reticulate 1.31

Python Installation Management

• reticulate will no longer prompt users to install miniconda. Instead,
  reticulate will now prompt users to create a default r-reticulate venv.

• The search that reticulate conducts to select which Python installation to load
  has changed. See the updated Python "Order of Discover" in the "versions" vignette.
  vignette("versions", package = "reticulate").

• Updated recommendations in the "python_dependencies" vignette for how R packages
  can approach Python dependency management.
  vignette("python_dependencies", package = "reticulate")

• New function virtualenv_starter(), which can be used to find a suitable
  python binary for creating a virtual environmnent. This is now the default
  method for finding the python binary when calling
  virtualenv_create(version = <version>).

• virtualenv_create() and virtualenv_install() gain a requirements argument,
  accepting a filepath to a python requirements file.

• virtualenv_create() gains a force argument.

• virtualenv_install() gains a python_version argument, allowing users to customize
  which python version is used when bootstrapping a new virtual environment.

• Fixed an issue where the list of available python versions used by
  install_python() would be out-of-date.

• install_python() now gives a better error message if git is not installed.

• install_python() on macOS will now will use brew, if it's available, to install
  build dependencies, substantially speeding up python build times.

• New function conda_search(), contributed by @mkoohafkan in PR #1364.

Language

• New [ and [<- methods that invoke Python __getitem__, __setitem__ and
  __delitem__. The R generics [ and [<- now accept python-style slice
  syntax like x[1:2:3]. See examples in ?py_get_item.

• py_iterator() gains a prefetch argument, primarily to avoid deadlocks
  where the main thread is blocked, waiting for the iterator, which is waiting
  to run on the main thread, as encountered in TensorFlow/Keras. (#1405).

• String columns from Pandas data frames containing None, pd.NA or np.nan
  are now simplified into character vectors and missing values replaced by NA
  (#1428).

• Converting from Pandas data frames containing columns with Pandas nullable
  data types are now correctly converted into R data.frames preserving the
  missing values (#1427).

Knitr

• The knitr engine gains a jupyter_compat option, enabling
  reticulate to better match the behavior of Jupyter. When this chunk
  option is set to TRUE, only the return value from the last
  expression in a chunk is auto-printed. (#1391, #1394, contributed by
  @matthew-brett)

• The knitr engine now more reliably detects and displays matplotlib
  pending plots, without the need for a matplotlib artist object to be
  returned as a top-level expression. E.g., the knitr engine will now
  display plots when the matplotlib api returns something other than
  an artist object, (plt.bar()), or the matplotlib return value is
  not auto-printed due to being assigned, (x = plt.plot()), or
  suppressed with a ;, (plt.plot();). (#1391, #1401, contributed
  by @matthew-brett)

• Fixed an issue where knitr engine would not respect chunk options
  fig.width / fig.height when rendering matplotlib plots. (#1398)

• Fixed an issue where the reticulate knitr engine would not capture output
  printed from python. (PR #1412, fixing #1378, #331)

Miscellanous

• Reticulate now periodically flushes python stdout and stderr buffers even
  while the main thread is blocked executing Python code. Streaming output
  from a long-running Python function call will now appear in the R console
  while the Python function is still executing. (Previously, output might not
  appear until the Python function had finished and control of the main thread
  had returned to R).

• Updated sparse matrix conversion routines for compatibility with
  scipy 1.11.0.

• Fixed an issue where a py capsule finalizer could access the R API from
  a background thread. (#1406)

• Fixed issue where R would segfault (crash) in long-lived R sessions where both
  rpy2 and reticulate were in use (#1236).

• Fixed an issue where exceptions from reticulate would not be formatted properly
  when running tests under testthat (r-lib/rlang#1637, #1413).

• Fixed an issue where py_get_attr(silent = TRUE) would not return an R NULL,
  if the attribute was missing, as documented. (#1413)

• Fixed an issue where py_get_attr(silent = TRUE) would leave a python global
  exception set if the attribute was missing, resulting in fatal errors when
  running python under debug mode. (#1396)