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Updated glue.ligolw calls to latest stable release

Duncan Macleod requested to merge github/fork/duncanmmacleod/ligolw-deprecations into master

The latest release of glue is backwards incompatible with previous, with a number of objects and methods being removed (DeprecationWarnings have been in place for a while). This PR updates any broken glue.ligolw calls in a backwards compatible manner.

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