chore: 📦 Update dependencies (#613)

This PR updates the lockfile to the latest versions of the dependencies.
Please review the changes and merge when ready.

---------

Co-authored-by: Dion Häfner <dion.haefner@simulation.science>
Co-authored-by: Jonathan Brodrick <jonathanbrodrick@gmail.com>

Author: 3 people

.github/workflows/build_docs.yml

@@ -34,6 +34,13 @@ jobs:
         run: |
           uv sync --extra docs --frozen
 
+      # TEMPORARY: sphinx-click cannot introspect typer's vendored click (typer
+      # >= 0.26), which breaks the CLI reference pages. Pin to the last real-click
+      # typer for the docs build only (does not affect the shipped package) until
+      # we settle on a long-term docs fix. See the docs CLI reference pages.
+      - name: Pin typer < 0.26 for docs build (sphinx-click compatibility)
+        run: uv pip install 'typer<0.26'
+
       - name: Build docs
         working-directory: docs
         run: |

demo/_showcase/ansys-shapeopt/jax_fem/tesseract_config.yaml

@@ -10,7 +10,7 @@ description: |
 build_config:
   target_platform: "native"
   # conda-forge has binaries for gmsh and friends, even on ARM64
-  base_image: "condaforge/miniforge3:latest"
+  base_image: "condaforge/miniforge3:26.1.1-3"
   requirements:
     provider: conda
   extra_packages:

demo/fem-shape-optimization/fem_tess/tesseract_config.yaml

@@ -10,7 +10,7 @@ description: |
 build_config:
   target_platform: "native"
   # conda-forge has binaries for gmsh and friends, even on ARM64
-  base_image: "condaforge/miniforge3:latest"
+  base_image: "condaforge/miniforge3:26.1.1-3"
   requirements:
     provider: conda
   extra_packages:

examples/conda/tesseract_config.yaml

@@ -3,6 +3,6 @@ version: "1.0.0"
 description: "Custom venv creation."
 
 build_config:
-  base_image: "condaforge/miniforge3:latest"
+  base_image: "condaforge/miniforge3:26.1.1-3"
   requirements:
     provider: conda

production.uv.lock

@@ -8,10 +8,9 @@ authors = [
 license = { text = "Apache-2.0" }
 requires-python = ">=3.10,<3.15"
 dependencies = [
-    "click",
     "jinja2",
     "rich",
-    "typer",
+    "typer>=0.16",
     "pyyaml",
     "pydantic",
     "numpy",
@@ -44,8 +43,10 @@ runtime = [
     "fastapi<=0.136.3,>=0.115",
     "requests<=2.34.2,>=2.32.4",
     "uvicorn<=0.48.0,>=0.34",
-    "click<=8.4.1,>=8.1",
-    "typer<=0.25.1,>=0.15",
+    # NOTE: typer 0.15.0 ships a TyperArgument.make_metavar() without the ``ctx``
+    # arg that click >= 8.2 passes, and declares no click upper bound, so it is
+    # broken with modern click. 0.16.0 is the first version that supports it.
+    "typer<=0.26.4,>=0.16",
     "fsspec[http,s3]<=2026.4.0,>=2024.12",
     "pybase64<=1.4.3,>=1.4",
     "orjson<=3.11.9,>=3.10",

pyproject.toml

@@ -8,13 +8,9 @@ certifi==2026.5.20
     # via requests
 charset-normalizer==3.4.7
     # via requests
-click==8.4.1
-    # via
-    #   tesseract-core
-    #   typer
 colorama==0.4.6 ; sys_platform == 'win32'
-    # via click
-idna==3.16
+    # via typer
+idna==3.17
     # via requests
 jinja2==3.1.6
     # via tesseract-core
@@ -34,7 +30,7 @@ orjson==3.11.9
     # via tesseract-core
 packaging==26.2
     # via tesseract-core
-pip==26.1.1
+pip==26.1.2
     # via tesseract-core
 pybase64==1.4.3
     # via tesseract-core
@@ -54,7 +50,7 @@ rich==15.0.0
     #   typer
 shellingham==1.5.4
     # via typer
-typer==0.25.1
+typer==0.26.4
     # via tesseract-core
 typing-extensions==4.15.0
     # via

requirements.txt

@@ -19,7 +19,6 @@
     get_origin,
 )
 
-import click
 import typer
 from pydantic import ValidationError
 from pydantic_core import from_json
@@ -45,6 +44,15 @@
     check_gradients as check_gradients_,
 )
 
+# typer >= 0.26 vendors its own click (and drops the click dependency), so the
+# Context type and exceptions must come from the click typer actually runs;
+# fall back to real click on older typer (which still ships it).
+try:
+    from typer._click.core import Context
+    from typer._click.exceptions import BadParameter, UsageError
+except ImportError:  # typer < 0.26
+    from click import BadParameter, Context, UsageError
+
 CONFIG_FIELDS = {
     str(field_name): field.annotation
     for field_name, field in RuntimeConfig.model_fields.items()
@@ -66,7 +74,7 @@ def _enum_to_val(val: Any) -> Any:
 class SpellcheckedTyperGroup(typer.core.TyperGroup):
     """A Typer group that suggests similar commands if a command is not found."""
 
-    def get_command(self, ctx: click.Context, invoked_command: str) -> Any:
+    def get_command(self, ctx: Context, invoked_command: str) -> Any:
         """Get a command from the Typer group, suggesting similar commands if the command is not found."""
         import difflib
 
@@ -76,7 +84,7 @@ def get_command(self, ctx: click.Context, invoked_command: str) -> Any:
                 invoked_command, possible_commands, n=1, cutoff=0.6
             )
             if close_match:
-                raise click.UsageError(
+                raise UsageError(
                     f"No such command '{invoked_command}'. Did you mean '{close_match[0]}'?",
                     ctx,
                 )
@@ -111,7 +119,7 @@ def _parse_payload(value: Any) -> dict[str, Any]:
         try:
             value = read_from_path(value[1:]).decode("utf-8")
         except Exception as e:
-            raise click.BadParameter(f"Could not read data from path {value}.") from e
+            raise BadParameter(f"Could not read data from path {value}.") from e
 
     # Use pydantic from_json here because it is much faster, and the payload may be large.
     return from_json(value)
@@ -407,7 +415,7 @@ def _callback_wrapper(**kwargs: Any):
                     context={"base_dir": input_path},
                 )
             except ValidationError as e:
-                raise click.BadParameter(
+                raise BadParameter(
                     str(e),
                     param_hint="payload",
                 ) from e

tesseract_core/runtime/cli.py

@@ -18,7 +18,6 @@
 from types import SimpleNamespace
 from typing import Annotated, Any, NoReturn
 
-import click
 import typer
 import yaml
 from jinja2 import Environment, PackageLoader, StrictUndefined
@@ -48,6 +47,16 @@
 from .exceptions import UserError
 from .logs import DEFAULT_CONSOLE, set_logger
 
+# typer >= 0.26 vendors its own click (and drops the click dependency), so the
+# Context type, exceptions, and context lookups must come from the click typer
+# actually runs; fall back to real click on older typer (which still ships it).
+try:
+    from typer._click.core import Context
+    from typer._click.exceptions import UsageError
+    from typer._click.globals import get_current_context
+except ImportError:  # typer < 0.26
+    from click import Context, UsageError, get_current_context
+
 logger = getLogger("tesseract")
 
 # Jinja2 Template Environment
@@ -62,7 +71,7 @@
 class SpellcheckedTyperGroup(typer.core.TyperGroup):
     """A Typer group that suggests similar commands if a command is not found."""
 
-    def get_command(self, ctx: click.Context, invoked_command: str) -> Any:
+    def get_command(self, ctx: Context, invoked_command: str) -> Any:
         """Get a command from the Typer group, suggesting similar commands if the command is not found."""
         import difflib
 
@@ -72,7 +81,7 @@ def get_command(self, ctx: click.Context, invoked_command: str) -> Any:
                 invoked_command, possible_commands, n=1, cutoff=0.6
             )
             if close_match:
-                raise click.UsageError(
+                raise UsageError(
                     f"No such command '{invoked_command}'. Did you mean '{close_match[0]}'?",
                     ctx,
                 )
@@ -1124,7 +1133,7 @@ def run_container(
 
     if not tesseract_image:
         if invoke_help:
-            click.get_current_context().get_help()
+            get_current_context().get_help()
             return
         raise typer.BadParameter(
             "Tesseract image name is required.",
@@ -1133,7 +1142,7 @@ def run_container(
 
     if not cmd:
         if invoke_help:
-            click.get_current_context().get_help()
+            get_current_context().get_help()
             return
         else:
             error_string = f"Command is required. Are you sure your Tesseract image name is `{tesseract_image}`?"