Replace vcr-py for tests

.github/workflows/ci.yml

@@ -166,7 +166,10 @@ jobs:
         with:
           # Install a specific version of uv.
           version: "0.4.22"
-
+
+      - name: Install proxay
+        run: npm install -g proxay
+
       - name: Set up Python ${{ matrix.python-version }}
         run: uv python install ${{ matrix.python-version }}
 
@@ -182,6 +185,9 @@ jobs:
         if: ${{ matrix.group == 1 && matrix.python-version == '3.11' }}
         run: ./typecheck.sh
 
+      - name: Setup tmate session
+        uses: mxschmitt/action-tmate@v3
+
       - name: Python tests
         timeout-minutes: 30
         env:

CONTRIBUTING.md

@@ -133,15 +133,20 @@ Internal workflows for scalable minds:
 
 The `webknossos` folder contains examples, which are not part of the package, but are tested via `tests/test_examples.py` and added to the documentation (see `docs/src/webknossos-py/examples`).
 
+To run the `./test.sh` script it is necessary to install `proxay`. This is either done with [NPM](https://www.npmjs.com) or [yarn](https://yarnpkg.com/getting-started/install):
+```bash
+npm install --global proxay
+
+# or if you're using yarn
+yarn global add proxay
+```
+
 The tests also contain functionality for the WEBKNOSSOS client. There a two modes to run the tests:
 
 1. `./test.sh --refresh-snapshots`, sending network requests to a WEBKNOSSOS instance:
-  This expects a local WEBKNOSSOS setup with specific test data, which is shipped with WEBKNOSSOS. If you're starting and running WEBKNOSSOS manually, please use port 9000 (the default) and run the `tools/postgres/dbtool.js prepare-test-db` script in the WEBKNOSSOS repository (⚠️ this overwrites your local WEBKNOSSOS database). Alternatively, a `docker compose` setup is started automatically for the tests, see `./test.sh` and `tests/docker-compose.yml` for details. The network requests & response are recorded as "cassettes" by [vcr.py](https://vcrpy.readthedocs.io), see next point:
-2. `./test.sh` replays responses from previous network snapshots using [vcr.py](https://vcrpy.readthedocs.io) via [pytest-recording](https://github.com/kiwicom/pytest-recording). No additional network requests are allowed in this mode.
+  This expects a local WEBKNOSSOS setup with specific test data, which is shipped with WEBKNOSSOS. If you're starting and running WEBKNOSSOS manually, please use port 9000 (the default) and run the `tools/postgres/dbtool.js prepare-test-db` script in the WEBKNOSSOS repository (⚠️ this overwrites your local WEBKNOSSOS database). Alternatively, a `docker compose` setup is started automatically for the tests, see `./test.sh` and `tests/docker-compose.yml` for details. The network requests & response are recorded as "cassettes" by [proxay](https://github.com/airtasker/proxay), see next point:
+2. `./test.sh` replays responses from previous network snapshots using [proxay](https://github.com/airtasker/proxay).
 
-`./test.sh --store-durations` updates the durations for
-[`pytest-split`](https://jerry-git.github.io/pytest-split),
-which is used in the CI to split the tests for different runners.
 
 #### `cluster_tools` package
 

cluster_tools/dockered-slurm/docker-compose.yml

@@ -1,5 +1,3 @@
-version: "2.2"
-
 services:
   mysql:
     image: mysql:5.7
@@ -16,7 +14,7 @@ services:
 
   slurmdbd:
     image: scalableminds/slurm-docker-cluster:master__11274637426
-    command: ["slurmdbd"]
+    command: [ "slurmdbd" ]
     container_name: slurmdbd
     hostname: slurmdbd
     volumes:
@@ -32,7 +30,7 @@ services:
 
   slurmctld:
     image: scalableminds/slurm-docker-cluster:master__11274637426
-    command: ["slurmctld"]
+    command: [ "slurmctld" ]
     container_name: slurmctld
     environment:
       USER: "root"
@@ -53,7 +51,7 @@ services:
 
   c1:
     image: scalableminds/slurm-docker-cluster:master__11274637426
-    command: ["slurmd"]
+    command: [ "slurmd" ]
     hostname: c1
     container_name: c1
     volumes:
@@ -71,7 +69,7 @@ services:
 
   c2:
     image: scalableminds/slurm-docker-cluster:master__11274637426
-    command: ["slurmd"]
+    command: [ "slurmd" ]
     hostname: c2
     container_name: c2
     volumes:

webknossos/Changelog.md

@@ -17,6 +17,7 @@ For upgrade instructions, please check the respective _Breaking Changes_ section
 ### Added
 
 ### Changed
+- Removes vcr-py from developer dependencies for testing and adds proxay for recording and replaying API requests. [#1198](https://github.com/scalableminds/webknossos-libs/pull/1198)
 
 ### Fixed
 

webknossos/examples/accessing_metadata.py

@@ -2,19 +2,18 @@
 
 
 def main() -> None:
-    with wk.webknossos_context(url="https://webknossos.org/"):
-        l4_sample_dataset = wk.Dataset.open_remote("l4_sample")
-        # Access the metadata of the dataset
-        print(l4_sample_dataset.metadata)
+    l4_sample_dataset = wk.Dataset.open_remote("l4_sample")
+    # Access the metadata of the dataset
+    print(l4_sample_dataset.metadata)
 
-        # Edit the metadata of the dataset
-        l4_sample_dataset.metadata["new_key"] = "new_value"
+    # Edit the metadata of the dataset
+    l4_sample_dataset.metadata["new_key"] = "new_value"
 
-        # Access metadata of a folder
-        print(l4_sample_dataset.folder.metadata)
+    # Access metadata of a folder
+    print(l4_sample_dataset.folder.metadata)
 
-        # Edit the metadata of the folder
-        l4_sample_dataset.folder.metadata["new_folder_key"] = "new_folder_value"
+    # Edit the metadata of the folder
+    l4_sample_dataset.folder.metadata["new_folder_key"] = "new_folder_value"
 
 
 if __name__ == "__main__":

webknossos/examples/apply_merger_mode.py

@@ -20,10 +20,9 @@ def main() -> None:
     ###############################################
 
     dataset = wk.Dataset.download(
-        "l4_sample_dev",
-        "scalable_minds",
+        "l4_sample",
+        "Organization_X",
         path="testoutput/l4_sample_dev",
-        webknossos_url="https://webknossos.org",
     )
     in_layer = cast(wk.SegmentationLayer, dataset.get_layer("segmentation"))
     in_mag1 = in_layer.get_mag("1")

webknossos/examples/learned_segmenter.py

@@ -1,7 +1,6 @@
 import os
 from functools import partial
 from tempfile import TemporaryDirectory
-from time import gmtime, strftime
 
 import numpy as np
 from skimage import feature
@@ -20,8 +19,7 @@ def main() -> None:
     # Step 1: Read the training data from the annotation and the dataset's color
     # layer (the data will be streamed from WEBKNOSSOS to our local computer)
     training_data_bbox = annotation.user_bounding_boxes[0]  # type: ignore[index]
-    time_str = strftime("%Y-%m-%d_%H-%M-%S", gmtime())
-    new_dataset_name = annotation.dataset_name + f"_segmented_{time_str}"
+    new_dataset_name = f"{annotation.dataset_name}_segmented"
     with wk.webknossos_context("https://webknossos.org"):
         dataset = annotation.get_remote_annotation_dataset()
 

webknossos/examples/upload_dicom_stack.py

@@ -1,14 +1,12 @@
 from pathlib import Path
-from time import gmtime, strftime
 
 import webknossos as wk
 
 
 def main() -> None:
-    time_str = strftime("%Y-%m-%d_%H-%M-%S", gmtime())
     dataset = wk.Dataset.from_images(
         str(Path(__file__).parent.parent / "testdata" / "dicoms"),
-        f"dicom_dataset_{time_str}",
+        "dicom_dataset_upload",
         voxel_size=(12, 12, 12),
     )
     dataset.compress()

webknossos/examples/upload_image_data.py

@@ -1,5 +1,3 @@
-from time import gmtime, strftime
-
 import numpy as np
 from skimage import data
 
@@ -19,12 +17,8 @@ def main() -> None:
     # we expect the following dimensions: Channels, X, Y, Z.
     img = np.transpose(img, [1, 3, 2, 0])
 
-    # choose a name for our dataset
-    time_str = strftime("%Y-%m-%d_%H-%M-%S", gmtime())
-    name = f"cell_{time_str}"
-
-    # voxel_size is defined in nm
-    ds = wk.Dataset(name, voxel_size=(260, 260, 290))
+    # choose name and voxel size (voxel_size is defined in nm)
+    ds = wk.Dataset("cell_dataset", voxel_size=(260, 260, 290))
 
     ds.default_view_configuration = DatasetViewConfiguration(zoom=0.35)
 

webknossos/examples/upload_tiff_stack.py

@@ -1,14 +1,12 @@
 from pathlib import Path
-from time import gmtime, strftime
 
 import webknossos as wk
 
 
 def main() -> None:
-    time_str = strftime("%Y-%m-%d_%H-%M-%S", gmtime())
     dataset = wk.Dataset.from_images(
         str(Path(__file__).parent.parent / "testdata" / "tiff"),
-        f"tiff_dataset_{time_str}",
+        "tiff_dataset_upload",
         voxel_size=(12, 12, 12),
     )
     dataset.compress()

webknossos/local_wk_setup.sh

@@ -6,12 +6,12 @@ function export_vars {
 
 function ensure_local_test_wk {
     export_vars
+    WK_DOCKER_DIR="tests"
 
     if ! curl -sf localhost:9000/api/health; then
         echo "Using docker compose setup with the docker tag $DOCKER_TAG"
         echo "  To change this, please update DOCKER_TAG in local_wk_setup.sh"
 
-        WK_DOCKER_DIR="tests"
         pushd $WK_DOCKER_DIR > /dev/null
         docker compose pull webknossos
         if [ ! -d binaryData/Organization_X/l4_sample ]; then
@@ -34,6 +34,10 @@ function ensure_local_test_wk {
         while ! curl -sf localhost:9000/api/health; do
             sleep 5
         done
+        # docker compose exec -T --user root webknossos sh -c "echo name,url,publicUrl,key,isScratch,isDeleted,allowsUpload,onlyAllowedOrganization,reportUsedStorageEnabled\n'http://localhost','http://localhost:9000','http://localhost:3000','something-secure',f,f,t,,f > test/db/dataStores.csv"
+        # docker compose exec -T --user root webknossos sh -c "sed -i 's|publicUri = \${http.uri}|publicUri = \"localhost:3000\"|' conf/application.conf"
+        docker compose exec -T --user root webknossos sh -c "sed -i \"s|f,t,'l4_sample'|t,t,'l4_sample'|\" test/db/dataSets.csv"
+        # docker compose exec -T --user root webknossos sh -c "cat test/db/dataSets.csv"
         OUT=$(docker compose exec -T webknossos tools/postgres/dbtool.js prepare-test-db 2>&1) || echo "$OUT"
         popd > /dev/null
     else

webknossos/pyproject.toml

@@ -96,8 +96,6 @@ dev-dependencies = [
     "mypy ~=1.10.0",
     "pytest ~=8.3.2",
     "pytest-custom-exit-code ~=0.3.0",
-    "pytest-recording ~=0.13.0",
-    "vcrpy ~=6.0",
     "pytest-split ~=0.9.0",
     "pytest-sugar ~=1.0.0",
     "pytest-timeout ~=2.3.0",
@@ -179,7 +177,7 @@ indent-style = "space"
 line-ending = "auto"
 
 [tool.pytest.ini_options]
-markers = ["with_vcr: Runs with VCR recording and optionally blocked network"]
+markers = ["use_proxay: Runs with a proxay instance recording/replaying http responses", "serial"]
 testpaths = ["tests"]
 
 [build-system]

webknossos/test.sh

@@ -3,31 +3,56 @@ set -eEuo pipefail
 
 source local_wk_setup.sh
 
-export_vars
-
 
 # Note that pytest should be executed via `python -m`, since
 # this will ensure that the current directory is added to sys.path
 # (which is standard python behavior). This is necessary so that the imports
 # refer to the checked out (and potentially modified) code.
 PYTEST="uv run --all-extras --frozen python -m pytest --suppress-no-test-exit-code"
 
+find tests/binaryData/Organization_X -mindepth 1 -maxdepth 1 -type d ! -name 'l4_sample' ! -name 'e2006_knossos' -exec rm -rf {} +
+
 
 if [ $# -gt 0 ] && [ "$1" = "--refresh-snapshots" ]; then
     ensure_local_test_wk
 
     rm -rf tests/cassettes
-    rm -rf tests/**/cassettes
+
+    # Starts a proxy server in record mode on port 3000 and sets the HTTP_PROXY env var
+    proxay --mode record --host http://localhost:9000 --tapes-dir tests/cassettes &
+    PROXAY_PID=$!
 
     shift
-    $PYTEST --record-mode once -m "with_vcr" "$@"
-    stop_local_test_wk
-elif [ $# -gt 0 ] && [ "$1" = "--add-snapshots" ]; then
-    ensure_local_test_wk
-    shift
-    $PYTEST --record-mode once -m "with_vcr" "$@"
+    $PYTEST "-m" "use_proxay" "$@"
+    PYTEST_EXIT_CODE=$?
+
+    # Kill the proxy server
+    kill $PROXAY_PID
+    wait $PROXAY_PID
+
     stop_local_test_wk
+
+    exit $PYTEST_EXIT_CODE
+elif [ $# -gt 0 ] && [ "$1" = "--debug-cassettes" ]; then
+    # This will start a proxay server in replay mode so that the stored cassettes can be used for debugging tests.
+
+    export_vars
+
+    proxay --mode replay --tapes-dir tests/cassettes &
+    PROXAY_PID=$!
+    echo "Proxay server is running in replay mode. Press Ctrl+C to stop."
+    trap 'kill $PROXAY_PID; exit' INT
+    wait $PROXAY_PID
 else
-    $PYTEST --block-network -m "with_vcr" "$@"
+    export_vars
+
+    proxay --mode replay --tapes-dir tests/cassettes 2>&1 > /dev/null &
+    PROXAY_PID=$!
+
+    $PYTEST "$@"
+    PYTEST_EXIT_CODE=$?
+
+    kill $PROXAY_PID
+
+    exit $PYTEST_EXIT_CODE
 fi
-$PYTEST --disable-recording -m "not with_vcr" "$@"