tests/server/conftest.py

@@ -1,21 +1,11 @@
-# This code is derived from the conftest.py file from the ezomero library,
-# which is licensed under the GNU General Public License v2.0 as published by
-# the Free Software Foundation.
+# This code is derived from the conftest.py file in the ezomero project:
+#   https://github.com/erickmartins/ezomero
+#   Copyright (c) 2020-2025, Erick Ratamero, Dave Mellert, and contributors
 #
-# Copyright (c) 2020-2025, Erick Ratamero, Dave Mellert, and contributors
-#
-# This program is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation, either version 3 of the License, or
-# (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# GNU General Public License for more details.
-#
-# For the original code, please see:
-# https://github.com/erickmartins/ezomero
+# ezomero is distributed under the GNU General Public License, version 2
+# (GPL-2.0). napari-omero is GPL-2.0-or-later, which is compatible. This file is
+# distributed under the same terms; it comes with NO WARRANTY, to the extent
+# permitted by law. See the GNU General Public License for more details.
 #
 # Note that these fixtures are only used for the OMERO server tests.
 import os
@@ -35,7 +25,7 @@
 DEFAULT_OMERO_HOST = "localhost"
 DEFAULT_OMERO_WEB_HOST = "http://localhost:4080"
 DEFAULT_OMERO_PORT = "4064"
-DEFAULT_OMERO_SECURE = 1
+DEFAULT_OMERO_SECURE = True
 
 # [[group, permissions], ...]
 GROUPS_TO_CREATE = [["test_group_1", "read-only"], ["test_group_2", "read-only"]]
@@ -77,7 +67,7 @@ def pytest_addoption(parser):
     parser.addoption(
         "--omero-secure",
         action="store",
-        default=bool(os.environ.get("OMERO_SECURE", DEFAULT_OMERO_SECURE)),
+        default=os.environ.get("OMERO_SECURE", DEFAULT_OMERO_SECURE),
     )
 
 
@@ -89,7 +79,14 @@ def omero_params(request):
     host = request.config.getoption("--omero-host")
     web_host = request.config.getoption("--omero-web-host")
     port = request.config.getoption("--omero-port")
-    secure = request.config.getoption("--omero-secure")
+    secure_opt = request.config.getoption("--omero-secure")
+    # the option default is a real bool, but an OMERO_SECURE env var arrives as
+    # a string ("0"/"false" should mean False), so coerce explicitly.
+    secure = (
+        secure_opt
+        if isinstance(secure_opt, bool)
+        else str(secure_opt).strip().lower() in ("1", "true", "yes")
+    )
     return (user, password, host, web_host, port, secure)
 
 
@@ -205,7 +202,7 @@ def users_groups(conn, omero_params):
 
 @pytest.fixture(scope="session")
 def conn(omero_params):
-    user, password, host, web_host, port, secure = omero_params
+    user, password, host, _web_host, port, secure = omero_params
     conn = BlitzGateway(user, password, host=host, port=port, secure=secure)
     conn.connect()
     yield conn

tests/server/test_server.py

@@ -8,7 +8,7 @@ def test_server_connection(conn):
 def test_omero_browser_login(make_napari_viewer, omero_params, qtbot):
     from napari_omero import OMEROWidget
 
-    user, password, host, web_host, port, secure = omero_params
+    user, password, host, _web_host, port, _secure = omero_params
 
     viewer = make_napari_viewer()
     widget = OMEROWidget()