Update Python 3.13 support: bump dependencies and fix numpy constraints

Update template to Python 3.13 base image and bump key packages for compatibility:
- numpy 1.26.4 → 2.3.5 (Python 3.13 requires numpy 2.x)
- scipy 1.13.1 → 1.17.0, gensim 4.3.3 → 4.4.0, numba 0.61.2 → 0.63.1, spacy 3.8.2 → 3.8.11
- e2b_charts: relax numpy constraint from ^1.26.4 to >=1.26.4 for numpy 2 compatibility

Co-Authored-By: Claude Haiku 4.5 <noreply@anthropic.com>

Author: mishushakov

chart_data_extractor/pyproject.toml

@@ -12,13 +12,13 @@ packages = [{ include = "e2b_charts" }]
 [tool.poetry.dependencies]
 python = "^3.10"
 
-numpy = "^1.26.4"
-matplotlib = "^3.9.2"
-pydantic = "^2.8.2"
+numpy = ">=1.26.4"
+matplotlib = "^3.10.3"
+pydantic = "^2.9.1"
 
 [tool.poetry.group.dev.dependencies]
-pytest = "^7.4.0"
-python-dotenv = "^1.0.0"
+pytest = "^8.3.5"
+python-dotenv = "^1.2.1"
 pytest-dotenv = "^0.5.2"
 ruff = "^0.11.12"
 

template/requirements.txt

@@ -15,13 +15,13 @@ e2b_charts
 aiohttp==3.13.3
 beautifulsoup4==4.13.4
 bokeh==3.8.2
-gensim==4.3.3 # unmaintained, blocking numpy and scipy bump
+gensim==4.4.0
 imageio==2.37.0
 joblib==1.5.0
 librosa==0.11.0
 nltk==3.9.1
-numpy==1.26.4 # bump blocked by gensim
-numba==0.61.2
+numpy==2.3.5
+numba==0.63.1
 opencv-python==4.11.0.86
 openpyxl==3.1.5
 plotly==6.0.1
@@ -32,10 +32,10 @@ pytz==2025.2
 requests==2.32.4
 scikit-image==0.25.2
 scikit-learn==1.6.1
-scipy==1.13.1 # bump blocked by gensim
+scipy==1.17.0
 seaborn==0.13.2
 soundfile==0.13.1
-spacy==3.8.2 # doesn't work on 3.13.x
+spacy==3.8.11
 textblob==0.19.0
 tornado==6.5.1
 urllib3==2.6.3

template/template.py

@@ -9,7 +9,7 @@ def make_template(
     # Start with base template
     template = (
         Template()
-        .from_image("python:3.12")
+        .from_image("python:3.13")
         .set_user("root")
         .set_workdir("/root")
         .set_envs(