Merge pull request #33 from genotoul-bioinfo/dev

 Merge dev branch into Main to release version 1.0.4

.github/workflows/binette_ci.yml

@@ -96,3 +96,16 @@ jobs:
         python scripts/compare_results.py expected_results/final_bins_quality_reports.tsv test_results_from_dirs/final_bins_quality_reports.tsv
 
 
+    - name: Run simple test case from bin dirs and with proteins input
+      run: |
+        cd test_data
+        binette -d binning_results/A/ binning_results/B/ binning_results/C/ \
+                --contigs all_contigs.fna --checkm2_db checkm2_tiny_db/checkm2_tiny_db.dmnd  -v -o test_results_from_dirs_and_prot_input --proteins proteins.faa
+
+    - name: Compare results from bin dirs with expectation
+      run: |
+        cd test_data
+        head  expected_results/final_bins_quality_reports.tsv test_results_from_dirs_and_prot_input/final_bins_quality_reports.tsv
+        python scripts/compare_results.py expected_results/final_bins_quality_reports.tsv test_results_from_dirs_and_prot_input/final_bins_quality_reports.tsv
+
+

.github/workflows/black_lint.yml

@@ -0,0 +1,10 @@
+name: Lint
+
+on: [push, pull_request]
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: psf/black@stable

.gitignore

@@ -63,3 +63,10 @@ cython_debug/
 # Custome folder
 # testing
 test_data/
+
+
+.vscode/
+
+.pytest_cache/
+
+Binette_TestData/

README.md

@@ -177,7 +177,7 @@ To report bugs, request new features, or seek help and support, please open an [
 This program is released as an open source software under the terms of [MIT License](LICENSE).
 
 
-## Citations
+## Citation
 
 Binette is scientific software, with a [published paper](https://joss.theoj.org/papers/10.21105/joss.06782) in the [Journal of Open-Source Software](https://joss.theoj.org/). 
 If you use Binette in academic research, please cite the following paper:

binette/__init__.py

@@ -1 +1 @@
-__version__ = '1.0.3'
+__version__ = "1.0.4"