Made the package pip installable and updated ci

.github/workflows/build.yml

@@ -34,7 +34,7 @@ jobs:
           environment-file: environment.yml
 
       - name: Install package
-        run: pip install .
+        run: pip install -e .
 
       - name: Pytest
         run: pytest

pyproject.toml

@@ -1,6 +1,44 @@
 [build-system]
-requires = [
-    "setuptools>=42",
-    "wheel"
+requires = ["setuptools>=61.0", "setuptools_scm>=6.2"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "paste"
+authors = [
+    {name="Max Land", email="max.ruikang.land@gmail.com"}
 ]
-build-backend = "setuptools.build_meta"
+description = "A computational method to align and integrate spatial transcriptomics experiments."
+readme = "README.md"
+requires-python = ">=3.6"
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "License :: OSI Approved :: BSD License",
+    "Operating System :: OS Independent",
+]
+
+dependencies = [
+    "anndata>=0.7.6",
+    "scanpy>=1.7.2",
+    "POT==0.9.0",
+    "numpy",
+    "scipy",
+    "scikit-learn>=0.24.0",
+    "IPython>=7.18.1",
+]
+dynamic = ["version"]
+
+[project.scripts]
+paste = "paste.__main__:main"
+
+[tool.setuptools]
+package-dir = {"" = "src"}
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+addopts = "-sv"
+
+[project.optional-dependencies]
+dev = [
+    "build",
+    "pytest",
+]

paste-cmd-line.py → src/paste/paste-cmd-line.py

@@ -56,7 +56,7 @@ def main(args):
         pis_init = [pd.read_csv(args.start[i],index_col=0).to_numpy() for i in range(len(args.start))]
 
     # create output folder
-    output_path = os.path.join(args.direc, "paste_output")
+    output_path = os.path.join(args.direc, "../../paste_output")
     if not os.path.exists(output_path):
         os.mkdir(output_path)
 
@@ -82,8 +82,8 @@ def main(args):
         center_slice, pis = center_align(initial_slice, slices, lmbda, args.alpha, args.n_components, args.threshold, dissimilarity=args.cost, distributions=[slices[i].obsm['weights'] for i in range(n_slices)], pis_init=pis_init)
         W = pd.DataFrame(center_slice.uns['paste_W'], index = center_slice.obs.index)
         H = pd.DataFrame(center_slice.uns['paste_H'], columns = center_slice.var.index)
-        W.to_csv(os.path.join(args.direc,"paste_output/W_center"))
-        H.to_csv(os.path.join(args.direc,"paste_output/H_center"))
+        W.to_csv(os.path.join(args.direc, "../../paste_output/W_center"))
+        H.to_csv(os.path.join(args.direc, "../../paste_output/H_center"))
         for i in range(len(pis)):
             output_filename = "paste_output/slice_center_slice" + str(i+1) + "_pairwise.csv"
             pi = pd.DataFrame(pis[i], index = center_slice.obs.index, columns = slices[i].obs.index)

tests/test_paste.py

@@ -6,7 +6,9 @@
 import pandas as pd
 import tempfile
 
-from paste import pairwise_align, center_align, center_ot, intersect, center_NMF
+from paste import pairwise_align, center_align
+from paste.PASTE import center_ot, intersect, center_NMF
+
 
 test_dir = Path(__file__).parent
 input_dir = test_dir / "data/input"