Update Python versions and dependencies

.github/workflows/build-docs.yml

@@ -6,19 +6,19 @@ on:
   workflow_dispatch:
 jobs:
   build-docs:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     steps:
       - name: Git checkout
         uses: actions/checkout@v2
 
       - name: Setup Python env
         uses: actions/setup-python@v2
         with:
-          python-version: "3.9"
+          python-version: "3.11"
 
       - name: Install Poetry
         run: |
-          pip install poetry==1.5.1
+          pip install poetry==1.*
           poetry config virtualenvs.create false
 
       - name: Install autodisc-server-libs dependencies

README.md

@@ -101,13 +101,13 @@ For development work on the Python libraries, we recommend starting a new conda
 environment with
 
 ```bash
-conda create -n adtool python=3.9 poetry=1.5.1
+conda create -n adtool python=3.11 poetry=1.* -y
 ```
 
 or, if you are running on the new Macbooks with M1 processors
 
 ```bash
-CONDA_SUBDIR=osx-64 conda create -n adtool python=3.9 poetry=1.5.1
+CONDA_SUBDIR=osx-64 conda create -n adtool python=3.11 poetry=1.* -y
 ```
 
 Please see the online documentation at https://developmentalsystems.org/adtool/.

configs/remote_experiments/additional_files/jeanzay.sh

@@ -13,7 +13,7 @@ sbatch <<EOT
 #SBATCH --array=0-$(($1-1))
 
 module purge
-module load python/3.7.3
+module load python/3.11
 conda activate autoDiscTool
 
 srun python auto_disc/auto_disc/run.py --seed \$SLURM_ARRAY_TASK_ID ${@:2}

services/base/AutoDiscServer/Dockerfile

@@ -1,23 +1,23 @@
-FROM --platform=linux/amd64 nvidia/cuda:12.1.1-base-ubuntu20.04 as library
+FROM --platform=linux/amd64 nvidia/cuda:12.3.2-base-ubuntu22.04 as library
 
 # install pip and virtualenv for the system python environment (python3.8)
 ENV DEBIAN_FRONTEND="noninteractive"
 # TODO: load tz dynamically, would also fix the issue #210
 ENV TZ="Etc/UTC"
 RUN apt-get update -y && apt-get install -y python3-pip virtualenv python-is-python3
 
-# bootstrap a virtual env in python3.9 for poetry
-RUN apt-get install -y python3.9
+# bootstrap a virtual env in python3.11 for poetry
+RUN apt-get install -y python3.11
 ENV POETRY_HOME=/opt/poetry
 ENV VIRTUAL_ENV=$POETRY_HOME
-RUN virtualenv -p /usr/bin/python3.9 $VIRTUAL_ENV
+RUN virtualenv -p /usr/bin/python3.11 $VIRTUAL_ENV
 # activate virtual environment and install poetry
 ENV PATH="$VIRTUAL_ENV/bin:$PATH"
-RUN pip install poetry==1.5.1
+RUN pip install poetry==1.*
 
 # create and activate the autodisc-env virtualenv for the server
 ENV VIRTUAL_ENV=/autodisc-env
-RUN virtualenv -p /usr/bin/python3.9 /autodisc-env
+RUN virtualenv -p /usr/bin/python3.11 /autodisc-env
 ENV PATH="$VIRTUAL_ENV/bin:$PATH"
 # at this point, the $PATH prefers /autodisc-env, then /opt/poetry, then system
 

services/base/AutoDiscServer/flask_app/requirements.txt

@@ -1,6 +1,6 @@
-flask==2.1.2
-flask-cors==3.0.10
-pyyaml==6.0
-pexpect==4.8.0
-addict==2.4.0
-gunicorn==20.1.0
+flask==3
+flask-cors==4
+pyyaml==6
+pexpect==4.8
+addict==2.4
+gunicorn==21

services/base/AutoDiscServer/libs/docs/README_INSTALL.md

@@ -90,7 +90,7 @@ The software is implemented in various microservices
 1. If you do not already have it, please install
    [Conda](https://www.anaconda.com/)
 2. Create _autoDiscTool_ conda environment: `conda env create --name
-autoDiscTool python=3.7 `
+autoDiscTool python=3.11 `
 3. Activate _autoDiscTool_ conda environment: `conda activate autoDiscTool`
 4. Go to package: `cd libs/auto_disc`
 5. Install package: `pip install -e .`

services/base/AutoDiscServer/libs/pyproject.toml

@@ -1,5 +1,5 @@
 [build-system]
-requires = [ "poetry-core>=1.5.1",]
+requires = [ "poetry-core>=1",]
 build-backend = "poetry.core.masonry.api"
 
 [tool.poetry]
@@ -21,22 +21,23 @@ include = "adtool_default"
 addict = "2.4.0"
 filetype = "1.2.0"
 graphviz = "0.20.1"
-imageio = "2.28.0"
-imageio-ffmpeg = "0.4.7"
-matplotlib = "^3.7.1"
+imageio = "2.34.0"
+imageio-ffmpeg = "0.4.9"
+matplotlib = "^3.8"
 mergedeep = "1.3.4"
 neat-python = "0.92"
-numpy = "1.21.6"
+numpy = "^1.26"
 pexpect = "^4.8.0"
-pillow = "9.2.0"
-python = ">=3.9,<3.11"
-requests = "2.28.1"
-sqlalchemy = "2.0.3"
-tinydb = "4.7.0"
+pillow = "10.2.0"
+python = ">=3.9,<3.13"
+requests = "^2"
+sqlalchemy = "^2.0"
+tinydb = "4.8.0"
 toml = "^0.10.2"
 torch = "^1.7.1"
-urllib3 = ">=1.21.1,<1.27"
-watchdog = "^3.0.0"
+urllib3 = "2.2.1"
+watchdog = "^4.0.0"
+Werkzeug= "^2.3"
 
 [tool.poetry.group.test.dependencies]
 coverage = "^7.2.7"

services/base/ExpeDB/API/Dockerfile

@@ -1,4 +1,4 @@
-FROM python:3.8-slim
+FROM python:3.11-slim
 
 RUN apt-get update -y && apt-get install -y gcc
 

services/base/docker-compose.yml

@@ -1,5 +1,5 @@
 # docker-compose.yml
-version: "3" # TODO
+version: "3.7" # TODO
 services:
   ##### FRONTEND APP #####
   app:
@@ -86,7 +86,7 @@ services:
     hostname: autodisc-server
     platform: linux/amd64
     build:
-      context: ./AutoDiscServer
+      context: ../base/AutoDiscServer
     environment:
       EXPEDB_CALLER_HOST: expe-db-api
       EXPEDB_CALLER_PORT: 80

services/dev/utils/Dockerfile

@@ -1,4 +1,4 @@
-FROM python:3.7.14-slim
+FROM python:3.11-slim
 
 RUN apt-get update -y && apt-get install -y gcc
 

services/prod/docker-compose.yml

@@ -1,46 +1,53 @@
 # docker-compose.yml
-version: "3"
+version: "3.7"
 services:
   ##### FRONTEND APP #####
   app:
-    extends:
-      file: ../base/docker-compose.yml
-      service: app
+    # extends:
+    #   file: ../base/docker-compose.yml
+    #   service: app
+   # <<: *app
     image: ${DOCKER_REGISTRY-adtool}/app:${RELEASE_TAG-latest}
+
   ##### GATEWAY #####
   gateway:
-    extends:
-      file: ../base/docker-compose.yml
-      service: gateway
+    # extends:
+    #   file: ../base/docker-compose.yml
+    #   service: gateway
     image: ${DOCKER_REGISTRY-adtool}/gateway:${RELEASE_TAG-latest}
-  ##### APP DB #####
-  app-db:
-    extends:
-      file: ../base/docker-compose.yml
-      service: app-db
-  app-db-api:
-    extends:
-      file: ../base/docker-compose.yml
-      service: app-db-api
-  ##### EXPE DB #####
-  expe-db:
-    extends:
-      file: ../base/docker-compose.yml
-      service: expe-db
+
+
+  # ##### APP DB #####
+  # app-db:
+  #   extends:
+  #     file: ../base/docker-compose.yml
+  #     service: app-db
+  # app-db-api:
+  #   extends:
+  #     file: ../base/docker-compose.yml
+  #     service: app-db-api
+  # ##### EXPE DB #####
+  # expe-db:
+  #   extends:
+  #     file: ../base/docker-compose.yml
+  #     service: expe-db
   expe-db-api:
-    extends:
-      file: ../base/docker-compose.yml
-      service: expe-db-api
+    # extends:
+    #   file: ../base/docker-compose.yml
+    #   service: expe-db-api
     image: ${DOCKER_REGISTRY-adtool}/expe-db-api:${RELEASE_TAG-latest}
+
   ##### AUTODISC SERVER #####
   autodisc-server:
-    extends:
-      file: ../base/docker-compose.yml
-      service: autodisc-server
+    # extends:
+    #   file: ../base/docker-compose.yml
+    #   service: autodisc-server
     image: ${DOCKER_REGISTRY-adtool}/autodisc-server:${RELEASE_TAG-latest}
+
   ##### JUPYTER LAB #####
   jupyter:
-    extends:
-      file: ../base/docker-compose.yml
-      service: jupyter
+    # extends:
+    #   file: ../base/docker-compose.yml
+    #   service: jupyter
     image: ${DOCKER_REGISTRY-adtool}/jupyter:${RELEASE_TAG-latest}
+