/WikidPad

WikidPad is a single user desktop wiki

Primary LanguagePython

Setuptools (pip) package for WikidPad (WikidPadMP)

Wikidpad (WP) is a personal wiki written in Python. See the original repository for more information here.

There are two important differences between this version and the original (see at the end of this page).

  1. The original wikidpad is usually installed via a binary installer. This version is installed as a conda or pip package.

    pip install WikidPadMP

  2. A series of plugins are distributed along with wikidpad. These are located in the WikidPad/user_extensions directory and can be removed.

We call these plugins "mecplugins" and they help us with biology and molecular biology work.

Installation with Anaconda

  1. Install Anaconda or Miniconda.

  2. Create a new conda environment with python 3.8 conda create python=3.8 -n wp38

  3. Activate this environment conda activate wp38

  4. Install wikidpad by conda install -c bjornfjohansson wikidpadmp

  5. run from terminal by ~/anaconda3/envs/wp38/bin/wikidpad

  6. conda info

(bjorn39) bjorn@bjorn-ThinkPad-T450s:~$ conda info

 active environment : bjorn39
active env location : /home/bjorn/anaconda3/envs/bjorn39
        shell level : 2
   user config file : /home/bjorn/.condarc

populated config files : /home/bjorn/.condarc conda version : 4.9.2 conda-build version : 3.20.5 python version : 3.8.3.final.0 virtual packages : __glibc=2.31=0 __unix=0=0 __archspec=1=x86_64 base environment : /home/bjorn/anaconda3 (writable) channel URLs : https://conda.anaconda.org/conda-forge/linux-64 https://conda.anaconda.org/conda-forge/noarch https://repo.anaconda.com/pkgs/main/linux-64 https://repo.anaconda.com/pkgs/main/noarch https://repo.anaconda.com/pkgs/r/linux-64 https://repo.anaconda.com/pkgs/r/noarch https://conda.anaconda.org/BjornFJohansson/linux-64 https://conda.anaconda.org/BjornFJohansson/noarch package cache : /home/bjorn/anaconda3/pkgs /home/bjorn/.conda/pkgs envs directories : /home/bjorn/anaconda3/envs /home/bjorn/.conda/envs platform : linux-64 user-agent : conda/4.9.2 requests/2.25.1 CPython/3.8.3 Linux/5.4.0-64-generic linuxmint/20.1 glibc/2.31 UID:GID : 1000:1000 netrc file : None offline mode : False

active env location : /home/bjorn/anaconda3/envs/bjorn39

.desktop file for linux:

#!/usr/bin/env xdg-open
[Desktop Entry]
Name=wikidpad
Type=Application
Exec=/home/bjorn/bin/wikidpad
Terminal=false
StartupNotify=true
MimeType=
Icon=/home/bjorn/Desktop/python_packages/WikidPad/WikidPad/Wikidpad_128x128x32.png
Categories=Office;

Conda packages

WikidPadMP can also be run from source in editable mode by downloading this repository:

conda install wxpython pillow matplotlib natsort scipy dateparser appdirs biopython prettytable networkx pyparsing gspread

pip install --editable . --no-deps

Where is what?