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Author SHA1 Message Date
dependabot[bot] 9b3d47311c build(deps): bump mistune from 3.2.1 to 3.3.0 in /docs (#5075) 
Bumps [mistune](https://github.com/lepture/mistune) from 3.2.1 to 3.3.0.
- [Release notes](https://github.com/lepture/mistune/releases)
- [Changelog](https://github.com/lepture/mistune/blob/main/docs/changes.rst)
- [Commits](https://github.com/lepture/mistune/compare/v3.2.1...v3.3.0)

---
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- dependency-name: mistune
  dependency-version: 3.3.0
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 2026-07-13 16:38:08 +02:00
dependabot[bot] 43d027b8a3 build(deps): bump soupsieve from 2.8.3 to 2.8.4 in /docs (#5074) 
Bumps [soupsieve](https://github.com/facelessuser/soupsieve) from 2.8.3 to 2.8.4.
- [Release notes](https://github.com/facelessuser/soupsieve/releases)
- [Commits](https://github.com/facelessuser/soupsieve/compare/2.8.3...2.8.4)

---
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- dependency-name: soupsieve
  dependency-version: 2.8.4
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 2026-07-13 16:37:47 +02:00
Zhihao Dai e6dd1f5b36 ENH: Move optional-dep into dep-groups (#4589) 
* Move optional dep into dep groups

* Recommend uv for development

* Add missing dot

* Fix mypy errors

Co-authored-by: Zhihao Dai <zhihao.dai@eng.ox.ac.uk>

* Fix mypy selenium error

Co-authored-by: Zhihao Dai <zhihao.dai@eng.ox.ac.uk>

* Fix a DeepExplainer bug

Co-authored-by: Zhihao Dai <zhihao.dai@eng.ox.ac.uk>

* Use dep groups for cibuildwheel

Co-authored-by: Zhihao Dai <zhihao.dai@eng.ox.ac.uk>

* Update contributing guide w/ cuda install

Co-authored-by: Zhihao Dai <zhihao.dai@eng.ox.ac.uk>

* Ignore auto-generated pyi

Co-authored-by: Zhihao Dai <zhihao.dai@eng.ox.ac.uk>

* Use uv where possible

Co-authored-by: Zhihao Dai <zhihao.dai@eng.ox.ac.uk>

* Fix mypy error

Co-authored-by: Zhihao Dai <zhihao.dai@eng.ox.ac.uk>

* Upgrade mypy if needed

Co-authored-by: Zhihao Dai <zhihao.dai@eng.ox.ac.uk>

* Update GPU tree notebook

Co-authored-by: Zhihao Dai <zhihao.dai@eng.ox.ac.uk>

* Use uv for mypy tests

Co-authored-by: Zhihao Dai <zhihao.dai@eng.ox.ac.uk>

* Revert all py changes

Co-authored-by: Zhihao Dai <zhihao.dai@eng.ox.ac.uk>

* Use system mypy

Co-authored-by: Zhihao Dai <zhihao.dai@eng.ox.ac.uk>

* Remove outdated comments

Co-authored-by: Zhihao Dai <zhihao.dai@eng.ox.ac.uk>

* Apply tobias comments

Co-authored-by: Zhihao Dai <zhihao.dai@eng.ox.ac.uk>
 2026-06-29 16:33:19 +02:00
dependabot[bot] 45cb46557a build(deps): bump tornado from 6.5.6 to 6.5.7 (#5050) 
Bumps [tornado](https://github.com/tornadoweb/tornado) from 6.5.6 to 6.5.7.
- [Changelog](https://github.com/tornadoweb/tornado/blob/master/docs/releases.rst)
- [Commits](https://github.com/tornadoweb/tornado/compare/v6.5.6...v6.5.7)

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- dependency-name: tornado
  dependency-version: 6.5.7
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 2026-06-21 22:08:36 +02:00
dependabot[bot] 44e69e3c6c build(deps): bump bleach from 6.3.0 to 6.4.0 in /docs (#5051) 
Bumps [bleach](https://github.com/mozilla/bleach) from 6.3.0 to 6.4.0.
- [Changelog](https://github.com/mozilla/bleach/blob/main/CHANGES)
- [Commits](https://github.com/mozilla/bleach/compare/v6.3.0...v6.4.0)

---
updated-dependencies:
- dependency-name: bleach
  dependency-version: 6.4.0
  dependency-type: direct:production
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 2026-06-21 22:08:15 +02:00
dependabot[bot] 286086a6af build(deps): bump tornado from 6.5.5 to 6.5.6 (#5042) 
Bumps [tornado](https://github.com/tornadoweb/tornado) from 6.5.5 to 6.5.6.
- [Changelog](https://github.com/tornadoweb/tornado/blob/master/docs/releases.rst)
- [Commits](https://github.com/tornadoweb/tornado/compare/v6.5.5...v6.5.6)

---
updated-dependencies:
- dependency-name: tornado
  dependency-version: 6.5.6
  dependency-type: direct:production
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 2026-06-15 11:12:06 +02:00
Tobias Pitters 3be70014c9 remove webpack dependency for sickness scores (#5018) 
* build(deps): bump qs and express in /javascript

Bumps [qs](https://github.com/ljharb/qs) and [express](https://github.com/expressjs/express). These dependencies needed to be updated together.

Updates `qs` from 6.14.2 to 6.15.2
- [Changelog](https://github.com/ljharb/qs/blob/main/CHANGELOG.md)
- [Commits](https://github.com/ljharb/qs/compare/v6.14.2...v6.15.2)

Updates `express` from 4.22.1 to 4.22.2
- [Release notes](https://github.com/expressjs/express/releases)
- [Changelog](https://github.com/expressjs/express/blob/v4.22.2/History.md)
- [Commits](https://github.com/expressjs/express/compare/v4.22.1...v4.22.2)

---
updated-dependencies:
- dependency-name: qs
  dependency-version: 6.15.2
  dependency-type: indirect
- dependency-name: express
  dependency-version: 4.22.2
  dependency-type: indirect
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* update sickness scores; remove webpack dependency

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 2026-05-27 19:37:24 +02:00
dependabot[bot] 9be5435bb8 build(deps): bump idna from 3.11 to 3.15 in /docs (#5007) 
Bumps [idna](https://github.com/kjd/idna) from 3.11 to 3.15.
- [Release notes](https://github.com/kjd/idna/releases)
- [Changelog](https://github.com/kjd/idna/blob/master/HISTORY.md)
- [Commits](https://github.com/kjd/idna/compare/v3.11...v3.15)

---
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- dependency-name: idna
  dependency-version: '3.15'
  dependency-type: direct:production
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 2026-05-27 12:27:49 +02:00
dependabot[bot] ce4abd7693 build(deps): bump mistune from 3.2.0 to 3.2.1 (#4990) 
Bumps [mistune](https://github.com/lepture/mistune) from 3.2.0 to 3.2.1.
- [Release notes](https://github.com/lepture/mistune/releases)
- [Changelog](https://github.com/lepture/mistune/blob/main/docs/changes.rst)
- [Commits](https://github.com/lepture/mistune/compare/v3.2.0...v3.2.1)

---
updated-dependencies:
- dependency-name: mistune
  dependency-version: 3.2.1
  dependency-type: direct:production
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 2026-05-13 14:46:07 +02:00
dependabot[bot] 4264d6c6bc build(deps): bump urllib3 from 2.6.3 to 2.7.0 (#5000) 
Bumps [urllib3](https://github.com/urllib3/urllib3) from 2.6.3 to 2.7.0.
- [Release notes](https://github.com/urllib3/urllib3/releases)
- [Changelog](https://github.com/urllib3/urllib3/blob/main/CHANGES.rst)
- [Commits](https://github.com/urllib3/urllib3/compare/2.6.3...2.7.0)

---
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- dependency-name: urllib3
  dependency-version: 2.7.0
  dependency-type: direct:production
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 2026-05-13 14:45:12 +02:00
dependabot[bot] 0852948ca6 build(deps): bump nbconvert from 7.17.0 to 7.17.1 in /docs (#4722) 
Bumps [nbconvert](https://github.com/jupyter/nbconvert) from 7.17.0 to 7.17.1.
- [Release notes](https://github.com/jupyter/nbconvert/releases)
- [Changelog](https://github.com/jupyter/nbconvert/blob/main/CHANGELOG.md)
- [Commits](https://github.com/jupyter/nbconvert/compare/v7.17.0...v7.17.1)

---
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- dependency-name: nbconvert
  dependency-version: 7.17.1
  dependency-type: direct:production
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 2026-04-22 08:51:00 +02:00
Samudraneel Sarkar 413f063220 Remove unused typing-extensions dependency (#4629) 2026-04-18 21:48:49 +02:00
Abhishek e4ddc195ea add cross-links between API Reference and API Examples pages 2026-04-08 13:43:45 +05:30
Tobias Pitters 05c0e77708 follow SPEC 0 and update dependencies (#4310) 
* update dependencies for notebooks, wheels, readthedocs, etc. to follow spec0 and upgrade dependencies to newer versions

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* update type annotations to new python version

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 2026-04-02 00:48:34 +02:00
dependabot[bot] 0d79fa0f87 build(deps): bump tornado from 6.5.1 to 6.5.5 in /docs (#4293) 
Bumps [tornado](https://github.com/tornadoweb/tornado) from 6.5.1 to 6.5.5.
- [Changelog](https://github.com/tornadoweb/tornado/blob/master/docs/releases.rst)
- [Commits](https://github.com/tornadoweb/tornado/compare/v6.5.1...v6.5.5)

---
updated-dependencies:
- dependency-name: tornado
  dependency-version: 6.5.5
  dependency-type: direct:production
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 2026-04-01 21:41:19 +02:00
James Lamb c5dedf6a10 update LightGBM links (#4296) 2026-03-31 23:15:11 +02:00
dependabot[bot] 6c46f99aa8 build(deps): bump requests from 2.32.4 to 2.33.0 in /docs (#4304) 
Bumps [requests](https://github.com/psf/requests) from 2.32.4 to 2.33.0.
- [Release notes](https://github.com/psf/requests/releases)
- [Changelog](https://github.com/psf/requests/blob/main/HISTORY.md)
- [Commits](https://github.com/psf/requests/compare/v2.32.4...v2.33.0)

---
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- dependency-name: requests
  dependency-version: 2.33.0
  dependency-type: direct:production
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 2026-03-31 12:37:28 +02:00
dependabot[bot] 502eed8eac build(deps): bump pygments from 2.18.0 to 2.20.0 in /docs (#4306) 
Bumps [pygments](https://github.com/pygments/pygments) from 2.18.0 to 2.20.0.
- [Release notes](https://github.com/pygments/pygments/releases)
- [Changelog](https://github.com/pygments/pygments/blob/master/CHANGES)
- [Commits](https://github.com/pygments/pygments/compare/2.18.0...2.20.0)

---
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- dependency-name: pygments
  dependency-version: 2.20.0
  dependency-type: direct:production
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 2026-03-31 12:37:05 +02:00
dependabot[bot] adc3f0c6d6 build(deps): bump nbconvert from 7.16.4 to 7.17.0 in /docs (#4262) 
* build(deps): bump nbconvert from 7.16.4 to 7.17.0 in /docs

Bumps [nbconvert](https://github.com/jupyter/nbconvert) from 7.16.4 to 7.17.0.
- [Release notes](https://github.com/jupyter/nbconvert/releases)
- [Changelog](https://github.com/jupyter/nbconvert/blob/main/CHANGELOG.md)
- [Commits](https://github.com/jupyter/nbconvert/compare/v7.16.4...v7.17.0)

---
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- dependency-name: nbconvert
  dependency-version: 7.17.0
  dependency-type: direct:production
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* update requirements-docs.txt

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 2026-02-11 23:06:22 +01:00
dependabot[bot] f28b20aaf4 build(deps): bump pillow from 10.4.0 to 12.1.1 (#4265) 
Bumps [pillow](https://github.com/python-pillow/Pillow) from 10.4.0 to 12.1.1.
- [Release notes](https://github.com/python-pillow/Pillow/releases)
- [Changelog](https://github.com/python-pillow/Pillow/blob/main/CHANGES.rst)
- [Commits](https://github.com/python-pillow/Pillow/compare/10.4.0...12.1.1)

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- dependency-name: pillow
  dependency-version: 12.1.1
  dependency-type: direct:production
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 2026-02-11 22:59:01 +01:00
dependabot[bot] 825dbf5e8e build(deps): bump urllib3 from 2.6.0 to 2.6.3 in /docs (#4246) 
Bumps [urllib3](https://github.com/urllib3/urllib3) from 2.6.0 to 2.6.3.
- [Release notes](https://github.com/urllib3/urllib3/releases)
- [Changelog](https://github.com/urllib3/urllib3/blob/main/CHANGES.rst)
- [Commits](https://github.com/urllib3/urllib3/compare/2.6.0...2.6.3)

---
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- dependency-name: urllib3
  dependency-version: 2.6.3
  dependency-type: direct:production
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 2026-01-13 21:22:12 +01:00
dependabot[bot] 256c93a836 build(deps): bump urllib3 from 2.5.0 to 2.6.0 in /docs (#4233) 
Bumps [urllib3](https://github.com/urllib3/urllib3) from 2.5.0 to 2.6.0.
- [Release notes](https://github.com/urllib3/urllib3/releases)
- [Changelog](https://github.com/urllib3/urllib3/blob/main/CHANGES.rst)
- [Commits](https://github.com/urllib3/urllib3/compare/2.5.0...2.6.0)

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- dependency-name: urllib3
  dependency-version: 2.6.0
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 2025-12-09 09:24:03 +01:00
dependabot[bot] b4511146b6 build(deps): bump fonttools from 4.54.1 to 4.61.0 in /docs (#4231) 
Bumps [fonttools](https://github.com/fonttools/fonttools) from 4.54.1 to 4.61.0.
- [Release notes](https://github.com/fonttools/fonttools/releases)
- [Changelog](https://github.com/fonttools/fonttools/blob/main/NEWS.rst)
- [Commits](https://github.com/fonttools/fonttools/compare/4.54.1...4.61.0)

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- dependency-name: fonttools
  dependency-version: 4.61.0
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 2025-12-09 09:12:53 +01:00
Stefano Borzì 6c2f2417ac docs(shap_nips.bib): update reference (#4141) 2025-07-25 23:21:08 +02:00
dependabot[bot] 74d5b10347 build(deps): bump urllib3 from 2.2.3 to 2.5.0 in /docs (#4115) 
Bumps [urllib3](https://github.com/urllib3/urllib3) from 2.2.3 to 2.5.0.
- [Release notes](https://github.com/urllib3/urllib3/releases)
- [Changelog](https://github.com/urllib3/urllib3/blob/main/CHANGES.rst)
- [Commits](https://github.com/urllib3/urllib3/compare/2.2.3...2.5.0)

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- dependency-name: urllib3
  dependency-version: 2.5.0
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 2025-06-25 22:02:50 +02:00
dependabot[bot] 6b7251d782 build(deps): bump tornado from 6.4.2 to 6.5.1 in /docs (#4094) 
Bumps [tornado](https://github.com/tornadoweb/tornado) from 6.4.2 to 6.5.1.
- [Changelog](https://github.com/tornadoweb/tornado/blob/master/docs/releases.rst)
- [Commits](https://github.com/tornadoweb/tornado/compare/v6.4.2...v6.5.1)

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- dependency-name: tornado
  dependency-version: 6.5.1
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 2025-06-11 09:12:54 +02:00
dependabot[bot] fe4f12a571 build(deps): bump requests from 2.32.3 to 2.32.4 in /docs (#4106) 
Bumps [requests](https://github.com/psf/requests) from 2.32.3 to 2.32.4.
- [Release notes](https://github.com/psf/requests/releases)
- [Changelog](https://github.com/psf/requests/blob/main/HISTORY.md)
- [Commits](https://github.com/psf/requests/compare/v2.32.3...v2.32.4)

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- dependency-name: requests
  dependency-version: 2.32.4
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 2025-06-11 09:10:44 +02:00
dependabot[bot] cadb4d0300 build(deps): bump tornado from 6.4.1 to 6.4.2 in /docs (#3913) 
Bumps [tornado](https://github.com/tornadoweb/tornado) from 6.4.1 to 6.4.2.
- [Changelog](https://github.com/tornadoweb/tornado/blob/v6.4.2/docs/releases.rst)
- [Commits](https://github.com/tornadoweb/tornado/compare/v6.4.1...v6.4.2)

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 2025-03-08 20:04:22 +01:00
dependabot[bot] da0ce7da00 Bump jinja2 from 3.1.5 to 3.1.6 in /docs (#4012) 
Bumps [jinja2](https://github.com/pallets/jinja) from 3.1.5 to 3.1.6.
- [Release notes](https://github.com/pallets/jinja/releases)
- [Changelog](https://github.com/pallets/jinja/blob/main/CHANGES.rst)
- [Commits](https://github.com/pallets/jinja/compare/3.1.5...3.1.6)

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 2025-03-06 21:26:59 +01:00
dependabot[bot] ac1af960f5 build(deps): bump jinja2 from 3.1.4 to 3.1.5 in /docs (#3950) 
Bumps [jinja2](https://github.com/pallets/jinja) from 3.1.4 to 3.1.5.
- [Release notes](https://github.com/pallets/jinja/releases)
- [Changelog](https://github.com/pallets/jinja/blob/main/CHANGES.rst)
- [Commits](https://github.com/pallets/jinja/compare/3.1.4...3.1.5)

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 2025-01-10 23:00:48 +00:00
connortann bf4b10e1dc DOCS: Pin docs dependencies for reproducibility (#3885) 2024-10-09 13:44:06 +01:00
Jeremy Goh 972ea9948a docs: use intersphinx for some external links (#3851) 
* feat: enable intersphinx extension

* fix: some sphinx build warnings

* minor spelling errors

* add intersphinx links to clean up slightly

* Use proper external syntax

* Add mpl and python intersphinx

* Remove stdlib inv
 2024-09-14 12:41:57 +08:00
Jeremy Goh 8ad94df18c refactor: Cohorts internals, use @property, add type hinting and expose it in docs (#3779) 
* refactor: use property to enforce types in cohorts

* fix: remove __call__ since Explanation has no call

NOTE: this is because we had enforced `cohorts[k]` to always be an
Explanation upon property setting.
And Explanation has no `__call__` attribute (error thrown by mypy), so
it makes no sense for cohorts to have it as well.

* docs: Expose Cohorts as public API in the docs

* apply review suggestions

* fix: populate cohorts dict rather than modify one by one

This prevents the subtle bug where we can accidentally add in a non-Explanation object

* chore: add tests for Cohorts

* fix: add __call__ back

for invoking methods after they have been getattr-ed, e.g. cohort.mean(axis=0)

* fix: mypy complaints

* include review suggestion

Co-authored-by: connortann <71127464+connortann@users.noreply.github.com>

* docs: add comment to docstring

* fix: remove cast after assert

---------

Co-authored-by: connortann <71127464+connortann@users.noreply.github.com>
 2024-08-11 22:10:29 +08:00
connortann 2857009995 Remove old bar notebook (#3755) 2024-07-24 19:02:12 +01:00
connortann 45587666fd Deprecate the legacy bar plot, add migration guide to new Explainer API (#3739) 
* Add deprecationwarning to  bar_legacy

* Add notebook on Explanation API

* Update docs and warning

* Update wording of docs
 2024-07-05 16:59:11 +01:00
connortann fc8a60f9b0 Maint: apply ruff formatter to all python files (#3722) 
* Include py files in ruff formatter

* Rerun precommit formatter
 2024-06-28 17:12:55 +01:00
connortann 434d0fdedb Add Contributing guide to published Sphinx docs (#3405) 
* Add myst-parser

* Include contributing guide

* Update include statement

* Enable mys_parser extension

* Wording
 2023-12-04 20:20:59 +00:00
Jeremy Goh b91b11a468 chore: Add a Jupyter style guide and supporting infra (#3074) 
* add watermark to docs requirements

* add precommit checks

* use autosectionlabel to generate targets automatically

* add style guide to CONTRIBUTING

* refactor: code review

* remove watermark

* refactor: adjust prose about cross-references in notebooks

Couldn't get the cross references to work, I'm following this
'https://nbsphinx.readthedocs.io/en/0.9.3/markdown-cells.html#Links-to-Domain-Objects'
instead
 2023-10-15 10:37:41 +01:00
connortann 7992f6b7f3 DOCS: Lint notebooks/text_examples (#3302) 
* DOCS: Lint notebooks/text_examples

* Lint bar.ipynb, simplify pre-commit patterns
 2023-10-09 12:02:29 +01:00
Jeremy Goh 3ec6d1d414 refactor: remove boston dataset as promised (#3316) 2023-10-07 10:54:06 +01:00
connortann 1cf6838fbf docs: Remove redundant toctree levels (#3253) 
Co-authored-by: Jeremy Goh <30731072+thatlittleboy@users.noreply.github.com>
 2023-10-01 14:36:32 +08:00
connortann ca08229b8b ENH: Rename explainers to usual long-form names for consistency with docs (#3247) 
* Use long form of explainers in API docs

* Use long-form names as canonical definition
 2023-09-15 10:25:20 +01:00
dsgibbons e8a176e45a DOCS: Remove boston dataset from the README (#3200) 
* docs: remove boston dataset and add figure returns for non-waterfalls

* docs: render html plots to png

* fix: remove tight layout conflict with constrained mode in summary_plot

* tests: update image mpl baselines

* chore: limit number of points for force plot

* fix: revert plotting functionality

* docs: remove old boston plots
 2023-09-13 13:17:21 +09:30
connortann f826fcf5b9 DOCS: Fixup sidebar, add captions and restore logo (#3183) 
* Add captions to toctree

* Bump sphinx_rtd_theme

* Remove lower caption

* Comment empty toctree directive

---------

Co-authored-by: Jeremy Goh <30731072+thatlittleboy@users.noreply.github.com>
 2023-08-20 01:49:28 +08:00
connortann df056ff308 MAINT: Bulk update repo links to point to new shap GH org (#3142) 
* Bulk update repo links to point to new shap GH org

* Rename link in pyproject.toml

---------

Co-authored-by: Jeremy Goh <30731072+thatlittleboy@users.noreply.github.com>
 2023-07-27 16:13:05 +01:00
connortann b92aef0b6a DOCS: Add Sphinx release notes, remove manual Changelog (#3104) 
* Add Sphinx release notes

* Add dependency

* Remove changelog, simplify PR template

* Update fallback url

* Add link to unreleased changes

* Switch to rst_epilog

* Typo fix

* Formatting

* Better wording

* PR comments

* Quote toml key
 2023-07-22 22:48:24 +01:00
connortann 37dcc01a92 Fix rather a lot of typos (#3105) 
* Doing god's work here

* More fixes

* Rename Coefficent to Coefficient

* Apply suggestions from code review

Co-authored-by: Jeremy Goh <30731072+thatlittleboy@users.noreply.github.com>

* Better deprecation note

---------

Co-authored-by: Jeremy Goh <30731072+thatlittleboy@users.noreply.github.com>
 2023-07-21 19:10:04 +01:00
Scott Lundberg ae0b9867c1 Update Approve Hits.ipynb 2023-07-21 10:36:30 -07:00
Jeremy Goh 022498a119 chore: Apply black to docs conf.py (#3072) 
* blacken docs conf.py

* single line
 2023-07-08 23:55:15 +08:00
Jeremy Goh ab63310aad docs: Missing datasets documentation (#3039) 2023-06-25 10:05:46 +08:00