fixing merge conflicts

.gitlab/merge_request_templates/Default.md

@@ -30,11 +30,12 @@ The `CREDIT.md` file and `credit/` directory shall be completed and updated acco
 
 General:
 
-* give a glance to [DoD](https://fedbiomed.gitlabpages.inria.fr/latest/developer/Fed-BioMed_DoD.pdf)
-* check [coding rules and coding style](https://fedbiomed.gitlabpages.inria.fr/latest/developer/usage_and_tools/#coding-style)
+* give a glance to [DoD](http://fedbiomed.org/latest/developer/Fed-BioMed_DoD.pdf)
+* check [coding rules and coding style](http://fedbiomed.org/latest/developer/usage_and_tools/#coding-style)
 * check docstrings (eg run `tests/docstrings/check_docstrings`)
 
 Specific to some cases:
 
 * update all conda envs consistently (`development` and `vpn`, Linux and MacOS)
 * if modified researcher (eg new attributes in classes) check if breakpoint needs update (`breakpoint`/`load_breakpoint` in `Experiment()`, `save_state`/`load_state` in aggregators, strategies, secagg, etc.)
+* if modified a component with versioning (config files, breakpoint, messaging protocol) then update the version following the rules in `common/utils/_versions.py`

CONTRIBUTING.md

@@ -14,7 +14,7 @@ Here is a brief summary of how it is structured:
 
 ## Getting started
 
-Please **read carefully** [the Developer guide on the Fed-BioMed webpage](https://fedbiomed.gitlabpages.inria.fr/latest/developer/usage_and_tools/).
+Please **read carefully** [the Developer guide on the Fed-BioMed webpage](http://fedbiomed.org/latest/developer/usage_and_tools/).
 
 When done please contact `fedbiomed _at_ inria _dot_ fr` to receive your contributor credentials consisting of: an account on `gitlab.inria.fr` with access to the gitlab repository, the registration to the developer mailing lists, the invitation to the developers team's Discord server. Please feel free to ask for a meeting on Discord to meet Fed-BioMed developers, to explain your interests in the framework and envisagd contributions, to ask questions, etc.
 

README.md

@@ -11,7 +11,7 @@ Fed-BioMed is an open source project focused on empowering biomedical research u
 
 The project is currently based on Python, PyTorch and Scikit-learn, and enables developing and deploying federated learning analysis in real-world machine learning applications.
 
-The code is regularly released and available on the **master** branch of this repository. The documentation of the releases can be found at https://fedbiomed.gitlabpages.inria.fr
+The code is regularly released and available on the **master** branch of this repository. The documentation of the releases can be found at http://fedbiomed.org
 
 Curious users may also be interested by the current developments, occuring in the **develop** branch (https://gitlab.inria.fr/fedbiomed/fedbiomed/-/tree/develop)
 According to our coding rules, the develop branch is usable, tests and tutorials will run, but the documentation may be not fully available or desynchronized with the code. We only provide support for the last release (currently v4.3) aka the master branch.
@@ -24,9 +24,9 @@ It runs also smoothly on macOSX (mostly tested on macOSX 12: Monterey).
 
 This README.md file provide a quick start/installation guide for Linux.
 
-Full installation instruction are also available at: https://fedbiomed.gitlabpages.inria.fr/latest/tutorials/installation/0-basic-software-installation/
+Full installation instruction are also available at: http://fedbiomed.org/latest/tutorials/installation/0-basic-software-installation/
 
-An installation guide is also provided for Windows10, which relies on WSL2: https://fedbiomed.gitlabpages.inria.fr/latest/user-guide/installation/windows-installation/
+An installation guide is also provided for Windows10, which relies on WSL2: http://fedbiomed.org/latest/user-guide/installation/windows-installation/
 
 
 ### Prerequisites :
@@ -356,7 +356,7 @@ without paying action on visual of the site.
 ./tests/docstrings/check_docstrings
 ```
 
-Developer should do the last test on gitlabpages.
+Developer should do the last test before pushing documentation release.
 
 ## Using Tensorboard
 
@@ -649,4 +649,3 @@ ${FEDBIOMED_DIR}/scripts/fedbiomed_mpc (node | researcher) *WORKDIR* exec --help
 ${FEDBIOMED_DIR}/scripts/fedbiomed_mpc (node | researcher) *WORKDIR* shamir-server-key --help
 
 ```
-

RELEASE.md

@@ -1,6 +1,6 @@
 # Fed-BioMed release HOWTO
 
-Make coordinated release of software (this repo) and documentation (published on `fedbiomed.gitlabpages.inria.fr`)
+Make coordinated release of software (this repo) and documentation (published on `http://fedbiomed.org`)
   * using same version tag
   * corresponding to same software version
   * **release software before documentation** (for API documentation)
@@ -35,6 +35,7 @@ git checkout -b release/$RELEASE_TAG
 - in the `release` branch, do the release time updates:
   * `CHANGELOG.md`
   * `README.md` : change `v4.` occurences ; change `version 4` if major release
+  * `fedbiomed/common/constants.py` : change `v4.`
 - in the `release` branch, commit the release time updates
 ```bash
 git commit -a

envs/development/conda/fedbiomed-gui.yaml

@@ -23,6 +23,7 @@ dependencies:
   - jsonschema >=4.2.0,< 4.2.1
   - requests >=2.25.1,<3.0.0
   - git
+  - packaging >=23.0,<24.0
   # sklearn
   #   scipy >= 1.9 from conda-forge needs recent GLIBC thus causes issue 389
   #   with many current systems

envs/development/conda/fedbiomed-node-macosx.yaml

@@ -26,6 +26,7 @@ dependencies:
   - validators >=0.18.2,<0.19.0
   - tqdm >=4.59.0,<5.0.0
   - git
+  - packaging >=23.0,<24.0
   # these two have to be aligned
   - cryptography ~=39.0
   - pyopenssl ~=23.0

envs/development/conda/fedbiomed-node.yaml

@@ -25,6 +25,7 @@ dependencies:
   - validators >=0.18.2,<0.19.0
   - tqdm >=4.59.0,<5.0.0
   - git
+  - packaging >=23.0,<24.0
   # these two have to be aligned
   - cryptography ~=39.0
   - pyopenssl ~=23.0

envs/development/conda/fedbiomed-researcher-macosx.yaml

@@ -31,6 +31,7 @@ dependencies:
   - validators >=0.18.2,<0.19.0
   - tqdm >=4.59.0,<5.0.0
   - git
+  - packaging >=23.0,<24.0
   # these two have to be aligned
   - cryptography ~=39.0
   - pyopenssl ~=23.0

envs/development/conda/fedbiomed-researcher.yaml

@@ -30,6 +30,7 @@ dependencies:
   - validators >=0.18.2,<0.19.0
   - tqdm >=4.59.0,<5.0.0
   - git
+  - packaging >=23.0,<24.0
   # these two have to be aligned
   - cryptography ~=39.0
   - pyopenssl ~=23.0

envs/vpn/README.md

@@ -454,7 +454,7 @@ Use the node gui from outside the gui container :
 By default, only connections from `localhost` are authorized. To enable connection to the GUI from any IP address
   - specify the bind IP address at container launch time (eg: your node public IP address `NODE_IP`, or `0.0.0.0` to listen on all node addresses)
 ```bash
-[user@node $] GUI_HOST=0.0.0.0 docker-compose up -d gui
+[user@node $] GUI_SERVER_IP=0.0.0.0 docker-compose up -d gui
 ```
   - connect to `http://${NODE_IP}:8484`
   - **warning** allowing connections from non-`localhost` exposes the gui to attacks from the network. Only use with proper third party security measures (web proxy, firewall, etc.) Currently, the provided gui container does not include a user authentication mechanism or encrypted communications for the user.
@@ -566,7 +566,7 @@ my_notebook.ipynb
 ## GPU support in container
 
 You can access the host machine GPU accelerator from a node container to speed up training.
-- reminder: Fed-BioMed currently [supports only](https://fedbiomed.gitlabpages.inria.fr/user-guide/nodes/using-gpu/) (1) Nvidia GPUs (2) for PyTorch training (3) on node side
+- reminder: Fed-BioMed currently [supports only](http://fedbiomed.org/latest/user-guide/nodes/using-gpu/) (1) Nvidia GPUs (2) for PyTorch training (3) on node side
 
 Before using a GPU for Fed-BioMed in a `node` docker container, you need to meet the requirements for the host machine:
 

envs/vpn/conda/fedbiomed-gui.yaml

@@ -23,6 +23,7 @@ dependencies:
   - jsonschema >=4.2.0,< 4.2.1
   - requests >=2.25.1,<3.0.0
   - git
+  - packaging >=23.0,<24.0
   # sklearn
   #   scipy >= 1.9 from conda-forge needs recent GLIBC thus causes issue 389
   #   with many current systems

envs/vpn/conda/fedbiomed-node.yaml

@@ -25,6 +25,7 @@ dependencies:
   - validators >=0.18.2,<0.19.0
   - tqdm >=4.59.0,<5.0.0
   - git
+  - packaging >=23.0,<24.0
   # these two have to be aligned
   - cryptography ~=39.0
   - pyopenssl ~=23.0

envs/vpn/conda/fedbiomed-researcher.yaml

@@ -30,6 +30,7 @@ dependencies:
   - validators >=0.18.2,<0.19.0
   - tqdm >=4.59.0,<5.0.0
   - git
+  - packaging >=23.0,<24.0
   # these two have to be aligned
   - cryptography ~=39.0
   - pyopenssl ~=23.0

envs/vpn/docker/docker-compose.yml

@@ -196,15 +196,16 @@ services:
     environment:
     # enable overloading build-time id with a run-time id
       - SSL_ON=true
+      - GUI_SERVER_NAME
       - NGINX_PORT_SSL=8443
       - NGINX_PORT_NOSSL=8484
       - CONTAINER_UID
       - CONTAINER_GID
       - CONTAINER_USER
       - CONTAINER_GROUP
     ports:
-      - "${GUI_HOST:-127.0.0.1}:8484:8484" # nginx + flask HTTP server
-      - "${GUI_HOST:-127.0.0.1}:8443:8443" # nginx + gunicorn HTTPS server
+      - "${GUI_SERVER_IP:-127.0.0.1}:8484:8484" # nginx + flask HTTP server
+      - "${GUI_SERVER_IP:-127.0.0.1}:8443:8443" # nginx + gunicorn HTTPS server
     volumes:
       # caution: /data /etc /var directory must be shared with node
       - ./gui/run_mounts/certs:/certs
@@ -225,15 +226,16 @@ services:
     environment:
     # enable overloading build-time id with a run-time id
       - SSL_ON=true
+      - GUI_SERVER_NAME
       - NGINX_PORT_SSL=8444
       - NGINX_PORT_NOSSL=8485
       - CONTAINER_UID
       - CONTAINER_GID
       - CONTAINER_USER
       - CONTAINER_GROUP
     ports:
-      - "${GUI_HOST:-127.0.0.1}:8485:8485" # nginx + gunicorn HTTP server
-      - "${GUI_HOST:-127.0.0.1}:8444:8444" # nginx + gunicorn HTTPS server
+      - "${GUI_SERVER_IP:-127.0.0.1}:8485:8485" # nginx + gunicorn HTTP server
+      - "${GUI_SERVER_IP:-127.0.0.1}:8444:8444" # nginx + gunicorn HTTPS server
     volumes:
       # caution: /data /etc /var directory must be shared with node
       - ./gui2/run_mounts/certs:/certs

envs/vpn/docker/docker-compose_run_node.yml

@@ -88,15 +88,16 @@ services:
     environment:
       # enable overloading build-time id with a run-time id
       - SSL_ON=true
+      - GUI_SERVER_NAME
       - NGINX_PORT_SSL=8443
       - NGINX_PORT_NOSSL=8484
       - CONTAINER_UID
       - CONTAINER_GID
       - CONTAINER_USER
       - CONTAINER_GROUP
     ports:
-      - "${GUI_HOST:-127.0.0.1}:8484:8484" # nginx + flask HTTP server
-      - "${GUI_HOST:-127.0.0.1}:8443:8443" # nginx + gunicorn HTTPS server
+      - "${GUI_SERVER_IP:-127.0.0.1}:8484:8484" # nginx + flask HTTP server
+      - "${GUI_SERVER_IP:-127.0.0.1}:8443:8443" # nginx + gunicorn HTTPS server
     volumes:
       # caution: /data /etc /var directory must be shared with node
       - ./gui/run_mounts/certs:/certs
@@ -113,15 +114,16 @@ services:
     environment:
     # enable overloading build-time id with a run-time id
       - SSL_ON=true
+      - GUI_SERVER_NAME
       - NGINX_PORT_SSL=8444
       - NGINX_PORT_NOSSL=8485
       - CONTAINER_UID
       - CONTAINER_GID
       - CONTAINER_USER
       - CONTAINER_GROUP
     ports:
-      - "${GUI_HOST:-127.0.0.1}:8485:8485" # nginx + flask HTTP server
-      - "${GUI_HOST:-127.0.0.1}:8444:8444" # nginx + gunicorn HTTPS server
+      - "${GUI_SERVER_IP:-127.0.0.1}:8485:8485" # nginx + flask HTTP server
+      - "${GUI_SERVER_IP:-127.0.0.1}:8444:8444" # nginx + gunicorn HTTPS server
     volumes:
       # caution: /data /etc /var directory must be shared with node
       - ./gui2/run_mounts/certs:/certs

envs/vpn/docker/gui/build_files/entrypoint.bash

@@ -13,14 +13,20 @@ change_path_owner "/fedbiomed" "/home/$CONTAINER_BUILD_USER"
 # To avoid envsubst to over write default nginx variables
 export DOLLAR='$'
 
-if [ -z "$GUI_SERVER_NAME" ]; then
-  export GUI_SERVER_NAME=127.0.0.1
-fi
-
 # Set Gunicorn PORT and HOST
 export GUI_PORT=8000
 export GUI_HOST=localhost
 
+# Set variable for nginx handling with/without specific domain
+if [ -z "$GUI_SERVER_NAME" ] ; then
+  export SERVER_NAME_DIRECTIVE=
+  export DEFAULT_FAIL=
+  export DEFAULT_SUCCEED=' default_server'
+else
+  export SERVER_NAME_DIRECTIVE="server_name ${GUI_SERVER_NAME};"
+  export DEFAULT_FAIL=' default_server'
+  export DEFAULT_SUCCEED=
+fi
 
 echo "SSL activation status:  $SSL_ON"
 

envs/vpn/docker/gui/build_files/nginx/no-ssl.conf.template

@@ -3,12 +3,19 @@ upstream fedbiomed_gunicorn {
        server ${GUI_HOST}:${GUI_PORT};
 }
 
+server {
+
+    listen ${NGINX_PORT_NOSSL} ${DEFAULT_FAIL};
+
+    server_name "";
+    return 444;
+}
 
 server {
-    listen ${NGINX_PORT_NOSSL} default_server;
+    listen ${NGINX_PORT_NOSSL}${DEFAULT_SUCCEED};
     listen [::]:${NGINX_PORT_NOSSL};
 
-    server_name $GUI_SERVER_NAME;
+    ${SERVER_NAME_DIRECTIVE}
 
     location / {
         proxy_pass http://fedbiomed_gunicorn;
@@ -32,9 +39,21 @@ server {
 }
 
 server {
-    listen ${NGINX_PORT_SSL} ssl;
 
-    server_name $GUI_SERVER_NAME;
+    listen ${NGINX_PORT_SSL} ssl${DEFAULT_FAIL};
+
+    server_name "";
+
+    ssl_certificate ${SSL_CERTIFICATE};
+    ssl_certificate_key ${SSL_KEY};
+
+    return 444;
+}
+
+server {
+    listen ${NGINX_PORT_SSL} ssl${DEFAULT_SUCCEED};
+
+    ${SERVER_NAME_DIRECTIVE}
 
     ssl_certificate ${SSL_CERTIFICATE};
     ssl_certificate_key ${SSL_KEY};

envs/vpn/docker/gui/build_files/nginx/ssl.conf.template

@@ -4,12 +4,19 @@ upstream fedbiomed_gunicorn {
        server localhost:${GUI_PORT};
 }
 
+server {
+
+    listen ${NGINX_PORT_NOSSL} ${DEFAULT_FAIL};
+
+    server_name "";
+    return 444;
+}
 
 server {
-    listen ${NGINX_PORT_NOSSL} default_server;
-    listen [::]:${NGINX_PORT_NOSSL} default_server;
+    listen ${NGINX_PORT_NOSSL}${DEFAULT_SUCCEED};
+    listen [::]:${NGINX_PORT_NOSSL};
 
-    server_name $GUI_SERVER_NAME;
+    ${SERVER_NAME_DIRECTIVE}
 
     location / {
         return 302 https://${DOLLAR}host:${NGINX_PORT_SSL}${DOLLAR}request_uri;
@@ -18,9 +25,21 @@ server {
 
 server {
 
-    listen ${NGINX_PORT_SSL} ssl;
+    listen ${NGINX_PORT_SSL} ssl${DEFAULT_FAIL};
+
+    server_name "";
+
+    ssl_certificate ${SSL_CERTIFICATE};
+    ssl_certificate_key ${SSL_KEY};
+
+    return 444;
+}
+
+server {
+
+    listen ${NGINX_PORT_SSL} ssl${DEFAULT_SUCCEED};
 
-    server_name $GUI_SERVER_NAME;
+    ${SERVER_NAME_DIRECTIVE}
 
     ssl_certificate ${SSL_CERTIFICATE};
     ssl_certificate_key ${SSL_KEY};

fedbiomed/__init__.py

@@ -0,0 +1 @@
+from fedbiomed.common.constants import __version__

fedbiomed/common/constants.py

@@ -3,6 +3,7 @@
 
 """Fed-BioMed constants/enums"""
 
+from packaging.version import Version as FBM_Component_Version
 from enum import Enum
 
 CONFIG_FOLDER_NAME = "etc"
@@ -32,6 +33,10 @@
 
 MPSPDZ_certificate_prefix = "MPSPDZ_certificate"
 
+__version__ = FBM_Component_Version('4.3')  # Fed-BioMed software version
+__researcher_config_version__ = FBM_Component_Version('1')  # researcher config file version
+__node_config_version__ = FBM_Component_Version('1')  # node config file version
+
 
 class _BaseEnum(Enum):
     """