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Contents 1 Installation 2 Python3 compliance 2.1 getbirch 3 BIRCH 4 Phylogeny

Installation

Python3 compliance

Based on testing on macos-arm64 on which python2 is not installed, BIRCH should now be completely Python3 compliant. We will fix remaining noncompliant scripts, if any, as they show up.

getbirch

• revise birchtally.cgi to replace the deprecated cgi module using urlparse.
• revise getbirch to eliminate the check for csh/tcsh. This is found in java-src/install/Main.java.

BIRCH

• Elimination of tcsh/csh dependency
• Remove obsolete csh scripts from $birch/script (do a grep csh * in script to find these)
  • Rewriting of features to features.py
• Python3 - deprecation of escape sequences. Python3 gives a warning for escape sequences in regular expressions such as re.match eg. '\s'. This must be changed to '\\s'.
  See [1]. This has been fixed in htmldoc.py, and the revised htmldoc.py appears to work. In future releases, we will have to go through all python scripts and change these. Acckkk!!!

Phylogeny

• When doing bootstrapping, the treefile and outfile don't get decoded, so they have the names from uniqid.py, rather than the original names.