Update Python 3.13 support and bump dependencies (#192)

* 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>

* Regenerate poetry.lock for updated dependencies

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

* Install e2b_charts with --no-deps to bypass numpy<2 pin on PyPI

The published e2b_charts 0.0.4 on PyPI still has numpy<2.0.0.
Until a new version is published, install it separately with --no-deps.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

* Revert template/requirements.txt and build script changes

Keep these files as-is on main; e2b_charts updates will be in a separate PR.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

* moved the changes here to separate pr

* keep comment

* added changeset

* re-try with fix missing

* return

* skip cache

* return

* install r-base with fix missing

* simplify r install

---------

Co-authored-by: Claude Haiku 4.5 <noreply@anthropic.com>
Co-authored-by: Jakub Novák <jakub@e2b.dev>

Author: 3 people

.changeset/tangy-grapes-crash.md

@@ -0,0 +1,5 @@
+---
+'@e2b/code-interpreter-template': minor
+---
+
+updated Python version to 3.13

template/requirements.txt

@@ -15,13 +15,13 @@ e2b_charts
 aiohttp==3.13.3
 beautifulsoup4==4.14.3
 bokeh==3.8.2
-gensim==4.3.3 # unmaintained, blocking numpy and scipy bump
+gensim==4.4.0
 imageio==2.37.2
 joblib==1.5.3
 librosa==0.11.0
 nltk==3.9.3
-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==2.32.5
 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==3.8.11 # doesn't work on 3.13.x
+spacy==3.8.11
 textblob==0.19.0
 tornado==6.5.4
 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(
@@ -51,21 +51,11 @@ def make_template(
 
     # Install R Kernel if requested
     if "r" in enabled_kernels:
-        template = (
-            template.run_cmd(
-                [
-                    "sudo gpg --keyserver keyserver.ubuntu.com --recv-key 95C0FAF38DB3CCAD0C080A7BDC78B2DDEABC47B7",
-                    "sudo gpg --armor --export 95C0FAF38DB3CCAD0C080A7BDC78B2DDEABC47B7 | sudo tee /etc/apt/trusted.gpg.d/cran_debian_key.asc",
-                    'echo "deb https://cloud.r-project.org/bin/linux/debian trixie-cran40/" | sudo tee /etc/apt/sources.list.d/cran.list',
-                ]
-            )
-            .apt_install("r-base=${R_VERSION} r-base-dev")
-            .run_cmd(
-                [
-                    "R -e \"install.packages('IRkernel', repos='https://cloud.r-project.org')\"",
-                    "R -e \"IRkernel::installspec(user = FALSE, name = 'r', displayname = 'R')\"",
-                ]
-            )
+        template = template.apt_install("r-base=${R_VERSION} r-base-dev").run_cmd(
+            [
+                "R -e \"install.packages('IRkernel', repos='https://cloud.r-project.org')\"",
+                "R -e \"IRkernel::installspec(user = FALSE, name = 'r', displayname = 'R')\"",
+            ]
         )
 
     # Install JavaScript Kernel if requested