Merge branch 'dev' into 238-dev-async-job-worker

.gitignore

@@ -33,7 +33,6 @@ deps
 _darcs
 *.pdf
 *.png
-*.sql
 *.ini
 *.toml
 !test-data/test_config.ini

.gitlab-ci.yml

 # Optimising CI speed by using tips from https://blog.nimbleways.com/let-s-make-faster-gitlab-ci-cd-pipelines/
-image: adinapoli/gargantext:v3.4
+#image: adinapoli/gargantext:v3.4
+image: cgenie/gargantext:9.4.8
 
 variables:
   STACK_ROOT: "${CI_PROJECT_DIR}/.stack-root"

CHANGELOG.md

+## Version 0.0.7.3 [/!\ Maintenance command inside]
+
+* [BACK][FIX][Upgrade to GHC 9.4.8][Switch from .ini to TOML? (#304)](https://gitlab.iscpif.fr/gargantext/haskell-gargantext/issues/304)
+* [BACK][CLEAN][Unused trigger](https://gitlab.iscpif.fr/gargantext/haskell-gargantext/merge_requests/345)
+  * ``` $ ./bin/psql gargantext.ini < devops/postgres/upgrade/0.0.7.3.sql```
+* [BACK][Update Readme](https://gitlab.iscpif.fr/gargantext/haskell-gargantext/merge_requests/346)
+* [FRONT][FIX][[Node document] Display the db source of a document (with authors, etc.) (#695)](https://gitlab.iscpif.fr/gargantext/purescript-gargantext/issues/695)
+* [FRONT][FIX][Add separators between keywords in phylo (#696)](https://gitlab.iscpif.fr/gargantext/purescript-gargantext/issues/696)
+* [FRONT][FIX][[Node Terms] In settings, on the download tab, put JSON as default selectbox choice, instead of the current JSON (zipped) (#691)](https://gitlab.iscpif.fr/gargantext/purescript-gargantext/issues/691)
+* [BACK][FIX][Order 2] Back to previous parameter WIP
+
 ## Version 0.0.7.2.8
 
 * [BACK][FEAT][Switch from .ini to TOML? (#304)](https://gitlab.iscpif.fr/gargantext/haskell-gargantext/issues/304)
@@ -7,7 +18,6 @@
 * [DOC][README][Little update to README, docs and .gitignore
   interface](https://gitlab.iscpif.fr/gargantext/haskell-gargantext/merge_requests/343)
 
-
 ## Version 0.0.7.2.7
 
 * [BACK][FEAT][Switch from .ini to TOML? (#304)](https://gitlab.iscpif.fr/gargantext/haskell-gargantext/issues/304)

README.md

@@ -190,9 +190,11 @@ The initialization schema should be loaded automatically from `devops/postgres/s
 $ cp gargantext-settings.toml_toModify gargantext-settings.toml
 ```
 
-**NOTE** If you had the `gargantext.ini` file before, you can automatically generate toml with:
+**NOTE** If you had the `gargantext.ini` file before, you can automatically
+convert it into a file `gargantext-settings.toml` by running the following
+from a Nix shell:
 ```shell
-n$ cabal v2-run gargantext-cli -- ini --ini-path ./gargantext.ini > gargantext-settings.toml
+n$ cabal v2-run gargantext-cli -- ini
 ```
 
 > `.gitignore` excludes this file, so you don't need to worry about
@@ -236,6 +238,27 @@ If you want to run particular tests, use:
 cabal v2-test garg-test-tasty --test-show-details=streaming --test-option=--pattern='/job status update and tracking/
 ```
 
+### CI
+
+The CI is on gitlab and is controlled by the `.gitlab-ci.yml` file.
+
+The Docker image that is used can be built with:
+```shell
+podman build -t cgenie/gargantext:9.4.8 -f ./devops/docker/Dockerfile --format=docker .
+```
+or
+```shell
+docker build -t cgenie/gargantext:9.4.8 -f ./devops/docker/Dockerfile .
+```
+
+NOTE: if podman/docker complains about not enough space, it's probably
+about tmpfs. In that case you can set
+```shell
+mkdir _build
+export TMPDIR=$(pwd)/_build
+```
+(https://stackoverflow.com/questions/75845647/changing-podman-build-to-path-with-more-space).
+
 ### Working on libraries
 
 When a devlopment is needed on libraries (for instance, the HAL crawler in https://gitlab.iscpif.fr/gargantext/crawlers):

bin/update-project-dependencies

@@ -18,13 +18,12 @@ fi
 # with the `sha256sum` result calculated on the `cabal.project` and
 # `cabal.project.freeze`. This ensures the files stay deterministic so that CI
 # cache can kick in.
-expected_cabal_project_hash="5abb6f7a57b0d90232d829c662d08caec87a82b4a302fba095bf22e8e3fd840a"
-expected_cabal_project_freeze_hash="7f170787195aa7ab37bbfbe6a530b64e4ecf44eb0fd8e34a76c3769d2d9cc042"
+expected_cabal_project_hash="9714d7562e90ad8438108ac87d47c9afdb741b67e34349efb9f65ead0f94cfd8"
+expected_cabal_project_freeze_hash="30dd1cf2cb2015351dd0576391d22b187443b1935c2be23599b821ad1ab95f23"
 
 
 cabal --store-dir=$STORE_DIR v2-build --dry-run
-cabal2stack --system-ghc --allow-newer --resolver lts-21.17 --resolver-file devops/stack/lts-21.17.yaml -o stack.yaml
-cabal --store-dir=$STORE_DIR v2-freeze
+cabal2stack --system-ghc --allow-newer --resolver lts-21.25 --resolver-file devops/stack/lts-21.25.yaml -o stack.yaml
 
 # Run 'sed' to remove the constraint for 'gargantext', as it doesn't make sense and
 # for the test we need to run this with a different flag.

cabal.project

@@ -3,7 +3,7 @@
 -- index-state: 2023-12-10T10:34:46Z
 index-state: 2024-09-12T03:02:26Z
 
-with-compiler: ghc-9.4.7
+with-compiler: ghc-9.4.8
 optimization: 2
 
 packages:

cabal.project.freeze

@@ -9,9 +9,7 @@ constraints: any.Boolean ==0.2.4,
              any.JuicyPixels ==3.3.9,
              JuicyPixels -mmap,
              any.KMP ==0.2.0.0,
-             any.MemoTrie ==0.6.11,
-             MemoTrie -examples,
-             any.MissingH ==1.4.3.1,
+             any.MissingH ==1.6.0.1,
              MissingH +network--ge-3_0_0,
              any.MonadRandom ==0.6,
              any.NumInstances ==1.4,
@@ -61,7 +59,7 @@ constraints: any.Boolean ==0.2.4,
              any.authenticate-oauth ==1.7,
              any.auto-update ==0.1.6,
              any.barbies ==2.1.1.0,
-             any.base ==4.17.2.0,
+             any.base ==4.17.2.1,
              any.base-compat ==0.13.1,
              any.base-compat-batteries ==0.13.1,
              any.base-orphans ==0.9.2,
@@ -88,8 +86,7 @@ constraints: any.Boolean ==0.2.4,
              any.bsb-http-chunked ==0.0.0.4,
              any.byteable ==0.1.1,
              any.byteorder ==1.0.4,
-             any.bytes ==0.17.3,
-             any.bytestring ==0.11.5.2,
+             any.bytestring ==0.11.5.3,
              any.bytestring-builder ==0.10.8.2.0,
              bytestring-builder +bytestring_has_builder,
              any.bytestring-lexing ==0.5.0.14,
@@ -210,13 +207,13 @@ constraints: any.Boolean ==0.2.4,
              any.generic-monoid ==0.1.0.1,
              any.generically ==0.1.1,
              any.generics-sop ==0.5.1.3,
-             any.ghc ==9.4.7,
+             any.ghc ==9.4.8,
              any.ghc-bignum ==1.3,
-             any.ghc-boot ==9.4.7,
-             any.ghc-boot-th ==9.4.7,
-             any.ghc-heap ==9.4.7,
+             any.ghc-boot ==9.4.8,
+             any.ghc-boot-th ==9.4.8,
+             any.ghc-heap ==9.4.8,
              any.ghc-prim ==0.9.1,
-             any.ghci ==9.4.7,
+             any.ghci ==9.4.8,
              any.githash ==0.1.7.0,
              any.graphviz ==2999.20.2.0,
              graphviz -test-parsing,
@@ -410,7 +407,7 @@ constraints: any.Boolean ==0.2.4,
              any.primitive ==0.7.4.0,
              any.primitive-extras ==0.10.2,
              any.primitive-unlifted ==2.1.0.0,
-             any.process ==1.6.17.0,
+             any.process ==1.6.18.0,
              any.product-profunctors ==0.11.1.1,
              any.profunctors ==5.6.2,
              any.promises ==0.3,

devops/docker/Dockerfile

@@ -3,7 +3,7 @@ FROM ubuntu:noble
 ## NOTA BENE: In order for this to be built successfully, you have to run ./devops/coreNLP/build.sh first.
 
 ARG DEBIAN_FRONTEND=noninteractive
-ARG GHC=9.4.7
+ARG GHC=9.4.8
 ARG CORENLP=4.5.4
 ARG CORE
 COPY ./shell.nix                                       /builds/gargantext/shell.nix

devops/postgres/upgrade/0.0.7.3.sql

+-- This removes the trigger prevening ngrams deletion
+-- because the function was not working.
+
+DROP TRIGGER check_ngrams_json_trg ON ngrams;
+DROP FUNCTION check_ngrams_json;

devops/stack/lts-21.17.yaml

+# https://github.com/commercialhaskell/stackage-snapshots/blob/master/lts/21/17.yaml
 flags:
   HsOpenSSL:
     fast-bignum: false

gargantext.cabal

@@ -5,7 +5,7 @@ cabal-version: 3.4
 -- see: https://github.com/sol/hpack
 
 name:           gargantext
-version: 0.0.7.2.8
+version: 0.0.7.3
 synopsis:       Search, map, share
 description:    Please see README.md
 category:       Data
@@ -477,7 +477,7 @@ library
     cpp-options: -DNO_PHYLO_DEBUG_LOGS
   build-depends:
       KMP ^>= 0.2.0.0
-    , MissingH ^>= 1.4.3.0
+    , MissingH ^>= 1.6.0.1
     , MonadRandom ^>= 0.6
     , QuickCheck ^>= 2.14.2
     , accelerate ^>= 1.3.0.0
@@ -490,14 +490,14 @@ library
     , base64-bytestring ^>= 1.2.1.0
     , bimap >= 0.5.0
     , boolexpr ^>= 0.3
-    , bytestring ^>= 0.11.5.2
+    , bytestring ^>= 0.11.5.3
     , cache >= 0.1.3.0
     , case-insensitive ^>= 1.2.1.0
     , cassava ^>= 0.5.2.0
     , cereal ^>= 0.5.8.2
     , clock >= 0.8
     , conduit ^>= 1.3.4.2
-    , containers ^>= 0.6.5.1
+    , containers ^>= 0.6.7
     , crawlerArxiv
     , crawlerHAL
     , crawlerISTEX
@@ -506,16 +506,16 @@ library
     , cron ^>= 0.7.0
     , data-time-segment ^>= 0.1.0.0
     , deferred-folds >= 0.9.18 && < 0.10
-    , directory ^>= 1.3.6.0
+    , directory ^>= 1.3.7.1
     , discrimination >= 0.5
     , ekg-core ^>= 0.1.1.7
     , ekg-json ^>= 0.1.0.7
     , epo-api-client
-    , exceptions ^>= 0.10.4
+    , exceptions ^>= 0.10.5
     , extra ^>= 1.7.9
     , fast-logger ^>= 3.2.2
     , fgl ^>= 5.8.0.0
-    , filepath ^>= 1.4.2.1
+    , filepath ^>= 1.4.2.2
     , fmt
     , formatting ^>= 7.2.0
     , fullstop ^>= 0.1.4
@@ -559,11 +559,11 @@ library
     , opaleye-textsearch >= 0.2.0.0
     , openalex
     , parallel ^>= 3.2.2.0
-    , parsec ^>= 3.1.14.0
+    , parsec ^>= 3.1.16.1
     , patches-class ^>= 0.1.0.1
     , patches-map ^>= 0.1.0.1
     , postgresql-simple ^>= 0.6.4
-    , process ^>= 1.6.13.2
+    , process ^>= 1.6.18.0
     , product-profunctors ^>= 0.11.0.3
     , protolude ^>= 0.3.3
     , quickcheck-instances ^>= 0.3.25.2
@@ -657,11 +657,11 @@ executable gargantext-cli
       aeson ^>= 2.1.2.1
     , aeson-pretty
     , async ^>= 2.2.4
-    , bytestring ^>= 0.11.5.2
+    , bytestring ^>= 0.11.5.3
     , cassava ^>= 0.5.2.0
-    , containers ^>= 0.6.5.1
+    , containers ^>= 0.6.7
     , cryptohash ^>= 0.11.9
-    , directory ^>= 1.3.6.0
+    , directory ^>= 1.3.7.1
     , extra ^>= 1.7.9
     , gargantext
     , gargantext-prelude
@@ -700,7 +700,7 @@ executable gargantext-server
       bin/gargantext-server
   build-depends:
       cassava ^>= 0.5.2.0
-    , containers ^>= 0.6.5.1
+    , containers ^>= 0.6.7
     , extra ^>= 1.7.9
     , gargantext
     , gargantext-prelude
@@ -720,14 +720,14 @@ common testDependencies
     , aeson-qq
     , async ^>= 2.2.4
     , boolexpr ^>= 0.3
-    , bytestring ^>= 0.11.5.2
+    , bytestring ^>= 0.11.5.3
     , cache >= 0.1.3.0
     , case-insensitive
     , conduit ^>= 1.3.4.2
-    , containers ^>= 0.6.5.1
+    , containers ^>= 0.6.7
     , crawlerArxiv
     , cryptohash
-    , directory
+    , directory ^>= 1.3.7.1
     , epo-api-client
     , extra ^>= 1.7.9
     , fast-logger ^>= 3.2.2
@@ -749,13 +749,13 @@ common testDependencies
     , monad-control >= 1.0.3 && < 1.1
     , mtl ^>= 2.2.2
     , network-uri
-    , parsec ^>= 3.1.14.0
+    , parsec ^>= 3.1.16.1
     , patches-class ^>= 0.1.0.1
     , patches-map ^>= 0.1.0.1
     , postgres-options >= 0.2 && < 0.3
     , postgresql-simple >= 0.6.4 && < 0.7
-    , pretty
-    , process ^>= 1.6.13.2
+    , pretty ^>= 1.1.3.6
+    , process ^>= 1.6.18.0
     , protolude ^>= 0.3.3
     , quickcheck-instances ^>= 0.3.25.2
     , raw-strings-qq
@@ -889,7 +889,7 @@ benchmark garg-bench
   other-modules:
       Paths_gargantext
   build-depends: base
-               , bytestring ^>= 0.11.5.2
+               , bytestring ^>= 0.11.5.3
                , gargantext
                , gargantext-prelude
                , tasty-bench

nix/pkgs.nix

@@ -2,8 +2,8 @@
 
 rec {
   inherit pkgs;
-  ghc947 = if pkgs.stdenv.isDarwin
-           then pkgs.haskell.compiler.ghc947.overrideAttrs (finalAttrs: previousAttrs: {
+  ghc948 = if pkgs.stdenv.isDarwin
+           then pkgs.haskell.compiler.ghc948.overrideAttrs (finalAttrs: previousAttrs: {
                 patches = previousAttrs.patches ++ [
                             # Reverts the linking behavior of GHC to not resolve `-libc++` to `c++`.
                             (pkgs.fetchpatch {
@@ -12,8 +12,8 @@ rec {
                             })
                           ];
                 })
-           else pkgs.haskell.compiler.ghc947;
-  cabal_install_3_10_1_0 = pkgs.haskell.lib.compose.justStaticExecutables pkgs.haskell.packages.ghc947.cabal-install;
+           else pkgs.haskell.compiler.ghc948;
+  cabal_install_3_10_2_1 = pkgs.haskell.lib.compose.justStaticExecutables pkgs.haskell.packages.ghc948.cabal-install;
   graphviz_dev = pkgs.graphviz.overrideAttrs (finalAttrs: previousAttrs: {
     version = "11.0.0~dev";
     src = pkgs.fetchFromGitLab {
@@ -95,8 +95,8 @@ rec {
 
   });
   hsBuildInputs = [
-    ghc947
-    cabal_install_3_10_1_0
+    ghc948
+    cabal_install_3_10_2_1
     pkgs.haskellPackages.alex
     pkgs.haskellPackages.happy
     pkgs.haskellPackages.pretty-show

src/Gargantext/Core/Methods/Similarities/Accelerate/Distributional.hs

@@ -205,8 +205,8 @@ logDistributional' n m' = trace ("logDistributional'") result
     -- m_{i,j} = 0 if n_{i,j} = 0 or i = j, 
     -- m_{i,j} = log(to * n_{i,j} / s_{i,j}) otherwise.
     mi = (.*) (matrixEye n)
-              (map (lift1 (\x -> let x' = x * to in cond (x' < 0.5) 0 (log x'))) ((./) m ss))
-              -- (map (lift1 (\x -> let x' = x * to in cond (x' < 1) 0 (log x'))) ((./) m ss))
+              -- (map (lift1 (\x -> let x' = x * to in cond (x' < 0.5) 0 (log x'))) ((./) m ss))
+              (map (lift1 (\x -> let x' = x * to in cond (x' < 1) 0 (log x'))) ((./) m ss))
     -- mi_nnz :: Int
     -- mi_nnz = flip indexArray Z . run $
     --   foldAll (+) 0 $ map (\a -> ifThenElse (abs a < 10^(-6 :: Exp Int)) 0 1) mi

stack.yaml

@@ -2,13 +2,11 @@
 "extra-deps":
 - "JuicyPixels-3.3.9"
 - "KMP-0.2.0.0"
-- "MissingH-1.4.3.1"
 - "OneTuple-0.4.2"
 - "aeson-pretty-0.8.10"
 - "alex-3.5.1.0"
 - "ansi-terminal-1.0.2"
 - "assoc-1.1.1"
-- "async-2.2.5"
 - "atomic-primops-0.8.8"
 - "barbies-2.1.1.0"
 - "base-compat-0.13.1"
@@ -24,7 +22,6 @@
 - "cabal-doctest-1.0.10"
 - "cassava-0.5.3.2"
 - "cassava-conduit-0.6.6"
-- "cborg-0.2.10.0"
 - "concurrent-output-1.10.21"
 - "conduit-1.3.6"
 - "criterion-measurement-0.2.2.0"
@@ -33,7 +30,6 @@
 - "crypton-x509-1.7.7"
 - "data-fix-0.3.4"
 - "dec-0.0.6"
-- "deferred-folds-0.9.18.6"
 - "digest-0.0.2.1"
 - "double-conversion-2.0.5.0"
 - "extra-1.7.16"
@@ -44,7 +40,6 @@
 - "foldl-1.4.17"
 - "free-5.2"
 - "fullstop-0.1.4"
-- "graphviz-2999.20.2.0"
 - "hashable-1.4.4.0"
 - "haskell-src-meta-0.8.14"
 - "hedgehog-1.5"
@@ -57,24 +52,21 @@
 - "hspec-expectations-0.8.4"
 - "http-accept-0.2"
 - "http-api-data-0.5.1"
+- "http-client-0.7.14"
 - "http-conduit-2.3.8.3"
-- "http-types-0.12.4"
 - "http2-5.0.1"
 - "indexed-traversable-0.1.4"
 - "invariant-0.6.3"
 - "iproute-1.7.14"
-- "jose-0.10.0.1"
 - "json-stream-0.4.6.0"
 - "kan-extensions-5.2.6"
 - "language-c-0.9.3"
 - "libyaml-0.1.4"
 - "libyaml-clib-0.2.5"
-- "lifted-async-0.10.2.5"
 - "linear-1.23"
 - "logict-0.8.1.0"
 - "lzma-0.0.1.1"
 - "math-functions-0.3.4.4"
-- "matrix-0.3.6.3"
 - "megaparsec-9.6.1"
 - "microlens-th-0.4.3.15"
 - "mono-traversable-1.0.17.0"
@@ -89,7 +81,6 @@
 - "morpheus-graphql-subscriptions-0.24.3"
 - "mwc-random-0.15.1.0"
 - "network-control-0.0.2"
-- "old-time-1.1.0.4"
 - "ordered-containers-0.2.4"
 - "os-string-2.0.6"
 - "password-3.0.4.0"
@@ -98,14 +89,12 @@
 - "primitive-extras-0.10.2"
 - "primitive-unlifted-2.1.0.0"
 - "protolude-0.3.4"
-- "psqueues-0.2.8.0"
 - "rake-0.0.1"
 - "random-1.2.1.2"
 - "recover-rtti-0.4.3"
 - "reflection-2.1.8"
 - "resourcet-1.3.0"
 - "safe-0.3.21"
-- "serialise-0.2.6.1"
 - "servant-0.20.2"
 - "servant-auth-0.4.2.0"
 - "servant-auth-client-0.4.2.0"
@@ -150,7 +139,6 @@
 - "validity-0.12.1.0"
 - "vector-0.12.3.1"
 - "vector-algorithms-0.9.0.2"
-- "wai-3.2.4"
 - "wai-app-static-3.1.9"
 - "wai-extra-3.1.15"
 - "wai-logger-2.4.1"
@@ -721,5 +709,5 @@ flags:
     standalone: true
 packages:
 - .
-resolver: "lts-21.17"
+resolver: "lts-21.25"
 "system-ghc": true

test/Test/Utils/Jobs.hs

@@ -472,7 +472,7 @@ test = do
       testExceptions
     it "fairly picks equal-priority-but-different-kind jobs" $
       testFairness
-  describe "job status update and tracking" $ do
+  describe "job status update and tracking" $ sequential $ do
     it "can fetch the latest job status" $
       testFetchJobStatus
     it "can spin two separate jobs and track their status separately" $