Installation on macOS Big Sur with M1 ARM chip

[felixriese]

Describe the bug I want to install alphapept on my Macbook with M1 chip (ARM). This does not work out-of-the-box. I want to share my learnings and open issues here for others to be more efficient in solving them with new dependency versions available.

Several packages will not work, such as numba, PyQt5 and pythonnet. One error message (regarding numba) is:

FileNotFoundError: [Errno 2] No such file or directory: 'llvm-config'

To Reproduce Steps to reproduce the behavior:

conda create --name alphapept python=3.8
conda activate alphapept
cd
git clone https://github.com/MannLabs/alphapept.git
cd alphapept
pip install -r requirements.txt
pip install .

Expected behavior Installation runs through with out an error and within the python console, I can run:

import alphapept

Version (please complete the following information):

• OS: macOS Big Sur 11.2.2
• Version: Current version (commit 10600097a566b95d9e99bebaabf0c0b51792a5f1)
• Installation Type: pip (see above)

[felixriese]

Quick-and-dirty solution:

1. Install conda miniforge

2. Change requirements.txt to:

biopython==1.78
comtypes==1.1.7
lxml==4.6.1
matplotlib==3.3.3
networkx==2.5
numpy==1.20.1
pandas==1.2.3
psutil==5.7.3
pyyaml==5.3.1
qdarkstyle==2.8.1
qroundprogressbar==1.0.0
tqdm==4.51.0
SQLAlchemy==1.3.20
SQLAlchemy==1.3.20
fastcore==1.3.5
nbdev==1.1.5
click==7.1.2

3. Install alphapept as follows:

conda create --name alphapept python=3.8
conda activate alphapept
cd
git clone https://github.com/MannLabs/alphapept.git
cd alphapept
conda install numpy pandas scikit-learn scipy seaborn pytables h5py
pip install -r requirements.txt
pip install .
conda install numba

TODO: Install two missing packages: PyQt5 and pythonnet.