The recommended way to build GGTX is via cabal anyway, and stack
shouldn't get in the way of a successful build.

BREAKING CHANGE: this requires a newer version of `nix-shell`, at least
2.18 onwards. You can upgrade following the steps at:

https://nixos.org/download/

In particular, these are the bumped packages:

* GHC (9.4.8 -> 9.6.6)
* Cabal ( -> 3.12.1.0)
* Fortran ( 7 -> pinned)

[worker] various fixes

See merge request !389

Replace performance-critical parts of the algorithm with `massiv` (and ditch `accelerate-llvm`)

See merge request !382

We are now around 6/7 times slower than the LLVM code.

This also changes the cabal.project to not pull the accelerate-llvm or
the llvm-hs dependencies.

There are some rounding errors in the tests, but otherwise
the implementation seems correct.

It's crucial to be able to understand the API surface area when porting
the old code to `massiv`. It turns out that other than distributional,
the other piece of code using the LLVM interpreter is
`logDistributional2`.

This commit starts introducing `massiv` in the codebase,
initially for simple functions like `termDivNan`. The main
goal is to extend the linear algebra toolkit up to the
point where we can implement `distributional` in terms of
`massive` and measure its performance.

The previous code was sometimes yielding a matrix of NaN numbers as
it was attempting the division of the input matrix with the diagonal,
which would be 0 in case of an input matrix of 0, resulting in a
division by 0 error.

The main idea is trying to refactor/improve the existing linear algebra
functions one function at the time, using reference implementations and
benchmarks along the way.

Related to
gargantext/crawlers/openalex#6

- fix openalex parser
- fix cli message about 'init' needed
- more granular progress reports for node updates
- fix error message when worker fails (though I'm not sure such a
- detailed message is neede for the end user?)

release candidate 0.0.7.4.3

See merge request !385

commit be879b1e
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Thu Jan 30 18:22:44 2025 +0100

    [ngrams] code fixes according to review

    Related MR:
    !378

commit bf89561b
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Wed Jan 22 21:11:47 2025 +0100

    [test] notification on node move

    Also, some small refactorings.

commit 3d5d74ab
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Wed Jan 22 20:13:44 2025 +0100

    [tests] add notifications func comment, fix core/notifications indent

commit b8ea3af2
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Wed Jan 22 19:13:35 2025 +0100

    [update-project-dependencies]

commit 1217baf4
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Wed Jan 22 19:09:17 2025 +0100

    [tests] notifications: test async notifications for update tree

    Related to
    #418

commit 874785e9
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Tue Jan 21 06:06:27 2025 +0100

    [refactor] unify Database & ExternalIDs

    These types are the same, except for Database.Empty

    I managed to have backwards compatibility with the frontend format,
    hence the frontend doesn't need any changes.

commit e7b16520
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Tue Jan 21 06:05:57 2025 +0100

    [cabal] upgrade haskell-bee to fix TSRetry and ESRepeat issues

commit ad045ae0
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Mon Jan 20 06:32:49 2025 +0100

    [cabal] upgrade haskell-bee tag

commit b3910bb4
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Tue Jan 14 10:56:12 2025 +0100

    [test] move some Arbitrary instances to Test/Instances.hs

commit bb282d02
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Tue Jan 14 09:17:23 2025 +0100

    [test] WithQuery offline test (with EPO constructor)

commit c0fe2e51
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Tue Jan 14 06:59:45 2025 +0100

    [query] move EPO user/token into the datafield

    This simplifies the WithQuery structure even more

commit 93586adc
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Mon Jan 13 17:45:42 2025 +0100

    [tests] fix WithQuery frontend serialization test

    Also, add WithQuery pubmed test (with api_key)

commit bc29319c
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Mon Jan 13 10:13:15 2025 +0100

    [ngrams] simplify WithQuery json structure

    There is now only a 'datafield' field, no need for duplicated
    'database'.

    Related to #441

commit e6fdbee4
Merge: 95dc32b3 13457ca8
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Fri Jan 10 12:03:59 2025 +0100

    Merge branch 'dev' into 224-dev-understanding-ngrams

commit 95dc32b3
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Tue Jan 7 20:01:11 2025 +0100

    [ngrams] refactor PubMed DB type (to include Maybe APIKey)

commit baa2491f
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Tue Jan 7 18:09:04 2025 +0100

    [refactor] searx search refactoring

commit fcf83bf7
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Tue Jan 7 11:14:03 2025 +0100

    [ngrams] more types annotations

commit 0d8a77c4
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Mon Dec 30 16:15:07 2024 +0100

    [ngrams, test] refactor: Count -> Terms

commit 85f1dffe
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Mon Dec 30 14:35:05 2024 +0100

    [ngrams] refactor opaque Int into TermsWeight newtype

commit a81ea049
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Mon Dec 30 14:34:39 2024 +0100

    [CLI] fix limit removal

    It wasn't used anyways.

commit d1dfbf79
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Mon Dec 30 11:35:41 2024 +0100

    [ngrams] one more simplification in ngramsByDoc'

commit fcb48b8f
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Mon Dec 30 11:33:33 2024 +0100

    [ngrams] some more simplification of ngramsByDoc'

commit ab7c1766
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Mon Dec 30 11:00:19 2024 +0100

    [ngrams, tests] understanding ngramsByDoc better

commit 35c2d0b0
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Mon Dec 23 21:20:29 2024 +0100

    [ngrams] small simplification to docNgrams function

commit 161ac077
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Mon Dec 23 18:35:59 2024 +0100

    [ngrams] annotate types of ngrams algorithms

commit 08c7c91c
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Sat Dec 21 09:45:00 2024 +0100

    [ngrams] improve function documentation, add types, add unit tests

    I want to understand ngrams algorithms better.