From 67984c0fe7612be1772f187af136c0567a319dd5 Mon Sep 17 00:00:00 2001
From: Yoann Apel <yoann.apel@ign.fr>
Date: Wed, 9 Oct 2024 17:15:54 +0200
Subject: [PATCH 01/36] add github actions to deploy docker on ghcr

---
 .github/workflows/cicd_deploy.yml | 69 +++++++++++++++++++++++++++++++
 Makefile                          | 18 ++++++--
 2 files changed, 84 insertions(+), 3 deletions(-)
 create mode 100644 .github/workflows/cicd_deploy.yml

diff --git a/.github/workflows/cicd_deploy.yml b/.github/workflows/cicd_deploy.yml
new file mode 100644
index 00000000..2b6f721a
--- /dev/null
+++ b/.github/workflows/cicd_deploy.yml
@@ -0,0 +1,69 @@
+
+name: cicd_deploy
+
+on:
+  # Also run when the pull request merges  (which generates a push)
+  # So that we can tag the docker image appropriately.
+  push:
+    tags: [ 'v*.*.*' ]
+
+env:
+  IMAGE_NAME:  ${{ github.repository }}
+  REGISTRY: ghcr.io
+  TEST_TAG:  ${{ github.repository }}:test
+
+jobs:
+  deploy_docker:
+    runs-on: ubuntu-latest
+
+    permissions:
+      packages: write
+
+    steps:
+    - name: Checkout branch
+      uses: actions/checkout@v4
+
+    - name: Build the Docker image
+      id: build
+      uses: docker/build-push-action@v5
+      with:
+        load: true
+        tags: ${{ env.TEST_TAG }}
+
+    # run the test on the docker image
+    - name: Run tests in docker image
+      run: >
+        docker run
+        --ipc=host
+        ${{ env.TEST_TAG }}
+        python -m pytest ./test -s --log-cli-level DEBUG
+
+    # Login against a Docker registry except on PR
+    # https://github.com/docker/login-action
+    - name: Log into registry ${{ env.REGISTRY }}
+      if: github.event_name != 'pull_request'
+      uses: docker/login-action@v2
+      with:
+        registry: ${{ env.REGISTRY }}
+        username: ${{ github.actor }}
+        password: ${{ secrets.GITHUB_TOKEN }}
+
+    # Extract metadata (tags, labels) for Docker
+    # https://github.com/docker/metadata-action
+    - name: Extract Docker metadata
+      if: github.event_name != 'pull_request'
+      id: meta
+      uses: docker/metadata-action@v5
+      with:
+        images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+
+    # Build an Docker image with Buildx (don't on PR)
+    # https://github.com/docker/build-push-action
+    - name: Build and push Docker image
+      id: build-and-push
+      uses: docker/build-push-action@v5
+      with:
+        context: .
+        push: true
+        tags: ${{ steps.meta.outputs.tags }}
+        labels: ${{ steps.meta.outputs.labels }}
\ No newline at end of file
diff --git a/Makefile b/Makefile
index 49748893..676546be 100644
--- a/Makefile
+++ b/Makefile
@@ -21,12 +21,24 @@ mamba-env-update:
 # Docker
 ##############################
 
-PROJECT_NAME=lidar_hd/lidro
+REGISTRY=ghcr.io
+IMAGE_NAME=lidro
+NAMESPACE=ignf
 VERSION=`python -m lidro._version`
+FULL_IMAGE_NAME=${REGISTRY}/${NAMESPACE}/${IMAGE_NAME}:${VERSION}
+
 
 docker-build:
-	docker build -t ${PROJECT_NAME}:${VERSION} -f Dockerfile .
+	docker build --no-cache -t ${IMAGE_NAME}:${VERSION} -f Dockerfile .
+
+docker-test:
+	docker run --rm -it ${IMAGE_NAME}:${VERSION} python -m pytest -s
 
 docker-remove:
-	docker rmi -f `docker images | grep ${PROJECT_NAME} | tr -s ' ' | cut -d ' ' -f 3`
+	docker rmi -f `docker images | grep ${IMAGE_NAME} | tr -s ' ' | cut -d ' ' -f 3`
 	docker rmi -f `docker images -f "dangling=true" -q`
+
+docker-deploy:
+	docker tag ${IMAGE_NAME}:${VERSION} ${FULL_IMAGE_NAME}
+	docker push ${FULL_IMAGE_NAME}
+

From 19ee9cc992eb2525ee77d7ef1681c76ca563c03a Mon Sep 17 00:00:00 2001
From: Yoann Apel <yoann.apel@ign.fr>
Date: Wed, 9 Oct 2024 17:25:52 +0200
Subject: [PATCH 02/36] test cicd file

---
 .github/workflows/cicd_deploy.yml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/cicd_deploy.yml b/.github/workflows/cicd_deploy.yml
index 2b6f721a..79e447bf 100644
--- a/.github/workflows/cicd_deploy.yml
+++ b/.github/workflows/cicd_deploy.yml
@@ -2,10 +2,10 @@
 name: cicd_deploy
 
 on:
-  # Also run when the pull request merges  (which generates a push)
-  # So that we can tag the docker image appropriately.
-  push:
-    tags: [ 'v*.*.*' ]
+  pull_request:
+    branches:
+      - main
+      - dev
 
 env:
   IMAGE_NAME:  ${{ github.repository }}

From 2857ef24843fe676e7f65601c40060627f8a3783 Mon Sep 17 00:00:00 2001
From: Yoann Apel <yoann.apel@ign.fr>
Date: Wed, 9 Oct 2024 17:54:28 +0200
Subject: [PATCH 03/36] to fixup

---
 .github/workflows/cicd_deploy.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/cicd_deploy.yml b/.github/workflows/cicd_deploy.yml
index 79e447bf..e9f9d7c2 100644
--- a/.github/workflows/cicd_deploy.yml
+++ b/.github/workflows/cicd_deploy.yml
@@ -63,6 +63,8 @@ jobs:
       id: build-and-push
       uses: docker/build-push-action@v5
       with:
+        ssh-key: ${{ secrets.DEPLOYER_SSHKEY }}
+        submodules: true
         context: .
         push: true
         tags: ${{ steps.meta.outputs.tags }}

From e0645c60c09263d03ae102c34a0c4750ea0b8192 Mon Sep 17 00:00:00 2001
From: Yoann Apel <yoann.apel@ign.fr>
Date: Wed, 9 Oct 2024 17:56:29 +0200
Subject: [PATCH 04/36] to fixup

---
 .github/workflows/cicd_deploy.yml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/.github/workflows/cicd_deploy.yml b/.github/workflows/cicd_deploy.yml
index e9f9d7c2..0495fcee 100644
--- a/.github/workflows/cicd_deploy.yml
+++ b/.github/workflows/cicd_deploy.yml
@@ -63,8 +63,7 @@ jobs:
       id: build-and-push
       uses: docker/build-push-action@v5
       with:
-        ssh-key: ${{ secrets.DEPLOYER_SSHKEY }}
-        submodules: true
+        submodules: false
         context: .
         push: true
         tags: ${{ steps.meta.outputs.tags }}

From 2a7169148e326422c6db11bd5f1be0edb952df8e Mon Sep 17 00:00:00 2001
From: Yoann Apel <yoann.apel@ign.fr>
Date: Wed, 9 Oct 2024 18:11:19 +0200
Subject: [PATCH 05/36] to fixup

---
 .github/workflows/cicd_deploy.yml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/cicd_deploy.yml b/.github/workflows/cicd_deploy.yml
index 0495fcee..13d0a83b 100644
--- a/.github/workflows/cicd_deploy.yml
+++ b/.github/workflows/cicd_deploy.yml
@@ -63,7 +63,9 @@ jobs:
       id: build-and-push
       uses: docker/build-push-action@v5
       with:
-        submodules: false
+        submodules:
+          include: []
+          recursive: false
         context: .
         push: true
         tags: ${{ steps.meta.outputs.tags }}

From 0abe69149d1f6a1dee97c5eb23902e8b8630ba5f Mon Sep 17 00:00:00 2001
From: Yoann Apel <yoann.apel@ign.fr>
Date: Wed, 9 Oct 2024 18:12:19 +0200
Subject: [PATCH 06/36] to fixup

---
 .github/workflows/cicd_deploy.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/cicd_deploy.yml b/.github/workflows/cicd_deploy.yml
index 13d0a83b..346c71aa 100644
--- a/.github/workflows/cicd_deploy.yml
+++ b/.github/workflows/cicd_deploy.yml
@@ -62,10 +62,10 @@ jobs:
     - name: Build and push Docker image
       id: build-and-push
       uses: docker/build-push-action@v5
+      submodules:
+        include: []
+        recursive: false
       with:
-        submodules:
-          include: []
-          recursive: false
         context: .
         push: true
         tags: ${{ steps.meta.outputs.tags }}

From 5d9b13caf0035bda9e4884df8c83b2861d0bf948 Mon Sep 17 00:00:00 2001
From: Yoann Apel <yoann.apel@ign.fr>
Date: Wed, 16 Oct 2024 11:24:50 +0200
Subject: [PATCH 07/36] fix submodules

---
 .github/workflows/cicd_deploy.yml | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/.github/workflows/cicd_deploy.yml b/.github/workflows/cicd_deploy.yml
index 346c71aa..79e447bf 100644
--- a/.github/workflows/cicd_deploy.yml
+++ b/.github/workflows/cicd_deploy.yml
@@ -62,9 +62,6 @@ jobs:
     - name: Build and push Docker image
       id: build-and-push
       uses: docker/build-push-action@v5
-      submodules:
-        include: []
-        recursive: false
       with:
         context: .
         push: true

From 3627180549098418ba0700bd09d7ca7f23c5118a Mon Sep 17 00:00:00 2001
From: Yoann Apel <yoann.apel@ign.fr>
Date: Tue, 12 Nov 2024 14:43:53 +0100
Subject: [PATCH 08/36] to fixup data

---
 Dockerfile | 3 ++-
 data       | 2 +-
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 54970eec..db063a0e 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -16,4 +16,5 @@ ARG MAMBA_DOCKERFILE_ACTIVATE=1
 
 
 COPY lidro lidro
-COPY configs configs
\ No newline at end of file
+COPY configs configs
+COPY data data
\ No newline at end of file
diff --git a/data b/data
index 031c3315..2ae2dfcc 160000
--- a/data
+++ b/data
@@ -1 +1 @@
-Subproject commit 031c3315127a9c972d622779a25aed3274789fa4
+Subproject commit 2ae2dfcc4fd4f5e89c4510c49fd4e6676e247421

From 80a06f30eb92494a5b5f06066154e1181b8aeff4 Mon Sep 17 00:00:00 2001
From: Yoann Apel <yoann.apel@ign.fr>
Date: Tue, 12 Nov 2024 15:35:38 +0100
Subject: [PATCH 09/36] to fixup data

---
 Dockerfile | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index db063a0e..af48a61d 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -14,7 +14,7 @@ RUN micromamba install -y -n base -f /tmp/env.yaml && \
 ENV ENV=base
 ARG MAMBA_DOCKERFILE_ACTIVATE=1
 
-
+RUN mkdir data
+RUN mkdir tmp
 COPY lidro lidro
 COPY configs configs
-COPY data data
\ No newline at end of file

From 2cedfa92af3d2578efb20b04574ecfed86fd4b8b Mon Sep 17 00:00:00 2001
From: Yoann Apel <yoann.apel@ign.fr>
Date: Tue, 12 Nov 2024 15:48:22 +0100
Subject: [PATCH 10/36] to fixup data

---
 Dockerfile | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/Dockerfile b/Dockerfile
index af48a61d..01a4777d 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -15,6 +15,11 @@ ENV ENV=base
 ARG MAMBA_DOCKERFILE_ACTIVATE=1
 
 RUN mkdir data
+RUN cd /data && git clone git@github.com:IGNF/lidro-data.git
+RUN cd ..
 RUN mkdir tmp
 COPY lidro lidro
 COPY configs configs
+RUN git submodule update --remote --merge
+
+

From b78f5d680469244f488bbe70709577a92c5122b6 Mon Sep 17 00:00:00 2001
From: Yoann Apel <yoann.apel@ign.fr>
Date: Tue, 12 Nov 2024 16:03:58 +0100
Subject: [PATCH 11/36] to fixup data

---
 .github/workflows/cicd_deploy.yml | 5 +++++
 Dockerfile                        | 5 ++---
 2 files changed, 7 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/cicd_deploy.yml b/.github/workflows/cicd_deploy.yml
index 79e447bf..5a5d3af8 100644
--- a/.github/workflows/cicd_deploy.yml
+++ b/.github/workflows/cicd_deploy.yml
@@ -20,6 +20,11 @@ jobs:
       packages: write
 
     steps:
+    - name: Checkout with submodules
+      uses: actions/checkout@v3
+      with:
+        ssh-key: ${{ secrets.DEPLOYER_SSHKEY }}
+        submodules: true
     - name: Checkout branch
       uses: actions/checkout@v4
 
diff --git a/Dockerfile b/Dockerfile
index 01a4777d..77e3e5e3 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -15,11 +15,10 @@ ENV ENV=base
 ARG MAMBA_DOCKERFILE_ACTIVATE=1
 
 RUN mkdir data
-RUN cd /data && git clone git@github.com:IGNF/lidro-data.git
-RUN cd ..
+## RUN cd /data && git clone git@github.com:IGNF/lidro-data.git
 RUN mkdir tmp
 COPY lidro lidro
 COPY configs configs
-RUN git submodule update --remote --merge
+## RUN git submodule update --remote --merge
 
 

From 87ce4d41dfcfe367538a8c08cf646d3a9a130991 Mon Sep 17 00:00:00 2001
From: Yoann Apel <yoann.apel@ign.fr>
Date: Tue, 12 Nov 2024 16:26:18 +0100
Subject: [PATCH 12/36] to fixup data

---
 .github/workflows/cicd_deploy.yml | 127 ++++++++++++++++++------------
 1 file changed, 76 insertions(+), 51 deletions(-)

diff --git a/.github/workflows/cicd_deploy.yml b/.github/workflows/cicd_deploy.yml
index 5a5d3af8..8a379e2d 100644
--- a/.github/workflows/cicd_deploy.yml
+++ b/.github/workflows/cicd_deploy.yml
@@ -12,63 +12,88 @@ env:
   REGISTRY: ghcr.io
   TEST_TAG:  ${{ github.repository }}:test
 
+
 jobs:
-  deploy_docker:
+  build-docker:
     runs-on: ubuntu-latest
+    steps:
+      - name: Checkout with submodules
+        uses: actions/checkout@v3
+        with:
+          ssh-key: ${{ secrets.DEPLOYER_SSHKEY }}
+          submodules: true
+      - name: Log in to the Container registry
+        uses: docker/login-action@65b78e6e13532edd9afa3aa52ac7964289d1a9c1
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GHCR_TOKEN }}
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v2
+      - name: Build and push
+        uses: docker/build-push-action@v3
+        with:
+          context: .
+          push: true
+          tags: 'user/app:tag'
 
-    permissions:
-      packages: write
+# jobs:
+#   deploy_docker:
+#     runs-on: ubuntu-latest
 
-    steps:
-    - name: Checkout with submodules
-      uses: actions/checkout@v3
-      with:
-        ssh-key: ${{ secrets.DEPLOYER_SSHKEY }}
-        submodules: true
-    - name: Checkout branch
-      uses: actions/checkout@v4
+#     permissions:
+#       packages: write
+
+#     steps:
+#     - name: Checkout with submodules
+#       uses: actions/checkout@v3
+#       with:
+#         ssh-key: ${{ secrets.DEPLOYER_SSHKEY }}
+#         submodules: true
+#     - name: Checkout branch
+#       uses: actions/checkout@v4
 
-    - name: Build the Docker image
-      id: build
-      uses: docker/build-push-action@v5
-      with:
-        load: true
-        tags: ${{ env.TEST_TAG }}
+#     - name: Build the Docker image
+#       id: build
+#       uses: docker/build-push-action@v5
+#       with:
+#         load: true
+#         tags: ${{ env.TEST_TAG }}
 
-    # run the test on the docker image
-    - name: Run tests in docker image
-      run: >
-        docker run
-        --ipc=host
-        ${{ env.TEST_TAG }}
-        python -m pytest ./test -s --log-cli-level DEBUG
+#     # run the test on the docker image
+#     - name: Run tests in docker image
+#       run: >
+#         docker run
+#         --ipc=host
+#         ${{ env.TEST_TAG }}
+#         python -m pytest ./test -s --log-cli-level DEBUG
 
-    # Login against a Docker registry except on PR
-    # https://github.com/docker/login-action
-    - name: Log into registry ${{ env.REGISTRY }}
-      if: github.event_name != 'pull_request'
-      uses: docker/login-action@v2
-      with:
-        registry: ${{ env.REGISTRY }}
-        username: ${{ github.actor }}
-        password: ${{ secrets.GITHUB_TOKEN }}
+#     # Login against a Docker registry except on PR
+#     # https://github.com/docker/login-action
+#     - name: Log into registry ${{ env.REGISTRY }}
+#       if: github.event_name != 'pull_request'
+#       uses: docker/login-action@v2
+#       with:
+#         registry: ${{ env.REGISTRY }}
+#         username: ${{ github.actor }}
+#         password: ${{ secrets.GITHUB_TOKEN }}
 
-    # Extract metadata (tags, labels) for Docker
-    # https://github.com/docker/metadata-action
-    - name: Extract Docker metadata
-      if: github.event_name != 'pull_request'
-      id: meta
-      uses: docker/metadata-action@v5
-      with:
-        images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+#     # Extract metadata (tags, labels) for Docker
+#     # https://github.com/docker/metadata-action
+#     - name: Extract Docker metadata
+#       if: github.event_name != 'pull_request'
+#       id: meta
+#       uses: docker/metadata-action@v5
+#       with:
+#         images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
 
-    # Build an Docker image with Buildx (don't on PR)
-    # https://github.com/docker/build-push-action
-    - name: Build and push Docker image
-      id: build-and-push
-      uses: docker/build-push-action@v5
-      with:
-        context: .
-        push: true
-        tags: ${{ steps.meta.outputs.tags }}
-        labels: ${{ steps.meta.outputs.labels }}
\ No newline at end of file
+#     # Build an Docker image with Buildx (don't on PR)
+#     # https://github.com/docker/build-push-action
+#     - name: Build and push Docker image
+#       id: build-and-push
+#       uses: docker/build-push-action@v5
+#       with:
+#         context: .
+#         push: true
+#         tags: ${{ steps.meta.outputs.tags }}
+#         labels: ${{ steps.meta.outputs.labels }}
\ No newline at end of file

From 7be901719974c0dce6182f6f800ab63b72ba9159 Mon Sep 17 00:00:00 2001
From: Yoann Apel <yoann.apel@ign.fr>
Date: Tue, 12 Nov 2024 16:33:28 +0100
Subject: [PATCH 13/36] to fixup data

---
 .github/workflows/cicd_deploy.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/cicd_deploy.yml b/.github/workflows/cicd_deploy.yml
index 8a379e2d..b9f7476b 100644
--- a/.github/workflows/cicd_deploy.yml
+++ b/.github/workflows/cicd_deploy.yml
@@ -37,7 +37,7 @@ jobs:
           push: true
           tags: 'user/app:tag'
 
-# jobs:
+## jobs:
 #   deploy_docker:
 #     runs-on: ubuntu-latest
 

From ecfc99c42041c8a437fb2a6722ed9e868e3b9802 Mon Sep 17 00:00:00 2001
From: Yoann Apel <yoann.apel@ign.fr>
Date: Tue, 12 Nov 2024 16:42:36 +0100
Subject: [PATCH 14/36] to fixup data

---
 .github/workflows/cicd_deploy.yml | 146 +++++++++++++-----------------
 1 file changed, 64 insertions(+), 82 deletions(-)

diff --git a/.github/workflows/cicd_deploy.yml b/.github/workflows/cicd_deploy.yml
index b9f7476b..349eaa6f 100644
--- a/.github/workflows/cicd_deploy.yml
+++ b/.github/workflows/cicd_deploy.yml
@@ -1,99 +1,81 @@
-
 name: cicd_deploy
 
 on:
-  pull_request:
-    branches:
-      - main
-      - dev
+  push:
+    # Run deployment on every new version tag and every push to main
+    branches: [ "main" ]
+    tags: [ '*.*.*' ]
 
 env:
-  IMAGE_NAME:  ${{ github.repository }}
+  IMAGE_NAME: ${{ github.repository }}
   REGISTRY: ghcr.io
-  TEST_TAG:  ${{ github.repository }}:test
-
+  DOCKER_IMAGE_NAME: lidro
+  TEST_TAG: lidro:test
 
 jobs:
-  build-docker:
+  deploy_docker:
     runs-on: ubuntu-latest
-    steps:
-      - name: Checkout with submodules
-        uses: actions/checkout@v3
-        with:
-          ssh-key: ${{ secrets.DEPLOYER_SSHKEY }}
-          submodules: true
-      - name: Log in to the Container registry
-        uses: docker/login-action@65b78e6e13532edd9afa3aa52ac7964289d1a9c1
-        with:
-          registry: ${{ env.REGISTRY }}
-          username: ${{ github.actor }}
-          password: ${{ secrets.GHCR_TOKEN }}
-      - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v2
-      - name: Build and push
-        uses: docker/build-push-action@v3
-        with:
-          context: .
-          push: true
-          tags: 'user/app:tag'
 
-## jobs:
-#   deploy_docker:
-#     runs-on: ubuntu-latest
+    steps:
+    - name: Checkout branch
+      uses: actions/checkout@v4
 
-#     permissions:
-#       packages: write
+    # build the image
+    - name: Build Docker image for tests
+      id: build
+      uses: docker/build-push-action@v5
+      with:
+        load: true
+        tags: ${{ env.TEST_TAG }}
 
-#     steps:
-#     - name: Checkout with submodules
-#       uses: actions/checkout@v3
-#       with:
-#         ssh-key: ${{ secrets.DEPLOYER_SSHKEY }}
-#         submodules: true
-#     - name: Checkout branch
-#       uses: actions/checkout@v4
+    - name: Run tests in docker
+      run: >
+        docker run
+        --ipc=host
+        ${{ env.TEST_TAG }}
+        python -m pytest -m docker -s --log-cli-level DEBUG
 
-#     - name: Build the Docker image
-#       id: build
-#       uses: docker/build-push-action@v5
-#       with:
-#         load: true
-#         tags: ${{ env.TEST_TAG }}
+    - name: Set version number
+      run: |
+        echo "VERSION=v$(python -m lidro.version)" >> $GITHUB_ENV
 
-#     # run the test on the docker image
-#     - name: Run tests in docker image
-#       run: >
-#         docker run
-#         --ipc=host
-#         ${{ env.TEST_TAG }}
-#         python -m pytest ./test -s --log-cli-level DEBUG
+    - name: Check tag and version number consistency
+      if: ${{ github.event_name == 'tag' }}
+      run: |
+        if [[ ${{ github.ref_name }} == ${{ env.VERSION }} ]]
+        then
+        echo "OK: Tag name and VERSION.md (${{ env.VERSION }}) version number (${{ github.ref_name }}) match"
+        else
+        echo "NOK: Tag name and VERSION.md (${{ env.VERSION }}) version number (${{ github.ref_name }}) don't match"
+        exit 1
+        fi
 
-#     # Login against a Docker registry except on PR
-#     # https://github.com/docker/login-action
-#     - name: Log into registry ${{ env.REGISTRY }}
-#       if: github.event_name != 'pull_request'
-#       uses: docker/login-action@v2
-#       with:
-#         registry: ${{ env.REGISTRY }}
-#         username: ${{ github.actor }}
-#         password: ${{ secrets.GITHUB_TOKEN }}
+    # Login against a Docker registry except on PR
+    # https://github.com/docker/login-action
+    - name: Log into registry ${{ env.REGISTRY }}
+      if: github.event_name != 'pull_request'
+      uses: docker/login-action@v2
+      with:
+        registry: ${{ env.REGISTRY }}
+        username: ${{ github.actor }}
+        password: ${{ secrets.GITHUB_TOKEN }}
 
-#     # Extract metadata (tags, labels) for Docker
-#     # https://github.com/docker/metadata-action
-#     - name: Extract Docker metadata
-#       if: github.event_name != 'pull_request'
-#       id: meta
-#       uses: docker/metadata-action@v5
-#       with:
-#         images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+    # Extract metadata (tags, labels) for Docker
+    # https://github.com/docker/metadata-action
+    - name: Extract Docker metadata
+      id: meta
+      uses: docker/metadata-action@v5
+      with:
+        images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
 
-#     # Build an Docker image with Buildx (don't on PR)
-#     # https://github.com/docker/build-push-action
-#     - name: Build and push Docker image
-#       id: build-and-push
-#       uses: docker/build-push-action@v5
-#       with:
-#         context: .
-#         push: true
-#         tags: ${{ steps.meta.outputs.tags }}
-#         labels: ${{ steps.meta.outputs.labels }}
\ No newline at end of file
+    # Build and push Docker image with Buildx (don't on PR)
+    # https://github.com/docker/build-push-action
+    - name: Build and push Docker image
+      id: build-and-push
+      if: ${{ github.event_name != 'pull_request' }}
+      uses: docker/build-push-action@v5
+      with:
+        context: .
+        push: true
+        tags: ${{ steps.meta.outputs.tags }}
+        labels: ${{ steps.meta.outputs.labels }}
\ No newline at end of file

From e68678ae80d306db9a21677fb798524525fe2b60 Mon Sep 17 00:00:00 2001
From: Yoann Apel <yoann.apel@ign.fr>
Date: Tue, 12 Nov 2024 16:43:58 +0100
Subject: [PATCH 15/36] to fixup data

---
 .github/workflows/cicd_deploy.yml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/cicd_deploy.yml b/.github/workflows/cicd_deploy.yml
index 349eaa6f..78e0fe5c 100644
--- a/.github/workflows/cicd_deploy.yml
+++ b/.github/workflows/cicd_deploy.yml
@@ -1,11 +1,11 @@
 name: cicd_deploy
 
 on:
-  push:
-    # Run deployment on every new version tag and every push to main
-    branches: [ "main" ]
-    tags: [ '*.*.*' ]
-
+  pull_request:
+    branches:
+      - main
+      - dev
+      
 env:
   IMAGE_NAME: ${{ github.repository }}
   REGISTRY: ghcr.io

From 0e10b9faf34e36cfd2ee5f4694482eaededce335 Mon Sep 17 00:00:00 2001
From: Yoann Apel <yoann.apel@ign.fr>
Date: Tue, 12 Nov 2024 16:45:15 +0100
Subject: [PATCH 16/36] to fixup data

---
 .github/workflows/cicd_deploy.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/cicd_deploy.yml b/.github/workflows/cicd_deploy.yml
index 78e0fe5c..ea248cc7 100644
--- a/.github/workflows/cicd_deploy.yml
+++ b/.github/workflows/cicd_deploy.yml
@@ -5,7 +5,7 @@ on:
     branches:
       - main
       - dev
-      
+
 env:
   IMAGE_NAME: ${{ github.repository }}
   REGISTRY: ghcr.io
@@ -58,7 +58,7 @@ jobs:
       with:
         registry: ${{ env.REGISTRY }}
         username: ${{ github.actor }}
-        password: ${{ secrets.GITHUB_TOKEN }}
+        password: ${{ secrets.GHCR_TOKEN }}
 
     # Extract metadata (tags, labels) for Docker
     # https://github.com/docker/metadata-action

From 7f7493e0b2e5dabb5be099ef1c9ff606ecaf6b6d Mon Sep 17 00:00:00 2001
From: Yoann Apel <yoann.apel@ign.fr>
Date: Tue, 12 Nov 2024 17:02:46 +0100
Subject: [PATCH 17/36] to fixup data

---
 .github/workflows/cicd_deploy.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/cicd_deploy.yml b/.github/workflows/cicd_deploy.yml
index ea248cc7..140f9785 100644
--- a/.github/workflows/cicd_deploy.yml
+++ b/.github/workflows/cicd_deploy.yml
@@ -20,7 +20,7 @@ jobs:
     - name: Checkout branch
       uses: actions/checkout@v4
 
-    # build the image
+    ## build the image
     - name: Build Docker image for tests
       id: build
       uses: docker/build-push-action@v5

From c948485370a7818ffe98ef208d4cd20855c55248 Mon Sep 17 00:00:00 2001
From: Yoann Apel <yoann.apel@ign.fr>
Date: Tue, 12 Nov 2024 17:14:30 +0100
Subject: [PATCH 18/36] to fixup data

---
 .github/workflows/cicd_deploy.yml | 4 +++-
 .gitmodules                       | 2 +-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/cicd_deploy.yml b/.github/workflows/cicd_deploy.yml
index 140f9785..362106db 100644
--- a/.github/workflows/cicd_deploy.yml
+++ b/.github/workflows/cicd_deploy.yml
@@ -19,7 +19,9 @@ jobs:
     steps:
     - name: Checkout branch
       uses: actions/checkout@v4
-
+      with:
+        submodules: recursive
+        token: ${{ secrets.GHCR_TOKEN }}
     ## build the image
     - name: Build Docker image for tests
       id: build
diff --git a/.gitmodules b/.gitmodules
index ca441591..938af87f 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -1,3 +1,3 @@
 [submodule "data"]
 	path = data
-	url = git@github.com:IGNF/lidro-data.git
+	url = https://github.com/IGNF/lidro-data.git

From a577780733e80e48d07e344a3c9e1c170f9315d5 Mon Sep 17 00:00:00 2001
From: Yoann Apel <yoann.apel@ign.fr>
Date: Tue, 12 Nov 2024 17:15:54 +0100
Subject: [PATCH 19/36] to fixup data

---
 .gitmodules | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.gitmodules b/.gitmodules
index 938af87f..ca441591 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -1,3 +1,3 @@
 [submodule "data"]
 	path = data
-	url = https://github.com/IGNF/lidro-data.git
+	url = git@github.com:IGNF/lidro-data.git

From 0038d0f9ad51ba08a0d1831cadde5a5f8c26752b Mon Sep 17 00:00:00 2001
From: Yoann Apel <yoann.apel@ign.fr>
Date: Tue, 12 Nov 2024 17:24:05 +0100
Subject: [PATCH 20/36] to fixup data

---
 .github/workflows/cicd_deploy.yml | 2 +-
 .gitmodules                       | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/cicd_deploy.yml b/.github/workflows/cicd_deploy.yml
index 362106db..8a0454d1 100644
--- a/.github/workflows/cicd_deploy.yml
+++ b/.github/workflows/cicd_deploy.yml
@@ -22,7 +22,7 @@ jobs:
       with:
         submodules: recursive
         token: ${{ secrets.GHCR_TOKEN }}
-    ## build the image
+    # build the image
     - name: Build Docker image for tests
       id: build
       uses: docker/build-push-action@v5
diff --git a/.gitmodules b/.gitmodules
index ca441591..938af87f 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -1,3 +1,3 @@
 [submodule "data"]
 	path = data
-	url = git@github.com:IGNF/lidro-data.git
+	url = https://github.com/IGNF/lidro-data.git

From 211e4e709813c4e2be42c456e10a7e2208fc460c Mon Sep 17 00:00:00 2001
From: Yoann Apel <yoann.apel@ign.fr>
Date: Tue, 12 Nov 2024 17:29:46 +0100
Subject: [PATCH 21/36] to fixup data

---
 .github/workflows/cicd_deploy.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/cicd_deploy.yml b/.github/workflows/cicd_deploy.yml
index 8a0454d1..3c3a70c3 100644
--- a/.github/workflows/cicd_deploy.yml
+++ b/.github/workflows/cicd_deploy.yml
@@ -20,7 +20,7 @@ jobs:
     - name: Checkout branch
       uses: actions/checkout@v4
       with:
-        submodules: recursive
+        submodules: true
         token: ${{ secrets.GHCR_TOKEN }}
     # build the image
     - name: Build Docker image for tests

From 37eadf9f9a669b99c5f6b67ba902850b3538747a Mon Sep 17 00:00:00 2001
From: mdupays <malvina.dupays@ign.fr>
Date: Tue, 12 Nov 2024 17:36:51 +0100
Subject: [PATCH 22/36] update ghcr_token

---
 .github/workflows/ci.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index 21b7395a..373c31e9 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -18,7 +18,7 @@ jobs:
         uses: actions/checkout@v4
         with:
           submodules: recursive
-          token: ${{ secrets.PAT_TOKEN }}
+          token: ${{ secrets.GHCR_TOKEN }}
       # See https://github.com/marketplace/actions/setup-micromamba
       - name: Install conda env
         uses: mamba-org/setup-micromamba@v1.8.1

From c9789a6be4c1d10d20743f68671b1e591fa0f7e3 Mon Sep 17 00:00:00 2001
From: mdupays <malvina.dupays@ign.fr>
Date: Tue, 12 Nov 2024 17:38:23 +0100
Subject: [PATCH 23/36] update ghcr_token

---
 .github/workflows/ci.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index 373c31e9..b984d337 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -17,7 +17,7 @@ jobs:
       - name: Checkout branch
         uses: actions/checkout@v4
         with:
-          submodules: recursive
+          submodules: True
           token: ${{ secrets.GHCR_TOKEN }}
       # See https://github.com/marketplace/actions/setup-micromamba
       - name: Install conda env

From a96cd3024e5ba61f0a9fe49ca94c70782d3beec2 Mon Sep 17 00:00:00 2001
From: mdupays <malvina.dupays@ign.fr>
Date: Tue, 12 Nov 2024 17:47:14 +0100
Subject: [PATCH 24/36] update ghcr_token

---
 .github/workflows/ci.yaml | 22 ++++++++++++++++++----
 .netrc                    |  3 +++
 2 files changed, 21 insertions(+), 4 deletions(-)
 create mode 100644 .netrc

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index b984d337..1e84be1b 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -17,17 +17,31 @@ jobs:
       - name: Checkout branch
         uses: actions/checkout@v4
         with:
-          submodules: True
-          token: ${{ secrets.GHCR_TOKEN }}
-      # See https://github.com/marketplace/actions/setup-micromamba
+          submodules: recursive
+          token: ${{ secrets.GHRC_TOKEN }}
+
+      - name: Configure .netrc for Docker submodule access
+        run: |
+          echo "machine github.com login ${{ secrets.GHRC_TOKEN }}" > ~/.netrc
+          chmod 600 ~/.netrc
+
+      - name: Build Docker image for tests
+        uses: docker/build-push-action@v3
+        with:
+          context: .
+          load: true
+          tags: ${{ env.TEST_TAG }}
+          secrets: id=netrc,src=$HOME/.netrc
+
       - name: Install conda env
         uses: mamba-org/setup-micromamba@v1.8.1
         with:
           environment-file: environment.yml
-          environment-name: lidro  # activate the environment
+          environment-name: lidro
           cache-environment: true
           cache-downloads: true
           generate-run-shell: true
+
       - name: Unit test
         shell: micromamba-shell {0}
         run: |
diff --git a/.netrc b/.netrc
new file mode 100644
index 00000000..865ebcaa
--- /dev/null
+++ b/.netrc
@@ -0,0 +1,3 @@
+machine github.com
+login GITHUB_USERNAME
+password GITHUB_TOKEN
\ No newline at end of file

From fa484e928e180096900cc94666b2efbcebc61d62 Mon Sep 17 00:00:00 2001
From: mdupays <malvina.dupays@ign.fr>
Date: Tue, 12 Nov 2024 17:50:26 +0100
Subject: [PATCH 25/36] update ghcr_token

---
 .github/workflows/ci.yaml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index 1e84be1b..d1f07386 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -18,7 +18,8 @@ jobs:
         uses: actions/checkout@v4
         with:
           submodules: recursive
-          token: ${{ secrets.GHRC_TOKEN }}
+          token: ${{ secrets.GITHUB_TOKEN }}
+
 
       - name: Configure .netrc for Docker submodule access
         run: |

From 14e51427df6960de70b918f6ce4fd1705a704a16 Mon Sep 17 00:00:00 2001
From: mdupays <malvina.dupays@ign.fr>
Date: Tue, 12 Nov 2024 17:58:30 +0100
Subject: [PATCH 26/36] update ghcr_token

---
 .github/workflows/ci.yaml |  8 +-------
 .netrc                    |  3 ---
 Dockerfile                | 22 ++++++++++++++++++----
 3 files changed, 19 insertions(+), 14 deletions(-)
 delete mode 100644 .netrc

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index d1f07386..e35e5352 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -18,13 +18,7 @@ jobs:
         uses: actions/checkout@v4
         with:
           submodules: recursive
-          token: ${{ secrets.GITHUB_TOKEN }}
-
-
-      - name: Configure .netrc for Docker submodule access
-        run: |
-          echo "machine github.com login ${{ secrets.GHRC_TOKEN }}" > ~/.netrc
-          chmod 600 ~/.netrc
+          token: ${{ secrets.GHRC_TOKEN }}
 
       - name: Build Docker image for tests
         uses: docker/build-push-action@v3
diff --git a/.netrc b/.netrc
deleted file mode 100644
index 865ebcaa..00000000
--- a/.netrc
+++ /dev/null
@@ -1,3 +0,0 @@
-machine github.com
-login GITHUB_USERNAME
-password GITHUB_TOKEN
\ No newline at end of file
diff --git a/Dockerfile b/Dockerfile
index 77e3e5e3..3027b97a 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -2,6 +2,13 @@ FROM mambaorg/micromamba:latest
 
 USER root
 
+
+# Switch to root to install additional packages
+USER root
+
+# Install Git to enable submodule sync/update commands
+RUN apt-get update && apt-get install -y git && rm -rf /var/lib/apt/lists/*
+
 WORKDIR /lidro
 
 # # Set up the Conda environment: cf https://github.com/mamba-org/micromamba-docker
@@ -11,14 +18,21 @@ RUN chown $MAMBA_USER:$MAMBA_USER /tmp/env.yaml
 RUN micromamba install -y -n base -f /tmp/env.yaml && \
     micromamba clean --all --yes
 
+
+# Set environment variables
 ENV ENV=base
 ARG MAMBA_DOCKERFILE_ACTIVATE=1
 
-RUN mkdir data
-## RUN cd /data && git clone git@github.com:IGNF/lidro-data.git
-RUN mkdir tmp
+# Sync and update submodules (ensure they are configured in the repository)
+RUN git submodule sync && \
+    git submodule update --init --recursive
+
+# Create directories
+RUN mkdir data tmp
+
+# Copy the application files
 COPY lidro lidro
 COPY configs configs
-## RUN git submodule update --remote --merge
+
 
 

From e68864abdb142d43d5d7367f8ee1ea5a119f369a Mon Sep 17 00:00:00 2001
From: mdupays <malvina.dupays@ign.fr>
Date: Tue, 12 Nov 2024 18:03:16 +0100
Subject: [PATCH 27/36] update ghcr_token

---
 .github/workflows/ci.yaml | 15 +++------------
 1 file changed, 3 insertions(+), 12 deletions(-)

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index e35e5352..373c31e9 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -18,25 +18,16 @@ jobs:
         uses: actions/checkout@v4
         with:
           submodules: recursive
-          token: ${{ secrets.GHRC_TOKEN }}
-
-      - name: Build Docker image for tests
-        uses: docker/build-push-action@v3
-        with:
-          context: .
-          load: true
-          tags: ${{ env.TEST_TAG }}
-          secrets: id=netrc,src=$HOME/.netrc
-
+          token: ${{ secrets.GHCR_TOKEN }}
+      # See https://github.com/marketplace/actions/setup-micromamba
       - name: Install conda env
         uses: mamba-org/setup-micromamba@v1.8.1
         with:
           environment-file: environment.yml
-          environment-name: lidro
+          environment-name: lidro  # activate the environment
           cache-environment: true
           cache-downloads: true
           generate-run-shell: true
-
       - name: Unit test
         shell: micromamba-shell {0}
         run: |

From ac77a7332de3386abb15baf56d83625f985239fa Mon Sep 17 00:00:00 2001
From: mdupays <malvina.dupays@ign.fr>
Date: Tue, 12 Nov 2024 18:10:09 +0100
Subject: [PATCH 28/36] update ghcr_token

---
 .gitmodules | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.gitmodules b/.gitmodules
index 938af87f..5c50f01d 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -1,3 +1,3 @@
-[submodule "data"]
+[submodule "lidro-data"]
 	path = data
 	url = https://github.com/IGNF/lidro-data.git

From 49b55c4603b7fa9638a41a0da4185d58e91abbaa Mon Sep 17 00:00:00 2001
From: mdupays <malvina.dupays@ign.fr>
Date: Tue, 12 Nov 2024 18:12:13 +0100
Subject: [PATCH 29/36] update ghcr_token

---
 .github/workflows/cicd_deploy.yml | 2 +-
 .gitmodules                       | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/cicd_deploy.yml b/.github/workflows/cicd_deploy.yml
index 3c3a70c3..8a0454d1 100644
--- a/.github/workflows/cicd_deploy.yml
+++ b/.github/workflows/cicd_deploy.yml
@@ -20,7 +20,7 @@ jobs:
     - name: Checkout branch
       uses: actions/checkout@v4
       with:
-        submodules: true
+        submodules: recursive
         token: ${{ secrets.GHCR_TOKEN }}
     # build the image
     - name: Build Docker image for tests
diff --git a/.gitmodules b/.gitmodules
index 5c50f01d..4b1a0fd7 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -1,3 +1,3 @@
 [submodule "lidro-data"]
-	path = data
+	path = lidro/data
 	url = https://github.com/IGNF/lidro-data.git

From aba4e393e652459e7c75285ec20cb51b420eaac6 Mon Sep 17 00:00:00 2001
From: mdupays <malvina.dupays@ign.fr>
Date: Tue, 12 Nov 2024 18:13:32 +0100
Subject: [PATCH 30/36] update ghcr_token

---
 .gitmodules | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.gitmodules b/.gitmodules
index 4b1a0fd7..938af87f 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -1,3 +1,3 @@
-[submodule "lidro-data"]
-	path = lidro/data
+[submodule "data"]
+	path = data
 	url = https://github.com/IGNF/lidro-data.git

From 01670a33c7df5b60c4ca01300525e9c177775ae6 Mon Sep 17 00:00:00 2001
From: mdupays <malvina.dupays@ign.fr>
Date: Wed, 13 Nov 2024 09:34:51 +0100
Subject: [PATCH 31/36] update ghcr_token

---
 .github/workflows/ci.yaml |  2 +-
 Dockerfile                | 14 ++++++++------
 2 files changed, 9 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index 373c31e9..ee8ef460 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -18,7 +18,7 @@ jobs:
         uses: actions/checkout@v4
         with:
           submodules: recursive
-          token: ${{ secrets.GHCR_TOKEN }}
+          #token: ${{ secrets.GHCR_TOKEN }}
       # See https://github.com/marketplace/actions/setup-micromamba
       - name: Install conda env
         uses: mamba-org/setup-micromamba@v1.8.1
diff --git a/Dockerfile b/Dockerfile
index 3027b97a..3b2f724e 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -11,9 +11,11 @@ RUN apt-get update && apt-get install -y git && rm -rf /var/lib/apt/lists/*
 
 WORKDIR /lidro
 
+COPY . .
+
 # # Set up the Conda environment: cf https://github.com/mamba-org/micromamba-docker
-COPY environment.yml /tmp/env.yaml
-COPY requirements.txt /tmp/requirements.txt
+# COPY environment.yml /tmp/env.yaml
+# COPY requirements.txt /tmp/requirements.txt
 RUN chown $MAMBA_USER:$MAMBA_USER /tmp/env.yaml
 RUN micromamba install -y -n base -f /tmp/env.yaml && \
     micromamba clean --all --yes
@@ -28,11 +30,11 @@ RUN git submodule sync && \
     git submodule update --init --recursive
 
 # Create directories
-RUN mkdir data tmp
+RUN mkdir tmp
 
-# Copy the application files
-COPY lidro lidro
-COPY configs configs
+# # Copy the application files
+# COPY lidro lidro
+# COPY configs configs
 
 
 

From 91d6e040c798ae62066b3adc0dc4d3d2a3e93380 Mon Sep 17 00:00:00 2001
From: mdupays <malvina.dupays@ign.fr>
Date: Wed, 13 Nov 2024 09:39:12 +0100
Subject: [PATCH 32/36] update ghcr_token

---
 Dockerfile | 25 +++++++++++++++----------
 1 file changed, 15 insertions(+), 10 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 3b2f724e..5102ad3d 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -6,19 +6,28 @@ USER root
 # Switch to root to install additional packages
 USER root
 
-# Install Git to enable submodule sync/update commands
-RUN apt-get update && apt-get install -y git && rm -rf /var/lib/apt/lists/*
+# # Install Git to enable submodule sync/update commands
+# RUN apt-get update && apt-get install -y git && rm -rf /var/lib/apt/lists/*
 
 WORKDIR /lidro
 
 COPY . .
 
-# # Set up the Conda environment: cf https://github.com/mamba-org/micromamba-docker
+RUN chown $MAMBA_USER:$MAMBA_USER environment.yml
+RUN micromamba install -y -n base -f environment.yml && \
+    micromamba clean --all --yes
+
+    
+# # # Set up the Conda environment: cf https://github.com/mamba-org/micromamba-docker
 # COPY environment.yml /tmp/env.yaml
 # COPY requirements.txt /tmp/requirements.txt
-RUN chown $MAMBA_USER:$MAMBA_USER /tmp/env.yaml
-RUN micromamba install -y -n base -f /tmp/env.yaml && \
-    micromamba clean --all --yes
+# RUN chown $MAMBA_USER:$MAMBA_USER /tmp/env.yaml
+# RUN micromamba install -y -n base -f /tmp/env.yaml && \
+#     micromamba clean --all --yes
+
+# # Copy the application files
+# COPY lidro lidro
+# COPY configs configs
 
 
 # Set environment variables
@@ -32,9 +41,5 @@ RUN git submodule sync && \
 # Create directories
 RUN mkdir tmp
 
-# # Copy the application files
-# COPY lidro lidro
-# COPY configs configs
-
 
 

From 4a6304c14db26d27bda8b6c58b0a8395034ae1c8 Mon Sep 17 00:00:00 2001
From: mdupays <malvina.dupays@ign.fr>
Date: Wed, 13 Nov 2024 09:41:12 +0100
Subject: [PATCH 33/36] update dockerfile with submodule

---
 Dockerfile | 15 +++++++++------
 1 file changed, 9 insertions(+), 6 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 5102ad3d..c04c0b45 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -11,13 +11,21 @@ USER root
 
 WORKDIR /lidro
 
+
+# Create directories
+RUN mkdir tmp data
+
 COPY . .
 
+# Sync and update submodules (ensure they are configured in the repository)
+RUN git submodule sync && \
+    git submodule update --init --recursive
+    
 RUN chown $MAMBA_USER:$MAMBA_USER environment.yml
 RUN micromamba install -y -n base -f environment.yml && \
     micromamba clean --all --yes
 
-    
+
 # # # Set up the Conda environment: cf https://github.com/mamba-org/micromamba-docker
 # COPY environment.yml /tmp/env.yaml
 # COPY requirements.txt /tmp/requirements.txt
@@ -34,12 +42,7 @@ RUN micromamba install -y -n base -f environment.yml && \
 ENV ENV=base
 ARG MAMBA_DOCKERFILE_ACTIVATE=1
 
-# Sync and update submodules (ensure they are configured in the repository)
-RUN git submodule sync && \
-    git submodule update --init --recursive
 
-# Create directories
-RUN mkdir tmp
 
 
 

From c0d04fe48508bef8fd84f81d264fd1110985d32b Mon Sep 17 00:00:00 2001
From: mdupays <malvina.dupays@ign.fr>
Date: Wed, 13 Nov 2024 09:52:53 +0100
Subject: [PATCH 34/36] update dockerfile with submodule

---
 .github/workflows/ci.yaml |  3 ++-
 Dockerfile                | 14 ++++++++------
 2 files changed, 10 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index ee8ef460..bb20131a 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -18,7 +18,8 @@ jobs:
         uses: actions/checkout@v4
         with:
           submodules: recursive
-          #token: ${{ secrets.GHCR_TOKEN }}
+          token: ${{ secrets.GHCR_TOKEN }}
+          fetch-depth: 1
       # See https://github.com/marketplace/actions/setup-micromamba
       - name: Install conda env
         uses: mamba-org/setup-micromamba@v1.8.1
diff --git a/Dockerfile b/Dockerfile
index c04c0b45..70d52d10 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -12,15 +12,11 @@ USER root
 WORKDIR /lidro
 
 
-# Create directories
-RUN mkdir tmp data
+# # Create directories
+RUN mkdir tmp 
 
 COPY . .
 
-# Sync and update submodules (ensure they are configured in the repository)
-RUN git submodule sync && \
-    git submodule update --init --recursive
-    
 RUN chown $MAMBA_USER:$MAMBA_USER environment.yml
 RUN micromamba install -y -n base -f environment.yml && \
     micromamba clean --all --yes
@@ -43,6 +39,12 @@ ENV ENV=base
 ARG MAMBA_DOCKERFILE_ACTIVATE=1
 
 
+# Sync and update submodules (ensure they are configured in the repository)
+RUN git submodule sync && \
+    git submodule update --init --recursive
+
+RUN mkdir tmp
+
 
 
 

From d2dec1364e4e50204c6b1339f416249cbaf16bde Mon Sep 17 00:00:00 2001
From: mdupays <malvina.dupays@ign.fr>
Date: Wed, 13 Nov 2024 09:58:46 +0100
Subject: [PATCH 35/36] update dockerfile with submodule

---
 .github/workflows/ci.yaml |  2 +-
 Dockerfile                | 10 +++++++---
 2 files changed, 8 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index bb20131a..84b0ccb3 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -19,7 +19,7 @@ jobs:
         with:
           submodules: recursive
           token: ${{ secrets.GHCR_TOKEN }}
-          fetch-depth: 1
+          #fetch-depth: 1
       # See https://github.com/marketplace/actions/setup-micromamba
       - name: Install conda env
         uses: mamba-org/setup-micromamba@v1.8.1
diff --git a/Dockerfile b/Dockerfile
index 70d52d10..077b37f1 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -38,10 +38,14 @@ RUN micromamba install -y -n base -f environment.yml && \
 ENV ENV=base
 ARG MAMBA_DOCKERFILE_ACTIVATE=1
 
+# Use ARG to pass the authentication token
+ARG GIT_AUTH_TOKEN
 
-# Sync and update submodules (ensure they are configured in the repository)
-RUN git submodule sync && \
-    git submodule update --init --recursive
+# Configure Git to use the token in the submodule URLs
+RUN git config --global url."https://${GIT_AUTH_TOKEN}@github.com/".insteadOf "https://github.com/"
+
+# Initialize and update submodules
+RUN git submodule update --init --recursive
 
 RUN mkdir tmp
 

From fb916f9525ebc68aa3ca6335d42c35f73c96d89b Mon Sep 17 00:00:00 2001
From: mdupays <malvina.dupays@ign.fr>
Date: Wed, 13 Nov 2024 10:02:01 +0100
Subject: [PATCH 36/36] update dockerfile with submodule

---
 Dockerfile | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 077b37f1..306d28fe 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -3,9 +3,6 @@ FROM mambaorg/micromamba:latest
 USER root
 
 
-# Switch to root to install additional packages
-USER root
-
 # # Install Git to enable submodule sync/update commands
 # RUN apt-get update && apt-get install -y git && rm -rf /var/lib/apt/lists/*
 
@@ -38,6 +35,9 @@ RUN micromamba install -y -n base -f environment.yml && \
 ENV ENV=base
 ARG MAMBA_DOCKERFILE_ACTIVATE=1
 
+
+RUN mkdir tmp data
+
 # Use ARG to pass the authentication token
 ARG GIT_AUTH_TOKEN
 
@@ -47,7 +47,6 @@ RUN git config --global url."https://${GIT_AUTH_TOKEN}@github.com/".insteadOf "h
 # Initialize and update submodules
 RUN git submodule update --init --recursive
 
-RUN mkdir tmp