From 715c42a4d3f343cfe2950ebc55ac5bc1390721f6 Mon Sep 17 00:00:00 2001 From: rettigl Date: Mon, 24 Jun 2024 23:40:01 +0200 Subject: [PATCH 1/5] update poetry, limit numpy --- poetry.lock | 12 ++++++------ pyproject.toml | 4 ++-- 2 files changed, 8 insertions(+), 8 deletions(-) diff --git a/poetry.lock b/poetry.lock index f1b02cae..35b7b394 100644 --- a/poetry.lock +++ b/poetry.lock @@ -851,20 +851,20 @@ tests = ["pytest", "pytest-cov", "pytest-xdist"] [[package]] name = "dask" -version = "2023.12.0" +version = "2024.6.2" description = "Parallel PyData with Task Scheduling" optional = false python-versions = ">=3.9" files = [ - {file = "dask-2023.12.0-py3-none-any.whl", hash = "sha256:6cef2fa43815adc8fe895dd3ea473a311249ba0e15e1f7eb9b1b68302339d998"}, - {file = "dask-2023.12.0.tar.gz", hash = "sha256:3f687e647ced0d3f2cadbef113c730b6555b9499b62e3a220535438841001c91"}, + {file = "dask-2024.6.2-py3-none-any.whl", hash = "sha256:81b80ee015b2e057b93bb2d1bf13a866136e762e2b24bf54b6b621e8b86b7708"}, + {file = "dask-2024.6.2.tar.gz", hash = "sha256:d429d6b19e85fd1306ac37c188aaf99d03bbe69a6fe59d2b42882b2ac188686f"}, ] [package.dependencies] click = ">=8.1" cloudpickle = ">=1.5.0" fsspec = ">=2021.09.0" -importlib-metadata = ">=4.13.0" +importlib-metadata = {version = ">=4.13.0", markers = "python_version < \"3.12\""} packaging = ">=20.0" partd = ">=1.2.0" pyyaml = ">=5.3.1" @@ -873,9 +873,9 @@ toolz = ">=0.10.0" [package.extras] array = ["numpy (>=1.21)"] complete = ["dask[array,dataframe,diagnostics,distributed]", "lz4 (>=4.3.2)", "pyarrow (>=7.0)", "pyarrow-hotfix"] -dataframe = ["dask[array]", "pandas (>=1.3)"] +dataframe = ["dask-expr (>=1.1,<1.2)", "dask[array]", "pandas (>=1.3)"] diagnostics = ["bokeh (>=2.4.2)", "jinja2 (>=2.10.3)"] -distributed = ["distributed (==2023.12.0)"] +distributed = ["distributed (==2024.6.2)"] test = ["pandas[test]", "pre-commit", "pytest", "pytest-cov", "pytest-rerunfailures", "pytest-timeout", "pytest-xdist"] [[package]] diff --git a/pyproject.toml b/pyproject.toml index 75e4892b..92a10c7e 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -13,9 +13,9 @@ keywords = ["sed", "mpes", "flash", "arpes"] license = "MIT" [tool.poetry.dependencies] -python = ">=3.9, <3.12.3, !=3.11.9" +python = ">=3.9, <3.13" bokeh = ">=2.4.2" -dask = ">=2021.12.0, <2023.12.1" +dask = ">=2021.12.0" fastdtw = ">=0.3.4" h5py = ">=3.6.0" ipympl = ">=0.9.1" From a70529a050201a07e43a92c7a74576bc85559fc8 Mon Sep 17 00:00:00 2001 From: rettigl Date: Wed, 11 Sep 2024 21:35:38 +0200 Subject: [PATCH 2/5] update lockfile --- poetry.lock | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/poetry.lock b/poetry.lock index 35b7b394..5a026897 100644 --- a/poetry.lock +++ b/poetry.lock @@ -851,13 +851,13 @@ tests = ["pytest", "pytest-cov", "pytest-xdist"] [[package]] name = "dask" -version = "2024.6.2" +version = "2024.8.0" description = "Parallel PyData with Task Scheduling" optional = false python-versions = ">=3.9" files = [ - 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[tool.poetry.dependencies] python = ">=3.9, <3.13" bokeh = ">=2.4.2" -dask = ">=2021.12.0" +dask = ">=2021.12.0, <2024.8" fastdtw = ">=0.3.4" h5py = ">=3.6.0" ipympl = ">=0.9.1" From 1aa4a83ec7ae94fa615c3c5e733536419a905bf7 Mon Sep 17 00:00:00 2001 From: rettigl Date: Sat, 12 Oct 2024 00:06:07 +0200 Subject: [PATCH 4/5] disable dask query-planning as workaround for bugs in dask-expr --- sed/__init__.py | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/sed/__init__.py b/sed/__init__.py index 50850279..3d03ef82 100644 --- a/sed/__init__.py +++ b/sed/__init__.py @@ -1,7 +1,11 @@ """sed module easy access APIs.""" import importlib.metadata -from .core.processor import SedProcessor +import dask + +dask.config.set({"dataframe.query-planning": False}) + +from .core.processor import SedProcessor # noqa: E402 __version__ = importlib.metadata.version("sed-processor") __all__ = ["SedProcessor"] From 41f05ef209acd32fa9be284fe0295251fc3c090b Mon Sep 17 00:00:00 2001 From: rettigl Date: Sat, 12 Oct 2024 00:17:46 +0200 Subject: [PATCH 5/5] remove limits on python versions for tests --- .github/workflows/testing_multiversion.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/testing_multiversion.yml b/.github/workflows/testing_multiversion.yml index 0c016113..f0efc943 100644 --- a/.github/workflows/testing_multiversion.yml +++ b/.github/workflows/testing_multiversion.yml @@ -13,7 +13,7 @@ jobs: # Using matrix strategy strategy: matrix: - python-version: ["3.9", "3.10", "3.11.8", "3.12.2"] + python-version: ["3.9", "3.10", "3.11", "3.12"] runs-on: ubuntu-latest steps: # Check out repo and set up Python