Graeme Winter

DYLD_LIBRARY does not work as expected

1

``` if [ -n "$DYLD_FALLBACK_LIBRARY_PATH" ]; then DYLD_FALLBACK_LIBRARY_PATH="$LIBTBX_BUILD/lib:$LIBTBX_BUILD/../conda_base/lib:$DYLD_FALLBACK_LIBRARY_PATH" export DYLD_FALLBACK_LIBRARY_PATH else DYLD_FALLBACK_LIBRARY_PATH="$LIBTBX_BUILD/lib:$LIBTBX_BUILD/../conda_base/lib:/usr/X11/lib:/usr/lib::" export DYLD_FALLBACK_LIBRARY_PATH fi ``` does not do what we would expect ``` silver-surfer viewer :( $ python3 -c...

Proposal: extract PHIL into a standard python package

4

I would like to be able to use PHIL for input for a non-cctbx / non-DIALS Python project and it would be very nice to be able to ``` pip...

Fix treatment of NaN in histogram

1

Includes test to assert this behaviour. Means histogram behaves as expected for #478 however issues with min() and max() remain.

Treatment of NaN in flex

8

It seems that NaN's confuse flex histogram... ``` ratio = flex.log10(t_i.select(t_nn) / r_i.select(r_nn)).as_double() print("Min: %f" % flex.min(ratio)) print("Number < -5: %d" % (ratio < -5).count(True)) r_hist = flex.histogram(ratio, data_min=-10, data_max=10,...

In PHIL - should we add the option for a deprecated=True bool flag...

1

... and if this is deprecated and changed by the user a deprecation warning emitted - see https://github.com/dials/dials/pull/1207#issuecomment-604289311 for inspiration

At: https://github.com/cctbx/cctbx_project/wiki/cctbx-Developer-Guidance Contains e.g. "Printing output Use `print >> log, bla` and not `print bla` . Use show function to print a summary or result of code execution instead of...

Numerically stable cell reduction isn't

2

```from __future__ import print_function from cctbx import crystal, uctbx, sgtbx uc = uctbx.unit_cell((82, 82, 87, 90, 90, 120)) cs = crystal.symmetry(unit_cell=uc, space_group_info=sgtbx.space_group_info("P3")) for i in range(10): cb_op = cs.change_of_basis_op_to_minimum_cell() cs...

https://github.com/cctbx/cctbx_project/blob/e85a70581599585a10ff6e19e109dcc69a254e06/scitbx/array_family/boost_python/flex_double_matrix.cpp#L134 Pointed out by @ndevenish in passing but ... `exercise_packed_u_accessor();` in `wrap_flex_double_matrix`? While it has been there for 14 years surely some mistake?

``` C:\Users\gw56\Work\cctbx\build>python ..\cctbx_project\libtbx\configure.py libtbx Traceback (most recent call last): File "..\cctbx_project\libtbx\configure.py", line 34, in if not run(): File "..\cctbx_project\libtbx\configure.py", line 29, in run libtbx.env_config.cold_start(sys.argv) File "C:\Users\gw56\Work\cctbx\cctbx_project\libtbx\env_config.py", line 2608, in cold_start...

```xray.scattering_type_registry()``` behaves like a dictionary i.e. has ```has_key``` methods and is indexed by string keys but is not iterable so cannot ask if thing in reg. Since it looks like...