Merge branch 'develop' into feature/401-scripts-for-certificate-and-i…

…p-address-registration

AUTHORS.md

@@ -26,6 +26,7 @@ Each author can mention his/her name only or give more information in the follow
 - Yann Fraboni
 - Thibaud Kloczko
 - Lena Le Quintrec
+- Nathan Lapel
 - Jonathan Levy
 - Marco Lorenzi
 - Riham Nehmeh

envs/development/conda/fedbiomed-gui.yaml

@@ -33,7 +33,7 @@ dependencies:
   - pip:
       # nn
       - torch >=1.8.0,<2.0.0
-      - torchvision >=0.9.0,<0.14.0
+      - torchvision >=0.9.0,<0.15.0
       - monai >=1.0.0,<1.1.0
       # other
       - pandas >=1.2.3,<2.0.0

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

@@ -33,7 +33,7 @@ dependencies:
   - pip:
       # nn
       - torch >=1.8.0,<2.0.0
-      - torchvision >=0.9.0,<0.14.0
+      - torchvision >=0.9.0,<0.15.0
       - opacus >=1.2.0,<1.3.0
       - monai >=1.0.0,<1.1.0
       # other

envs/development/conda/fedbiomed-node.yaml

@@ -40,7 +40,7 @@ dependencies:
   - pip:
       # nn
       - torch >=1.8.0,<2.0.0
-      - torchvision >=0.9.0,<0.14.0
+      - torchvision >=0.9.0,<0.15.0
       - opacus >=1.2.0,<1.3.0
       - monai >=1.0.0,<1.1.0
       # other

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

@@ -38,7 +38,7 @@ dependencies:
   - pip:
       # nn
       - torch >=1.8.0,<2.0.0
-      - torchvision >=0.9.0,<0.14.0
+      - torchvision >=0.9.0,<0.15.0
       - opacus >=1.2.0,<1.3.0
       - monai >=1.0.0,<1.1.0
       # other

envs/development/conda/fedbiomed-researcher.yaml

@@ -44,7 +44,7 @@ dependencies:
   - pip:
       # nn
       - torch >=1.8.0,<2.0.0
-      - torchvision >=0.9.0,<0.14.0
+      - torchvision >=0.9.0,<0.15.0
       - opacus >=1.2.0,<1.3.0
       - monai >=1.0.0,<1.1.0
       # other

envs/vpn/README.md

@@ -25,7 +25,7 @@ Supported operating systems for using containers :
 Pre-requisites for using containers :
 
 * **`docker >= 20.10.0`** is needed to build mqtt, see [there](https://wiki.alpinelinux.org/wiki/Release_Notes_for_Alpine_3.14.0#faccessat2). With older docker version it fails with a `make: sh: Operation not permitted`
-* **`docker-compose` >= 1.27.0 and < 2.0** is needed for extended file format for [GPU support in docker](https://docs.docker.com/compose/gpu-support/) even if you're not using GPU in container.
+* **`docker-compose` >= 1.27.0** is needed for extended file format for [GPU support in docker](https://docs.docker.com/compose/gpu-support/) even if you're not using GPU in container.
   -  some distributions (eg Ubuntu 20.04) don't provide a package with a recent enough version.
   - Type `docker-compose --version` to check installed version.
   - You can use your usual package manager to  install up-to-date version (eg: `sudo apt-get update && sudo apt-get install docker-compose` for apt, `sudo dnf clean metadata && sudo dnf update docker-compose` for dnf).
@@ -579,7 +579,7 @@ Before using a GPU for Fed-BioMed in a `node` docker container, you need to meet
   - not supported on MacOS (few Nvidia cards, docker virtualized)
 * **Nvidia drivers and CUDA >= 11.5.0** (the version used by Fed-BioMed container with GPU support)
 * **[Nvidia container toolkit](https://docs.nvidia.com/datacenter/cloud-native/container-toolkit/install-guide.html)**
-* **`docker-compose` version >= 1.27.0 and < 2.0** (already installed for container support)
+* **`docker-compose` version >= 1.27.0** (already installed for container support)
 
 
 Installation guidelines for requirements:

envs/vpn/conda/fedbiomed-gui.yaml

@@ -33,7 +33,7 @@ dependencies:
   - pip:
       # nn
       - torch >=1.8.0,<2.0.0
-      - torchvision >=0.9.0,<0.14.0
+      - torchvision >=0.9.0,<0.15.0
       - monai >=1.0.0,<1.1.0
       # other
       - pandas >=1.2.3,<2.0.0

envs/vpn/conda/fedbiomed-node.yaml

@@ -40,7 +40,7 @@ dependencies:
   - pip:
       # nn
       - torch >=1.8.0,<2.0.0
-      - torchvision >=0.9.0,<0.14.0
+      - torchvision >=0.9.0,<0.15.0
       - opacus >=1.2.0,<1.3.0
       - monai >=1.0.0,<1.1.0
       # other

envs/vpn/conda/fedbiomed-researcher.yaml

@@ -44,7 +44,7 @@ dependencies:
   - pip:
       # nn
       - torch >=1.8.0,<2.0.0
-      - torchvision >=0.9.0,<0.14.0
+      - torchvision >=0.9.0,<0.15.0
       - opacus >=1.2.0,<1.3.0
       - monai >=1.0.0,<1.1.0
       # other

envs/vpn/docker/docker-compose.yml

@@ -1,4 +1,38 @@
 version: "3.7"
+
+#
+# node component template
+x-node:
+  &standard-node
+  container_name: fedbiomed-vpn-node
+  hostname: fedbiomed-vpn-node
+  build:
+    context: ../../..
+    dockerfile: envs/vpn/docker/node/build_files/Dockerfile
+    args:
+      - CONTAINER_UID
+      - CONTAINER_GID
+      - CONTAINER_USER
+      - CONTAINER_GROUP
+  image: fedbiomed/vpn-node
+  environment:
+  # enable overloading build-time id with a run-time id
+    - CONTAINER_UID
+    - CONTAINER_GID
+    - CONTAINER_USER
+    - CONTAINER_GROUP
+  cap_add:
+    - net_admin
+    - sys_module
+  devices:
+    - /dev/net/tun
+  volumes:
+    - ./node/run_mounts/config:/config # contains VPN configurations
+    - ./node/run_mounts/data:/data # datasets can be added here
+    - ./node/run_mounts/etc:/fedbiomed/etc # contains fedbiomed config files
+    - ./node/run_mounts/var:/fedbiomed/var # contains fedbiomed db, exp results ...
+    - ./node/run_mounts/envs/common:/fedbiomed/envs/common # contains fedbiomed default training plans...
+
 services:
   #
   # intermediate step : image for building wireguard for base image
@@ -78,38 +112,6 @@ services:
       - ./vpnserver/run_mounts/config:/config # contains VPN configurations
     ports:
       - 51820:51820/udp # wireguard server
-  #
-  # node component
-  x-node:
-    &standard-node
-    container_name: fedbiomed-vpn-node
-    hostname: fedbiomed-vpn-node
-    build:
-      context: ../../..
-      dockerfile: envs/vpn/docker/node/build_files/Dockerfile
-      args:
-        - CONTAINER_UID
-        - CONTAINER_GID
-        - CONTAINER_USER
-        - CONTAINER_GROUP
-    image: fedbiomed/vpn-node
-    environment:
-    # enable overloading build-time id with a run-time id
-      - CONTAINER_UID
-      - CONTAINER_GID
-      - CONTAINER_USER
-      - CONTAINER_GROUP
-    cap_add:
-      - net_admin
-      - sys_module
-    devices:
-      - /dev/net/tun
-    volumes:
-      - ./node/run_mounts/config:/config # contains VPN configurations
-      - ./node/run_mounts/data:/data # datasets can be added here
-      - ./node/run_mounts/etc:/fedbiomed/etc # contains fedbiomed config files
-      - ./node/run_mounts/var:/fedbiomed/var # contains fedbiomed db, exp results ...
-      - ./node/run_mounts/envs/common:/fedbiomed/envs/common # contains fedbiomed default training plans...
 
   # not using gpu
   node:

envs/vpn/docker/docker-compose_run_node.yml

@@ -1,36 +1,38 @@
 version: "3.7"
+
+#
+# Minimal configuration for only running a node component from a saved image
+#
+# Minimal dockerfile permits minimal file tree
+# because *all* files dependencies referenced in `docker-compose.yml`
+# (eg: `./*/build_files`, `./*/run_mounts/config/config.env`)
+# need to exist for *all* containers everytime we run a docker-compose command
+# thus we would have to copy file trees for vpnserver, researcher, etc. when only
+# running a node
+x-node:
+  &standard-node
+  container_name: fedbiomed-vpn-node
+  hostname: fedbiomed-vpn-node
+  image: fedbiomed/vpn-node
+  environment:
+    # enable overloading build-time id with a run-time id
+    - CONTAINER_UID
+    - CONTAINER_GID
+    - CONTAINER_USER
+    - CONTAINER_GROUP
+  cap_add:
+    - net_admin
+    - sys_module
+  devices:
+    - /dev/net/tun
+  volumes:
+    - ./node/run_mounts/config:/config # contains VPN configurations
+    - ./node/run_mounts/data:/data # datasets can be added here
+    - ./node/run_mounts/etc:/fedbiomed/etc # contains fedbiomed config files
+    - ./node/run_mounts/var:/fedbiomed/var # contains fedbiomed db, exp results ...
+    - ./node/run_mounts/envs/common:/fedbiomed/envs/common # contains fedbiomed default training plans..
+
 services:
-  #
-  # Minimal configuration for only running a node component from a saved image
-  #
-  # Minimal dockerfile permits minimal file tree
-  # because *all* files dependencies referenced in `docker-compose.yml`
-  # (eg: `./*/build_files`, `./*/run_mounts/config/config.env`)
-  # need to exist for *all* containers everytime we run a docker-compose command
-  # thus we would have to copy file trees for vpnserver, researcher, etc. when only
-  # running a node
-  x-node:
-    &standard-node
-    container_name: fedbiomed-vpn-node
-    hostname: fedbiomed-vpn-node
-    image: fedbiomed/vpn-node
-    environment:
-      # enable overloading build-time id with a run-time id
-      - CONTAINER_UID
-      - CONTAINER_GID
-      - CONTAINER_USER
-      - CONTAINER_GROUP
-    cap_add:
-      - net_admin
-      - sys_module
-    devices:
-      - /dev/net/tun
-    volumes:
-      - ./node/run_mounts/config:/config # contains VPN configurations
-      - ./node/run_mounts/data:/data # datasets can be added here
-      - ./node/run_mounts/etc:/fedbiomed/etc # contains fedbiomed config files
-      - ./node/run_mounts/var:/fedbiomed/var # contains fedbiomed db, exp results ...
-      - ./node/run_mounts/envs/common:/fedbiomed/envs/common # contains fedbiomed default training plans..
   # not using gpu
   node:
     << : *standard-node

tests/test_medical_datasets.py

@@ -221,7 +221,7 @@ def test_nifti_folder_dataset_09_dataloader(self):
         dataset = NIFTIFolderDataset(self.root)
         batch_size = len(dataset) // 2
         loader = DataLoader(dataset, batch_size=batch_size, shuffle=True)
-        img_batch, targets = iter(loader).next()
+        img_batch, targets = next(iter(loader))
 
         self.assertEqual(len(targets), batch_size)
         self.assertEqual(len(img_batch), batch_size)
@@ -704,7 +704,7 @@ def _assert_batch_types_and_sizes(self, dataset: Dataset):
             AssertionError if test fails
         """
         data_loader = DataLoader(dataset, batch_size=self.batch_size)
-        (images, demographics), targets = iter(data_loader).next()  # get the first iteration of dataloader
+        (images, demographics), targets = next(iter(data_loader))  # get the first iteration of dataloader
 
         self.assertIsInstance(images, dict)
         self.assertIsInstance(targets, dict)