Mailman 3 - fastlmm-user

New version of FaST-LMM, PySnpTools, & Bed-Reader with support for Python 3.13
by Carl K Nov. 3, 2024

Nov. 3, 2024

Greetings, We're happy to announce Python 3.13 support for all programs. Also, we now support both ARM and x64 on Linux and Mac. (Windows is still x64, only) To upgrade: * pip install --upgrade fastlmm pysnptools bed-reader Carl Kadie, Ph.D. FaST-LMM & PySnpTools Team<https://fastlmm.github.io/> (Microsoft Research, retired) https://medium.com/@carlmkadie https://www.linkedin.com/in/carlk/

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New versions of FaST-LMM, PySnpTools, and Bed-Reader
by Carl K July 5, 2024

July 5, 2024

Greetings, We have new versions of all the programs. What's new: * Compatibility with the new NumPy 2.0. * Support for MacOS on Arm and Linux on Arm. * Support for BGEN file format everywhere. pip install --upgrade fastlmm bed-reader pysnptools Thanks as always for using our tools in your own important work. * Carl Carl Kadie, Ph.D. FaST-LMM & PySnpTools Team<https://fastlmm.github.io/> (Microsoft Research, retired) https://www.linkedin.com/in/carlk/ Join the … [View More]

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New FaST-LMM and PySnpTools support for Python 3.12 (also 3.9, 3.10, and 3.11)
by Carl K June 3, 2024

June 3, 2024

Greetings, We are pleased to announce Python 3.12 is now supported by both FaST-LMM and PySnpTools. To make this happen, we've made support for the BGEN format optional. The BGEN format now available optionally on Linux and Windows for Python versions 3.11 and before. Yours, Carl Carl Kadie, Ph.D. FaST-LMM & PySnpTools Team<https://fastlmm.github.io/> (Microsoft Research, retired) https://www.linkedin.com/in/carlk/ Join the FaST-LMM user discussion and announcement list via … [View More]

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FaST-LMM 0.6.8: fixes SciPy issues
by Carl K April 30, 2024

April 30, 2024

Greetings, We're happy to announce FaST-LMM version 0.6.8. It contains hundreds of little changes to let it work with newer versions of SciPy, NumPy, and matplotlib. To get the new version, just: * pip install fastlmm==0.6.8 Yours, Carl

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New bed-reader feature: Support for writing very large PLINK 1.9 Bed Files
by Carl K April 22, 2024

April 22, 2024

Greetings, The Python version of the bed-reader package (1.0.3) now supports writing out large PLINK 1.9 Bed Files too big to fit in memory. Documentation on the new features: https://fastlmm.github.io/bed-reader/#bed_reader.create_bed Here is a notebook that shows the creation of a 1M sample x 250K SNP Bed file (In just, 5 minutes). Also, you can convert between individual-major to SNP-major mode (In about 1 hour). https://github.com/fastlmm/bed-reader/blob/master/bed_reader/tests/benchmar…… [View More]

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New version of Bed-Reader and PySnpTools
by Carl K Nov. 12, 2023

Nov. 12, 2023

Greetings, We're happy to announce new versions of Bed-Reader (1.0.0) and PySnpTools (0.5.11): Bed-reader The Python version of Bed-Reader now supports SciPy's sparse matrix format. Also, by default, it now depends only on NumPy. If you want that minimal version use pip install bed-reader If you want support for downloading example files and creating sparse matrices use: pip install bed-reader[samples,sparse] Rust version: The Rust version of Bed-Reader now returns a smaller "result … [View More]

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New version: FaST-LMM 0.6.7
by Carl K Aug. 11, 2023

Aug. 11, 2023

Greetings, We are happy to announce a new version of FaST-LMM (https://pypi.org/project/fastlmm/). It now supports Python 3.11 and newer versions of NumPy and SciPy. * Carl Carl Kadie, Ph.D. FaST-LMM & PySnpTools Team<https://fastlmm.github.io/> (Microsoft Research, retired) https://www.linkedin.com/in/carlk/ Join the FaST-LMM user discussion and announcement list via email<mailto:fastlmm-user-join@python.org?subject=Subscribe> (or use web sign up<https://mail.python.org/mailman3/lists/fastlmm-user.python.org>)

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Bed-Reader and PySnpTools now support Mac on Arm (and also Python 3.11)
by Carl K May 21, 2023

May 21, 2023

Greetings, We're happy to announce that Bed-Reader and PySnpTools now support MacOS Arm when installed via "pip". Also, we've bumped our supported Python versions up so we now support Python 3.8, 3.9, 3.10, and 3.11. Yours, Carl Carl Kadie, Ph.D. FaST-LMM & PySnpTools Team<https://fastlmm.github.io/> (Microsoft Research, retired) https://www.linkedin.com/in/carlk/ Join the FaST-LMM user discussion and announcement list via email<mailto:fastlmm-user-join@python.org?subject=… [View More]

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New versions of FaST-LMM, PySnpTools, and Bed-Reader
by Carl K May 2, 2023

May 2, 2023

Greetings, We're released a new version of the tools. The main change is adding support for Python 3.10 on Windows. * bed-reader 0.2.34<https://pypi.org/project/bed-reader/> - Updated to use latest version of Rust tools that we use under the covers. (Also updated: article about creating Python extensions in Rust<https://medium.com/towards-data-science/nine-rules-for-writing-python-exten…>.) * pysnptools 0.5.9<https://pypi.org/project/pysnptools/>, now supports Python … [View More]

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New version of PySnpTools: 0.5.8
by Carl K Feb. 1, 2023

Feb. 1, 2023

Greetings, We've updated PySnpTools to work with NumPy 1.24. (PySnpTools is also used by FaST-LMM.) pip uninstall pysnptools pip install pysnptools Yours, Carl Carl Kadie, Ph.D. FaST-LMM & PySnpTools Team<https://fastlmm.github.io/> (Microsoft Research, retired) https://www.linkedin.com/in/carlk/ Join the FaST-LMM user discussion and announcement list via email<mailto:fastlmm-user-join@python.org?subject=Subscribe> (or use web sign up<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.pyth…>)

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