fixed style inconsistencies

wisdomadingo · Jun 23, 2023 · 8f78451 · 8f78451
1 parent c58c0bc
commit 8f78451
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Showing 2 changed files with 20 additions and 34 deletions.
diff --git a/jupyter-book/annotation/annotation.ipynb b/jupyter-book/annotation/annotation.ipynb
@@ -52,7 +52,7 @@
     "import numba\n",
     "from numba.core.errors import NumbaDeprecationWarning, NumbaPendingDeprecationWarning\n",
     "\n",
-    "warnings.simplefilter('ignore', category=NumbaDeprecationWarning)"
+    "warnings.simplefilter(\"ignore\", category=NumbaDeprecationWarning)"
    ]
   },
   {
@@ -801,9 +801,9 @@
    "source": [
     "cl_annotation = {\n",
     "    \"4\": \"Naive CD20+ B\",\n",
-    "    \"6\": \"Naive CD20+ B\", # 6\n",
+    "    \"6\": \"Naive CD20+ B\",\n",
     "    \"8\": \"Transitional B\",\n",
-    "    \"18\": \"B1 B\",  # note that IGHD and IGHM are negative markers, in this case more lowly expressed than in the other B cell clusters \n",
+    "    \"18\": \"B1 B\",  # note that IGHD and IGHM are negative markers, in this case more lowly expressed than in the other B cell clusters\n",
     "}"
    ]
   },
@@ -2129,7 +2129,7 @@
     "scarches_model = sca.models.SCVI.load_query_data(\n",
     "    adata=adata_to_map_augmented,\n",
     "    reference_model=os.path.join(dir_reference_model, \"model\"),\n",
-    "    freeze_dropout=True\n",
+    "    freeze_dropout=True,\n",
     ")"
    ]
   },
@@ -2582,8 +2582,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "adata_emb.obs[\"transf_cell_type\"] = labels.loc[adata_emb.obs.index,\"cell_type\"]\n",
-    "adata_emb.obs['transf_cell_type_unc'] = uncert.loc[adata_emb.obs.index, \"cell_type\"]"
+    "adata_emb.obs[\"transf_cell_type\"] = labels.loc[adata_emb.obs.index, \"cell_type\"]\n",
+    "adata_emb.obs[\"transf_cell_type_unc\"] = uncert.loc[adata_emb.obs.index, \"cell_type\"]"
    ]
   },
   {
@@ -2599,8 +2599,12 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "adata.obs.loc[adata_emb.obs.index, \"transf_cell_type\"] = adata_emb.obs[\"transf_cell_type\"]\n",
-    "adata.obs.loc[adata_emb.obs.index, \"transf_cell_type_unc\"] = adata_emb.obs[\"transf_cell_type_unc\"]"
+    "adata.obs.loc[adata_emb.obs.index, \"transf_cell_type\"] = adata_emb.obs[\n",
+    "    \"transf_cell_type\"\n",
+    "]\n",
+    "adata.obs.loc[adata_emb.obs.index, \"transf_cell_type_unc\"] = adata_emb.obs[\n",
+    "    \"transf_cell_type_unc\"\n",
+    "]"
    ]
   },
   {
@@ -2623,7 +2627,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "sc.set_figure_params(figsize=(5,5))"
+    "sc.set_figure_params(figsize=(5, 5))"
    ]
   },
   {
@@ -2655,11 +2659,7 @@
     }
    ],
    "source": [
-    "sc.pl.umap(\n",
-    "    adata,\n",
-    "    color=\"transf_cell_type\",\n",
-    "    frameon=False,\n",
-    ")"
+    "sc.pl.umap(adata, color=\"transf_cell_type\", frameon=False)"
    ]
   },
   {
@@ -2691,11 +2691,7 @@
     }
    ],
    "source": [
-    "sc.pl.umap(\n",
-    "    adata,\n",
-    "    color=\"transf_cell_type_unc\",\n",
-    "    frameon=False,\n",
-    ")"
+    "sc.pl.umap(adata, color=\"transf_cell_type_unc\", frameon=False)"
    ]
   },
   {
@@ -2806,11 +2802,7 @@
     }
    ],
    "source": [
-    "sc.pl.umap(\n",
-    "    adata,\n",
-    "    color=\"transf_cell_type_certain\",\n",
-    "    frameon=False\n",
-    ")"
+    "sc.pl.umap(adata, color=\"transf_cell_type_certain\", frameon=False)"
    ]
   },
   {
@@ -2842,11 +2834,7 @@
     }
    ],
    "source": [
-    "sc.pl.umap(\n",
-    "    adata,\n",
-    "    color=\"transf_cell_type_certain\",\n",
-    "    groups=\"Unknown\"\n",
-    ")"
+    "sc.pl.umap(adata, color=\"transf_cell_type_certain\", groups=\"Unknown\")"
    ]
   },
   {
@@ -2956,9 +2944,7 @@
    ],
    "source": [
     "sc.pl.umap(\n",
-    "    adata,\n",
-    "    color=[\"transf_cell_type_unc\", \"transf_cell_type_certain\"],\n",
-    "    frameon=False\n",
+    "    adata, color=[\"transf_cell_type_unc\", \"transf_cell_type_certain\"], frameon=False\n",
     ")"
    ]
   },

diff --git a/jupyter-book/annotation/annotation.yml b/jupyter-book/annotation/annotation.yml
@@ -16,5 +16,5 @@ dependencies:
   - anaconda::pandas<2.0.0
   - anaconda::pip
   - pip:
-    - scarches>=0.5.8
-    - scvi-tools>=0.20.3
+      - scarches>=0.5.8
+      - scvi-tools>=0.20.3