From d7973903b51bc519434b8b0bfbb896226eb245fb Mon Sep 17 00:00:00 2001
From: Ladislav Hovan <19410951+ladislav-hovan@users.noreply.github.com>
Date: Thu, 26 Mar 2026 11:14:57 +0100
Subject: [PATCH 1/3] Pin requirements.txt versions, modify CLI test

---
 requirements.txt     | 18 +++++++++---------
 tests/test_sponge.py | 12 +++++++++---
 2 files changed, 18 insertions(+), 12 deletions(-)

diff --git a/requirements.txt b/requirements.txt
index 0584610..fbab6bb 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,9 +1,9 @@
-bioframe
-matplotlib
-numpy
-pandas
-pybbi
-pyjaspar
-scikit-learn
-setuptools-scm
-tqdm
\ No newline at end of file
+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
diff --git a/tests/test_sponge.py b/tests/test_sponge.py
index f33cf11..0df14ee 100644
--- a/tests/test_sponge.py
+++ b/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'))
 

From 8689b8e62ec590570580d28e0d00537dbfd15406 Mon Sep 17 00:00:00 2001
From: Ladislav Hovan <19410951+ladislav-hovan@users.noreply.github.com>
Date: Thu, 26 Mar 2026 11:27:44 +0100
Subject: [PATCH 2/3] Potentially fix CLI test when run on GH

---
 .github/workflows/test.yaml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml
index 27c0602..f2bc8af 100644
--- a/.github/workflows/test.yaml
+++ b/.github/workflows/test.yaml
@@ -28,6 +28,8 @@ jobs:
     steps:
     - name: Checkout repository
       uses: actions/checkout@v6
+      with:
+        fetch-depth: 0
 
     - name: Setup Python
       uses: actions/setup-python@v6

From c70e32f150638639f320c0682af59eba342fff04 Mon Sep 17 00:00:00 2001
From: Ladislav Hovan <19410951+ladislav-hovan@users.noreply.github.com>
Date: Thu, 26 Mar 2026 12:52:38 +0100
Subject: [PATCH 3/3] Add Zenodo badge, restrict test running scenarios

---
 .github/workflows/test.yaml | 1 -
 README.md                   | 1 +
 2 files changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml
index f2bc8af..2f3ec77 100644
--- a/.github/workflows/test.yaml
+++ b/.github/workflows/test.yaml
@@ -3,7 +3,6 @@ name: SPONGE tests
 on:
   push:
     branches:
-    - main
     - devel
   pull_request:
     branches:
diff --git a/README.md b/README.md
index de1a4de..e8ab097 100644
--- a/README.md
+++ b/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