test refactor wip + partially named list fix

Author: genmeblog

CHANGELOG.md

@@ -1,6 +1,14 @@
 # Change Log
 All notable changes to this project will be documented in this file. This change log follows the conventions of [keepachangelog.com](http://keepachangelog.com/).
 
+## [unreleased]
+- all operators are added
+- support for `switch` in codegen
+- `vrkrasana` moved out of `src` (also `vrkrasana` branch is created)
+- set of not used or internal functions deprecated in the main namespace (`function`, `apply-function`, `print-help`, `str-md`, `println-r-lines`, `r-lines->md`, `println-captured-str`)
+- `object-structure` - function returning result of `utils::str` as a string.
+- fixed: partially named list conversion to a map had wrong id for unnamed values
+
 ## [1.1.0]
 - added more operators `%/%`, `%%` ,`%in%`, `xor`
 - use devcontainer setup following template

src/clojisr/v1/codegen.clj

@@ -124,9 +124,15 @@
   [vs session ctx]
   (let [[pred f1 f2] (map #(form->code % session ctx) (take 3 vs))]
     (if f2
-      (format "if(%s) {%s} else {%s}"  pred f1 f2)
+      (format "if(%s) {%s} else {%s}" pred f1 f2)
       (format "if(%s) {%s}" pred f1))))
 
+(defn switch->code
+  "Create switch"
+  [vs session ctx]
+  (let [forms (map #(form->code % session ctx) (take 3 vs))]
+    (format "switch(%s)" (join "," forms))))
+
 (defn for-loop->code
   "Create for loop"
   [bindings body session ctx]  
@@ -232,6 +238,7 @@
         (= "do" fs) (format "{%s}" (join ";" (map #(form->code % session ctx) r)))
         (= "for" fs) (for-loop->code (first r) (rest r) session ctx)
         (= "while" fs) (while-loop->code (first r) (rest r) session ctx)
+        (= "switch" fs) (switch->code r session ctx)
         (contains? bracket-data fs) (bracket-call->code (bracket-data fs) r session ctx)
         (= 'clojure.core/unquote f) (unquote-form->code r session ctx)
         :else (symbol-form->code fs r session ctx)))

src/clojisr/v1/functions.clj

@@ -24,15 +24,15 @@
     (let [autorefreshing (refresh/auto-refresing-object
                           r-object)]
       (fn ([& args]
-           (let [explicit-session-args
-                 (when (some-> args butlast last (= :session-args))
-                   (last args))]
-             (apply-function
-              @autorefreshing
-              (if explicit-session-args
-                (-> args butlast butlast)
-                args)
-              (session/fetch-or-make explicit-session-args))))))))
+          (let [explicit-session-args
+                (when (some-> args butlast last (= :session-args))
+                  (last args))]
+            (apply-function
+             @autorefreshing
+             (if explicit-session-args
+               (-> args butlast butlast)
+               args)
+             (session/fetch-or-make explicit-session-args))))))))
 
 (defn function
   [r-object]

src/clojisr/v1/help.clj

@@ -6,21 +6,22 @@
             [clojisr.v1.session :as session]
 
             [clojisr.v1.help :as help]))
+
 (defn- un-back-quote [s]
   (str/replace s  "`" "" ))
 
 
 (defn _get-help[function package]
- ;(println :obtain-help (format  "%s/%s " (name package) (un-back-quote (name function))))
- (->>
-  (evl/r (format  
-          "tryCatch(capture.output(tools:::Rd2txt(utils:::.getHelpFile(as.character(help(%s,%s))), options=list(underline_titles=FALSE))),error=function(e) {return( \"no doc available\")})"
-                  (name function) (name package))
-         (session/fetch-or-make nil))
-
-  (using-sessions/r->java)
-  (java2clj/java->clj)
-  (str/join "\n")))
+                                        ;(println :obtain-help (format  "%s/%s " (name package) (un-back-quote (name function))))
+  (->>
+   (evl/r (format  
+           "tryCatch(capture.output(tools:::Rd2txt(utils:::.getHelpFile(as.character(help(%s,%s))), options=list(underline_titles=FALSE))),error=function(e) {return( \"no doc available\")})"
+           (name function) (name package))
+          (session/fetch-or-make nil))
+
+   (using-sessions/r->java)
+   (java2clj/java->clj)
+   (str/join "\n")))
 
 (def get-help (memoize _get-help))
 

src/clojisr/v1/impl/clj_to_java.clj

@@ -4,8 +4,7 @@
             [tech.v3.dataset.protocols :as ds-prot]
             [tech.v3.dataset.column :as col]
             [tech.v3.dataset :as dataset]
-            [tech.v3.datatype :as dtype]
-            [tech.v3.dataset :as ds])
+            [tech.v3.datatype :as dtype])
   (:import [clojisr.v1.robject RObject]))
 
 (declare clj->java)

src/clojisr/v1/impl/common.clj

@@ -37,7 +37,7 @@
   "Create key names for partially named lists"
   [names]
   (map-indexed (fn [^long id k]
-                 (if (empty? k) id (usually-keyword k))) names))
+                 (if (empty? k) (inc id) (usually-keyword k))) names))
 
 ;; REXP/SEXP helpers for dataset conversion
 
@@ -52,8 +52,8 @@
   prot/RProto
   (inherits? [_ _] false)
   prot/Clojable
-  (->clj [obj] obj)
-  (->native [obj] obj))
+  (->clj [_] nil)
+  (->native [_] nil))
 
 (defn ->seq-with-missing
   [xs missing]

src/clojisr/v1/impl/rserve/printing.clj

@@ -10,3 +10,4 @@
                           (prot/eval-r->java session))]
     (->> (.asStrings output)       
          (string/join "\n"))))
+

src/clojisr/v1/impl/rserve/rexp.clj

@@ -5,7 +5,7 @@
                                             valid-list-names]]
             [clojisr.v1.impl.types :as types])
   (:import (org.rosuda.REngine REXP REXPDouble REXPInteger REXPLogical REXPString REXPFactor REXPSymbol REXPNull
-                               REXPUnknown REXPGenericVector REXPList
+                               REXPLanguage REXPUnknown REXPGenericVector REXPList
                                RFactor RList)))
 
 ;;;;;;;;;;;;;;;;;;;;
@@ -97,6 +97,12 @@
   (->column [exp _] (prot/->clj exp)) ;; same as above
   (->columns [exp] (list->columns exp)))
 
+;; probably needs to be treated differently...
+(extend-type REXPLanguage
+  prot/Clojable
+  (->clj [exp] (list->map-or-vector exp prot/->clj))
+  (->native [exp] (list->map-or-vector exp prot/->native)))
+
 ;;;;;;;;;;;;;;;;;;;;
 ;; Clojure -> REXP
 ;;;;;;;;;;;;;;;;;;;;
@@ -130,6 +136,6 @@
       (REXPGenericVector. (REXPList. nil))))
 
 (defn ->rexp-named-list [^java.util.Collection ks
-                         ^java.util.Collection vs]
+                      ^java.util.Collection vs]
   (-> (RList. vs ks)
       (REXPGenericVector.))) ;; named list creates attr already 

src/clojisr/v1/impl/rserve/session.clj

@@ -104,7 +104,7 @@
         port (or port (get-free-port))
         rserve (when spawn-rserve?
                  (proc/start-rserve port init-r))]
-
+    
     (when rserve ;; be sure the process is spawned
       (loop [attempts (int 5)]
         (Thread/sleep 500)