Bump version to 0.4.6.9000

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: stochtree
 Title: Stochastic Tree Ensembles (XBART and BART) for Supervised Learning and Causal Inference
-Version: 0.4.5
+Version: 0.4.6.9000
 Authors@R: 
   c(
     person("Drew", "Herren", email = "drewherrenopensource@gmail.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0003-4109-6611")), 

Doxyfile

@@ -48,7 +48,7 @@ PROJECT_NAME           = "StochTree"
 # could be handy for archiving the generated documentation or if some version
 # control system is used.
 
-PROJECT_NUMBER         = 0.4.5
+PROJECT_NUMBER         = 0.4.6.9000
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer a

NEWS.md

@@ -1,3 +1,5 @@
+# stochtree 0.4.6.9000
+
 # stochtree 0.4.5
 
 ## Bug Fixes

RELEASING.md

@@ -38,6 +38,7 @@ This document describes the end-to-end process for releasing a new version of st
 - No empty version section in `NEWS.md` (CRAN will flag this)
 - `MANIFEST.in` includes any new C++ dependency header trees added since the last release
 - All tests pass locally (`source venv/bin/activate && python -m pytest` and `NOT_CRAN=true Rscript -e "devtools::load_all('.'); testthat::test_dir('test/R/testthat')"`)
+- If sampler output changed this cycle, regenerate the reproducibility references under `tools/reproducibility/{R,python}` and confirm the `reproducibility_check` workflow **fails on drift** against the new references. (A stale-reference / lenient-check mismatch caused a post-tag follow-up in 0.4.5.)
 
 ---
 
@@ -81,6 +82,13 @@ git push origin --delete v0.4.2
 
 Then you can start a new draft and pre-release it as above
 
+## Do post-tag fixes need a re-tag?
+
+When a fix lands on `main` after the release tag is cut, decide by what it touches:
+
+- **Re-tag** if it changes anything shipped in the R/Python packages — `R/`, `src/`, `stochtree/`, the version files, or `NEWS.md`.
+- **Leave the tag** if it only touches things outside the distributed packages — CI workflows, `tools/reproducibility/` references, benchmarks, docs-site config. The tagged artifact is unchanged, so moving the tag buys nothing. (In 0.4.5, a CI-only reproducibility fix landed post-tag and was correctly left out of the release.)
+
 ## Updating a full release (minor fixes after promotion)
 
 For small fixes (doc corrections, man page updates, typos) discovered after promoting to a full release, delete-and-recreate is overkill. Instead, merge the fix to `main` and force-move the tag:
@@ -143,9 +151,36 @@ Review the Actions tab for results. If a check fails, fix the issue on `main`, t
 Promoting the pre-release to a full release fires `published`, which:
 
 - **Automatically updates the `r-dev` branch** (via `r-cran-branch.yml`) and tags the R release as `r-x.y.z` (which from 0.4.2-on is a git tag but not a separate github release)
-- **Triggers wheel builds** (via `pypi-wheels.yml`); PyPI publication is currently a **manual step** — download the wheel artifacts from the Actions run and upload via `twine upload dist/*`. Setting up [PyPI trusted publishing](https://docs.pypi.org/trusted-publishers/) (OIDC) will automate this and in upcoming release cycles.
+- **Triggers wheel builds** (via `pypi-wheels.yml`); PyPI publication is currently a **manual step** — see [PyPI publication](#pypi-publication-manual) below.
+
+**How (UI):** Edit the pre-release → uncheck **"Set as a pre-release"** → click **"Update release"**.
+
+**How (CLI):**
+
+```bash
+gh release edit vx.y.z --repo StochasticTree/stochtree --prerelease=false --latest
+```
+
+`--latest` forces the "Latest" badge (and `/releases/latest` redirect) onto this release rather than relying on GitHub's auto-detection. A release cannot be both prerelease and latest, so these two flags work together. This does not affect which workflows fire — the `published`/`released` events trigger regardless.
+
+### PyPI publication (manual)
+
+After promotion, the `pypi-wheels.yml` run on the `published` event builds the per-platform **wheels** as artifacts (it does **not** build an sdist). Download the wheels, build the sdist locally, then upload both:
+
+```bash
+# 1. download the wheel artifacts from the release run
+# find the run id (event=release, workflow "Build Python Wheels for PyPI")
+gh run list --repo StochasticTree/stochtree --event release
+gh run download <run-id> --repo StochasticTree/stochtree --dir dist_wheels
+
+# 2. build the sdist locally (the CI workflow does not produce one)
+rm -rf dist && pipx run build --sdist
+
+# 3. upload wheels + sdist
+twine upload dist_wheels/**/*.whl dist/*.tar.gz
+```
 
-**How:** Edit the pre-release → uncheck **"Set as a pre-release"** → click **"Update release"**.
+Confirm `x.y.z` appears at https://pypi.org/project/stochtree/. Setting up [PyPI trusted publishing](https://docs.pypi.org/trusted-publishers/) (OIDC) will automate this in an upcoming release cycle.
 
 ---
 

configure

@@ -1,6 +1,6 @@
 #! /bin/sh
 # Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.72 for stochtree 0.4.5.
+# Generated by GNU Autoconf 2.72 for stochtree 0.4.6.9000.
 #
 #
 # Copyright (C) 1992-1996, 1998-2017, 2020-2023 Free Software Foundation,
@@ -600,8 +600,8 @@ MAKEFLAGS=
 # Identity of this package.
 PACKAGE_NAME='stochtree'
 PACKAGE_TARNAME='stochtree'
-PACKAGE_VERSION='0.4.5'
-PACKAGE_STRING='stochtree 0.4.5'
+PACKAGE_VERSION='0.4.6.9000'
+PACKAGE_STRING='stochtree 0.4.6.9000'
 PACKAGE_BUGREPORT=''
 PACKAGE_URL=''
 
@@ -1204,7 +1204,7 @@ if test "$ac_init_help" = "long"; then
   # Omit some internal or obsolete options to make the list less imposing.
   # This message is too long to be a string in the A/UX 3.1 sh.
   cat <<_ACEOF
-'configure' configures stochtree 0.4.5 to adapt to many kinds of systems.
+'configure' configures stochtree 0.4.6.9000 to adapt to many kinds of systems.
 
 Usage: $0 [OPTION]... [VAR=VALUE]...
 
@@ -1266,7 +1266,7 @@ fi
 
 if test -n "$ac_init_help"; then
   case $ac_init_help in
-     short | recursive ) echo "Configuration of stochtree 0.4.5:";;
+     short | recursive ) echo "Configuration of stochtree 0.4.6.9000:";;
    esac
   cat <<\_ACEOF
 
@@ -1334,7 +1334,7 @@ fi
 test -n "$ac_init_help" && exit $ac_status
 if $ac_init_version; then
   cat <<\_ACEOF
-stochtree configure 0.4.5
+stochtree configure 0.4.6.9000
 generated by GNU Autoconf 2.72
 
 Copyright (C) 2023 Free Software Foundation, Inc.
@@ -1371,7 +1371,7 @@ cat >config.log <<_ACEOF
 This file contains any messages produced by compilers while
 running configure, to aid debugging if configure makes a mistake.
 
-It was created by stochtree $as_me 0.4.5, which was
+It was created by stochtree $as_me 0.4.6.9000, which was
 generated by GNU Autoconf 2.72.  Invocation command line was
 
   $ $0$ac_configure_args_raw
@@ -2380,7 +2380,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
 # report actual input values of CONFIG_FILES etc. instead of their
 # values after options handling.
 ac_log="
-This file was extended by stochtree $as_me 0.4.5, which was
+This file was extended by stochtree $as_me 0.4.6.9000, which was
 generated by GNU Autoconf 2.72.  Invocation command line was
 
   CONFIG_FILES    = $CONFIG_FILES
@@ -2435,7 +2435,7 @@ ac_cs_config_escaped=`printf "%s\n" "$ac_cs_config" | sed "s/^ //; s/'/'\\\\\\\\
 cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
 ac_cs_config='$ac_cs_config_escaped'
 ac_cs_version="\\
-stochtree config.status 0.4.5
+stochtree config.status 0.4.6.9000
 configured by $0, generated by GNU Autoconf 2.72,
   with options \\"\$ac_cs_config\\"
 

configure.ac

@@ -3,7 +3,7 @@
 # https://github.com/microsoft/LightGBM/blob/master/R-package/configure.ac
 
 AC_PREREQ(2.69)
-AC_INIT([stochtree], [0.4.5], [], [stochtree], [])
+AC_INIT([stochtree], [0.4.6.9000], [], [stochtree], [])
 # Note: consider making version number dynamic as in 
 # https://github.com/microsoft/LightGBM/blob/195c26fc7b00eb0fec252dfe841e2e66d6833954/build-cran-package.sh
 

pyproject.toml

@@ -9,7 +9,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "stochtree"
-version = "0.4.5"
+version = "0.4.6-dev"
 dependencies = [
     "matplotlib",
     "numpy",