Quarto output

Makefile

@@ -1,41 +1,58 @@
 .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)))
+BASENAME = $(CURDIR)
+
+CONDA_ACTIVATE = source $$(conda info --base)/etc/profile.d/conda.sh ; conda activate ; conda activate
 CONDA_ENV_DIR := $(foreach i,$(REQ),$(shell conda info --base)/envs/$(i))
 KERNEL_DIR := $(foreach i,$(REQ),$(shell jupyter --data-dir)/kernels/$(i))
-CONDA_ACTIVATE = source $$(conda info --base)/etc/profile.d/conda.sh ; conda activate ; conda activate
 
 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 --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/

_toc.yml

@@ -3,13 +3,4 @@ parts:
 - caption: Preamble
   chapters:
   - file: notebooks/how-to-cite
-- caption: Classification
-  chapters:
-  - file: notebooks/01_classification
-- caption: Floodmapping
-  chapters:
-  - file: notebooks/02_floodmapping
-- caption: References
-  chapters:
-  - file: notebooks/references
 root: README

notebooks/01_classification.yml

@@ -1,25 +1,23 @@
 name: 01_classification
 channels:
   - conda-forge
-  - defaults
 dependencies:
+  - python=3.12
+  - pip
+  - mamba
+  - jupyter
   - cmcrameri
   - dask
   - geopandas
-  - ipykernel
-  - jupyter
-  - mamba
   - matplotlib
   - nbformat
   - numpy
   - odc-stac
   - openssl
-  - python==3.10
   - rasterio
   - rioxarray
   - scikit-learn
   - seaborn
   - stackstac
   - xarray
-  - pip:
-      - pystac-client
+  - pystac-client

notebooks/02_floodmapping.yml

@@ -2,7 +2,7 @@ name: 02_floodmapping
 channels:
   - conda-forge
 dependencies:
-  - python=3.10
+  - python=3.12
   - pip
   - mamba
   - jupyter

notebooks/Makefile

@@ -1,41 +1,58 @@
 .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)))
+BASENAME = $(CURDIR)
+
+CONDA_ACTIVATE = source $$(conda info --base)/etc/profile.d/conda.sh ; conda activate ; conda activate
 CONDA_ENV_DIR := $(foreach i,$(REQ),$(shell conda info --base)/envs/$(i))
 KERNEL_DIR := $(foreach i,$(REQ),$(shell jupyter --data-dir)/kernels/$(i))
-CONDA_ACTIVATE = source $$(conda info --base)/etc/profile.d/conda.sh ; conda activate ; conda activate
 
 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 --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/