Adds missing notebooks to user.clj

.envrc

@@ -0,0 +1,5 @@
+#! /bin/env bash
+echo "Either start nREPL server directly:"
+echo "'clj -M:nrepl'"
+echo "or connect to it inside nvim(vim-jack-in): "
+echo "':Clj'"

deps.edn

@@ -1,7 +1,13 @@
 {:paths ["dev" "notebooks" "resources"]
+ :mvn/repos {"central" {:url "https://repo1.maven.org/maven2/"}
+             "clojars" {:url "https://clojars.org/repo"}}
  :deps {io.github.nextjournal/clerk {:git/sha "6c710b552f7b3591e34c93ea635c435a7e35231e"}
         io.github.nextjournal/clerk-slideshow {:git/sha "5fe197ca0c8f28128379849dc677cd718be71524"}
 
+        ;; python integration
+        ; clj-python/libpython-clj {:mvn/version "1.37"}
+        org.clojure/data.csv {:mvn/version "0.1.4"}
+        ;; /python integration
         ;; keep 1.10 until `kixi/stats` and `sicmutils` fix warnings
         org.clojure/clojure {:mvn/version "1.10.3"}
 
@@ -22,6 +28,7 @@
         ;; semantic web goodies and box/arrow graphs
         io.github.jackrusher/mundaneum {:git/sha "d2c934a12388d88ddb3e53fef92ec2eef97d6140"}
         arrowic/arrowic {:mvn/version "0.1.1"}
+        clj-python/libpython-clj {:mvn/version "2.024"}
 
         ;; OSC server
         com.illposed.osc/javaosc-core      {:mvn/version "0.8" :exclusions [org.slf4j/slf4j-api org.slf4j/slf4j-log4j12]}
@@ -45,4 +52,12 @@
                                                    "notebooks/sicmutils.clj"
                                                    "notebooks/rule_30.clj"
                                                    "notebooks/zipper_with_scars.clj"]}
-                               :main-opts ["-m" "babashka.cli.exec"]}}}
+                               :main-opts ["-m" "babashka.cli.exec"]}
+           :test {:extra-paths ["test"]
+                  :extra-deps {org.clojure/test.check {:mvn/version "0.10.0"}}}
+           :runner
+           {:extra-deps {com.cognitect/test-runner
+                         {:git/url "https://github.com/cognitect-labs/test-runner"
+                          :sha "f7ef16dc3b8332b0d77bc0274578ad5270fbfedd"}}
+            :main-opts ["-m" "cognitect.test-runner"
+                        "-d" "test"]}}}

dev/user.clj

@@ -16,17 +16,25 @@
 
   ;; or call `clerk/show!` explicitly
   (clerk/show! "notebooks/introduction.clj")
+  (clerk/show! "notebooks/controls.clj")
   (clerk/show! "notebooks/data_science.clj")
   (clerk/show! "notebooks/sicmutils.clj")
+  (clerk/show! "notebooks/dictionary.clj")
+  (clerk/show! "notebooks/elements.clj")
+  (clerk/show! "notebooks/git.clj")
+  (clerk/show! "notebooks/logo.clj")
   (clerk/show! "notebooks/rule_30.clj")
   (clerk/show! "notebooks/semantic.clj")
   (clerk/show! "notebooks/images.clj")
+  (clerk/show! "notebooks/zipper_with_scars.clj")
+  (clerk/show! "notebooks/numpy_plot.clj")
+  (clerk/show! "notebooks/python.clj")
 
   (clerk/show! "index.md")
 
   ;; TODO If you would like more details about how Clerk works, here's a
   ;; notebook with some implementation details.
-  ;; (clerk/show! "notebooks/how_clerk_works.clj")
+  (clerk/show! "notebooks/how_clerk_works.clj")
 
   ;; produce a static app
   (clerk/build-static-app! {:paths (mapv #(str "notebooks/" % ".clj")

notebooks/gigasquid/numpy_plot.clj

@@ -0,0 +1,110 @@
+; from https://raw.githubusercontent.com/gigasquid/libpython-clj-examples/master/src/gigasquid/numpy_plot.clj
+(ns gigasquid.numpy-plot
+  {:nextjournal.clerk/visibility {:code :fold}
+   :nextjournal.clerk/no-cache true}
+  (:require
+   [clojure.zip :as zip]
+   [arrowic.core :as a]
+   [nextjournal.clerk :as clerk]
+   [nextjournal.clerk.viewer :as v]
+   [gigasquid.plot :as plot]
+   [clojure.string :as str]
+   [libpython-clj2.python
+    :refer [as-python as-jvm
+            ->python ->jvm
+            get-attr call-attr call-attr-kw
+            get-item initialize!
+            run-simple-string
+            add-module module-dict
+            import-module
+            python-type]
+    :as py]))
+
+(py/initialize!)
+; Clojure
+(require '[libpython-clj2.require :refer [require-python]])
+(require-python '[matplotlib.pyplot :as pyplot])
+(require-python '[numpy :as np])
+(require-python '[pandas :as pd])
+(require-python '[numpy :as numpy])
+
+(def dates (pd/date_range "1/1/2000" :periods 8))
+(def table (pd/DataFrame (call-attr np/random :randn 8 4) :index dates :columns ["A" "B" "C" "D"]))
+(def row-date (pd/date_range :start "2000-01-01" :end "2000-01-01"))
+(get-item (get-attr table :loc) row-date)
+;;;; you will need matplotlib, numpy, and pillow installed to run this in python3
+
+;;; This uses a macro from printing in the plot namespace that uses the shell "open" command
+;;; to show a saved image from pyplot. If you don't have a mac you will need to modify that
+;;; to whatever shell command you have.
+
+(comment
+  (def x (numpy/linspace 0 2 50))
+
+  (plot/with-show (matplotlib.pyplot/plot [[1 2 3 4 5] [1 2 3 4 10]] :label "linear"))
+
+  (plot/with-show
+    (pyplot/plot [x x] :label "linear")
+    (pyplot/plot [x (py. x "__pow__" 2)] :label "quadratic")
+    (pyplot/plot [x (py. x "__pow__" 3)] :label "cubic")
+    (pyplot/xlabel "x label")
+    (pyplot/ylabel "y label")
+    (pyplot/title "Simple Plot"))
+
+;;; numpy printing tutorial http://cs231n.github.io/python-numpy-tutorial/#matplotlib-plotting
+  (let [x (numpy/arange 0 (* 3 numpy/pi) 0.1)
+        y (numpy/sin x)]
+    (plot/with-show
+      (pyplot/plot x y)))
+
+  (let [x (numpy/arange 0 (* 3 numpy/pi) 0.1)
+        y-sin (numpy/sin x)
+        y-cos (numpy/cos x)]
+    (plot/with-show
+      (pyplot/plot x y-sin)
+      (pyplot/plot x y-cos)
+      (pyplot/xlabel "x axis label")
+      (pyplot/ylabel "y axis label")
+      (pyplot/title "Sine and Cosine")
+      (pyplot/legend ["Sine" "Cosine"])))
+
+  ;;;; Subplots
+
+  (let [x (numpy/arange 0 (* 3 numpy/pi) 0.1)
+        y-sin (numpy/sin x)
+        y-cos (numpy/cos x)]
+    (plot/with-show
+      ;;; set up a subplot gird that has a height of 2 and width of 1
+      ;; and set the first such subplot as active
+      (pyplot/subplot 2 1 1)
+      (pyplot/plot x y-sin)
+      (pyplot/title "Sine")
+
+      ;;; set the second subplot as active and make the second plot
+      (pyplot/subplot 2 1 2)
+      (pyplot/plot x y-cos)
+      (pyplot/title "Cosine")))
+
+;;;;; Images
+
+  (let [img (pyplot/imread "resources/cat.jpg")
+        img-tinted (numpy/multiply img [1 0.95 0.9])]
+    (plot/with-show
+      (pyplot/subplot 1 2 1)
+      (pyplot/imshow img)
+      (pyplot/subplot 1 2 2)
+      (pyplot/imshow (numpy/uint8 img-tinted))))
+
+;;;;; pie chart
+;;;; from https://org/3.1.1/gallery/pie_and_polar_charts/pie_features.html
+
+  (let [labels ["Frogs" "Hogs" "Dogs" "Logs"]
+        sizes [15 30 45 10]
+        explode [0 0.1 0 0] ; only explode the 2nd slice (Hogs)
+        ]
+    (plot/with-show
+      (let [[fig1 ax1] (pyplot/subplots)]
+        (py. ax1 "pie" sizes :explode explode :labels labels :autopct "%1.1f%%"
+             :shadow true :startangle 90)
+        (py. ax1 "axis" "equal")) ;equal aspec ration ensures that pie is drawn as circle
+      )))

notebooks/gigasquid/plot.clj

@@ -0,0 +1,79 @@
+(ns gigasquid.plot
+  (:require
+            ; [libpython-clj.python :as py :refer [py. py.. py.-]]
+   [libpython-clj2.python
+    :refer [as-python as-jvm
+            ->python ->jvm
+            get-attr call-attr call-attr-kw
+            get-item initialize!
+            run-simple-string
+            add-module module-dict
+            import-module
+            python-type
+            py. py.. py.-]
+    :as py]
+   [libpython-clj2.require :refer [require-python]]
+   [gigasquid.utils :refer [display-image create-tmp-file]]
+   [clojure.java.shell :as sh]))
+
+;;; This uses the headless version of matplotlib to generate a graph then copy it to the JVM
+;;; where we can then print it
+
+;;; have to set the headless mode before requiring pyplot
+(def mplt (py/import-module "matplotlib"))
+(py. mplt "use" "Agg")
+
+(require-python '[matplotlib.pyplot :as pyplot])
+(require-python 'matplotlib.backends.backend_agg)
+(require-python 'numpy)
+
+(defmacro with-show
+  "Takes forms with mathplotlib.pyplot to then show locally"
+  [& body]
+  `(let [_# (pyplot/clf)
+         fig# (pyplot/figure)
+         agg-canvas# (matplotlib.backends.backend_agg/FigureCanvasAgg fig#)
+         temp-file# (create-tmp-file "tmp-image" ".png")
+         temp-image# (.getAbsolutePath temp-file#)]
+     ~(cons 'do body)
+     (py. agg-canvas# "draw")
+     (pyplot/savefig temp-image#)
+     (display-image temp-image#)
+     (.deleteOnExit temp-file#)))
+
+;;;; If you run into mem problems with temporary files try this one
+
+(defmacro with-show-one
+  "Takes forms with mathplotlib.pyplot to then show locally"
+  [& body]
+  `(let [_# (pyplot/clf)
+         fig# (pyplot/figure)
+         agg-canvas# (matplotlib.backends.backend_agg/FigureCanvasAgg fig#)]
+     ~(cons 'do body)
+     (py. agg-canvas# "draw")
+     (pyplot/savefig "temp.png")
+     (sh/sh "open" "temp.png")))
+
+(defmacro with-save
+  "Takes forms with mathplotlib.pyplot to then show locally"
+  [fname & body]
+  `(let [_# (pyplot/clf)
+         fig# (pyplot/figure)
+         agg-canvas# (matplotlib.backends.backend_agg/FigureCanvasAgg fig#)]
+     ~(cons 'do body)
+     (py. agg-canvas# "draw")
+     (pyplot/savefig  ~fname)))
+
+(comment
+
+  (def x (numpy/linspace 0 2 100))
+
+  (with-show
+    (pyplot/plot [x x] :label "linear")
+    (pyplot/plot [x (py. x "__pow__" 2)] :label "quadratic")
+    (pyplot/plot [x (py. x "__pow__" 3)] :label "cubic")
+    (pyplot/xlabel "x label")
+    (pyplot/ylabel "y label")
+    (pyplot/title "Simple Plot"))
+
+  (with-show (pyplot/plot [[1 2 3 4 5] [1 2 3 4 10]] :label "linear")))

notebooks/gigasquid/utils.clj

@@ -0,0 +1,36 @@
+(ns gigasquid.utils
+  (:require
+   [clojure.string :as string]
+   [clojure.java.shell :as sh]
+   [clojure.pprint :refer [pprint]])
+  (:import [java.io File]))
+
+(def is-linux?
+  (= "linux"
+     (-> "os.name"
+         System/getProperty
+         string/lower-case)))
+
+(def is-mac?
+  (-> "os.name"
+      System/getProperty
+      string/lower-case
+      (string/starts-with? "mac")))
+
+(defn display-image
+  "Display image on OSX or on Linux based system"
+  [image-file]
+  (cond
+    is-mac?
+    (sh/sh "open" image-file)
+
+    is-linux?
+    (sh/sh "display" image-file)))
+
+(defn create-tmp-file
+  "Return full path of temporary file.
+
+  Example:
+  (create-tmp-file \"tmp-image\" \".png\") "
+  [prefix ext]
+  (File/createTempFile prefix ext))

utils.clj

@@ -0,0 +1,36 @@
+(ns gigasquid.utils
+  (:require
+   [clojure.string :as string]
+   [clojure.java.shell :as sh]
+   [clojure.pprint :refer [pprint]])
+  (:import [java.io File]))
+
+(def is-linux?
+  (= "linux"
+     (-> "os.name"
+         System/getProperty
+         string/lower-case)))
+
+(def is-mac?
+  (-> "os.name"
+      System/getProperty
+      string/lower-case
+      (string/starts-with? "mac")))
+
+(defn display-image
+  "Display image on OSX or on Linux based system"
+  [image-file]
+  (cond
+    is-mac?
+    (sh/sh "open" image-file)
+
+    is-linux?
+    (sh/sh "display" image-file)))
+
+(defn create-tmp-file
+  "Return full path of temporary file.
+
+  Example:
+  (create-tmp-file \"tmp-image\" \".png\") "
+  [prefix ext]
+  (File/createTempFile prefix ext))