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add CI description to contributing guide - #13837
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CI failure seems unrelated (PyVista/VTK on Python 3.13). |
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drammock
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Co-authored-by: Daniel McCloy <[email protected]>
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* [pre-commit.ci] pre-commit autoupdate (mne-tools#13646) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: mne[bot] <[email protected]> * Fix and extend anonymize_info (mne-tools#13647) * Fix epochs.plot() scrollbar issue (mne-tools#13654) * ENH: Add optional channel name overlay to plot_alignment (mne-tools#13570) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Daniel McCloy <[email protected]> * Fix docstrings for get_data() (mne-tools#13652) * DOC: Add detail to make_watershed_bem volume parameter (mne-tools#13658) * [pre-commit.ci] pre-commit autoupdate (mne-tools#13663) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: mne[bot] <[email protected]> * update maintainers lists (mne-tools#13631) * Fixes make_scalp_surfaces (mne-tools#13024) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Marijn van Vliet <[email protected]> Co-authored-by: Eric Larson <[email protected]> * DOC: Add pybvrf [skip azp] [skip actions] (mne-tools#13665) * Expose bem submodule (mne-tools#13669) * Rename `Epochs.reset_drop_log_selection()` to `Epochs.reset_index()` (mne-tools#13675) * MAINT: Work around NumPy deprecation (mne-tools#13677) * [pre-commit.ci] pre-commit autoupdate (mne-tools#13678) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: mne[bot] <[email protected]> * Allow reading alternative nasion label (Nz) from snirf file (mne-tools#13672) Co-authored-by: Daniel McCloy <[email protected]> * use a lockfile for "old" CI job (mne-tools#13490) Co-authored-by: Carina Forster <[email protected]> Co-authored-by: Thomas S. Binns <[email protected]> Co-authored-by: Scott Huberty <[email protected]> Co-authored-by: Erica Peterson <[email protected]> Co-authored-by: Eric Larson <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Fix bad cross-ref syntax (mne-tools#13690) * Doc- clarify return types as instance of original type (mne-tools#13674) Co-authored-by: Marijn van Vliet <[email protected]> * update partner institution list (mne-tools#13668) * MAINT: Update code credit (mne-tools#13709) Co-authored-by: Eric Larson <[email protected]> * [pre-commit.ci] pre-commit autoupdate (mne-tools#13716) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: mne[bot] <[email protected]> * DOC: clarify index mismatch in Epochs.drop when epochs are auto-dropped (mne-tools#13688) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Thomas S. Binns <[email protected]> Co-authored-by: Daniel McCloy <[email protected]> * ENH: support per-vertex opacity in 3D overlays (mne-tools#13706) Co-authored-by: Eric Larson <[email protected]> * FIX: Spelling [ci skip] * Fix generation of lockfile for old job (mne-tools#13724) * eyetrack should not count as picks=data (mne-tools#13723) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Scott Huberty <[email protected]> * BUG: prevent NaNs in layered overlay compositing when resulting alpha is zero (mne-tools#13714) Co-authored-by: Marijn van Vliet <[email protected]> * Added HEDAnnotations (mne-tools#13059) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Daniel McCloy <[email protected]> Co-authored-by: Bru <[email protected]> Co-authored-by: Stefan Appelhoff <[email protected]> * [dependabot]: Bump the actions group with 2 updates (mne-tools#13728) Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: mne[bot] <[email protected]> Co-authored-by: Eric Larson <[email protected]> * [pre-commit.ci] pre-commit autoupdate (mne-tools#13734) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: mne[bot] <[email protected]> Co-authored-by: Eric Larson <[email protected]> * Raising meaningful warnings/errors for interpolate_bads, when supplie… (mne-tools#13518) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * BUG: Fix bug with default (mne-tools#13744) * DOC: document first_samp behavior after crop and RawArray workaround (mne-tools#13685) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * FIX: do not print dev_head_t if not available (mne-tools#13741) Co-authored-by: Eric Larson <[email protected]> * FIX: Link [ci skip] * Update name [ci skip] * MAINT: cleanup Python 3.9 compat from __future__ import annotations (mne-tools#13749) Co-authored-by: Marijn van Vliet <[email protected]> * FIX: Handle hidden annotations during deletion in mpl plot (mne-tools#13703) * ENH: Log scaling better (mne-tools#13758) * [pre-commit.ci] pre-commit autoupdate (mne-tools#13762) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: mne[bot] <[email protected]> Co-authored-by: Eric Larson <[email protected]> * FORWARD: assert invariant for unreachable rref branch in _lead_dots (mne-tools#13764) * Improve handling of dropped epochs in ica.plot_properties (mne-tools#13746) * Support mixed hed annotations, concat and solve version registration (mne-tools#13736) * ENH: compute CSD directly for upper-triangle channel pairs in Fourier/multitaper (mne-tools#13719) * Extend plot_csd support to SEEG, ECoG, and DBS channel types (mne-tools#13713) Co-authored-by: Thomas S. Binns <[email protected]> Co-authored-by: Marijn van Vliet <[email protected]> * Add example for Python/R interoperability using mass univariate t-test (mne-tools#13729) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Eric Larson <[email protected]> Co-authored-by: Daniel McCloy <[email protected]> * [BUG] `IndexError` in `set_montage()` for MEG+EEG recordings when digitization is skipped (mne-tools#13700) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * FIX: remap lowpass <= 0 to Nyquist in GDF/EDF reader (mne-tools#13769) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * FIX: correct spacing attribute in SourceMorph when src_to is provided (mne-tools#13687) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * [pre-commit.ci] pre-commit autoupdate (mne-tools#13779) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: mne[bot] <[email protected]> Co-authored-by: Eric Larson <[email protected]> * fix bad xrefs in changelog (mne-tools#13783) * DOC: fix invalid cross-reference in 13700 changelog entry (mne-tools#13785) * FIX: raise clear ValueError when no ECG events found in create_ecg_ep… (mne-tools#13771) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Daniel McCloy <[email protected]> * ENH: Add native save and read support for SSD (mne-tools#13718) Co-authored-by: Thomas S. Binns <[email protected]> * ENH: Add variance regularization to F-statistic in f_oneway (mne-tools#13698) Co-authored-by: Daniel McCloy <[email protected]> * [pre-commit.ci] pre-commit autoupdate (mne-tools#13802) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: mne[bot] <[email protected]> * ENH: allow per-channel colors in raw.plot via channel name dict keys (mne-tools#13765) * Fix top and bottom clipping in raw.plot() (mne-tools#13787) * MAINT: Update code credit (mne-tools#13805) * FIX: short-circuit n_jobs=None to n_jobs=1 without Parallel setup (mne-tools#13777) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Daniel McCloy <[email protected]> Co-authored-by: autofix-ci[bot] <114827586+autofix-ci[bot]@users.noreply.github.com> * Replacing abstractclassmethod with abstractmethod (mne-tools#13806) * ENH: expose font_file in Brain.add_text (mne-tools#13778) Co-authored-by: Daniel McCloy <[email protected]> Co-authored-by: Marijn van Vliet <[email protected]> * ENH: add cmap parameter to Evoked.animate_topomap (mne-tools#13756) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * MAINT: Install SciPy pre (mne-tools#13807) * ENH: Replace custom _whosmat_hdf5 with pymatreader.whosmat (mne-tools#13753) * MAINT: Make sys_info more robust (mne-tools#13810) * MAINT: Remove tomli, tomlsort, and ruff from `test` group (mne-tools#13809) * BUG: Fix bug with fwd.info["dev_head_t"] setting (mne-tools#13619) * ENH: Add initial BCI2000 .dat reader (preload-only) (mne-tools#13699) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: autofix-ci[bot] <114827586+autofix-ci[bot]@users.noreply.github.com> Co-authored-by: Eric Larson <[email protected]> * Add pybispectra as related software (mne-tools#13812) * DOC: Fix type annotation for order parameter in Epochs.plot() (mne-tools#13639) Co-authored-by: Daniel McCloy <[email protected]> Co-authored-by: Scott Huberty <[email protected]> * [dependabot]: Bump the actions group with 2 updates (mne-tools#13817) Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: mne[bot] <[email protected]> * fixed some info fields in MEG interpolation across sensor types using… (mne-tools#13759) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * ENH: Add support for plotting ICA source timecourses in Report.add_ica (mne-tools#13697) * FIX: correct sensor name ordering in plot_topomap when using Info object (mne-tools#13686) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * MAINT: Update dependency specifiers (mne-tools#13814) Co-authored-by: autofix-ci[bot] <114827586+autofix-ci[bot]@users.noreply.github.com> Co-authored-by: Thomas S. Binns <[email protected]> * [pre-commit.ci] pre-commit autoupdate (mne-tools#13818) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: mne[bot] <[email protected]> * MAINT: Update code credit [ci skip] (mne-tools#13823) Co-authored-by: Eric Larson <[email protected]> * Update values to int64 (mne-tools#13548) Co-authored-by: Eric Larson <[email protected]> Co-authored-by: autofix-ci[bot] <114827586+autofix-ci[bot]@users.noreply.github.com> Co-authored-by: Daniel McCloy <[email protected]> * FIX: Installer links etc [ci skip] * TST: Doc * FIX: correct mode parameter in get_point_spread and get_cross_talk (mne-tools#13754) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * DOC: Add epoch quality example (mne-tools#13710) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Thomas S. Binns <[email protected]> * Change syncing of dependencies with `README` (mne-tools#13832) * DOC: Fix changelog [circle deploy] (mne-tools#13833) Co-authored-by: Thomas S. Binns <[email protected]> * Exclude private submodules (e.g., _edf) from Credits page (mne-tools#13673) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * BUG: Fix bug with backward compat [circle deploy] (mne-tools#13835) * Fix bug with credit [circle deploy] (mne-tools#13841) * ENH: broaden OPM coil handling for colocated topomaps (mne-tools#13825) * DOC: Add artifact-cleaning note to epoch quality example. (mne-tools#13827) * [pre-commit.ci] pre-commit autoupdate (mne-tools#13839) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: mne[bot] <[email protected]> Co-authored-by: Eric Larson <[email protected]> * FIX: Ref [skip azp] [skip actions] * BUG: Fix bug with logging level (mne-tools#13843) * fix env var in actions (mne-tools#13844) Co-authored-by: Scott Huberty <[email protected]> * TST: Add regression coverage for OPM topomap grouping via `plot_joint()` and `ICA` (mne-tools#13842) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Customize annotation colors (mne-tools#13838) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * DOC: Remove invalid ndarray option from colormap docstrings (mne-tools#13797) * Fix versionadded for annotation_colors (mne-tools#13853) * [dependabot]: Bump the actions group with 2 updates (mne-tools#13852) Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: mne[bot] <[email protected]> * [pre-commit.ci] pre-commit autoupdate (mne-tools#13854) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: mne[bot] <[email protected]> * MAINT: Links [circle deploy] [skip azp] [skip actions] * MAINT: add OPM overlap grouping helper (mne-tools#13847) * FIX: Correct fNIRS interpolation with reordered picks (mne-tools#13856) * MAINT: Modernize numpydoc checks (mne-tools#13865) * Allow concatenating `BaseRaw` objects (mne-tools#13263) Co-authored-by: Copilot <[email protected]> Co-authored-by: Eric Larson <[email protected]> * Add dark theme to Matplotlib-based raw.plot (mne-tools#13861) Co-authored-by: Copilot <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * FIX: Check [ci skip] * FIX: Sets [ci skip] * Update towncrier change type descriptions (mne-tools#13829) * fix numpydoc (missed YD01 ignore) (mne-tools#13868) * FIX: correct label orientation for 0-90 deg nodes in plot_connectivity_circle (mne-tools#13855) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Daniel McCloy <[email protected]> * [dependabot]: Bump the actions group with 3 updates (mne-tools#13871) Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: mne[bot] <[email protected]> * [pre-commit.ci] pre-commit autoupdate (mne-tools#13873) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: mne[bot] <[email protected]> * Add preload keyward argument to Inst.load_data() method call (mne-tools#13858) * MAINT: Make test dir read-only (mne-tools#13872) * BUG: improve FreeSurfer error message when executable not found (mne-tools#13874) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Eric Larson <[email protected]> * add CI description to contributing guide (mne-tools#13837) Co-authored-by: Daniel McCloy <[email protected]> * Fix grammar [ci skip] (mne-tools#13881) * FIX: handle missing __version__ in check_version (mne-tools#13870) Co-authored-by: Claude Sonnet 4.6 <[email protected]> * apply diataxis to tutorials/inverse/80_brainstorm_phantom_elekta.py (mne-tools#13584) Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * add AI policy (mne-tools#13883) * MAINT: Switch to pip for macOS and minimal jobs (mne-tools#13882) * MAINT: Update code credit (mne-tools#13878) * ENH: Allow passing source detector distances to beer lambert law (mne-tools#13875) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * MAINT: Update for vtk deprecation (mne-tools#13886) * ENH: Add overrides= parameter to read_raw_brainvision for BIDS header repair (mne-tools#13884) * Fix bug with ica.plot_properties (mne-tools#13885) * Fix `picks` being ignored in `Epochs.apply_function()` (mne-tools#13894) * Update describing changes in contributing guide (mne-tools#13895) * Add Zuna to related software list (mne-tools#13849) Co-authored-by: Daniel McCloy <[email protected]> * [dependabot]: Bump github/codeql-action from 4.35.2 to 4.35.3 in the actions group (mne-tools#13897) Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: mne[bot] <[email protected]> Co-authored-by: Eric Larson <[email protected]> * DOC: Fix apply_function shape description for Epochs (mne-tools#13891) Co-authored-by: Eric Larson <[email protected]> * Raise warning and errors when np.nan provided to mne.stats.permutation_t_test(). (mne-tools#13813) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Erica R Peterson <[email protected]> * MAINT: Update dependency specifiers (mne-tools#13899) Co-authored-by: autofix-ci[bot] <114827586+autofix-ci[bot]@users.noreply.github.com> Co-authored-by: Eric Larson <[email protected]> * [dependabot]: Bump github/codeql-action from 4.35.3 to 4.35.4 in the actions group (mne-tools#13901) Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: mne[bot] <[email protected]> * [pre-commit.ci] pre-commit autoupdate (mne-tools#13902) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: mne[bot] <[email protected]> * MAINT: Remove workaround for old PySide6 (mne-tools#13900) * Add spherical montages (mne-tools#13903) * [dependabot]: Bump the actions group with 2 updates (mne-tools#13918) Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: mne[bot] <[email protected]> * [pre-commit.ci] pre-commit autoupdate (mne-tools#13919) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: mne[bot] <[email protected]> * MAINT: Update dependency specifiers (mne-tools#13916) Co-authored-by: autofix-ci[bot] <114827586+autofix-ci[bot]@users.noreply.github.com> Co-authored-by: Eric Larson <[email protected]> * BUG: set_eeg_reference list ch_type now applies per-type CAR by default (mne-tools#13920) * FIX: Avoid iteration errors caused by None when reading Nihon Kohden .LOG files (mne-tools#13915) * Fix drop_log dtype (mne-tools#13923) * Doc: add guidance on taking over a stale pull request (mne-tools#13877) Co-authored-by: Thomas S. Binns <[email protected]> Co-authored-by: Daniel McCloy <[email protected]> * FIX: Make set_eeg_reference working with a string for a channel name (mne-tools#13917) --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: mne[bot] <[email protected]> Co-authored-by: Clemens Brunner <[email protected]> Co-authored-by: Aman Srivastava <[email protected]> Co-authored-by: Daniel McCloy <[email protected]> Co-authored-by: Himanshu Mahor <[email protected]> Co-authored-by: Scott Huberty <[email protected]> Co-authored-by: Victor Férat <[email protected]> Co-authored-by: Marijn van Vliet <[email protected]> Co-authored-by: Eric Larson <[email protected]> Co-authored-by: Aniket <[email protected]> Co-authored-by: Carina Forster <[email protected]> Co-authored-by: Thomas S. Binns <[email protected]> Co-authored-by: Erica Peterson <[email protected]> Co-authored-by: Horizon_Architect_07 <[email protected]> Co-authored-by: Pragnya <[email protected]> Co-authored-by: Benedikt Ehinger <[email protected]> Co-authored-by: Kay Robbins <[email protected]> Co-authored-by: Bru <[email protected]> Co-authored-by: Stefan Appelhoff <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Johannes Herforth <[email protected]> Co-authored-by: Hansuja <[email protected]> Co-authored-by: Simon Kern <[email protected]> Co-authored-by: autofix-ci[bot] <114827586+autofix-ci[bot]@users.noreply.github.com> Co-authored-by: Akhilesh <[email protected]> Co-authored-by: CHH <[email protected]> Co-authored-by: Teon L Brooks <[email protected]> Co-authored-by: Lifeng <[email protected]> Co-authored-by: Kalle Mäkelä <[email protected]> Co-authored-by: Copilot <[email protected]> Co-authored-by: Pavel Popov <[email protected]> Co-authored-by: Ayushi Satodiya <[email protected]> Co-authored-by: Seth Bashford <[email protected]> Co-authored-by: Baris <[email protected]> Co-authored-by: Claude Sonnet 4.6 <[email protected]> Co-authored-by: Jonas Mago <[email protected]> Co-authored-by: Bhargav Kowshik <[email protected]> Co-authored-by: Erica R Peterson <[email protected]> Co-authored-by: Ben Tang <[email protected]> Co-authored-by: myd7349 <[email protected]> Co-authored-by: Michael Straube <[email protected]>
Merged
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This PR updates the Contributing Guide to improve clarity and usability of the CI (Continuous Integration) section.
The current contributing guide links to a Wikipedia page on CI but does not explain why we use CI.
This update aims to make it easier for new contributors to:
Understand what CI is doing and why it is important to run checks locally before pushing changes. This is particularly relevant, as we receive many user comments about CircleCI and failing doc builds for unregistered users.