chore: create helper make command to rebuild project

makefile

@@ -4,6 +4,14 @@ format:
 lint:
 	ruff check --fix 
 
+rebuild: compile sync install
+
+compile:
+	uv pip compile --all-extras pyproject.toml -o requirements.txt
+
+sync:
+	uv pip sync requirements.txt
+
 install:
 	uv pip install -e ".[dev,medical]"
 
@@ -14,7 +22,7 @@ test:
 	pytest
 
 coverage:
-	pytest --cov=blazingai tests
+	pytest --cov=blazingai
 
 static-checks:
 	mypy . --ignore-missing-imports --exclude build/

pyproject.toml

@@ -39,3 +39,14 @@ medical = [
   "pylibjpeg-libjpeg>=1.3.2",
   "pylibjpeg-openjpeg>=1.2.1",
 ]
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+norecursedirs = [
+  "*.egg-info",
+  ".*",
+  "blazingai",
+  "build",
+  "dist",
+]
+markers = ["slow"]

requirements.txt

@@ -10,8 +10,6 @@ antlr4-python3-runtime==4.9.3
     # via omegaconf
 asttokens==2.4.1
     # via stack-data
-async-timeout==4.0.3
-    # via aiohttp
 attrs==23.2.0
     # via
     #   aiohttp
@@ -35,10 +33,6 @@ dill==0.3.8
     # via
     #   datasets
     #   multiprocess
-exceptiongroup==1.2.0
-    # via
-    #   ipython
-    #   pytest
 executing==2.0.1
     # via stack-data
 filelock==3.13.1
@@ -85,7 +79,7 @@ joblib==1.3.2
 libcst==1.2.0
     # via usort
 lightning==2.2.1
-lightning-utilities==0.10.1
+lightning-utilities==0.11.0
     # via
     #   lightning
     #   pytorch-lightning
@@ -112,9 +106,9 @@ mypy-extensions==1.0.0
     # via
     #   mypy
     #   typing-inspect
-networkx==3.1
+networkx==3.2.1
     # via torch
-numpy==1.24.4
+numpy==1.26.4
     # via
     #   datasets
     #   lightning
@@ -171,7 +165,7 @@ packaging==24.0
     #   pytorch-lightning
     #   torchmetrics
     #   transformers
-pandas==2.0.3
+pandas==2.2.1
     # via datasets
 parso==0.8.3
     # via jedi
@@ -189,7 +183,7 @@ ptyprocess==0.7.0
     # via pexpect
 pure-eval==0.2.2
     # via stack-data
-pyarrow==15.0.1
+pyarrow==15.0.2
     # via datasets
 pyarrow-hotfix==0.6
     # via datasets
@@ -198,11 +192,11 @@ pygments==2.17.2
     # via ipython
 pylibjpeg==2.0.0
 pylibjpeg-libjpeg==2.0.2
-pylibjpeg-openjpeg==2.1.1
+pylibjpeg-openjpeg==2.2.0
 pynvim==0.5.0
 pytest==8.1.1
     # via pytest-cov
-pytest-cov==4.1.0
+pytest-cov==5.0.0
 python-dateutil==2.9.0.post0
     # via pandas
 pytorch-lightning==2.2.1
@@ -226,13 +220,13 @@ requests==2.31.0
     #   datasets
     #   huggingface-hub
     #   transformers
-ruff==0.3.3
+ruff==0.3.4
 safetensors==0.4.2
     # via
     #   timm
     #   transformers
-scikit-learn==1.3.2
-scipy==1.10.1
+scikit-learn==1.4.1.post1
+scipy==1.12.0
     # via scikit-learn
 sentencepiece==0.2.0
 setuptools==69.2.0
@@ -247,27 +241,21 @@ stdlibs==2024.1.28
     # via usort
 sympy==1.12
     # via torch
-threadpoolctl==3.3.0
+threadpoolctl==3.4.0
     # via scikit-learn
 timm==0.9.16
 tokenizers==0.15.2
     # via transformers
 toml==0.10.2
     # via usort
-tomli==2.0.1
-    # via
-    #   coverage
-    #   ipdb
-    #   mypy
-    #   pytest
 torch==2.2.1
     # via
     #   lightning
     #   pytorch-lightning
     #   timm
     #   torchmetrics
     #   torchvision
-torchmetrics==1.3.1
+torchmetrics==1.3.2
     # via
     #   lightning
     #   pytorch-lightning
@@ -286,7 +274,7 @@ traitlets==5.14.2
     # via
     #   ipython
     #   matplotlib-inline
-transformers==4.38.2
+transformers==4.39.1
 triton==2.2.0
     # via torch
 typing-extensions==4.10.0

tests/test_convert_images.py

@@ -15,6 +15,7 @@ def dicom_file(tmpdir_factory):
     return Path(fpath)
 
 
+@pytest.mark.slow
 def test_happy_case(dicom_file, tmp_path):
     # given
     assert dicom_file.exists()