Merge branch 'main' into Joe-example

Code4NP · Jan 8, 2025 · ceedc8f · ceedc8f
2 parents 0fea19c + 274a855
commit ceedc8f
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diff --git a/Makefile b/Makefile
@@ -25,13 +25,16 @@ build_docker_dev:
 
 ## render:	Render a post (e.g. make render posts/example_dir/index.ipynb)
 render: build_docker_dev
-	mkdir -p $$(dirname $${i})/index_files $$(dirname $${i})/index_cache && \
+	mkdir -p $(realpath $(dir $(filter-out $@,$(MAKECMDGOALS))))/index_files $(realpath $(dir $(filter-out $@,$(MAKECMDGOALS))))/index_cache && \
 	docker run -it \
-		-v "$(realpath $(dir $(filter-out $@,$(MAKECMDGOALS))))":/repo \
+		-v $(realpath $(dir $(filter-out $@,$(MAKECMDGOALS)))):/repo \
 		-u $(shell id -u):$(shell id -g) \
 		code4np_base:dev \
 		/bin/bash -c 'pixi run quarto render $(notdir $(filter-out $@,$(MAKECMDGOALS)))'
 
+
+
+
 ## render_all_posts :	Render all posts
 render_all_posts: build_docker_dev
 		for i in $$(find posts -name "index.ipynb" -o -name "index.qmd"); do \

diff --git a/posts/chemsim_2024_02_28/index.html b/posts/chemsim_2024_02_28/index.html
diff --git a/posts/intro_to_mass_spec/1_intro/collapse-callout.lua b/posts/intro_to_mass_spec/1_intro/collapse-callout.lua
@@ -0,0 +1,9 @@
+function Callout(el)
+    if quarto.doc.isFormat("html") then
+      -- Set default collapse to true if unset
+      if not el.collapse then
+        el.collapse = true
+      end
+      return el
+    end
+  end
diff --git a/posts/intro_to_mass_spec/1_intro/index.html b/posts/intro_to_mass_spec/1_intro/index.html
diff --git a/posts/intro_to_mass_spec/1_intro/index.qmd b/posts/intro_to_mass_spec/1_intro/index.qmd
@@ -7,16 +7,16 @@ author:
 categories: [beginner, mass spectrometry, r]
 date: "2024-02-01"
 description: "First in a series of introductory posts about working with mass spectrometry data in R"
-execute: 
+execute:
   cache: true
   freeze: true
 format:
   html:
     df-print: paged
 filters:
-  - collapse-callout
+  - collapse-callout.lua
 collapse-callout:
-  all: true  
+  all: true
 ---
 
 

diff --git a/posts/intro_to_mass_spec/2_mzml/collapse-callout.lua b/posts/intro_to_mass_spec/2_mzml/collapse-callout.lua
@@ -0,0 +1,9 @@
+function Callout(el)
+    if quarto.doc.isFormat("html") then
+      -- Set default collapse to true if unset
+      if not el.collapse then
+        el.collapse = true
+      end
+      return el
+    end
+  end
diff --git a/posts/intro_to_mass_spec/2_mzml/index.html b/posts/intro_to_mass_spec/2_mzml/index.html
diff --git a/posts/intro_to_mass_spec/2_mzml/index.qmd b/posts/intro_to_mass_spec/2_mzml/index.qmd
@@ -7,16 +7,16 @@ author:
 categories: [beginner, mass spectrometry, r]
 date: "2024-02-02"
 description: "What mass spectrometry data looks like, using R"
-execute: 
+execute:
   cache: true
   freeze: true
 format:
   html:
     df-print: paged
 filters:
-  - collapse-callout
+  - collapse-callout.lua
 collapse-callout:
-  all: true  
+  all: true
 ---
 
 This is a continuation from [Part 1](../1_intro/).

diff --git a/posts/intro_to_mass_spec/3_spectra/collapse-callout.lua b/posts/intro_to_mass_spec/3_spectra/collapse-callout.lua
@@ -0,0 +1,9 @@
+function Callout(el)
+    if quarto.doc.isFormat("html") then
+      -- Set default collapse to true if unset
+      if not el.collapse then
+        el.collapse = true
+      end
+      return el
+    end
+  end
diff --git a/posts/intro_to_mass_spec/3_spectra/index.html b/posts/intro_to_mass_spec/3_spectra/index.html
diff --git a/posts/intro_to_mass_spec/3_spectra/index.qmd b/posts/intro_to_mass_spec/3_spectra/index.qmd
@@ -7,16 +7,16 @@ author:
 categories: [beginner, mass spectrometry, r]
 date: "2024-02-03"
 description: "An introduction to working with mass spectrometry data in R"
-execute: 
+execute:
   cache: true
   freeze: true
 format:
   html:
     df-print: paged
 filters:
-  - collapse-callout
+  - collapse-callout.lua
 collapse-callout:
-  all: true  
+  all: true
 ---
 
 This is a continuation from [Part 2](../2_mzml/).

diff --git a/posts/intro_to_mass_spec/3_spectra/pixi.toml b/posts/intro_to_mass_spec/3_spectra/pixi.toml
@@ -10,7 +10,7 @@ platforms = ["linux-64"]
 [dependencies]
 quarto = "==1.4.550"
 r-base = "4.3.*"
-r-rmarkdown = ""
-r-knitr = ""
+r-rmarkdown = "*"
+r-knitr = "*"
 bioconductor-mzr = "==2.36.0"
-r-codetools = ""
+r-codetools = "*"
diff --git a/posts/intro_to_mass_spec/4_reanalysis/collapse-callout.lua b/posts/intro_to_mass_spec/4_reanalysis/collapse-callout.lua
@@ -0,0 +1,9 @@
+function Callout(el)
+    if quarto.doc.isFormat("html") then
+      -- Set default collapse to true if unset
+      if not el.collapse then
+        el.collapse = true
+      end
+      return el
+    end
+  end
diff --git a/posts/intro_to_mass_spec/4_reanalysis/index.html b/posts/intro_to_mass_spec/4_reanalysis/index.html
diff --git a/posts/intro_to_mass_spec/4_reanalysis/index.qmd b/posts/intro_to_mass_spec/4_reanalysis/index.qmd
@@ -7,16 +7,16 @@ author:
 categories: [beginner, mass spectrometry, r]
 date: "2024-02-04"
 description: "An introduction to working with mass spectrometry data in R"
-execute: 
+execute:
   cache: true
   freeze: true
 format:
   html:
     df-print: paged
 filters:
-  - collapse-callout
+  - collapse-callout.lua
 collapse-callout:
-  all: true  
+  all: true
 ---
 
 This is a continuation from [Part 3](../3_spectra/).

diff --git a/posts/intro_to_mass_spec/4_reanalysis/pixi.toml b/posts/intro_to_mass_spec/4_reanalysis/pixi.toml
@@ -11,8 +11,8 @@ platforms = ["linux-64"]
 quarto = "==1.4.550"
 r-base = "4.3.*"
 r-ggplot2 = "==3.4.4"
-r-rmarkdown = ""
-r-knitr = ""
+r-rmarkdown = "*"
+r-knitr = "*"
 bioconductor-mzr = "==2.36.0"
-r-codetools = ""
-r-plotly = ""
+r-codetools = "*"
+r-plotly = "*"
diff --git a/posts/intro_to_python_and_jupyter/NPAtlas_download.tsv b/posts/intro_to_python_and_jupyter/NPAtlas_download.tsv
diff --git a/posts/intro_to_python_and_jupyter/index.html b/posts/intro_to_python_and_jupyter/index.html