AMORPH 1.1.0

The graphical interface shows the estimate of a run while the sampler
works, reports several seeds of one sample together and draws their
figures for LaTeX. The sampler and its results are those of 1.0.2.
Pre-releases (v1.1.0-rc.1, ...) come before the release, on GitHub only.

Added

• «Прогоны» shows the estimate of the run while the sampler works: the
  amorphous fraction with its 50% and 90% intervals from all the saves so
  far with their posterior weights, how it moved over the saves, the
  effective sample size, log(Z) and whether the estimate has settled; and
  the background, the amorphous halo, the crystalline peaks and the model,
  each a layer that can be hidden, for the posterior mean so far, the best
  sample or the last saved one, with their levels among those of the
  sampler. It used to show only the last saved sample, which once the
  levels are built is usually from a low level and fits the data worse
  than the posterior. The estimate is updated every second; when it takes
  longer, as on a slow computer or late in a long run, it waits four
  times as long as it took, and the plots are redrawn only for a new
  estimate.

• «Сравнение»: the options file and the saves of each run, its effective
  sample size, log(Z) against the best run of the same data and settings,
  and its checks; a run 5 nats or more below the best did not converge
  and is unticked. The ticked runs make a joint report (the fraction of
  all the seeds together, the spread of their medians, warnings, a line
  for a paper) and a figure, in the style of doc/figures/xrd_fit.tex or
  with two panels (doc/figures/xrd_seeds.tex), exported as the tables of
  PGFPlots, a folder for LaTeX, PDF and SVG built with the LaTeX
  installed, or PNG. «Добавить папку…» adds every archive of a folder.
  Every run shown on «Результаты» has a row on «Сравнение», once: a run
  done here (in 1.0.2 only the seeds of a batch of two or more came
  there), opened from its folder, or an archive opened.

• «Данные для PGFPlots…» on «Результаты» writes the tables of
  export_pgf.py for the run.

• «Отчёт LaTeX…» on «Результаты» and «Сравнение» writes a folder with
  report.tex to build with pdflatex: the result of the run or of the
  ticked seeds together and the line for a paper, the table of the runs
  with their checks, the data and the settings, the diagnostic cards of
  each run, both figures with their tables, and how to read the numbers,
  in Russian or in English as chosen in the menu of the button
  (src/amorph_gui/report.py, the English texts in strings_en.py).

• doc/figures/xrd_fit.tex also builds SVG: latex and dvisvgm.

• src/amorph_seeds.py pools the seeds of a sample;
  export_pgf.write_tables writes the tables from curves in memory;
  src/amorph_tex.py writes the folders of the figures and builds them.

• «Открыть прогоны…» on «Прогоны» (or a folder chosen on «Сравнение», or
  folders dropped on the window) opens runs done earlier or on another
  computer from their folders, many at a time: each on «Прогоны» with its
  output and its estimate rebuilt from its saves, on «Результаты» and on
  «Сравнение». A run without an up-to-date archive is post-processed.

• Explanations in the GUI: a «?» next to each card, figure and group of
  settings explains in plain words what it shows, and «Справка» (F1) has
  all these explanations on one page; the numbers, the columns of the
  tables, the views and the layers have tooltips. The intervals read
  "с вероятностью 50% — от … до …" instead of "50% [ , ]", and the
  column «Доля [25%, 75%]» of «Сравнение» is «Доля [50% интервал]».

• A splash screen shows as soon as the GUI starts, with the step under way:
  the first start of a newly unpacked package can take a minute while the
  system checks its files, and without a window the program was started
  again and again. The README says so too.

Changed

• The fraction on the figure of doc/figures/xrd_fit.tex, and on its
  preview in the GUI, is the median with its 50% interval, as
  $62.1^{+3.0}{-3.9}$ %: the numbers that the GUI and the line for a
  paper give. It was the mean: 61.4% where the median is 62.1%, as the
  distribution has a longer tail towards lower fractions. The interval
  is not symmetric and stays within 0-100%: near 100% it reads
  $98.0^{+1.5}{-5.0}$, not 98 ± 10. export_pgf.py writes it in
  \xrdamorph, its numbers in \xrdamorphmedian, \xrdamorphlo and
  \xrdamorphhi; tables of an older export_pgf.py still show the mean.
• The words of both figures (xrd_fit, xrd_seeds) come with their
  tables, in English or in Russian (src/figure_labels.py):
  export_pgf.py --language ru, the switch «язык» of «Сравнение» for the
  preview and every export, the menu of «Данные для PGFPlots…» on
  «Результаты», and the language of «Отчёт LaTeX…». In Russian the
  fraction in percent reads «Степень аморфности», as «доля» is 0-1
  everywhere else. The .tex files of the figures load Tempora, a
  Times-like font with Cyrillic, with newtxmath, instead of newtxtext;
  tables of an older export_pgf.py get the English words.

Fixed

• The axes of the plots of the GUI no longer scale numbers with an SI
  prefix: the histogram of the fraction read 200-800 "(x0.001)".
• The layout of rc.1: an empty table of «Сравнение» squeezed «Архив» and
  «Настройки» to a few letters, and its hint was cut off; the table of
  «Прогоны» scrolled sideways; the empty plot of the fraction ran from
  -0.4 to 0.4.
• In rc.1 and rc.2 the plots of «Прогоны» were updated every 5 seconds,
  behind a fast sampler, and the chips of the layers were all struck
  through, as if hidden.

Build and CI

• A tag v-rc. (or -beta., -alpha.) makes a GitHub
  pre-release of the version, with the notes of the version.