Replace requirements.txt with environment.yml, fix python-package pipeline

.github/workflows/python-package.yml

@@ -20,20 +20,25 @@ jobs:
     steps:
     - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v3
+      uses: conda-incubator/setup-miniconda@v3
       with:
         python-version: ${{ matrix.python-version }}
+        environment-file: environment.yml
+        auto-activate-base: false
+        activate-environment: probest
+        channels: conda-forge,bioconda,defaults
     - name: Install dependencies
+      shell: bash -l {0}
       run: |
-        python -m pip install --upgrade pip
-        python -m pip install flake8 pytest pytest-cov
-        pip install -e .[dev]
+        python setup.py install
     - name: Lint with flake8
+      shell: bash -l {0}
       run: |
         # stop the build if there are Python syntax errors or undefined names
         flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
         # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
         flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
     - name: Test with pytest
+      shell: bash -l {0}
       run: |
         pytest

README.md

@@ -17,9 +17,8 @@ At the core of PROBEst is an AI-enhanced workflow that combines Primer3 for init
 ```bash
 git clone https://github.com/CTLab-ITMO/PROBEst.git
 cd PROBEst
-conda create -n probest
+conda env create -f environment.yml
 conda activate probest
-conda install --file requirements.txt
 python setup.py install
 ```
 

environment.yml

@@ -0,0 +1,27 @@
+name: probest
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - biopython>=1.81
+  - pandas>=1.5.0
+  - numpy>=1.21.0
+  - requests>=2.28.0
+  - beautifulsoup4>=4.11.0
+  - pytest>=7.0.0
+  - pytest-cov>=4.0.0
+  - tqdm>=4.67.1
+  - scikit-learn>=1.0.2
+  - matplotlib>=3.5.0
+  - seaborn>=0.12.0
+  - pytorch>=2.0.0
+  - blast>=2.16.0
+  - primer3>=2.6.1
+  - flake8>=7.3.0
+  - pip:
+    - ViennaRNA==2.6.4
+  #optional: PDF parsing
+  #- PyMuPDF>=1.23.0
+  #- pdfplumber>=0.9.0
+  #- PyPDF2>=3.0.0

setup.py

@@ -1,18 +1,12 @@
 from setuptools import setup, find_packages
 import os
 
-def read_requirements():
-    """Read requirements from requirements.txt."""
-    with open('requirements.txt') as f:
-        return [line.strip() for line in f if line.strip() and not line.startswith('#')]
-
 setup(
     name='PROBESt',
     version='0.1.4',
     packages=find_packages(where='src'),
     package_dir={'': 'src'},
     python_requires='>=3.8',
-    install_requires=read_requirements(),
     author='Your Name',
     author_email='your.email@example.com',
     description='PROBESt: package for nucleotide probes generation',