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.

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.

commit b4755ad5
Author: Alfredo Di Napoli <alfredo.dinapoli@gmail.com>
Date:   Wed Jan 29 11:41:32 2025 +0100

    Code review, part II

    This commit splits the /export (renaming it to just remote) and tuck it
    under the /node hierarchy. The import also lives tucked in the /node.

commit 483bd3e5
Author: Alfredo Di Napoli <alfredo.dinapoli@gmail.com>
Date:   Tue Jan 28 09:34:14 2025 +0100

    Code review feedback

    * Rename `exampleS` into `exampleSchema`;
    * Revert commit about the public keys & co;

commit 18d207f0
Author: Alfredo Di Napoli <alfredo.dinapoli@gmail.com>
Date:   Tue Jan 28 09:50:56 2025 +0100

    Revert "Add _env_remote_transfer_keys field"

    This reverts commit 3ea32b50.

commit 9cc5159a
Author: Alfredo Di Napoli <alfredo.dinapoli@gmail.com>
Date:   Mon Jan 20 10:00:53 2025 +0100

    Support transfering of notes

commit 1fe60d75
Author: Alfredo Di Napoli <alfredo.dinapoli@gmail.com>
Date:   Fri Jan 17 08:37:53 2025 +0100

    Refactor exporting and transfering of nodes

commit b39c1805
Author: Alfredo Di Napoli <alfredo.dinapoli@gmail.com>
Date:   Thu Jan 16 09:54:38 2025 +0100

    Preliminary work to transfer notes

commit b2f7a9a8
Author: Alfredo Di Napoli <alfredo.dinapoli@gmail.com>
Date:   Mon Jan 13 15:25:34 2025 +0100

    Chunks the insertion of remote docs

commit 0d4e0554
Author: Alfredo Di Napoli <alfredo.dinapoli@gmail.com>
Date:   Mon Jan 13 14:43:16 2025 +0100

    Move terms updating to separate job as well

commit c62480c7
Author: Alfredo Di Napoli <alfredo.dinapoli@gmail.com>
Date:   Mon Jan 13 12:30:19 2025 +0100

    Proper support for importing documents

commit 6019587c
Author: Alfredo Di Napoli <alfredo.dinapoli@gmail.com>
Date:   Mon Jan 6 15:44:13 2025 +0100

    Initial support for importing ngrams

commit 842b3d36
Author: Alfredo Di Napoli <alfredo.dinapoli@gmail.com>
Date:   Mon Jan 6 15:07:21 2025 +0100

    Support exporting docs and ngrams (but not importing them yet)

commit 98708c2e
Author: Alfredo Di Napoli <alfredo.dinapoli@gmail.com>
Date:   Mon Jan 6 12:32:17 2025 +0100

    Support exporting of tree hierarchies (with proviso)

    Exporting a corpus works, as it also exports its children, but for
    example the docs and terms nodes do not have any associated content.
    This is because those are stored in separate DB tables, and we need
    to find a way to export those as well.

commit c248eaf1
Author: Alfredo Di Napoli <alfredo.dinapoli@gmail.com>
Date:   Mon Jan 6 11:50:14 2025 +0100

    Support trees of export nodes (to be tested)

commit dd2049aa
Author: Alfredo Di Napoli <alfredo.dinapoli@gmail.com>
Date:   Mon Jan 6 11:23:30 2025 +0100

    Add getNodes function to Database.Query.Table.Node

commit c429cbb1
Author: Alfredo Di Napoli <alfredo.dinapoli@gmail.com>
Date:   Mon Jan 6 10:39:37 2025 +0100

    Restrict export of nodes to only a few types

commit c648699e
Author: Alfredo Di Napoli <alfredo.dinapoli@gmail.com>
Date:   Mon Jan 6 09:27:28 2025 +0100

    Update deps again (after rebase)

commit 7337820e
Author: Alfredo Di Napoli <alfredo.dinapoli@gmail.com>
Date:   Mon Dec 16 16:07:49 2024 +0100

    Basic Remote API testing

commit 1eb59c52
Author: Alfredo Di Napoli <alfredo.dinapoli@gmail.com>
Date:   Mon Dec 16 15:31:47 2024 +0100

    Barebone (non-streaming) storage of nodes

commit be5e9faf
Author: Alfredo Di Napoli <alfredo.dinapoli@gmail.com>
Date:   Mon Dec 16 14:20:16 2024 +0100

    Send serialised nodes instead of dummy strings

commit aff15b60
Author: Alfredo Di Napoli <alfredo.dinapoli@gmail.com>
Date:   Mon Dec 16 12:07:49 2024 +0100

    Remove redundant test imports

commit 6d776767
Author: Alfredo Di Napoli <alfredo.dinapoli@gmail.com>
Date:   Mon Dec 16 12:01:55 2024 +0100

    Bolt-on ownership check for /remote/export

commit 58d9fcb0
Author: Alfredo Di Napoli <alfredo.dinapoli@gmail.com>
Date:   Mon Dec 16 11:08:11 2024 +0100

    Proper error handling for remote import and export handlers

commit 23a06d28
Author: Alfredo Di Napoli <alfredo.dinapoli@gmail.com>
Date:   Mon Dec 9 15:37:29 2024 +0100

    Update project deps

commit d5096e40
Author: Alfredo Di Napoli <alfredo.dinapoli@gmail.com>
Date:   Mon Dec 2 17:05:04 2024 +0100

    Make a start on the remote (streaming) endpoints

    It typechecks but it exchange only a very simple string and
    it prints it.

commit 3ea32b50
Author: Alfredo Di Napoli <alfredo.dinapoli@gmail.com>
Date:   Mon Dec 2 11:26:11 2024 +0100

    Add _env_remote_transfer_keys field

    This adds a new randomly-generated pair of (PublicKey, PrivateKey) to be
    later used to send messages between instances.

    It also:

    * Returns a remote transfer pub key inside an AuthResponse
    * Adds pubKey roundtrip test

commit 7dd23297
Author: Fabien Maniere <fabien.maniere@cnrs.fr>
Date:   Wed Jan 15 12:33:12 2025 +0100

    update the main gargantext command to lauch app within the start script

commit 8e19bf65
Author: Grégoire Locqueville <gregoire.locqueville@cnrs.fr>
Date:   Wed Jan 8 18:25:01 2025 +0100

    Remove call to `recursiveClustering'`

    Also removed some dead and commented code around the edited area.

    Note: `recursiveClustering'` was not actually recursive, it just went
    one level deeper.

commit 28e2927e
Author: Grégoire Locqueville <gregoire.locqueville@cnrs.fr>
Date:   Mon Dec 2 17:06:29 2024 +0100

    Deal with error with a proper error

    ... instead of returning a `Maybe` to the frontend

commit 54675ae8
Author: Grégoire Locqueville <gregoire.locqueville@cnrs.fr>
Date:   Mon Dec 2 16:27:03 2024 +0100

    Return Maybe (node ID) upon creating a subcorpus

commit d7948acb
Author: Fabien Maniere <fabien.maniere@cnrs.fr>
Date:   Wed Jan 15 17:36:49 2025 +0100

    export to GEXF: adding the weight attribute to all nodes

commit d937e72e
Author: Fabien Manière <fmaniere.pro@gmail.com>
Date:   Wed Apr 24 17:09:27 2024 +0200

    adding weight attribute

[graphql] fix droping field prefixes

See merge request !379

Upgrade 'haskell-bee' version, also bump up versions of some packages

See merge request !377

Resolve "Fix test build warnings"

See merge request !376