Forever issue python 2.7 vs 3; missing tables in one and in "3.*" it just make even more issues

[StanleeKol]

$python2.7 PartitionFinder.py MyrsPart/ ERROR Could not find the dependency tables, please check that you have followed the installation instructions in the manual and try again.

$pip2 install tables DEPRECATION: Python 2.7 reached the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 is no longer maintained. pip 21.0 will drop support for Python 2.7 in January 2021. More details about Python 2 support in pip can be found at https://pip.pypa.io/en/latest/development/release-process/#python-2-support pip 21.0 will remove support for this functionality. Collecting tables Using cached tables-3.5.2-cp27-cp27m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl (4.3 MB) Collecting numexpr>=2.6.2 Using cached numexpr-2.8.1.tar.gz (94 kB) Installing build dependencies ... error ERROR: Command errored out with exit status 1: command: /Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pip install --ignore-installed --no-user --prefix /private/var/folders/fj/3rr110l52cs7ctvhzy_ggvpw0000gn/T/pip-build-env-VCwMMv/overlay --no-warn-script-location --no-binary :none: --only-binary :none: -i https://pypi.org/simple -- setuptools wheel oldest-supported-numpy cwd: None Complete output (7 lines): DEPRECATION: Python 2.7 reached the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 is no longer maintained. pip 21.0 will drop support for Python 2.7 in January 2021. More details about Python 2 support in pip can be found at https://pip.pypa.io/en/latest/development/release-process/#python-2-support pip 21.0 will remove support for this functionality. Collecting setuptools Using cached setuptools-44.1.1-py2.py3-none-any.whl (583 kB) Collecting wheel Using cached wheel-0.37.1-py2.py3-none-any.whl (35 kB) ERROR: Could not find a version that satisfies the requirement oldest-supported-numpy (from versions: none) ERROR: No matching distribution found for oldest-supported-numpy

ERROR: Command errored out with exit status 1: /Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pip install --ignore-installed --no-user --prefix /private/var/folders/fj/3rr110l52cs7ctvhzy_ggvpw0000gn/T/pip-build-env-VCwMMv/overlay --no-warn-script-location --no-binary :none: --only-binary :none: -i https://pypi.org/simple -- setuptools wheel oldest-supported-numpy Check the logs for full command output.

Any recommendations?

[roblanf]

hi @stanleewild - as you've identified, PF2 is coming to the end of it's life.

Luckily, it is superceded by something much better - IQTREE2. Most of what PF2 does is already implemented in IQTREE2, we are just finalising a few details. But if you use MFP+MERGE at the commandline with IQ-TREE2, you'll e able to optimise partitioning schemes.

Details here: http://www.iqtree.org/doc/Advanced-Tutorial (scroll down to 'choosing the right partitioning scheme')

[StanleeKol]

Hi @roblanf Thank you very much for the clarification! I have one more question - please, regarding IQTREE2 having better capability than PF2 itself, how could I generate partitioning scheme or "partition file". PF2 was giving me best_scheme file with these data. Otherwise I don't know how can I provide to IQTree partitions file (except codon positions, but that is something else). Thanks a lot!

Stan

[roblanf]

It's all there in the tutorial I think...

The tutorial shows you how to start from scratch (i.e. with data blocks, the same as you would start in PF2). It also shows you how to define a partitioning scheme.

If anything doesn't make sense, best to use the iq-tree google group: https://groups.google.com/g/iqtree

[StanleeKol]

Thank you @roblanf for the reply. Unfortunately, I was not able to find out from the manual this thing. There is always only "example.nex" mentioned which has already defined the partitions. I did not find any function where I could just specify codon positions (data blocks) and then to get partitions. I send this question also to IQTree group, but without the response.