update tutorials

kaizhang · Sep 10, 2023 · 7a2c999 · 7a2c999
1 parent 1aaac4e
commit 7a2c999
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Showing 7 changed files with 25 additions and 11 deletions.
diff --git a/docs/_static/versions.json b/docs/_static/versions.json
@@ -7,7 +7,8 @@
     {
         "name": "2.3.1 (stable)",
         "version": "2.3.1",
-        "url": "https://kzhang.org/SnapATAC2/version/2.3.1/"
+        "url": "https://kzhang.org/SnapATAC2/version/2.3.1/",
+        "preferred": true
     },
     {
         "name": "2.3.0",

diff --git a/docs/conf.py b/docs/conf.py
@@ -121,11 +121,20 @@
     switcher_version = f"{version}"
 
 html_theme_options = {
+     "logo": {
+        "text": "SnapATAC2",
+        "image_dark": "_static/logo-dark.svg",
+        "alt_text": "SnapATAC2",
+    },
+
     "github_url": "https://github.com/kaizhang/SnapATAC2",
     "external_links": [
         {"name": "Learn", "url": "https://kzhang.org/epigenomics-analysis/"}
     ],
-    "navbar_end": ["version-switcher", "theme-switcher", "navbar-icon-links"],
+
+    "navbar_center": ["version-switcher", "navbar-nav"],
+    "navbar_end": ["theme-switcher", "navbar-icon-links"],
+    "show_version_warning_banner": True,
 
     "switcher": {
         "version_match": switcher_version,

diff --git a/docs/tutorials/integration.ipynb b/docs/tutorials/integration.ipynb
diff --git a/docs/tutorials/pbmc.ipynb b/docs/tutorials/pbmc.ipynb
diff --git a/snapatac2-python/setup.py b/snapatac2-python/setup.py
@@ -39,7 +39,7 @@
         "MACS2>=2.2.7",
         "natsort",
         "numpy>=1.16.0",
-        "pandas",
+        "pandas>=1.0",
         "plotly>=5.6.0",
         "polars>=0.14.0, <=0.18.0",
         "pooch>=1.6.0",

diff --git a/snapatac2-python/snapatac2/preprocessing/_knn.py b/snapatac2-python/snapatac2/preprocessing/_knn.py
@@ -21,6 +21,9 @@ def knn(
     """
     Compute a neighborhood graph of observations.
 
+    Computes a neighborhood graph of observations stored in `adata` using
+    the method specified by `method`. The distance metric used is Euclidean.
+
     Parameters
     ----------
     adata
@@ -32,7 +35,8 @@ def knn(
     use_rep
         The key for the matrix
     method
-        'hora', 'pynndescent', or 'exact'
+        'hora', 'pynndescent', or 'exact'. The default is 'hora', which uses the
+        HNSW algorithm to approximate the nearest neighbors.
     n_jobs
         number of CPUs to use
     inplace

diff --git a/snapatac2-python/tests/test_pipeline.py b/snapatac2-python/tests/test_pipeline.py
@@ -7,7 +7,6 @@ def h5ad(dir=Path("./")):
     dir.mkdir(exist_ok=True)
     return str(dir / Path(str(uuid.uuid4()) + ".h5ad"))
 
-'''
 def test_exclude():
     fragment_file = snap.datasets.pbmc500(True)
 
@@ -49,8 +48,7 @@ def test_backed(tmp_path):
     snap.pp.knn(data)
     snap.tl.leiden(data)
 
-    snap.pp.make_gene_matrix(data, gene_anno=snap.genome.hg38, file = h5ad(tmp_path))
-'''
+    snap.pp.make_gene_matrix(data, gene_anno=snap.genome.hg38, file=h5ad(tmp_path))
 
 def test_in_memory():
     fragment_file = snap.datasets.pbmc500(True)
@@ -63,6 +61,8 @@ def test_in_memory():
     snap.pp.add_tile_matrix(data)
 
     snap.pp.filter_cells(data)
+    snap.pp.select_features(data, whitelist=snap.datasets.cre_HEA())
+    snap.pp.select_features(data, blacklist=snap.datasets.cre_HEA())
     snap.pp.select_features(data)
 
     snap.tl.spectral(data, sample_size=100)