fix quarto ordering and make kernel target

.gitignore

@@ -2,9 +2,11 @@
 .env
 
 # Temporary and binary files
-/.quarto/
-/_book/
-/data/
+.quarto/
+_book/
+data/
+_freeze/
+notebooks/
 *_files/
 .jupyter_cache/
 *~
@@ -60,6 +62,7 @@ MANIFEST
 # Per-project virtualenvs
 .venv*/
 venv
+.conda_envs/
 
 # Make file markers
 .install*

Makefile

@@ -1,41 +1,57 @@
 .ONESHELL:
 SHELL = /bin/bash
-.PHONY: help clean environment kernel post-render data
+.PHONY: help clean environment kernel teardown post-render data
+
 YML = $(wildcard notebooks/*.yml)
 QMD = $(wildcard chapters/*.qmd)
 REQ = $(basename $(notdir $(YML)))
-CONDA_ENV_DIR := $(foreach i,$(REQ),$(shell conda info --base)/envs/$(i))
-KERNEL_DIR := $(foreach i,$(REQ),$(shell jupyter --data-dir)/kernels/$(i))
+BASENAME = $(CURDIR)
+
 CONDA_ACTIVATE = source $$(conda info --base)/etc/profile.d/conda.sh ; conda activate ; conda activate
+PREFIX = $(BASENAME)/.conda_envs
+CONDA_ENV_DIR := $(foreach i,$(REQ),$(PREFIX)/$(i))
+KERNEL_DIR := $(foreach i,$(REQ),$(shell jupyter --data-dir)/kernels/$(i))
 
 help:
-	@echo "make clean"
-	@echo " clean all jupyter checkpoints"
-	@echo "make environment"
-	@echo " create a conda environment"
-	@echo "make kernel"
-	@echo " make ipykernel based on conda lock file"
+	@echo "Makefile for setting up environment, kernel, and pulling notebooks"
+	@echo ""
+	@echo "Usage:"
+	@echo "  make environment  - Create Conda environments"
+	@echo "  make kernel       - Create Conda environments and Jupyter kernels"
+	@echo "  "
+	@echo "  make teardown     - Remove Conda environments and Jupyter kernels"
+	@echo "  make clean        - Removes ipynb_checkpoints"
+	@echo "  make help         - Display this help message"
 
 clean:
-	rm --force --recursive .ipynb_checkpoints/
-	for i in $(REQ); do conda remove -n $$i --all -y ; jupyter kernelspec uninstall -y $$i ; done
+	rm --force --recursive .ipynb_checkpoints/ **/.ipynb_checkpoints/ _book/ \
+		_freeze/ .quarto/
+
+teardown:
+	$(foreach f, $(REQ), \
+		$(CONDA_ACTIVATE) $(f); \
+		jupyter kernelspec uninstall -y $(f); \
+		conda deactivate; \
+		conda remove -n $(f) --all -y ; \
+		conda deactivate; )
 
-$(CONDA_ENV_DIR):
-	for i in $(YML); do conda env create -f $$i; done
+$(CONDA_ENV_DIR): $(YML)
+	- conda update -n base -c conda-forge conda -y
+	$(foreach f, $^, conda env create --file $(f); )
 
 environment: $(CONDA_ENV_DIR)
 	@echo -e "conda environments are ready."
 
 $(KERNEL_DIR): $(CONDA_ENV_DIR)
-	pip install --upgrade pip
-	pip install jupyter
-	for i in $(REQ); do $(CONDA_ACTIVATE) $$i ; python -m ipykernel install --user --name $$i --display-name $$i ; conda deactivate; done
+	$(foreach f, $(REQ), \
+		$(CONDA_ACTIVATE) $(f); \
+		python -m ipykernel install --user --name $(f) --display-name $(f); \
+		conda deactivate; )
 
 kernel: $(KERNEL_DIR)
 	@echo -e "conda jupyter kernel is ready."
 
 post-render:
-	for i in $(QMD); do quarto convert $$i; done
 	- mv chapters/*.ipynb notebooks/ >/dev/null 2>&1
 	- for f in chapters/*.quarto_ipynb ; do mv -- "$f" "${f%.quarto_ipynb}.ipynb"  >/dev/null 2>&1; done
 	cp Makefile notebooks/

_quarto.yml

@@ -11,10 +11,12 @@ book:
   date: "7/10/2024"
   chapters:
     - index.qmd
-    - chapters/Courses
-      - chapter/Microwave Remote Sensing
-    - chapters/01_classification.qmd
-    - chapters/02_floodmapping.qmd
+    - part: "Courses"
+      chapters:
+        - chapters/01_classification.qmd
+        - chapters/02_floodmapping.qmd
+    - part: "Tutorials"
+    - part: "Lessons"
     - chapters/references.qmd
   navbar: 
     logo: assets/images/tuw-geo-logo.svg
@@ -27,3 +29,7 @@ format:
     theme: cosmo
     title-block-banner: "#006699"
     title-block-banner-color: white
+
+execute:
+  freeze: auto
+  keep-ipynb: true