Patch/restore mdf client (#472)

* Restore missing mdf_client.py from design-renaissance branch

This file was part of PR #469 but was not included in the merge,
causing ModuleNotFoundError when importing foundry.

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

* Fix DOI search to return correct dataset

The forge DOI search can return multiple results where only one
actually has the matching DOI. Previously, get_metadata_by_doi()
blindly returned the first result, which often didn't have the
requested DOI.

Now it iterates through results to find the one with the exact
DOI match, fixing test_dataframe_search_by_doi and
test_dataframe_download_by_doi tests.

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

* Move torch/tensorflow to optional extras to fix CI disk space

The combined size of torch, tensorflow, and NVIDIA CUDA dependencies
exceeded GitHub Actions runner disk space (~4GB+). These ML frameworks
are now available as optional extras via pip install .[torch] or
pip install .[tensorflow].

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

* Fix flake8 linting errors

- Remove unused imports (sys, rprint, Optional, pandas, numpy)
- Fix unused exception variable
- Remove f-string without placeholders
- Split long line in MCP server description
- Add noqa comment for intentional re-export

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

* Replace mdf_forge with internal MDFClient in tests

Update test imports to use foundry.mdf_client.MDFClient instead of
mdf_forge.Forge, which is no longer a required dependency.

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

* Add optional extras and document installation

Move heavy ML dependencies to optional extras to reduce default
install size:
- pip install foundry-ml[torch]
- pip install foundry-ml[tensorflow]
- pip install foundry-ml[huggingface]
- pip install foundry-ml[excel]
- pip install foundry-ml[examples]
- pip install foundry-ml[dev]

Update README with extras install instructions and NumPy 2.0
compatibility note.

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

---------

Co-authored-by: Claude Opus 4.5 <noreply@anthropic.com>

Author: blaiszik

README.md

@@ -23,6 +23,17 @@
 pip install foundry-ml
 ```
 
+Need optional integrations? Install extras only when you need them:
+
+```bash
+pip install "foundry-ml[torch]"        # Enable dataset.get_as_torch()
+pip install "foundry-ml[tensorflow]"   # Enable dataset.get_as_tensorflow()
+pip install "foundry-ml[huggingface]"  # Enable push-to-hub
+pip install "foundry-ml[excel]"        # Excel import support via openpyxl
+```
+
+> PyTorch/TensorFlow extras expect wheels compiled against NumPy 2.0. Install PyTorch 2.3+ and TensorFlow 2.18+ (or newer builds with NumPy 2 support) to avoid ABI errors.
+
 ```python
 from foundry import Foundry
 
@@ -79,10 +90,10 @@ foundry mcp install  # Add to Claude Code
 |---------|-------------|
 | Search | Find datasets by keyword, DOI, or browse catalog |
 | Load | Automatic download, caching, and format conversion |
-| PyTorch/TensorFlow | `dataset.get_as_torch()`, `dataset.get_as_tensorflow()` |
+| PyTorch/TensorFlow (extras) | `dataset.get_as_torch()`, `dataset.get_as_tensorflow()` |
 | CLI | Terminal-based workflows |
 | MCP Server | AI assistant integration |
-| HuggingFace Export | Publish to HuggingFace Hub |
+| HuggingFace Export (extra) | Publish to HuggingFace Hub |
 
 ## Available Datasets
 
@@ -125,4 +136,4 @@ See [CONTRIBUTING.md](docs/how-to-contribute/contributing.md) for details.
 
 This work was supported by the National Science Foundation under NSF Award Number: 1931306 "Collaborative Research: Framework: Machine Learning Materials Innovation Infrastructure".
 
-Foundry integrates with [Materials Data Facility](https://materialsdatafacility.org), [DLHub](https://www.dlhub.org), and [MAST-ML](https://mastmldocs.readthedocs.io/).
+Foundry integrates with [Materials Data Facility](https://materialsdatafacility.org), [FuncX](https://www.funcx.org), and [MAST-ML](https://mastmldocs.readthedocs.io/).

setup.py

@@ -14,25 +14,45 @@
     long_description=long_description,
     long_description_content_type="text/markdown",
     install_requires=[
-        "mdf_toolbox>=0.6.0",
+        "mdf_toolbox>=0.7.1",
         "globus-sdk>=3,<4",
-        "dlhub_sdk>=1.0.0",
-        "numpy>=1.15.4",
-        "pandas>=0.23.4",
-        "pydantic>=2.7.2",
         "mdf_connect_client>=0.5.0",
-        "h5py>=2.10.0",
-        "json2table",
-        "openpyxl>=3.1.0",
+        "requests>=2.31.0",
+        "tqdm>=4.66.0",
+        "numpy>=2.0.0",
+        "pandas>=2.2.2",
+        "h5py>=3.11.0",
+        "pydantic>=2.7.2",
+        "json2table>=1.1.5",
         # CLI and agent support (core)
-        "typer[all]>=0.9.0",
-        "rich>=13.0.0",
+        "typer>=0.12.0",
+        "rich>=13.7.0",
     ],
     extras_require={
+        "torch": [
+            "torch>=2.1.0",
+        ],
+        "tensorflow": [
+            "tensorflow>=2.12.0",
+        ],
+        "excel": [
+            "openpyxl>=3.1.0",
+        ],
         "huggingface": [
             "datasets>=2.14.0",
             "huggingface_hub>=0.17.0",
         ],
+        "examples": [
+            "scikit-learn>=1.4.0",
+        ],
+        "dev": [
+            "pytest>=7.4",
+            "pytest-cov>=4.1",
+            "pytest-mock>=3.12",
+            "flake8>=7.0",
+            "jsonschema>=4.19",
+            "mock>=5.1",
+        ],
     },
     entry_points={
         "console_scripts": [