Merge branch 'master' of github.com:mmagnus/geekbook

* 'master' of github.com:mmagnus/geekbook:
  Update quickref.rst
  Update quickref.rst
  Update quickref.rst
  Update rna.rst
  Update requirements.txt
  Update quickref.rst
  Update quickref.rst
  Update find_files.py
  Update view.rst
  Update getstarted.rst
  Update CHANGELOG.md
  start & test: it should go with --update to generate html page
  webserverflask.py: remove some prints
  Fix a bug, not public is not public now
  conf: fix, FIND_FILES_PLUGIN should go before conf_local
  corrected version, no alert if file is found
  new way to open files
  Update README.md
  slides: fix missing lib
  workshop: prepare a presentation for workshops

# Conflicts:
#	CHANGELOG.md
#	docs/source/quickref.rst
#	engine/plugins/find_files.py
#	engine/webserverflask.py
#	geekbookapp.py

CHANGELOG.md

@@ -5,9 +5,8 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
 ## [Pre-release]
-(TODO)
+## 2.2 Last Python2 version!
 - Introduce ``#short`` to make it shorter 190719
-
 ## 2.1
 ### Added
 - Insert files (drag and drop) from Apple Photos

docs/requirements.txt

@@ -3,3 +3,4 @@ markdown==2.6.11
 py-gfm==0.1.3
 Flask
 pandas
+pygments

docs/source/getstarted.rst

@@ -29,5 +29,3 @@ open your browser and copy-paste the ```html path``` (in my case is ```file:///p
 To make a new note, create a file in ```<path to your geekbook>/notes/<notes here>```.
 
 Remember to keep geekbookapp.py running all the time, it will detect a new note and compile it for you.
-
-**To force your browser to refresh html files whenevery there is a change on you drive (when geekbook compiles something new) please use something like this Auto-load (https://addons.mozilla.org/en-US/firefox/addon/auto-reload/?src=api) (this works for me in Firefox).**

docs/source/quickref.rst

@@ -3,21 +3,39 @@ Quick Reference
 
 ::
 
+     find a full path to your file and insert it in the given place in a generated html
      [ff:<file>]
      [ff:uniq-name.pse]
-        find a full path to your file and insert it in the given place in a generated html
-
-::
 
+     insert an external file
      [if:<file>]
      [if:/Users/magnus/work-src/fenzymes/examples/readme.txt]
-        insert an external file
 
-::
+     insert the table of content in here
+     [tableofcontent] or {{TOC}}
+
+     to get the current date 2017-01-13
+     [date]
+
+     define only width for a image:
+     ![](imgs/Screen_Shot_2017-02-12_at_1.17.04_AM.png =500x)
+
+     only height:
+     ![](imgs/Screen_Shot_2017-02-12_at_1.17.04_AM.png =x400)
+
+     and both:
+     ![](imgs/Screen_Shot_2017-02-12_at_1.17.04_AM.png =400x400)
+
+     you can put to images next to each other and sqeeze them to the left
+     <div style="width:300px">
+     ![](imgs/190409_L4yjm119T5aONVO9BVeCTQ_thumb_7a17.jpg)![](imgs/190409_thumb_7a18.jpg)
+     </div>
+
+     #short - set for image (``max-height:400px``) to make it shorter
 
      [tableofcontent] or {{TOC}}
         insert the table of content in here
 
-Images::
 
-     #short - set for image (``max-height:400px``) to make it shorter
+     add description of a note in the Index page
+     [desc:info on TN]

docs/source/rna.rst

@@ -1,7 +1,7 @@
-RNA-pdb-tools
+mmagnus/rna-tools
 ============================================================
 
-You need to install rna-pdb-tools (http://rna-pdb-tools.readthedocs.io/en/latest/) first.
+You need to install rna-tools (http://rna-tools.readthedocs.io/en/latest/) first.
 
 Draw VARNA-based image of RNA secondary structure
 ------------------------------------------------------------

docs/source/view.rst

@@ -4,18 +4,4 @@ Out | Read
 .. image:: ../imgs/view.png
 **Fig**. The index in Safari.
 
-Of course you can browser your notes in any browser. I'm using (mmagnus) Firefox with following addons to improve the experience, and Safari for screenshots ;-) 
-
-Auto-reload
---------------------------------------------------------------
-
-To force your browser to refresh HTML files whenever there is a change on you drive (when geekbook compiles something new) please use something like this Auto-load (https://addons.mozilla.org/en-US/firefox/addon/auto-reload/?src=api)
-
-Old default image style
---------------------------------------------------------------
-
-To get "old default image style" (white background) in Firefox install this add-on (https://addons.mozilla.org/en-US/firefox/addon/old-default-image-style/)
-
-.. image:: ../imgs/firefox_img_old.png
-
-
+Of course you can browser your notes in any browser. I used to use Firefox, then Chrome, and now Safari :-)

engine/conf.py

@@ -18,7 +18,6 @@
 
 SCREENSHOT_INBOX = None
 
-
 # find files plugin off/on
 FIND_FILES_PLUGIN = False
 

engine/plugins/find_files.py

@@ -17,60 +17,6 @@
 JSON_DB = os.path.dirname(os.path.abspath(__file__)) + os.sep + 'find_file.json'
 
 
-## def file_search(filename, verbose):
-##     """Search for filename. Returns dirname of the filename's path, and the full path.
-
-##     181120 Test on my OSX. I might work on Linux as well. But this requires further
-##     testing.
-
-##     170107 add cache. If the db is not found, create an empty pandas df
-##     and populate this df with append later. If the filename is not in the db
-##     run g/locate. Then, save the found path to the db (using pandas, via df, to json)"""
-##     import pandas as pd
-##     # cache
-##     if os.path.isfile(JSON_DB):
-##         df = pd.read_json(JSON_DB, orient='records')
-##         #filename = 'x.pse'
-##         pathdf = df[df['fn'] == filename]['path']
-##         # test if the file still exists there
-##         path = pathdf.to_string(index=False)
-##         if not pathdf.empty and os.path.isfile(path):
-##             logger.info('[from the db]:' + filename)
-##             return os.path.dirname(path), path
-##             # ok, here the function will finished if the results were cashed and
-##             # file still exists there
-##     else:
-##         df = pd.DataFrame()
-
-##     # if filename is not found in the db
-##     logger.info('find file:' + filename)
-
-##     if platform.system() == "Linux":
-##         out = commands.getoutput('locate ' + filename)
-##     if platform.system() == "Darwin":
-##         # out = commands.getoutput('glocate ' + filename)
-##         out = commands.getoutput('mdfind -name ' + filename)
-##     first_hit = out.split('\n')[0]
-##     logger.info('# of hits ' + str(len(out.split('\n'))) + " " + out.replace('\n',', '))
-##     if not first_hit:
-##         logger.info('not found')
-##         return ('Not found', '~~' + filename + '~~')
-##     else:
-##         logger.info('hit ' + first_hit)
-
-##     # update cache
-##     dffile = pd.DataFrame([[filename, first_hit],], columns=['fn', 'path'])
-##     if verbose: print(df)
-##     try:
-##         df[df['fn'] == filename]['path']
-##     except KeyError:
-##         pass
-##     df = df.append(dffile, ignore_index=True)
-##     # save to json
-##     df.to_json(JSON_DB, orient='records')
-##     return os.path.dirname(first_hit), first_hit
-
-
 def find_files(text, verbose=False):
     """
     The search was completely re-written in a way that now the files
@@ -92,7 +38,7 @@ def find_files(text, verbose=False):
             if verbose: print '# file_finder.search()', output
             # remove for now folder link, it does not work @todo
             #output += l.replace('[ff:' + filename + ']',' <a href="' + folderpath + '"><code>[+]</code></a> ' + '<a target="_blank" href="/open' + filepath + '"> <span class="mantext">' + os.path.basename(filepath) + '</span></a>')
-            output += l.replace('[ff:' + filename + ']', '<a  href="#" address="' + filepath + '" id="openfile"> <span class="mantext">' + os.path.basename(filepath) + '</span></a>\n')
+            output += l.replace('[ff:' + filename + ']', '<a  href="#" address="' + filepath + '" id="openfile"> <span class="mantext">' + os.path.basename(filepath) + '</span></a>\n') # or without '\n
         else:
             output += l + '\n'
     output = output.replace('[files-not-found]', msg_listofnotfoundfiles)

engine/webserverflask.py

@@ -142,7 +142,6 @@ def view(note_title):
     """Open a note with your edit
     http://flask.pocoo.org/snippets/76/
     """
-    print(note_title)
     if request.remote_addr not in ['127.0.0.1', '0.0.0.0']:
         if note_title not in OPEN_ACCESS:
             return 'Hmm...'