Python environment engine + generic check_module() gate - #2
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reticulate is a hard Imports dependency, so requireNamespace() can never fail here; remove the guard.
Drop the import-based py_module_info() and the separate py_module_info2(); keep the metadata (no-import) implementation under the name py_module_info(). It reports module/available/version without importing, which is cheaper and safe for modules with heavy or side-effecting imports. module_version() now reads that metadata first and only falls back to importing + __version__ (module_version_by_import) when metadata yields nothing, so versions still resolve for namespace/editable installs and when importlib.metadata is unavailable. The now-unused python_module_path() and the dead reticulate guards in the introspectors are removed.
Port fafbseg's simple_python provisioning family into nat.python as the ecosystem's shared entry point for setting up a managed miniconda Python environment, including the curated basic/full/extra package bundles. Messaging uses cli rather than usethis, and the fafbseg.condaenv option is generalised to nat.python.condaenv (default r-reticulate). check_reticulate() collapses to a Python-availability gate now that reticulate is a hard dependency. Adds cli and jsonlite to Imports; reframes the Title/Description around managing Python for the natverse (this package is opinionated about how the environment should be set up, unlike bare reticulate).
A single entry point for code that needs a particular Python module: it checks
the module is installed (from distribution metadata, no import), imports it,
optionally enforces a minimum version, and on absence either installs it or
errors with actionable guidance. Ordered installed-first / load-second so a
failed import of an installed module is reported as an environment problem
(wrong Python) rather than a missing package.
install = c("ask", "never", "always") is self-documenting; instructions are
always shown, only the install action is gated. Results are memoised (cache =
TRUE) via check_module_impl, and simple_python() forgets that cache after an
install so later checks see newly installed packages. Package-specific checks
(fafbseg's check_seatable etc.) become thin wrappers over this and need not
memoise themselves.
Adds memoise to Imports.
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Summary
Brings fafbseg's Python provisioning engine and module install/load gate into
nat.python, so the natverse ecosystem has one place to set Python up and one
generic way to check a module is usable.
seatabler(and laterfafbseg,bancr) can then depend on nat.python for provisioning rather than on fafbseg.Four logically discrete commits, each builds on its own:
rids2pyint()— reticulate is a hardImportsdependency, so therequireNamespace()guard can never fire.py_module_info()to a single metadata-based introspector —drop the import-based
py_module_info()and the separatepy_module_info2(); keep the metadata (no-import) implementation under thename
py_module_info()(columnsmodule/available/version).module_version()now reads metadata first and falls back to importing +__version__only when metadata yields nothing, so versions still resolvefor namespace/editable installs and when
importlib.metadatais absent.Removes the now-unused
python_module_path().simple_python,check_reticulate) —ported near-verbatim from fafbseg's
simple_pythonfamily, including thecurated
basic/full/extrabundles. Messaging usesclirather thanusethis;fafbseg.condaenv→nat.python.condaenv(defaultr-reticulate).check_reticulate()collapses to a Python-availability gate.Reframes the Title/Description around managing Python for the natverse.
check_module()install/load gate — installed-first /load-second ordering so a failed import of an installed module is reported
as an environment problem (wrong Python) rather than a missing package.
install = c("ask", "never", "always")gates only the install action, neverthe instructions. Results are memoised (
cache = TRUE);simple_python()forgets that cache after an install. Package-specific checks (fafbseg's
check_seatableetc.) become thin wrappers over this and need not memoisethemselves.
Dependency changes
Adds
cli,jsonlite,memoisetoImports.Testing
Full suite green offline (
check-modulecovers every decision branch bymocking the Python-touching pieces;
py_module_info/module_versiontests passunchanged — numpy resolves via metadata, a bogus module via the import
fallback).
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