Incorporate latest changes and small fixes

.github/workflows/test.yaml

@@ -3,7 +3,6 @@ name: SPONGE tests
 on:
   push:
     branches:
-    - main
     - devel
   pull_request:
     branches:
@@ -28,6 +27,8 @@ jobs:
     steps:
     - name: Checkout repository
       uses: actions/checkout@v6
+      with:
+        fetch-depth: 0
 
     - name: Setup Python
       uses: actions/setup-python@v6

README.md

@@ -1,6 +1,7 @@
 [![main](https://img.shields.io/github/actions/workflow/status/kuijjerlab/sponge/test.yaml?branch=main&label=main)](https://github.com/kuijjerlab/sponge/actions/workflows/test.yaml)
 [![devel](https://img.shields.io/github/actions/workflow/status/kuijjerlab/sponge/test.yaml?branch=devel&label=devel)](https://github.com/kuijjerlab/sponge/actions/workflows/test.yaml)
 [![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.13628784.svg)](https://doi.org/10.5281/zenodo.13628784)
 
 
 # SPONGE - Simple Prior Omics Network GEnerator

requirements.txt

@@ -1,9 +1,9 @@
-bioframe
-matplotlib
-numpy
-pandas
-pybbi
-pyjaspar
-scikit-learn
-setuptools-scm
-tqdm
+bioframe == 0.8.0
+matplotlib == 3.10.8
+numpy == 2.2.6
+pandas == 2.3.3
+pybbi == 0.4.2
+pyjaspar == 4.0.0
+scikit-learn == 1.7.2
+setuptools-scm == 8.3.1
+tqdm == 4.67.1

tests/test_sponge.py

@@ -746,9 +746,15 @@ def test_file_writer(input, prior_frame, tmp_path):
 
 ### CLI tests ###
 def test_basic_cli(tmp_path):
-    subprocess.run(['netzoopy-sponge', '-h'], cwd=tmp_path)
-    subprocess.run(['netzoopy-sponge', '-v'], cwd=tmp_path)
-    subprocess.run(['netzoopy-sponge', '-e'], cwd=tmp_path)
+    for flag in ['-h', '-v', '-e']:
+        result = subprocess.run(['netzoopy-sponge', flag], cwd=tmp_path,
+            capture_output=True, text=True)
+        # This ensures that if something went wrong, we will see the whole
+        # error message - check=True may only show a tiny part
+        stderr_output = result.stderr
+        if stderr_output:
+            print (stderr_output)
+        assert not stderr_output
 
     assert os.path.exists(os.path.join(tmp_path, 'user_config.yaml'))