Update requirements and Dockerfile to fix issues (#414)

with Docker build. - remove Pandas - remove psycopg2 - update typing-extensions for Pydantic
codeforboston · Nov 4, 2024 · b49b4b3 · b49b4b3
1 parent d1cb0d3
commit b49b4b3
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Showing 10 changed files with 35 additions and 105 deletions.
diff --git a/backend/Dockerfile b/backend/Dockerfile
@@ -1,6 +1,18 @@
 FROM python:3-slim-bookworm AS base
 
-RUN apt-get update && apt-get install curl -y && apt-get install g++ libpq-dev gcc python3-dev -y
+# Install dependencies
+RUN apt-get update -y && apt-get install -y \
+    curl \
+    g++ \
+    libpq-dev \
+    gcc \
+    python3-dev \
+    libffi-dev
+
+# Install Rust
+RUN curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh -s -- -y
+ENV PATH="/root/.cargo/bin:${PATH}"
+
 
 ADD https://github.com/ufoscout/docker-compose-wait/releases/download/2.12.1/wait /wait
 RUN chmod +x /wait

diff --git a/backend/database/__init__.py b/backend/database/__init__.py
@@ -1,5 +1,5 @@
 # flake8: noqa: F401
-from backend.database.core import db_cli, execute_query
+from backend.database.core import db_cli
 
 # Neo4j / NeoModel related imports
 from neomodel import config as neo_config

diff --git a/backend/database/core.py b/backend/database/core.py
@@ -8,12 +8,12 @@
 from typing import Optional
 
 import click
-import pandas as pd
 from flask import current_app
 from flask.cli import AppGroup, with_appcontext
 from werkzeug.utils import secure_filename
 from neomodel import install_all_labels
 from neo4j import Driver
+from typing import List, Dict, Any
 
 from ..utils import dev_only
 
@@ -23,10 +23,10 @@
 )
 
 
-def execute_query(filename: str) -> Optional[pd.DataFrame]:
+def execute_query(filename: str) -> Optional[List[Dict[str, Any]]]:
     """Run a Cypher query from a file using the provided Neo4j connection.
 
-    It returns a Pandas DataFrame if the query yields results; otherwise,
+    It returns a list of dictionaries if the query yields results; otherwise,
     it returns None.
     """
     # Read the query from the file
@@ -45,9 +45,7 @@ def execute_query(filename: str) -> Optional[pd.DataFrame]:
         if records:
             # Convert Neo4j records to a list of dictionaries
             data = [record.data() for record in records]
-            # Create a DataFrame
-            df = pd.DataFrame(data)
-            return df
+            return data
         else:
             return None
 

diff --git a/requirements/_core.in b/requirements/_core.in
@@ -5,9 +5,9 @@ celery
 flake8
 flask
 gunicorn
-pandas>=2.2.2
 pip-tools
 pydantic==2.9.2
+typing-extensions>=4.12.2 # Required for pydantic
 pytest
 pytest-env
 pytest-cov
@@ -32,6 +32,5 @@ jupyter
 mixpanel
 ua-parser
 ujson
-testcontainers
 neo4j
 neomodel==5.3.3
diff --git a/requirements/dev_unix.in b/requirements/dev_unix.in
@@ -1,3 +1 @@
--r _core.in
-psycopg2-binary
-psycopg-binary
+-r _core.in
diff --git a/requirements/dev_unix.txt b/requirements/dev_unix.txt
@@ -12,8 +12,6 @@ anyio==4.3.0
     # via
     #   httpx
     #   jupyter-server
-appnope==0.1.4
-    # via ipykernel
 argon2-cffi==23.1.0
     # via jupyter-server
 argon2-cffi-bindings==21.2.0
@@ -94,8 +92,6 @@ defusedxml==0.7.1
     # via nbconvert
 dnspython==2.6.1
     # via email-validator
-docker==7.1.0
-    # via testcontainers
 email-validator==2.1.1
     # via -r requirements/_core.in
 et-xmlfile==1.1.0
@@ -280,9 +276,7 @@ notebook-shim==0.2.4
     #   jupyterlab
     #   notebook
 numpy==1.26.4
-    # via
-    #   -r requirements/_core.in
-    #   pandas
+    # via -r requirements/_core.in
 openpyxl==3.0.9
     # via -r requirements/_core.in
 overrides==7.7.0
@@ -300,8 +294,6 @@ packaging==24.0
     #   pytest
     #   qtconsole
     #   qtpy
-pandas==2.2.2
-    # via -r requirements/_core.in
 pandocfilters==1.5.1
     # via nbconvert
 parso==0.8.3
@@ -329,10 +321,6 @@ prompt-toolkit==3.0.43
     #   jupyter-console
 psutil==5.9.8
     # via ipykernel
-psycopg-binary==3.1.18
-    # via -r requirements/dev_unix.in
-psycopg2-binary==2.9.9
-    # via -r requirements/dev_unix.in
 ptyprocess==0.7.0
     # via
     #   pexpect
@@ -381,15 +369,12 @@ python-dateutil==2.9.0
     #   botocore
     #   celery
     #   jupyter-client
-    #   pandas
 python-dotenv==1.0.1
     # via -r requirements/_core.in
 python-json-logger==2.0.7
     # via jupyter-events
 pytz==2024.1
-    # via
-    #   neo4j
-    #   pandas
+    # via neo4j
 pyyaml==6.0.1
     # via
     #   -r requirements/_core.in
@@ -413,7 +398,6 @@ referencing==0.34.0
 requests==2.32.3
     # via
     #   -r requirements/_core.in
-    #   docker
     #   jupyterlab-server
     #   mixpanel
 rfc3339-validator==0.1.4
@@ -455,8 +439,6 @@ terminado==0.18.1
     # via
     #   jupyter-server
     #   jupyter-server-terminals
-testcontainers==4.8.1
-    # via -r requirements/_core.in
 tinycss2==1.2.1
     # via nbconvert
 tornado==6.4
@@ -486,15 +468,13 @@ traitlets==5.14.2
     #   qtconsole
 types-python-dateutil==2.9.0.20240316
     # via arrow
-typing-extensions==4.10.0
+typing-extensions==4.12.2
     # via
+    #   -r requirements/_core.in
     #   pydantic
     #   pydantic-core
-    #   testcontainers
 tzdata==2024.1
-    # via
-    #   celery
-    #   pandas
+    # via celery
 ua-parser==0.18.0
     # via -r requirements/_core.in
 ujson==5.10.0
@@ -504,10 +484,8 @@ uri-template==1.3.0
 urllib3==1.26.18
     # via
     #   botocore
-    #   docker
     #   mixpanel
     #   requests
-    #   testcontainers
 vine==5.1.0
     # via
     #   amqp
@@ -531,8 +509,6 @@ wheel==0.43.0
     # via pip-tools
 widgetsnbextension==4.0.10
     # via ipywidgets
-wrapt==1.16.0
-    # via testcontainers
 wtforms==2.3.3
     # via
     #   -r requirements/_core.in

diff --git a/requirements/dev_windows.in b/requirements/dev_windows.in
@@ -1,3 +1 @@
 -r _core.in
-psycopg2
-psycopg
diff --git a/requirements/dev_windows.txt b/requirements/dev_windows.txt
@@ -12,8 +12,6 @@ anyio==4.3.0
     # via
     #   httpx
     #   jupyter-server
-appnope==0.1.4
-    # via ipykernel
 argon2-cffi==23.1.0
     # via jupyter-server
 argon2-cffi-bindings==21.2.0
@@ -94,8 +92,6 @@ defusedxml==0.7.1
     # via nbconvert
 dnspython==2.6.1
     # via email-validator
-docker==7.1.0
-    # via testcontainers
 email-validator==2.1.1
     # via -r requirements/_core.in
 et-xmlfile==1.1.0
@@ -280,9 +276,7 @@ notebook-shim==0.2.4
     #   jupyterlab
     #   notebook
 numpy==1.26.4
-    # via
-    #   -r requirements/_core.in
-    #   pandas
+    # via -r requirements/_core.in
 openpyxl==3.0.9
     # via -r requirements/_core.in
 overrides==7.7.0
@@ -300,8 +294,6 @@ packaging==24.0
     #   pytest
     #   qtconsole
     #   qtpy
-pandas==2.2.2
-    # via -r requirements/_core.in
 pandocfilters==1.5.1
     # via nbconvert
 parso==0.8.3
@@ -329,10 +321,6 @@ prompt-toolkit==3.0.43
     #   jupyter-console
 psutil==5.9.8
     # via ipykernel
-psycopg==3.1.18
-    # via -r requirements/dev_windows.in
-psycopg2==2.9.9
-    # via -r requirements/dev_windows.in
 ptyprocess==0.7.0
     # via
     #   pexpect
@@ -381,15 +369,12 @@ python-dateutil==2.9.0
     #   botocore
     #   celery
     #   jupyter-client
-    #   pandas
 python-dotenv==1.0.1
     # via -r requirements/_core.in
 python-json-logger==2.0.7
     # via jupyter-events
 pytz==2024.1
-    # via
-    #   neo4j
-    #   pandas
+    # via neo4j
 pyyaml==6.0.1
     # via
     #   -r requirements/_core.in
@@ -413,7 +398,6 @@ referencing==0.34.0
 requests==2.32.3
     # via
     #   -r requirements/_core.in
-    #   docker
     #   jupyterlab-server
     #   mixpanel
 rfc3339-validator==0.1.4
@@ -455,8 +439,6 @@ terminado==0.18.1
     # via
     #   jupyter-server
     #   jupyter-server-terminals
-testcontainers==4.8.1
-    # via -r requirements/_core.in
 tinycss2==1.2.1
     # via nbconvert
 tornado==6.4
@@ -486,16 +468,13 @@ traitlets==5.14.2
     #   qtconsole
 types-python-dateutil==2.9.0.20240316
     # via arrow
-typing-extensions==4.10.0
+typing-extensions==4.12.2
     # via
-    #   psycopg
+    #   -r requirements/_core.in
     #   pydantic
     #   pydantic-core
-    #   testcontainers
 tzdata==2024.1
-    # via
-    #   celery
-    #   pandas
+    # via celery
 ua-parser==0.18.0
     # via -r requirements/_core.in
 ujson==5.10.0
@@ -505,10 +484,8 @@ uri-template==1.3.0
 urllib3==1.26.18
     # via
     #   botocore
-    #   docker
     #   mixpanel
     #   requests
-    #   testcontainers
 vine==5.1.0
     # via
     #   amqp
@@ -532,8 +509,6 @@ wheel==0.43.0
     # via pip-tools
 widgetsnbextension==4.0.10
     # via ipywidgets
-wrapt==1.16.0
-    # via testcontainers
 wtforms==2.3.3
     # via
     #   -r requirements/_core.in

diff --git a/requirements/prod.in b/requirements/prod.in
@@ -1,3 +1 @@
 -r _core.in
-psycopg2-binary==2.9.9
-psycopg-binary==3.1.18