Merge pull request #70 from TUW-GEO/fix-kernel

add set kernel to cookbook processing chain

Author: npikall

Makefile

@@ -13,7 +13,7 @@ CONDA_ACTIVATE := source $(CONDA_ENV)/etc/profile.d/conda.sh ; \
 	conda activate ; conda activate
 PREFIX = $(CURDIR)/.conda_envs
 CONDA_ENV_DIR := $(foreach i,$(REQ),$(PREFIX)/$(i))
-KERNEL_DIR != $(CONDA_ACTIVATE) eo-datascience; jupyter --data-dir
+KERNEL_DIR != jupyter --data-dir
 KERNEL_DIR := $(foreach i,$(REQ),$(KERNEL_DIR)/kernels/$(i))
 
 help:
@@ -31,10 +31,6 @@ help:
 		temporary files"
 	@echo "  make help         - Display this help message"
 
-$(CONDA_ENV)/envs/eo-datascience:
-	- conda update -n base -c conda-forge conda -y
-	conda env create --file environment.yml
-
 $(CONDA_ENV_DIR):
 	$(foreach f, $(YML), \
 		conda env create --file $(f) \
@@ -49,7 +45,7 @@ $(KERNEL_DIR):
 		python -m ipykernel install --user --name $(f) --display-name $(f); \
 			conda deactivate; )
 
-kernel: $(CONDA_ENV)/envs/eo-datascience $(CONDA_ENV_DIR) $(KERNEL_DIR)
+kernel: $(CONDA_ENV_DIR) $(KERNEL_DIR)
 	@echo -e "jupyter kernels are ready."
 
 post-render:
@@ -63,8 +59,7 @@ convert:
 		quarto convert $(f); \
 		mv $(subst .ipynb,.qmd, $(f)) $(subst notebooks,chapters,$(subst .ipynb,.qmd,$(f))); )
 
-preview: $(CONDA_ENV)/envs/eo-datascience $(CONDA_ENV_DIR) $(KERNEL_DIR)
-	$(CONDA_ACTIVATE) $(PREFIX)/eo-datascience
+preview: $(CONDA_ENV_DIR) $(KERNEL_DIR)
 	- mkdir -p _preview/notebooks
 	python -m pip install .
 	cp ./chapters/references.bib ./_preview/notebooks/
@@ -73,8 +68,11 @@ preview: $(CONDA_ENV)/envs/eo-datascience $(CONDA_ENV_DIR) $(KERNEL_DIR)
 	wget https://raw.githubusercontent.com/TUW-GEO/eo-datascience-cookbook/refs/heads/main/_config.yml -nc -P ./_preview
 	wget https://raw.githubusercontent.com/TUW-GEO/eo-datascience-cookbook/refs/heads/main/notebooks/how-to-cite.md -nc -P ./_preview/notebooks
 	render_sfinx_toc ./_preview
+	merge_envs --out ./_preview/environment.yml --name eo-datascience-dev
+	conda env create --file _preview/environment.yml --prefix $(PREFIX)/eo-datascience-cookbook-dev
+	$(CONDA_ACTIVATE) $(PREFIX)/eo-datascience-cookbook-dev
+	python -m ipykernel install --user --name eo-datascience-cookbook-dev --display-name eo-datascience-cookbook-dev
 	clean_nb ./notebooks ./_preview/notebooks
-	merge_envs --out environment.yml --name eo-datascience-dev
 	jupyter-book build ./_preview
 	jupyter-book build ./_preview
 
@@ -85,7 +83,6 @@ clean:
 		**/**/*.quarto_ipynb **/__pycache__ **/**/__pycache__ __pycache__
 
 teardown:
-	conda remove -n $(PREFIX)/eo-datascience --all -y
 	$(foreach f, $(REQ), \
 		$(CONDA_ACTIVATE) $(PREFIX)/$(f); \
 		jupyter kernelspec uninstall -y $(f); \
@@ -95,4 +92,4 @@ teardown:
 
 master:
 	python -m pip install .
-	merge_envs --out environment.yml --name eo-datascience-dev
+	merge_envs --out environment.yml --name eo-datascience-cookbook-dev

environment.yml

@@ -2,48 +2,14 @@ name: eo-datascience
 channels:
   - conda-forge
 dependencies:
-  - aiohttp
-  - bokeh
-  - cartopy
-  - cmcrameri
-  - dask
-  - datashader
-  - folium
-  - geopandas
-  - geoviews
-  - graphviz
-  - holoviews
-  - huggingface_hub
-  - hvplot
-  - intake
-  - intake-xarray
+  - python=3.12
+  - pip
+  - mamba
   - jupyter
-  - jupyter-book
   - jupyter-cache
-  - jupyter_bokeh
-  - mamba
-  - matplotlib
   - nbformat
-  - nbstripout
-  - nodejs
-  - numpy
-  - odc-stac
-  - openssl
-  - pip
   - pre-commit
-  - pyproj
-  - pystac-client
+  - nbstripout
   - pytest
-  - python=3.12
-  - rasterio
-  - requests
-  - rioxarray
-  - scikit-image
-  - scikit-learn
-  - scipy
-  - seaborn
-  - snaphu
+  - jupyter-book
   - sphinx-pythia-theme
-  - stackstac
-  - xarray
-  - zarr=2.18.4

src/eo_datascience/clean_nb.py

@@ -1,7 +1,24 @@
-import nbformat
-from pathlib import Path
-import re
 import argparse
+import re
+from pathlib import Path
+
+import nbformat
+
+
+def set_kernel_all_notebooks(
+    dir="./notebooks", out=None, save=True, name="eo-datascience-cookbook-dev"
+):
+    nb_paths = find_ipynb(dir)
+    for nb_path in nb_paths:
+        nb = nbformat.read(nb_path, as_version=4)
+        nb.metadata.kernelspec.name = name
+        nb.metadata.kernelspec.display_name = name
+    # Save notebook
+    nb_path = substitute_path(nb_path, dir, out)
+    if save:
+        nbformat.write(nb, nb_path)
+    else:
+        return nb
 
 
 def clean_up_frontmatter(dir="./notebooks", out=None, save=True):
@@ -29,7 +46,7 @@ def clean_up_frontmatter(dir="./notebooks", out=None, save=True):
                 i += 1
                 line = fm[i]
 
-            new_text += fm[i + 1 :]
+            new_text += fm[i + 1 :]  # noqa
             nb.cells[0].source = "\n".join(new_text) + "\n"
             nb.cells[0].cell_type = "markdown"
         # Save notebook
@@ -44,8 +61,9 @@ def convert_bibliography(nb_path="./notebooks/references.ipynb", out=None, save=
     nb_path = Path(nb_path)
     if nb_path.exists():
         nb = nbformat.read(nb_path, as_version=4)
-        nb.cells[0].source = \
-"""# References
+        nb.cells[
+            0
+        ].source = """# References
 ```{bibliography}
 :style: plain
 ```
@@ -150,6 +168,7 @@ def main():
     args = parser.parse_args()
 
     clean_up_frontmatter(args.dir, args.out)
+    set_kernel_all_notebooks(args.out)
     convert_callout_notes(args.out)
     convert_refs(args.out)
     convert_bibliography(out=args.out)

src/eo_datascience/merge_envs.py

@@ -57,7 +57,7 @@ def resolve_dependency_versions(
 
 
 def create_master_environment(
-    final_dependencies: List | Set, name: str = "eo-datascience-dev"
+    final_dependencies: List | Set, name: str = "eo-datascience-cookbook-dev"
 ) -> Dict:
     master_env = {
         "name": name,
@@ -103,7 +103,7 @@ def main() -> None:
         "--name",
         type=str,
         help="Name of the environment",
-        default="eo-datascience-dev",
+        default="eo-datascience-cookbook-dev",
     )
     args = parser.parse_args()
 

tests/mock.ipynb

@@ -1,40 +1,35 @@
 {
  "cells": [
   {
-   "cell_type": "raw",
+   "cell_type": "markdown",
    "metadata": {},
    "source": [
     "---\n",
     "title: This a mock Jupyter file\n",
     "subtitle: We use it for testing\n",
     "author: anonymous\n",
+    "jupyter:\n",
+    "  kernelspec:\n",
+    "    name: \"eo-datascience\"\n",
+    "    language: \"python\"\n",
+    "    display_name: \"eo-datascience\"\n",
     "---\n",
     "\n",
-    "Some other text, which should not be deleted!"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
     "::: {.callout-note}\n",
     "This a callout note.\n",
-    ":::"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "lorem ipsum [@anon2024] and [@anon2025] and lorem ipsum @anon2024 and @anon2025"
+    ":::\n",
+    "\n",
+    "lorem ipsum [@anon2024] and [@anon2025] and lorem ipsum @anon2024 and @anon2025\n"
    ]
   }
  ],
  "metadata": {
-  "language_info": {
-   "name": "python"
+  "kernelspec": {
+   "display_name": "eo-datascience",
+   "language": "python",
+   "name": "eo-datascience"
   }
  },
  "nbformat": 4,
- "nbformat_minor": 2
+ "nbformat_minor": 4
 }

tests/mock.qmd

@@ -2,12 +2,15 @@
 title: This a mock Jupyter file
 subtitle: We use it for testing
 author: anonymous
-jupyter: python3
+jupyter:
+  kernelspec:
+    name: "eo-datascience"
+    language: "python"
+    display_name: "eo-datascience"
 ---
 
 ::: {.callout-note}
 This a callout note.
 :::
 
 lorem ipsum [@anon2024] and [@anon2025] and lorem ipsum @anon2024 and @anon2025
-

tests/test_quarto_nb_conversions.py

@@ -11,6 +11,7 @@
     quarto_note_replace,
     quarto_ref_person_replace,
     quarto_ref_time_replace,
+    set_kernel_all_notebooks,
     substitute_path,
 )
 from eo_datascience.render_sfinx_toc import (
@@ -95,10 +96,12 @@ def test_toc_conversion():
                     "file": "notebooks/courses/microwave-remote-sensing",
                     "sections": [
                         {
-                            "file": "notebooks/courses/microwave-remote-sensing/01_in_class_exercise"
+                            "file": "notebooks/courses/microwave-remote-"
+                            + "sensing/01_in_class_exercise"
                         },
                         {
-                            "file": "notebooks/courses/microwave-remote-sensing/02_in_class_exercise"
+                            "file": "notebooks/courses/microwave-remote-"
+                            + "sensing/02_in_class_exercise"
                         },
                     ],
                 },
@@ -145,7 +148,8 @@ def test_remove_front_matter():
     )
     assert (
         clean_up_frontmatter("./tests", None, False)["cells"][0]["source"]
-        == "# This a mock Jupyter file\n**We use it for testing**\n\nSome other text, which should not be deleted!\n"
+        == "# This a mock Jupyter file\n**We use it for testing**\n\nSome"
+        + " other text, which should not be deleted!\n"
     )
 
 
@@ -174,11 +178,21 @@ def test_conversion_of_refs():
     ]
     assert (
         convert_refs("./tests", None, False)["cells"][2]["source"]
-        == r"lorem ipsum {cite:p}`anon2024` and {cite:p}`anon2025` and lorem ipsum {cite:t}`anon2024` and {cite:t}`anon2025`"
+        == r"lorem ipsum {cite:p}`anon2024` and {cite:p}`anon2025` and lorem"
+        + " ipsum {cite:t}`anon2024` and {cite:t}`anon2025`"
     )
 
 
 def test_conversion_of_callout_notes():
     rst = ":::{note}\nThis a callout note.\n:::"
     assert quarto_note_replace(r"::: {.callout-note}\nThis a callout note.\n:::") == rst
     assert convert_callout_notes("./tests", None, False)["cells"][1]["source"] == rst
+
+
+def test_setting_kernelspec():
+    meta_mock_nb = nbformat.read("tests/mock.ipynb", as_version=4).metadata
+    kernel_display_name_mock_nb = meta_mock_nb.kernelspec.display_name
+    kernel_name_mock_nb = meta_mock_nb.kernelspec.name
+    new_meta_mock_nb = set_kernel_all_notebooks(dir="tests", save=False).metadata
+    assert kernel_display_name_mock_nb != new_meta_mock_nb.kernelspec.display_name
+    assert kernel_name_mock_nb != new_meta_mock_nb.kernelspec.name