# fivepseq upgrade

## upgrade process

python3.8 -m venv fivepseq-env
cd fivepseq-env
source bin/activate

## Try 1: this doesn't work
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/mnt/home/lilit/fivepseq-env/lib/python3.8/site-packages/plastid/__init__.py", line 39, in <module>
from plastid.genomics.roitools import (
File "plastid/genomics/roitools.pyx", line 1, in init plastid.genomics.roitools
ImportError: numpy.core.multiarray failed to import (auto-generated because you didn't call 'numpy.import_array()' after cimporting numpy; use '<void>numpy._import_array' to disable if you are certain you don't need it).

git clone https://github.com/joshuagryphon/plastid
cd plastid
pip install -r requirements.txt
pip install --install-option='--recythonize' plastid

## Try 2: trying the development branch which is two commits ahead of master - this one does work!
This thread (
https://github.com/joshuagryphon/plastid/issues/42) claims that the issue has been solved in this branch

Nope! this one doesn't work either!
ModuleNotFoundError: No module named 'plastid.genomics.roitools'

git clone https://github.com/joshuagryphon/plastid -b develop
cd plastid
pip uninstall plastid
python setup.py install

## Install fivepseq

git clone https://github.com/lilit-nersisyan/fivepseq.git
cd fivepseq
python install setup.py
    
pip uninstall bokeh
pip install bokeh=2.4.3
    
python install setup.py
    
fivepseq works, but throws an error: ModuleNotFoundError: No module named '_sqlite3 
    
Trying downgrading biopython to 1.77
    
pip uninstall biopython 
pip install biopython==1.77
    
cd fivepseq
python setup.py install

### Error #1
error: pandas 1.1.5 is installed but pandas>=1.2 is required by {'bokeh'}

## plastid 0.6.1 dependencies

biopython==1.79 (but need 1.77 for fivepseq)
Cython==0.29.28
matplotlib==3.3.4
numpy==1.19.5
pandas==1.1.5
pysam==0.19.0
scipy==1.5.4
termcolor==1.1.0
twobitreader==3.1.7

## fivpeseq dependencies

plastid==0.6.1
pathlib2==2.3.7 (latest)
preconditions==0.1 (latest)
numpy==1.19.5 (plastid req)
pandas==1.1.5 (error with bokeh, which requires >=1.2; bokeh 2.4.3 doesn't enforce pandas versions)
pysam==0.19.0 (plastid req)
dill==0.3.8 (latest)
colorlover==0.3.0 (latest)
bokeh==2.4.3 (downgraded from latest)
logging==0.4.9.6 (latest)