fix all weird bugs

.dockerignore

@@ -0,0 +1,10 @@
+# Ignore all but src/
+*
+!src/neuroagent/*
+!pyproject.toml
+
+# Ignore the __pycache__ that are in the whitelisted folders.
+*/__pycache__/
+*/*/__pycache__/
+*/*/*/__pycache__/
+

.env.example

@@ -0,0 +1,54 @@
+# required.
+NEUROAGENT_TOOLS__LITERATURE__URL=
+NEUROAGENT_KNOWLEDGE_GRAPH__BASE_URL=
+NEUROAGENT_GENERATIVE__OPENAI__TOKEN=
+
+# Important but not required
+NEUROAGENT_AGENT__MODEL=
+NEUROAGENT_AGENT__CHAT=
+NEUROAGENT_KNOWLEDGE_GRAPH__USE_TOKEN=
+NEUROAGENT_KNOWLEDGE_GRAPH__TOKEN=
+NEUROAGENT_KNOWLEDGE_GRAPH__DOWNLOAD_HIERARCHY=
+
+# Useful but not required.
+NEUROAGENT_DB__PREFIX=
+NEUROAGENT_DB__USER=
+NEUROAGENT_DB__PASSWORD=
+NEUROAGENT_DB__HOST=
+NEUROAGENT_DB__PORT=
+NEUROAGENT_DB__NAME=
+NEUROAGENT_TOOLS__LITERATURE__RETRIEVER_K=
+NEUROAGENT_TOOLS__LITERATURE__RERANKER_K=
+NEUROAGENT_TOOLS__LITERATURE__USE_RERANKER=
+
+NEUROAGENT_TOOLS__KNOWLEDGE_GRAPH__SEARCH_SIZE=
+
+NEUROAGENT_TOOLS__TRACE__SEARCH_SIZE=
+
+NEUROAGENT_TOOLS__KG_MORPHO__SEARCH_SIZE=
+
+NEUROAGENT_GENERATIVE__LLM_TYPE= # can only be openai for now
+NEUROAGENT_GENERATIVE__OPENAI__MODEL=
+NEUROAGENT_GENERATIVE__OPENAI__TEMPERATURE=
+NEUROAGENT_GENERATIVE__OPENAI__MAX_TOKENS=
+
+NEUROAGENT_COHERE__TOKEN=
+
+NEUROAGENT_LOGGING__LEVEL=
+NEUROAGENT_LOGGING__EXTERNAL_PACKAGES=
+
+NEUROAGENT_KNOWLEDGE_GRAPH__BR_SAVING_PATH=
+NEUROAGENT_KNOWLEDGE_GRAPH__CT_SAVING_PATH=
+
+NEUROAGENT_MISC__APPLICATION_PREFIX=
+NEUROAGENT_MISC__CORS_ORIGINS=
+
+NEUROAGENT_KEYCLOAK__ISSUER=
+NEUROAGENT_KEYCLOAK__VALIDATE_TOKEN=
+NEUROAGENT_KEYCLOAK__CLIENT_ID=
+NEUROAGENT_KEYCLOAK__USERNAME=
+NEUROAGENT_KEYCLOAK__PASSWORD=
+
+# other.
+SSL_CERT_FILE=(path to cert file)(etc/ssl/certs/ca-certificates.crt for ubuntu, for mac check Nicolas tutorial)
+REQUESTS_CA_BUNDLE=(path to cert file)(etc/ssl/certs/ca-certificates.crt for ubuntu, for mac check Nicolas tutorial)

.gitignore

@@ -0,0 +1,154 @@
+# Custom entries
+/.idea/
+.DS_Store
+.env*
+!.env*.example
+.python-version
+.vscode
+.pypirc
+
+# Version file
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# static files generated from Django application using `collectstatic`
+media
+static

.pre-commit-config.yaml

@@ -0,0 +1,35 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    hooks:
+      - id: check-added-large-files
+      - id: check-json
+      - id: check-toml
+      - id: check-yaml
+      - id: requirements-txt-fixer
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: no-commit-to-branch
+        args: [--branch, master, --branch, main]
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.5.5
+    hooks:
+      - id: ruff
+        args: [ --fix ]
+      - id: ruff-format
+
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.8.0
+    hooks:
+    - id: mypy
+      files: ^src/
+      additional_dependencies: ['pydantic', 'types-requests']
+
+  - repo: https://github.com/PyCQA/bandit
+    rev: 1.7.4
+    hooks:
+    - id: bandit
+      args: [-c, pyproject.toml, -qr]
+      files: ^src/
+      additional_dependencies: ["bandit[toml]"]

AUTHORS.txt

@@ -0,0 +1,8 @@
+
+
+- [Boris Bergsma](https://github.com/BoBer78) @ Blue Brain Project, EPFL
+- [Emilie Delattre](https://github.com/EmilieDel) @ Blue Brain Project, EPFL
+- [Nicolas Frank](https://github.com/WonderPG) @ Blue Brain Project, EPFL
+- [Jan Krepl](https://github.com/jankrepl) @ Blue Brain Project, EPFL
+- [Kerem Kurban](https://github.com/KeremKurban) @ Blue Brain Project, EPFL
+- [Csaba Zsolnai]() @ Blue Brain Project, EPFL

CHANGELOG.md

@@ -2,10 +2,13 @@
 
 All notable changes to this project will be documented in this file.
 
-The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
 ## [Unreleased]
 
 ### Removed
-- Github action to create the docs.
+- Github action to create the docs.
+
+### Changed
+- Migration to pydantic V2.

Dockerfile

@@ -1,3 +1,16 @@
-FROM python:3.10-slim
+FROM python:3.10
 
-CMD python
+ENV PYTHONUNBUFFERED=1
+
+RUN apt-get -y update
+RUN apt-get -y install curl
+
+RUN pip install --no-cache-dir --upgrade pip
+COPY ./ /code
+RUN pip install --no-cache-dir /code[api]
+RUN rm -rf /code
+
+WORKDIR /
+
+EXPOSE 8078
+CMD neuroagent-api --host 0.0.0.0 --port 8078