Merge branch 'ClojureCivitas:main' into main

Author: Schroedingberg

…flows/render-and-publish-incremental.yml …s/render-and-publish-incremental.yml.bak.github/workflows/render-and-publish-incremental.yml renamed to .github/workflows/render-and-publish-incremental.yml.bak .github/workflows/render-and-publish-incremental.yml renamed to .github/workflows/render-and-publish-incremental.yml.bak

@@ -23,6 +23,7 @@ jobs:
       - name: Install dependencies
         run: |
           pip install plotly kaleido
+          pip install --index-url https://download.pytorch.org/whl/cpu torch numpy
 
       - name: Set up Java
         uses: actions/setup-java@v4

.github/workflows/render-and-publish.yml

@@ -3,7 +3,7 @@
 .clj-kondo/
 .quarto/
 _site/
-.calva/output-window/
+.calva
 .classpath
 .clj-kondo/.cache
 .cpcache
@@ -13,8 +13,7 @@ _site/
 .hgignore
 .java-version
 .lein-*
-.lsp/.cache
-.lsp/sqlite.db
+.lsp/
 .nrepl-history
 .nrepl-port
 .project

.gitignore

@@ -138,7 +138,7 @@ clojure -M:clay -A:markdown
 quarto preview site
 ```
 
-(`bb site-preview` will run these two commands for you.)
+(`bb preview` will run these two commands for you.)
 
 This will open a browser displaying the site locally.
 

README.md

@@ -3,6 +3,7 @@
  :deps
  {org.clojure/clojure                         {:mvn/version "1.12.3"}
   org.scicloj/noj                             {:mvn/version "2-beta18"}
+  org.scicloj/tablecloth.time                 {:mvn/version "1.00-alpha-6"}
   ;; Tableplot can be removed after updating Noj:
   org.scicloj/tableplot                       {:mvn/version "1-beta14"}
   markdown-clj/markdown-clj                   {:mvn/version "1.12.4"}
@@ -14,8 +15,10 @@
   metosin/malli                               {:mvn/version "0.19.1"}
   clj-fuzzy/clj-fuzzy                         {:mvn/version "0.4.1"}
   clj-thamil/clj-thamil                       {:mvn/version "0.2.0"}
-  org.scicloj/clay                            {:mvn/version "2.0.5"}
-  org.scicloj/kindly                          {:mvn/version "4-beta21"}
+  org.scicloj/clay                            {#_#_:mvn/version "2.0.5"
+                                               :git/url "https://github.com/scicloj/clay"
+                                               :git/sha "a52102ac993fa4f6b455e8f37d6a653030e69920"}
+  org.scicloj/kindly                          {:mvn/version "4-beta23"}
   thi.ng/geom                                 {:mvn/version "1.0.1"}
   org.eclipse.elk/org.eclipse.elk.core        {:mvn/version "0.10.0"}
   org.eclipse.elk/org.eclipse.elk.graph       {:mvn/version "0.10.0"}
@@ -48,6 +51,8 @@
   dev.data-star.clojure/malli-schemas         {:mvn/version "1.0.0-RC4"}
   dev.data-star.clojure/http-kit-malli-schemas {:mvn/version "1.0.0-RC4"}
   dev.data-star.clojure/ring-malli-schemas    {:mvn/version "1.0.0-RC4"}
+  ;; required by mentat_collective/emmy
+  io.github.nextjournal/clerk                 {:mvn/version "0.18.1158"}
 
   ;; libraries for GIS work
   org.apache.sis.storage/sis-geotiff          {:mvn/version "1.5"}
@@ -61,6 +66,8 @@
 
   generateme/fastmath                         {:mvn/version "3.0.0-alpha4"}
   clojure2d/clojure2d                         {:mvn/version "1.5.0-alpha1"}
+  org.scicloj/wadogo                          {:mvn/version "1.1.0-alpha1"}
+  quil/quil                                   {:mvn/version "4.3.1563"}
 
   com.github.psambit9791/jdsp                 {:mvn/version "3.1.0"}
 
@@ -74,8 +81,9 @@
                                                :deps/root "core"}
   com.hyperphor/multitool                     {:mvn/version "0.2.3"}
   datascript/datascript                       {:mvn/version "1.7.8"}
-  io.github.pbaille/noon                      {:git/url "https://github.com/pbaille/noon.git"
-                                               :git/sha "e63bb7c82671293c5610da6a02e3148a48ad71dd"}}
+  ;; io.github.pbaille/noon                      {:git/url "https://github.com/pbaille/noon.git"
+  ;;                                              :git/sha "97677727bff20243dc15d5cafb821d4af9019842"}
+  }
 
  :mvn/repos {"osgeo" {:url "https://repo.osgeo.org/repository/release/"}}
 

deps.edn

@@ -35,10 +35,10 @@ website:
           text: "Prologue"
         - section: "Chapters"
           contents:
-            - href: mentat_collective/emmy/fdg_ch01.qmd
-              text: "FDG Chapter 1"
             - href: mentat_collective/emmy/sicm_original_ch01.qmd
               text: "SICM Chapter 1"
+            - href: mentat_collective/emmy/fdg_ch01.qmd
+              text: "FDG Chapter 1"
             - href: mentat_collective/emmy/fdg_ch02.qmd
               text: "FDG Chapter 2"
             - href: mentat_collective/emmy/fdg_ch03.qmd
@@ -47,6 +47,18 @@ website:
               text: "FDG Chapter 4"
             - href: mentat_collective/emmy/fdg_ch05.qmd
               text: "FDG Chapter 5"
+            - href: mentat_collective/emmy/fdg_ch06.qmd
+              text: "FDG Chapter 6"
+            - href: mentat_collective/emmy/fdg_ch07.qmd
+              text: "FDG Chapter 7"
+            - href: mentat_collective/emmy/fdg_ch08.qmd
+              text: "FDG Chapter 8"
+            - href: mentat_collective/emmy/fdg_ch09.qmd
+              text: "FDG Chapter 9"
+            - href: mentat_collective/emmy/fdg_ch10.qmd
+              text: "FDG Chapter 10"
+            - href: mentat_collective/emmy/fdg_ch11.qmd
+              text: "FDG Chapter 11"
             - href: mentat_collective/emmy/fdg_ch01_ys.qmd
               text: "FDG Ch01 Infix"
             - href: mentat_collective/emmy/sicm_ch01.qmd

site/_quarto.yml

@@ -24,7 +24,7 @@
    :name        "Daniel Slutsky"
    :image       "https://avatars.githubusercontent.com/u/5673102?v=4"
    :url         "https://scicloj.github.io/contributors/daslu/"
-   :affiliation [:scicloj :endor]
+   :affiliation [:scicloj]
    :links       [{:icon "github" :href "https://github.com/daslu"}]}
   {:id          :danielsz
    :name        "Daniel Szmulewicz"
@@ -176,6 +176,10 @@
    :image       "https://avatars.githubusercontent.com/burinc"
    :links       [{:icon "github" :href "https://github.com/burinc"}]
    :affiliation []}
+  {:id          :annieliu
+   :name        "Annie Liu"
+   :url         "https://github.com/humanni-e"
+   :email       "u3629374@connect.hku.hk"}
   {:id          :proffitt
    :name        "William Proffitt"
    :url         "https://github.com/doogiecode"
@@ -202,7 +206,12 @@
    :name        "Pierre Baille"
    :image       "https://avatars.githubusercontent.com/u/4739483"
    :url         "https://github.com/pbaille"
-   :links       []}]
+   :links       []}
+  {:id          :ezmiller
+   :name        "Ethan Miller"
+   :image       "https://avatars.githubusercontent.com/u/772738?v=4&size=64"
+   :url         "https://github.com/ezmiller"
+   :links       ["https://humanscodes.com"]}]
 
  :affiliation
  [{:id   :clojure.core

site/db.edn

@@ -1,15 +1,21 @@
 ---
 title: "Drafts"
 listing:
-  contents: [".", "!./*.qmd"]
-  include:
-    type: post
-    draft: true
-  sort:
-    - "date desc"
-    - "title desc"
-  sort-ui: true
-  filter-ui: true
-  feed:
-    type: metadata
+  - contents: [".", "!./*.qmd"]
+    include:
+      type: post
+      draft: true
+    sort:
+      - "date desc"
+      - "title desc"
+    sort-ui: true
+    filter-ui: true
+  - contents: [".", "!./*.qmd"]
+    include:
+      type: draft
+    sort:
+      - "date desc"
+      - "title desc"
+    sort-ui: true
+    filter-ui: true
 ---

site/drafts.qmd

@@ -32,16 +32,23 @@ This article gets you started with computing and rendering volumetric clouds.
 
 ## Dependencies
 
-To download the required libraries, we use a `deps.edn` file with the following content:
+To download the required libraries, we use a `deps.edn` file with the following content.
+Replace the *natives-linux* classifier with *natives-macos* or *natives-windows* as required.
 
 ```Clojure
 {:deps
  {
-  org.clojure/clojure {:mvn/version "1.12.3"}
-  org.scicloj/noj     {:mvn/version "2-beta18"}
-  midje/midje         {:mvn/version "1.10.10"}
-  generateme/fastmath {:mvn/version "3.0.0-alpha4"}
-  comb/comb           {:mvn/version "1.0.0"}
+  org.clojure/clojure                  {:mvn/version "1.12.3"}
+  org.scicloj/noj                      {:mvn/version "2-beta18"}
+  midje/midje                          {:mvn/version "1.10.10"}
+  generateme/fastmath                  {:mvn/version "3.0.0-alpha4"}
+  org.lwjgl/lwjgl                      {:mvn/version "3.4.0"}
+  org.lwjgl/lwjgl$natives-linux        {:mvn/version "3.4.0"}
+  org.lwjgl/lwjgl-opengl               {:mvn/version "3.4.0"}
+  org.lwjgl/lwjgl-opengl$natives-linux {:mvn/version "3.4.0"}
+  org.lwjgl/lwjgl-glfw                 {:mvn/version "3.4.0"}
+  org.lwjgl/lwjgl-glfw$natives-linux   {:mvn/version "3.4.0"}
+  comb/comb                            {:mvn/version "1.0.0"}
   }
 }
 ```

site/volumetric_clouds/main.qmd

@@ -90,8 +90,7 @@
                                  :template "trestles")
                       :author  author
                       :listing {:contents  [".", "!./*.qmd"]
-                                :include   {:type   :post
-                                            :author (str "{" (:name author) "}" "*")}
+                                :include   {:author (str "{" (:name author) "}*")}
                                 :sort      ["date desc" "title desc"]
                                 :sort-ui   true
                                 :filter-ui true}}]