From 1edf9c57020be416e67697b91799f55231e83be6 Mon Sep 17 00:00:00 2001
From: patnr <patrick.n.raanes@gmail.com>
Date: Tue, 15 Sep 2026 09:52:58 +0200
Subject: [PATCH 1/4] Colab-first deps; vendor mpl-tools helpers; no build
 backend

Dependencies:
- pyproject.toml documents why Colab-preinstalled packages are unconstrained
  and where reproducibility comes from (uv.lock locally).
- colab_bootstrap.sh installs requirements-colab.txt with --no-deps: only what
  Colab lacks, never touching preinstalled (already imported) packages, so no
  runtime restart. Also no more PEP 517 build just to read a dependency list.
- Runtime deps now list what the notebooks import; jupyter moved to dev.
- Dropped jupyterlab~=3.6, ipympl, jupyter_nbextensions_configurator and the
  jupyter-server<2 pin they forced. Dev frontend is now notebook 7.
- No [build-system]; [tool.uv] package = false.

Vendoring:
- freshfig, nRowCol and is_notebook (was mpl_tools.is_notebook_or_qt) were the
  only things used from mpl-tools; rewritten in tools/plotting.py using only
  stable, public matplotlib/IPython API. mpl-tools kept breaking on Colab's
  matplotlib upgrades via its use of internals.

Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
---
 .pre-commit-config.yaml     |   2 +-
 colab_bootstrap.sh          |  60 ++++--
 notebooks/tools/geostat.py  |   3 +-
 notebooks/tools/plotting.py | 176 +++++++++--------
 pyproject.toml              |  94 ++++++---
 requirements-colab.txt      |  23 +++
 uv.lock                     | 385 +++++++++++-------------------------
 7 files changed, 343 insertions(+), 400 deletions(-)
 mode change 100644 => 100755 colab_bootstrap.sh
 create mode 100644 requirements-colab.txt

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 077520d..a2b39f9 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -35,7 +35,7 @@ repos:
           - tags
 
   - repo: https://github.com/mwouts/jupytext
-    rev: v1.15.1 # ensure equal to main venv
+    rev: v1.15.2 # keep equal to the `jupytext` pin in pyproject.toml
     hooks:
       - id: jupytext
         args: [--sync]
diff --git a/colab_bootstrap.sh b/colab_bootstrap.sh
old mode 100644
new mode 100755
index a49422d..4a77ea0
--- a/colab_bootstrap.sh
+++ b/colab_bootstrap.sh
@@ -1,42 +1,60 @@
 #!/usr/bin/env bash
 
-# Colab doesn't provide
-# - Auto-installing dependencies (neither pyproject.toml nor requirements.txt)
-# - Pre-loading data/modules (aside from the notebook itself)
-# This script takes care of the above by cloning the full (shallow) repo.
+# Bootstrap for Google Colab, invoked from the first code cell of each notebook:
+#
+#     !wget -qO- https://raw.githubusercontent.com/patnr/HistoryMatching/master/colab_bootstrap.sh | bash -s
+#
+# Colab does not auto-install a project's dependencies (no pyproject/requirements
+# support), nor does it fetch anything but the notebook itself. So this script
+# 1. shallow-clones the repo (or copies it from `--repo=PATH`, for tests),
+# 2. installs ONLY the packages Colab lacks, with `--no-deps`, so that nothing
+#    preinstalled (and already imported) gets touched, which would otherwise
+#    require a runtime restart. See requirements-colab.txt and pyproject.toml.
+# 3. copies the notebooks dir (incl. `tools/`) into the working directory.
+#
+# Options: `--debug`/`-v` for verbose output; `--branch=NAME` (default: master).
 
 main () {
     set -e
 
-    # Clear any existing REPO for a fresh git clone
+    # Clear any existing REPO for a fresh copy
     rm -rf REPO
 
-    # Download repo
-    URL=https://github.com/patnr/HistoryMatching.git
-    if [[ ! -d REPO ]]; then git clone --depth=1 $URL REPO; fi
-
-    # https://pythonspeed.com/articles/upgrade-pip/
-    pip install --upgrade pip
+    if [[ -n "$SRC" ]]; then
+        # Local checkout (used by tests/colab/smoke.sh)
+        mkdir REPO
+        tar -C "$SRC" --exclude=.git -cf - . | tar -C REPO -xf -
+    else
+        git clone --depth=1 --branch "$BRANCH" https://github.com/patnr/HistoryMatching.git REPO
+    fi
 
-    # Install dependencies (declared in REPO/pyproject.toml)
-    pip install ./REPO
+    # Install what Colab lacks. NB: no pip upgrade, no dependency resolution.
+    pip install --no-deps -r REPO/requirements-colab.txt
 
-    # Put repo contents (including hidden files) in PWD
+    # Put notebooks (including hidden files) in PWD
     shopt -s dotglob
     cp -r REPO/notebooks/* ./
 }
 
-# Only run if we're on colab
-if python -c "import google.colab" 2>/dev/null; then
-
-    # Use `bash -s -- --debug` to get verbose output
-    if echo $@ | grep -E -- '(--debug|-v)' > /dev/null ; then
+# Parse args
+SRC=""
+BRANCH="master"
+DEBUG=""
+for arg in "$@"; do
+    case "$arg" in
+        --repo=*)   SRC="${arg#--repo=}" ;;
+        --branch=*) BRANCH="${arg#--branch=}" ;;
+        --debug|-v) DEBUG=1 ;;
+    esac
+done
+
+# Only run if we're on Colab (the env var is also set in Colab's runtime image)
+if [[ -n "$COLAB_RELEASE_TAG" ]] || python -c "import google.colab" 2>/dev/null; then
+    if [[ -n "$DEBUG" ]]; then
         main
     else
-        # Quiet
         main > /dev/null 2>&1
     fi
-
     echo "Initialization for Colab done."
 else
     echo "Not running on Colab => Didn't do anything."
diff --git a/notebooks/tools/geostat.py b/notebooks/tools/geostat.py
index 0d2d576..8b5094e 100644
--- a/notebooks/tools/geostat.py
+++ b/notebooks/tools/geostat.py
@@ -3,9 +3,10 @@
 import numpy as np
 import scipy.linalg as sla
 from matplotlib import pyplot as plt
-from mpl_tools.misc import nRowCol
 from numpy.random import randn
 
+from tools.plotting import nRowCol
+
 
 def variogram_gauss(xx, r, n=0, a=1 / 3):
     """Compute the Gaussian variogram for the 1D points xx.
diff --git a/notebooks/tools/plotting.py b/notebooks/tools/plotting.py
index ad50cfb..ba9f875 100644
--- a/notebooks/tools/plotting.py
+++ b/notebooks/tools/plotting.py
@@ -2,18 +2,17 @@
 
 import copy
 import warnings
+from math import sqrt
 
 import ipywidgets as wg
 import matplotlib as mpl
-import mpl_tools
-import mpl_tools.place
 import numpy as np
 import struct_tools
+from IPython import get_ipython
 from IPython.display import display
 from matplotlib import pyplot as plt
 from matplotlib.gridspec import GridSpec
 from matplotlib.ticker import MaxNLocator, LogLocator
-from mpl_tools.misc import nRowCol
 from struct_tools import DotDict as Dict
 from minires.plotting import styles
 
@@ -58,10 +57,82 @@
 from matplotlib.colors import LogNorm, AsinhNorm  # noqa  # type: ignore
 
 
-def freshfig(*args, **kwargs):
-    if not kwargs.get("figsize", None):
-        kwargs["figsize"] = (8, 4)
-    return mpl_tools.place.freshfig(*args, **kwargs)
+# The following 3 helpers used to come from `mpl-tools` (also by patnr).
+# They were vendored (and reduced to what this repo uses) so that the tutorials
+# depend only on stable, public matplotlib/IPython API. This matters because
+# on Colab the base environment is outside our control (see pyproject.toml).
+
+
+def freshfig(num=None, figsize=None, sup=True, **kwargs):
+    """Like `plt.subplots(num=num, figsize=figsize, **kwargs)`, but re-using figures.
+
+    If a figure labelled `num` (a descriptive string, please) already exists,
+    it is *cleared*, not closed and re-opened. Thus its window keeps its
+    position and size on screen, which is what you want when re-running
+    the `.py` mirror of a notebook with `%run` in IPython (GUI backend).
+
+    The inline (Jupyter/Colab) backend does not show the figure label,
+    so there (if `sup`) the label is set as `fig.suptitle` instead.
+    """
+    if figsize is None:
+        figsize = (8, 4)
+    fig, ax = plt.subplots(num=num, figsize=figsize, clear=True, **kwargs)
+    if sup and isinstance(num, str) and "inline" in mpl.get_backend():
+        fig.suptitle(num)
+    return fig, ax
+
+
+def nRowCol(nTotal, figsize=None, axsize=None):
+    """Compute `(nrows, ncols)` such that `nTotal ≈ nrows*ncols`.
+
+    Takes into account the `figsize` and `axsize`, either of which
+    may be given as a tuple, or a number (the ratio width/height).
+    Defaults are taken from `mpl.rcParams`.
+
+    Examples
+    --------
+    >>> nRowCol(4)
+    {'nrows': 2, 'ncols': 2}
+    >>> nRowCol(4, (4, 1), (1, 1))
+    {'nrows': 1, 'ncols': 4}
+    >>> nRowCol(4, (4, 1), (4, 1))
+    {'nrows': 2, 'ncols': 2}
+    >>> nRowCol(12, (4, 3), (1, 1))
+    {'nrows': 3, 'ncols': 4}
+    """
+    if figsize is None:
+        figsize = mpl.rcParams["figure.figsize"]
+    if axsize is None:
+        rc = {k: mpl.rcParams["figure.subplot." + k] for k in ["bottom", "left", "right", "top"]}
+        axsize = (rc["right"] - rc["left"], rc["top"] - rc["bottom"])
+
+    def ratio(size):
+        try:
+            w, h = size
+            return w / h
+        except TypeError:
+            return size
+
+    ratio = ratio(figsize) / ratio(axsize)
+    nrows = round(sqrt(nTotal / ratio)) or 1
+    ncols = nTotal // nrows
+    if nrows * ncols < nTotal:  # since `//` rounds down
+        ncols += 1
+    return {"nrows": nrows, "ncols": ncols}
+
+
+def is_notebook():
+    """Detect a Jupyter-type frontend (local Jupyter, Colab, VS Code, nbclient, ...).
+
+    Returns `False` in plain Python and in terminal IPython.
+    Relies only on the shell class, which has been stable for a decade:
+    `ZMQInteractiveShell` for Jupyter kernels, `google.colab._shell.Shell` on Colab.
+    """
+    ip = get_ipython()
+    if ip is None:
+        return False
+    cls = type(ip)
+    return cls.__name__ == "ZMQInteractiveShell" or "colab" in cls.__module__
 
 
 def fields(
@@ -151,51 +222,28 @@ def fields(
 
 
 def init():
-    """Configure mpl.
-
-    ## On the choice of backend:
-
-    - In scripts, `Qt5Agg` is nice coz it (is interactive and) allows
-      programmatic (automatic) placement of figures on screen.
-    - In notebooks `%matplotib notebook` (nbAgg) is interactive,
-      so cooler than `%matplotlib inline`.
-    - On my local machine, `%matplotlib inline` always makes figures display
-      as string: <Figure size ...>, despite `plt.show()`, `plt.pause(0.1)`, etc.
-    - However, `%matplotlib widget/ipympl` ('module://ipympl.backend_nbagg')
-      is also interactive, and compatible with BOTH jupyter-notebook and -lab.
-      It may also be selected via `import ipympl`.
-    - Colab only supports `%matplotlib inline` (but could look into "plotly")
-      https://stackoverflow.com/a/64297121
-
-    ## On IPython magics vs `mpl.use()`:
-
-    The magics (like `%matplotlib notebook/ipympl`) set `plt.ion()` and some rcParams.
-    They could probably be used in a module via `get_ipython().run_line_magic()`
-    however, here I choose to instead use `mpl.use(...)` or `import ipympl`.
-    - Obsolete? If you do `import ipympl` BEFORE `import matplotlib.pyplot` then
-      the figures only display as the text string <Figure size ...>.
-    - If you do mpl.use("nbAgg") BEFORE `import matplotlib.pyplot` then
-      you must remember to do `plt.ion()` too.
-      PS: this "interactive" is not to be confused with "interactive backends".
-      PS: check status with `plt.isinteractive`.
-
-    ## About "run all (cells)":
-
-    On my Mac, the figures sometimes don't display, or are "inline" instead of "nbAgg".
-
-    ## About animation displaying twice:
-
-    The solution seems to be to split the creation and display cells, and using %%capture.
-    This worked both locally and on Colab.
-    - [Ref](https://stackoverflow.com/q/47138023)
-    - [Ref](https://stackoverflow.com/a/36685236)
-    On my Mac, `%matplotlib inline` did not have this issue, but plenty others (see above).
-    However, on Colab (i.e. `%matplotlib inline`), the animation still displayed double.
+    """Configure mpl (backend, rcParams).
+
+    ## Backend
+    In notebooks, we always use the "inline" backend, which is the default
+    of Jupyter kernels, and the only one supported by Colab. The interactive
+    alternatives (`%matplotlib widget`, i.e. `ipympl`, and `nbAgg`) were
+    dropped: they don't work on Colab, are slower and flicker when embedded
+    in `ipywidgets` controls, and testing a single backend is simpler.
+    NB: this means `init()` must not `mpl.use()` anything in notebooks.
+
+    In scripts (e.g. `%run HistoryMatch.py` in IPython), `Qt5Agg` is preferred
+    since it allows programmatic placement of figure windows. Otherwise
+    (e.g. on macOS without Qt) the default GUI backend is used, and figure
+    windows at least keep their placement across re-runs thanks to `freshfig`.
+
+    ## Animations displaying twice
+    Split the creation and display into separate cells, using `%%capture`.
+    Refs: <https://stackoverflow.com/q/47138023>, <https://stackoverflow.com/a/36685236>.
     """
-    if mpl_tools.is_notebook_or_qt:
+    if is_notebook():
         mpl.rc("animation", html="jshtml")
 
-        # mpl.rcParams["figure.figsize"] = [5, 3.5]
         # NB: Non-default figsize/fontsize may cause axis labels/titles
         # that do not fit within the figure, or trespass into the axes
         # (unless fixed by tight_layout, but that is sometimes not possible)
@@ -205,32 +253,6 @@ def init():
         mpl.rcParams.update({"legend.fontsize": "large"})
         mpl.rcParams["font.size"] = 11
 
-        try:
-            # Colab
-            import google.colab  # type: ignore  # noqa: F401
-            # [colab-specific adjustments]
-
-        except ImportError:
-            # Local Jupyter
-
-            # ipympl is nice but when embedded in ipywidget controls
-            # - it is a bit slower than inline
-            # - it flickers (in classic notebook, not jupyter-lab)
-            # Also it's nice to only have to test for one backend,
-            # i.e. the one that works on Colab
-            pass  # use "inline"
-
-            # try:
-            #     # Similar to `%matplotlib widget/ipympl`
-            #     # or `mpl.use('module://ipympl.backend_nbagg')`
-            #     # import ipympl  # type: ignore
-
-            # except ImportError:
-            #     pass  # use "inline"
-
-            #     # Similar to `%matplotlib notebook`:
-            #     # mpl.use("nbAgg")  # NB: must be installed!
-
     else:
         # Script run
         mpl.rcParams.update({"font.size": 10})
@@ -464,8 +486,8 @@ def ens_style(label, N=100):
     return style
 
 
-# NOTE: This uses IPython/jupyter widgets. Another solution, using interactive
-# mpl backends (=> not available on Colab), can be found in mpl_tools.
+# NOTE: This uses IPython/jupyter widgets (works on Colab), rather than
+# an interactive mpl backend (not available on Colab).
 def toggle_items(wrapped):
     """Include checkboxes/checkmarks to toggle plotted data series on/off."""
 
diff --git a/pyproject.toml b/pyproject.toml
index bdb29a9..ef0df33 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -5,51 +5,85 @@ description = "Tutorial on history matching and production optimisation."
 readme = "README.md"
 license = "MIT"
 authors = [{ name = "Patrick N. Raanes", email = "patrick.n.raanes@gmail.com" }]
+
+# ── Dependency policy ────────────────────────────────────────────────────────
+#
+# The tutorials must run with a single click on Google Colab, whose base
+# environment we do not control and which gets upgraded every few weeks.
+# That single fact shapes everything below. There are two install targets:
+#
+# (A) Local (`uv sync`): exact reproducibility comes from `uv.lock`,
+#     not from pins in this file. Refresh with `uv lock --upgrade`.
+#
+# (B) Colab (`colab_bootstrap.sh`): installs `requirements-colab.txt`
+#     with `pip install --no-deps`, i.e. it adds ONLY the packages Colab lacks,
+#     and never touches a preinstalled one. Reason: numpy/scipy/matplotlib/
+#     ipywidgets are already *imported* when a Colab kernel starts, so
+#     re-installing them (up- or downgrade) requires a runtime restart.
+#     Hence the constraints below on Colab-preinstalled packages must accept
+#     whatever Colab ships. In practice this means: no upper bounds here
+#     (our own `minires` carries `matplotlib<4`), and lower bounds only
+#     where the code demands them. If Colab's upgrades break us, we fix the
+#     code, not the pins -- and `tests/colab/` exists to catch that early.
+#
+# Consequently `pyproject.toml` and `requirements-colab.txt` must be kept in
+# sync by hand (they are short). The Colab smoke test fails loudly on drift
+# (ImportError for a missing package, or a mutated preinstalled package).
+#
+# Python: 3.12 (`.python-version`) because that is what Colab runs
+# (runtime 2026.08). Newer versions work too (`requires-python` is open),
+# but 3.12 is what gets tested.
+
 requires-python = ">=3.12"
 dependencies = [
-  # Pinned to a commit (rather than a release) -- bump as needed.
+  # Our own toy reservoir simulator. Pinned to a commit until the PyPI release,
+  # then this becomes `minires>=X.Y` (and `requirements-colab.txt` likewise).
+  # For local hacking: `uv pip install -e ${HOME}/path/MiniRes`
   "minires @ git+https://github.com/patnr/MiniRes.git@1b9f8d56010a",
-  # "Editable" mode: install with `uv pip install -e ${HOME}/path/MiniRes`
-  "jupyter",
-  "pathos",
+  # Preinstalled on Colab => deliberately unconstrained (see policy above).
+  "numpy",
+  "scipy",
+  "matplotlib",
+  "ipywidgets",
+  "ipython",
   "threadpoolctl",
-  "adjustText==0.8",
-  # NB: 0.4.0 uses `mpl.rcsetup.interactive_bk`, removed in matplotlib 3.11
-  # (and 0.4.1 has a `freshfig` bug) -- so this floor is load-bearing.
-  "mpl-tools>=0.4.2,<0.5",
-  # Used by the notebooks; used to arrive transitively, via TPFA-ResSim.
+  # NOT preinstalled on Colab => also listed in `requirements-colab.txt`.
+  # `pathos` (multiprocessing with dill pickling) drags in
+  # dill/multiprocess/pox/ppft, all pure-Python, so also cheap on Colab.
+  "pathos",
+  # Zero dependencies, by design (it is our own).
   "struct-tools",
+  # Label de-overlapping in `tools/utils.py`. Exact-pinned since it was added
+  # (2023, when 0.8 was current); the 1.x releases rewrote the algorithm and
+  # the pin has simply not been re-evaluated against them. Not preinstalled on
+  # Colab (only depends on numpy+matplotlib), so the exact pin is harmless there.
+  "adjustText==0.8",
 ]
 
 [dependency-groups]
+# Local-only tooling. Never installed on Colab, which has its own frontend.
 dev = [
-  # Extensions for classic notebook
-  "jupyter_nbextensions_configurator",
-  "jupyter-server<2.0.0",
-  # For jupyterlab
-  # NB: jupyterlab>=4 breaks complex widgets and throws errors in console.
-  # NB: `.python-version` pins 3.12, since `jupyterlab~=3.6` has no wheels for later versions.
-  "jupyterlab~=3.6",
+  # Notebook frontend (v7, i.e. built on JupyterLab 4). Classic notebook (v6)
+  # and `jupyterlab~=3.6` were dropped: they forced `jupyter-server<2` and
+  # Python 3.12, and doubled the surface to test. `ipympl` was also dropped:
+  # all notebooks use the inline backend (the only one that works on Colab).
+  "notebook",
+  # Executes notebooks headlessly (`tests/colab/run_nb.py`).
+  "nbclient",
+  # Keep in sync with the `jupytext` rev in `.pre-commit-config.yaml`.
   "jupytext~=1.15.2",
-  "ipympl~=0.9.3",
-  "ipython",
   "ipdb",
   "pre-commit",
   "ruff~=0.5.0",
 ]
 
-[build-system]
-requires = ["hatchling"]
-build-backend = "hatchling.build"
-
-# Needed for the `minires @ git+...` pin above.
-[tool.hatch.metadata]
-allow-direct-references = true
-
-# This "project" is just a dependency set (the notebooks are run in-place,
-# not imported), so the wheel ships no files.
-[tool.hatch.build.targets.wheel]
-bypass-selection = true
+# Not a package: nothing is imported from this project, the notebooks are run
+# in place. Hence no `[build-system]` (a PEP 517 build would only serve to
+# read the dependency list). Install with `uv sync`, or, for pip users,
+# `pip install -r requirements-colab.txt` is NOT the way (it is Colab-specific);
+# use `uv pip install -r pyproject.toml` or just `pip install uv && uv sync`.
+[tool.uv]
+package = false
 
 [tool.ruff]
 line-length = 100
diff --git a/requirements-colab.txt b/requirements-colab.txt
new file mode 100644
index 0000000..ba1a9c0
--- /dev/null
+++ b/requirements-colab.txt
@@ -0,0 +1,23 @@
+# Packages that Google Colab does NOT preinstall, and that the notebooks need.
+#
+# Installed by `colab_bootstrap.sh` with `pip install --no-deps -r <this>`.
+# `--no-deps` guarantees that pip never up/downgrades a package Colab already
+# ships (numpy, scipy, matplotlib, ipywidgets, tqdm, ...): those are already
+# imported when the kernel starts, so changing them would require a runtime
+# restart. The price is that transitive dependencies must be listed here by
+# hand. Drift shows up as an ImportError, which `tests/colab/smoke.sh` catches.
+#
+# Keep in sync with `pyproject.toml` (the policy is documented there).
+# Colab's current package list: https://github.com/googlecolab/backend-info
+
+# Pin must equal the one in pyproject.toml (until the PyPI release of minires).
+minires @ git+https://github.com/patnr/MiniRes.git@1b9f8d56010a
+struct-tools
+adjustText==0.8
+# pathos and its (pure-Python) dependencies. Colab ships dill and multiprocess
+# already; they are listed anyway so that this file does not depend on that.
+pathos
+dill
+multiprocess
+pox
+ppft
diff --git a/uv.lock b/uv.lock
index e3b474c..36d3704 100644
--- a/uv.lock
+++ b/uv.lock
@@ -19,35 +19,17 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/44/36/ac4a2dfefe115be67403bb8c622edf5b6adacbb3afd2ac921af37138ec1c/adjustText-0.8-py3-none-any.whl", hash = "sha256:6da99f9d739c496f79346753a3fcadb6354d8d09699cde112fed46cfb837d271", size = 9132, upload-time = "2023-02-17T10:54:26.116Z" },
 ]
 
-[[package]]
-name = "aiofiles"
-version = "22.1.0"
-source = { registry = "https://pypi.org/simple" }
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From 24eb76a4f063790914c035c7deb7e7ba140bfd33 Mon Sep 17 00:00:00 2001
From: patnr <patrick.n.raanes@gmail.com>
Date: Tue, 15 Sep 2026 09:53:58 +0200
Subject: [PATCH 2/4] Add Colab smoke tests (GitHub Actions + local)

Run inside Google's published Colab runtime image: bootstrap, check that no
preinstalled package changed (the restart hazard), execute both notebooks.
Monthly cron catches Colab's upgrades; also on PRs/pushes touching Colab files.

Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
---
 .github/workflows/colab-compat.yml | 44 +++++++++++++++++++++
 README.md                          | 61 +++++++++++++++++++++---------
 tests/colab/check_freeze.py        | 44 +++++++++++++++++++++
 tests/colab/run_nb.py              | 58 ++++++++++++++++++++++++++++
 tests/colab/smoke.sh               | 56 +++++++++++++++++++++++++++
 tests/colab/smoke_inner.sh         | 39 +++++++++++++++++++
 6 files changed, 284 insertions(+), 18 deletions(-)
 create mode 100644 .github/workflows/colab-compat.yml
 create mode 100644 tests/colab/check_freeze.py
 create mode 100644 tests/colab/run_nb.py
 create mode 100755 tests/colab/smoke.sh
 create mode 100755 tests/colab/smoke_inner.sh

diff --git a/.github/workflows/colab-compat.yml b/.github/workflows/colab-compat.yml
new file mode 100644
index 0000000..4117403
--- /dev/null
+++ b/.github/workflows/colab-compat.yml
@@ -0,0 +1,44 @@
+name: Colab compatibility
+
+# Runs the tutorials inside Google's published Colab runtime image
+# (which lags the live Colab runtime by a few weeks), checking that
+# - colab_bootstrap.sh installs cleanly,
+# - it modifies no preinstalled package (=> no "restart runtime" prompt),
+# - both notebooks execute end-to-end.
+# See tests/colab/ and the dependency policy in pyproject.toml.
+
+on:
+  workflow_dispatch:
+  schedule:
+    - cron: "0 8 1 * *" # 1st of every month: catches Colab's upgrades
+  push:
+    branches: [master]
+    paths:
+      - requirements-colab.txt
+      - colab_bootstrap.sh
+      - notebooks/**
+      - tests/colab/**
+      - .github/workflows/colab-compat.yml
+  pull_request:
+    paths:
+      - requirements-colab.txt
+      - colab_bootstrap.sh
+      - notebooks/**
+      - tests/colab/**
+      - .github/workflows/colab-compat.yml
+
+jobs:
+  colab:
+    runs-on: ubuntu-latest
+    timeout-minutes: 90
+    container:
+      image: us-docker.pkg.dev/colab-images/public/runtime:latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Smoke test (bootstrap, freeze diff, execute notebooks)
+        env:
+          REPO_DIR: ${{ github.workspace }}
+          SMOKE_MODE: local
+        run: bash tests/colab/smoke_inner.sh
diff --git a/README.md b/README.md
index e1e73bd..48d3940 100644
--- a/README.md
+++ b/README.md
@@ -18,24 +18,20 @@ Use this option for development, or if you simply want faster computations
 *You could instead download & unzip, but then you will
 have to manually download any later updates.*
 
-**Install** (Python >= 3.12) with either
+**Install** (Python >= 3.12) with
+[uv](https://docs.astral.sh/uv/getting-started/installation/),
+a single, cross-platform tool that also fetches Python for you:
 
-- [uv](https://docs.astral.sh/uv/getting-started/installation/) -- recommended:
-  a single, cross-platform tool that also fetches Python for you.
+```bash
+uv sync
+uv run jupyter notebook
+```
 
-  ```bash
-  uv sync
-  uv run jupyter notebook
-  ```
-
-- Or any other installer, e.g. `pip` inside an active environment
-  created by [venv](https://docs.python.org/3/library/venv.html),
-  [conda](https://www.anaconda.com/download), ... :
-
-  ```bash
-  pip install .
-  jupyter notebook
-  ```
+*Without uv:* this project is not a package (nothing is imported from it),
+so there is nothing to `pip install .`. Instead, in an active environment
+(venv, conda, ...) do `pip install uv && uv pip install -r pyproject.toml`.
+Or, if you already have the scientific stack, just add what
+`requirements-colab.txt` lists.
 
 The `jupyter notebook` command opens a file navigator in your web browser.
 Click on `notebooks/HistoryMatch.ipynb`.
@@ -44,8 +40,7 @@ Click on `notebooks/HistoryMatch.ipynb`.
 
 The dev tooling (jupytext, ruff, pre-commit, ...) lives in the `dev`
 [dependency group](https://peps.python.org/pep-0735/),
-which `uv sync` installs by default
-(with `pip`: `pip install --group dev`).
+which `uv sync` installs by default.
 
 I prefer to develop mostly in the format of standard python script,
 which is why each notebook corresponds to a `.py` file synced via [jupytext](https://jupytext.readthedocs.io/en/latest/).
@@ -56,6 +51,36 @@ then the notebooks will get synced with the `.py` files before committing.
 Linting (which is, as of now, just a suggestion) can be run with
 `ruff check --output-format=grouped`.
 
+### Dependencies and Colab
+
+The single-click Colab experience is the design constraint for dependencies:
+Colab's base environment is not ours to control and gets upgraded regularly,
+and re-installing anything it has already imported (numpy, matplotlib, ...)
+forces a runtime restart.
+Therefore `colab_bootstrap.sh` installs `requirements-colab.txt` with `--no-deps`,
+i.e. only what Colab lacks, while `pyproject.toml` leaves Colab-preinstalled
+packages unconstrained and `uv.lock` provides reproducibility locally.
+The full reasoning is documented in `pyproject.toml`.
+The two files must be kept in sync by hand.
+
+### Smoke tests
+
+Google publishes the Colab runtime image, so the Colab experience can be tested
+without Colab. This runs monthly (and on relevant pushes) on GitHub Actions,
+see `.github/workflows/colab-compat.yml`, which is the primary way to catch
+breakage from Colab's upgrades. The same test can be run locally
+(requires `podman` or `docker`; the image is large, see the script):
+
+```bash
+tests/colab/smoke.sh            # local checkout
+tests/colab/smoke.sh --remote   # exactly what students get (GitHub master)
+```
+
+It checks that the bootstrap installs cleanly, that it modifies no
+preinstalled package, and that both notebooks execute end-to-end.
+The notebook runner also works locally, without the image:
+`uv run tests/colab/run_nb.py notebooks/HistoryMatch.ipynb --skip-bootstrap`.
+
 ## Contributors
 
 This work has been developed by *Patrick N. Raanes*, researcher at *NORCE*.
diff --git a/tests/colab/check_freeze.py b/tests/colab/check_freeze.py
new file mode 100644
index 0000000..bf4158a
--- /dev/null
+++ b/tests/colab/check_freeze.py
@@ -0,0 +1,44 @@
+"""Compare two `pip freeze` outputs: fail if any pre-existing package changed.
+
+Usage: check_freeze.py BEFORE.txt AFTER.txt
+
+Rationale: on Colab, packages present at kernel start are already imported;
+re-installing them would require a runtime restart. `colab_bootstrap.sh` must
+therefore only *add* packages. This check makes that contract testable.
+"""
+
+import sys
+
+
+def parse(path):
+    pkgs = {}
+    for line in open(path):
+        line = line.strip()
+        if not line or line.startswith("#"):
+            continue
+        for sep in ("==", " @ "):
+            if sep in line:
+                name, ver = line.split(sep, 1)
+                break
+        else:
+            name, ver = line, ""
+        pkgs[name.lower().replace("_", "-")] = ver
+    return pkgs
+
+
+def main(before_path, after_path):
+    before, after = parse(before_path), parse(after_path)
+    changed = {k: (v, after.get(k)) for k, v in before.items() if after.get(k) != v}
+    added = sorted(set(after) - set(before))
+    print(f"Added packages ({len(added)}):", ", ".join(added) or "none")
+    if changed:
+        print("FAIL: preinstalled packages were modified (=> Colab would need a restart):")
+        for k, (old, new) in sorted(changed.items()):
+            print(f"  {k}: {old} -> {new if new is not None else '(removed)'}")
+        return 1
+    print("OK: no preinstalled package was modified.")
+    return 0
+
+
+if __name__ == "__main__":
+    sys.exit(main(*sys.argv[1:3]))
diff --git a/tests/colab/run_nb.py b/tests/colab/run_nb.py
new file mode 100644
index 0000000..9fc1ec2
--- /dev/null
+++ b/tests/colab/run_nb.py
@@ -0,0 +1,58 @@
+"""Execute a notebook headlessly (via `nbclient`), as a smoke test.
+
+Usage: run_nb.py NOTEBOOK.ipynb [--timeout SECONDS] [--skip-bootstrap] [--out PATH]
+
+- `--skip-bootstrap` removes the cell that runs `colab_bootstrap.sh` (so that
+  a test of a local checkout does not fetch and install `master` on top).
+- Fails (exit 1) on the first cell error, printing that cell's source and traceback.
+
+Runs both locally (`uv run tests/colab/run_nb.py notebooks/HistoryMatch.ipynb`)
+and inside the Colab runtime image (see smoke.sh), which ships `nbclient`.
+"""
+
+import argparse
+import sys
+import time
+from pathlib import Path
+
+import nbformat
+from nbclient import NotebookClient
+from nbclient.exceptions import CellExecutionError
+
+
+def main():
+    ap = argparse.ArgumentParser()
+    ap.add_argument("notebook", type=Path)
+    ap.add_argument("--timeout", type=int, default=1800, help="per-cell timeout (s)")
+    ap.add_argument("--skip-bootstrap", action="store_true")
+    ap.add_argument("--out", type=Path, help="write the executed notebook here")
+    args = ap.parse_args()
+
+    nb = nbformat.read(args.notebook, as_version=4)
+    if args.skip_bootstrap:
+        n = len(nb.cells)
+        nb.cells = [c for c in nb.cells if "colab_bootstrap.sh" not in c.source]
+        print(f"Skipped {n - len(nb.cells)} bootstrap cell(s).")
+
+    client = NotebookClient(
+        nb,
+        timeout=args.timeout,
+        kernel_name="python3",
+        resources={"metadata": {"path": str(args.notebook.parent)}},
+    )
+    t0 = time.time()
+    try:
+        client.execute()
+    except CellExecutionError as e:
+        print(f"FAIL: {args.notebook} after {time.time() - t0:.0f}s\n{e}")
+        return 1
+    finally:
+        if args.out:
+            nbformat.write(nb, args.out)
+    ncode = sum(c.cell_type == "code" for c in nb.cells)
+    print(f"OK: {args.notebook}: {ncode} code cells in {time.time() - t0:.0f}s")
+    return 0
+
+
+if __name__ == "__main__":
+    sys.exit(main())
diff --git a/tests/colab/smoke.sh b/tests/colab/smoke.sh
new file mode 100755
index 0000000..2ab3fc6
--- /dev/null
+++ b/tests/colab/smoke.sh
@@ -0,0 +1,56 @@
+#!/usr/bin/env bash
+# Smoke-test the tutorials inside Google's published Colab runtime image,
+# LOCALLY. The same test runs monthly on GitHub Actions
+# (.github/workflows/colab-compat.yml), which is the primary way to run it:
+# native x86-64 and a fast network. Use this script when you need to iterate
+# without pushing.
+#
+#   tests/colab/smoke.sh                  # local checkout, both notebooks
+#   tests/colab/smoke.sh --remote         # what students get: bootstrap from GitHub master
+#   SMOKE_NOTEBOOKS=HistoryMatch.ipynb tests/colab/smoke.sh
+#   COLAB_IMAGE=us-docker.pkg.dev/colab-images/public/runtime:<tag> tests/colab/smoke.sh
+#
+# Checks (see smoke_inner.sh): the bootstrap runs, it modifies no preinstalled
+# package (=> no "restart runtime"), and every notebook executes without error.
+#
+# The image is x86-64 and ~23 GB compressed (it is the GPU image: CUDA, torch,
+# TF, ...), so the first run takes a while; later runs use the cached image.
+# On Apple silicon it runs emulated (Rosetta via `podman machine`), i.e. slowly.
+# Tags: `latest`, or dated ones like `release-colab_20250925-060051_RC00`;
+# list with `podman search --list-tags us-docker.pkg.dev/colab-images/public/runtime`.
+# Note the public image lags Colab's actual runtime by a few weeks; for what
+# students *currently* have, see https://github.com/googlecolab/backend-info .
+set -euo pipefail
+
+IMAGE=${COLAB_IMAGE:-us-docker.pkg.dev/colab-images/public/runtime:latest}
+ENGINE=${CONTAINER_ENGINE:-$(command -v podman || command -v docker)}
+REPO=$(cd "$(dirname "$0")/../.." && pwd)
+
+MODE=local
+for arg in "$@"; do
+    case "$arg" in
+        --remote) MODE=remote ;;
+        *) echo "Unknown arg: $arg"; exit 2 ;;
+    esac
+done
+
+# The repo is copied into the container rather than bind-mounted: it is a few
+# MB, and bind mounts are unreliable in some `podman machine` setups
+# (e.g. "statfs ...: connection refused" with the libkrun provider on macOS).
+name=hm-colab-smoke-$$
+staging=$(mktemp -d)
+trap '"$ENGINE" rm -f "$name" >/dev/null 2>&1; rm -rf "$staging"' EXIT
+
+mkdir "$staging/repo"
+tar -C "$REPO" --exclude=.git --exclude=.claude --exclude=.ipynb_checkpoints \
+    --exclude=.ruff_cache --exclude=.pytest_cache -cf - . | tar -C "$staging/repo" -xf -
+
+"$ENGINE" create --name "$name" --platform linux/amd64 \
+    -e REPO_DIR=/repo \
+    -e SMOKE_MODE="$MODE" \
+    -e SMOKE_BRANCH="${SMOKE_BRANCH:-master}" \
+    -e SMOKE_NOTEBOOKS="${SMOKE_NOTEBOOKS:-HistoryMatch.ipynb Optimise.ipynb}" \
+    -e SMOKE_TIMEOUT="${SMOKE_TIMEOUT:-1800}" \
+    --entrypoint bash "$IMAGE" /repo/tests/colab/smoke_inner.sh >/dev/null
+"$ENGINE" cp "$staging/repo" "$name":/repo
+"$ENGINE" start --attach "$name"
diff --git a/tests/colab/smoke_inner.sh b/tests/colab/smoke_inner.sh
new file mode 100755
index 0000000..5d3ccd7
--- /dev/null
+++ b/tests/colab/smoke_inner.sh
@@ -0,0 +1,39 @@
+#!/usr/bin/env bash
+# Runs INSIDE the Colab runtime image, either on GitHub Actions
+# (.github/workflows/colab-compat.yml) or locally via smoke.sh.
+#
+# Env: REPO_DIR (checkout of this repo, default /repo),
+#      SMOKE_MODE=local|remote (default local), SMOKE_BRANCH (remote mode),
+#      SMOKE_NOTEBOOKS (default: both), SMOKE_TIMEOUT (per cell, default 1800).
+set -euo pipefail
+REPO_DIR=${REPO_DIR:-/repo}
+
+MODE=${SMOKE_MODE:-local}
+NOTEBOOKS=${SMOKE_NOTEBOOKS:-"HistoryMatch.ipynb Optimise.ipynb"}
+TIMEOUT=${SMOKE_TIMEOUT:-1800}
+
+mkdir -p /content && cd /content
+echo "== Image: ${COLAB_RELEASE_TAG:-unknown}  |  $(python --version)  |  $(which python) $(which pip)"
+echo "== Mode: $MODE"
+
+pip freeze > /tmp/before.txt
+
+echo "== 1/3 bootstrap"
+if [[ "$MODE" == remote ]]; then
+    remote=https://raw.githubusercontent.com/patnr/HistoryMatching
+    wget -qO- "$remote/${SMOKE_BRANCH:-master}/colab_bootstrap.sh" | bash -s -- --debug --branch="${SMOKE_BRANCH:-master}"
+else
+    bash "$REPO_DIR/colab_bootstrap.sh" --debug --repo="$REPO_DIR"
+fi
+
+echo "== 2/3 preinstalled packages untouched?"
+pip freeze > /tmp/after.txt
+python "$REPO_DIR/tests/colab/check_freeze.py" /tmp/before.txt /tmp/after.txt
+
+echo "== 3/3 execute notebooks"
+skip=""; [[ "$MODE" == local ]] && skip="--skip-bootstrap"
+status=0
+for nb in $NOTEBOOKS; do
+    python "$REPO_DIR/tests/colab/run_nb.py" "$nb" --timeout "$TIMEOUT" $skip || status=1
+done
+exit $status

From c1d9add51f7eec0ba234fafd9907f984da41284f Mon Sep 17 00:00:00 2001
From: patnr <patrick.n.raanes@gmail.com>
Date: Tue, 15 Sep 2026 11:21:46 +0200
Subject: [PATCH 3/4] Depend on minires 0.3.0 from PyPI, pinned to the minor

`minires~=0.3.0` replaces the git-commit pin, in `pyproject.toml`,
`requirements-colab.txt` and the lockfile. minires is 0.x, so a minor bump
may break the API; the pin therefore advances deliberately, with the
notebooks checked against the new version.

Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
---
 pyproject.toml         | 17 +++++++++++------
 requirements-colab.txt |  4 ++--
 uv.lock                | 16 +++++++++++-----
 3 files changed, 24 insertions(+), 13 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index ef0df33..c69fd2e 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -36,10 +36,12 @@ authors = [{ name = "Patrick N. Raanes", email = "patrick.n.raanes@gmail.com" }]
 
 requires-python = ">=3.12"
 dependencies = [
-  # Our own toy reservoir simulator. Pinned to a commit until the PyPI release,
-  # then this becomes `minires>=X.Y` (and `requirements-colab.txt` likewise).
-  # For local hacking: `uv pip install -e ${HOME}/path/MiniRes`
-  "minires @ git+https://github.com/patnr/MiniRes.git@1b9f8d56010a",
+  # Our own toy reservoir simulator, from PyPI since its 0.3.0 (2026-09-15).
+  # Pinned to the minor: `minires` is 0.x, so a minor bump may break the API
+  # (keep `requirements-colab.txt` in step). An unreleased snapshot is
+  # `"minires @ git+https://github.com/patnr/MiniRes.git@<hash>"`; for local
+  # hacking, `uv pip install -e ${HOME}/path/MiniRes`.
+  "minires~=0.3.0",
   # Preinstalled on Colab => deliberately unconstrained (see policy above).
   "numpy",
   "scipy",
@@ -68,8 +70,11 @@ dev = [
   # Python 3.12, and doubled the surface to test. `ipympl` was also dropped:
   # all notebooks use the inline backend (the only one that works on Colab).
   "notebook",
-  # Executes notebooks headlessly (`tests/colab/run_nb.py`).
-  "nbclient",
+  # `tests/colab/run_nb.py` executes notebooks headlessly with these two
+  # (deliberately not nbclient, see its docstring). Both come with `notebook`
+  # anyway, and Colab ships them.
+  "jupyter_client",
+  "nbformat",
   # Keep in sync with the `jupytext` rev in `.pre-commit-config.yaml`.
   "jupytext~=1.15.2",
   "ipdb",
diff --git a/requirements-colab.txt b/requirements-colab.txt
index ba1a9c0..7366e0f 100644
--- a/requirements-colab.txt
+++ b/requirements-colab.txt
@@ -10,8 +10,8 @@
 # Keep in sync with `pyproject.toml` (the policy is documented there).
 # Colab's current package list: https://github.com/googlecolab/backend-info
 
-# Pin must equal the one in pyproject.toml (until the PyPI release of minires).
-minires @ git+https://github.com/patnr/MiniRes.git@1b9f8d56010a
+# Pin must equal the one in pyproject.toml.
+minires~=0.3.0
 struct-tools
 adjustText==0.8
 # pathos and its (pure-Python) dependencies. Colab ships dill and multiprocess
diff --git a/uv.lock b/uv.lock
index 36d3704..2b6d30e 100644
--- a/uv.lock
+++ b/uv.lock
@@ -695,8 +695,9 @@ dependencies = [
 [package.dev-dependencies]
 dev = [
     { name = "ipdb" },
+    { name = "jupyter-client" },
     { name = "jupytext" },
-    { name = "nbclient" },
+    { name = "nbformat" },
     { name = "notebook" },
     { name = "pre-commit" },
     { name = "ruff" },
@@ -708,7 +709,7 @@ requires-dist = [
     { name = "ipython" },
     { name = "ipywidgets" },
     { name = "matplotlib" },
-    { name = "minires", git = "https://github.com/patnr/MiniRes.git?rev=1b9f8d56010a" },
+    { name = "minires", specifier = "~=0.3.0" },
     { name = "numpy" },
     { name = "pathos" },
     { name = "scipy" },
@@ -719,8 +720,9 @@ requires-dist = [
 [package.metadata.requires-dev]
 dev = [
     { name = "ipdb" },
+    { name = "jupyter-client" },
     { name = "jupytext", specifier = "~=1.15.2" },
-    { name = "nbclient" },
+    { name = "nbformat" },
     { name = "notebook" },
     { name = "pre-commit" },
     { name = "ruff", specifier = "~=0.5.0" },
@@ -1434,14 +1436,18 @@ wheels = [
 
 [[package]]
 name = "minires"
-version = "0.2.0"
-source = { git = "https://github.com/patnr/MiniRes.git?rev=1b9f8d56010a#1b9f8d56010a8c1cd36b65481b2a0d81c094bf0f" }
+version = "0.3.0"
+source = { registry = "https://pypi.org/simple" }
 dependencies = [
     { name = "matplotlib" },
     { name = "scipy" },
     { name = "struct-tools" },
     { name = "tqdm" },
 ]
+sdist = { url = "https://files.pythonhosted.org/packages/35/95/45fe49d0e8fd79f7efe1ed9e730935e4ed3ab9147651f4fd3027051060b7/minires-0.3.0.tar.gz", hash = "sha256:858b91e089ac25fe9df002d30e71e8d1f1d8c3d51134d7f598af33edaba7dd47", size = 63406, upload-time = "2026-09-15T08:37:23.147Z" }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/7c/94/e15c1963ff7026bd0dbbf978e421054ee66cecaa6bf8cd1eba9aebda1116/minires-0.3.0-py3-none-any.whl", hash = "sha256:fdb7f331fc1606d8b4e9efc2b9804c183a3dc5ad99cfe84d9562abb52a4f0fcf", size = 67341, upload-time = "2026-09-15T08:37:21.882Z" },
+]
 
 [[package]]
 name = "mistune"

From 33850269bd275c63b528449221309d879b4abf1e Mon Sep 17 00:00:00 2001
From: patnr <patrick.n.raanes@gmail.com>
Date: Tue, 15 Sep 2026 11:23:31 +0200
Subject: [PATCH 4/4] Smoke tests: notebook runner on jupyter_client instead of
 nbclient

nbclient's asyncio loop intermittently misses the execute-reply of cells
that emit a burst of ipywidgets comm messages (our interact/toggle_items
cells), stalling for the full per-cell timeout ~50% of the time. Seen with
nbclient 0.11, jupyter_client 8.10, pyzmq 25-27, ipykernel 6 and 7.
The blocking client polls synchronously and is unaffected (8/8 fast).
Also: -v prints each cell with its duration; timeouts are failures.

Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
---
 tests/colab/run_nb.py | 97 ++++++++++++++++++++++++++++++++++---------
 1 file changed, 78 insertions(+), 19 deletions(-)

diff --git a/tests/colab/run_nb.py b/tests/colab/run_nb.py
index 9fc1ec2..bf362b1 100644
--- a/tests/colab/run_nb.py
+++ b/tests/colab/run_nb.py
@@ -1,13 +1,21 @@
-"""Execute a notebook headlessly (via `nbclient`), as a smoke test.
+"""Execute a notebook headlessly, as a smoke test.
 
-Usage: run_nb.py NOTEBOOK.ipynb [--timeout SECONDS] [--skip-bootstrap] [--out PATH]
+Usage: run_nb.py NOTEBOOK.ipynb [--timeout SECONDS] [--skip-bootstrap] [--out PATH] [-v]
 
 - `--skip-bootstrap` removes the cell that runs `colab_bootstrap.sh` (so that
   a test of a local checkout does not fetch and install `master` on top).
-- Fails (exit 1) on the first cell error, printing that cell's source and traceback.
+- Fails (exit 1) on the first cell error or timeout, printing that cell's source.
+- `-v` prints each code cell (index, first line, duration) as it runs.
 
 Runs both locally (`uv run tests/colab/run_nb.py notebooks/HistoryMatch.ipynb`)
-and inside the Colab runtime image (see smoke.sh), which ships `nbclient`.
+and inside the Colab runtime image (see smoke.sh).
+
+Why not `nbclient` (or `jupyter nbconvert --execute`, `papermill`, which wrap it)?
+Its asyncio message loop intermittently misses the execute-reply of cells that
+emit a burst of ipywidgets comm messages (our `interact`/`toggle_items` cells),
+so such cells stall for the full per-cell timeout, ~50% of the time (seen 2026-09
+with nbclient 0.11, jupyter_client 8.10, pyzmq 25-27, ipykernel 6 and 7).
+`jupyter_client`'s blocking client polls synchronously and does not have this.
 """
 
 import argparse
@@ -16,8 +24,47 @@
 from pathlib import Path
 
 import nbformat
-from nbclient import NotebookClient
-from nbclient.exceptions import CellExecutionError
+from jupyter_client.manager import start_new_kernel
+from nbformat.v4 import output_from_msg
+
+
+class CellFailed(Exception):
+    pass
+
+
+def run_cell(kc, cell, timeout):
+    """Execute one code cell; collect its outputs; raise `CellFailed` on error/timeout."""
+    msg_id = kc.execute(cell.source)
+    cell.outputs = []
+    deadline = time.monotonic() + timeout
+    reply = idle = False
+    while not (reply and idle):
+        remaining = deadline - time.monotonic()
+        if remaining <= 0:
+            raise CellFailed(f"Timed out after {timeout}s")
+        # Drain iopub (outputs, status), then check for the shell reply.
+        try:
+            msg = kc.get_iopub_msg(timeout=min(remaining, 0.1))
+        except Exception:  # queue.Empty
+            msg = None
+        if msg and msg["parent_header"].get("msg_id") == msg_id:
+            mt = msg["msg_type"]
+            if mt == "status":
+                idle = msg["content"]["execution_state"] == "idle"
+            elif mt in ("stream", "display_data", "execute_result", "error"):
+                cell.outputs.append(output_from_msg(msg))
+            elif mt == "clear_output":
+                cell.outputs = []
+        if not reply:
+            try:
+                r = kc.get_shell_msg(timeout=0)
+            except Exception:
+                r = None
+            if r and r["parent_header"].get("msg_id") == msg_id:
+                reply = True
+                if r["content"]["status"] == "error":
+                    c = r["content"]
+                    raise CellFailed(f"{c.get('ename')}: {c.get('evalue')}\n" + "\n".join(c.get("traceback", [])))
 
 
 def main():
@@ -26,6 +73,7 @@ def main():
     ap.add_argument("--timeout", type=int, default=1800, help="per-cell timeout (s)")
     ap.add_argument("--skip-bootstrap", action="store_true")
     ap.add_argument("--out", type=Path, help="write the executed notebook here")
+    ap.add_argument("-v", "--verbose", action="store_true", help="print each cell as it runs")
     args = ap.parse_args()
 
     nb = nbformat.read(args.notebook, as_version=4)
@@ -34,24 +82,35 @@ def main():
         nb.cells = [c for c in nb.cells if "colab_bootstrap.sh" not in c.source]
         print(f"Skipped {n - len(nb.cells)} bootstrap cell(s).")
 
-    client = NotebookClient(
-        nb,
-        timeout=args.timeout,
-        kernel_name="python3",
-        resources={"metadata": {"path": str(args.notebook.parent)}},
-    )
+    km, kc = start_new_kernel(kernel_name="python3", cwd=str(args.notebook.parent.resolve()))
     t0 = time.time()
+    status = 0
     try:
-        client.execute()
-    except CellExecutionError as e:
-        print(f"FAIL: {args.notebook} after {time.time() - t0:.0f}s\n{e}")
-        return 1
+        for i, cell in enumerate(nb.cells):
+            if cell.cell_type != "code":
+                continue
+            if args.verbose:
+                head = cell.source.strip().splitlines()[0][:70] if cell.source.strip() else ""
+                print(f"[{i:3}] {head}", end=" ", flush=True)
+            t1 = time.time()
+            try:
+                run_cell(kc, cell, args.timeout)
+            except CellFailed as e:
+                print(f"\nFAIL: {args.notebook} at cell {i} after {time.time() - t0:.0f}s: {e}")
+                print("-" * 19 + f"\n{cell.source}\n" + "-" * 19)
+                status = 1
+                break
+            if args.verbose:
+                print(f"{time.time() - t1:6.1f}s", flush=True)
     finally:
+        kc.stop_channels()
+        km.shutdown_kernel(now=True)
         if args.out:
             nbformat.write(nb, args.out)
-    ncode = sum(c.cell_type == "code" for c in nb.cells)
-    print(f"OK: {args.notebook}: {ncode} code cells in {time.time() - t0:.0f}s")
-    return 0
+    if status == 0:
+        ncode = sum(c.cell_type == "code" for c in nb.cells)
+        print(f"OK: {args.notebook}: {ncode} code cells in {time.time() - t0:.0f}s")
+    return status
 
 
 if __name__ == "__main__":