From e99a59627340156c84a588c9fe84dd44d86bb184 Mon Sep 17 00:00:00 2001 From: Pradeep Rajasekhar Date: Fri, 24 Jan 2025 00:31:43 +1100 Subject: [PATCH 1/9] constrain numpy to versions below 2.0 --- core/pyproject.toml | 2 +- plugin/pyproject.toml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/core/pyproject.toml b/core/pyproject.toml index 41b6b53f..bc897865 100644 --- a/core/pyproject.toml +++ b/core/pyproject.toml @@ -48,7 +48,7 @@ dependencies = [ # Older tifffile are not compatible with aicsimageio, see: https://github.com/AllenCellModeling/aicsimageio/issues/518 "napari-workflows>=0.2.8", "npy2bdv", - "numpy", + "numpy<2", "pandas", "pyclesperanto_prototype>=0.20.0", "pyopencl", diff --git a/plugin/pyproject.toml b/plugin/pyproject.toml index a69aa6a8..62299063 100644 --- a/plugin/pyproject.toml +++ b/plugin/pyproject.toml @@ -54,7 +54,7 @@ dependencies = [ "napari-workflows>=0.2.8", "napari>=0.4.11", "npy2bdv", - "numpy", + "numpy<2", "psutil", "pyclesperanto_prototype>=0.20.0", "pydantic", From adda7769d2834ac0dd03e45c13dc34487aa7ec2d Mon Sep 17 00:00:00 2001 From: Pradeep Rajasekhar Date: Fri, 24 Jan 2025 00:32:07 +1100 Subject: [PATCH 2/9] enable napari-aicsimageio dependency --- plugin/pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/plugin/pyproject.toml b/plugin/pyproject.toml index 62299063..06282ed8 100644 --- a/plugin/pyproject.toml +++ b/plugin/pyproject.toml @@ -48,7 +48,7 @@ dependencies = [ "magicgui<0.8.0", # Currently commented out to avoid installation issues, although # This can be reinstated once https://github.com/pypa/pip/pull/12095 is merged - # "napari-aicsimageio>=0.7.2", + "napari-aicsimageio>=0.7.2", "napari-spreadsheet", "napari-workflow-inspector", "napari-workflows>=0.2.8", From 0304488bb12dd916547c1b1c539d1a4131082822 Mon Sep 17 00:00:00 2001 From: Pradeep Rajasekhar Date: Sat, 25 Jan 2025 13:37:12 +1100 Subject: [PATCH 3/9] napari version --- plugin/pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/plugin/pyproject.toml b/plugin/pyproject.toml index 06282ed8..a0d1901b 100644 --- a/plugin/pyproject.toml +++ b/plugin/pyproject.toml @@ -52,7 +52,7 @@ dependencies = [ "napari-spreadsheet", "napari-workflow-inspector", "napari-workflows>=0.2.8", - "napari>=0.4.11", + "napari[all]>=0.4.11, "npy2bdv", "numpy<2", "psutil", From aaf0594761545d4311812959666cf0bc8c96da3f Mon Sep 17 00:00:00 2001 From: Pradeep Rajasekhar Date: Sat, 25 Jan 2025 22:33:48 +1100 Subject: [PATCH 4/9] remove comment --- plugin/pyproject.toml | 2 -- 1 file changed, 2 deletions(-) diff --git a/plugin/pyproject.toml b/plugin/pyproject.toml index a0d1901b..ac28f60d 100644 --- a/plugin/pyproject.toml +++ b/plugin/pyproject.toml @@ -46,8 +46,6 @@ dependencies = [ # The upper bound is because we are waiting on https://github.com/hanjinliu/magic-class/issues/128 "magic-class>=0.7.5,<0.8.0", "magicgui<0.8.0", - # Currently commented out to avoid installation issues, although - # This can be reinstated once https://github.com/pypa/pip/pull/12095 is merged "napari-aicsimageio>=0.7.2", "napari-spreadsheet", "napari-workflow-inspector", From 6b984d92d9cc99357b3cb1f2a2db9abbb117dbd8 Mon Sep 17 00:00:00 2001 From: Pradeep Rajasekhar Date: Sat, 25 Jan 2025 22:35:57 +1100 Subject: [PATCH 5/9] fixed typo --- plugin/pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/plugin/pyproject.toml b/plugin/pyproject.toml index ac28f60d..fc1da1b2 100644 --- a/plugin/pyproject.toml +++ b/plugin/pyproject.toml @@ -50,7 +50,7 @@ dependencies = [ "napari-spreadsheet", "napari-workflow-inspector", "napari-workflows>=0.2.8", - "napari[all]>=0.4.11, + "napari[all]>=0.4.11", "npy2bdv", "numpy<2", "psutil", From 07d2334c6f9a37dcb81d1472546fded26348538c Mon Sep 17 00:00:00 2001 From: Pradeep Rajasekhar Date: Mon, 27 Jan 2025 15:13:47 +1100 Subject: [PATCH 6/9] remove repetitions from core --- core/pyproject.toml | 1 - plugin/pyproject.toml | 7 +------ 2 files changed, 1 insertion(+), 7 deletions(-) diff --git a/core/pyproject.toml b/core/pyproject.toml index bc897865..5de50c7f 100644 --- a/core/pyproject.toml +++ b/core/pyproject.toml @@ -45,7 +45,6 @@ dependencies = [ "dask[distributed]", "fsspec>=2022.8.2", "importlib_resources", - # Older tifffile are not compatible with aicsimageio, see: https://github.com/AllenCellModeling/aicsimageio/issues/518 "napari-workflows>=0.2.8", "npy2bdv", "numpy<2", diff --git a/plugin/pyproject.toml b/plugin/pyproject.toml index fc1da1b2..377d0250 100644 --- a/plugin/pyproject.toml +++ b/plugin/pyproject.toml @@ -36,18 +36,15 @@ classifiers = [ ] requires-python = ">=3.8" dependencies = [ - "aicsimageio>=4.6.3", "dask[distributed]", # This isn't used directly, but we need to pin this version "fsspec>=2022.8.2", "importlib_resources", "lls_core", # The lower bound is because we need this Python 3.8 fix: https://github.com/hanjinliu/magic-class/pull/108 - # The upper bound is because we are waiting on https://github.com/hanjinliu/magic-class/issues/128 - "magic-class>=0.7.5,<0.8.0", + "magic-class>=0.7.5", "magicgui<0.8.0", "napari-aicsimageio>=0.7.2", - "napari-spreadsheet", "napari-workflow-inspector", "napari-workflows>=0.2.8", "napari[all]>=0.4.11", @@ -55,12 +52,10 @@ dependencies = [ "numpy<2", "psutil", "pyclesperanto_prototype>=0.20.0", - "pydantic", "qtpy", "typing_extensions>=4.7.0", "rich", "StrEnum", - "xarray" ] [project.urls] From 34e1a7ca2105134903d3897febc79fce72673479 Mon Sep 17 00:00:00 2001 From: Pradeep Rajasekhar Date: Mon, 27 Jan 2025 15:13:58 +1100 Subject: [PATCH 7/9] remove python 3.11 testing --- .github/workflows/test_and_deploy.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/test_and_deploy.yml b/.github/workflows/test_and_deploy.yml index 61b4309c..18358883 100644 --- a/.github/workflows/test_and_deploy.yml +++ b/.github/workflows/test_and_deploy.yml @@ -21,7 +21,7 @@ jobs: strategy: fail-fast: false matrix: - python-version: ["3.8", "3.9", "3.10", "3.11"] + python-version: ["3.8", "3.9", "3.10"] env: DISPLAY: ":99.0" steps: From 3261140b52b2ce9ab9d4a18e6f2270908aa0d273 Mon Sep 17 00:00:00 2001 From: Pradeep Rajasekhar Date: Mon, 27 Jan 2025 22:08:18 +1100 Subject: [PATCH 8/9] revert depdendency deletions_fawltydeps error --- plugin/pyproject.toml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/plugin/pyproject.toml b/plugin/pyproject.toml index 377d0250..afae0e9a 100644 --- a/plugin/pyproject.toml +++ b/plugin/pyproject.toml @@ -36,6 +36,7 @@ classifiers = [ ] requires-python = ">=3.8" dependencies = [ + "aicsimageio>=4.6.3", "dask[distributed]", # This isn't used directly, but we need to pin this version "fsspec>=2022.8.2", @@ -52,10 +53,12 @@ dependencies = [ "numpy<2", "psutil", "pyclesperanto_prototype>=0.20.0", + "pydantic", "qtpy", "typing_extensions>=4.7.0", "rich", "StrEnum", + "xarray" ] [project.urls] From a211b8a3548fb89ef5e149e17ca6df3c6a0ea66f Mon Sep 17 00:00:00 2001 From: Pradeep Rajasekhar Date: Wed, 29 Jan 2025 08:54:22 +1100 Subject: [PATCH 9/9] change deploy actions to python v3.10 --- .github/workflows/test_and_deploy.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/test_and_deploy.yml b/.github/workflows/test_and_deploy.yml index 18358883..4b1b66a4 100644 --- a/.github/workflows/test_and_deploy.yml +++ b/.github/workflows/test_and_deploy.yml @@ -95,7 +95,7 @@ jobs: - name: Set up Python uses: actions/setup-python@v4 with: - python-version: "3.11" + python-version: "3.10" - name: Install dependencies run: | python -m pip install --upgrade pip setuptools wheel