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868 discussions

IMP 2.13.0 release
by Ben Webb 14 May '20

14 May '20

IMP 2.13.0 is now available. This is contains major updates, most notably support for Ubuntu 20.04, Focal Fossa, and a new IMP::sampcon module to estimate the highest precision at which the sampling is exhaustive. See https://integrativemodeling.org/2.13.0/doc/manual/changelog.html for the full change log. Check it out at https://integrativemodeling.org/ Ben -- ben(a)salilab.org https://salilab.org/~ben/ "It is a capital mistake to theorize before one has data." - Sir Arthur Conan Doyle

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IMP Homebrew package and Python 3.8
by Ben Webb 28 Apr '20

28 Apr '20

Hi all, just FYI I will likely be moving the Homebrew IMP package to Python 3.8 in the near future. The Homebrew folks seem to be having a lot of trouble switching from Python 3.7 to 3.8; see https://github.com/Homebrew/homebrew-core/issues/47274 which they have been working on since November. They gave up on a simple switch and now they are migrating formulae individually. Most formulae now use Python 3.8 but the default (/usr/local/bin/python3) is still 3.7. Since IMP uses the default it is increasingly broken since common dependencies (numpy, scipy) now only work with 3.8. If you want to build IMP on a Homebrew Mac against Python 3.8, this is pretty easy - just set in bashrc/zshrc export PATH="/usr/local/opt/python@3.8/bin:$PATH" as recommended by "brew info python(a)3.8" to make "python3" be 3.8 and export CMAKE_FRAMEWORK_PATH="/usr/local/Cellar/python(a)3.8/3.8.2/Frameworks" for CMake to pick up 3.8 when you build IMP. I will likely also adjust the Homebrew IMP package to use Python 3.8 at some point in the next few weeks. Ben -- ben(a)salilab.org https://salilab.org/~ben/ "It is a capital mistake to theorize before one has data." - Sir Arthur Conan Doyle

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IMP 2.12.0 release
by Ben Webb 06 Dec '19

06 Dec '19

IMP 2.12.0 is now available. This is contains major updates, most notably support for Python 3.8 and RHEL/CentOS 8, and a new IMP::bayesianem module for Bayesian handling of cryo-electron microscopy density map data. See https://integrativemodeling.org/2.12.0/doc/manual/changelog.html for the full change log. Check it out at https://integrativemodeling.org/ Ben -- ben(a)salilab.org https://salilab.org/~ben/ "It is a capital mistake to theorize before one has data." - Sir Arthur Conan Doyle

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IMP 2.11.1 release
by Ben Webb 18 Jul '19

18 Jul '19

IMP 2.11.1 is now available. This is a bugfix release, which fixes some issues with the build system, failures to read RMF files, and cloning of molecular hierarchies. See https://integrativemodeling.org/2.11.1/doc/manual/changelog.html for the full change log. Check it out at https://integrativemodeling.org/ Ben -- ben(a)salilab.org https://salilab.org/~ben/ "It is a capital mistake to theorize before one has data." - Sir Arthur Conan Doyle

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IMP 2.11.0 release
by Ben Webb 25 Jun '19

25 Jun '19

IMP 2.11.0 is now available. This is a bugfix and major update release. Most notably a number of new tutorials are now available covering a variety of topics from modeling complexes with IMP::pmi to writing new C++ code. The build system has also been overhauled to better support multiple versions of Python, to allow building IMP extensions modules outside of the IMP build tree, and to support using IMP as a library in other programs. See https://integrativemodeling.org/2.11.0/doc/manual/changelog.html for the full change log. Check it out at https://integrativemodeling.org/ Ben -- ben(a)salilab.org https://salilab.org/~ben/ "It is a capital mistake to theorize before one has data." - Sir Arthur Conan Doyle

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IMP CMake builds now default to Python3
by Ben Webb 04 Jun '19

04 Jun '19

Note that in IMP's develop branch (as of 9f63080a6, committed earlier today) CMake will now default to using Python 3 if available: https://github.com/salilab/imp/commit/9f63080a6 This new logic should make building IMP on systems with multiple Pythons (e.g. Macs with Homebrew) much simpler, as CMake should handle this without needing to manually set PYTHON_INCLUDE_PATH or PYTHON_LIBRARY directly. If you still want to build IMP with Python 2 on a system that has Python 3, pass -DUSE_PYTHON2=on to your cmake invocation. (But note that Python 2 is - very slowly - being phased out so switching to 3 might make sense. For example Fedora 30 no longer has Python 2 scikit-learn or biopython packages.) Ben -- ben(a)salilab.org https://salilab.org/~ben/ "It is a capital mistake to theorize before one has data." - Sir Arthur Conan Doyle

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IMP 2.10.1 release
by Ben Webb 26 Feb '19

26 Feb '19

IMP 2.10.1 is now available. This is a minor bugfix release. It adds support for building with OpenCV 4, and fixes some minor bugs in the create_gmm.py script and with using command line tools on systems with multiple Python installations. See https://integrativemodeling.org/2.10.1/doc/manual/changelog.html for the full change log. Check it out at https://integrativemodeling.org/ Ben -- ben(a)salilab.org https://salilab.org/~ben/ "It is a capital mistake to theorize before one has data." - Sir Arthur Conan Doyle

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IMP 2.10.0 release
by Ben Webb 08 Jan '19

08 Jan '19

IMP 2.10.0 is now available. This is a bugfix and major update release. Most notably the IMP::pmi module has been overhauled; the IMP::pmi::representation::Representation class is now deprecated (and will be removed in the next release) and the IMP::pmi::topology::System class should be used instead. A legacy IMP::pmi1 module is now provided to support old published applications of IMP that use the old Representation class, but should not be used for new applications. This release also includes a number of bug fixes and performance improvements. See https://integrativemodeling.org/2.10.0/doc/manual/changelog.html for the full change log. Check it out at https://integrativemodeling.org/ Ben -- ben(a)salilab.org https://salilab.org/~ben/ "It is a capital mistake to theorize before one has data." - Sir Arthur Conan Doyle

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Preparation for IMP 2.10.0 release
by Ben Webb 30 Nov '18

30 Nov '18

I'll be making a new IMP release shortly - probably branching within a week or two and releasing at the end of this month. This is primarily to get the new PMI2 code out there so we can start cleaning out the old PMI1 classes. So now is a good time for any polishing, bug fixing, documentation fixes etc. (and a really bad time for any sweeping changes!) Ben -- ben(a)salilab.org https://salilab.org/~ben/ "It is a capital mistake to theorize before one has data." - Sir Arthur Conan Doyle

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IMP 2.9.0 release
by Ben Webb 03 Jul '18

03 Jul '18

IMP 2.9.0 is now available. This is a bugfix and major update release. Most notably a number of new applications of IMP are now available, including the elucidation of the structure of the entire yeast nuclear pore complex. This release also includes a number of bug fixes and performance improvements. See https://integrativemodeling.org/2.9.0/doc/manual/changelog.html for the full change log. Check it out at https://integrativemodeling.org/ Ben -- ben(a)salilab.org https://salilab.org/~ben/ "It is a capital mistake to theorize before one has data." - Sir Arthur Conan Doyle

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