microsoft · fepegar · Jan 25, 2023 · Jan 25, 2023 · Jan 25, 2023 · Jan 25, 2023
diff --git a/.github/workflows/multimodal-pr.yml b/.github/workflows/multimodal-pr.yml
@@ -13,7 +13,7 @@ on:
     - cron: "0 4 * * *"  # every day at 4 AM UTC
 
 env:
-  pythonVersion: 3.7
+  pythonVersion: "3.10"
   folder: hi-ml-multimodal
   HIML_TENANT_ID: ${{ secrets.HIML_TENANT_ID }}
   HIML_RESOURCE_GROUP: ${{ secrets.HIML_RESOURCE_GROUP }}

diff --git a/hi-ml-multimodal/.mypy.ini b/hi-ml-multimodal/.mypy.ini
@@ -1,5 +1,5 @@
 [mypy]
-python_version=3.7
+python_version=3.10
 scripts_are_modules=True
 namespace_packages=True
 show_traceback=True

diff --git a/hi-ml-multimodal/MANIFEST.in b/hi-ml-multimodal/MANIFEST.in
@@ -1,3 +1,2 @@
 include LICENSE
-include requirements_run.txt
 include README.md
diff --git a/hi-ml-multimodal/Makefile b/hi-ml-multimodal/Makefile
@@ -1,22 +1,16 @@
 ## Package management
 
-# Create a Conda environment for this folder only
-env:
-	conda env create --file environment.yml
-	pip install -r requirements_test.txt
-	pip install -r requirements_build.txt
-
 # pip upgrade
 pip_upgrade:
 	python -m pip install --upgrade pip
 
 # pip upgrade and install build requirements
 pip_build: pip_upgrade
-	pip install -r requirements_build.txt
+	pip install .[build]
 
 # pip upgrade and install test requirements
 pip_test: pip_upgrade
-	pip install -r requirements_test.txt
+	pip install .[test]
 
 pip_publish: pip_upgrade
 	pip install --upgrade build twine
@@ -26,7 +20,8 @@ pip_local:
 	pip install -e .
 
 # pip install everything for local development and testing
-pip: pip_build pip_test pip_local
+pip:
+	pip install -e .[dev]
 
 ## Actions
 
@@ -48,7 +43,6 @@ flake8:
 
 # run mypy, assuming test requirements already installed
 mypy:
-	mypy --install-types --show-error-codes --non-interactive setup.py
 	mypy --install-types --show-error-codes --non-interactive src
 	mypy --install-types --show-error-codes --non-interactive test_multimodal
 

diff --git a/hi-ml-multimodal/README.md b/hi-ml-multimodal/README.md
@@ -6,7 +6,7 @@ The code is available on [GitHub][1] and [Hugging Face 🤗][6].
 ## Getting started
 
 The best way to get started is by running the [phrase grounding notebook][2].
-All the dependencies will be installed upon execution, so Python 3.7 and [Jupyter][3] are the only requirements to get started.
+All the dependencies will be installed upon execution, so [Jupyter][3] is the only requirements to get started.
 
 The notebook can also be run on [Binder][4], without the need to download any code or install any libraries:
 

diff --git a/hi-ml-multimodal/environment.yml b/hi-ml-multimodal/environment.yml
diff --git a/hi-ml-multimodal/pyproject.toml b/hi-ml-multimodal/pyproject.toml
@@ -0,0 +1,5 @@
+[build-system]
+requires = [
+  "setuptools>=42",
+]
+build-backend = "setuptools.build_meta"
diff --git a/hi-ml-multimodal/requirements_build.txt b/hi-ml-multimodal/requirements_build.txt
diff --git a/hi-ml-multimodal/requirements_run.txt b/hi-ml-multimodal/requirements_run.txt
diff --git a/hi-ml-multimodal/requirements_test.txt b/hi-ml-multimodal/requirements_test.txt
diff --git a/hi-ml-multimodal/setup.cfg b/hi-ml-multimodal/setup.cfg
@@ -0,0 +1,74 @@
+[metadata]
+name = hi-ml-multimodal
+version = 0.1.2
+author = Biomedical Imaging Team @ Microsoft Health Futures
+author_email = innereyedev@microsoft.com
+url = https://github.com/microsoft/hi-ml
+description = Microsoft Health Futures package to work with multi-modal health data
+long_description = file: README.md
+long_description_content_type = text/markdown
+license_file = MIT License
+platforms = OS Independent
+classifiers =
+    Intended Audience :: Science/Research
+    Natural Language :: English
+    Operating System :: OS Independent
+    Programming Language :: Python
+    Programming Language :: Python :: 3
+    Programming Language :: Python :: 3 :: Only
+    Programming Language :: Python :: 3.10
+    Topic :: Scientific/Engineering
+    Topic :: Scientific/Engineering :: Artificial Intelligence
+    Topic :: Scientific/Engineering :: Image Processing
+    Topic :: Scientific/Engineering :: Medical Science Apps.
+    Typing :: Typed
+    Development Status :: 3 - Alpha
+    License :: OSI Approved :: MIT License
+
+[options]
+install_requires =
+    huggingface-hub
+    matplotlib
+    pillow
+    pydicom
+    scikit-image
+    SimpleITK
+    torch
+    torchvision
+    transformers
+python_requires = >=3.10,<3.11
+include_package_data = True
+zip_safe = False
+
+[options.packages.find]
+where = src
+
+[options.extras_require]
+dev =
+    %(build)s
+    %(test)s
+    bump2version
+    pre-commit
+build =
+    docutils
+    myst-parser
+    sphinx
+    sphinx-autodoc-typehints
+    sphinx-automodapi
+    sphinx-rtd-theme
+    twine
+test =
+    coverage
+    flake8
+    ipykernel
+    ipython
+    mypy
+    papermill
+    pycobertura
+    pytest
+    pytest-cov
+    pytest-rerunfailures
+    pytest-timeout
+
+[bdist_wheel]
+universal = 1
diff --git a/hi-ml-multimodal/test_multimodal/vlp/test_zero_shot_classification.py b/hi-ml-multimodal/test_multimodal/vlp/test_zero_shot_classification.py
@@ -1,7 +1,7 @@
 import tempfile
 from enum import Enum, unique
 from pathlib import Path
-from typing import List, Tuple, Union
+from typing import List, Optional, Tuple, Union
 
 import requests
 from torchvision.datasets.utils import check_integrity
@@ -46,7 +46,7 @@ def _get_default_text_prompts_for_pneumonia() -> Tuple[List, List]:
     return pos_query, neg_query
 
 
-def save_img_from_url(image_url: str, local_path: Union[str, Path], md5: str = None) -> None:
+def save_img_from_url(image_url: str, local_path: Union[str, Path], md5: Optional[str] = None) -> None:
     """
     Pull an image from a URL and save it to a local path
     """

diff --git a/readthedocs_requirements.txt b/readthedocs_requirements.txt
@@ -1,4 +1,4 @@
 -r build_requirements.txt
 -r hi-ml/run_requirements.txt
 -r hi-ml-azure/run_requirements.txt
--r hi-ml-multimodal/requirements_run.txt
+./hi-ml-multimodal