From 267ef1f29d4c0bd499af97bb2561c8000559e4c7 Mon Sep 17 00:00:00 2001
From: JeanMainguy <jean.mainguy@outlook.fr>
Date: Sat, 4 Nov 2023 09:23:12 +0100
Subject: [PATCH] install binette from bioconda and then install current
 version

---
 .github/workflows/python-package.yml | 63 ----------------------------
 1 file changed, 63 deletions(-)
 delete mode 100644 .github/workflows/python-package.yml

diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
deleted file mode 100644
index 24d7a4c..0000000
--- a/.github/workflows/python-package.yml
+++ /dev/null
@@ -1,63 +0,0 @@
-# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
-# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
-
-name: Python Package using Conda
-
-on: [push] #to any branch
-
-jobs:
-  build:
-
-    runs-on: ubuntu-latest
-    strategy:
-      fail-fast: false
-      matrix:
-        python-version: [3.9] #["3.8", "3.9", "3.10"]
-
-    steps:
-    - uses: actions/checkout@v3
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v3
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Add conda to system path
-      run: |
-        # $CONDA is an environment variable pointing to the root of the miniconda directory
-        echo $CONDA/bin >> $GITHUB_PATH
-    - name: Install mamba
-      run: |
-        conda install -c conda-forge mamba
-    - name: Install binette dependencies
-      run: |
-        mamba env update --file binette.yaml --name base
-    - name: Install binette
-      run: |
-        pip install .
-        binette -h
-    - name: Lint with flake8
-      run: |
-        conda install flake8
-        # 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
-      run: |
-        conda install pytest
-        pytest
-
-    - name: Download test data
-      uses: actions/checkout@v3
-      with:
-        repository: genotoul-bioinfo/Binette_TestData
-        path: test_data
-
-    - name: Run simple test case
-      run: |
-        cd test_data
-        binette -b binning_results/* --contigs all_contigs.fna --checkm2_db checkm2_tiny_db/checkm2_tiny_db.dmnd  -v -o test_results
-    - name: Compare results with expectation
-      run: |
-        cd test_data
-        head  expected_results/final_bins_quality_reports.tsv test_results/final_bins_quality_reports.tsv
-        python scripts/compare_results.py expected_results/final_bins_quality_reports.tsv test_results/final_bins_quality_reports.tsv