Merge pull request ioos#175 from ocefpaf/add_colab_script

add colab missing dependencies script

.pre-commit-config.yaml

@@ -14,17 +14,16 @@ repos:
       - id: check-docstring-first
       - id: check-json
       - id: check-yaml
-      - id: double-quote-string-fixer
 
   - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: v4.0.0-alpha.3
+    rev: v4.0.0-alpha.8
     hooks:
       - id: prettier
         types_or: [html]
         exclude: "_templates/layout.html"
 
   - repo: https://github.com/psf/black
-    rev: 23.11.0
+    rev: 23.12.0
     hooks:
       - id: black
         language_version: python3
@@ -35,7 +34,7 @@ repos:
       - id: add-trailing-comma
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.1.6
+    rev: v0.1.9
     hooks:
       - id: ruff
 

jupyterbook/content/add_colab_install_missing_deps.py

@@ -0,0 +1,105 @@
+from pathlib import Path
+
+from depfinder import notebook_path_to_dependencies
+
+notebook_path = Path(".")
+notebooks = list(notebook_path.glob("**/*.ipynb"))
+
+## Get modules that are absent on GoogleColab
+# required = []
+
+# for notebook in notebooks:
+#     try:
+#         ret = notebook_path_to_dependencies(notebook)
+#     except Exception as err:
+#         print(f"Could not parse {notebook=}. {err}")
+#     required.extend(ret["required"])
+
+# modules = sorted(set(required))
+
+## go to colab with this list and run to obtain the absent list
+
+# """
+# import importlib
+# for module in modules:
+#     if importlib.util.find_spec(module) is None:
+#         print(module)
+# """
+
+## update notebooks
+import nbformat
+
+absent = [
+    "bagit",
+    "cartopy",
+    "cf-units",
+    "cf_xarray",
+    "compliance-checker",
+    "erddapy",
+    "geoplot",
+    "gridgeo",
+    "ioos-tools",
+    "ioos_qc",
+    "ipyleaflet",
+    "iris",
+    "netcdf4",
+    "oceans",
+    "odvc",
+    "owslib",
+    "palettable",
+    "pocean-core",
+    "pyobis",
+    "pyoos",
+    "pysgrid",
+    "pyugrid",
+    "pyworms",
+    "retrying",
+    "seawater",
+    "zarr",
+]
+
+
+code = """\
+import subprocess
+import sys
+COLAB = "google.colab" in sys.modules
+
+def _install(package):
+    if COLAB:
+        ans = input(f"Install {{ package }}? [y/n]:")
+        if ans.lower() in ["y", "yes"]:
+            subprocess.check_call([sys.executable, "-m", "pip", "install", "--quiet", package])
+            print(f"{{ package }} installed!")
+
+def _colab_install_missing_deps(deps):
+    import importlib
+    for dep in deps:
+        if importlib.util.find_spec(dep) is None:
+            if dep == "iris":
+                dep = "scitools-iris"
+            _install(dep)
+
+deps = {}
+_colab_install_missing_deps(deps)"""
+
+
+def update_notebook(notebook, code):
+    nb = nbformat.read(notebook, as_version=4)
+
+    new_cell = nbformat.v4.new_code_cell(code)
+    new_cell.pop("id")  # cannot save mod nb with this
+    new_cell["metadata"] = {"tags": ["remove-cell"]}  # won't render on jupyterbook
+    # nb.cells.insert(0, new_cell)
+    nb.cells[0] = new_cell
+    nbformat.write(nb, notebook, version=4)
+
+
+for notebook in notebooks:
+    if "archived" not in str(notebook):
+        try:
+            required = notebook_path_to_dependencies(notebook)["required"]
+            missing_from_colab = [module for module in absent if module in required]
+            update_notebook(notebook, code.format(missing_from_colab))
+        except Exception as err:
+            print(f"Could not parse {notebook=}. {err}")
+            continue