Fix weasyprint patch with --force-reinstall & move warning filter in example notebook

Author: jairideout

Dockerfile

@@ -143,7 +143,7 @@ RUN chown -R $NB_USER:root /usr/local/lib/python3.8
 # Fix for transparency issue
 # Pin in onecodex/onecodex once version w/ fix is released
 # https://github.com/Kozea/WeasyPrint/commit/4dfe6079c2d1bd91cccfd9a7d78f8924e2dfabef
-RUN pip install 'git+https://github.com/Kozea/WeasyPrint.git@4dfe6079c2d1bd91cccfd9a7d78f8924e2dfabef'
+RUN pip install --force-reinstall 'git+https://github.com/Kozea/WeasyPrint.git@4dfe6079c2d1bd91cccfd9a7d78f8924e2dfabef'
 
 # Switch to unprivileged user, jovyan
 USER $NB_USER

test/notebooks/example.ipynb

@@ -39,20 +39,17 @@
     "project = ocx.Projects.get(\"d53ad03b010542e3\")  # get DIABIMMUNE project by ID\n",
     "samples = ocx.Samples.where(project=project.id, public=True, limit=50)\n",
     "\n",
-    "# filter warning because timestamp shows up in diff-pdf\n",
-    "with warnings.catch_warnings():\n",
-    "    warnings.filterwarnings(\"ignore\", message=\".*SampleCollection contains multiple.*\")\n",
-    "    md_table = samples.metadata[[\n",
-    "        \"gender\",\n",
-    "        \"host_age\",\n",
-    "        \"geo_loc_name\",\n",
-    "        \"totalige\",\n",
-    "        \"eggs\",\n",
-    "        \"vegetables\",\n",
-    "        \"milk\",\n",
-    "        \"wheat\",\n",
-    "        \"rice\",\n",
-    "    ]]\n",
+    "md_table = samples.metadata[[\n",
+    "    \"gender\",\n",
+    "    \"host_age\",\n",
+    "    \"geo_loc_name\",\n",
+    "    \"totalige\",\n",
+    "    \"eggs\",\n",
+    "    \"vegetables\",\n",
+    "    \"milk\",\n",
+    "    \"wheat\",\n",
+    "    \"rice\",\n",
+    "]]\n",
     "    \n",
     "display(md_table)"
    ]
@@ -72,9 +69,13 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "observed_taxa = samples.plot_metadata(vaxis=\"observed_taxa\", haxis=\"geo_loc_name\", return_chart=True)\n",
-    "simpson = samples.plot_metadata(vaxis=\"simpson\", haxis=\"geo_loc_name\", return_chart=True)\n",
-    "shannon = samples.plot_metadata(vaxis=\"shannon\", haxis=\"geo_loc_name\", return_chart=True)\n",
+    "# filter warning because timestamp shows up in diff-pdf\n",
+    "with warnings.catch_warnings():\n",
+    "    warnings.filterwarnings(\"ignore\", message=\".*SampleCollection contains multiple.*\")\n",
+    "    \n",
+    "    observed_taxa = samples.plot_metadata(vaxis=\"observed_taxa\", haxis=\"geo_loc_name\", return_chart=True)\n",
+    "    simpson = samples.plot_metadata(vaxis=\"simpson\", haxis=\"geo_loc_name\", return_chart=True)\n",
+    "    shannon = samples.plot_metadata(vaxis=\"shannon\", haxis=\"geo_loc_name\", return_chart=True)\n",
     "\n",
     "observed_taxa | simpson | shannon"
    ]
@@ -259,7 +260,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.3"
+   "version": "3.11.4"
   },
   "onecodex_notebook": true
  },