feat: script to check all examples in doc/python.

-   Updates `pyproject.toml` to install packages previously listed in `doc/requirements.txt`.
-   Removes `doc/requirements.txt`.
-   Run `python bin/check-all-md.py doc/python/*.md` to re-run all examples.

Author: gvwilson

bin/check-all-md.py

@@ -0,0 +1,18 @@
+from pathlib import Path
+import os
+import re
+import sys
+
+PAT = re.compile(r"^```python\n(.+?)\n```", re.MULTILINE | re.DOTALL)
+TMP_FILE = "tmp.py"
+
+for filename in sys.argv[1:]:
+    content = Path(filename).read_text()
+    blocks = PAT.findall(content)
+    for i, b in enumerate(blocks):
+        Path(TMP_FILE).write_text(b.strip())
+        sys.stdout.write(f"\n{'=' * 40}\n{filename}: {i}\n")
+        sys.stdout.flush()
+        sys.stdout.write(f"{'-' * 40}\n")
+        sys.stdout.flush()
+        os.system(f"python {TMP_FILE} > /dev/null")

doc/requirements.txt

@@ -63,9 +63,13 @@ dev_optional = [
     "plotly[kaleido]",
     "anywidget",
     "colorcet",
+    "dash_bio",
+    "datashader",
     # fiona>1.9.6 is not compatible with geopandas<1; geopandas>=1 is not compatible with python 3.8
     "fiona<=1.9.6;python_version<='3.8'",
     "geopandas",
+    "google",
+    "igraph",
     "inflect",
     "numpy",
     "orjson",
@@ -74,15 +78,19 @@ dev_optional = [
     "pillow",
     "plotly-geo",
     "polars[timezone]",
+    "pooch",
     "pyarrow",
     "pydoclint",
     "pyshp",
     "pytz",
     "scikit-image",
+    "scikit-learn",
     "scipy",
     "shapely",
     "statsmodels",
+    "umap",
     "vaex;python_version<='3.9'",
+    "wget",
     "xarray"
 ]
 dev = [