| Age | Commit message (Collapse) | Author |
|---|
|
This commit replaces image.crystals with an array of small structs, each
consisting of a Crystal-RefList pair. index.c and stream.c are updated,
more to follow.
|
|
This is a terrible bit of API. A Crystal contains both the parameters
for a calculation (e.g. prediction) and the results. Just look at
post-refinement.c for an example of the mess this makes when trying to
do calculations.
This commit removes the reflection list from the Crystal structure.
Future commits in this series will fix the resulting build carnage.
This also gets rid of vestigial field pr_dud, and adds initialisers for
all (remaining) fields.
|
|
|
|
|
|
|
|
It hasn't been needed for ages.
|
|
|
|
|
|
|
|
I don't understand the correct way to do this dependency, and I've run
out of time to figure it out. Contributions welcome! But in the
meantime, users probably have Python+Numpy installed on their systems
some other way.
|
|
These should be handled via the formula's dependencies.
|
|
Ok, I interpreted the documentation a little too literatlly.
|
|
|
|
Needed for peakogram-stream.
|
|
Indexamajig --help causes a segfault on MacOS due to a bug in
argp-standalone. That package is unlikely to be updated any time soon.
Eventually, Homebrew might switch to one of the non-crashy forks, but
probably not soon. We aren't the only ones affected - see
https://www.openwall.com/lists/musl/2021/02/10/1
This commit adds a warning message to state that we already know about
it, and it's not "our" fault. It also removes the corresponding test,
since we know it fails.
|
|
|
|
|
|
Not used any more.
|
|
Pandoc >=2.0.0 needs "-f markdown-smart", which requests (amongst some
other things) not to convert "--" to an en-dash. We have a lot of
double hyphens in the documentation, and I would prefer not to have to
escape every single one of them.
Older Pandoc versions don't recognise "-smart", but also don't do the
en-dash thing by default. Here, we can simply use "-f markdown".
Note that older Pandoc versions don't quite render the manual pages
correctly, but it's near enough.
Fixes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/90
|
|
|
|
This paragraph isn't true. Our formula explicitly removes the
--wrap-mode=nofallback option, to allow the wrapped dependencies to be
installed.
What is true, however, is that this makes the formula unacceptable
upstream. We would need to create individual packages for all the
dependencies.
|
|
|
|
A little clearer than fftw_malloc(*sizeof)
|
|
This is only needed to reset FFTW to a "pristine" state, which is not
required here, and possibly even detrimental.
|
|
We don't need to fish out the arrays and use FFTW's "new array
execution" functions: http://fftw.org/fftw3_doc/New_002darray-Execute-Functions.html
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
This could be used for indexing, but it seems more transparent to have
the "real" filename in the script for auditing. The geometry copy will
be used for detector alignment. The alternative - extracting the
geometry from the stream - seems quite a lot more complicated.
|
|
|
|
|
|
Rationale: the refinement is very quick, and the output geometry file
name is central to the process.
|
|
|
|
|
|
Note that the indexamajig option --max-mille-level isn't implemented
yet.
|
|
|
|
The script has been replaced with align_detector --level=0.
|
|
There are still some rough edges, e.g. it only works with a simple
I/SIGI column (not I+/I-), and can't yet interpret the symmetry
information in the file. However, it's still better than the old
mtz2hkl script.
Closes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/7
|
|
|
|
The containers have all the development package dependencies and tools preinstalled to save
time and network bandwidth in the Fedora 32 & 37 and Centos7 jobs.
|
|
|
|
This also reduces the default timeout to 500 ms.
|
|
|
|
Example: group_all = q0,q1,q2,q2
|
|
|
|
|
