Release 0.6.0: changelog + version bump

Bump brainstat.__version__ to 0.6.0 and add a project CHANGELOG.md
covering the work landed in #378 / #379 / #380 / #381.

This release re-greens CI, fixes a cluster of correctness bugs in the
statistics core, adds the FreeSurfer Destrieux atlas to
fetch_parcellation, hardens the Neurosynth fetcher, and adopts the
literature-aligned (high = darker) default for BigBrain histology
profiles. Backwards-incompatible changes are called out at the top of
CHANGELOG.md.

Author: zihuaihuai

CHANGELOG.md

@@ -0,0 +1,133 @@
+# Changelog
+
+All notable changes to BrainStat are recorded here. The project adopts
+[Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [0.6.0] — 2026-05
+
+This release re-greens CI after a long stretch of upstream-driven breakage,
+fixes a cluster of high-severity correctness bugs in the statistics core,
+adds the FreeSurfer Destrieux atlas to `fetch_parcellation`, hardens the
+Neurosynth fetcher, and adopts a literature-aligned default for BigBrain
+histology profiles. It also closes the longest-standing maintenance items
+in the issue tracker.
+
+### Backwards-incompatible changes
+
+- **`brainstat.context.histology.read_histology_profile` now inverts BigBrain
+  intensities by default** (`invert=True`) so that higher = darker = more
+  cell-dense, matching Paquola et al. 2021 (eLife) and most downstream
+  BigBrain analyses. Pass `invert=False` to recover the previous behaviour.
+  MPC and gradient computations are correlation-based and therefore
+  invariant to this flip; only direct inspection of profile intensities is
+  affected. (#274)
+- **`SLM.__init__` now coerces `contrast` to numeric and `mask` to
+  boolean.** Pandas Series of object/categorical dtype now raise a clear
+  `TypeError` instead of producing the cryptic `can't multiply sequence by
+  non-int of type 'float'` deep inside `_t_test`. Integer 0/1 masks (the
+  natural shape of `nib.load(...).get_fdata().astype(int)`) are now
+  converted to bool rather than degenerating into fancy indexing inside
+  `_fdr`. (#342)
+- **Pin numpy<2 and pandas<2.1.** `abagen 0.1.3` still imports
+  `pkg_resources` and calls `DataFrame.groupby(axis=...)`; until upstream is
+  patched, BrainStat must stay on the numpy 1.x ABI to avoid runtime
+  binary-incompatibility errors. Will be lifted once abagen ships a
+  compatible release.
+
+### Bug fixes — statistics core
+
+- `SLM._surfstat_to_brainstat_rft`: fix off-by-one in Yeo7 indexing.
+  `peak_clus` returns 1-based vertex IDs (a SurfStat carry-over); these
+  were being used to index a 0-based numpy array, raising `IndexError`
+  when a peak landed on the final mesh vertex and silently mis-labelling
+  Yeo networks for every other peak. (#347)
+- `SLM.py`: `from cmath import sqrt` was importing the **complex** square
+  root; switched to `math.sqrt`. The expression was always real but the
+  surrounding code would have silently propagated complex values had the
+  branch ever been negative.
+- `SLM.py`: removed a duplicate `fetch_template_surface` import.
+- `_t_test.py`: `sys.exit("Contrast is not estimable :-(")` would kill the
+  host Python process when invoked from a notebook or pipeline. Replaced
+  with `raise ValueError(...)`.
+- `_t_test.py`: replace `float(...)` with `.item()` on the t-statistic
+  computation. `numpy>=2.0` raises `TypeError: only 0-dimensional arrays
+  can be converted to Python scalars` for `float()` on size-1 ndarrays.
+
+### New features
+
+- `brainstat.datasets.fetch_parcellation(template, "destrieux", ...)`
+  now returns the FreeSurfer `aparc.a2009s` (Destrieux 2009)
+  parcellation, sourced via
+  `nilearn.datasets.fetch_atlas_surf_destrieux`. Native `fsaverage5`;
+  other `fsaverage*` templates resampled with nearest-neighbour
+  interpolation. `fslr32k` is rejected (FreeSurfer-specific). (#343)
+- The `surf=None + correction='rft'` error message now points users at
+  `correction='fdr'` for volumetric data instead of just refusing.
+
+### Maintenance
+
+- **CI fully restored.** Both Python and MATLAB suites had been red on
+  `master` for a long stretch. Root causes addressed:
+  - `setuptools >= 81` no longer ships `pkg_resources`, breaking
+    `abagen` import → pinned `setuptools<81` in CI and reinstalled it
+    after the editable install.
+  - `numpy.dtype size changed` from mixing pinned `pandas<2.1` (built
+    against numpy 1.x ABI) with `numpy>=2` → pinned `numpy<2` to keep
+    the stack consistent.
+  - `pandas 2.0.x` has no Python 3.12 wheels → temporarily dropped 3.12
+    from the matrix until abagen is patched and the pin can be lifted.
+  - `MATLAB:Python:PythonUnavailable` from the precomputed-pickle tests
+    → bumped to `matlab-actions/setup-matlab@v2` +
+    `matlab-actions/run-command@v2`, configure `pyenv()` before
+    `runtests`, add explicit `addpath(genpath('brainstat_matlab'))`.
+  - GitHub Actions versions: `actions/checkout@v4`,
+    `actions/setup-python@v5`. (PR #379)
+- **Drop `# type: ignore` from `SLM.py` and `_multiple_comparisons.py`.**
+  The class-body imports that were tripping
+  [python/mypy#10521](https://github.com/python/mypy/issues/10521) have
+  been lifted to module level and bound as class attributes (`_linear_model
+  = _linear_model`, etc.). mypy now runs to completion on both files
+  instead of crashing. The pre-existing untyped-code errors that the
+  blanket ignore was hiding are surfaced but tracked separately; the
+  `mypy` CI job remains commented out pending that triage. (#199)
+- **MATLAB R2019b/R2020a compatibility.** `peak_clus.column_vector`
+  replaced the `mustBeVector` validator (introduced in R2020b) with an
+  explicit `isvector` check. (#285)
+- **Resilient Neurosynth download.** `meta_analytic_decoder/fetch_neurosynth_data`
+  validates the downloaded zip via `java.util.zip.ZipFile` before
+  `unzip`, retries up to 3 times, cleans up partial zips between
+  attempts, and verifies the post-extract file count. Truncated
+  downloads no longer leave the toolbox in a permanently broken state.
+  (#341)
+
+### Issues closed
+
+- #199 — Remove `# type: ignore` from `SLM` class
+- #274 — Flip the bits on the histological profiles
+- #285 — `column_vector` uses `mustBeVector` from MATLAB 2020b+
+- #341 — Neurosynth data failed to get fetched
+- #342 — Volumetric mixed effects (input contract bugs; cluster-level
+  RFT/TFCE on volumes remains tracked separately as a feature request)
+- #343 — Atlas coverage for FreeSurfer GLM workflows (Destrieux added;
+  hosted Desikan-Killiany remains tracked for a follow-up)
+- #347 — Retrieval of yeo7 information has off-by-1 error
+
+### Known follow-ups
+
+- **Lift the numpy/pandas/3.12 pins** once `abagen` drops `pkg_resources`
+  and the `groupby(axis=)` call.
+- **Re-enable the commented-out `mypy` CI job** once the ~380 latent
+  typing errors uncovered by removing `# type: ignore` are triaged.
+- **Volumetric cluster-level RFT/TFCE** for `SLM` — present in SurfStat,
+  not yet ported.
+- **Hosted Desikan-Killiany (`aparc`) atlas** in `fetch_parcellation`
+  — needs a stable mirror (OSF / Zenodo) for the `.annot` files.
+
+## [0.5.2] — 2026-01
+
+Hotfixes only; no formal changelog was kept for this release.
+
+## [0.5.1] and earlier
+
+See `git log` and the merged-PR history for releases prior to the
+introduction of this changelog.

brainstat/__init__.py

@@ -1,2 +1,2 @@
 """Neuroimaging statistics toolbox."""
-__version__ = "0.5.2"
+__version__ = "0.6.0"