Merge remote-tracking branch 'origin/304-dev-toml-config-rewrite-and-update-deps-9.4.8' into dev

.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"

README.md

@@ -238,6 +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="3943da8b9f3ae918afadf2b302875b3b395b31b2f69c3d42135af2ac800b7a0c"
-expected_cabal_project_freeze_hash="af825192f1ec47b07e6001dd2556b59991c9e6c50094dc732ee933a41f0dc9bd"
+expected_cabal_project_hash="3afb11e01938b74ae8419caa160180d8f8628a67315a2d689c3a42a76463071e"
+expected_cabal_project_freeze_hash="de1726d350936da5f5e15140e3be29bb4f44757c5702defe995c2386f1b4a741"
 
 
 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

@@ -8,7 +8,7 @@ constraints: any.Cabal ==3.8.1.0,
              any.JuicyPixels ==3.3.9,
              JuicyPixels -mmap,
              any.KMP ==0.2.0.0,
-             any.MissingH ==1.4.3.1,
+             any.MissingH ==1.6.0.1,
              MissingH +network--ge-3_0_0,
              any.MonadRandom ==0.6,
              any.OneTuple ==0.4.2,
@@ -57,7 +57,7 @@ constraints: any.Cabal ==3.8.1.0,
              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,
@@ -84,7 +84,7 @@ constraints: any.Cabal ==3.8.1.0,
              any.bsb-http-chunked ==0.0.0.4,
              any.byteable ==0.1.1,
              any.byteorder ==1.0.4,
-             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.bzlib-conduit ==0.3.0.3,
@@ -203,13 +203,13 @@ constraints: any.Cabal ==3.8.1.0,
              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,
@@ -395,7 +395,7 @@ constraints: any.Cabal ==3.8.1.0,
              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/stack/lts-21.17.yaml

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

gargantext.cabal

@@ -472,7 +472,7 @@ 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
@@ -485,14 +485,14 @@ 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
@@ -501,16 +501,16 @@ 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
@@ -552,11 +552,11 @@ 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
@@ -649,11 +649,11 @@ 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
@@ -691,7 +691,7 @@ 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
@@ -711,14 +711,14 @@ 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
@@ -740,13 +740,13 @@ 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
@@ -879,7 +879,7 @@ 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

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"
@@ -23,7 +21,6 @@
 - "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"
@@ -32,7 +29,6 @@
 - "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"
@@ -43,7 +39,6 @@
 - "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"
@@ -56,23 +51,20 @@
 - "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"
 - "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"
@@ -87,7 +79,6 @@
 - "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"
@@ -96,14 +87,12 @@
 - "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"
@@ -147,7 +136,6 @@
 - "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"
@@ -703,5 +691,5 @@ flags:
     standalone: true
 packages:
 - .
-resolver: "lts-21.17"
+resolver: "lts-21.25"
 "system-ghc": true

test/Test/Utils/Jobs.hs

@@ -468,7 +468,7 @@ 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" $