From 766c5702c4d61403fd6c6217a67c19a01edff611 Mon Sep 17 00:00:00 2001
From: Kai Zhang <kai@kzhang.org>
Date: Mon, 11 Sep 2023 10:44:56 -0700
Subject: [PATCH] minor

---
 .github/workflows/docs.yml                    | 30 +++++++++++++++++--
 .../snapatac2/preprocessing/_basic.py         |  2 ++
 .../snapatac2/preprocessing/_knn.py           |  3 +-
 .../snapatac2/tools/_call_peaks.py            |  4 +--
 4 files changed, 32 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
index 0bf1b7b3c..ab43102e5 100644
--- a/.github/workflows/docs.yml
+++ b/.github/workflows/docs.yml
@@ -23,7 +23,7 @@ jobs:
 
     - name: Install dependency
       run: |
-        sudo apt-get install -y pandoc
+        sudo apt-get install -y pandoc jq
         sudo pip install --upgrade pip
         pip install --user sphinx==6.2.* pydata-sphinx-theme==0.13.* pandoc nbsphinx \
           Pygments==2.14.0 sphinx-autodoc-typehints myst-parser \
@@ -66,7 +66,7 @@ jobs:
         clean: true
         target-folder: /version/dev/
 
-    - name: Deploy (version)
+    - name: Deploy (version) 🚀
       uses: JamesIves/github-pages-deploy-action@v4
       if: ${{ env.DEPLOY_VERSION == 'true' }}
       with:
@@ -74,4 +74,28 @@ jobs:
         branch: gh-pages
         folder: _build/html
         clean: true
-        target-folder: /version/${{ env.VERSION }}/
\ No newline at end of file
+        target-folder: /version/${{ env.VERSION }}/
+
+    - name: Fetch JSON and Get Preferred Version
+      run: |
+        JSON=$(curl -s "https://raw.githubusercontent.com/kaizhang/SnapATAC2/main/docs/_static/versions.json")
+        VERSION=$(echo "$JSON" | jq -r '.[] | select(.preferred == true) | .version')
+        echo "PREFERRED_VERSION=$VERSION" >> $GITHUB_ENV
+        echo "Preferred version is $VERSION"
+
+    - name: Checkout code from gh-pages branch into folder
+      uses: actions/checkout@v2
+      with:
+        ref: 'gh-pages'
+        path: 'gh-pages-folder'
+
+    - name: Deploy (preferred version)
+      uses: JamesIves/github-pages-deploy-action@v4
+      with:
+        single-commit: true
+        branch: gh-pages
+        folder: gh-pages-folder/version/${{ env.PREFERRED_VERSION }}
+        clean: true
+        clean-exclude: version
+
+
diff --git a/snapatac2-python/snapatac2/preprocessing/_basic.py b/snapatac2-python/snapatac2/preprocessing/_basic.py
index 2d30fa4de..325e43396 100644
--- a/snapatac2-python/snapatac2/preprocessing/_basic.py
+++ b/snapatac2-python/snapatac2/preprocessing/_basic.py
@@ -200,6 +200,8 @@ def import_data(
             chrom_size = genome.chrom_sizes
         if gene_anno is None:
             gene_anno = genome.fetch_annotations()
+    if len(chrom_size) == 0:
+        raise ValueError("chrom_size cannot be empty")
 
     if whitelist is not None:
         if isinstance(whitelist, str) or isinstance(whitelist, Path):
diff --git a/snapatac2-python/snapatac2/preprocessing/_knn.py b/snapatac2-python/snapatac2/preprocessing/_knn.py
index e4699d3cb..8057ce283 100644
--- a/snapatac2-python/snapatac2/preprocessing/_knn.py
+++ b/snapatac2-python/snapatac2/preprocessing/_knn.py
@@ -12,7 +12,7 @@ def knn(
     adata: AnnData | AnnDataSet | np.ndarray,
     n_neighbors: int = 50,
     use_dims: int | list[int] | None = None,
-    use_rep: str | None = None,
+    use_rep: str = 'X_spectral',
     method: Literal['hora', 'pynndescent', 'exact'] = "hora",
     n_jobs: int = -1,
     inplace: bool = True,
@@ -51,7 +51,6 @@ def knn(
         Otherwise, return a sparse matrix.
     """
     if is_anndata(adata):
-        if use_rep is None: use_rep = "X_spectral"
         data = adata.obsm[use_rep]
     else:
         inplace = False
diff --git a/snapatac2-python/snapatac2/tools/_call_peaks.py b/snapatac2-python/snapatac2/tools/_call_peaks.py
index f77620882..32a4e7f10 100644
--- a/snapatac2-python/snapatac2/tools/_call_peaks.py
+++ b/snapatac2-python/snapatac2/tools/_call_peaks.py
@@ -63,8 +63,8 @@ def call_peaks(
     if isinstance(groupby, str):
         groupby = list(adata.obs[groupby])
     out_dir = out_dir if out_dir is None else str(out_dir)
-    res = _snapatac2.call_peaks(adata, groupby, selections, q_value, nolambda,
-        shift, extsize, blacklist, out_dir)
+    res = _snapatac2.call_peaks(adata, groupby, q_value, nolambda,
+        shift, extsize, selections, blacklist, out_dir)
     if inplace:
         if adata.isbacked:
             adata.uns[key_added] = res