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Development notes

20180319

  1. Problems with installing and running in a virtual environment. Get the error:

    RuntimeError: Python is not installed as a framework. The Mac OS X backend will not be able to fun

mmserver.py needs this BEFORE importing any matplotlib

import matplotlib
matplotlib.use('TkAgg')

  1. need to remove plot import from init.py

  2. write out and test full virtual env install, missing flask for example !!!

Using fresh install of Anaconda on OSX

# downgrade qt5 to qt4
conda uninstall pyqt
conda install pyqt=4

# we still need to get correct version of matplotlib
# stock install of anaconda on work osx does not have matplotlib
conda install -c conda-forge matplotlib=2.0.2
conda install -c conda-forge tifffile=0.12.1

# install PyMapMAnager
pip install -e Dropbox/PyMapManager

Install

Main archive folder has caps PyMapManager, this contains:

  • setup.py file
  • folder of pymapmanager code
  • auto generated docs folder

Code folder inside of PyMapManager is lower-case pymapmanager, at same level as setup.py and contians all the code

In this way pip install -e Dropbox/PyMapManager can then be used in python with import pymapmanager

Dropbox is NOT case sensitive, when I change case of enclosing pymapmanager folder it DOES NOT sync.

cd
pip install -e Dropbox/PyMapManager

spreadsheet for pandas in qt

https://github.com/draperjames/qtpandas

pip install qtpandas

Sphinx

sphinx-quickstart

sphinx readthedocs theme

pip install sphinx_rtd_theme

Make sure config.py has

from mock import MagicMock

class Mock(MagicMock):
    @classmethod
    def __getattr__(cls, name):
        return MagicMock()

MOCK_MODULES = ['pygtk', 'gtk', 'gobject', 'argparse', 'numpy', 'pandas','sip', 'PyQt4', 'PyQt4.QtGui', 'tifffile']
sys.modules.update((mod_name, Mock()) for mod_name in MOCK_MODULES)

import os
import sys
sys.path.insert(0, os.path.abspath('../..'))

html_theme = "sphinx_rtd_theme"

# remove duplicate modile name in every constructor
# e.g. mmMap.mmMap()
add_module_names = False

# exlude directories from build, in particular 'old'
exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store', 'old']

rebuild docs

sphinx-apidoc -o . ..
make html

Sphinx (Again)

Trying to use Sphinx napolean: http://www.sphinx-doc.org/en/stable/ext/napoleon.html

Tweek docs/source/conf.py

exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store', 'old', 'pdoc']

extensions = ['sphinx.ext.autodoc',
    'sphinx.ext.viewcode',
    'sphinx.ext.githubpages',
    'sphinx.ext.napoleon']

html_theme = "sphinx_rtd_theme"

To build the docs

cd ~/Dropbox/PyMapManager/pymapmanager/docs/
sphinx-apidoc -f -o docs ~/Dropbox/PyMapManager
make html

This should put output into root /docs/ folder (holding index.html) and github /docs/ option should work?

cd ~/Dropbox/PyMapManager/pymapmanager/docs/ #this has source directory with .rst files

# if i add a module i need to do this
sphinx-apidoc -f -o source ~/Dropbox/PyMapManager
# or
sphinx-apidoc -fe -o source ~/Dropbox/PyMapManager

# generic rebuild (do this all the time)
sphinx-build -b html source/ ../../docs

Github

Remove all references to .git

find . -name .git -print0 | xargs -0 rm -rf

mkdocs 20171129

PyMapManager/docs now has mkdocs website

PyMapManager/docs/api now has Sphinx API documentation

Push new Sphinx api with

sphinx-build -b html source/ ../../docs/api

Make new mkdocs with

cd ~/Dropbox/PyMapManager
mkdocs new docs

Push to mkdocs to github with

# need to do this in github repo, NOT Dropbox repo !!!
cd ~/Sites/PyMapManager/docs
mkdocs gh-deploy --clean

Make sure github repo is using gh-branch for docs

pdoc

Download forked git repo from https://github.com/j6k4m8/pdoc

# I am updating this code to tweek interface
# use pip install -e' and changes in code will propogate to python
pip install -e ~/Downloads/pdoc-master

#then this command works
pdoc PyMApManager --html --html-dir="docs" --overwrite --docstring-style=google

# then from package folder '/Users/cudmore/Dropbox/PyMapManager'
pdoc PyMapManager --html --html-dir="docs" --overwrite --docstring-style=google

#removed generation of mro by modifying html.maco 
% if 0 and len(mro) > 0:

Tweeked html.maco to hide init

    % if len(methods) > 0:
      <h3>Methods</h3>
      % for f in methods:
        % if f.name != "__init__":            	
          ${show_func(f)}
        % endif
      % endfor
    % endif

Changed init.py in module to strip out inherited class members/functions. See: mitmproxy/pdoc#15

	# abb ADDED
	# Only include attributes in this module or class, not inherited attributes
    cls_dict_names = self.cls.__dict__.keys()
    def is_in_dict(n):
        return n in cls_dict_names
    # /ADDED

    #return dict([(n, o) for n, o in idents.items() if exported(n)])
    return dict([(n, o) for n, o in idents.items() if exported(n) and is_in_dict(n)]) # abb MODIFIED

Added a link back to index.html in html.mako

#changed this
<div id="sidebar">
  <h1>Index</h1>

#to this
<div id="sidebar">
  <h1><A HREF="index.html">Index</A></h1>

To generate pdoc cd /Users/cudmore/Dropbox/ pip install -e PyMapManager cd PyMapManager pdoc PyMapManager --html --html-dir="docs" --overwrite --docstring-style="google"

# SHOULD make /doc/PyMapManager/ inside PyMapManager MODULE (not first level which is PACKAGE
  • check in in onpick() does it respect nan?

Downloaing data from BIL

One of my datasets is here and includes raw images and folders of txt files with annotations

https://download.brainimagelibrary.org/d9/01/d901fb2108458eca/rr30a/

line/                                              04-Jan-2018 09:19                   -
max/                                               02-Oct-2015 14:18                   -
stackdb/                                           04-Jan-2018 09:03                   -
rr30a_s0_ch1.tif                                   02-Oct-2015 14:30           146883164
rr30a_s0_ch2.tif                                   02-Oct-2015 14:30           146883164
rr30a_s1_ch1.tif                                   02-Oct-2015 14:30           136391514
rr30a_s1_ch2.tif                                   02-Oct-2015 14:30           136391514
rr30a_s2_ch1.tif                                   02-Oct-2015 14:30           146883164
rr30a_s2_ch2.tif                                   02-Oct-2015 14:30           146883164
rr30a_s3_ch1.tif                                   02-Oct-2015 14:30           146883164
rr30a_s3_ch2.tif                                   02-Oct-2015 14:30           146883164
rr30a_s4_ch1.tif                                   02-Oct-2015 14:30           146883164
rr30a_s4_ch2.tif                                   02-Oct-2015 14:30           146883164
rr30a_s5_ch1.tif                                   02-Oct-2015 14:30           167866464
rr30a_s5_ch2.tif                                   02-Oct-2015 14:30           167866464
rr30a_s6_ch1.tif                                   02-Oct-2015 14:30           146883164
rr30a_s6_ch2.tif                                   02-Oct-2015 14:30           146883164
rr30a_s7_ch1.tif                                   02-Oct-2015 14:30           167866464
rr30a_s7_ch2.tif                                   02-Oct-2015 14:30           167866464
rr30a_s8_ch1.tif                                   02-Oct-2015 14:30           146883164
rr30a_s8_ch2.tif                                   02-Oct-2015 14:30           146883164
rr30a_s9_ch1.tif                                   28-Apr-2016 18:37            25710592
rr30a_s9_ch2.tif                                   28-Apr-2016 18:37            25710592