Refactored test cases (#97)

* regenerated test file for test_align

* regenerated test file for test_model_selection

* regenerated test file for test_paste

* regenerated test file for test_paste_2

* regenerated test file for test_paste_helpers

* regenerated test file for test_visualization

* consolidating test files in a single directory; getting rid of tests/input and tests/output

* unpinned everything expect POT

docs/source/notebooks/paste2_tutorial.ipynb

@@ -51,10 +51,10 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "sliceA_filename = \"../../../tests/data/input/151673.h5ad\"\n",
-    "sliceB_filename = \"../../../tests/data/input/151674.h5ad\"\n",
-    "sliceC_filename = \"../../../tests/data/input/151675.h5ad\"\n",
-    "sliceD_filename = \"../../../tests/data/input/151676.h5ad\"\n",
+    "sliceA_filename = \"../../../tests/data/151673.h5ad\"\n",
+    "sliceB_filename = \"../../../tests/data/151674.h5ad\"\n",
+    "sliceC_filename = \"../../../tests/data/151675.h5ad\"\n",
+    "sliceD_filename = \"../../../tests/data/151676.h5ad\"\n",
     "sliceA = sc.read_h5ad(sliceA_filename)\n",
     "sliceB = sc.read_h5ad(sliceB_filename)\n",
     "sliceC = sc.read_h5ad(sliceC_filename)\n",

docs/source/notebooks/paste_tutorial.ipynb

@@ -54,7 +54,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "data_dir = \"../../../tests/data/input/\"\n",
+    "data_dir = \"../../../tests/data/\"\n",
     "\n",
     "\n",
     "# Assume that the coordinates of slices are named slice_name + \"_coor.csv\"\n",
@@ -609,7 +609,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "data_dir = \"../../../tests/data/input/\"\n",
+    "data_dir = \"../../../tests/data/\"\n",
     "\n",
     "\n",
     "# Assume that the coordinates of slices are named slice_name + \"_coor.csv\"\n",

pyproject.toml

@@ -18,10 +18,10 @@ classifiers = [
 ]
 
 dependencies = [
-    "anndata==0.10.9",
+    "anndata",
     "scanpy",
     "POT>=0.9.5",
-    "numpy<2",
+    "numpy",
     "scipy",
     "scikit-learn",
     "IPython",
@@ -50,7 +50,7 @@ dev = [
 ]
 
 docs = [
-    "sphinx==6.2.1",
+    "sphinx",
     "myst-parser",
     "sphinx-autodoc-typehints",
     "nbsphinx",