[cctbxbb] Scons for python3 released

Tue Oct 17 07:19:42 PDT 2017

Hi Robert

I think having more than one person independently look at the p3 problem is no bad thing - also with the geography it would seem perfectly possible for you / Nick to meet up and compare notes on this - it’s certainly something I would support.

Clearly there are a lot of things which could get caught up in the net with the p3 update - for example build system discussions, cleaning out cruft that is in there to support python 2.3 etc… however I did not read that Nick thought SCons3 was a waste of time - I think he was getting at the point that this is part of the move, and that there is also a lot of related work. Also that having p2 / p3 support for at least a transition rather than the “full Brexit” of no longer supporting p2 beyond the first date where p3 works would be good. I could imagine this transition period being O(1000 days) even.

I think the migration process is going to be a complex one, but doable. One thing I think we do need is to make sure that the code base as pushed by developers remains compatible with p2 and p3 - so perhaps extending find_clutter to check for things which only work in one or the other? Then developers would learn the tricks themselves and (ideally) not push p2-only or p3-only code, at least until post-transition. This I would compare with the svn to git move, which caused some grumbling and a little confusion but was ultimately successful…

Hope this is constructive, cheerio

Graeme

On 17 Oct 2017, at 13:50, R.D. Oeffner <rdo20 at cam.ac.uk<mailto:rdo20 at cam.ac.uk>> wrote:

Hi Nick and others,

That sounds like a great effort. A shame I didn't know about this. I have not had time to look in detail into your work but will nevertheless summarize my thoughts and work I have been doing lately in an effort to move CCTBX to python3.

I am not sure why it would be a waste of time to use SCons3.0 with python3 as I think you are suggesting. To me it seems as a necessary step in creating a codebase that runs both on python2 and python3. Do I understand correctly that as long as CCTBX code is changed to comply with python3 and remain python2 compliant then such a codebase can be used in place of the current python2 only codebase for derived projects such as Dials and Phenix? Assuming this is the case I think it is worth focusing just on CCTBX only for now.

My own attempt in porting CCTBX to python3 constitutes of the following steps:
* Replace Scons2 with Scons3
* Update the subset of Boost sources to version 1.63
* Run futurize stage1 and stage2 on the CCTBX
* Build base components like libtiff, hdf5, python3.6 + add-on modules)
* Run bootstrap.py build with Python3.6 repeatedly and provide mock-up fixes to allow the build to continue.

This work is almost near completion in the sense that the sources now can build but are unlikely to pass test due to the mock-up fixes which often constitutes of replacement of PyStringXXX functions with equivalent PyUnicodeXXX, PyBytestringXXX functions ignoring whether that is appropriate or not. These token fixes would also need to be guarded by #if PY_MAJOR_VERSION == 3 ... macros.

The sources are available on https://github.com/cctbx/cctbx_project/tree/Python3

The next steps are less well defined. One approach would be to set up a build system that migrates python2 code to python3 using the futurize script, then builds CCTBX and runs test and presents build log files online as in http://cci-vm-6.lbl.gov:8010/one_line_per_build. With a hook to GitHub this could also be done on the fly as people commit code to CCTBX. This should encourage people to write code that runs on python2 as well as python3. Eventually once all tests for CCTBX pass we are done and can merge this codebase into the master branch.

Robert

On 17/10/2017 11:56, Nicholas Devenish wrote:
Hi All,
I spent a little bit of time looking at python3/libtbx so have some
input on this.
On Tue, Oct 10, 2017 at 6:16 PM, Billy Poon <bkpoon at lbl.gov<mailto:bkpoon at lbl.gov>> wrote:
1) Use Python 2 to build Python 2 version of CCTBX (no work)
This might not be as simple as "No Work" - cctbx is a few years behind
on SCons versions (libtbx.scons --version suggests 2.2.0, from 2012)
so there *might* be other issues upgrading the SCons version to 3.0,
before trying python3.
I also feel that SCons-Python3 is something of a red herring - the
only thing that non-python3-SCons prevents is an 100% python3-only
codebase, and unless the plan is to migrate the entire codebase,
including all downstream dependencies (like dials) to python3-only in
one massive step (probably impossible), everything would need to be
dual 2/3 first, and only then a decision taken on deprecating 2.7
support.
More usefully, outside of a small core of libtbx code, not much of the
buildsystem files are bound to the main project so this shouldn't be
too difficult. In fact, I've experimented with converting to CMake,
and as one of the approaches I explored, I wrote a SCons-emulator that
read and parsed the build *without* any scons/cctbx dependencies. To
parse the entire "builder=dials" SCons-tree only required this subset
of libtbx:
https://github.com/ndevenish/read_scons/blob/master/tbx2cmake/import_env.py#L202-L235
[1]
(Note: my general CMake-work works but isn't complete/ready/documented
for general viewing, and still much resembles a hacky project, but I
thought that this was sufficient to decouple the buildsystem is
usefully illustrative of how simple the task might be)
Regarding general Python3 conversion, it's definitely not "Just
changing the print statements". I undertook a study in august to
convert libtbx (being the core that *everything* depends on) to dual
python2/3 and IIRC got most of the tests working in python3. It's a
couple of months out-of-date, but is probably useful as a benchmark of
the effort required. The repository links are:
   https://github.com/ndevenish/cctbx_project/tree/py3k-modernize [2]
   https://github.com/ndevenish/cctbx_project/tree/py3k [3]
Probably best looked at with a graphical viewer to get a top-down view
of the history. My approach was to separate manual/automatic changes
as follows:
1. Remove legacy code/modules - e.g. old compatibility. The Optik
removal came from this. We don't want to spend mental effort
converting absorbed external libraries from a decade ago (see also
e.g. pexpect, subprocess_with_fixes)
2. Make some manual fixes [Expanded as we go on]
3. Use futurize and modernize to update idioms ONLY e.g. remove
pre-2.7 deprecated ways of working. Each operation was done is a
separate commit (so that changes are more visible and I thought people
would have less objection than to a massive code-change dump), and
each commit ran the test suite for libtbx. Some of the 'fixers' in
each tool are complementary. If there are any problems with tests or
automatic conversion, then fix the problem, put the fix into step 2,
then start again. This step should be entirely scriptable. I had 17
commits for separate fixes in this chain.
This is the where the py3k-modernize branch stops, and should in
principle be kept entirely safe to push back onto the python2-only
repository. The next steps form the `py3k` branch (not being intended
for direct pushing, is a little less organised - some of my changes
could definitely be moved to step 2):
4. Run 'modernize' to convert the codebase to as much python2/3 as
possible. This introduces the dependency on 'six'
5. Run tests, implement various fixes, repeat. This work was ongoing
when I stopped working on the study.
Various (non-exhaustive) problems found:
- cStringIO isn't handled automatically, so these need to be fixed
manually ( e.g.
https://github.com/ndevenish/cctbx_project/commit/c793eb58acc37c60360dccbbbdd5205504ec3f1a
[4] )
- Iterators needed to be fixed in cases where they were missed (next
vs __next__)
- Rounding. Python3 uses 'Bankers Rounding' and there are formatting
tests where this changes the output. I didn't know enough about the
exact desired result to know the best way to fix this
- libtbx uses compiler.misc.mangle and I don't know why - this was
always a private interface and was removed in 3.
- Moving print statements to functions - there was several failed
tests relating to the old python2-print-soft-spacing behaviour, which
was removed. Not too difficult, but definitely causes
- A couple of text/binary mode file issues, which seemed to be simple
but may be more complicated than the test cases covered. I'd expect
more issues with this in the format readers though.
I evaluated both the futurize (using future library) and modernize
(using the well known six library) tools, both being different
approaches to 2to3, but for dual 2/3 codebases. I liked the approach
of futurize to attempt to make code look as python3-idiomatic
as-possible, but some of the performance implications were slightly
opaque: e.g. libtbx makes heavy use of cStringIO (presumably for a
good reason), and futurize converted all of these back to using
StringIO in the Python2 case, so settled on modernize as I felt two
different compatibility libraries would be messy. In either case,
using the library means that you can identify exactly everywhere that
needs to be removed when moving to python3 only.
My conclusions:
- Automatic tools are useful for the bulk of changes, but there are
still lots of edge cases
- The complexity means that a phased approach is *absolutely*
necessary - starting by converting the core to 2/3 and only moving to
3 once everything downstream is converted.Trying to convert everything
at once would likely mean months of feature-freeze.
- A separate "Remove legacy" cleaning phase might be very useful,
though obviously the domain of this could be endless
- SCons is probably the least important of the conversion worries
Nick
Links:
------
[1]
https://github.com/ndevenish/read_scons/blob/master/tbx2cmake/import_env.py#L202-L235
[2] https://github.com/ndevenish/cctbx_project/tree/py3k-modernize
[3] https://github.com/ndevenish/cctbx_project/tree/py3k
[4]
https://github.com/ndevenish/cctbx_project/commit/c793eb58acc37c60360dccbbbdd5205504ec3f1a
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