Installation problem

[annazhukova]

I have tried to install aPhyloGeo using these guidlines on Ubuntu 22.04.4 LTS

I get the following issue:

$:~/Downloads/aPhyloGeo$ make
python aphylogeo/main.py
~/Downloads/aPhyloGeo/aphylogeo/main.py:1: DeprecationWarning: 
Pyarrow will become a required dependency of pandas in the next major release of pandas (pandas 3.0),
(to allow more performant data types, such as the Arrow string type, and better interoperability with other libraries)
but was not found to be installed on your system.
If this would cause problems for you,
please provide us feedback at https://github.com/pandas-dev/pandas/issues/54466

  import pandas as pd
Traceback (most recent call last):
  File "~/Downloads/aPhyloGeo/aphylogeo/main.py", line 3, in <module>
    from aphylogeo.alignement import AlignSequences
ModuleNotFoundError: No module named 'aphylogeo'
make: *** [Makefile:2: aPhylogeo] Error 1

[geomarceau]

Hi annazhukova,

We are using Poetry as packager and installer for dev environment. The main.py is mostly there to give some guidelines for developers on how to use the library.

We got some instructions for dev setup (that could be clarified) here: https://github.com/tahiri-lab/aPhyloGeo/wiki/Contribution-Guidelines#development-setup

1 - install poetry if you dont already have it. best practice is to install it with their setup:

• curl -sSL https://install.python-poetry.org | python3
• OR can be simply installed with pip install poetry. 2 - Clone the repository: git clone https://github.com/tahiri-lab/aPhyloGeo.git. 3 - Install dependencies: poetry install (poetry create and handle the Virtual Environment for you) 4 - Open the Venv: poetry shell

And you should get:

`C:\aphylogeo\aPhyloGeo>poetry install Creating virtualenv aphylogeo-8DOfMLu--py3.11 in C:\Users\gmarceau\AppData\Local\pypoetry\Cache\virtualenvs Installing dependencies from lock file

Package operations: 33 installs, 1 update, 0 removals

• Installing certifi (2023.7.22)
• Installing charset-normalizer (3.3.2)
• Installing idna (3.4)
• ....`

`C:\aphylogeo\aPhyloGeo>poetry shell Spawning shell within C:\Users\gmarceau\AppData\Local\pypoetry\Cache\virtualenvs\aphylogeo-8DOfMLu--py3.11

C:\aphylogeo\aPhyloGeo>()

(aphylogeo-py3.11) C:\aphylogeo\aPhyloGeo>python aphylogeo/main.py

Starting alignement

Searching for the centroid Starting multiprocessing, this might take some time The first process is ran alone for calibration purposes

---

Available memory: 2.27 / 2.78 Gb Active processes: 0 / 83408 ....`

Hope it help.

[annazhukova]

Hi, thank you for adding the development setup instructions.

I managed to run them all right, however with a few minor adjustments that should probably be listed on the page:

1. It seems like python 3.9 is needed (worth specifying in theinstructions). When I tried with python 3.8 poetry install produced an issue "Current Python version (3.8.19) is not allowed by the project (>=3.9.0)."
2. Step 2 should be change the directory to aPhyloGeo: cd aPhyloGeo
3. If one uses conda poetry shell step is not needed (maybe also worth mentioning)
4. Step 4 currently states python.exe aphylogeo/main.py. It is maybe good for Windows, but for linux should be python aphylogeo/main.py (again would not hurt to mention)

Thanks!