From bad850f056209fd18b5f3a54697df4fe32025b12 Mon Sep 17 00:00:00 2001 From: Wouter-Michiel Vierdag Date: Tue, 15 Apr 2025 14:35:57 +0200 Subject: [PATCH 01/10] change assert to use exc_info --- tests/test_generic.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/test_generic.py b/tests/test_generic.py index d4dda1a7..466b7a3f 100644 --- a/tests/test_generic.py +++ b/tests/test_generic.py @@ -87,7 +87,7 @@ def test_cli_read_generic_image_invalid_data_axes(runner: CliRunner) -> None: ], ) assert result.exit_code != 0, result.output - assert "'invalid_axes' is not one of 'cyx', 'czyx'." in result.output + assert "data_axes must be a permutation of 'cyx' or 'czyx'." in result.exc_info[1].args[0] @pytest.mark.parametrize("cli", [True, False]) From 6ca3d05c7cc6603012741103e5a533d1e91e6f63 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Tue, 15 Apr 2025 12:39:33 +0000 Subject: [PATCH 02/10] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- README.md | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/README.md b/README.md index 02213221..f598404d 100644 --- a/README.md +++ b/README.md @@ -111,8 +111,7 @@ Marconato, L., Palla, G., Yamauchi, K.A. et al. SpatialData: an open and univers [link-docs]: https://spatialdata.scverse.org/projects/io/en/latest/ [link-api]: https://spatialdata.scverse.org/projects/io/en/latest/api.html [link-cli]: https://spatialdata.scverse.org/projects/io/en/latest/cli.html - -[//]: # (numfocus-fiscal-sponsor-attribution) +[//]: # "numfocus-fiscal-sponsor-attribution" spatialdata-io is part of the scverse® project ([website](https://scverse.org), [governance](https://scverse.org/about/roles)) and is fiscally sponsored by [NumFOCUS](https://numfocus.org/). If you like scverse® and want to support our mission, please consider making a tax-deductible [donation](https://numfocus.org/donate-to-scverse) to help the project pay for developer time, professional services, travel, workshops, and a variety of other needs. From ca742b2adf37616ab89fc9c0100d3e48307c4232 Mon Sep 17 00:00:00 2001 From: Wouter-Michiel Vierdag Date: Tue, 15 Apr 2025 14:47:37 +0200 Subject: [PATCH 03/10] use latest cache --- .github/workflows/test.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml index 8546b3d7..ba1b923e 100644 --- a/.github/workflows/test.yaml +++ b/.github/workflows/test.yaml @@ -37,7 +37,7 @@ jobs: run: | echo "::set-output name=dir::$(pip cache dir)" - name: Restore pip cache - uses: actions/cache@v2 + uses: actions/cache@v3 with: path: ${{ steps.pip-cache-dir.outputs.dir }} key: pip-${{ runner.os }}-${{ env.pythonLocation }}-${{ hashFiles('**/pyproject.toml') }} From 18194285a852f92922e14145f6e23a9491b9152f Mon Sep 17 00:00:00 2001 From: Wouter-Michiel Vierdag Date: Tue, 15 Apr 2025 15:12:08 +0200 Subject: [PATCH 04/10] use latest upload artifact --- .github/workflows/prepare_test_data.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/prepare_test_data.yaml b/.github/workflows/prepare_test_data.yaml index 77f984fc..685400bd 100644 --- a/.github/workflows/prepare_test_data.yaml +++ b/.github/workflows/prepare_test_data.yaml @@ -44,7 +44,7 @@ jobs: done - name: Upload artifacts - uses: actions/upload-artifact@v3 + uses: actions/upload-artifact@v4 with: name: data path: ./data From fda13e7e05b1a7dc23e869d3f2b95c2b8b78efc1 Mon Sep 17 00:00:00 2001 From: Wouter-Michiel Vierdag Date: Tue, 15 Apr 2025 15:16:58 +0200 Subject: [PATCH 05/10] update artifact download action --- .github/workflows/test.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml index ba1b923e..e754f073 100644 --- a/.github/workflows/test.yaml +++ b/.github/workflows/test.yaml @@ -53,7 +53,7 @@ jobs: - name: Download artifact of test data if: matrix.python == '3.12' - uses: dawidd6/action-download-artifact@v2 + uses: dawidd6/action-download-artifact@v9 with: workflow: prepare_test_data.yaml name: data From 590fdef6fe80a1959e3c571a9781a9168cd7de75 Mon Sep 17 00:00:00 2001 From: Wouter-Michiel Vierdag Date: Tue, 15 Apr 2025 15:23:46 +0200 Subject: [PATCH 06/10] require prepare-data --- .github/workflows/test.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml index e754f073..1f1de397 100644 --- a/.github/workflows/test.yaml +++ b/.github/workflows/test.yaml @@ -10,6 +10,7 @@ on: jobs: test: + needs: prepare-data runs-on: ${{ matrix.os }} defaults: run: From 116a0e17a5a83ea4c571a57e80be55d623164fff Mon Sep 17 00:00:00 2001 From: Wouter-Michiel Vierdag Date: Tue, 15 Apr 2025 15:26:18 +0200 Subject: [PATCH 07/10] rever need for prepare-data --- .github/workflows/test.yaml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml index 1f1de397..e754f073 100644 --- a/.github/workflows/test.yaml +++ b/.github/workflows/test.yaml @@ -10,7 +10,6 @@ on: jobs: test: - needs: prepare-data runs-on: ${{ matrix.os }} defaults: run: From 6c06b4123b70400b34cfbdd1ae14be6910e96b02 Mon Sep 17 00:00:00 2001 From: Wouter-Michiel Vierdag Date: Tue, 15 Apr 2025 15:32:08 +0200 Subject: [PATCH 08/10] try workflow trigger --- .github/workflows/test.yaml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml index e754f073..800fe3ff 100644 --- a/.github/workflows/test.yaml +++ b/.github/workflows/test.yaml @@ -7,6 +7,10 @@ on: - "v*" # Push events to matching v*, i.e. v1.0, v20.15.10, v1.0-rc.1, v2.1-alpha, v3.0-beta.3 pull_request: branches: [main] + workflow_run: + workflows: ["Prepare test data"] + types: + - completed jobs: test: From f1edfa340df0ee139003668d89224954cf4a494c Mon Sep 17 00:00:00 2001 From: Wouter-Michiel Vierdag Date: Tue, 15 Apr 2025 15:46:06 +0200 Subject: [PATCH 09/10] run prepare_test_data on a schedule --- .github/workflows/prepare_test_data.yaml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/prepare_test_data.yaml b/.github/workflows/prepare_test_data.yaml index 685400bd..bf979d96 100644 --- a/.github/workflows/prepare_test_data.yaml +++ b/.github/workflows/prepare_test_data.yaml @@ -1,6 +1,8 @@ name: Prepare test data on: + schedule: + - cron: "0 0 1 * *" # run once a month to prevent artifact expiration workflow_dispatch: # uncomment and adjust the branch name if you need to add new datasets to the artifact # push: From 386b6349f2a2cf6a04f0df32b64da29c2a08d702 Mon Sep 17 00:00:00 2001 From: Wouter-Michiel Vierdag Date: Tue, 15 Apr 2025 15:56:30 +0200 Subject: [PATCH 10/10] attempt fix --- .github/workflows/test.yaml | 10 ---------- 1 file changed, 10 deletions(-) diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml index 800fe3ff..c4d08869 100644 --- a/.github/workflows/test.yaml +++ b/.github/workflows/test.yaml @@ -7,10 +7,6 @@ on: - "v*" # Push events to matching v*, i.e. v1.0, v20.15.10, v1.0-rc.1, v2.1-alpha, v3.0-beta.3 pull_request: branches: [main] - workflow_run: - workflows: ["Prepare test data"] - types: - - completed jobs: test: @@ -63,12 +59,6 @@ jobs: name: data path: ./data - - name: List the data directory - if: matrix.python == '3.12' - run: | - ls -l ./data - pwd - - name: Test env: MPLBACKEND: agg