PyPI - py2ls - Versions diffs - 0.2.4.6__tar.gz → 0.2.4.8__tar.gz - Mend

py2ls 0.2.4.6tar.gz → 0.2.4.8tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (232) hide show

{py2ls-0.2.4.6 → py2ls-0.2.4.8}/PKG-INFO RENAMED Viewed

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: py2ls
-Version: 0.2.4.6
+Version: 0.2.4.8
 Summary: py(thon)2(too)ls
 Author: Jianfeng
 Author-email: Jianfeng.Liu0413@gmail.com
@@ -56,7 +56,7 @@ Requires-Dist: coverage (>=7.6.0)
 Requires-Dist: coveralls (>=4.0.1)
 Requires-Dist: crashtest (>=0.4.1)
 Requires-Dist: cycler (>=0.12.1)
-Requires-Dist: dask (>=2024.7.1)
+Requires-Dist: dask[dataframe] (>=2023.6,<2024.0)
 Requires-Dist: debugpy (>=1.8.2)
 Requires-Dist: decorator (>=5.1.1)
 Requires-Dist: defusedxml (>=0.7.1)

py2ls-0.2.4.8/py2ls/.git/index ADDED Viewed

Binary file

{py2ls-0.2.4.6 → py2ls-0.2.4.8}/py2ls/batman.py RENAMED Viewed

@@ -37,7 +37,38 @@ def convert_to_html(text_list, strict=False):
             text = text.replace(escape_seq, html_rep)
         html_content += text.replace("\n", "<br>")  # Add line breaks for newlines
     if strict:
-        html_content = "<html><body>\n" + html_content + "\n</body></html>"
+        # html_content = "<html><body>\n" + html_content + "\n</body></html>"
+                # Include mobile-friendly CSS for responsive tables
+        css_style = """
+        <style>
+            .table-container {
+                overflow-x: auto;
+                -webkit-overflow-scrolling: touch; /* Enable smooth scrolling on iOS */
+                margin-bottom: 20px;
+            }
+            table {
+                width: 100%;
+                border-collapse: collapse;
+            }
+            th, td {
+                padding: 8px;
+                border: 1px solid #ddd;
+                text-align: left;
+            }
+        </style>
+        """
+        # Wrap the HTML content in the responsive container div
+        html_content = f"""
+        <html>
+            <head>{css_style}</head>
+            <body>
+                <div class="table-container">
+                    {html_content}
+                </div>
+            </body>
+        </html>
+        """
     return html_content

{py2ls-0.2.4.6 → py2ls-0.2.4.8}/py2ls/bio.py RENAMED Viewed

@@ -166,9 +166,23 @@ def get_probe(
     if platform_id is None:
         df_meta = get_meta(geo=geo, dataset=dataset, verbose=False)
         platform_id = df_meta["platform_id"].unique().tolist()
-        platform_id = platform_id[0] if len(platform_id) == 1 else platform_id
         print(f"Platform: {platform_id}")
-    df_probe = geo[dataset].gpls[platform_id].table
+    if len(platform_id) > 1:
+        df_probe= geo[dataset].gpls[platform_id[0]].table
+        # df_probe=pd.DataFrame()
+        # # Iterate over each platform ID and collect the probe tables
+        # for platform_id_ in platform_id:
+        #     if platform_id_ in geo[dataset].gpls:
+        #         df_probe_ = geo[dataset].gpls[platform_id_].table
+        #         if not df_probe_.empty:
+        #             df_probe=pd.concat([df_probe, df_probe_])
+        #         else:
+        #             print(f"Warning: Probe table for platform {platform_id_} is empty.")
+        #     else:
+        #         print(f"Warning: Platform ID {platform_id_} not found in dataset {dataset}.")
+    else:
+        df_probe= geo[dataset].gpls[platform_id[0]].table
     if df_probe.empty:
         print(
             f"Warning: cannot find the probe info. 看一下是不是在单独的文件中包含了probe信息"
@@ -215,9 +229,12 @@ def get_data(geo: dict, dataset: str = "GSE25097", verbose=False):
     df_expression = get_expression_data(geo, dataset=dataset)
     if not df_expression.select_dtypes(include=["number"]).empty:
         # 如果数据全部是counts类型的话, 则使用TMM进行normalize
-        if 'counts' in get_data_type(df_expression):
-            print(f"{dataset}'s type is raw read counts, nomalized(transformed) via 'TMM'")
-            df_expression=counts2expression(df_expression.T).T
+        if 'counts' in get_data_type(df_expression):
+            try:
+                df_expression=counts2expression(df_expression.T).T
+                print(f"{dataset}'s type is raw read counts, nomalized(transformed) via 'TMM'")
+            except Exception as e:
+                print("raw counts data")
     if any([df_probe.empty, df_expression.empty]):
         print(
             f"got empty values, check the probe info. 看一下是不是在单独的文件中包含了probe信息"
@@ -237,23 +254,9 @@ def get_data(geo: dict, dataset: str = "GSE25097", verbose=False):
     # get meta info
     df_meta = get_meta(geo, dataset=dataset, verbose=False)
     col_rm = [
-        "channel_count",
-        "contact_web_link",
-        "contact_address",
-        "contact_city",
-        "contact_country",
-        "contact_department",
-        "contact_email",
-        "contact_institute",
-        "contact_laboratory",
-        "contact_name",
-        "contact_phone",
-        "contact_state",
-        "contact_zip/postal_code",
-        "contributor",
-        "manufacture_protocol",
-        "taxid",
-        "web_link",
+        "channel_count","contact_web_link","contact_address","contact_city","contact_country","contact_department",
+        "contact_email","contact_institute","contact_laboratory","contact_name","contact_phone","contact_state",
+        "contact_zip/postal_code","contributor","manufacture_protocol","taxid","web_link",
     ]
     # rm unrelavent columns
     df_meta = df_meta.drop(columns=[col for col in col_rm if col in df_meta.columns])

{py2ls-0.2.4.6 → py2ls-0.2.4.8}/py2ls/data/usages_sns.json RENAMED Viewed

@@ -21,5 +21,6 @@
     "residplot": "seaborn.residplot(data=None,*,x=None,y=None,x_partial=None,y_partial=None,lowess=False,order=1,robust=False,dropna=True,label=None,color=None,scatter_kws=None,line_kws=None,ax=None)\nhttps://seaborn.pydata.org/generated/seaborn.residplot.html",
     "pairplot": "seaborn.pairplot(data,*,hue=None,hue_order=None,palette=None,vars=None,x_vars=None,y_vars=None,kind='scatter',diag_kind='auto',markers=None,height=2.5,aspect=1,corner=False,dropna=False,plot_kws=None,diag_kws=None,grid_kws=None,size=None)\nhttps://seaborn.pydata.org/generated/seaborn.pairplot.html",
     "jointplot": "seaborn.jointplot(data=None,*,x=None,y=None,hue=None,kind='scatter',height=6,ratio=5,space=0.2,dropna=False,xlim=None,ylim=None,color=None,palette=None,hue_order=None,hue_norm=None,marginal_ticks=False,joint_kws=None,marginal_kws=None,**kwargs)\nhttps://seaborn.pydata.org/generated/seaborn.jointplot.html",
-    "plotting_context": "seaborn.plotting_context(context=None,font_scale=1,rc=None)\nhttps://seaborn.pydata.org/generated/seaborn.plotting_context.html"
+    "plotting_context": "seaborn.plotting_context(context=None,font_scale=1,rc=None)\nhttps://seaborn.pydata.org/generated/seaborn.plotting_context.html",
+    "swarmplot":"seaborn.swarmplot(data=None, *, x=None, y=None, hue=None, order=None, hue_order=None, dodge=False, orient=None, color=None, palette=None, size=5, edgecolor=None, linewidth=0, hue_norm=None, log_scale=None, native_scale=False, formatter=None, legend='auto', warn_thresh=0.05, ax=None, **kwargs)\nhttps://seaborn.pydata.org/generated/seaborn.swarmplot.html"
 }

py2ls 0.2.4.6__tar.gz → 0.2.4.8__tar.gz

py2ls 0.2.4.6tar.gz → 0.2.4.8tar.gz