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Originally Posted by Agama
Should there be a Python sub-folder somewhere in this structure? The Bazaar installer mentioned a bundled Python 2.6 interpreter.
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There is no python subfolder. Python is bundled with the calibre binary, which you must install as well. You will test by setting the environment variable as documented, then using calibre-debug -g to start using your source.
However, as you are building plugins, there is no particular reason to run from source. You could start the normal calibre, then install and test the plugin. Perhaps someone who does more plugin development will provide some best-practice hints.
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Is there a document describing the various sub-folders of the calibre source, (customize, db, gui2, library etc.)?
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No.
Almost certainly the only folders you are interested in are src/calibre and resources.
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How do I keep this source code up to date with each calibre release?
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Assuming you are not making changes to the calibre source, cd to the calibre folder (the one containing src) and run bzr pull. That will grab the newest source. If you are making changes, then you will need to commit those changes (bzr commit) then merge the changes from launchpad (bzr merge).