Merge branch 'dev' into dev-openalex

.gitignore

@@ -2,9 +2,6 @@
 
 *lock
 
-# Cabal
-*.cabal
-
 # Profiling
 *.prof
 profiling

.gitlab-ci.yml

@@ -2,7 +2,7 @@
 # https://vadosware.io/post/zero-to-continuous-integrated-testing-a-haskell-project-with-gitlab/
 #
 #
-image: adinapoli/gargantext:v1
+image: adinapoli/gargantext:v2
 
 variables:
   STACK_ROOT: "${CI_PROJECT_DIR}/.stack-root"
@@ -13,13 +13,13 @@ variables:
   #- apt-get install make xz-utils
 
 stages:
-  - deps
+  - stack
+  - cabal
   - test
   - docs
-  - cabal
 
-deps:
-  stage: deps
+stack:
+  stage: stack
   cache:
     # cache per branch name
     # key: ${CI_COMMIT_REF_SLUG}
@@ -29,8 +29,7 @@ deps:
       - target
   script:
     - echo "Building the project from '$CI_PROJECT_DIR'"
-    - hpack
-    - nix-shell --run "LC_ALL=C.UTF-8 stack build --no-terminal --haddock --no-haddock-deps --only-dependencies --fast"
+    - nix-shell --run "stack build --no-terminal --haddock --no-haddock-deps --only-dependencies --fast --dry-run"
 
 docs:
   stage: docs
@@ -42,8 +41,7 @@ docs:
       - .stack-work/
       - target
   script:
-    - hpack
-    - nix-shell --run "LC_ALL=C.UTF-8 stack build --no-terminal --haddock --no-haddock-deps --fast"
+    - nix-shell --run "stack build --no-terminal --haddock --no-haddock-deps --fast --dry-run"
     - cp -R "$(stack path --local-install-root)"/doc ./output
   artifacts:
     paths:
@@ -51,24 +49,22 @@ docs:
     expire_in: 1 week
   allow_failure: true
 
-test:
-  stage: test
+cabal:
+  stage: cabal
   cache:
     # cache per branch name
     # key: ${CI_COMMIT_REF_SLUG}
     paths:
       - .stack-root/
       - .stack-work/
+      - dist-newstyle/
       - target
   script:
-    - hpack
-    - nix-shell --run "stack test --no-terminal --fast"
-
-      # TOOO
+    - nix-shell --run "./bin/update-cabal-project && cabal v2-build"
+  allow_failure: false
 
-cabal:
-  # FIXME(adinapoli) A temporary hack until we switch to cabal 3.10.1.0 properly
-  stage: cabal
+test:
+  stage: test
   cache:
     # cache per branch name
     # key: ${CI_COMMIT_REF_SLUG}
@@ -78,7 +74,5 @@ cabal:
       - dist-newstyle/
       - target
   script:
-    - hpack
-    - nix-shell --run "./bin/update-cabal-project && cabal v2-build --dry-run"
-  allow_failure: false
+    - nix-shell --run "cabal v2-test --test-show-details=streaming"
 

README.md

@@ -47,7 +47,7 @@ cd haskell-gargantext
 #### 1. Installation
 
 This project can be built with either Stack or Cabal. For historical
-reasons, we generate a `cabal.project` from the `package.yaml`, and
+reasons, we generate a `cabal.project` from the `stack.yaml`, and
 we do not commit the former to the repo, to have a single "source of truth".
 However, it's always possible to generate a `cabal.project` thanks
 to [stack2cabal](https://hackage.haskell.org/package/stack2cabal).

bin/update-cabal-project

 #!/usr/bin/env bash
 
 cabal v2-update 'hackage.haskell.org,2023-06-25T00:00:00Z'
-cabal v2-install hpack-0.35.0 --overwrite-policy=always
 cabal v2-install stack2cabal-1.0.14 --overwrite-policy=always
 stack2cabal --no-run-hpack -p '2023-06-25'

devops/debian/install

@@ -18,84 +18,40 @@ sudo apt upgrade
 
 # Tmux to avoid disconnections during the installation process
 # Htop for visual monitoring
-sudo apt install tmux htop
+sudo apt install tmux htop git iptables curl
 
 ########################################################################
-sudo sed -i "s/stretch/buster/g" /etc/apt/sources.list
+sudo sed -i "s/bullseye/bookworm/g" /etc/apt/sources.list
 sudo apt update
 sudo apt dist-upgrade
 # sudo reboot #recommended
 ########################################################################
 
 #sudo apt update
-sudo apt install liblzma-dev libpcre3-dev libblas-dev liblapack-dev pkg-config libgsl-dev libbz2-dev postgresql postgresql-server-dev-11 nginx libigraph0-dev libgfortran-9-dev
+sudo apt install postgresql postgresql-server-dev-15
 
-sudo apt install git
 #git config --global user.email "contact@gargantext.org"
 #git config --global user.name "Gargantua"
 
 
 ########################################################################
-echo "Which user?"
-#read USER
-USER="gargantua"
-sudo adduser --disabled-password --gecos "" $USER
 
-########################################################################
-#cd /home
-#sudo mv -if /home/$USER /srv/
-#sudo ln -s /srv/$USER
-
-curl -sSL https://get.haskellstack.org/ | sh
-
-sudo apt install curl
-sudo su $USER
-stack update
-stack upgrade
-
-#git clone https://gitlab.iscpif.fr/gargantext/haskell-gargantext.git
-
-#cd haskell-gargantext
-##########
-
-if [[ ! -d "purescript-gargantext" ]]; then
-  ./devops/debian/install-purescript
-fi
-
-#########################################################################
-
-# stack install should be enough but all process is the following steps
-stack setup && stack build && stack install
+echo "Installing Nix"
+sh <(curl -L https://nixos.org/nix/install) --daemon
 
-#########################################################################
-# build deps
-
-
-if [[ ! -d "deps" ]]; then
-  mkdir -v deps
-  cd deps
-
-  sudo apt install default-jdk
-  if [[ ! -f "coreNLP.tar.bz2" ]]; then
-    wget https://dl.gargantext.org/coreNLP.tar.bz2
-  fi
-  if [[ ! -d "home" ]]; then
-    tar xvjf coreNLP.tar.bz2
-  fi
-  # CoreNLP needs to be started
-  # ./startServer.sh
-
-  cd ..
-fi
+#######################################################################
+# Get the Sources
+git clone https://gitlab.iscpif.fr/gargantext/haskell-gargantext.git
+cd haskell-gargantext
+git clone https://gitlab.iscpif.fr/gargantext/purescript-gargantext.git
 
 
-# Specific to our servers
 
 #### Configure timezone and locale ###################################
 # todo sync dates
 #echo "###########  LOCALES & TZ #################"
 #echo "Europe/Paris" > /etc/timezone
-#dpkg-reconfigure --frontend=noninteractive tzdata
+#sudo dpkg-reconfigure --frontend=noninteractive tzdata
 ##ENV TZ "Europe/Paris"
 #
 #sed -i -e 's/# en_GB.UTF-8 UTF-8/en_GB.UTF-8 UTF-8/' /etc/locale.gen && \
@@ -109,13 +65,12 @@ fi
 # Database configuration
 # CREATE USER gargantua WITH PASSWORD $(grep DB_PASS gargantext.ini)
 # GRANT ALL PRIVILEGES ON DATABASE gargandbV4 to gargantua
+# sudo su postgres
+# createdb gargandb
 
 #######################################################################
 ## POSTGRESQL DATA (as ROOT)
 #######################################################################
-
-./devops/debian/install-postgres
-
 # configure the database with script in devops/postgres
 # edit gargantext.ini
 

devops/docker/Dockerfile

@@ -4,9 +4,16 @@ ARG DEBIAN_FRONTEND=noninteractive
 ARG GHC=8.10.7
 ARG STACK=2.7.3
 ARG CABAL=3.10.1.0
-COPY ./shell.nix            /builds/gargantext/shell.nix
-COPY ./nix/pkgs.nix         /builds/gargantext/nix/pkgs.nix
-COPY ./nix/pinned-22.05.nix /builds/gargantext/nix/pinned-22.05.nix
+COPY ./shell.nix                                       /builds/gargantext/shell.nix
+COPY ./nix/pkgs.nix                                    /builds/gargantext/nix/pkgs.nix
+COPY ./nix/pinned-22.05.nix                            /builds/gargantext/nix/pinned-22.05.nix
+COPY ./nix/overlays/Cabal-3.10.1.0.nix                 /builds/gargantext/nix/overlays/Cabal-3.10.1.0.nix
+COPY ./nix/overlays/cabal-install-3.10.1.0.nix         /builds/gargantext/nix/overlays/cabal-install-3.10.1.0.nix
+COPY ./nix/overlays/cabal-install-solver-3.10.1.0.nix  /builds/gargantext/nix/overlays/cabal-install-solver-3.10.1.0.nix
+COPY ./nix/overlays/Cabal-syntax-3.10.1.0.nix          /builds/gargantext/nix/overlays/Cabal-syntax-3.10.1.0.nix
+COPY ./nix/overlays/directory-1.3.7.0.nix              /builds/gargantext/nix/overlays/directory-1.3.7.0.nix
+COPY ./nix/overlays/hackage-security-0.6.2.3.nix       /builds/gargantext/nix/overlays/hackage-security-0.6.2.3.nix
+COPY ./nix/overlays/process-1.6.15.0.nix               /builds/gargantext/nix/overlays/process-1.6.15.0.nix
 
 ENV TZ=Europe/Rome
 RUN apt-get update && \
@@ -61,19 +68,7 @@ ENV PATH=/root/.nix-profile/bin:$PATH
 
 RUN . $HOME/.bashrc && nix-env --version
 
-RUN \
-curl https://downloads.haskell.org/~ghcup/x86_64-linux-ghcup > /usr/bin/ghcup && \
-    chmod +x /usr/bin/ghcup && \
-    ghcup config set gpg-setting GPGLax && \
-    ghcup -v install ghc --force ${GHC} && \
-    ghcup -v install cabal --force ${CABAL} && \
-    ghcup -v install stack --force ${STACK}
-
-ENV PATH=/root/.ghcup/bin:$PATH
 ENV PATH=/root/.local/bin:$PATH
 
-
 RUN cd /builds/gargantext && nix-shell
-RUN ghcup set 8.10.7 && cabal v2-update && cabal v2-install hpack --overwrite-policy=always
-
 WORKDIR "/builds/gargantext/"

gargantext.cabal

 cabal-version: 1.12
 
--- This file has been generated from package.yaml by hpack version 0.35.1.
---
--- see: https://github.com/sol/hpack
-
 name:           gargantext
 version:        0.0.6.9.9.7
 synopsis:       Search, map, share
@@ -59,12 +55,13 @@ library
       Gargantext.Core.Text.Context
       Gargantext.Core.Text.Corpus.API
       Gargantext.Core.Text.Corpus.API.Arxiv
-      Gargantext.Core.Text.Corpus.API.Pubmed
       Gargantext.Core.Text.Corpus.API.OpenAlex
+      Gargantext.Core.Text.Corpus.API.Pubmed
       Gargantext.Core.Text.Corpus.Query
       Gargantext.Core.Text.Corpus.Parsers
       Gargantext.Core.Text.Corpus.Parsers.CSV
       Gargantext.Core.Text.Corpus.Parsers.Date.Parsec
+      Gargantext.Core.Text.Corpus.Parsers.JSON
       Gargantext.Core.Text.List.Formats.CSV
       Gargantext.Core.Text.Metrics
       Gargantext.Core.Text.Metrics.CharByChar
@@ -203,7 +200,6 @@ library
       Gargantext.Core.Text.Corpus.Parsers.GrandDebat
       Gargantext.Core.Text.Corpus.Parsers.Iramuteq
       Gargantext.Core.Text.Corpus.Parsers.Isidore
-      Gargantext.Core.Text.Corpus.Parsers.JSON
       Gargantext.Core.Text.Corpus.Parsers.Json2Csv
       Gargantext.Core.Text.Corpus.Parsers.RIS
       Gargantext.Core.Text.Corpus.Parsers.RIS.Presse