Unit-test results depend on the Python version: unbounded upper pins let 3.12 resolve dependencies CI never sees · Issue #9069 · Project-MONAI/MONAI · GitHub
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Unit-test results depend on the Python version: unbounded upper pins let 3.12 resolve dependencies CI never sees #9069

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Unit-test results depend on the Python version: unbounded upper pins let 3.12 resolve dependencies CI never sees#9069

Description

@hjmjohnson
hjmjohnson
opened on Aug 22, 2026

Describe the bug

Whether the unit-test suite passes depends on which Python version the environment was built with, because [project.optional-dependencies].all has no upper bounds. Several dependencies have moved to requires-python >= 3.11 or >= 3.12, so a Python 3.10 environment simply cannot reach the releases that break MONAI, while a 3.12 environment installs them by default.

CI pins PYTHON_VER1: '3.10' and uses it for static-checks and full-dep, so CI never resolves the versions that fail. A contributor following CONTRIBUTING.md on a current interpreter does.

To Reproduce

uv venv --python 3.12 /tmp/env312 && VIRTUAL_ENV=/tmp/env312 uv pip install -e ".[all,testing]"
uv venv --python 3.10 /tmp/env310 && VIRTUAL_ENV=/tmp/env310 uv pip install -e ".[all,testing]"
./runtests.sh -u --net --coverage

What each interpreter resolves, from the same unbounded specifiers:

dependency Python 3.12 Python 3.10 why 3.10 cannot reach it
zarr 3.3.0 2.18.3 requires-python >= 3.12
scipy 1.18.1 1.15.3 requires-python >= 3.12
matplotlib 3.11.1 3.10.9 requires-python >= 3.11

Full suite, unmodified dev (c1240a2d4), Python 3.12: 18196 tests, 15 failures, 26 errors. Rebuilding the same tree on Python 3.10 clears five of the seven affected modules.

Which modules fail on 3.12 and why
module cause 3.10
tests.inferers.test_zarr_avg_merger (20 errors) zarr 3.3.0: ValueError: True is not a valid chunk input. Use chunks=None or chunks="auto" ... from zarr/core/chunk_grids.py:781 passes
tests.metrics.test_compute_fid_metric scipy 1.18 removed disp from scipy.linalg.sqrtm; monai/metrics/fid.py:85 calls sqrtm(..., disp=False) and unpacks two return values passes
tests.data.test_threadcontainer matplotlib baseline-image comparison, RMS 23.6 vs tolerance 0.05 (the baseline PNG dates from 2021) passes
tests.visualize.utils.test_matshow3d same passes
tests.transforms.test_orientation 'LIP' != 'LPS', 'RSP' != 'RAS' passes
tests.data.test_nifti_rw, tests.data.test_image_rw unrelated — a genuine bug, filed separately as #9068 still fails

Note the zarr failure here is not the one in #8476 (compressor cannot be used for arrays with zarr_format 3); zarr 3.3.0 also rejects chunks=True. Related: #8380, #8459, #8476.

QUICKTEST=True, which full-dep sets, does not skip any of these — I checked. CI avoids them purely through the Python pin.

torch has the same shape of gap: torch>=2.8.0 is unbounded, while CI tests 2.8.0–2.11.0 (PYTORCH_VER1..PYTORCH_VER4). A fresh environment installs 2.13.0, two minor versions past anything exercised.

Expected behavior

A contributor who follows CONTRIBUTING.md should get an environment where the suite passes, or a clear failure at install time — not green-or-red depending on the interpreter they happened to use.

Additional context

Two directions, not mutually exclusive:

  1. Bound what is known to break. Upper caps for zarr, scipy and matplotlib state the supported range explicitly instead of leaving it to interpreter-driven resolution. This is bookkeeping and it goes stale, but it makes the constraint visible.
  2. Test a modern Python. The min-dep matrix covers 3.10–3.13 with pinned torch, but full-dep — the job that installs [all] — runs only PYTHON_VER1 (3.10). A full-dep leg on PYTHON_VER3/PYTHON_VER4 would surface these at the same time contributors hit them, rather than after the fact.

The matplotlib case may want handling on its own terms: a 2021 baseline PNG compared at 0.05 tolerance will drift with any renderer change, independent of pinning policy.

Activity

  1. agourakis82 commented on Sep 29, 2026

    @agourakis82
    agourakis82
    on Sep 29, 2026

    AI-assisted proposal (Codex). I would be happy to take a small first step on CI observability: an Ubuntu/Python 3.12 job that installs .[all,testing] and records the resolved dependency versions, initially informational so the known compatibility failures do not block unrelated PRs. This would leave the existing Python 3.10 full-dep test matrix and package bounds unchanged; it would not close this issue or claim 3.12 test compatibility. Follow-up fixes and a required 3.12 full-dep test leg could be handled separately. Would maintainers prefer this narrow dependency-resolution step, or should the first PR target a different part of the issue?

  2. Talhax55z commented on Oct 1, 2026

    @Talhax55z
    Talhax55z
    on Oct 1, 2026
    Contributor

    Since #9076 and #9077 fix the scipy and zarr breakages directly, would an upper cap on torch (≤ tested 2.11 range) be a useful standalone PR here? Happy to take just that piece.

  3. ericspod
    added a commit that references this issue on Oct 12, 2026

    Fix FID metric for scipy >= 1.18: sqrtm no longer accepts disp (#9076)

    03e208f

  4. ericspod commented on Oct 13, 2026

    @ericspod
    ericspod
    on Oct 13, 2026
    Member

    Hi @Talhax55z we will be updating the versions of libraries being tested soon when we drop Python 3.10 support and I can look into if we need to fix versions then.

  5. ericspod
    added this to MONAI v1.7on Oct 13, 2026
  6. github-project-automation
    moved this to Not Yet Included in MONAI v1.7on Oct 13, 2026
  7. ericspod
    moved this from Not Yet Included to In progress in MONAI v1.7on Oct 13, 2026

  8. Talhax55z commented on Oct 13, 2026

    @Talhax55z
    Talhax55z
    on Oct 13, 2026
    Contributor

    Hi @ericspod thanks
    And secondly can you assign some issues to me ? I am willing Tom contribute but can't find any if there is any abandoned or new issue i will love to solve it

  9. ericspod
    added a commit that references this issue on Oct 13, 2026

    Fix ZarrAvgMerger under zarr 3.3: map chunks=True to auto-chunking (#…

    64e6f7e

  10. ericspod commented on Oct 14, 2026

    @ericspod
    ericspod
    on Oct 14, 2026
    Member

    9. Hi @ericspod thanks
    And secondly can you assign some issues to me ? I am willing Tom contribute but can't find any if there is any abandoned or new issue i will love to solve it

    We do have #9162 to remove the MMAR code in places. These functions should be marked as deprecated with one specifically being disabled as well for security concerns. If you wanted to propose a PR for that one I can review in time, thanks.

  11. ericspod commented on Oct 14, 2026

    @ericspod
    ericspod
    on Oct 14, 2026
    Member

    @Talhax55z you can also have a look at #9174 to figure out how to use ruff format to get the same results as black so we don't modify 300 files.

  12. Talhax55z commented on Oct 14, 2026

    @Talhax55z
    Talhax55z
    on Oct 14, 2026
    Contributor

    @ericspod
    thanks for trusting me i will look into this issue, open a pr when everything is ready
    thankss!!!

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