From ff2ef755292f86878687bb1a151b233b569d0ee7 Mon Sep 17 00:00:00 2001
From: Andrea Amantini <lo.zampino@gmail.com>
Date: Tue, 18 Oct 2022 18:25:44 +0200
Subject: [PATCH 01/17] First sketch of Clerk in Babashka

---
 bb-runtime.edn                                | 27 +++++++++++
 bb/stubs/multihash/core.clj                   |  3 ++
 bb/stubs/multihash/digest.clj                 |  3 ++
 bb/stubs/nextjournal/beholder.clj             |  4 ++
 bb/stubs/nextjournal/clerk/analyzer.clj       | 41 ++++++++++++++++
 bb/stubs/nextjournal/markdown.clj             |  3 ++
 bb/stubs/nextjournal/markdown/parser.clj      |  3 ++
 bb/stubs/nextjournal/markdown/transform.clj   |  4 ++
 bb/stubs/taoensso/nippy.clj                   |  5 ++
 resources/viewer-js-hash                      |  2 +-
 src/nextjournal/{clerk.clj => clerk.cljc}     |  3 +-
 src/nextjournal/clerk/{eval.clj => eval.cljc} | 23 +++++----
 src/nextjournal/clerk/sci_viewer.cljs         |  2 +
 src/nextjournal/clerk/view.clj                |  4 +-
 src/nextjournal/clerk/viewer.cljc             | 48 +++++++++++--------
 src/nextjournal/clerk/webserver.clj           |  4 +-
 16 files changed, 146 insertions(+), 33 deletions(-)
 create mode 100644 bb-runtime.edn
 create mode 100644 bb/stubs/multihash/core.clj
 create mode 100644 bb/stubs/multihash/digest.clj
 create mode 100644 bb/stubs/nextjournal/beholder.clj
 create mode 100644 bb/stubs/nextjournal/clerk/analyzer.clj
 create mode 100644 bb/stubs/nextjournal/markdown.clj
 create mode 100644 bb/stubs/nextjournal/markdown/parser.clj
 create mode 100644 bb/stubs/nextjournal/markdown/transform.clj
 create mode 100644 bb/stubs/taoensso/nippy.clj
 rename src/nextjournal/{clerk.clj => clerk.cljc} (99%)
 rename src/nextjournal/clerk/{eval.clj => eval.cljc} (91%)

diff --git a/bb-runtime.edn b/bb-runtime.edn
new file mode 100644
index 000000000..bd252391c
--- /dev/null
+++ b/bb-runtime.edn
@@ -0,0 +1,27 @@
+{:min-bb-version "0.9.159"
+ :paths ["bb/stubs" "src" "notebooks" "resources"]
+ :deps {;; hash replacement?
+        io.replikativ/hasch {:mvn/version "0.3.7"}
+        weavejester/dependency {:mvn/version "0.2.1"}
+        ;; shiiiiet!
+        ;; io.github.nextjournal/markdown {:mvn/version "0.4.126"}
+        hiccup/hiccup {:mvn/version "2.0.0-alpha2"}
+        }
+ :tasks
+ {nrepl
+  {:requires ([babashka.fs :as fs]
+              [babashka.nrepl.server :as srv])
+
+   :task (do (srv/start-server! {:host "localhost" :port 1339})
+             (spit ".nrepl-port" "1339")
+             (-> (Runtime/getRuntime)
+               (.addShutdownHook (Thread. (fn [] (fs/delete ".nrepl-port")))))
+             (deref (promise)))}
+
+  serve
+  {:task (clerk/serve! {:port 9999})}
+
+  clerk
+  {#_ #_ :depends [nrepl #_ serve]
+   :parallel? true
+   :task (println (ns-publics 'hiccup2.core))}}}
diff --git a/bb/stubs/multihash/core.clj b/bb/stubs/multihash/core.clj
new file mode 100644
index 000000000..bf30c73ee
--- /dev/null
+++ b/bb/stubs/multihash/core.clj
@@ -0,0 +1,3 @@
+(ns multihash.core)
+
+(defn base58 [h] "base58")
diff --git a/bb/stubs/multihash/digest.clj b/bb/stubs/multihash/digest.clj
new file mode 100644
index 000000000..c722b226e
--- /dev/null
+++ b/bb/stubs/multihash/digest.clj
@@ -0,0 +1,3 @@
+(ns multihash.digest)
+
+(defn sha2-512 [o] "sha2")
diff --git a/bb/stubs/nextjournal/beholder.clj b/bb/stubs/nextjournal/beholder.clj
new file mode 100644
index 000000000..72b31f72e
--- /dev/null
+++ b/bb/stubs/nextjournal/beholder.clj
@@ -0,0 +1,4 @@
+(ns nextjournal.beholder)
+
+(defn watch [cb & args] nil)
+(defn stop [w] nil)
diff --git a/bb/stubs/nextjournal/clerk/analyzer.clj b/bb/stubs/nextjournal/clerk/analyzer.clj
new file mode 100644
index 000000000..2a007c793
--- /dev/null
+++ b/bb/stubs/nextjournal/clerk/analyzer.clj
@@ -0,0 +1,41 @@
+(ns nextjournal.clerk.analyzer
+  (:require [nextjournal.clerk.config :as config]
+            [edamame.core :as edamame]))
+
+(defn valuehash [value] "hash")
+(defn hash-codeblock [_ {:keys [hash]}] hash)
+(defn ->hash-str [value] "hash-str")
+(defn deref? [form] false)
+(defn hash [doc] doc)
+(defn hash-deref-deps [doc _cell] doc)
+
+(defn build-graph [doc]
+   (-> doc
+       (assoc :->analysis-info (fn [x] {:form x}))
+       ;; TODO: read first form, create sci.lang.Namespace
+       (assoc :ns *ns*)
+       (update :blocks
+               (partial into [] (map (fn [{:as b :keys [type text]}]
+                                       (cond-> b
+                                         (= :code type)
+                                         (assoc :form
+                                                (edamame/parse-string text
+                                                                      {:all true
+                                                                       :readers *data-readers*
+                                                                       :read-cond :allow
+                                                                       :regex #(list `re-pattern %)
+                                                                       :features #{:clj}
+                                                                       ;; TODO:
+                                                                       #_#_:auto-resolve (auto-resolves (or *ns* (find-ns 'user)))})))))))))
+
+(defn exceeds-bounded-count-limit? [x]
+  (reduce (fn [_ xs]
+            (try
+              (let [limit config/*bounded-count-limit*]
+                (if (and (seqable? xs) (<= limit (bounded-count limit xs)))
+                  (reduced true)
+                  false))
+              (catch Exception _e
+                (reduced true))))
+          false
+          (tree-seq seqable? seq x)))
diff --git a/bb/stubs/nextjournal/markdown.clj b/bb/stubs/nextjournal/markdown.clj
new file mode 100644
index 000000000..6bef596bd
--- /dev/null
+++ b/bb/stubs/nextjournal/markdown.clj
@@ -0,0 +1,3 @@
+(ns nextjournal.markdown)
+
+(defn parse [md] {:type :doc :content md})
diff --git a/bb/stubs/nextjournal/markdown/parser.clj b/bb/stubs/nextjournal/markdown/parser.clj
new file mode 100644
index 000000000..55a8c459b
--- /dev/null
+++ b/bb/stubs/nextjournal/markdown/parser.clj
@@ -0,0 +1,3 @@
+(ns nextjournal.markdown.parser)
+
+(defn add-title+toc [doc] doc)
diff --git a/bb/stubs/nextjournal/markdown/transform.clj b/bb/stubs/nextjournal/markdown/transform.clj
new file mode 100644
index 000000000..28968dfc7
--- /dev/null
+++ b/bb/stubs/nextjournal/markdown/transform.clj
@@ -0,0 +1,4 @@
+(ns nextjournal.markdown.transform)
+
+(defn ->text [node] "text")
+(defn table-alignment [attrs] {})
diff --git a/bb/stubs/taoensso/nippy.clj b/bb/stubs/taoensso/nippy.clj
new file mode 100644
index 000000000..e9ce3e8e1
--- /dev/null
+++ b/bb/stubs/taoensso/nippy.clj
@@ -0,0 +1,5 @@
+(ns taoensso.nippy)
+
+(defn freezable? [x] false)
+(defn freeze [x] x)
+(defn thaw-from-file [file] "thawed")
diff --git a/resources/viewer-js-hash b/resources/viewer-js-hash
index 7a589706c..b39c9d5d7 100644
--- a/resources/viewer-js-hash
+++ b/resources/viewer-js-hash
@@ -1 +1 @@
-46k5SeDmWgR6seZFSVzwdiCJ7BEi
\ No newline at end of file
+HqSvyTYhQi6sTyU5EVEMH3u4Dn6
\ No newline at end of file
diff --git a/src/nextjournal/clerk.clj b/src/nextjournal/clerk.cljc
similarity index 99%
rename from src/nextjournal/clerk.clj
rename to src/nextjournal/clerk.cljc
index 1613920d0..ecc39167a 100644
--- a/src/nextjournal/clerk.clj
+++ b/src/nextjournal/clerk.cljc
@@ -40,7 +40,8 @@
                    (throw (ex-info (str "`nextjournal.clerk/show!` cannot show `nil`.")
                                    {:file-or-ns file-or-ns}))
 
-                   (or (symbol? file-or-ns) (instance? clojure.lang.Namespace file-or-ns))
+                   ;; TODO: sci.lang.Namespace
+                   (or (symbol? file-or-ns) (instance? #?(:bb (type *ns*) :clj clojure.lang.Namespace) file-or-ns))
                    (or (some (fn [ext]
                                (io/resource (str (str/replace (namespace-munge file-or-ns) "." "/") ext)))
                              [".clj" ".cljc"])
diff --git a/src/nextjournal/clerk/eval.clj b/src/nextjournal/clerk/eval.cljc
similarity index 91%
rename from src/nextjournal/clerk/eval.clj
rename to src/nextjournal/clerk/eval.cljc
index 7898c7ef8..99723bab1 100644
--- a/src/nextjournal/clerk/eval.clj
+++ b/src/nextjournal/clerk/eval.cljc
@@ -11,8 +11,9 @@
             [nextjournal.clerk.parser :as parser]
             [nextjournal.clerk.viewer :as v]
             [taoensso.nippy :as nippy])
-  (:import (java.awt.image BufferedImage)
-           (javax.imageio ImageIO)))
+  #?(:bb (:import)
+     :clj (:import (java.awt.image BufferedImage)
+                   (javax.imageio ImageIO))))
 
 (comment
   (alter-var-root #'nippy/*freeze-serializable-allowlist* (fn [_] "allow-and-record"))
@@ -20,9 +21,11 @@
   (nippy/get-recorded-serializable-classes))
 
 ;; nippy tweaks
-(alter-var-root #'nippy/*thaw-serializable-allowlist* (fn [_] (conj nippy/default-thaw-serializable-allowlist "java.io.File" "clojure.lang.Var" "clojure.lang.Namespace")))
-(nippy/extend-freeze BufferedImage :java.awt.image.BufferedImage [x out] (ImageIO/write x "png" (ImageIO/createImageOutputStream out)))
-(nippy/extend-thaw :java.awt.image.BufferedImage [in] (ImageIO/read in))
+#?(:bb nil
+   :clj (do
+          (alter-var-root #'nippy/*thaw-serializable-allowlist* (fn [_] (conj nippy/default-thaw-serializable-allowlist "java.io.File" "clojure.lang.Var" "clojure.lang.Namespace")))
+          (nippy/extend-freeze BufferedImage :java.awt.image.BufferedImage [x out] (ImageIO/write x "png" (ImageIO/createImageOutputStream out)))
+          (nippy/extend-thaw :java.awt.image.BufferedImage [in] (ImageIO/read in))))
 
 #_(-> [(clojure.java.io/file "notebooks") (find-ns 'user)] nippy/freeze nippy/thaw)
 
@@ -107,6 +110,10 @@
       #_(prn :freeze-error e)
       nil)))
 
+;; NOTE: cannot add clojure.main to bb stubs
+(defn ex-triage [m] #?(:bb m :clj (main/ex-triage m)))
+(defn ex-str [m] #?(:bb (str m) :clj (main/ex-str m)))
+
 (defn ^:private eval+cache! [{:keys [form var ns-effect? no-cache? freezable?] :as form-info} hash digest-file]
   (try
     (let [{:keys [result]} (time-ms (binding [config/*in-clerk* true]
@@ -128,8 +135,8 @@
                      result)]
         (wrapped-with-metadata result blob-id)))
     (catch Throwable t
-      (let [triaged (main/ex-triage (Throwable->map t))]
-        (throw (ex-info (main/ex-str triaged) triaged))))))
+      (let [triaged (ex-triage (Throwable->map t))]
+        (throw (ex-info (ex-str triaged) triaged))))))
 
 (defn maybe-eval-viewers [{:as opts :nextjournal/keys [viewer viewers]}]
   (cond-> opts
@@ -196,7 +203,7 @@
   "Evaluates the given `parsed-doc` using the `in-memory-cache` and augments it with the results."
   [in-memory-cache parsed-doc]
   (let [{:as analyzed-doc :keys [ns]} (analyzer/build-graph parsed-doc)]
-    (binding [*ns* ns]
+    (binding [*ns* (or ns *ns*)]
       (-> analyzed-doc
           analyzer/hash
           (assoc :blob->result in-memory-cache)
diff --git a/src/nextjournal/clerk/sci_viewer.cljs b/src/nextjournal/clerk/sci_viewer.cljs
index 48ccb3a4e..4492af151 100644
--- a/src/nextjournal/clerk/sci_viewer.cljs
+++ b/src/nextjournal/clerk/sci_viewer.cljs
@@ -10,6 +10,7 @@
             [goog.string :as gstring]
             [nextjournal.clerk.viewer :as viewer :refer [code md plotly tex table vl row col with-viewer with-viewers]]
             [nextjournal.clerk.parser :as clerk.parser]
+            [nextjournal.markdown :as markdown]
             [nextjournal.markdown.transform :as md.transform]
             [nextjournal.ui.components.icon :as icon]
             [nextjournal.ui.components.localstorage :as ls]
@@ -752,6 +753,7 @@
    'col col
    'html html-render
    'md md
+   'md->hiccup markdown/->hiccup
    'plotly plotly
    'row row
    'table table
diff --git a/src/nextjournal/clerk/view.clj b/src/nextjournal/clerk/view.clj
index d584fe4cd..0e3efe28c 100644
--- a/src/nextjournal/clerk/view.clj
+++ b/src/nextjournal/clerk/view.clj
@@ -12,7 +12,7 @@
      (-> (merge doc opts) v/notebook v/present))))
 
 
-#_(doc->viewer (nextjournal.clerk/eval-file "notebooks/hello.clj"))
+#_(doc->viewer (nextjournal.clerk.eval/eval-file "notebooks/hello.clj"))
 #_(nextjournal.clerk/show! "notebooks/test.clj")
 #_(nextjournal.clerk/show! "notebooks/visibility.clj")
 
@@ -56,7 +56,7 @@ window.ws_send = msg => ws.send(msg)")]]))
    [:head
     [:title (or (and current-path (-> state :path->doc (get current-path) v/->value :title)) "Clerk")]
     [:meta {:charset "UTF-8"}]
-    [:meta {:name "viewport" :content "width=device-width, initial-scale=1"}]    
+    [:meta {:name "viewport" :content "width=device-width, initial-scale=1"}]
     (include-css+js)]
    [:body
     [:div#clerk-static-app]
diff --git a/src/nextjournal/clerk/viewer.cljc b/src/nextjournal/clerk/viewer.cljc
index c4e9f3c0b..f3560cbe5 100644
--- a/src/nextjournal/clerk/viewer.cljc
+++ b/src/nextjournal/clerk/viewer.cljc
@@ -14,7 +14,10 @@
                        [applied-science.js-interop :as j]])
             [nextjournal.markdown :as md]
             [nextjournal.markdown.transform :as md.transform])
-  #?(:clj (:import (com.pngencoder PngEncoder)
+  #?(:bb (:import (java.nio.file Files StandardOpenOption)
+                  (java.util Base64)
+                  (java.lang Throwable))
+     :clj (:import (com.pngencoder PngEncoder)
                    (clojure.lang IDeref)
                    (java.lang Throwable)
                    (java.awt.image BufferedImage)
@@ -466,7 +469,8 @@
 #?(:clj
    (defn datafy-scope [scope]
      (cond
-       (instance? clojure.lang.Namespace scope) {:namespace (-> scope str keyword)}
+       (instance? #?(:bb (type *ns*) :clj clojure.lang.Namespace) scope)
+       {:namespace (-> scope str keyword)}
        (keyword? scope) scope
        :else (throw (ex-info (str "Unsupported scope " scope) {:scope scope})))))
 
@@ -605,7 +609,8 @@
   {:pred (fn [e] (instance? #?(:clj Throwable :cljs js/Error) e))
    :name :error :render-fn 'v/throwable-viewer :transform-fn (comp mark-presented (update-val (comp demunge-ex-data datafy/datafy)))})
 
-(def buffered-image-viewer #?(:clj {:pred #(instance? BufferedImage %)
+(def buffered-image-viewer #?(:bb {}
+                              :clj {:pred #(instance? BufferedImage %)
                                     :transform-fn (fn [{image :nextjournal/value}]
                                                     (let [w (.getWidth image)
                                                           h (.getHeight image)
@@ -620,15 +625,16 @@
                                     :render-fn '(fn [blob] (v/html [:figure.flex.flex-col.items-center.not-prose [:img {:src (v/url-for blob)}]]))}))
 
 (def ideref-viewer
-  {:pred #(instance? IDeref %)
-   :transform-fn (update-val (fn [ideref]
-                               (with-viewer :tagged-value
-                                 {:tag "object"
-                                  :value (vector (symbol (pr-str (type ideref)))
-                                                 #?(:clj (with-viewer :number-hex (System/identityHashCode ideref)))
-                                                 (if-let [deref-as-map (resolve 'clojure.core/deref-as-map)]
-                                                   (deref-as-map ideref)
-                                                   ideref))})))})
+  #?(:bb {} :clj
+     {:pred #(instance? IDeref %)
+      :transform-fn (update-val (fn [ideref]
+                                  (with-viewer :tagged-value
+                                    {:tag "object"
+                                     :value (vector (symbol (pr-str (type ideref)))
+                                                    #?(:clj (with-viewer :number-hex (System/identityHashCode ideref)))
+                                                    (if-let [deref-as-map (resolve 'clojure.core/deref-as-map)]
+                                                      (deref-as-map ideref)
+                                                      ideref))})))}))
 
 (def regex-viewer
   {:pred #?(:clj (partial instance? java.util.regex.Pattern) :cljs regexp?)
@@ -660,12 +666,16 @@
   {:name :vega-lite :render-fn (quote v/vega-lite-viewer) :transform-fn mark-presented})
 
 (def markdown-viewer
-  {:name :markdown :transform-fn (fn [wrapped-value]
-                                   (-> wrapped-value
-                                       mark-presented
-                                       (update :nextjournal/value #(cond->> % (string? %) md/parse))
-                                       (update :nextjournal/viewers add-viewers markdown-viewers)
-                                       (with-md-viewer)))})
+  (-> {:name :markdown}
+      #?(:bb  (assoc :transform-fn (comp mark-presented (update-val :content)))
+         :clj (assoc :transform-fn
+                     (fn [wrapped-value]
+                       (-> wrapped-value
+                           mark-presented
+                           (update :nextjournal/value #(cond->> % (string? %) md/parse))
+                           (update :nextjournal/viewers add-viewers markdown-viewers)
+                           (with-md-viewer)))))
+      #?(:bb (assoc :render-fn '(fn [str] (js/console.log :str str) (v/html (v/md->hiccup str)))))))
 
 (def code-viewer
   {:name :code :render-fn (quote v/code-viewer) :transform-fn (comp mark-presented (update-val (fn [v] (if (string? v) v (str/trim (with-out-str (pprint/pprint v)))))))})
@@ -1275,7 +1285,7 @@
   ([viewers] (reset-viewers! *ns* viewers))
   ([scope viewers]
    (assert (or (#{:default} scope)
-               #?(:clj (instance? clojure.lang.Namespace scope))))
+               #?(:bb :default :clj (instance? clojure.lang.Namespace scope))))
    (swap! !viewers assoc scope viewers)))
 
 (defn add-viewers! [viewers]
diff --git a/src/nextjournal/clerk/webserver.clj b/src/nextjournal/clerk/webserver.clj
index 17e384578..b4637fa91 100644
--- a/src/nextjournal/clerk/webserver.clj
+++ b/src/nextjournal/clerk/webserver.clj
@@ -3,14 +3,14 @@
             [clojure.edn :as edn]
             [clojure.pprint :as pprint]
             [clojure.string :as str]
-            [lambdaisland.uri :as uri]
             [nextjournal.clerk.view :as view]
             [nextjournal.clerk.viewer :as v]
             [nextjournal.markdown :as md]
             [org.httpkit.server :as httpkit]))
 
 (def help-doc
-  {:blocks [{:type :markdown :doc (md/parse "Use `nextjournal.clerk/show!` to make your notebook appear…")}]})
+  {:ns *ns*
+   :blocks [{:type :markdown :doc (md/parse "Use `nextjournal.clerk/show!` to make your notebook appear…")}]})
 
 (defonce !clients (atom #{}))
 (defonce !doc (atom help-doc))

From 36ba59c08c409c4c12d90d0145232d793ee1386a Mon Sep 17 00:00:00 2001
From: Andrea Amantini <lo.zampino@gmail.com>
Date: Tue, 18 Oct 2022 18:47:43 +0200
Subject: [PATCH 02/17] Fix bb task

---
 bb-runtime.edn           | 21 ++++++++-------------
 resources/viewer-js-hash |  2 +-
 2 files changed, 9 insertions(+), 14 deletions(-)

diff --git a/bb-runtime.edn b/bb-runtime.edn
index bd252391c..0bed14042 100644
--- a/bb-runtime.edn
+++ b/bb-runtime.edn
@@ -8,20 +8,15 @@
         hiccup/hiccup {:mvn/version "2.0.0-alpha2"}
         }
  :tasks
- {nrepl
+ {clerk
   {:requires ([babashka.fs :as fs]
-              [babashka.nrepl.server :as srv])
-
+              [babashka.nrepl.server :as srv]
+              [nextjournal.clerk :as clerk])
    :task (do (srv/start-server! {:host "localhost" :port 1339})
              (spit ".nrepl-port" "1339")
+             (clerk/serve! {:port 9999})
              (-> (Runtime/getRuntime)
-               (.addShutdownHook (Thread. (fn [] (fs/delete ".nrepl-port")))))
-             (deref (promise)))}
-
-  serve
-  {:task (clerk/serve! {:port 9999})}
-
-  clerk
-  {#_ #_ :depends [nrepl #_ serve]
-   :parallel? true
-   :task (println (ns-publics 'hiccup2.core))}}}
+               (.addShutdownHook (Thread. (fn []
+                                            (clerk/halt!)
+                                            (fs/delete ".nrepl-port")))))
+             (deref (promise)))}}}
diff --git a/resources/viewer-js-hash b/resources/viewer-js-hash
index b39c9d5d7..3625ba889 100644
--- a/resources/viewer-js-hash
+++ b/resources/viewer-js-hash
@@ -1 +1 @@
-HqSvyTYhQi6sTyU5EVEMH3u4Dn6
\ No newline at end of file
+3E4A2XqsHVVWy5QvM6RCuu7ScjWw
\ No newline at end of file

From 066161f4e0375fe419b49c01e92dbe34e65b006d Mon Sep 17 00:00:00 2001
From: Andrea Amantini <lo.zampino@gmail.com>
Date: Tue, 18 Oct 2022 19:13:59 +0200
Subject: [PATCH 03/17] Require latest babashka

---
 bb-runtime.edn | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bb-runtime.edn b/bb-runtime.edn
index 0bed14042..6abe7ceee 100644
--- a/bb-runtime.edn
+++ b/bb-runtime.edn
@@ -1,4 +1,4 @@
-{:min-bb-version "0.9.159"
+{:min-bb-version "1.0.164"
  :paths ["bb/stubs" "src" "notebooks" "resources"]
  :deps {;; hash replacement?
         io.replikativ/hasch {:mvn/version "0.3.7"}

From ed9b56090c32c7963a9a02a6d002a0e73d146e7d Mon Sep 17 00:00:00 2001
From: Andrea Amantini <lo.zampino@gmail.com>
Date: Wed, 19 Oct 2022 09:23:33 +0200
Subject: [PATCH 04/17] clean bb deps

---
 bb-runtime.edn | 8 +-------
 1 file changed, 1 insertion(+), 7 deletions(-)

diff --git a/bb-runtime.edn b/bb-runtime.edn
index 6abe7ceee..43fadb4b7 100644
--- a/bb-runtime.edn
+++ b/bb-runtime.edn
@@ -1,12 +1,6 @@
 {:min-bb-version "1.0.164"
  :paths ["bb/stubs" "src" "notebooks" "resources"]
- :deps {;; hash replacement?
-        io.replikativ/hasch {:mvn/version "0.3.7"}
-        weavejester/dependency {:mvn/version "0.2.1"}
-        ;; shiiiiet!
-        ;; io.github.nextjournal/markdown {:mvn/version "0.4.126"}
-        hiccup/hiccup {:mvn/version "2.0.0-alpha2"}
-        }
+ :deps {hiccup/hiccup {:mvn/version "2.0.0-alpha2"}}
  :tasks
  {clerk
   {:requires ([babashka.fs :as fs]

From baa9660a368d9a3ef37c0dea88d2928182a84203 Mon Sep 17 00:00:00 2001
From: Andrea Amantini <lo.zampino@gmail.com>
Date: Wed, 19 Oct 2022 10:21:52 +0200
Subject: [PATCH 05/17] Rely on latest bb for namespace instance check

---
 resources/viewer-js-hash          |  2 +-
 src/nextjournal/clerk.cljc        |  3 +--
 src/nextjournal/clerk/view.clj    |  4 ++--
 src/nextjournal/clerk/viewer.cljc | 10 +++++-----
 4 files changed, 9 insertions(+), 10 deletions(-)

diff --git a/resources/viewer-js-hash b/resources/viewer-js-hash
index 3625ba889..87ead369c 100644
--- a/resources/viewer-js-hash
+++ b/resources/viewer-js-hash
@@ -1 +1 @@
-3E4A2XqsHVVWy5QvM6RCuu7ScjWw
\ No newline at end of file
+QHueRFEbfs7jTLGUVfX7SnJvJoo
\ No newline at end of file
diff --git a/src/nextjournal/clerk.cljc b/src/nextjournal/clerk.cljc
index ecc39167a..1613920d0 100644
--- a/src/nextjournal/clerk.cljc
+++ b/src/nextjournal/clerk.cljc
@@ -40,8 +40,7 @@
                    (throw (ex-info (str "`nextjournal.clerk/show!` cannot show `nil`.")
                                    {:file-or-ns file-or-ns}))
 
-                   ;; TODO: sci.lang.Namespace
-                   (or (symbol? file-or-ns) (instance? #?(:bb (type *ns*) :clj clojure.lang.Namespace) file-or-ns))
+                   (or (symbol? file-or-ns) (instance? clojure.lang.Namespace file-or-ns))
                    (or (some (fn [ext]
                                (io/resource (str (str/replace (namespace-munge file-or-ns) "." "/") ext)))
                              [".clj" ".cljc"])
diff --git a/src/nextjournal/clerk/view.clj b/src/nextjournal/clerk/view.clj
index 0e3efe28c..d584fe4cd 100644
--- a/src/nextjournal/clerk/view.clj
+++ b/src/nextjournal/clerk/view.clj
@@ -12,7 +12,7 @@
      (-> (merge doc opts) v/notebook v/present))))
 
 
-#_(doc->viewer (nextjournal.clerk.eval/eval-file "notebooks/hello.clj"))
+#_(doc->viewer (nextjournal.clerk/eval-file "notebooks/hello.clj"))
 #_(nextjournal.clerk/show! "notebooks/test.clj")
 #_(nextjournal.clerk/show! "notebooks/visibility.clj")
 
@@ -56,7 +56,7 @@ window.ws_send = msg => ws.send(msg)")]]))
    [:head
     [:title (or (and current-path (-> state :path->doc (get current-path) v/->value :title)) "Clerk")]
     [:meta {:charset "UTF-8"}]
-    [:meta {:name "viewport" :content "width=device-width, initial-scale=1"}]
+    [:meta {:name "viewport" :content "width=device-width, initial-scale=1"}]    
     (include-css+js)]
    [:body
     [:div#clerk-static-app]
diff --git a/src/nextjournal/clerk/viewer.cljc b/src/nextjournal/clerk/viewer.cljc
index f3560cbe5..82e1b4373 100644
--- a/src/nextjournal/clerk/viewer.cljc
+++ b/src/nextjournal/clerk/viewer.cljc
@@ -469,7 +469,7 @@
 #?(:clj
    (defn datafy-scope [scope]
      (cond
-       (instance? #?(:bb (type *ns*) :clj clojure.lang.Namespace) scope)
+       (instance? clojure.lang.Namespace scope)
        {:namespace (-> scope str keyword)}
        (keyword? scope) scope
        :else (throw (ex-info (str "Unsupported scope " scope) {:scope scope})))))
@@ -667,15 +667,15 @@
 
 (def markdown-viewer
   (-> {:name :markdown}
-      #?(:bb  (assoc :transform-fn (comp mark-presented (update-val :content)))
+      #?(:bb  (assoc :transform-fn (comp mark-presented (update-val :content))
+                     :render-fn '(fn [str] (js/console.log :str str) (v/html (v/md->hiccup str))))
          :clj (assoc :transform-fn
                      (fn [wrapped-value]
                        (-> wrapped-value
                            mark-presented
                            (update :nextjournal/value #(cond->> % (string? %) md/parse))
                            (update :nextjournal/viewers add-viewers markdown-viewers)
-                           (with-md-viewer)))))
-      #?(:bb (assoc :render-fn '(fn [str] (js/console.log :str str) (v/html (v/md->hiccup str)))))))
+                           (with-md-viewer)))))))
 
 (def code-viewer
   {:name :code :render-fn (quote v/code-viewer) :transform-fn (comp mark-presented (update-val (fn [v] (if (string? v) v (str/trim (with-out-str (pprint/pprint v)))))))})
@@ -1285,7 +1285,7 @@
   ([viewers] (reset-viewers! *ns* viewers))
   ([scope viewers]
    (assert (or (#{:default} scope)
-               #?(:bb :default :clj (instance? clojure.lang.Namespace scope))))
+               #?(:clj (instance? clojure.lang.Namespace scope))))
    (swap! !viewers assoc scope viewers)))
 
 (defn add-viewers! [viewers]

From 4fc352602793da1713287f9d3a1b9d026ffd28ff Mon Sep 17 00:00:00 2001
From: Andrea Amantini <lo.zampino@gmail.com>
Date: Wed, 19 Oct 2022 11:51:29 +0200
Subject: [PATCH 06/17] Move stubs to bb files

---
 bb/stubs/multihash/core.clj                   |   3 -
 bb/stubs/multihash/digest.clj                 |   3 -
 bb/stubs/nextjournal/beholder.clj             |   4 -
 bb/stubs/nextjournal/clerk/analyzer.clj       |  41 -----
 bb/stubs/nextjournal/markdown.clj             |   3 -
 bb/stubs/nextjournal/markdown/parser.clj      |   3 -
 bb/stubs/taoensso/nippy.clj                   |   5 -
 resources/viewer-js-hash                      |   2 +-
 src/nextjournal/beholder.bb                   |   5 +
 src/nextjournal/{clerk.cljc => clerk.clj}     |   0
 src/nextjournal/clerk/analyzer.bb             |   6 +
 src/nextjournal/clerk/builder.clj             |   4 +-
 src/nextjournal/clerk/eval.bb                 | 149 ++++++++++++++++++
 src/nextjournal/clerk/{eval.cljc => eval.clj} |  27 ++--
 src/nextjournal/markdown.bb                   |   4 +
 src/nextjournal/markdown/parser.bb            |   4 +
 .../nextjournal/markdown/transform.bb         |   3 +-
 17 files changed, 183 insertions(+), 83 deletions(-)
 delete mode 100644 bb/stubs/multihash/core.clj
 delete mode 100644 bb/stubs/multihash/digest.clj
 delete mode 100644 bb/stubs/nextjournal/beholder.clj
 delete mode 100644 bb/stubs/nextjournal/clerk/analyzer.clj
 delete mode 100644 bb/stubs/nextjournal/markdown.clj
 delete mode 100644 bb/stubs/nextjournal/markdown/parser.clj
 delete mode 100644 bb/stubs/taoensso/nippy.clj
 create mode 100644 src/nextjournal/beholder.bb
 rename src/nextjournal/{clerk.cljc => clerk.clj} (100%)
 create mode 100644 src/nextjournal/clerk/analyzer.bb
 create mode 100644 src/nextjournal/clerk/eval.bb
 rename src/nextjournal/clerk/{eval.cljc => eval.clj} (91%)
 create mode 100644 src/nextjournal/markdown.bb
 create mode 100644 src/nextjournal/markdown/parser.bb
 rename bb/stubs/nextjournal/markdown/transform.clj => src/nextjournal/markdown/transform.bb (50%)

diff --git a/bb/stubs/multihash/core.clj b/bb/stubs/multihash/core.clj
deleted file mode 100644
index bf30c73ee..000000000
--- a/bb/stubs/multihash/core.clj
+++ /dev/null
@@ -1,3 +0,0 @@
-(ns multihash.core)
-
-(defn base58 [h] "base58")
diff --git a/bb/stubs/multihash/digest.clj b/bb/stubs/multihash/digest.clj
deleted file mode 100644
index c722b226e..000000000
--- a/bb/stubs/multihash/digest.clj
+++ /dev/null
@@ -1,3 +0,0 @@
-(ns multihash.digest)
-
-(defn sha2-512 [o] "sha2")
diff --git a/bb/stubs/nextjournal/beholder.clj b/bb/stubs/nextjournal/beholder.clj
deleted file mode 100644
index 72b31f72e..000000000
--- a/bb/stubs/nextjournal/beholder.clj
+++ /dev/null
@@ -1,4 +0,0 @@
-(ns nextjournal.beholder)
-
-(defn watch [cb & args] nil)
-(defn stop [w] nil)
diff --git a/bb/stubs/nextjournal/clerk/analyzer.clj b/bb/stubs/nextjournal/clerk/analyzer.clj
deleted file mode 100644
index 2a007c793..000000000
--- a/bb/stubs/nextjournal/clerk/analyzer.clj
+++ /dev/null
@@ -1,41 +0,0 @@
-(ns nextjournal.clerk.analyzer
-  (:require [nextjournal.clerk.config :as config]
-            [edamame.core :as edamame]))
-
-(defn valuehash [value] "hash")
-(defn hash-codeblock [_ {:keys [hash]}] hash)
-(defn ->hash-str [value] "hash-str")
-(defn deref? [form] false)
-(defn hash [doc] doc)
-(defn hash-deref-deps [doc _cell] doc)
-
-(defn build-graph [doc]
-   (-> doc
-       (assoc :->analysis-info (fn [x] {:form x}))
-       ;; TODO: read first form, create sci.lang.Namespace
-       (assoc :ns *ns*)
-       (update :blocks
-               (partial into [] (map (fn [{:as b :keys [type text]}]
-                                       (cond-> b
-                                         (= :code type)
-                                         (assoc :form
-                                                (edamame/parse-string text
-                                                                      {:all true
-                                                                       :readers *data-readers*
-                                                                       :read-cond :allow
-                                                                       :regex #(list `re-pattern %)
-                                                                       :features #{:clj}
-                                                                       ;; TODO:
-                                                                       #_#_:auto-resolve (auto-resolves (or *ns* (find-ns 'user)))})))))))))
-
-(defn exceeds-bounded-count-limit? [x]
-  (reduce (fn [_ xs]
-            (try
-              (let [limit config/*bounded-count-limit*]
-                (if (and (seqable? xs) (<= limit (bounded-count limit xs)))
-                  (reduced true)
-                  false))
-              (catch Exception _e
-                (reduced true))))
-          false
-          (tree-seq seqable? seq x)))
diff --git a/bb/stubs/nextjournal/markdown.clj b/bb/stubs/nextjournal/markdown.clj
deleted file mode 100644
index 6bef596bd..000000000
--- a/bb/stubs/nextjournal/markdown.clj
+++ /dev/null
@@ -1,3 +0,0 @@
-(ns nextjournal.markdown)
-
-(defn parse [md] {:type :doc :content md})
diff --git a/bb/stubs/nextjournal/markdown/parser.clj b/bb/stubs/nextjournal/markdown/parser.clj
deleted file mode 100644
index 55a8c459b..000000000
--- a/bb/stubs/nextjournal/markdown/parser.clj
+++ /dev/null
@@ -1,3 +0,0 @@
-(ns nextjournal.markdown.parser)
-
-(defn add-title+toc [doc] doc)
diff --git a/bb/stubs/taoensso/nippy.clj b/bb/stubs/taoensso/nippy.clj
deleted file mode 100644
index e9ce3e8e1..000000000
--- a/bb/stubs/taoensso/nippy.clj
+++ /dev/null
@@ -1,5 +0,0 @@
-(ns taoensso.nippy)
-
-(defn freezable? [x] false)
-(defn freeze [x] x)
-(defn thaw-from-file [file] "thawed")
diff --git a/resources/viewer-js-hash b/resources/viewer-js-hash
index 87ead369c..58daa8e5c 100644
--- a/resources/viewer-js-hash
+++ b/resources/viewer-js-hash
@@ -1 +1 @@
-QHueRFEbfs7jTLGUVfX7SnJvJoo
\ No newline at end of file
+3iQsRk6fdHXvMb1dcpPuwPdat3ya
\ No newline at end of file
diff --git a/src/nextjournal/beholder.bb b/src/nextjournal/beholder.bb
new file mode 100644
index 000000000..e6d96e0c9
--- /dev/null
+++ b/src/nextjournal/beholder.bb
@@ -0,0 +1,5 @@
+(ns nextjournal.beholder
+  "Babashka runtime no-op stubs")
+
+(defn watch [cb & args] nil)
+(defn stop [w] nil)
diff --git a/src/nextjournal/clerk.cljc b/src/nextjournal/clerk.clj
similarity index 100%
rename from src/nextjournal/clerk.cljc
rename to src/nextjournal/clerk.clj
diff --git a/src/nextjournal/clerk/analyzer.bb b/src/nextjournal/clerk/analyzer.bb
new file mode 100644
index 000000000..3fbe94d7a
--- /dev/null
+++ b/src/nextjournal/clerk/analyzer.bb
@@ -0,0 +1,6 @@
+(ns nextjournal.clerk.analyzer
+  "Babashka runtime no-op stubs")
+
+;; TODO: consider using this in eval
+(defn valuehash [val] "valuehash")
+(defn ->hash-str [val] (valuehash val))
diff --git a/src/nextjournal/clerk/builder.clj b/src/nextjournal/clerk/builder.clj
index 126b50f3e..fa9d47efc 100644
--- a/src/nextjournal/clerk/builder.clj
+++ b/src/nextjournal/clerk/builder.clj
@@ -2,9 +2,7 @@
   "Clerk's Static App Builder."
   (:require [babashka.fs :as fs]
             [clojure.java.browse :as browse]
-            [clojure.set :as set]
             [clojure.string :as str]
-            [nextjournal.clerk.analyzer :as analyzer]
             [nextjournal.clerk.builder-ui :as builder-ui]
             [nextjournal.clerk.eval :as eval]
             [nextjournal.clerk.parser :as parser]
@@ -197,7 +195,7 @@
         {state :result duration :time-ms} (eval/time-ms (mapv (comp (partial parser/parse-file {:doc? true}) :file) state))
         _ (report-fn {:stage :parsed :state state :duration duration})
         {state :result duration :time-ms} (eval/time-ms (reduce (fn [state doc]
-                                                                  (try (conj state (-> doc analyzer/build-graph analyzer/hash))
+                                                                  (try (conj state (eval/analyze-doc doc))
                                                                        (catch Exception e
                                                                          (reduced {:error e}))))
                                                                 []
diff --git a/src/nextjournal/clerk/eval.bb b/src/nextjournal/clerk/eval.bb
new file mode 100644
index 000000000..bef482670
--- /dev/null
+++ b/src/nextjournal/clerk/eval.bb
@@ -0,0 +1,149 @@
+(ns nextjournal.clerk.eval
+  "Clerk's incremental evaluation with in-memory and disk-persisted caching layers."
+  (:require [babashka.fs :as fs]
+            [clojure.java.io :as io]
+            [edamame.core :as edamame]
+            [nextjournal.clerk.config :as config]
+            [nextjournal.clerk.parser :as parser]
+            [nextjournal.clerk.viewer :as v]))
+
+(defn wrapped-with-metadata [value hash]
+  (cond-> {:nextjournal/value value}
+    ;; TODO: maybe fix hash for blob serving
+    hash (assoc :nextjournal/blob-id (cond-> hash (not (string? hash)) str #_ multihash/base58))))
+
+#_(wrap-with-blob-id :test "foo")
+
+(defn elapsed-ms [from]
+  (/ (double (- (. System (nanoTime)) from)) 1000000.0))
+
+(defmacro time-ms
+  "Pure version of `clojure.core/time`. Returns a map with `:result` and `:time-ms` keys."
+  [expr]
+  `(let [start# (System/nanoTime)
+         ret# ~expr]
+     {:result ret#
+      :time-ms (elapsed-ms start#)}))
+
+(defn ^:private var-from-def [var]
+  (let [resolved-var (cond (var? var)
+                           var
+
+                           (symbol? var)
+                           (find-var var)
+
+                           :else
+                           (throw (ex-info "Unable to resolve into a variable" {:data var})))]
+    {:nextjournal.clerk/var-from-def resolved-var}))
+
+(defn ^:private eval-form [{:keys [form var ns-effect? no-cache?]} hash]
+  (try
+    (let [{:keys [result]} (time-ms (binding [config/*in-clerk* true]
+                                      (eval form)))
+          result (if (and (nil? result) var (= 'defonce (first form)))
+                   (find-var var)
+                   result)
+          var-value (cond-> result (and var (var? result)) deref)
+          no-cache? (or ns-effect? no-cache? config/cache-disabled?)]
+      (let [blob-id (cond no-cache? "valuehash" #_#_ TODO?/valuehash (analyzer/->hash-str var-value)
+                          (fn? var-value) nil
+                          :else hash)
+            result (if var (var-from-def var) result)]
+        (wrapped-with-metadata result blob-id)))
+    (catch Throwable t
+      (throw (ex-info (ex-message t) (Throwable->map t))))))
+
+(defn maybe-eval-viewers [{:as opts :nextjournal/keys [viewer viewers]}]
+  (cond-> opts
+    viewer
+    (update :nextjournal/viewer eval)
+    viewers
+    (update :nextjournal/viewers eval)))
+
+(defn read+eval-cached [{:as _doc :keys [blob->result]} {:as codeblock :keys [form vars var ns-effect? no-cache?]}]
+  (let [no-cache? (or ns-effect? no-cache?)
+        ;; TODO: hash for in-memory cache
+        hash (str (gensym))
+        opts-from-form-meta (-> (meta form)
+                                (select-keys [:nextjournal.clerk/viewer :nextjournal.clerk/viewers :nextjournal.clerk/width :nextjournal.clerk/opts])
+                                v/normalize-viewer-opts
+                                maybe-eval-viewers)]
+    (cond-> (or (when-let [cached-result (and (not no-cache?) (get-in blob->result [hash :nextjournal/value]))]
+                  (wrapped-with-metadata cached-result hash))
+                (eval-form codeblock hash))
+      (seq opts-from-form-meta)
+      (merge opts-from-form-meta))))
+
+#_(show! "notebooks/scratch_cache.clj")
+
+#_(eval-file "notebooks/test123.clj")
+#_(eval-file "notebooks/how_clerk_works.clj")
+
+;; no-op for public access from builder
+(defn analyze-doc [doc] doc)
+
+(defn eval-analyzed-doc [{:as analyzed-doc :keys [->hash blocks]}]
+  (let [{:as evaluated-doc :keys [blob-ids]}
+        (reduce (fn [state {:as cell :keys [type]}]
+                  (let [{:as result :nextjournal/keys [blob-id]} (when (= :code type) (read+eval-cached state cell))]
+                    (cond-> (update state :blocks conj (cond-> cell result (assoc :result result)))
+                      blob-id (update :blob-ids conj blob-id)
+                      blob-id (assoc-in [:blob->result blob-id] result))))
+                (assoc analyzed-doc :blocks [] :blob-ids #{})
+                blocks)]
+    (-> evaluated-doc
+        (update :blob->result select-keys blob-ids)
+        (dissoc :blob-ids))))
+
+(defn read-forms [doc]
+  (-> doc
+      ;; TODO: read first form, create sci.lang.Namespace and eval ns-effects
+      ;; TODO: restore var, vars
+      (assoc :ns *ns*)
+      (update :blocks
+              (partial into [] (map (fn [{:as b :keys [type text]}]
+                                      (cond-> b
+                                        (= :code type)
+                                        (assoc :form
+                                               (edamame/parse-string text
+                                                                     {:all true
+                                                                      :readers *data-readers*
+                                                                      :read-cond :allow
+                                                                      :regex #(list `re-pattern %)
+                                                                      :features #{:clj}
+                                                                      ;; TODO:
+                                                                      #_#_:auto-resolve (auto-resolves (or *ns* (find-ns 'user)))})))))))))
+
+(defn +eval-results
+  "Evaluates the given `parsed-doc` using the `in-memory-cache` and augments it with the results."
+  [in-memory-cache parsed-doc]
+  (let [{:as doc :keys [ns]} (read-forms parsed-doc)]
+    (binding [*ns* (or ns *ns*)]
+      (-> doc
+          (assoc :blob->result in-memory-cache)
+          eval-analyzed-doc))))
+
+(defn eval-doc
+  "Evaluates the given `doc`."
+  ([doc] (eval-doc {} doc))
+  ([in-memory-cache doc] (+eval-results in-memory-cache doc)))
+
+(defn eval-file
+  "Reads given `file` (using `slurp`) and evaluates it."
+  ([file] (eval-file {} file))
+  ([in-memory-cache file]
+   (->> file
+        (parser/parse-file {:doc? true})
+        (eval-doc in-memory-cache))))
+
+#_(eval-file "notebooks/hello.clj")
+#_(eval-file "notebooks/rule_30.clj")
+#_(eval-file "notebooks/visibility.clj")
+
+(defn eval-string
+  "Evaluated the given `code-string` using the optional `in-memory-cache` map."
+  ([code-string] (eval-string {} code-string))
+  ([in-memory-cache code-string]
+   (eval-doc in-memory-cache (parser/parse-clojure-string {:doc? true} code-string))))
+
+#_(eval-string "(+ 39 3)")
diff --git a/src/nextjournal/clerk/eval.cljc b/src/nextjournal/clerk/eval.clj
similarity index 91%
rename from src/nextjournal/clerk/eval.cljc
rename to src/nextjournal/clerk/eval.clj
index 99723bab1..9b0541f9e 100644
--- a/src/nextjournal/clerk/eval.cljc
+++ b/src/nextjournal/clerk/eval.clj
@@ -11,9 +11,8 @@
             [nextjournal.clerk.parser :as parser]
             [nextjournal.clerk.viewer :as v]
             [taoensso.nippy :as nippy])
-  #?(:bb (:import)
-     :clj (:import (java.awt.image BufferedImage)
-                   (javax.imageio ImageIO))))
+  (:import (java.awt.image BufferedImage)
+           (javax.imageio ImageIO)))
 
 (comment
   (alter-var-root #'nippy/*freeze-serializable-allowlist* (fn [_] "allow-and-record"))
@@ -21,11 +20,9 @@
   (nippy/get-recorded-serializable-classes))
 
 ;; nippy tweaks
-#?(:bb nil
-   :clj (do
-          (alter-var-root #'nippy/*thaw-serializable-allowlist* (fn [_] (conj nippy/default-thaw-serializable-allowlist "java.io.File" "clojure.lang.Var" "clojure.lang.Namespace")))
-          (nippy/extend-freeze BufferedImage :java.awt.image.BufferedImage [x out] (ImageIO/write x "png" (ImageIO/createImageOutputStream out)))
-          (nippy/extend-thaw :java.awt.image.BufferedImage [in] (ImageIO/read in))))
+(alter-var-root #'nippy/*thaw-serializable-allowlist* (fn [_] (conj nippy/default-thaw-serializable-allowlist "java.io.File" "clojure.lang.Var" "clojure.lang.Namespace")))
+(nippy/extend-freeze BufferedImage :java.awt.image.BufferedImage [x out] (ImageIO/write x "png" (ImageIO/createImageOutputStream out)))
+(nippy/extend-thaw :java.awt.image.BufferedImage [in] (ImageIO/read in))
 
 #_(-> [(clojure.java.io/file "notebooks") (find-ns 'user)] nippy/freeze nippy/thaw)
 
@@ -110,10 +107,6 @@
       #_(prn :freeze-error e)
       nil)))
 
-;; NOTE: cannot add clojure.main to bb stubs
-(defn ex-triage [m] #?(:bb m :clj (main/ex-triage m)))
-(defn ex-str [m] #?(:bb (str m) :clj (main/ex-str m)))
-
 (defn ^:private eval+cache! [{:keys [form var ns-effect? no-cache? freezable?] :as form-info} hash digest-file]
   (try
     (let [{:keys [result]} (time-ms (binding [config/*in-clerk* true]
@@ -135,8 +128,8 @@
                      result)]
         (wrapped-with-metadata result blob-id)))
     (catch Throwable t
-      (let [triaged (ex-triage (Throwable->map t))]
-        (throw (ex-info (ex-str triaged) triaged))))))
+      (let [triaged (main/ex-triage (Throwable->map t))]
+        (throw (ex-info (main/ex-str triaged) triaged))))))
 
 (defn maybe-eval-viewers [{:as opts :nextjournal/keys [viewer viewers]}]
   (cond-> opts
@@ -199,11 +192,14 @@
         (update :blob->result select-keys blob-ids)
         (dissoc :blob-ids))))
 
+;; TODO: used in builder to drop analyzer dependency, cfr. below
+(defn analyze-doc [doc] (-> doc analyzer/build-graph analyzer/hash))
+
 (defn +eval-results
   "Evaluates the given `parsed-doc` using the `in-memory-cache` and augments it with the results."
   [in-memory-cache parsed-doc]
   (let [{:as analyzed-doc :keys [ns]} (analyzer/build-graph parsed-doc)]
-    (binding [*ns* (or ns *ns*)]
+    (binding [*ns* ns]
       (-> analyzed-doc
           analyzer/hash
           (assoc :blob->result in-memory-cache)
@@ -233,4 +229,3 @@
    (eval-doc in-memory-cache (parser/parse-clojure-string {:doc? true} code-string))))
 
 #_(eval-string "(+ 39 3)")
-
diff --git a/src/nextjournal/markdown.bb b/src/nextjournal/markdown.bb
new file mode 100644
index 000000000..491da7063
--- /dev/null
+++ b/src/nextjournal/markdown.bb
@@ -0,0 +1,4 @@
+(ns nextjournal.markdown
+  "Babashka runtime stubs")
+
+(defn parse [md] {:type :doc :content md})
diff --git a/src/nextjournal/markdown/parser.bb b/src/nextjournal/markdown/parser.bb
new file mode 100644
index 000000000..932d45342
--- /dev/null
+++ b/src/nextjournal/markdown/parser.bb
@@ -0,0 +1,4 @@
+(ns nextjournal.markdown.parser
+  "Babashka runtime no-op stubs")
+
+(defn add-title+toc [doc] doc)
diff --git a/bb/stubs/nextjournal/markdown/transform.clj b/src/nextjournal/markdown/transform.bb
similarity index 50%
rename from bb/stubs/nextjournal/markdown/transform.clj
rename to src/nextjournal/markdown/transform.bb
index 28968dfc7..c4585c0a4 100644
--- a/bb/stubs/nextjournal/markdown/transform.clj
+++ b/src/nextjournal/markdown/transform.bb
@@ -1,4 +1,5 @@
-(ns nextjournal.markdown.transform)
+(ns nextjournal.markdown.transform
+  "Babashka runtime stubs")
 
 (defn ->text [node] "text")
 (defn table-alignment [attrs] {})

From 1493d7be715f3e5a2d3ed13652132b60b49a91e0 Mon Sep 17 00:00:00 2001
From: Andrea Amantini <lo.zampino@gmail.com>
Date: Wed, 19 Oct 2022 12:05:06 +0200
Subject: [PATCH 07/17] Pass cli args to bb task

---
 bb-runtime.edn                    | 5 +++--
 resources/viewer-js-hash          | 2 +-
 src/nextjournal/clerk/eval.bb     | 6 ++----
 src/nextjournal/clerk/viewer.cljc | 6 +++---
 4 files changed, 9 insertions(+), 10 deletions(-)

diff --git a/bb-runtime.edn b/bb-runtime.edn
index 43fadb4b7..ce6651ce4 100644
--- a/bb-runtime.edn
+++ b/bb-runtime.edn
@@ -5,10 +5,11 @@
  {clerk
   {:requires ([babashka.fs :as fs]
               [babashka.nrepl.server :as srv]
-              [nextjournal.clerk :as clerk])
+              [nextjournal.clerk :as clerk]
+              [babashka.cli :as cli])
    :task (do (srv/start-server! {:host "localhost" :port 1339})
              (spit ".nrepl-port" "1339")
-             (clerk/serve! {:port 9999})
+             (clerk/serve! (cli/parse-opts *command-line-args*))
              (-> (Runtime/getRuntime)
                (.addShutdownHook (Thread. (fn []
                                             (clerk/halt!)
diff --git a/resources/viewer-js-hash b/resources/viewer-js-hash
index 58daa8e5c..786f4b0ae 100644
--- a/resources/viewer-js-hash
+++ b/resources/viewer-js-hash
@@ -1 +1 @@
-3iQsRk6fdHXvMb1dcpPuwPdat3ya
\ No newline at end of file
+3DvNBfsJZstwCXFtQehkuSfLP5xH
\ No newline at end of file
diff --git a/src/nextjournal/clerk/eval.bb b/src/nextjournal/clerk/eval.bb
index bef482670..02508bf32 100644
--- a/src/nextjournal/clerk/eval.bb
+++ b/src/nextjournal/clerk/eval.bb
@@ -1,8 +1,6 @@
 (ns nextjournal.clerk.eval
-  "Clerk's incremental evaluation with in-memory and disk-persisted caching layers."
-  (:require [babashka.fs :as fs]
-            [clojure.java.io :as io]
-            [edamame.core :as edamame]
+  "Clerk's incremental evaluation (Babashka Edition) with in-memory caching layer."
+  (:require [edamame.core :as edamame]
             [nextjournal.clerk.config :as config]
             [nextjournal.clerk.parser :as parser]
             [nextjournal.clerk.viewer :as v]))
diff --git a/src/nextjournal/clerk/viewer.cljc b/src/nextjournal/clerk/viewer.cljc
index 82e1b4373..8aff6d5d0 100644
--- a/src/nextjournal/clerk/viewer.cljc
+++ b/src/nextjournal/clerk/viewer.cljc
@@ -469,8 +469,7 @@
 #?(:clj
    (defn datafy-scope [scope]
      (cond
-       (instance? clojure.lang.Namespace scope)
-       {:namespace (-> scope str keyword)}
+       (instance? clojure.lang.Namespace scope) {:namespace (-> scope str keyword)}
        (keyword? scope) scope
        :else (throw (ex-info (str "Unsupported scope " scope) {:scope scope})))))
 
@@ -625,7 +624,8 @@
                                     :render-fn '(fn [blob] (v/html [:figure.flex.flex-col.items-center.not-prose [:img {:src (v/url-for blob)}]]))}))
 
 (def ideref-viewer
-  #?(:bb {} :clj
+  #?(:bb {}
+     :clj
      {:pred #(instance? IDeref %)
       :transform-fn (update-val (fn [ideref]
                                   (with-viewer :tagged-value

From 840659118fe2ec9f03576ed8a8e90ec9f328b7ad Mon Sep 17 00:00:00 2001
From: Andrea Amantini <lo.zampino@gmail.com>
Date: Wed, 19 Oct 2022 14:53:32 +0200
Subject: [PATCH 08/17] Fix add-viewers! and auto-resolve of ::alias keywords

---
 src/nextjournal/clerk/eval.bb | 49 +++++++++++++++++++++--------------
 1 file changed, 30 insertions(+), 19 deletions(-)

diff --git a/src/nextjournal/clerk/eval.bb b/src/nextjournal/clerk/eval.bb
index 02508bf32..b33dcc430 100644
--- a/src/nextjournal/clerk/eval.bb
+++ b/src/nextjournal/clerk/eval.bb
@@ -1,5 +1,6 @@
 (ns nextjournal.clerk.eval
   "Clerk's incremental evaluation (Babashka Edition) with in-memory caching layer."
+  (:refer-clojure :exclude [read-string])
   (:require [edamame.core :as edamame]
             [nextjournal.clerk.config :as config]
             [nextjournal.clerk.parser :as parser]
@@ -34,7 +35,7 @@
                            (throw (ex-info "Unable to resolve into a variable" {:data var})))]
     {:nextjournal.clerk/var-from-def resolved-var}))
 
-(defn ^:private eval-form [{:keys [form var ns-effect? no-cache?]} hash]
+(defn ^:private eval-form [{:keys [form var no-cache?]} hash]
   (try
     (let [{:keys [result]} (time-ms (binding [config/*in-clerk* true]
                                       (eval form)))
@@ -42,7 +43,7 @@
                    (find-var var)
                    result)
           var-value (cond-> result (and var (var? result)) deref)
-          no-cache? (or ns-effect? no-cache? config/cache-disabled?)]
+          no-cache? (or no-cache? config/cache-disabled?)]
       (let [blob-id (cond no-cache? "valuehash" #_#_ TODO?/valuehash (analyzer/->hash-str var-value)
                           (fn? var-value) nil
                           :else hash)
@@ -93,24 +94,34 @@
         (update :blob->result select-keys blob-ids)
         (dissoc :blob-ids))))
 
+(defn read-string [s]
+  (edamame/parse-string s
+                        {:all true
+                         :readers *data-readers*
+                         :read-cond :allow
+                         :regex #(list `re-pattern %)
+                         :features #{:clj}
+                         :auto-resolve (as-> (ns-aliases (or *ns* (find-ns 'user))) $
+                                         (zipmap (keys $) (map ns-name (vals $)))
+                                         (assoc $ :current (ns-name *ns*)))}))
+
 (defn read-forms [doc]
-  (-> doc
-      ;; TODO: read first form, create sci.lang.Namespace and eval ns-effects
-      ;; TODO: restore var, vars
-      (assoc :ns *ns*)
-      (update :blocks
-              (partial into [] (map (fn [{:as b :keys [type text]}]
-                                      (cond-> b
-                                        (= :code type)
-                                        (assoc :form
-                                               (edamame/parse-string text
-                                                                     {:all true
-                                                                      :readers *data-readers*
-                                                                      :read-cond :allow
-                                                                      :regex #(list `re-pattern %)
-                                                                      :features #{:clj}
-                                                                      ;; TODO:
-                                                                      #_#_:auto-resolve (auto-resolves (or *ns* (find-ns 'user)))})))))))))
+  (binding [*ns* *ns*]
+    (reduce (fn [doc {:as b :keys [type text]}]
+              (let [form (read-string text)
+                    ns? (= 'ns (when (list? form) (first form)))]
+                (when ns? (eval form))
+                (-> doc
+                    (cond-> (and ns? (not (:ns doc))) (assoc :ns *ns*))
+                    (update :blocks conj
+                            (cond-> b
+                              (= :code type) (assoc :form form)
+                              ns? (assoc :no-cache? true))))))
+            (assoc doc :blocks [])
+            (:blocks doc))))
+
+#_(read-forms
+   (parser/parse-file "notebooks/hello.clj"))
 
 (defn +eval-results
   "Evaluates the given `parsed-doc` using the `in-memory-cache` and augments it with the results."

From e5ce7ab5f77327ea08cbde36cfcc6a49ccf01b5c Mon Sep 17 00:00:00 2001
From: Andrea Amantini <lo.zampino@gmail.com>
Date: Wed, 19 Oct 2022 16:00:08 +0200
Subject: [PATCH 09/17] Extract var from def

---
 resources/viewer-js-hash          |  2 +-
 src/nextjournal/clerk/eval.bb     | 20 +++++++++++---------
 src/nextjournal/clerk/viewer.cljc |  2 +-
 3 files changed, 13 insertions(+), 11 deletions(-)

diff --git a/resources/viewer-js-hash b/resources/viewer-js-hash
index 786f4b0ae..abe47eb89 100644
--- a/resources/viewer-js-hash
+++ b/resources/viewer-js-hash
@@ -1 +1 @@
-3DvNBfsJZstwCXFtQehkuSfLP5xH
\ No newline at end of file
+3KYTPPtm8ocErseHCqJNzLEUsByx
\ No newline at end of file
diff --git a/src/nextjournal/clerk/eval.bb b/src/nextjournal/clerk/eval.bb
index b33dcc430..7e6cc75ad 100644
--- a/src/nextjournal/clerk/eval.bb
+++ b/src/nextjournal/clerk/eval.bb
@@ -1,7 +1,8 @@
 (ns nextjournal.clerk.eval
   "Clerk's incremental evaluation (Babashka Edition) with in-memory caching layer."
   (:refer-clojure :exclude [read-string])
-  (:require [edamame.core :as edamame]
+  (:require [clojure.string :as str]
+            [edamame.core :as edamame]
             [nextjournal.clerk.config :as config]
             [nextjournal.clerk.parser :as parser]
             [nextjournal.clerk.viewer :as v]))
@@ -73,15 +74,10 @@
       (seq opts-from-form-meta)
       (merge opts-from-form-meta))))
 
-#_(show! "notebooks/scratch_cache.clj")
-
-#_(eval-file "notebooks/test123.clj")
-#_(eval-file "notebooks/how_clerk_works.clj")
-
 ;; no-op for public access from builder
 (defn analyze-doc [doc] doc)
 
-(defn eval-analyzed-doc [{:as analyzed-doc :keys [->hash blocks]}]
+(defn eval-analyzed-doc [{:as analyzed-doc :keys [blocks]}]
   (let [{:as evaluated-doc :keys [blob-ids]}
         (reduce (fn [state {:as cell :keys [type]}]
                   (let [{:as result :nextjournal/keys [blob-id]} (when (= :code type) (read+eval-cached state cell))]
@@ -105,18 +101,24 @@
                                          (zipmap (keys $) (map ns-name (vals $)))
                                          (assoc $ :current (ns-name *ns*)))}))
 
+(defn deflike? [form] (and (seq? form) (symbol? (first form)) (str/starts-with? (name (first form)) "def")))
+#_(deflike? (read-string "(def ^{:doc \"aloha\"} foo 123)"))
+#_(deflike? (read-string "(def ^{:doc \"aloha\"} foo 123)"))
+
 (defn read-forms [doc]
   (binding [*ns* *ns*]
     (reduce (fn [doc {:as b :keys [type text]}]
               (let [form (read-string text)
-                    ns? (= 'ns (when (list? form) (first form)))]
+                    ns? (= 'ns (when (list? form) (first form)))
+                    var (when (and (deflike? form) (symbol? (second form))) (second form))]
                 (when ns? (eval form))
                 (-> doc
                     (cond-> (and ns? (not (:ns doc))) (assoc :ns *ns*))
                     (update :blocks conj
                             (cond-> b
                               (= :code type) (assoc :form form)
-                              ns? (assoc :no-cache? true))))))
+                              ns? (assoc :no-cache? true)
+                              var (assoc :var (symbol (name (ns-name *ns*)) (name var))))))))
             (assoc doc :blocks [])
             (:blocks doc))))
 
diff --git a/src/nextjournal/clerk/viewer.cljc b/src/nextjournal/clerk/viewer.cljc
index 8aff6d5d0..d69992dfe 100644
--- a/src/nextjournal/clerk/viewer.cljc
+++ b/src/nextjournal/clerk/viewer.cljc
@@ -668,7 +668,7 @@
 (def markdown-viewer
   (-> {:name :markdown}
       #?(:bb  (assoc :transform-fn (comp mark-presented (update-val :content))
-                     :render-fn '(fn [str] (js/console.log :str str) (v/html (v/md->hiccup str))))
+                     :render-fn '(fn [str] (v/html (v/md->hiccup str))))
          :clj (assoc :transform-fn
                      (fn [wrapped-value]
                        (-> wrapped-value

From a4b37384219ab0f76aa59b1aa5a214f80bb3810d Mon Sep 17 00:00:00 2001
From: Andrea Amantini <lo.zampino@gmail.com>
Date: Wed, 19 Oct 2022 16:26:49 +0200
Subject: [PATCH 10/17] Fix static builder in bb runtime

---
 src/nextjournal/clerk/eval.bb | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/src/nextjournal/clerk/eval.bb b/src/nextjournal/clerk/eval.bb
index 7e6cc75ad..850e3ce66 100644
--- a/src/nextjournal/clerk/eval.bb
+++ b/src/nextjournal/clerk/eval.bb
@@ -74,10 +74,7 @@
       (seq opts-from-form-meta)
       (merge opts-from-form-meta))))
 
-;; no-op for public access from builder
-(defn analyze-doc [doc] doc)
-
-(defn eval-analyzed-doc [{:as analyzed-doc :keys [blocks]}]
+(defn eval-analyzed-doc [{:as analyzed-doc :keys [ns blocks]}]
   (let [{:as evaluated-doc :keys [blob-ids]}
         (reduce (fn [state {:as cell :keys [type]}]
                   (let [{:as result :nextjournal/keys [blob-id]} (when (= :code type) (read+eval-cached state cell))]
@@ -87,6 +84,7 @@
                 (assoc analyzed-doc :blocks [] :blob-ids #{})
                 blocks)]
     (-> evaluated-doc
+        (cond-> (not ns) (assoc :ns (find-ns 'user)))
         (update :blob->result select-keys blob-ids)
         (dissoc :blob-ids))))
 
@@ -125,6 +123,9 @@
 #_(read-forms
    (parser/parse-file "notebooks/hello.clj"))
 
+;; used in builder
+(def analyze-doc read-forms)
+
 (defn +eval-results
   "Evaluates the given `parsed-doc` using the `in-memory-cache` and augments it with the results."
   [in-memory-cache parsed-doc]

From a642887da479ba7e56bbd0d79f36ca3a033eaccc Mon Sep 17 00:00:00 2001
From: Andrea Amantini <lo.zampino@gmail.com>
Date: Wed, 19 Oct 2022 16:45:07 +0200
Subject: [PATCH 11/17] Fix markdown viewer for cljs consumption

---
 resources/viewer-js-hash          |  2 +-
 src/nextjournal/clerk/viewer.cljc | 16 ++++++++--------
 2 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/resources/viewer-js-hash b/resources/viewer-js-hash
index abe47eb89..f53aff06c 100644
--- a/resources/viewer-js-hash
+++ b/resources/viewer-js-hash
@@ -1 +1 @@
-3KYTPPtm8ocErseHCqJNzLEUsByx
\ No newline at end of file
+3dJJyLHsUmEC71T4CnGbFunsr74R
\ No newline at end of file
diff --git a/src/nextjournal/clerk/viewer.cljc b/src/nextjournal/clerk/viewer.cljc
index d69992dfe..c5288f888 100644
--- a/src/nextjournal/clerk/viewer.cljc
+++ b/src/nextjournal/clerk/viewer.cljc
@@ -667,15 +667,15 @@
 
 (def markdown-viewer
   (-> {:name :markdown}
-      #?(:bb  (assoc :transform-fn (comp mark-presented (update-val :content))
+      #?(:bb  (assoc :transform-fn (comp mark-presented (update-val #(cond-> % (map? %) :content)))
                      :render-fn '(fn [str] (v/html (v/md->hiccup str))))
-         :clj (assoc :transform-fn
-                     (fn [wrapped-value]
-                       (-> wrapped-value
-                           mark-presented
-                           (update :nextjournal/value #(cond->> % (string? %) md/parse))
-                           (update :nextjournal/viewers add-viewers markdown-viewers)
-                           (with-md-viewer)))))))
+         :default (assoc :transform-fn
+                         (fn [wrapped-value]
+                           (-> wrapped-value
+                               mark-presented
+                               (update :nextjournal/value #(cond->> % (string? %) md/parse))
+                               (update :nextjournal/viewers add-viewers markdown-viewers)
+                               (with-md-viewer)))))))
 
 (def code-viewer
   {:name :code :render-fn (quote v/code-viewer) :transform-fn (comp mark-presented (update-val (fn [v] (if (string? v) v (str/trim (with-out-str (pprint/pprint v)))))))})

From b6bd4c402b6ff831ca8d54f1b4d3e7d9e9bef5e1 Mon Sep 17 00:00:00 2001
From: Andrea Amantini <lo.zampino@gmail.com>
Date: Wed, 19 Oct 2022 17:40:17 +0200
Subject: [PATCH 12/17] Add build bb task

---
 bb-runtime.edn | 15 +++++++++++----
 1 file changed, 11 insertions(+), 4 deletions(-)

diff --git a/bb-runtime.edn b/bb-runtime.edn
index ce6651ce4..94321aac5 100644
--- a/bb-runtime.edn
+++ b/bb-runtime.edn
@@ -1,8 +1,9 @@
 {:min-bb-version "1.0.164"
- :paths ["bb/stubs" "src" "notebooks" "resources"]
- :deps {hiccup/hiccup {:mvn/version "2.0.0-alpha2"}}
+ :paths ["src" "notebooks" "resources"]
+ :deps {hiccup/hiccup {:mvn/version "2.0.0-alpha2"}
+        org.babashka/cli {:mvn/version "0.5.40"}}
  :tasks
- {clerk
+ {dev
   {:requires ([babashka.fs :as fs]
               [babashka.nrepl.server :as srv]
               [nextjournal.clerk :as clerk]
@@ -14,4 +15,10 @@
                (.addShutdownHook (Thread. (fn []
                                             (clerk/halt!)
                                             (fs/delete ".nrepl-port")))))
-             (deref (promise)))}}}
+             (deref (promise)))}
+
+  build
+  {:requires ([nextjournal.clerk :as clerk]
+              [babashka.cli :as cli])
+   :task (let [spec (-> (resolve 'nextjournal.clerk/build!) meta :org.babashka/cli)]
+           (clerk/build! (cli/parse-opts *command-line-args* spec)))}}}

From 7c95f89cf3771b8aa0a984fb7dcc56fbaf746c54 Mon Sep 17 00:00:00 2001
From: Andrea Amantini <lo.zampino@gmail.com>
Date: Thu, 20 Oct 2022 13:02:14 +0200
Subject: [PATCH 13/17] Implement no-cache?

---
 src/nextjournal/clerk/eval.bb | 13 ++++++++++---
 1 file changed, 10 insertions(+), 3 deletions(-)

diff --git a/src/nextjournal/clerk/eval.bb b/src/nextjournal/clerk/eval.bb
index 850e3ce66..28ad406f3 100644
--- a/src/nextjournal/clerk/eval.bb
+++ b/src/nextjournal/clerk/eval.bb
@@ -62,8 +62,7 @@
 
 (defn read+eval-cached [{:as _doc :keys [blob->result]} {:as codeblock :keys [form vars var ns-effect? no-cache?]}]
   (let [no-cache? (or ns-effect? no-cache?)
-        ;; TODO: hash for in-memory cache
-        hash (str (gensym))
+        hash (.encodeToString (java.util.Base64/getEncoder) (.getBytes (str form)))
         opts-from-form-meta (-> (meta form)
                                 (select-keys [:nextjournal.clerk/viewer :nextjournal.clerk/viewers :nextjournal.clerk/width :nextjournal.clerk/opts])
                                 v/normalize-viewer-opts
@@ -102,6 +101,14 @@
 (defn deflike? [form] (and (seq? form) (symbol? (first form)) (str/starts-with? (name (first form)) "def")))
 #_(deflike? (read-string "(def ^{:doc \"aloha\"} foo 123)"))
 #_(deflike? (read-string "(def ^{:doc \"aloha\"} foo 123)"))
+(defn no-cache-from-meta [form]
+  (when (contains? (meta form) :nextjournal.clerk/no-cache)
+    (-> form meta :nextjournal.clerk/no-cache)))
+(defn no-cache? [& subjects] (or (some no-cache-from-meta subjects) false))
+(defn deref? [form]
+  (and (seq? form)
+       (= (first form) `deref)
+       (= 2 (count form))))
 
 (defn read-forms [doc]
   (binding [*ns* *ns*]
@@ -115,7 +122,7 @@
                     (update :blocks conj
                             (cond-> b
                               (= :code type) (assoc :form form)
-                              ns? (assoc :no-cache? true)
+                              (or ns? (deref? form) (no-cache? form var *ns*)) (assoc :no-cache? true)
                               var (assoc :var (symbol (name (ns-name *ns*)) (name var))))))))
             (assoc doc :blocks [])
             (:blocks doc))))

From 995e2645487ba76c86175b1559526cf16e736a63 Mon Sep 17 00:00:00 2001
From: Andrea Amantini <lo.zampino@gmail.com>
Date: Thu, 20 Oct 2022 13:08:52 +0200
Subject: [PATCH 14/17] Parse markdown via quickjs

---
 bb-runtime.edn                        | 20 ++++++++++++----
 resources/viewer-js-hash              |  2 +-
 src/nextjournal/clerk/viewer.cljc     | 16 +++++--------
 src/nextjournal/markdown.bb           | 33 +++++++++++++++++++++++++--
 src/nextjournal/markdown/parser.bb    |  4 ----
 src/nextjournal/markdown/transform.bb |  5 ----
 6 files changed, 53 insertions(+), 27 deletions(-)
 delete mode 100644 src/nextjournal/markdown/parser.bb
 delete mode 100644 src/nextjournal/markdown/transform.bb

diff --git a/bb-runtime.edn b/bb-runtime.edn
index 94321aac5..8b6d234c4 100644
--- a/bb-runtime.edn
+++ b/bb-runtime.edn
@@ -1,19 +1,29 @@
 {:min-bb-version "1.0.164"
  :paths ["src" "notebooks" "resources"]
  :deps {hiccup/hiccup {:mvn/version "2.0.0-alpha2"}
-        org.babashka/cli {:mvn/version "0.5.40"}}
+        org.babashka/cli {:mvn/version "0.5.40"}
+        io.github.nextjournal/markdown {:mvn/version "0.4.126"}
+        io.github.nextjournal/clerk-slideshow {:git/sha "562f634494a1e1a9149ed78d5d39fd9486cc00ba"}}
  :tasks
- {dev
+ {:init
+  (let [md-mod (slurp (clojure.java.io/resource "js/markdown.mjs"))]
+    ;; FIXME: hack for having qjs relative module imports work
+    (when-not (babashka.fs/exists? "js/markdown.mjs")
+      (println "Copying nextjournal.markdown ES module:" (count md-mod))
+      (babashka.fs/create-dir "js")
+      (spit (clojure.java.io/file "js/markdown.mjs") (slurp (clojure.java.io/resource "js/markdown.mjs")))))
+
+  dev
   {:requires ([babashka.fs :as fs]
               [babashka.nrepl.server :as srv]
-              [nextjournal.clerk :as clerk]
               [babashka.cli :as cli])
    :task (do (srv/start-server! {:host "localhost" :port 1339})
              (spit ".nrepl-port" "1339")
-             (clerk/serve! (cli/parse-opts *command-line-args*))
+             ;; can't require clerk before copying md module
+             ((requiring-resolve 'nextjournal.clerk/serve!) (cli/parse-opts *command-line-args*))
              (-> (Runtime/getRuntime)
                (.addShutdownHook (Thread. (fn []
-                                            (clerk/halt!)
+                                            ((requiring-resolve 'nextjournal.clerk/halt!))
                                             (fs/delete ".nrepl-port")))))
              (deref (promise)))}
 
diff --git a/resources/viewer-js-hash b/resources/viewer-js-hash
index f53aff06c..98e4fca0e 100644
--- a/resources/viewer-js-hash
+++ b/resources/viewer-js-hash
@@ -1 +1 @@
-3dJJyLHsUmEC71T4CnGbFunsr74R
\ No newline at end of file
+jTDHst3WuaZZ65Kbk7vW4w7315u
\ No newline at end of file
diff --git a/src/nextjournal/clerk/viewer.cljc b/src/nextjournal/clerk/viewer.cljc
index c5288f888..aa2b157a3 100644
--- a/src/nextjournal/clerk/viewer.cljc
+++ b/src/nextjournal/clerk/viewer.cljc
@@ -666,16 +666,12 @@
   {:name :vega-lite :render-fn (quote v/vega-lite-viewer) :transform-fn mark-presented})
 
 (def markdown-viewer
-  (-> {:name :markdown}
-      #?(:bb  (assoc :transform-fn (comp mark-presented (update-val #(cond-> % (map? %) :content)))
-                     :render-fn '(fn [str] (v/html (v/md->hiccup str))))
-         :default (assoc :transform-fn
-                         (fn [wrapped-value]
-                           (-> wrapped-value
-                               mark-presented
-                               (update :nextjournal/value #(cond->> % (string? %) md/parse))
-                               (update :nextjournal/viewers add-viewers markdown-viewers)
-                               (with-md-viewer)))))))
+  {:name :markdown :transform-fn (fn [wrapped-value]
+                                   (-> wrapped-value
+                                       mark-presented
+                                       (update :nextjournal/value #(cond->> % (string? %) md/parse))
+                                       (update :nextjournal/viewers add-viewers markdown-viewers)
+                                       (with-md-viewer)))})
 
 (def code-viewer
   {:name :code :render-fn (quote v/code-viewer) :transform-fn (comp mark-presented (update-val (fn [v] (if (string? v) v (str/trim (with-out-str (pprint/pprint v)))))))})
diff --git a/src/nextjournal/markdown.bb b/src/nextjournal/markdown.bb
index 491da7063..22ad1b263 100644
--- a/src/nextjournal/markdown.bb
+++ b/src/nextjournal/markdown.bb
@@ -1,4 +1,33 @@
 (ns nextjournal.markdown
-  "Babashka runtime stubs")
+  "Babashka runtime stubs"
+  (:require [babashka.process :as p]
+            [clojure.data.json :as json]
+            [nextjournal.markdown.parser :as md.parser]
+            [clojure.string :as str]))
 
-(defn parse [md] {:type :doc :content md})
+(defn escape [t] (-> t (str/replace "`" "\\`") (str/replace "'" "\\'")))
+(defn tokenize [text]
+  (some-> (babashka.process/shell {:out :string :err :string}
+                              (str "qjs -e 'import(\"./js/markdown.mjs\").then((mod) => {print(mod.default.tokenizeJSON(`" (escape text) "`))})"
+                                   ".catch((e) => {import(\"std\").then((std) => { std.err.puts(\"cant find markdown module\"); std.exit(1)})})'"))
+      :out not-empty
+      (json/read-str {:key-fn keyword})))
+
+(defn parse [md] (some-> md tokenize md.parser/parse))
+
+(comment
+  (tokenize "# Hello")
+  (parse "# Hello
+* `this`
+* _is_
+* crazy as [hello](https://hell.is)
+
+$what$
+
+---
+```
+and this is code
+```
+")
+  (try (parse (slurp "notebooks/markdown.md"))
+       (catch Exception e (:err (ex-data e)))))
diff --git a/src/nextjournal/markdown/parser.bb b/src/nextjournal/markdown/parser.bb
deleted file mode 100644
index 932d45342..000000000
--- a/src/nextjournal/markdown/parser.bb
+++ /dev/null
@@ -1,4 +0,0 @@
-(ns nextjournal.markdown.parser
-  "Babashka runtime no-op stubs")
-
-(defn add-title+toc [doc] doc)
diff --git a/src/nextjournal/markdown/transform.bb b/src/nextjournal/markdown/transform.bb
deleted file mode 100644
index c4585c0a4..000000000
--- a/src/nextjournal/markdown/transform.bb
+++ /dev/null
@@ -1,5 +0,0 @@
-(ns nextjournal.markdown.transform
-  "Babashka runtime stubs")
-
-(defn ->text [node] "text")
-(defn table-alignment [attrs] {})

From 865c088548139dbaca7f772081b7f322863ed304 Mon Sep 17 00:00:00 2001
From: Andrea Amantini <lo.zampino@gmail.com>
Date: Thu, 20 Oct 2022 13:20:45 +0200
Subject: [PATCH 15/17] Check quickjs is available

---
 bb-runtime.edn              | 2 ++
 src/nextjournal/markdown.bb | 4 ++--
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/bb-runtime.edn b/bb-runtime.edn
index 8b6d234c4..243417086 100644
--- a/bb-runtime.edn
+++ b/bb-runtime.edn
@@ -8,6 +8,8 @@
  {:init
   (let [md-mod (slurp (clojure.java.io/resource "js/markdown.mjs"))]
     ;; FIXME: hack for having qjs relative module imports work
+    (assert (= 0 (:exit (deref (babashka.process/process "which qjs"))))
+      "Quickjs needs to be installed (brew install quickjs)")
     (when-not (babashka.fs/exists? "js/markdown.mjs")
       (println "Copying nextjournal.markdown ES module:" (count md-mod))
       (babashka.fs/create-dir "js")
diff --git a/src/nextjournal/markdown.bb b/src/nextjournal/markdown.bb
index 22ad1b263..ddfb03d5d 100644
--- a/src/nextjournal/markdown.bb
+++ b/src/nextjournal/markdown.bb
@@ -8,8 +8,8 @@
 (defn escape [t] (-> t (str/replace "`" "\\`") (str/replace "'" "\\'")))
 (defn tokenize [text]
   (some-> (babashka.process/shell {:out :string :err :string}
-                              (str "qjs -e 'import(\"./js/markdown.mjs\").then((mod) => {print(mod.default.tokenizeJSON(`" (escape text) "`))})"
-                                   ".catch((e) => {import(\"std\").then((std) => { std.err.puts(\"cant find markdown module\"); std.exit(1)})})'"))
+                                  (str "qjs -e 'import(\"./js/markdown.mjs\").then((mod) => {print(mod.default.tokenizeJSON(`" (escape text) "`))})"
+                                       ".catch((e) => {import(\"std\").then((std) => { std.err.puts(\"cant find markdown module\"); std.exit(1)})})'"))
       :out not-empty
       (json/read-str {:key-fn keyword})))
 

From 38997c8e21e9c0ab1347cb16ea0bfe50d3d2eade Mon Sep 17 00:00:00 2001
From: Andrea Amantini <lo.zampino@gmail.com>
Date: Thu, 20 Oct 2022 14:22:01 +0200
Subject: [PATCH 16/17] Lazily copy markdown js module

---
 bb-runtime.edn              | 18 ++++--------------
 src/nextjournal/markdown.bb | 31 ++++++++++++++++++++++---------
 2 files changed, 26 insertions(+), 23 deletions(-)

diff --git a/bb-runtime.edn b/bb-runtime.edn
index 243417086..dc40f93f1 100644
--- a/bb-runtime.edn
+++ b/bb-runtime.edn
@@ -5,27 +5,17 @@
         io.github.nextjournal/markdown {:mvn/version "0.4.126"}
         io.github.nextjournal/clerk-slideshow {:git/sha "562f634494a1e1a9149ed78d5d39fd9486cc00ba"}}
  :tasks
- {:init
-  (let [md-mod (slurp (clojure.java.io/resource "js/markdown.mjs"))]
-    ;; FIXME: hack for having qjs relative module imports work
-    (assert (= 0 (:exit (deref (babashka.process/process "which qjs"))))
-      "Quickjs needs to be installed (brew install quickjs)")
-    (when-not (babashka.fs/exists? "js/markdown.mjs")
-      (println "Copying nextjournal.markdown ES module:" (count md-mod))
-      (babashka.fs/create-dir "js")
-      (spit (clojure.java.io/file "js/markdown.mjs") (slurp (clojure.java.io/resource "js/markdown.mjs")))))
-
-  dev
+ {dev
   {:requires ([babashka.fs :as fs]
               [babashka.nrepl.server :as srv]
+              [nextjournal.clerk :as clerk]
               [babashka.cli :as cli])
    :task (do (srv/start-server! {:host "localhost" :port 1339})
              (spit ".nrepl-port" "1339")
-             ;; can't require clerk before copying md module
-             ((requiring-resolve 'nextjournal.clerk/serve!) (cli/parse-opts *command-line-args*))
+             (nextjournal.clerk/serve! (cli/parse-opts *command-line-args*))
              (-> (Runtime/getRuntime)
                (.addShutdownHook (Thread. (fn []
-                                            ((requiring-resolve 'nextjournal.clerk/halt!))
+                                            (nextjournal.clerk/halt!)
                                             (fs/delete ".nrepl-port")))))
              (deref (promise)))}
 
diff --git a/src/nextjournal/markdown.bb b/src/nextjournal/markdown.bb
index ddfb03d5d..0896a8e9d 100644
--- a/src/nextjournal/markdown.bb
+++ b/src/nextjournal/markdown.bb
@@ -1,21 +1,34 @@
 (ns nextjournal.markdown
   "Babashka runtime stubs"
-  (:require [babashka.process :as p]
+  (:require [babashka.fs :as fs]
+            [babashka.process :as p]
             [clojure.data.json :as json]
-            [nextjournal.markdown.parser :as md.parser]
-            [clojure.string :as str]))
+            [clojure.java.io :as io]
+            [clojure.string :as str]
+            [nextjournal.markdown.parser :as md.parser]))
+
+(defn assert-quickjs! [] (assert (= 0 (:exit @(p/process '[which qjs]))) "QuickJS needs to be installed (brew install quickjs)"))
+(def !md-mod-temp-dir (atom nil))
+(defn md-mod-temp-dir []
+  (or @!md-mod-temp-dir
+      (let [tempdir (fs/create-temp-dir)]
+        (assert-quickjs!)
+        (spit (fs/file tempdir "markdown.mjs") (slurp (io/resource "js/markdown.mjs")))
+        (reset! !md-mod-temp-dir (str tempdir)))))
 
 (defn escape [t] (-> t (str/replace "`" "\\`") (str/replace "'" "\\'")))
 (defn tokenize [text]
-  (some-> (babashka.process/shell {:out :string :err :string}
-                                  (str "qjs -e 'import(\"./js/markdown.mjs\").then((mod) => {print(mod.default.tokenizeJSON(`" (escape text) "`))})"
-                                       ".catch((e) => {import(\"std\").then((std) => { std.err.puts(\"cant find markdown module\"); std.exit(1)})})'"))
-      :out not-empty
-      (json/read-str {:key-fn keyword})))
+  (some-> (p/shell {:out :string :err :string :dir (md-mod-temp-dir)}
+                   (str "qjs -e 'import(\"./markdown.mjs\").then((mod) => {print(mod.default.tokenizeJSON(`" (escape text) "`))})"
+                        ".catch((e) => {import(\"std\").then((std) => { std.err.puts(\"cant find markdown module\"); std.exit(1)})})'"))
+          deref :out not-empty
+          (json/read-str {:key-fn keyword})))
 
-(defn parse [md] (some-> md tokenize md.parser/parse))
+(defn parse [md] {:type :doc :content []} (some-> md tokenize md.parser/parse))
 
 (comment
+  (assert-quickjs!)
+  (md-mod-temp-dir)
   (tokenize "# Hello")
   (parse "# Hello
 * `this`

From 10e95c4c498c0f55bb5277d60796da4745811ee4 Mon Sep 17 00:00:00 2001
From: Andrea Amantini <lo.zampino@gmail.com>
Date: Thu, 20 Oct 2022 14:34:54 +0200
Subject: [PATCH 17/17] More escapes

---
 src/nextjournal/markdown.bb | 8 +++-----
 1 file changed, 3 insertions(+), 5 deletions(-)

diff --git a/src/nextjournal/markdown.bb b/src/nextjournal/markdown.bb
index 0896a8e9d..66111f039 100644
--- a/src/nextjournal/markdown.bb
+++ b/src/nextjournal/markdown.bb
@@ -16,7 +16,7 @@
         (spit (fs/file tempdir "markdown.mjs") (slurp (io/resource "js/markdown.mjs")))
         (reset! !md-mod-temp-dir (str tempdir)))))
 
-(defn escape [t] (-> t (str/replace "`" "\\`") (str/replace "'" "\\'")))
+(defn escape [t] (-> t (str/replace "\\" "\\\\\\") (str/replace "`" "\\`") (str/replace "'" "\\'")))
 (defn tokenize [text]
   (some-> (p/shell {:out :string :err :string :dir (md-mod-temp-dir)}
                    (str "qjs -e 'import(\"./markdown.mjs\").then((mod) => {print(mod.default.tokenizeJSON(`" (escape text) "`))})"
@@ -32,13 +32,11 @@
   (tokenize "# Hello")
   (parse "# Hello
 * `this`
-* _is_
+* _is_ Some $\\mathfrak{M}$ formula
 * crazy as [hello](https://hell.is)
 
-$what$
-
 ---
-```
+```clojure
 and this is code
 ```
 ")