Release 0.1.4

.github/workflows/main.yml

@@ -7,9 +7,11 @@ on:
     branches: [ "main" ]
 
 jobs:
-  build:
+  test:
     runs-on: ubuntu-latest
-
+    strategy:
+      matrix:
+        python-version: [ '3.9', '3.10', '3.11', '3.12'  ]
     steps:
     - uses: actions/checkout@v3
     - name: Install Poetry
@@ -19,7 +21,7 @@ jobs:
       uses: snok/install-poetry@v1
     - uses: actions/setup-python@v4
       with:
-        python-version: '3.9'
+        python-version: ${{ matrix.python-version }}
         cache: 'poetry'
     - name: Install project
       if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
@@ -31,6 +33,23 @@ jobs:
     - name: Pytest
       run: |
         poetry run pytest
+
+  docs:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+    - name: Install Poetry
+      with:
+        virtualenvs-create: true
+        virtualenvs-in-project: true
+      uses: snok/install-poetry@v1
+    - uses: actions/setup-python@v4
+      with:
+        python-version: '3.12'
+        cache: 'poetry'
+    - name: Install project
+      if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
+      run: poetry install --with docs,dev --no-interaction
     - name: Build documentation
       run: |
           mkdir gh-pages

Dockerfile

@@ -1,4 +1,4 @@
-FROM python:3.10-slim
+FROM python:3.12-slim
 
 WORKDIR /code
 
@@ -25,7 +25,7 @@ ENV POETRY_HOME=/opt/poetry
 
 # install poetry into its own venv
 RUN python3 -m venv $POETRY_HOME && \
-    $POETRY_HOME/bin/pip install poetry==1.7.1
+    $POETRY_HOME/bin/pip install poetry==1.8.0
 
 ENV VIRTUAL_ENV=/poetry-env \
     PATH="/poetry-env/bin:$POETRY_HOME/bin:$PATH"
@@ -39,6 +39,6 @@ USER $USERNAME
 COPY --chown=${USER_UID}:${USER_GID} pyproject.toml poetry.lock README.md /code/
 COPY --chown=${USER_UID}:${USER_GID} starling/__init__.py /code/starling/__init__.py
 
-RUN poetry install --with docs,dev
+RUN poetry install --with docs,dev && poetry self add poetry-plugin-export
 
 COPY --chown=${USER_UID}:${USER_GID} . .

README.md

@@ -3,6 +3,8 @@
 ![build](https://github.com/camlab-bioml/starling/actions/workflows/main.yml/badge.svg)
 ![](https://img.shields.io/badge/Python-3.9-blue)
 ![](https://img.shields.io/badge/Python-3.10-blue)
+![](https://img.shields.io/badge/Python-3.11-blue)
+![](https://img.shields.io/badge/Python-3.12-blue)
 
 
 STARLING is a probabilistic model for clustering cells measured with spatial expression assays (e.g. IMC, MIBI, etc...) while accounting for segmentation errors.

pyproject.toml

@@ -1,7 +1,7 @@
 [tool.poetry]
 name = "biostarling"
 packages = [{ include = "starling" }]
-version = "0.1.3"
+version = "0.1.4"
 description = "Segmentation error aware clustering single-cell spatial expression data"
 repository = "https://github.com/camlab-bioml/starling"
 authors = ["Jett (Yuju) Lee <[email protected]>"]
@@ -10,17 +10,21 @@ keywords = ["imaging cytometry classifier single-cell"]
 classifiers = [
     "Intended Audience :: Science/Research",
     "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
 ]
 license = "See License.txt"
 
 [tool.poetry.dependencies]
-python = ">= 3.9, < 3.11"
+python = ">= 3.9, < 3.13"
 phenograph = "^1.5.7"
 flowsom = "^0.1.1"
 numpy = "^1.26"
-torch = "^2.4.0"
+pandas = ">= 0.23.0"
 pytorch-lightning = "^2.3.3"
 scanpy = "^1.10.2"
+torch = "^2.4.0"
 
 [tool.poetry.group.dev]
 optional = true

requirements.txt

@@ -1,68 +1,86 @@
-aiohttp==3.9.1 ; python_version >= "3.9" and python_version < "4.0"
-aiosignal==1.3.1 ; python_version >= "3.9" and python_version < "4.0"
-anndata==0.10.4 ; python_version >= "3.9" and python_version < "4.0"
-array-api-compat==1.4 ; python_version >= "3.9" and python_version < "4.0"
+aiohappyeyeballs==2.3.5 ; python_version >= "3.9" and python_version < "3.13"
+aiohttp==3.10.3 ; python_version >= "3.9" and python_version < "3.13"
+aiosignal==1.3.1 ; python_version >= "3.9" and python_version < "3.13"
+anndata==0.10.8 ; python_version >= "3.9" and python_version < "3.13"
+array-api-compat==1.8 ; python_version >= "3.9" and python_version < "3.13"
 async-timeout==4.0.3 ; python_version >= "3.9" and python_version < "3.11"
-attrs==23.2.0 ; python_version >= "3.9" and python_version < "4.0"
-certifi==2023.11.17 ; python_version >= "3.9" and python_version < "4.0"
-charset-normalizer==3.3.2 ; python_version >= "3.9" and python_version < "4.0"
-colorama==0.4.6 ; python_version >= "3.9" and python_version < "4.0" and platform_system == "Windows"
-contourpy==1.2.0 ; python_version >= "3.9" and python_version < "4.0"
-cycler==0.12.1 ; python_version >= "3.9" and python_version < "4.0"
-decorator==5.1.1 ; python_version >= "3.9" and python_version < "4.0"
-exceptiongroup==1.2.0 ; python_version >= "3.9" and python_version < "3.11"
-fcsparser==0.2.8 ; python_version >= "3.9" and python_version < "4.0"
-flowcytometrytools==0.5.1 ; python_version >= "3.9" and python_version < "4.0"
-flowsom==0.1.1 ; python_version >= "3.9" and python_version < "4.0"
-fonttools==4.47.2 ; python_version >= "3.9" and python_version < "4.0"
-frozenlist==1.4.1 ; python_version >= "3.9" and python_version < "4.0"
-fsspec[http]==2023.12.2 ; python_version >= "3.9" and python_version < "4.0"
-h5py==3.10.0 ; python_version >= "3.9" and python_version < "4.0"
-idna==3.6 ; python_version >= "3.9" and python_version < "4.0"
-igraph==0.10.8 ; python_version >= "3.9" and python_version < "4.0"
-importlib-resources==6.1.1 ; python_version >= "3.9" and python_version < "3.10"
-joblib==1.3.2 ; python_version >= "3.9" and python_version < "4.0"
-kiwisolver==1.4.5 ; python_version >= "3.9" and python_version < "4.0"
-leidenalg==0.10.1 ; python_version >= "3.9" and python_version < "4.0"
-lightning-utilities==0.10.0 ; python_version >= "3.9" and python_version < "4.0"
-llvmlite==0.41.1 ; python_version >= "3.9" and python_version < "4.0"
-matplotlib==3.8.2 ; python_version >= "3.9" and python_version < "4.0"
-minisom==2.3.1 ; python_version >= "3.9" and python_version < "4.0"
-multidict==6.0.4 ; python_version >= "3.9" and python_version < "4.0"
-natsort==8.4.0 ; python_version >= "3.9" and python_version < "4.0"
-networkx==3.2.1 ; python_version >= "3.9" and python_version < "4.0"
-numba==0.58.1 ; python_version >= "3.9" and python_version < "4.0"
-numpy==1.26.3 ; python_version >= "3.9" and python_version < "4.0"
-packaging==23.2 ; python_version >= "3.9" and python_version < "4.0"
-pandas==2.1.4 ; python_version >= "3.9" and python_version < "4.0"
-patsy==0.5.6 ; python_version >= "3.9" and python_version < "4.0"
-phenograph==1.5.7 ; python_version >= "3.9" and python_version < "4.0"
-pillow==10.2.0 ; python_version >= "3.9" and python_version < "4.0"
-psutil==5.9.7 ; python_version >= "3.9" and python_version < "4.0"
-pynndescent==0.5.11 ; python_version >= "3.9" and python_version < "4.0"
-pyparsing==3.1.1 ; python_version >= "3.9" and python_version < "4.0"
-python-dateutil==2.8.2 ; python_version >= "3.9" and python_version < "4.0"
-pytorch-lightning==2.1.0 ; python_version >= "3.9" and python_version < "4.0"
-pytz==2023.3.post1 ; python_version >= "3.9" and python_version < "4.0"
-pyyaml==6.0.1 ; python_version >= "3.9" and python_version < "4.0"
-requests==2.31.0 ; python_version >= "3.9" and python_version < "4.0"
-scanpy==1.9.5 ; python_version >= "3.9" and python_version < "4.0"
-scikit-learn==1.4.0 ; python_version >= "3.9" and python_version < "4.0"
-scipy==1.11.4 ; python_version >= "3.9" and python_version < "4.0"
-seaborn==0.13.1 ; python_version >= "3.9" and python_version < "4.0"
-session-info==1.0.0 ; python_version >= "3.9" and python_version < "4.0"
-setuptools==69.0.3 ; python_version >= "3.9" and python_version < "4.0"
-six==1.16.0 ; python_version >= "3.9" and python_version < "4.0"
-statsmodels==0.14.1 ; python_version >= "3.9" and python_version < "4.0"
-stdlib-list==0.10.0 ; python_version >= "3.9" and python_version < "4.0"
-texttable==1.7.0 ; python_version >= "3.9" and python_version < "4.0"
-threadpoolctl==3.2.0 ; python_version >= "3.9" and python_version < "4.0"
-torch==1.12.1 ; python_version >= "3.9" and python_version < "4.0"
-torchmetrics==1.3.0.post0 ; python_version >= "3.9" and python_version < "4.0"
-tqdm==4.66.1 ; python_version >= "3.9" and python_version < "4.0"
-typing-extensions==4.9.0 ; python_version >= "3.9" and python_version < "4.0"
-tzdata==2023.4 ; python_version >= "3.9" and python_version < "4.0"
-umap-learn==0.5.5 ; python_version >= "3.9" and python_version < "4.0"
-urllib3==2.1.0 ; python_version >= "3.9" and python_version < "4.0"
-yarl==1.9.4 ; python_version >= "3.9" and python_version < "4.0"
-zipp==3.17.0 ; python_version >= "3.9" and python_version < "3.10"
+attrs==24.2.0 ; python_version >= "3.9" and python_version < "3.13"
+colorama==0.4.6 ; python_version >= "3.9" and python_version < "3.13" and platform_system == "Windows"
+contourpy==1.2.1 ; python_version >= "3.9" and python_version < "3.13"
+cycler==0.12.1 ; python_version >= "3.9" and python_version < "3.13"
+decorator==5.1.1 ; python_version >= "3.9" and python_version < "3.13"
+exceptiongroup==1.2.2 ; python_version >= "3.9" and python_version < "3.11"
+fcsparser==0.2.8 ; python_version >= "3.9" and python_version < "3.13"
+filelock==3.15.4 ; python_version >= "3.9" and python_version < "3.13"
+flowcytometrytools==0.5.1 ; python_version >= "3.9" and python_version < "3.13"
+flowsom==0.1.1 ; python_version >= "3.9" and python_version < "3.13"
+fonttools==4.53.1 ; python_version >= "3.9" and python_version < "3.13"
+frozenlist==1.4.1 ; python_version >= "3.9" and python_version < "3.13"
+fsspec==2024.6.1 ; python_version >= "3.9" and python_version < "3.13"
+fsspec[http]==2024.6.1 ; python_version >= "3.9" and python_version < "3.13"
+get-annotations==0.1.2 ; python_version >= "3.9" and python_version < "3.10"
+h5py==3.11.0 ; python_version >= "3.9" and python_version < "3.13"
+idna==3.7 ; python_version >= "3.9" and python_version < "3.13"
+igraph==0.11.6 ; python_version >= "3.9" and python_version < "3.13"
+importlib-resources==6.4.0 ; python_version >= "3.9" and python_version < "3.10"
+jinja2==3.1.4 ; python_version >= "3.9" and python_version < "3.13"
+joblib==1.4.2 ; python_version >= "3.9" and python_version < "3.13"
+kiwisolver==1.4.5 ; python_version >= "3.9" and python_version < "3.13"
+legacy-api-wrap==1.4 ; python_version >= "3.9" and python_version < "3.13"
+leidenalg==0.10.2 ; python_version >= "3.9" and python_version < "3.13"
+lightning-utilities==0.11.6 ; python_version >= "3.9" and python_version < "3.13"
+llvmlite==0.43.0 ; python_version >= "3.9" and python_version < "3.13"
+markupsafe==2.1.5 ; python_version >= "3.9" and python_version < "3.13"
+matplotlib==3.9.1.post1 ; python_version >= "3.9" and python_version < "3.13"
+minisom==2.3.2 ; python_version >= "3.9" and python_version < "3.13"
+mpmath==1.3.0 ; python_version >= "3.9" and python_version < "3.13"
+multidict==6.0.5 ; python_version >= "3.9" and python_version < "3.13"
+natsort==8.4.0 ; python_version >= "3.9" and python_version < "3.13"
+networkx==3.2.1 ; python_version >= "3.9" and python_version < "3.13"
+numba==0.60.0 ; python_version >= "3.9" and python_version < "3.13"
+numpy==1.26.4 ; python_version >= "3.9" and python_version < "3.13"
+nvidia-cublas-cu12==12.1.3.1 ; platform_system == "Linux" and platform_machine == "x86_64" and python_version >= "3.9" and python_version < "3.13"
+nvidia-cuda-cupti-cu12==12.1.105 ; platform_system == "Linux" and platform_machine == "x86_64" and python_version >= "3.9" and python_version < "3.13"
+nvidia-cuda-nvrtc-cu12==12.1.105 ; platform_system == "Linux" and platform_machine == "x86_64" and python_version >= "3.9" and python_version < "3.13"
+nvidia-cuda-runtime-cu12==12.1.105 ; platform_system == "Linux" and platform_machine == "x86_64" and python_version >= "3.9" and python_version < "3.13"
+nvidia-cudnn-cu12==9.1.0.70 ; platform_system == "Linux" and platform_machine == "x86_64" and python_version >= "3.9" and python_version < "3.13"
+nvidia-cufft-cu12==11.0.2.54 ; platform_system == "Linux" and platform_machine == "x86_64" and python_version >= "3.9" and python_version < "3.13"
+nvidia-curand-cu12==10.3.2.106 ; platform_system == "Linux" and platform_machine == "x86_64" and python_version >= "3.9" and python_version < "3.13"
+nvidia-cusolver-cu12==11.4.5.107 ; platform_system == "Linux" and platform_machine == "x86_64" and python_version >= "3.9" and python_version < "3.13"
+nvidia-cusparse-cu12==12.1.0.106 ; platform_system == "Linux" and platform_machine == "x86_64" and python_version >= "3.9" and python_version < "3.13"
+nvidia-nccl-cu12==2.20.5 ; platform_system == "Linux" and platform_machine == "x86_64" and python_version >= "3.9" and python_version < "3.13"
+nvidia-nvjitlink-cu12==12.6.20 ; platform_system == "Linux" and platform_machine == "x86_64" and python_version >= "3.9" and python_version < "3.13"
+nvidia-nvtx-cu12==12.1.105 ; platform_system == "Linux" and platform_machine == "x86_64" and python_version >= "3.9" and python_version < "3.13"
+packaging==24.1 ; python_version >= "3.9" and python_version < "3.13"
+pandas==2.2.2 ; python_version >= "3.9" and python_version < "3.13"
+patsy==0.5.6 ; python_version >= "3.9" and python_version < "3.13"
+phenograph==1.5.7 ; python_version >= "3.9" and python_version < "3.13"
+pillow==10.4.0 ; python_version >= "3.9" and python_version < "3.13"
+psutil==6.0.0 ; python_version >= "3.9" and python_version < "3.13"
+pynndescent==0.5.13 ; python_version >= "3.9" and python_version < "3.13"
+pyparsing==3.1.2 ; python_version >= "3.9" and python_version < "3.13"
+python-dateutil==2.9.0.post0 ; python_version >= "3.9" and python_version < "3.13"
+pytorch-lightning==2.4.0 ; python_version >= "3.9" and python_version < "3.13"
+pytz==2024.1 ; python_version >= "3.9" and python_version < "3.13"
+pyyaml==6.0.2 ; python_version >= "3.9" and python_version < "3.13"
+scanpy==1.10.2 ; python_version >= "3.9" and python_version < "3.13"
+scikit-learn==1.5.1 ; python_version >= "3.9" and python_version < "3.13"
+scipy==1.13.1 ; python_version >= "3.9" and python_version < "3.13"
+seaborn==0.13.2 ; python_version >= "3.9" and python_version < "3.13"
+session-info==1.0.0 ; python_version >= "3.9" and python_version < "3.13"
+setuptools==72.1.0 ; python_version >= "3.9" and python_version < "3.13"
+six==1.16.0 ; python_version >= "3.9" and python_version < "3.13"
+statsmodels==0.14.2 ; python_version >= "3.9" and python_version < "3.13"
+stdlib-list==0.10.0 ; python_version >= "3.9" and python_version < "3.13"
+sympy==1.13.2 ; python_version >= "3.9" and python_version < "3.13"
+texttable==1.7.0 ; python_version >= "3.9" and python_version < "3.13"
+threadpoolctl==3.5.0 ; python_version >= "3.9" and python_version < "3.13"
+torch==2.4.0 ; python_version >= "3.9" and python_version < "3.13"
+torchmetrics==1.4.1 ; python_version >= "3.9" and python_version < "3.13"
+tqdm==4.66.5 ; python_version >= "3.9" and python_version < "3.13"
+triton==3.0.0 ; platform_system == "Linux" and platform_machine == "x86_64" and python_version < "3.13" and python_version >= "3.9"
+typing-extensions==4.12.2 ; python_version >= "3.9" and python_version < "3.13"
+tzdata==2024.1 ; python_version >= "3.9" and python_version < "3.13"
+umap-learn==0.5.6 ; python_version >= "3.9" and python_version < "3.13"
+yarl==1.9.4 ; python_version >= "3.9" and python_version < "3.13"
+zipp==3.20.0 ; python_version >= "3.9" and python_version < "3.10"

starling/utility.py

@@ -9,6 +9,8 @@
 import scanpy.external as sce
 import torch
 
+# patch outdated flowsom dependencies
+pd.DataFrame.as_matrix = pd.DataFrame.to_numpy
 collections.MutableMapping = abc.MutableMapping
 from flowsom import flowsom
 from scanpy import AnnData
@@ -107,7 +109,7 @@ def init_clustering(
     elif initial_clustering_method == "FS":
         ## needs to output to csv first
         # ofn = OPATH + "fs_" + ONAME + ".csv"
-        pd.DataFrame(X).to_csv("fs.csv")
+        pd.DataFrame(adata.X).to_csv("fs.csv")
         fsom = flowsom("fs.csv", if_fcs=False, if_drop=True, drop_col=["Unnamed: 0"])
 
         fsom.som_mapping(

tests/test_utility.py

@@ -35,6 +35,12 @@ def test_init_clustering_pg(simple_adata):
     assert_annotated(initialized, k)
 
 
+def test_init_clustering_fs(simple_adata):
+    k = 2
+    initialized = init_clustering("FS", simple_adata, k)
+    assert_annotated(initialized, k)
+
+
 def test_init_clustering_user(simple_adata):
     k = 3
     initialized = init_clustering(