Merge pull request #423 from DFKI-NI/updateLinksAfterOrgMove

update all links after move to DFKI-NI org

.devcontainer/devcontainer.json

@@ -1,5 +1,5 @@
 {
-    "image": "ghcr.io/agri-gaia/seerep_base:latest",
+    "image": "ghcr.io/dfki-ni/seerep_base:latest",
     "name": "seerep_dev",
     "customizations": {
         "vscode": {
@@ -36,5 +36,5 @@
     "containerEnv": {
         "TZ": "Europe/Berlin"
     },
-    "postStartCommand": "git -C ./src pull || git clone [email protected]:agri-gaia/seerep.git ./src; ./src/.devcontainer/postCreateCommand.sh"
+    "postStartCommand": "git -C ./src pull || git clone [email protected]:DFKI-NI/seerep.git ./src; ./src/.devcontainer/postCreateCommand.sh"
 }

.github/workflows/test.yml

@@ -8,7 +8,7 @@ jobs:
     name: Unit Tests
     runs-on: ubuntu-latest
     container:
-      image: ghcr.io/agri-gaia/seerep_base:latest
+      image: ghcr.io/dfki-ni/seerep_base:latest
     steps:
 
     - name: Checkout Code
@@ -39,7 +39,7 @@ jobs:
     name: Integration Tests
     runs-on: ubuntu-latest
     container:
-      image: ghcr.io/agri-gaia/seerep_base:latest
+      image: ghcr.io/dfki-ni/seerep_base:latest
     steps:
 
     - name: Checkout Code

CITATION.cff

@@ -4,7 +4,7 @@ authors:
 - family-names: "Niemeyer"
   given-names: "Mark"
 title: "SEEREP: a spatio-temporal-SEmantic Environment REPresentation"
-url: "https://github.com/agri-gaia/seerep"
+url: "https://github.com/DFKI-NI/seerep"
 preferred-citation:
   type: conference-paper
   authors:

README.md

@@ -6,14 +6,14 @@
 <h3> Spatio-Temporal-Semantic Sensor Data Management <br>
 for Agricultural Robotics </h3>
 
-  [![catkin build workflow](https://github.com/agri-gaia/seerep/actions/workflows/main.yml/badge.svg)](https://github.com/agri-gaia/seerep/actions)
+  [![catkin build workflow](https://github.com/DFKI-NI/seerep/actions/workflows/main.yml/badge.svg)](https://github.com/DFKI-NI/seerep/actions)
   ![unstable](https://img.shields.io/badge/Stability-experimental-orange)
   [![License](https://img.shields.io/badge/License-BSD_3-brightgreen)](./LICENSE)
 
-  <b><a href="https://agri-gaia.github.io/seerep/mkdocs/home/index.html">
+  <b><a href="https://dfki-ni.github.io/seerep/mkdocs/home/index.html">
   Documentation</a></b>
   |
-  <b><a href="https://github.com/agri-gaia/seerep/tree/main/examples/python/gRPC">
+  <b><a href="https://github.com/DFKI-NI/seerep/tree/main/examples/python/gRPC">
   Examples</a></b>
 </div>
 
@@ -60,7 +60,7 @@ The simplest way to start SEEREP is by using `docker compose` with the
 configuration provided in the `docker/server` directory:
 
 ```bash
-git clone https://github.com/agri-gaia/seerep.git
+git clone https://github.com/DFKI-NI/seerep.git
 cd seerep/docker/server
 docker compose up
 ```
@@ -79,9 +79,9 @@ seerep_server | [2024-07-11 13:40:00.903333]<info>: Serving gRPC Server on "[::]
 ```
 
 For other ways to deploy SEEREP, check the
-[documentation](https://agri-gaia.github.io/seerep/mkdocs/getting-started/server_deployment/).
+[documentation](https://dfki-ni.github.io/seerep/mkdocs/getting-started/server_deployment/).
 
-Refer to the [examples section](https://github.com/agri-gaia/seerep/tree/update-readme/examples/python/gRPC)
+Refer to the [examples section](https://github.com/DFKI-NI/seerep/tree/update-readme/examples/python/gRPC)
 for instructions on uploading data.
 
 ## :wrench: Maintainer

docker/README.md

@@ -3,15 +3,15 @@
 The seerep-image is divided into two parts: base and server.
 
 All images are stored in the
-[github-registry](https://github.com/orgs/agri-gaia/packages?repo_name=seerep)
+[github-registry](https://github.com/orgs/DFKI-NI/packages?repo_name=seerep)
 
 ## Base Image
 
 The base image itself is derived from [ros:neotic](http://wiki.ros.org/noetic)
 and installs all neccessary dependencies for ros and seerep. This image is also
 used for the vs-code dev-container.
 
-- source: <https://github.com/agri-gaia/seerep/pkgs/container/seerep_base>
+- source: <https://github.com/DFKI-NI/seerep/pkgs/container/seerep_base>
 - folder: ./base
 
 ## Server Container

docker/kustomize/base/deployment.yaml

@@ -16,7 +16,7 @@ spec:
     spec:
       containers:
         - name: seerep-server
-          image: 'ghcr.io/agri-gaia/seerep_server:latest'
+          image: 'ghcr.io/dfki-ni/seerep_server:latest'
           tty: true
           ports:
             - containerPort: 9090

docker/server/docker-compose.yml

@@ -7,7 +7,7 @@ services:
       - seerep_log:${SEEREP_LOG_PATH}
     command: chown -R ${USER_ID}:${GROUP_ID} ${SEEREP_DATA_FOLDER} ${SEEREP_LOG_PATH}
   seerep:
-    image: ghcr.io/agri-gaia/seerep_server:latest
+    image: ghcr.io/dfki-ni/seerep_server:latest
     platform: linux/x86_64
     user: "${USER_ID}:${GROUP_ID}"
     tty: true

docs/doxygen/header.html

@@ -55,7 +55,7 @@
 </head>
 <body>
 
-<a href="https://github.com/agri-gaia/seerep" class="github-corner" title="View source on GitHub" target="_blank">
+<a href="https://github.com/DFKI-NI/seerep" class="github-corner" title="View source on GitHub" target="_blank">
     <svg viewBox="0 0 250 250" width="40" height="40" style="position: absolute; top: 0; border: 0; right: 0; z-index: 99;" aria-hidden="true">
         <path d="M0,0 L115,115 L130,115 L142,142 L250,250 L250,0 Z"></path>
         <path d="M128.3,109.0 C113.8,99.7 119.0,89.6 119.0,89.6 C122.0,82.7 120.5,78.6 120.5,78.6 C119.2,72.0 123.4,76.3 123.4,76.3 C127.3,80.9 125.5,87.3 125.5,87.3 C122.9,97.6 130.6,101.9 134.4,103.2" fill="currentColor" style="transform-origin: 130px 106px;" class="octo-arm"></path>

docs/mkdocs/data-protection-notice.md

@@ -12,7 +12,7 @@ our web site.
 Deutsches Forschungszentrum für Künstliche Intelligenz GmbH (DFKI)<br>
 Phone: [+49 631 20575 0](tel:+49631205750)<br>
 [[email protected]](mailto:[email protected])<br>
-[Legal Notice](https://agri-gaia.github.io/seerep/mkdocs/legal-notice/index.html)
+[Legal Notice](https://dfki-ni.github.io/seerep/mkdocs/legal-notice/index.html)
 
 ## Data protection officer
 

docs/mkdocs/getting-started/dev_setup.md

@@ -15,13 +15,13 @@ Clone the repository with:
 === "ssh"
 
     ```bash
-    git clone [email protected]:agri-gaia/seerep.git
+    git clone [email protected]:DFKI-NI/seerep.git
     ```
 
 === "https"
 
     ```bash
-    git clone https://github.com/agri-gaia/seerep
+    git clone https://github.com/DFKI-NI/seerep
     ```
 
 For the development, it is assumed that the directory designated for SEEREP's
@@ -69,7 +69,7 @@ Or in case this window doesn't open, use either ++f1++ or ++ctrl+shift+p++ and i
 
 Starting the Dev-Container the first time may take a while as it involves
 downloading the required
-[SEEREP Docker image](https://github.com/agri-gaia/seerep/pkgs/container/seerep_base)
+[SEEREP Docker image](https://github.com/DFKI-NI/seerep/pkgs/container/seerep_base)
 (around 4 GB). Additionally Visual Studio Code extensions, Intellisense, and
 pre-commit checks are setup in the container.
 
@@ -95,7 +95,7 @@ The main hooks are:
 - [Markdownlint](https://github.com/igorshubovych/markdownlint-cli) for Markdown
 
 Along with other checks for Dockerfiles and YAML, see the complete list in the
-[configuration](https://github.com/agri-gaia/seerep/blob/main/.pre-commit-config.yaml).
+[configuration](https://github.com/DFKI-NI/seerep/blob/main/.pre-commit-config.yaml).
 
 ## Debugging with VS-Code
 

docs/mkdocs/getting-started/docs.md

@@ -1,9 +1,9 @@
 # Documentation Setup
 
 The documentation is divided into two main parts:
-[MkDocs](https://agri-gaia.github.io/seerep/mkdocs/home/index.html) is used for
+[MkDocs](https://dfki-ni.github.io/seerep/mkdocs/home/index.html) is used for
 general documentation and
-[Doxygen](https://agri-gaia.github.io/seerep/doxygen/index.html) is used for C++
+[Doxygen](https://dfki-ni.github.io/seerep/doxygen/index.html) is used for C++
 code documentation.
 
 ## Dependencies
@@ -74,7 +74,7 @@ python3 -m http.server 9000
 ## GitHub Pages Deployment
 
 Both documentation pages are automatically deployed to GitHub Pages through a
-[workflow](https://github.com/agri-gaia/seerep/blob/mkdocs-update-getting-started/.github/workflows/build-docs.yml).
+[workflow](https://github.com/DFKI-NI/seerep/blob/mkdocs-update-getting-started/.github/workflows/build-docs.yml).
 A new version is released after a pull request to the main branch.
 Publishing both documentations requires a workaround, as a repository typically
 only supports one URL. The main page is a simple HTML document that links to the

docs/mkdocs/getting-started/grpc_clients.md

@@ -41,7 +41,7 @@ from seerep.fb import image_service_grpc_fb as image_service_fb
 ```
 
 For more advanced examples have a look at the
-[examples section](https://github.com/agri-gaia/seerep/tree/main/examples/python/gRPC).
+[examples section](https://github.com/DFKI-NI/seerep/tree/main/examples/python/gRPC).
 
 ### Building Locally
 
@@ -69,11 +69,11 @@ is required, to see the changes reflected
 
 A new version of the package is automatically released whenever there is a new
 SEEREP release, using the
-[main workflow](https://github.com/agri-gaia/seerep/blob/88ea59605446caf2d1500f111d6f16bb6a6e2bba/.github/workflows/main.yml#L138-L144).
+[main workflow](https://github.com/DFKI-NI/seerep/blob/88ea59605446caf2d1500f111d6f16bb6a6e2bba/.github/workflows/main.yml#L138-L144).
 
 ## C++ API
 
 The C++ bindings for the interfaces and messages are also generated within the
 Dev-Container and can be included in other packages using standard CMake methods.
 As an example use the `examples_cpp` package from the
-[repository](https://github.com/agri-gaia/seerep/tree/main/examples/cpp/gRPC).
+[repository](https://github.com/DFKI-NI/seerep/tree/main/examples/cpp/gRPC).

docs/mkdocs/getting-started/server_deployment.md

@@ -31,7 +31,7 @@ permissions without hard-coding the mount locations in the Dockerfile. To change
 the permissions, a very small container mounts the volumes and changes the
 permission to the specified `uid` and `guid` after which SEEREP is started with
 the same user. Additional information can be found in the
-[PR#376](https://github.com/agri-gaia/seerep/pull/376) discussion.
+[PR#376](https://github.com/DFKI-NI/seerep/pull/376) discussion.
 
 ## Kubernetes
 

docs/mkdocs/getting-started/tests.md

@@ -10,11 +10,11 @@ Action with every push.
 
 Currently unit tests are set up for:
 
-- [Flatbuffer ROS Conversions](https://github.com/agri-gaia/seerep/blob/main/seerep_ros/seerep_ros_conversions_fb/test/ros_to_fb_conversion_test.cpp):
+- [Flatbuffer ROS Conversions](https://github.com/DFKI-NI/seerep/blob/main/seerep_ros/seerep_ros_conversions_fb/test/ros_to_fb_conversion_test.cpp):
     Functions for converting ROS message to Flatbuffers message and vice versa.
-- [HDF5 PB Image Interface](https://github.com/agri-gaia/seerep/blob/main/seerep_hdf5/seerep_hdf5_pb/test/pb_write_load_test.cpp)
+- [HDF5 PB Image Interface](https://github.com/DFKI-NI/seerep/blob/main/seerep_hdf5/seerep_hdf5_pb/test/pb_write_load_test.cpp)
     : Reading and writing of Protocol Buffer image messages to HDF5.
-- [HDF5 FB Image Interface](https://github.com/agri-gaia/seerep/blob/main/seerep_hdf5/seerep_hdf5_fb/test/fb_write_load_test.cpp)
+- [HDF5 FB Image Interface](https://github.com/DFKI-NI/seerep/blob/main/seerep_hdf5/seerep_hdf5_fb/test/fb_write_load_test.cpp)
     : Reading and writing of Flatbuffer image messages to HDF5.
 
 ### Using catkin
@@ -29,7 +29,7 @@ catkin test <specific-package> # run all tests from a specific package
 ## Python Integration Tests
 
 The integration tests, based on the
-[Python examples](https://github.com/agri-gaia/seerep/tree/main/examples/python/gRPC),
+[Python examples](https://github.com/DFKI-NI/seerep/tree/main/examples/python/gRPC),
 cover most of the send and receive operations of SEEREP.
 
 ### Using pytest

docs/mkdocs/home/index.md

@@ -39,7 +39,7 @@ on the context.
   [gRPC](https://grpc.io/docs/what-is-grpc/introduction/).
 - Storage of data generated by the robotic system:
   - Offline on the robot (no or slow internet connection), currently in Progress
-        [#89](https://github.com/agri-gaia/seerep/issues/89)
+        [#89](https://github.com/DFKI-NI/seerep/issues/89)
   - Online on a server-cluster, with
         [gRPC](https://grpc.io/docs/what-is-grpc/introduction/).
 - Shifting computation loads away from the robot and into the cloud.

docs/mkdocs/legal-notice.md

@@ -3,7 +3,7 @@
 ## Responsible service provider
 
 Responsible for the content of the domain
-*[agri-gaia.github.io/seerep](https://agri-gaia.github.io/seerep/)* from the
+*[dfki-ni.github.io/seerep](https://dfki-ni.github.io/seerep/)* from the
 point of view of § 5 TMG:
 
 **Deutsches Forschungszentrum für Künstliche Intelligenz GmbH (DFKI)**</br>
@@ -23,7 +23,7 @@ Register Number: HRB 2313
 ID-Number: DE 148 646 973
 
 The person responsible for the editorial content of the domain
-*[agri-gaia.github.io/seerep](https://agri-gaia.github.io/seerep/)*
+*[dfki-ni.github.io/seerep](https://dfki-ni.github.io/seerep/)*
 of the German Research Center for Artificial Intelligence GmbH within the
 meaning of § 18 para. 2 MStV is:
 

docs/mkdocs/reference/pytests-message-abstractions.md

@@ -8,7 +8,7 @@ should get decoupled in a more elegant way.
 
 It is currently used to create variations for tests of `gRPC_fb_getInstances.py`.
 The tests can be found under
-[test_gRPC_fb_getInstances.py](https://github.com/agri-gaia/seerep/blob/main/tests/python/gRPC/instances/test_gRPC_fb_getInstances.py).
+[test_gRPC_fb_getInstances.py](https://github.com/DFKI-NI/seerep/blob/main/tests/python/gRPC/instances/test_gRPC_fb_getInstances.py).
 
 The idea is to provide default implementations for common datatypes, but still
 allow for modification of parts of that datatype. In some `flatbuffers`
@@ -23,28 +23,28 @@ should happen if a component is active.
 
 Datatype implementations for `Query` and `QueryInstance` and their abstraction
 model can be found
-[here](https://github.com/agri-gaia/seerep/blob/main/tests/python/gRPC/util/msg_abs/msgs.py).
+[here](https://github.com/DFKI-NI/seerep/blob/main/tests/python/gRPC/util/msg_abs/msgs.py).
 
 ## Defining new datatypes for variation testing
 
 First the datatype has to be defined as a class inheriting from FrozenEnum
 provided through
-[datastructures.py](https://github.com/agri-gaia/seerep/blob/main/tests/python/gRPC/util/datastructures.py),
+[datastructures.py](https://github.com/DFKI-NI/seerep/blob/main/tests/python/gRPC/util/datastructures.py),
 which is essentially a unmodifiable enum.
 
 This is done for the `FbQuery` datatype, which corresponding `flatbuffers`
 definition can be found
-[here](https://github.com/agri-gaia/seerep/blob/main/seerep_msgs/fbs/query.fbs).
+[here](https://github.com/DFKI-NI/seerep/blob/main/seerep_msgs/fbs/query.fbs).
 
 ```python
---8<-- "https://raw.githubusercontent.com/agri-gaia/seerep/main/tests/python/gRPC/util/msg_abs/msgs.py:27:41"
+--8<-- "https://raw.githubusercontent.com/DFKI-NI/seerep/main/tests/python/gRPC/util/msg_abs/msgs.py:27:41"
 ```
 
 Then `FbQuery` inherits from `MsgsFb`, which itself is a template type defined in
-[msgs_base.py](https://github.com/agri-gaia/seerep/blob/main/tests/python/gRPC/util/msg_abs/msgs_base.py).
+[msgs_base.py](https://github.com/DFKI-NI/seerep/blob/main/tests/python/gRPC/util/msg_abs/msgs_base.py).
 
 ```python
---8<-- "https://raw.githubusercontent.com/agri-gaia/seerep/main/tests/python/gRPC/util/msg_abs/msgs.py:49:138"
+--8<-- "https://raw.githubusercontent.com/DFKI-NI/seerep/main/tests/python/gRPC/util/msg_abs/msgs.py:49:138"
 ```
 
 In `MsgsFb` `_set_enum_func_mapping()` is a abstractmethod which return type is
@@ -57,7 +57,7 @@ gets called when the component is set active.
 On runtime it is checked if all elements of the enum are mapped. The functions
 are mostly mapped to default implementations for that specific component datatype.
 The default functions implementations can be inspected
-[here](https://github.com/agri-gaia/seerep/blob/main/tests/python/gRPC/util/msg_abs/msgs.py)
+[here](https://github.com/DFKI-NI/seerep/blob/main/tests/python/gRPC/util/msg_abs/msgs.py)
 at the bottom.
 
 The `@expect_component` decorator can be used to define dependencies between the
@@ -72,7 +72,7 @@ the components at this point are set.
 ## Using message abstractions for testing
 
 ```python
---8<-- "https://raw.githubusercontent.com/agri-gaia/seerep/main/tests/python/gRPC/instances/test_gRPC_fb_getInstances.py:82:122"
+--8<-- "https://raw.githubusercontent.com/DFKI-NI/seerep/main/tests/python/gRPC/instances/test_gRPC_fb_getInstances.py:82:122"
 ```
 
 In this function all the possible datatypes with attached instances are tested
@@ -111,7 +111,7 @@ Another snippet to highlight is the following where one of the components of the
 datatype itself is inheriting from `MsgsFb`.
 
 ```python
---8<-- "https://raw.githubusercontent.com/agri-gaia/seerep/main/tests/python/gRPC/instances/test_gRPC_fb_getInstances.py:234:310"
+--8<-- "https://raw.githubusercontent.com/DFKI-NI/seerep/main/tests/python/gRPC/instances/test_gRPC_fb_getInstances.py:234:310"
 ```
 
 Here `query_builder` is used to build the `Query.Query` datatype in order to

docs/mkdocs/reference/python-helpers.md

@@ -6,7 +6,7 @@ Contains common functions like `get_grpc_channel()` and some functions for
 passing into `boltons.iterutils.remap`.
 
 The source is located
-[here](https://github.com/agri-gaia/seerep/blob/main/examples/python/gRPC/util/common.py).
+[here](https://github.com/DFKI-NI/seerep/blob/main/examples/python/gRPC/util/common.py).
 
 ## fb_helper.py
 
@@ -19,23 +19,23 @@ composition into another datatype. If the component itself should be serialized
 the function retrieved value.
 
 The source is located
-[here](https://github.com/agri-gaia/seerep/blob/main/examples/python/gRPC/util/fb_helper.py).
+[here](https://github.com/DFKI-NI/seerep/blob/main/examples/python/gRPC/util/fb_helper.py).
 
 ## service_manager.py
 
 Contains a class `ServiceManager` which when instantiated can be used to
 instantly call the services with the return values of the `fb_helper.py`
 functions, i.e. the `builder.Finish()` and `builder.Output()` calls are done in
 the `ServiceManager` methods. Example usage can be found in
-[msg_abs/msgs.py](https://github.com/agri-gaia/seerep/blob/main/tests/python/gRPC/util/msg_abs/msgs.py)
+[msg_abs/msgs.py](https://github.com/DFKI-NI/seerep/blob/main/tests/python/gRPC/util/msg_abs/msgs.py)
 , e.g.:
 
 ```python
---8<-- "https://raw.githubusercontent.com/agri-gaia/seerep/main/tests/python/gRPC/util/msg_abs/msgs.py:274:309"
+--8<-- "https://raw.githubusercontent.com/DFKI-NI/seerep/main/tests/python/gRPC/util/msg_abs/msgs.py:274:309"
 ```
 
 The source is located
-[here](https://github.com/agri-gaia/seerep/blob/main/examples/python/gRPC/util/service_manager.py).
+[here](https://github.com/DFKI-NI/seerep/blob/main/examples/python/gRPC/util/service_manager.py).
 
 **Note**: This module is currently incomplete and contains only a subset of the
 available service calls.
@@ -49,15 +49,15 @@ objects to a python dictionary. More information can be found by looking at the
 docstring:
 
 ```python
---8<-- "https://raw.githubusercontent.com/agri-gaia/seerep/main/examples/python/gRPC/util/fb_to_dict.py:105:119"
+--8<-- "https://raw.githubusercontent.com/DFKI-NI/seerep/main/examples/python/gRPC/util/fb_to_dict.py:105:119"
 ```
 
 ### catkin_find_schema_dir()
 
 Looking at the docstring should reveal everything to know about this function:
 
 ```python
---8<-- "https://raw.githubusercontent.com/agri-gaia/seerep/main/examples/python/gRPC/util/fb_to_dict.py:63:77"
+--8<-- "https://raw.githubusercontent.com/DFKI-NI/seerep/main/examples/python/gRPC/util/fb_to_dict.py:63:77"
 ```
 
 ### SchemaFileNames