[cctbxbb] bootstrap.py not overwriting modified sources

markus.gerstel at diamond.ac.uk markus.gerstel at diamond.ac.uk
Tue Feb 14 05:00:48 PST 2017

Hi Rob

I would say that this would be a rather dangerous default. You would lose any uncommitted changes and there is no way back. At least (assuming a git repository) do a git stash instead -- although to the unsuspecting non-expert user this would still look like the changes are lost.

How about: If changes present, warn the user and advise that they can irrevocably reset the repository with eg.
 git reset --hard HEAD; git clean -dffx

(I only ever use ‘update’ to do the initial checkout, so whatever the decision it wouldn’t affect me.)

From: cctbxbb-bounces at phenix-online.org [mailto:cctbxbb-bounces at phenix-online.org] On Behalf Of R.D. Oeffner
Sent: 14 February 2017 12:49
To: cctbx mailing list <cctbxbb at phenix-online.org>
Subject: [cctbxbb] bootstrap.py not overwriting modified sources

Hi all,

It appears that when bootstrap.py is invoked to update sources then unsurprisingly it doesn't overwrite existing sources if these are more recent, as in someone has modified them and not committed the changes. Occasionally this leads to broken builds.

To prevent this from happening would it not be a good idea to change bootstrap.py to default to overwrite any uncommitted changes unless some flag is set on the command line?


Robert Oeffner, Ph.D.

Research Associate, The Read Group

Department of Haematology,

Cambridge Institute for Medical Research

University of Cambridge

Cambridge Biomedical Campus

Wellcome Trust/MRC Building

Hills Road

Cambridge CB2 0XY


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