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Aryan-SINGH-GITAryan-SINGH-GIT
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Fix linting errors
Signed-off-by: Aryan-SINGH-GIT <aryansingh12oct2005@gmail.com>
1 parent d9dc96e commit 027c7eb

27 files changed

Lines changed: 172 additions & 151 deletions

‎malariagen_data/adir1.py‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -174,7 +174,7 @@ def _repr_html_(self):
174174
<th style="text-align: left">
175175
Data releases available
176176
</th>
177-
<td>{', '.join(self._available_releases)}</td>
177+
<td>{", ".join(self._available_releases)}</td>
178178
</tr>
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<tr>
180180
<th style="text-align: left">
@@ -222,7 +222,7 @@ def _repr_html_(self):
222222
<th style="text-align: left">
223223
Relevant data releases
224224
</th>
225-
<td>{', '.join(self.releases)}</td>
225+
<td>{", ".join(self.releases)}</td>
226226
</tr>
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</tbody>
228228
</table>

‎malariagen_data/af1.py‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -179,7 +179,7 @@ def _repr_html_(self):
179179
<th style="text-align: left">
180180
Data releases available
181181
</th>
182-
<td>{', '.join(self._available_releases)}</td>
182+
<td>{", ".join(self._available_releases)}</td>
183183
</tr>
184184
<tr>
185185
<th style="text-align: left">
@@ -227,7 +227,7 @@ def _repr_html_(self):
227227
<th style="text-align: left">
228228
Relevant data releases
229229
</th>
230-
<td>{', '.join(self.releases)}</td>
230+
<td>{", ".join(self.releases)}</td>
231231
</tr>
232232
</tbody>
233233
</table>

‎malariagen_data/ag3.py‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -264,7 +264,7 @@ def _repr_html_(self):
264264
<th style="text-align: left">
265265
Data releases available
266266
</th>
267-
<td>{', '.join(self._available_releases)}</td>
267+
<td>{", ".join(self._available_releases)}</td>
268268
</tr>
269269
<tr>
270270
<th style="text-align: left">
@@ -318,7 +318,7 @@ def _repr_html_(self):
318318
<th style="text-align: left">
319319
Relevant data releases
320320
</th>
321-
<td>{', '.join(self.releases)}</td>
321+
<td>{", ".join(self.releases)}</td>
322322
</tr>
323323
</tbody>
324324
</table>

‎malariagen_data/amin1.py‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -177,7 +177,7 @@ def _repr_html_(self):
177177
<th style="text-align: left">
178178
Data releases available
179179
</th>
180-
<td>{', '.join(self.releases)}</td>
180+
<td>{", ".join(self.releases)}</td>
181181
</tr>
182182
<tr>
183183
<th style="text-align: left">
@@ -225,7 +225,7 @@ def _repr_html_(self):
225225
<th style="text-align: left">
226226
Relevant data releases
227227
</th>
228-
<td>{', '.join(self.releases)}</td>
228+
<td>{", ".join(self.releases)}</td>
229229
</tr>
230230
</tbody>
231231
</table>

‎malariagen_data/anoph/karyotype_params.py‎

Lines changed: 0 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,5 @@
11
"""Parameter definitions for karyotype analysis functions."""
22

3-
43
from typing_extensions import Annotated, TypeAlias
54

65
inversion_param: TypeAlias = Annotated[

‎malariagen_data/anoph/pca.py‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -152,7 +152,7 @@ def pca(
152152
# df_pca.index = df_pca.index.astype(str)
153153

154154
# Name the DataFrame's columns as PC1, PC2, etc.
155-
df_pca.columns = pd.Index([f"PC{i+1}" for i in range(coords.shape[1])])
155+
df_pca.columns = pd.Index([f"PC{i + 1}" for i in range(coords.shape[1])])
156156

157157
# Load the sample metadata.
158158
df_samples = self.sample_metadata(

‎malariagen_data/anopheles.py‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -2424,9 +2424,9 @@ def plot_haplotype_network(
24242424
# charts
24252425
for i, (v, c) in enumerate(color_discrete_map_prepped.items()):
24262426
node_style[f"pie-{i + 1}-background-color"] = c
2427-
node_style[
2428-
f"pie-{i + 1}-background-size"
2429-
] = f"mapData({v}, 0, 100, 0, 100)"
2427+
node_style[f"pie-{i + 1}-background-size"] = (
2428+
f"mapData({v}, 0, 100, 0, 100)"
2429+
)
24302430
node_stylesheet = {
24312431
"selector": "node",
24322432
"style": node_style,

‎malariagen_data/mjn.py‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -263,7 +263,7 @@ def _mjn_graph_edges(
263263

264264
# add further intermediate nodes as necessary
265265
for k in range(1, sep - 1):
266-
source = f"anon_{i}_{j}_{k-1}"
266+
source = f"anon_{i}_{j}_{k - 1}"
267267
target = f"anon_{i}_{j}_{k}"
268268
graph_node = {
269269
"id": target,
@@ -279,7 +279,7 @@ def _mjn_graph_edges(
279279
graph_edges.append(graph_edge)
280280

281281
# add edge from final intermediate node to node j
282-
source = f"anon_{i}_{j}_{sep-2}"
282+
source = f"anon_{i}_{j}_{sep - 2}"
283283
target = j
284284
graph_node = {
285285
"id": source,
@@ -288,7 +288,7 @@ def _mjn_graph_edges(
288288
}
289289
graph_nodes.append(graph_node)
290290
graph_edge = {
291-
"id": f"edge_{i}_{j}_{sep-1}",
291+
"id": f"edge_{i}_{j}_{sep - 1}",
292292
"source": source,
293293
"target": target,
294294
}

‎malariagen_data/util.py‎

Lines changed: 1 addition & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -851,9 +851,7 @@ def _value_error(
851851
value,
852852
expectation,
853853
):
854-
message = (
855-
f"Bad value for parameter {name}; expected {expectation}, " f"found {value!r}"
856-
)
854+
message = f"Bad value for parameter {name}; expected {expectation}, found {value!r}"
857855
raise ValueError(message)
858856

859857

‎notebooks/auto_chunks.ipynb‎

Lines changed: 6 additions & 10 deletions
Original file line numberDiff line numberDiff line change
@@ -39,9 +39,7 @@
3939
"metadata": {},
4040
"outputs": [],
4141
"source": [
42-
"ds = ag3.snp_calls(\n",
43-
" region=\"3R\", sample_sets=\"AG1000G-BF-A\"\n",
44-
")"
42+
"ds = ag3.snp_calls(region=\"3R\", sample_sets=\"AG1000G-BF-A\")"
4543
]
4644
},
4745
{
@@ -80,7 +78,9 @@
8078
"outputs": [],
8179
"source": [
8280
"ds = ag3.snp_calls(\n",
83-
" region=\"3R\", sample_sets=\"AG1000G-BF-A\", chunks=\"300MB\",\n",
81+
" region=\"3R\",\n",
82+
" sample_sets=\"AG1000G-BF-A\",\n",
83+
" chunks=\"300MB\",\n",
8484
")"
8585
]
8686
},
@@ -119,9 +119,7 @@
119119
"metadata": {},
120120
"outputs": [],
121121
"source": [
122-
"ds = ag3.snp_calls(\n",
123-
" region=\"3R\", sample_sets=\"AG1000G-BF-A\", chunks=\"auto\"\n",
124-
")"
122+
"ds = ag3.snp_calls(region=\"3R\", sample_sets=\"AG1000G-BF-A\", chunks=\"auto\")"
125123
]
126124
},
127125
{
@@ -159,9 +157,7 @@
159157
"metadata": {},
160158
"outputs": [],
161159
"source": [
162-
"ds = ag3.snp_calls(\n",
163-
" region=\"3R\", sample_sets=\"AG1000G-BF-A\", chunks=\"ndauto\"\n",
164-
")"
160+
"ds = ag3.snp_calls(region=\"3R\", sample_sets=\"AG1000G-BF-A\", chunks=\"ndauto\")"
165161
]
166162
},
167163
{

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