test.py instead of test.sh (#1379)

* test.py

* lint

* npx

* shell

* rm proxay from ci

* print

* ci

* ci

* pre-install proxay

* comments

* win!

* changelog

* pr feedback

* better handle sigint

* pr feedback

Author: normanrz

.github/workflows/ci.yml

@@ -149,7 +149,7 @@ jobs:
           cache-dependency-glob: "webknossos/uv.lock"
 
       - name: Install proxay
-        run: npm install -g proxay
+        run: npm install -g proxay@1.9.0
 
       - name: Set up Python ${{ matrix.python-version }}
         run: uv python install ${{ matrix.python-version }}
@@ -176,14 +176,14 @@ jobs:
         timeout-minutes: 30
         env:
           PYTHON_VERSION: ${{ matrix.python-version }}
-        run: ./test.sh --splits 3 --group ${{ matrix.group }} --splitting-algorithm least_duration --cov=webknossos --cov-report=
+        run: uv run test.py --splits 3 --group ${{ matrix.group }} --splitting-algorithm least_duration --cov=webknossos --cov-report=
 
       - name: Python tests
         if: ${{ matrix.python-version != '3.11' }}
         timeout-minutes: 30
         env:
           PYTHON_VERSION: ${{ matrix.python-version }}
-        run: ./test.sh --splits 3 --group ${{ matrix.group }} --splitting-algorithm least_duration
+        run: uv run test.py --splits 3 --group ${{ matrix.group }} --splitting-algorithm least_duration
 
       - name: Persist coverage reports
         if: ${{ matrix.python-version == '3.11' }}
@@ -222,22 +222,21 @@ jobs:
           enable-cache: true
           cache-dependency-glob: "webknossos/uv.lock"
 
-      - name: Install proxay
-        run: npm install -g proxay
-
       - name: Install minio
         run: Invoke-WebRequest -Uri "https://dl.min.io/server/minio/release/windows-amd64/minio.exe" -OutFile "minio.exe"
 
+      - name: Install proxay
+        run: npm install -g [email protected]
+
       - name: Set up Python ${{ matrix.python-version }}
         run: uv python install ${{ matrix.python-version }}
 
       - name: Python tests
         timeout-minutes: 30
-        shell: bash
         env:
           PYTHON_VERSION: ${{ matrix.python-version }}
           MULTIPROCESSING_DEFAULT_START_METHOD: spawn
-        run: ./test.sh --splits 3 --group ${{ matrix.group }} --splitting-algorithm least_duration
+        run: uv run test.py --splits 3 --group ${{ matrix.group }} --splitting-algorithm least_duration
 
   coverage_report:
     needs: [webknossos_linux]

.github/workflows/nightly.yml

@@ -2,7 +2,7 @@ name: nightly
 
 on:
   schedule:
-    - cron:  '00 06 * * *'
+    - cron: "00 06 * * *"
   workflow_dispatch: ~
 
 jobs:
@@ -19,46 +19,46 @@ jobs:
         working-directory: webknossos
 
     steps:
-    - uses: actions/checkout@v3
+      - uses: actions/checkout@v3
 
-    - name: Install uv
-      uses: astral-sh/setup-uv@v3
+      - name: Install uv
+        uses: astral-sh/setup-uv@v3
 
-    - name: Install proxay
-      run: npm install -g proxay
+      - name: Install proxay
+        run: npm install -g proxay
 
-    - name: Set up Python ${{ matrix.python-version }}
-      run: uv python install ${{ matrix.python-version }}
+      - name: Set up Python ${{ matrix.python-version }}
+        run: uv python install ${{ matrix.python-version }}
 
-    - name: Check if git is dirty
-      run: |
-        git diff --no-ext-diff --quiet --exit-code
-        [[ -z $(git status -s) ]]
+      - name: Check if git is dirty
+        run: |
+          git diff --no-ext-diff --quiet --exit-code
+          [[ -z $(git status -s) ]]
 
-    - name: Python tests, refreshing the network snapshots
-      env:
-        WK_TOKEN: ${{ secrets.WK_TOKEN }}
-      run: ./test.sh --refresh-snapshots --splits 3 --group ${{ matrix.group }}
+      - name: Python tests, refreshing the network snapshots
+        env:
+          WK_TOKEN: ${{ secrets.WK_TOKEN }}
+        run: uv run test.py --refresh-snapshots --splits 3 --group ${{ matrix.group }}
 
-    - name: Python tests, using the new snapshots
-      env:
-        WK_TOKEN: ${{ secrets.WK_TOKEN }}
-      run: ./test.sh --refresh-snapshots --splits 3 --group ${{ matrix.group }}
+      - name: Python tests, using the new snapshots
+        env:
+          WK_TOKEN: ${{ secrets.WK_TOKEN }}
+        run: uv run test.py --refresh-snapshots --splits 3 --group ${{ matrix.group }}
 
-    - uses: slackapi/[email protected]
-      if: failure() || cancelled()
-      with:
-        webhook: ${{ secrets.SLACK_WEBHOOK_URL }}
-        webhook-type: incoming-webhook
-        payload: |
-          attachments:
-            - color: "#f00"
-              blocks:
-                - type: "section"
-                  text:
-                    type: "mrkdwn"
-                    text: ':fire: Job <${{github.server_url}}/${{github.repository}}/actions/runs/${{github.run_id}}|${{github.job}}> of workflow "${{github.workflow}}" failed'
-                - type: "context"
-                  elements:
-                    - type: mrkdwn
-                      text: '<${{github.repositoryUrl}}|${{github.repository}}>'
+      - uses: slackapi/[email protected]
+        if: failure() || cancelled()
+        with:
+          webhook: ${{ secrets.SLACK_WEBHOOK_URL }}
+          webhook-type: incoming-webhook
+          payload: |
+            attachments:
+              - color: "#f00"
+                blocks:
+                  - type: "section"
+                    text:
+                      type: "mrkdwn"
+                      text: ':fire: Job <${{github.server_url}}/${{github.repository}}/actions/runs/${{github.run_id}}|${{github.job}}> of workflow "${{github.workflow}}" failed'
+                  - type: "context"
+                    elements:
+                      - type: mrkdwn
+                        text: '<${{github.repositoryUrl}}|${{github.repository}}>'

CONTRIBUTING.md

@@ -114,7 +114,7 @@ See below for specifics of the different packages. Let's have a look at the comm
     * `./format.sh`: ruff
     * `./lint.sh`: ruff
     * `./typecheck.sh`: mypy
-    * `./test.sh`: pytest and custom scripts
+    * `./test.py`: pytest and custom scripts
 
   Those are also accessible via make commands from the top-level directory, running the respective scripts for each sub-project
   , e.g. `make format`, `make lint`, …
@@ -133,26 +133,26 @@ 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):
+To run the `uv run test.py` 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
 ```
-When running the `./test.sh` script on MacOS, it is also necessary to install `minio` using the following command:
+When running the `uv run test.py` script on MacOS, it is also necessary to install `minio` using the following command:
 
 ```bash
 brew install minio
 ```
 
 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 [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).
+1. `uv run test.py --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 `uv run test.py` 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. `uv run test.py` replays responses from previous network snapshots using [proxay](https://github.com/airtasker/proxay).
 
-`./test.sh --store-durations` updates the durations for
+`uv run test.py --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.
 

webknossos/Changelog.md

@@ -15,6 +15,13 @@ For upgrade instructions, please check the respective _Breaking Changes_ section
 ### Breaking Changes
 - The `endpoint_url` in `UPath` objects is now stored directly in the `storage_options` dict, instead of being stored in the `storage_options["client_kwargs"]` dict. [#1365](https://github.com/scalableminds/webknossos-libs/pull/1365)
 - Removed Docker image `scalableminds/webknossos-cli` build. It will not be released further. [#1376](https://github.com/scalableminds/webknossos-libs/pull/1376)
+
+### Added
+- Dataset.add_layer_as_ref() now accepts RemoteLayer objects as well as Layer objects. [#1371](https://github.com/scalableminds/webknossos-libs/pull/1371])
+- RemoteDataset.annotation_id is now exposed, when available. [#1380](https://github.com/scalableminds/webknossos-libs/pull/1380)
+- RemoteDataset.open() now accepts an annotation url as well. [#1380](https://github.com/scalableminds/webknossos-libs/pull/1380)
+### Changed
+- Ported `test.sh` to `test.py`, run with `uv run test.py`. [#1379](https://github.com/scalableminds/webknossos-libs/pull/1379)
 - `Dataset.add_layer_as_ref(remote_layer.path)` does not work anymore. Please use `Dataset.add_layer_as_ref(remote_layer)` instead. [#1371](https://github.com/scalableminds/webknossos-libs/pull/1371])
 - Due to the refactoring, the imports of various classes have changed. Please update your code accordingly. [#1371](https://github.com/scalableminds/webknossos-libs/pull/1371])
 - Deprecated a number of methods [#1371](https://github.com/scalableminds/webknossos-libs/pull/1371]):
@@ -24,13 +31,6 @@ For upgrade instructions, please check the respective _Breaking Changes_ section
   - `Dataset.download()`, use `RemoteDataset.download()` instead.
   - `mag_view.is_foreign`, use `layer.is_mag_view_foreign(mag_view)` instead.
   - `Dataset.trigger_reload_in_datastore()`, use `RemoteDataset.trigger_reload_in_datastore()` instead.
-
-### Added
-- Dataset.add_layer_as_ref() now accepts RemoteLayer objects as well as Layer objects. [#1371](https://github.com/scalableminds/webknossos-libs/pull/1371])
-- RemoteDataset.annotation_id is now exposed, when available. [#1380](https://github.com/scalableminds/webknossos-libs/pull/1380)
-- RemoteDataset.open() now accepts an annotation url as well. [#1380](https://github.com/scalableminds/webknossos-libs/pull/1380)
-
-### Changed
 - Replaced `pathlib.Path` for `upath.UPath` internally. `pathlib.Path` is still supported for user-facing APIs. Adds support for `universal_pathlib` version 0.3.x. [#1374](https://github.com/scalableminds/webknossos-libs/pull/1374)
 - Only use fs-based copy for mags on local file systems and S3. Other protocols, e.g. memory and HTTP, have caveats that break fs-based copying. [#1365](https://github.com/scalableminds/webknossos-libs/pull/1365)
 - The `add_*` methods in `Attachments` now return the created attachment objects, similar to `add_layer` and `add_mag`. [#1365](https://github.com/scalableminds/webknossos-libs/pull/1365)