Merge pull request #405 from weese/hotfix/fiona-vs8

[FIX] fixed fiona issues and mingw warnings
Merge pull request #402 from singerj/hotfix-knime-flexbar

Hotfix knime flexbar
Merge pull request #407 from singerj/hotfix-knime-flexbar

[FIX] Fixed a default value problem with the output files.
Merge branch 'master' into develop