Let me know if you need something else.

Build Info (Successful)

(python3) [user@nuc blog] $ nikola build
[2017-02-23T16:36:28Z] WARNING: Nikola: In order to USE_BUNDLES, you must install the "webassets" Python package.
[2017-02-23T16:36:28Z] WARNING: bundles: Setting USE_BUNDLES to False.
Scanning posts...........done!
.  render_taxonomies:output/archive.html
.  render_sources:output/posts/test-org-mode.org
.  render_posts:timeline_changes
.  render_posts:cache/posts/test-org-mode.html
Loading /usr/share/emacs/site-lisp/site-start.d/asy-init.el (source)...
Loading /usr/share/emacs/site-lisp/site-start.d/cmake-init.el (source)...
Loading /usr/share/emacs/site-lisp/site-start.d/desktop-entry-mode-init.el (source)...
Loading /usr/share/emacs/site-lisp/site-start.d/git-init.el (source)...
Loading /usr/share/emacs/site-lisp/site-start.d/htmlize-init.el (source)...
Loading /home/user/Dropbox/blog/plugins/orgmode/conf.el (source)...
Loading /home/user/.emacs.d/lisp/ob-stata.el (source)...
executing Python code block...
Code block evaluation complete.
Can’t guess python-indent-offset, using defaults: 4
.  render_taxonomies:output/2017/index.html
.  render_taxonomies:output/blog/index.html
.  render_pages:output/posts/test-org-mode.html
.  render_pages:output/posts/reproducible-research.html
.  render_taxonomies:output/rss.xml
.  sitemap:output/sitemap.xml
.  sitemap:output/sitemapindex.xml

Build Info Unsuccessful

Setting (setq org-html-htmlize-output-type nil) in conf.el, gives me this:

(python3) [user@nuc posts] $ nikola build
[2017-02-23T17:05:23Z] WARNING: Nikola: In order to USE_BUNDLES, you must install the "webassets" Python package.
[2017-02-23T17:05:23Z] WARNING: bundles: Setting USE_BUNDLES to False.
Scanning posts...........done!
.  render_sources:output/posts/test-org-mode.org
.  render_posts:timeline_changes
.  render_posts:cache/posts/test-org-mode.html
Loading /usr/share/emacs/site-lisp/site-start.d/asy-init.el (source)...
Loading /usr/share/emacs/site-lisp/site-start.d/cmake-init.el (source)...
Loading /usr/share/emacs/site-lisp/site-start.d/desktop-entry-mode-init.el (source)...
Loading /usr/share/emacs/site-lisp/site-start.d/git-init.el (source)...
Loading /usr/share/emacs/site-lisp/site-start.d/htmlize-init.el (source)...
Loading /home/user/Dropbox/blog/plugins/orgmode/conf.el (source)...
Loading /home/user/.emacs.d/lisp/ob-stata.el (source)...
executing Python code block...
Code block evaluation complete.
Can’t guess python-indent-offset, using defaults: 4
Symbol’s function definition is void: nil
########################################
TaskError - taskid:render_posts:cache/posts/test-org-mode.html
PythonAction Error
Traceback (most recent call last):
  File "/home/user/Dropbox/blog/plugins/orgmode/orgmode.py", line 73, in compile_html
    subprocess.check_call(command)
  File "/home/user/anaconda/envs/python3/lib/python3.5/subprocess.py", line 581, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['emacs', '--batch', '-l', '/home/user/Dropbox/blog/plugins/orgmode/init.el', '--eval', '(nikola-html-export "/home/user/Dropbox/blog/posts/test-org-mode.org" "/home/user/Dropbox/blog/cache/posts/test-org-mode.html")']' returned non-zero exit status 255

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/user/anaconda/envs/python3/lib/python3.5/site-packages/doit/action.py", line 403, in execute
    returned_value = self.py_callable(*self.args, **kwargs)
  File "/home/user/anaconda/envs/python3/lib/python3.5/site-packages/nikola/post.py", line 540, in compile
    lang)
  File "/home/user/anaconda/envs/python3/lib/python3.5/site-packages/nikola/plugin_categories.py", line 304, in compile
    self.compile_html(source, dest, is_two_file)
  File "/home/user/Dropbox/blog/plugins/orgmode/orgmode.py", line 97, in compile_html
    source, e.returncode))
Exception: Cannot compile posts/test-org-mode.org -- bad org-mode configuration (return code 255)

conf.el

(when (>= emacs-major-version 24)
  (require 'package)
  (add-to-list
   'package-archives
   '("melpa" . "http://melpa.org/packages/")
   t)
  (package-initialize))


(require `ob-ipython)
(require `pyvenv)
(require `htmlize)

;; pyvenv setup
;; this is required for many code blocks to execute
;; Specifically, R and python
(setenv "WORKON_HOME" "~/anaconda/envs")
(setq pyvenv-workon "python3")
(setenv "WORKON" "python3")
(pyvenv-mode 1)

;; sets up stata execution
(require 'ess-site)
;; turns off prompts
(setq ess-ask-for-ess-directory nil)
;; Tell emacs where is your personal elisp lib dir
(add-to-list 'load-path "~/.emacs.d/lisp/")
;; load ob-stata
(load "ob-stata")

;; sets up org-babel
(org-babel-do-load-languages
 'org-babel-load-languages
 '((python . t)
   (ipython . t)
   (R . t)
   (sh . t)
   (matlab . t)
   (stata . t)
 ))

(setq org-confirm-babel-evaluate nil) ;; C-c C-c without typing yes

;; work around for bad htmlize
;; (setq org-html-htmlize-output-type nil) 

init.el

;; Init file to use with the orgmode plugin.

;; Load org-mode
;; Requires org-mode v8.x

;; Uncomment these lines and change the path to your org source to
;; add use it.
;; (let* ((org-lisp-dir "~/.emacs.d/src/org/lisp"))
;;   (when (file-directory-p org-lisp-dir)
;;       (add-to-list 'load-path org-lisp-dir)
;;       (require 'org)))

(require 'ox-html)

;;; Custom configuration for the export. ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;

;;; Add any custom configuration that you would like to 'conf.el'.
(setq
 nikola-use-pygments t
 org-export-with-toc nil
 org-export-with-section-numbers nil
 org-startup-folded 'showeverything)

;; Load additional configuration from conf.el
(let ((conf (expand-file-name "conf.el" (file-name-directory load-file-name))))
  (if (file-exists-p conf)
      (load-file conf)))

;;; Macros ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;

;; Load Nikola macros
(setq nikola-macro-templates
      (with-current-buffer
          (find-file
           (expand-file-name "macros.org" (file-name-directory load-file-name)))
        (org-macro--collect-macros)))


;;; Code highlighting ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
(defun org-html-decode-plain-text (text)
       "Convert HTML character to plain TEXT. i.e. do the inversion of
     `org-html-encode-plain-text`. Possible conversions are set in
     `org-html-protect-char-alist'."
       (mapc
        (lambda (pair)
          (setq text (replace-regexp-in-string (cdr pair) (car pair) text t t)))
        (reverse org-html-protect-char-alist))
       text)

;; Use pygments highlighting for code
(defun pygmentize (lang code)
  "Use Pygments to highlight the given code and return the output"
  (with-temp-buffer
    (insert code)
    (let ((lang (or (cdr (assoc lang org-pygments-language-alist)) "text")))
      (shell-command-on-region (point-min) (point-max)
                               (format "pygmentize -f html -l %s" lang)
                               (buffer-name) t))

    (buffer-string)))


(defconst org-pygments-language-alist
  '(
    ("asymptote" . "asymptote")
    ("awk" . "awk")
    ("C" . "c")
    ("cpp" . "cpp")
    ("clojure" . "clojure")
    ("css" . "css")
    ("D" . "d")
    ("emacs-lisp" . "scheme")
    ("F90" . "fortran")
    ("gnuplot" . "gnuplot")
    ("groovy" . "groovy")
    ("haskell" . "haskell")
    ("java" . "java")
    ("js" . "js")
    ("julia" . "julia")
    ("latex" . "latex")
    ("lisp" . "lisp")
    ("makefile" . "makefile")
    ("matlab" . "matlab")
    ("mscgen" . "mscgen")
    ("ocaml" . "ocaml")
    ("octave" . "octave")
    ("perl" . "perl")
    ("picolisp" . "scheme")
    ("python" . "python")
    ("R" . "r")
    ("ruby" . "ruby")
    ("sass" . "sass")
    ("scala" . "scala")
    ("scheme" . "scheme")
    ("sh" . "sh")
    ("sql" . "sql")
    ("sqlite" . "sqlite3")
    ("tcl" . "tcl")
    )
  "Alist between org-babel languages and Pygments lexers.

See: http://orgmode.org/worg/org-contrib/babel/languages.html and
http://pygments.org/docs/lexers/ for adding new languages to the
mapping. ")

;; Override the html export function to use pygments
(defun org-html-src-block (src-block contents info)
  "Transcode a SRC-BLOCK element from Org to HTML.
CONTENTS holds the contents of the item.  INFO is a plist holding
contextual information."
  (if (org-export-read-attribute :attr_html src-block :textarea)
      (org-html--textarea-block src-block)
    (let ((lang (org-element-property :language src-block))
	  (code (org-html-format-code src-block info)))
      (if nikola-use-pygments
          (pygmentize lang (org-html-decode-plain-text code))
        code))))

;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;

;; Export function used by Nikola.
(defun nikola-html-export (infile outfile)
  "Export the body only of the input file and write it to
specified location."

  (with-current-buffer (find-file infile)
    (org-macro-replace-all nikola-macro-templates)
    (org-html-export-as-html nil nil t t)
    (write-file outfile nil)))

test-org-mode.org

print("Hello World")

I will try reproducing the issue with your config, Thanks.

But to begin with can you try fixing these requires? The backtick needs to be a single-quote.

(require `ob-ipython)
(require `pyvenv)
(require `htmlize)

(require 'ob-ipython)
(require 'pyvenv)
(require 'htmlize)