From a48300c9d9536ce0a6adcb7f35a8057120ca266d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Edwin=20Carre=C3=B1o?= Date: Fri, 27 Feb 2026 07:31:37 +0100 Subject: [PATCH 1/2] fix: change Numpy version to allow newer version and newer release (>=1.26.4) --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 31b8dfb..c5e4528 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -38,7 +38,7 @@ toml = "*" pypath-common = { git = "https://github.com/saezlab/pypath-common.git", branch = "master" } python-dateutil = "^2.9.0.post0" platformdirs = "^4.2.2" -numpy = "^1.26.4" +numpy = ">=1.26.4" [tool.poetry.dev-dependencies] pytest = ">=6.0" From 7a2812d9287df51bef3b97edf8b4249ac356dde9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Edwin=20Carre=C3=B1o?= Date: Mon, 9 Mar 2026 14:21:47 +0100 Subject: [PATCH 2/2] chores: update poetry lock file --- poetry.lock | 316 +++++++++++++++++++++++++++++++++++++++++++++++----- 1 file changed, 291 insertions(+), 25 deletions(-) diff --git a/poetry.lock b/poetry.lock index cb6e424..6074b5b 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,16 +1,23 @@ -# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.4 and should not be changed by hand. [[package]] name = "accessible-pygments" version = "0.0.5" -description = "" +description = "A collection of accessible pygments styles" optional = false -python-versions = "*" +python-versions = ">=3.9" files = [ {file = "accessible_pygments-0.0.5-py3-none-any.whl", hash = "sha256:88ae3211e68a1d0b011504b2ffc1691feafce124b845bd072ab6f9f66f34d4b7"}, {file = "accessible_pygments-0.0.5.tar.gz", hash = "sha256:40918d3e6a2b619ad424cb91e556bd3bd8865443d9f22f1dcdf79e33c8046872"}, ] +[package.dependencies] +pygments = ">=1.5" + +[package.extras] +dev = ["pillow", "pkginfo (>=1.10)", "playwright", "pre-commit", "setuptools", "twine (>=5.0)"] +tests = ["hypothesis", "pytest"] + [package.source] type = "legacy" url = "https://pypi.org/simple" @@ -189,6 +196,25 @@ type = "legacy" url = "https://pypi.org/simple" reference = "pypi-public" +[[package]] +name = "async-lru" +version = "2.0.5" +description = "Simple LRU cache for asyncio" +optional = false +python-versions = ">=3.9" +files = [ + {file = "async_lru-2.0.5-py3-none-any.whl", hash = "sha256:ab95404d8d2605310d345932697371a5f40def0487c03d6d0ad9138de52c9943"}, + {file = "async_lru-2.0.5.tar.gz", hash = "sha256:481d52ccdd27275f42c43a928b4a50c3bfb2d67af4e78b170e3e0bb39c66e5bb"}, +] + +[package.dependencies] +typing_extensions = {version = ">=4.0.0", markers = "python_version < \"3.11\""} + +[package.source] +type = "legacy" +url = "https://pypi.org/simple" +reference = "pypi-public" + [[package]] name = "attrs" version = "24.2.0" @@ -258,6 +284,28 @@ type = "legacy" url = "https://pypi.org/simple" reference = "pypi-public" +[[package]] +name = "bleach" +version = "6.2.0" +description = "An easy safelist-based HTML-sanitizing tool." +optional = false +python-versions = ">=3.9" +files = [ + {file = "bleach-6.2.0-py3-none-any.whl", hash = "sha256:117d9c6097a7c3d22fd578fcd8d35ff1e125df6736f554da4e432fdd63f31e5e"}, + {file = "bleach-6.2.0.tar.gz", hash = "sha256:123e894118b8a599fd80d3ec1a6d4cc7ce4e5882b1317a7e1ba69b56e95f991f"}, +] + +[package.dependencies] +webencodings = "*" + +[package.extras] +css = ["tinycss2 (>=1.1.0,<1.5)"] + +[package.source] +type = "legacy" +url = "https://pypi.org/simple" +reference = "pypi-public" + [[package]] name = "bump2version" version = "1.0.1" @@ -755,6 +803,22 @@ type = "legacy" url = "https://pypi.org/simple" reference = "pypi-public" +[[package]] +name = "defusedxml" +version = "0.7.1" +description = "XML bomb protection for Python stdlib modules" +optional = false +python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" +files = [ + {file = "defusedxml-0.7.1-py2.py3-none-any.whl", hash = "sha256:a352e7e428770286cc899e2542b6cdaedb2b4953ff269a210103ec58f6198a61"}, + {file = "defusedxml-0.7.1.tar.gz", hash = "sha256:1bb3032db185915b62d7c6209c5a8792be6a32ab2fedacc84e01b52c51aa3e69"}, +] + +[package.source] +type = "legacy" +url = "https://pypi.org/simple" +reference = "pypi-public" + [[package]] name = "distlib" version = "0.3.8" @@ -825,6 +889,25 @@ type = "legacy" url = "https://pypi.org/simple" reference = "pypi-public" +[[package]] +name = "fastjsonschema" +version = "2.21.2" +description = "Fastest Python implementation of JSON schema" +optional = false +python-versions = "*" +files = [ + {file = "fastjsonschema-2.21.2-py3-none-any.whl", hash = "sha256:1c797122d0a86c5cace2e54bf4e819c36223b552017172f32c5c024a6b77e463"}, + {file = "fastjsonschema-2.21.2.tar.gz", hash = "sha256:b1eb43748041c880796cd077f1a07c3d94e93ae84bba5ed36800a33554ae05de"}, +] + +[package.extras] +devel = ["colorama", "json-spec", "jsonschema", "pylint", "pytest", "pytest-benchmark", "pytest-cache", "validictory"] + +[package.source] +type = "legacy" +url = "https://pypi.org/simple" +reference = "pypi-public" + [[package]] name = "filelock" version = "3.16.1" @@ -1697,6 +1780,26 @@ type = "legacy" url = "https://pypi.org/simple" reference = "pypi-public" +[[package]] +name = "jupyter-lsp" +version = "2.3.0" +description = "Multi-Language Server WebSocket proxy for Jupyter Notebook/Lab server" +optional = false +python-versions = ">=3.8" +files = [ + {file = "jupyter_lsp-2.3.0-py3-none-any.whl", hash = "sha256:e914a3cb2addf48b1c7710914771aaf1819d46b2e5a79b0f917b5478ec93f34f"}, + {file = "jupyter_lsp-2.3.0.tar.gz", hash = "sha256:458aa59339dc868fb784d73364f17dbce8836e906cd75fd471a325cba02e0245"}, +] + +[package.dependencies] +importlib_metadata = {version = ">=4.8.3", markers = "python_version < \"3.10\""} +jupyter_server = ">=1.1.2" + +[package.source] +type = "legacy" +url = "https://pypi.org/simple" +reference = "pypi-public" + [[package]] name = "jupyter-nbextensions-configurator" version = "0.6.4" @@ -1791,13 +1894,50 @@ reference = "pypi-public" [[package]] name = "jupyterlab" -version = "4.2.2" -description = "" +version = "4.0.13" +description = "JupyterLab computational environment" optional = false -python-versions = "*" +python-versions = ">=3.8" +files = [ + {file = "jupyterlab-4.0.13-py3-none-any.whl", hash = "sha256:3aa81c364d50cc715f6c2935674c7cca8936bd74b5898d6ad6598aef08c43808"}, + {file = "jupyterlab-4.0.13.tar.gz", hash = "sha256:e8950f94e0d8ab8aa7d8166b19db27f4d4fea5000ee04ba372c50116e98fb733"}, +] + +[package.dependencies] +async-lru = ">=1.0.0" +importlib-metadata = {version = ">=4.8.3", markers = "python_version < \"3.10\""} +ipykernel = "*" +jinja2 = ">=3.0.3" +jupyter-core = "*" +jupyter-lsp = ">=2.0.0" +jupyter-server = ">=2.4.0,<3" +jupyterlab-server = ">=2.19.0,<3" +notebook-shim = ">=0.2" +packaging = "*" +tomli = {version = "*", markers = "python_version < \"3.11\""} +tornado = ">=6.2.0" +traitlets = "*" + +[package.extras] +dev = ["build", "bump2version", "coverage", "hatch", "pre-commit", "pytest-cov", "ruff (==0.2.0)"] +docs = ["jsx-lexer", "myst-parser", "pydata-sphinx-theme (>=0.13.0)", "pytest", "pytest-check-links", "pytest-tornasync", "sphinx (>=1.8,<7.2.0)", "sphinx-copybutton"] +docs-screenshots = ["altair (==5.0.1)", "ipython (==8.14.0)", "ipywidgets (==8.0.6)", "jupyterlab-geojson (==3.4.0)", "jupyterlab-language-pack-zh-cn (==4.0.post0)", "matplotlib (==3.7.1)", "nbconvert (>=7.0.0)", "pandas (==2.2.0)", "scipy (==1.12.0)", "vega-datasets (==0.9.0)"] +test = ["coverage", "pytest (>=7.0)", "pytest-check-links (>=0.7)", "pytest-console-scripts", "pytest-cov", "pytest-jupyter (>=0.5.3)", "pytest-timeout", "pytest-tornasync", "requests", "requests-cache", "virtualenv"] + +[package.source] +type = "legacy" +url = "https://pypi.org/simple" +reference = "pypi-public" + +[[package]] +name = "jupyterlab-pygments" +version = "0.3.0" +description = "Pygments theme using JupyterLab CSS variables" +optional = false +python-versions = ">=3.8" files = [ - {file = "jupyterlab-4.2.2-py3-none-any.whl", hash = "sha256:59ee9b839f43308c3dfd55d72d1f1a299ed42a7f91f2d1afe9c12a783f9e525f"}, - {file = "jupyterlab-4.2.2.tar.gz", hash = "sha256:a534b6a25719a92a40d514fb133a9fe8f0d9981b0bbce5d8a5fcaa33344a3038"}, + {file = "jupyterlab_pygments-0.3.0-py3-none-any.whl", hash = "sha256:841a89020971da1d8693f1a99997aefc5dc424bb1b251fd6322462a1b8842780"}, + {file = "jupyterlab_pygments-0.3.0.tar.gz", hash = "sha256:721aca4d9029252b11cfa9d185e5b5af4d54772bb8072f9b7036f4170054d35d"}, ] [package.source] @@ -2189,6 +2329,25 @@ type = "legacy" url = "https://pypi.org/simple" reference = "pypi-public" +[[package]] +name = "mistune" +version = "3.2.0" +description = "A sane and fast Markdown parser with useful plugins and renderers" +optional = false +python-versions = ">=3.8" +files = [ + {file = "mistune-3.2.0-py3-none-any.whl", hash = "sha256:febdc629a3c78616b94393c6580551e0e34cc289987ec6c35ed3f4be42d0eee1"}, + {file = "mistune-3.2.0.tar.gz", hash = "sha256:708487c8a8cdd99c9d90eb3ed4c3ed961246ff78ac82f03418f5183ab70e398a"}, +] + +[package.dependencies] +typing-extensions = {version = "*", markers = "python_version < \"3.11\""} + +[package.source] +type = "legacy" +url = "https://pypi.org/simple" +reference = "pypi-public" + [[package]] name = "myst-nb" version = "1.1.1" @@ -2283,14 +2442,41 @@ reference = "pypi-public" [[package]] name = "nbconvert" version = "7.16.4" -description = "" +description = "Converting Jupyter Notebooks (.ipynb files) to other formats. Output formats include asciidoc, html, latex, markdown, pdf, py, rst, script. nbconvert can be used both as a Python library (`import nbconvert`) or as a command line tool (invoked as `jupyter nbconvert ...`)." optional = false -python-versions = "*" +python-versions = ">=3.8" files = [ {file = "nbconvert-7.16.4-py3-none-any.whl", hash = "sha256:05873c620fe520b6322bf8a5ad562692343fe3452abda5765c7a34b7d1aa3eb3"}, {file = "nbconvert-7.16.4.tar.gz", hash = "sha256:86ca91ba266b0a448dc96fa6c5b9d98affabde2867b363258703536807f9f7f4"}, ] +[package.dependencies] +beautifulsoup4 = "*" +bleach = "!=5.0.0" +defusedxml = "*" +importlib-metadata = {version = ">=3.6", markers = "python_version < \"3.10\""} +jinja2 = ">=3.0" +jupyter-core = ">=4.7" +jupyterlab-pygments = "*" +markupsafe = ">=2.0" +mistune = ">=2.0.3,<4" +nbclient = ">=0.5.0" +nbformat = ">=5.7" +packaging = "*" +pandocfilters = ">=1.4.1" +pygments = ">=2.4.1" +tinycss2 = "*" +traitlets = ">=5.1" + +[package.extras] +all = ["flaky", "ipykernel", "ipython", "ipywidgets (>=7.5)", "myst-parser", "nbsphinx (>=0.2.12)", "playwright", "pydata-sphinx-theme", "pyqtwebengine (>=5.15)", "pytest (>=7)", "sphinx (==5.0.2)", "sphinxcontrib-spelling", "tornado (>=6.1)"] +docs = ["ipykernel", "ipython", "myst-parser", "nbsphinx (>=0.2.12)", "pydata-sphinx-theme", "sphinx (==5.0.2)", "sphinxcontrib-spelling"] +qtpdf = ["pyqtwebengine (>=5.15)"] +qtpng = ["pyqtwebengine (>=5.15)"] +serve = ["tornado (>=6.1)"] +test = ["flaky", "ipykernel", "ipywidgets (>=7.5)", "pytest (>=7)"] +webpdf = ["playwright"] + [package.source] type = "legacy" url = "https://pypi.org/simple" @@ -2299,14 +2485,24 @@ reference = "pypi-public" [[package]] name = "nbformat" version = "5.10.4" -description = "" +description = "The Jupyter Notebook format" optional = false -python-versions = "*" +python-versions = ">=3.8" files = [ {file = "nbformat-5.10.4-py3-none-any.whl", hash = "sha256:3b48d6c8fbca4b299bf3982ea7db1af21580e4fec269ad087b9e81588891200b"}, {file = "nbformat-5.10.4.tar.gz", hash = "sha256:322168b14f937a5d11362988ecac2a4952d3d8e3a2cbeb2319584631226d5b3a"}, ] +[package.dependencies] +fastjsonschema = ">=2.15" +jsonschema = ">=2.6" +jupyter-core = ">=4.12,<5.0.dev0 || >=5.1.dev0" +traitlets = ">=5.1" + +[package.extras] +docs = ["myst-parser", "pydata-sphinx-theme", "sphinx", "sphinxcontrib-github-alt", "sphinxcontrib-spelling"] +test = ["pep440", "pre-commit", "pytest", "testpath"] + [package.source] type = "legacy" url = "https://pypi.org/simple" @@ -2369,26 +2565,26 @@ reference = "pypi-public" [[package]] name = "notebook" -version = "7.2.2" +version = "7.0.8" description = "Jupyter Notebook - A web-based notebook environment for interactive computing" optional = false python-versions = ">=3.8" files = [ - {file = "notebook-7.2.2-py3-none-any.whl", hash = "sha256:c89264081f671bc02eec0ed470a627ed791b9156cad9285226b31611d3e9fe1c"}, - {file = "notebook-7.2.2.tar.gz", hash = "sha256:2ef07d4220421623ad3fe88118d687bc0450055570cdd160814a59cf3a1c516e"}, + {file = "notebook-7.0.8-py3-none-any.whl", hash = "sha256:7f421b3fd46a17d91830e724b94e8e9ae922af152ebfd48b1e13ae4a07d8193c"}, + {file = "notebook-7.0.8.tar.gz", hash = "sha256:3957ecd956056b0014677afc76d3bb44c2d2f29649f87b24d13606ff1d18938f"}, ] [package.dependencies] jupyter-server = ">=2.4.0,<3" -jupyterlab = ">=4.2.0,<4.3" -jupyterlab-server = ">=2.27.1,<3" +jupyterlab = ">=4.0.2,<4.1" +jupyterlab-server = ">=2.22.1,<3" notebook-shim = ">=0.2,<0.3" tornado = ">=6.2.0" [package.extras] dev = ["hatch", "pre-commit"] docs = ["myst-parser", "nbsphinx", "pydata-sphinx-theme", "sphinx (>=1.3.6)", "sphinxcontrib-github-alt", "sphinxcontrib-spelling"] -test = ["importlib-resources (>=5.0)", "ipykernel", "jupyter-server[test] (>=2.4.0,<3)", "jupyterlab-server[test] (>=2.27.1,<3)", "nbval", "pytest (>=7.0)", "pytest-console-scripts", "pytest-timeout", "pytest-tornasync", "requests"] +test = ["importlib-resources (>=5.0)", "ipykernel", "jupyter-server[test] (>=2.4.0,<3)", "jupyterlab-server[test] (>=2.22.1,<3)", "nbval", "pytest (>=7.0)", "pytest-console-scripts", "pytest-timeout", "pytest-tornasync", "requests"] [package.source] type = "legacy" @@ -2499,6 +2695,22 @@ type = "legacy" url = "https://pypi.org/simple" reference = "pypi-public" +[[package]] +name = "pandocfilters" +version = "1.5.1" +description = "Utilities for writing pandoc filters in python" +optional = false +python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" +files = [ + {file = "pandocfilters-1.5.1-py2.py3-none-any.whl", hash = "sha256:93be382804a9cdb0a7267585f157e5d1731bbe5545a85b268d6f5fe6232de2bc"}, + {file = "pandocfilters-1.5.1.tar.gz", hash = "sha256:002b4a555ee4ebc03f8b66307e287fa492e4a77b4ea14d3f934328297bb4939e"}, +] + +[package.source] +type = "legacy" +url = "https://pypi.org/simple" +reference = "pypi-public" + [[package]] name = "parso" version = "0.8.4" @@ -2837,14 +3049,17 @@ reference = "pypi-public" [[package]] name = "pygments" version = "2.18.0" -description = "" +description = "Pygments is a syntax highlighting package written in Python." optional = false -python-versions = "*" +python-versions = ">=3.8" files = [ {file = "pygments-2.18.0-py3-none-any.whl", hash = "sha256:b8e6aca0523f3ab76fee51799c488e38782ac06eafcf95e7ba832985c8e7b13a"}, {file = "pygments-2.18.0.tar.gz", hash = "sha256:786ff802f32e91311bff3889f6e9a86e81505fe99f2735bb6d60ae0c5004f199"}, ] +[package.extras] +windows-terminal = ["colorama (>=0.4.6)"] + [package.source] type = "legacy" url = "https://pypi.org/simple" @@ -3793,14 +4008,22 @@ reference = "pypi-public" [[package]] name = "sphinx-remove-toctrees" version = "1.0.0.post1" -description = "" +description = "Reduce your documentation build size by selectively removing toctrees from pages." optional = false -python-versions = "*" +python-versions = ">=3.9" files = [ {file = "sphinx_remove_toctrees-1.0.0.post1-py3-none-any.whl", hash = "sha256:22a96579d7899cc034de194195916717a54a122cc101f16ec79c996fe0baa2be"}, {file = "sphinx_remove_toctrees-1.0.0.post1.tar.gz", hash = "sha256:4808d1edf151c06eff6d2c3922ec7ebc9fd3aa1762de1b2e1674a37f5ac9ce2d"}, ] +[package.dependencies] +sphinx = ">=5" + +[package.extras] +code-style = ["pre-commit (>=2.12)"] +docs = ["ipython", "myst-parser", "sphinx-book-theme"] +tests = ["ipython", "myst-parser", "pytest", "sphinx-book-theme"] + [package.source] type = "legacy" url = "https://pypi.org/simple" @@ -4240,6 +4463,29 @@ type = "legacy" url = "https://pypi.org/simple" reference = "pypi-public" +[[package]] +name = "tinycss2" +version = "1.4.0" +description = "A tiny CSS parser" +optional = false +python-versions = ">=3.8" +files = [ + {file = "tinycss2-1.4.0-py3-none-any.whl", hash = "sha256:3a49cf47b7675da0b15d0c6e1df8df4ebd96e9394bb905a5775adb0d884c5289"}, + {file = "tinycss2-1.4.0.tar.gz", hash = "sha256:10c0972f6fc0fbee87c3edb76549357415e94548c1ae10ebccdea16fb404a9b7"}, +] + +[package.dependencies] +webencodings = ">=0.4" + +[package.extras] +doc = ["sphinx", "sphinx_rtd_theme"] +test = ["pytest", "ruff"] + +[package.source] +type = "legacy" +url = "https://pypi.org/simple" +reference = "pypi-public" + [[package]] name = "toml" version = "0.10.2" @@ -4332,14 +4578,18 @@ reference = "pypi-public" [[package]] name = "traitlets" version = "5.14.3" -description = "" +description = "Traitlets Python configuration system" optional = false -python-versions = "*" +python-versions = ">=3.8" files = [ {file = "traitlets-5.14.3-py3-none-any.whl", hash = "sha256:b74e89e397b1ed28cc831db7aea759ba6640cb3de13090ca145426688ff1ac4f"}, {file = "traitlets-5.14.3.tar.gz", hash = "sha256:9ed0579d3502c94b4b3732ac120375cda96f923114522847de4b3bb98b96b6b7"}, ] +[package.extras] +docs = ["myst-parser", "pydata-sphinx-theme", "sphinx"] +test = ["argcomplete (>=3.0.3)", "mypy (>=1.7.0)", "pre-commit", "pytest (>=7.0,<8.2)", "pytest-mock", "pytest-mypy-testing"] + [package.source] type = "legacy" url = "https://pypi.org/simple" @@ -4572,6 +4822,22 @@ type = "legacy" url = "https://pypi.org/simple" reference = "pypi-public" +[[package]] +name = "webencodings" +version = "0.5.1" +description = "Character encoding aliases for legacy web content" +optional = false +python-versions = "*" +files = [ + {file = "webencodings-0.5.1-py2.py3-none-any.whl", hash = "sha256:a0af1213f3c2226497a97e2b3aa01a7e4bee4f403f95be16fc9acd2947514a78"}, + {file = "webencodings-0.5.1.tar.gz", hash = "sha256:b36a1c245f2d304965eb4e0a82848379241dc04b865afcc4aab16748587e1923"}, +] + +[package.source] +type = "legacy" +url = "https://pypi.org/simple" +reference = "pypi-public" + [[package]] name = "websocket-client" version = "1.8.0" @@ -4620,4 +4886,4 @@ reference = "pypi-public" [metadata] lock-version = "2.0" python-versions = "^3.9" -content-hash = "67de55f1b7dacc3393331ae310bf38699d8f7d2a2ea81b537b6ca89bb9e986ae" +content-hash = "b0653a19b5ce8c5366580929c2b8fd49b661f42621b30dbe8372fd2c25a7eba2"