From 7b3cfd2a6373d11b61f600615f18f197da18fbb1 Mon Sep 17 00:00:00 2001
From: Ladislav Hovan <19410951+ladislav-hovan@users.noreply.github.com>
Date: Mon, 3 Aug 2026 16:30:10 +0200
Subject: [PATCH 1/8] Fix a tiny typo

---
 src/sponge/modules/protein_id_mapper/protein_id_mapper.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/sponge/modules/protein_id_mapper/protein_id_mapper.py b/src/sponge/modules/protein_id_mapper/protein_id_mapper.py
index afbbcd1..3d2e793 100644
--- a/src/sponge/modules/protein_id_mapper/protein_id_mapper.py
+++ b/src/sponge/modules/protein_id_mapper/protein_id_mapper.py
@@ -103,7 +103,7 @@ def get_uniprot_mapping(
         if 'results' not in uniprot_status.json():
             # Unable to retrieve the results within the given time
             raise ConnectionError('No results have been retrieved from UniProt'
-                'in the given time')
+                ' in the given time')
 
         # Retrieve the results
         uniprot_results = requests.get(self.mapping_url + f'stream/{job_id}')

From 45a5ecc66f886bf1af78120264b85cab066f056f Mon Sep 17 00:00:00 2001
From: Ladislav Hovan <19410951+ladislav-hovan@users.noreply.github.com>
Date: Tue, 15 Sep 2026 13:53:14 +0200
Subject: [PATCH 2/8] Replace versioning for SPONGE with importlib, eliminate
 setuptools-scm dependency

---
 pyproject.toml       | 1 -
 requirements.txt     | 1 -
 src/sponge/cli.py    | 8 ++------
 src/sponge/sponge.py | 9 +++------
 4 files changed, 5 insertions(+), 14 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 3fe71a5..4ab5fc9 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -25,7 +25,6 @@ dependencies = [
     "pybbi>=0.4.0,<0.5",
     "pyjaspar>=4.0.0,<5",
     "scikit-learn>=1.7.2,<2",
-    "setuptools-scm>=8.3.0,<9",
     "tqdm>=4.67.1,<5",
 ]
 
diff --git a/requirements.txt b/requirements.txt
index fbab6bb..d66fb1c 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -5,5 +5,4 @@ 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/src/sponge/cli.py b/src/sponge/cli.py
index 122f69d..99a3464 100644
--- a/src/sponge/cli.py
+++ b/src/sponge/cli.py
@@ -21,8 +21,8 @@
 
 from argparse import (ArgumentDefaultsHelpFormatter, ArgumentParser,
     RawDescriptionHelpFormatter)
+from importlib.metadata import version
 from pathlib import Path
-from setuptools_scm import get_version
 
 from .sponge import Sponge
 
@@ -77,11 +77,7 @@ def cli(
     args = parser.parse_args()
 
     if args.show_version:
-        print (get_version(
-            Path(__file__).parents[2],
-            version_scheme='only-version',
-            local_scheme='no-local-version',
-        ))
+        print (version('netzoopy-sponge'))
     elif args.example_config:
         file_dir = Path(__file__).parents[0]
         shutil.copy(os.path.join(file_dir, 'user_config.yaml'),
diff --git a/src/sponge/sponge.py b/src/sponge/sponge.py
index 1dbfd27..848368f 100644
--- a/src/sponge/sponge.py
+++ b/src/sponge/sponge.py
@@ -20,8 +20,8 @@
 
 from bioframe import assembly_info
 from functools import wraps
+from importlib.metadata import version
 from pathlib import Path
-from setuptools_scm import get_version
 from typing import Callable, Union
 
 from sponge.config_manager import ConfigManager
@@ -132,11 +132,8 @@ def __init__(
         # Fill in the default values in the user config
         self.fill_default_values()
         self.version_logger = VersionLogger(temp_folder)
-        self.version_logger.write_retrieved('SPONGE', get_version(
-            Path(__file__).parents[2],
-            version_scheme='only-version',
-            local_scheme='no-local-version',
-        ))
+        self.version_logger.write_retrieved('SPONGE',
+            version('netzoopy-sponge'))
         # Retrieve necessary files if required
         self.retrieve_data()
         # Run the default workflow if selected

From ca83fdbc5b03fe1484a864636f6fcbbca1888936 Mon Sep 17 00:00:00 2001
From: Ladislav Hovan <19410951+ladislav-hovan@users.noreply.github.com>
Date: Tue, 15 Sep 2026 13:55:29 +0200
Subject: [PATCH 3/8] Update JASPAR links

---
 src/sponge/config.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/sponge/config.yaml b/src/sponge/config.yaml
index 850572f..5d123b8 100644
--- a/src/sponge/config.yaml
+++ b/src/sponge/config.yaml
@@ -2,12 +2,12 @@
 url:
   motif:
     full:
-    - "https://mencius.uio.no/JASPAR/JASPAR_TFBSs/{year}/\
+    - "https://mencius-pub.uio.no/JASPAR/JASPAR_TFBSs/{year}/\
        JASPAR{year}_{genome_assembly}.bb"
     - "http://expdata.cmmt.ubc.ca/JASPAR/downloads/UCSC_tracks/{year}/\
        JASPAR{year}_{genome_assembly}.bb"
     by_tf:
-    - "https://mencius.uio.no/JASPAR/JASPAR_TFBSs/{year}/\
+    - "https://mencius-pub.uio.no/JASPAR/JASPAR_TFBSs/{year}/\
        {genome_assembly}/"
     - "http://expdata.cmmt.ubc.ca/JASPAR/downloads/UCSC_tracks/{year}/\
        {genome_assembly}/"

From 03c649489f6ffaac930b0b50d5a823b2a770e2d3 Mon Sep 17 00:00:00 2001
From: Ladislav Hovan <19410951+ladislav-hovan@users.noreply.github.com>
Date: Tue, 15 Sep 2026 15:55:06 +0200
Subject: [PATCH 4/8] Change plotting backend for testing

---
 tests/test_sponge.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/tests/test_sponge.py b/tests/test_sponge.py
index 0df14ee..7794238 100644
--- a/tests/test_sponge.py
+++ b/tests/test_sponge.py
@@ -18,6 +18,7 @@
 ### Imports ###
 import bioframe
 import datetime
+import matplotlib
 import os
 import pytest
 import subprocess
@@ -34,6 +35,9 @@
 from sponge.modules.match_aggregator import MatchAggregator
 from sponge.modules.ppi_retriever import PPIRetriever
 
+# Change plotting backend to avoid issues with headless environments
+matplotlib.use('Agg')
+
 ### Fixtures ###
 # Core config fixture
 @pytest.fixture

From 856147d57bc34a076ddcf3180a6cde62dd13b86f Mon Sep 17 00:00:00 2001
From: Ladislav Hovan <19410951+ladislav-hovan@users.noreply.github.com>
Date: Tue, 15 Sep 2026 16:27:51 +0200
Subject: [PATCH 5/8] Change the BioMart link again, add a bit of documentation

---
 src/sponge/config.yaml                     | 2 +-
 src/sponge/modules/utils/data_retrieval.py | 6 +++++-
 2 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/src/sponge/config.yaml b/src/sponge/config.yaml
index 5d123b8..0d15715 100644
--- a/src/sponge/config.yaml
+++ b/src/sponge/config.yaml
@@ -12,7 +12,7 @@ url:
     - "http://expdata.cmmt.ubc.ca/JASPAR/downloads/UCSC_tracks/{year}/\
        {genome_assembly}/"
   region:
-    xml: "http://www.ensembl.org/biomart"
+    xml: "http://jun2026.archive.ensembl.org/biomart"
     rest: "https://rest.ensembl.org"
   protein: "https://rest.uniprot.org/idmapping/"
   ppi: "https://string-db.org/api/tsv/"
diff --git a/src/sponge/modules/utils/data_retrieval.py b/src/sponge/modules/utils/data_retrieval.py
index 8893b9f..6d38c65 100644
--- a/src/sponge/modules/utils/data_retrieval.py
+++ b/src/sponge/modules/utils/data_retrieval.py
@@ -26,7 +26,7 @@
 from io import BytesIO
 from pathlib import Path
 from tqdm import tqdm
-from typing import Iterable, List, Optional, Tuple, Union
+from typing import Iterable, List, Optional, Union
 
 ### Functions ###
 def download_with_progress(
@@ -179,10 +179,14 @@ def retrieve_ensembl_data(
     BytesIO
         Bytes retrieved from the server
     """
+
+    # Formulate the XML query
     xml_query = create_xml_query(dataset_name, requested_fields, filters)
     REQUEST_STRING = '/martservice?query='
+    # Build a full link to the Ensembl BioMart service
     link = ensembl_url + REQUEST_STRING + xml_query
     MAX_ITERATIONS = 50
+    # Various failure messages that can be returned by Ensembl
     FAILURE = ['Query ERROR', 'Service unavailable']
     for _ in range(MAX_ITERATIONS):
         r = requests.get(link, stream=True)

From fabd3a81d82839c1512f4f347db776a641c2eb99 Mon Sep 17 00:00:00 2001
From: Ladislav Hovan <19410951+ladislav-hovan@users.noreply.github.com>
Date: Wed, 16 Sep 2026 11:21:09 +0200
Subject: [PATCH 6/8] Properly close Pools and file handles

---
 src/sponge/config_manager.py                      |  3 ++-
 src/sponge/modules/utils/data_retrieval.py        |  2 ++
 src/sponge/modules/utils/tfbs_filtering.py        |  2 ++
 .../modules/version_logger/version_logger.py      |  8 ++++----
 tests/test_sponge.py                              | 15 ++++++++++-----
 5 files changed, 20 insertions(+), 10 deletions(-)

diff --git a/src/sponge/config_manager.py b/src/sponge/config_manager.py
index c52f738..1895fda 100644
--- a/src/sponge/config_manager.py
+++ b/src/sponge/config_manager.py
@@ -88,7 +88,8 @@ def __del__(
 
         if self.temp_folder is not None:
             log_file = os.path.join(self.temp_folder, self._log_filename)
-            yaml.safe_dump(self.config, open(log_file, 'w', encoding='utf-8'))
+            with open(log_file, 'w', encoding='utf-8') as f:
+                yaml.safe_dump(self.config, f)
 
 
     def __getitem__(
diff --git a/src/sponge/modules/utils/data_retrieval.py b/src/sponge/modules/utils/data_retrieval.py
index 6d38c65..839787c 100644
--- a/src/sponge/modules/utils/data_retrieval.py
+++ b/src/sponge/modules/utils/data_retrieval.py
@@ -106,6 +106,8 @@ def download_with_progress(
 
     if file_path is None:
         return BytesIO(stream.getvalue())
+    else:
+        stream.close()
 
 
 def create_xml_query(
diff --git a/src/sponge/modules/utils/tfbs_filtering.py b/src/sponge/modules/utils/tfbs_filtering.py
index 06a280e..846f640 100644
--- a/src/sponge/modules/utils/tfbs_filtering.py
+++ b/src/sponge/modules/utils/tfbs_filtering.py
@@ -163,6 +163,7 @@ def iterate_chromosomes(
         results_list += edges_chrom_list
         elapsed_chr = time.time() - st_chr
         print (f'Done in: {elapsed_chr // 60:n} m {elapsed_chr % 60:.2f} s')
+    p.close()
 
     return results_list
 
@@ -254,6 +255,7 @@ def process_motif(
     result = p.starmap_async(process_chromosome, input_tuples,
         chunksize=n_processes)
     result_list = result.get()
+    p.close()
     # Merge the results
     df = pd.concat(result_list, ignore_index=True, copy=False)
 
diff --git a/src/sponge/modules/version_logger/version_logger.py b/src/sponge/modules/version_logger/version_logger.py
index eaad214..5be4fae 100644
--- a/src/sponge/modules/version_logger/version_logger.py
+++ b/src/sponge/modules/version_logger/version_logger.py
@@ -58,8 +58,8 @@ def __init__(
         self.data = defaultdict(dict)
         if os.path.exists(self.log_file):
             try:
-                self.data = defaultdict(dict,
-                    yaml.safe_load(open(self.log_file)))
+                with open(self.log_file, 'r', encoding='utf-8') as f:
+                    self.data = yaml.safe_load(f)
             except TypeError:
                 # Most likely means an empty log file, ignore
                 pass
@@ -80,8 +80,8 @@ def __del__(
         """
 
         if len(self.data) > 0:
-            yaml.safe_dump(dict(self.data),
-                open(self.log_file, 'w', encoding='utf-8'))
+            with open(self.log_file, 'w', encoding='utf-8') as f:
+                yaml.safe_dump(dict(self.data), f)
 
 
     def __getitem__(
diff --git a/tests/test_sponge.py b/tests/test_sponge.py
index 7794238..84a8783 100644
--- a/tests/test_sponge.py
+++ b/tests/test_sponge.py
@@ -225,9 +225,11 @@ def test_download_with_progress(input, compare_to, tmp_path):
     else:
         file_path = os.path.join(tmp_path, input[1])
         data_f.download_with_progress(input[0], file_path)
-        data = open(file_path, 'r').read()
+        with open(file_path, 'r', encoding='utf-8') as f:
+            data = f.read()
 
-    comp_data = open(compare_to, 'r').read()
+    with open(compare_to, 'r', encoding='utf-8') as f:
+        comp_data = f.read()
 
     assert data == comp_data
 
@@ -440,7 +442,8 @@ def test_config_manager(c_path, input, expected_length, tmp_path):
 
     assert os.path.exists(config_file)
 
-    data = yaml.safe_load(open(config_file, 'r', encoding='utf-8'))
+    with open(config_file, 'r', encoding='utf-8') as f:
+        data = yaml.safe_load(f)
 
     assert len(data) == expected_length
 
@@ -471,7 +474,8 @@ def test_version_logger(input, expected_length, tmp_path):
 
     assert os.path.exists(fp_file)
 
-    data = yaml.safe_load(open(fp_file, 'r', encoding='utf-8'))
+    with open(fp_file, 'r', encoding='utf-8') as f:
+        data = yaml.safe_load(f)
 
     assert len(data) == expected_length
 
@@ -790,7 +794,8 @@ def run_integration_test_common(
     motif_output = os.path.join(tmp_path, 'motif_prior.tsv')
     ppi_output = os.path.join(tmp_path, 'ppi_prior.tsv')
 
-    settings = yaml.safe_load(open(config_file, 'r'))
+    with open(config_file, 'r', encoding='utf-8') as f:
+        settings = yaml.safe_load(f)
     settings['motif_output']['file_name'] = motif_output
     settings['ppi_output']['file_name'] = ppi_output
 

From 8c0c27fef9611f1940bcbe7a246a8c5a64c0d738 Mon Sep 17 00:00:00 2001
From: Ladislav Hovan <19410951+ladislav-hovan@users.noreply.github.com>
Date: Wed, 16 Sep 2026 14:42:45 +0200
Subject: [PATCH 7/8] Add xfail behaviour for Ensembl-related tests

---
 tests/test_sponge.py | 26 ++++++++++++++++++++++++++
 1 file changed, 26 insertions(+)

diff --git a/tests/test_sponge.py b/tests/test_sponge.py
index 84a8783..acc1c96 100644
--- a/tests/test_sponge.py
+++ b/tests/test_sponge.py
@@ -29,6 +29,7 @@
 from Bio.motifs.jaspar import Motif
 from pathlib import Path
 from pyjaspar import jaspardb, JASPAR_LATEST_RELEASE
+from requests.exceptions import HTTPError
 from typing import Any, Iterable, Tuple
 
 from sponge.config_manager import ConfigManager
@@ -255,6 +256,11 @@ def test_create_xml_query(input):
     ('hsapiens_gene_ensembl', ['ensembl_transcript_id'],
         {'chromosome_name': ['chr19', 'chrX']}),
 ])
+@pytest.mark.xfail(
+    reason='Ensembl server may be down, so this test can fail',
+    raises=[ConnectionError, HTTPError],
+    strict=False,
+)
 def test_retrieve_ensembl_data(dataset, fields, filters, core_config):
     ensembl_url = core_config['url']['region']['xml']
     df = pd.read_table(data_f.retrieve_ensembl_data(dataset, fields,
@@ -544,6 +550,11 @@ def test_tfbs_retriever(settings, assembly, on_the_fly, default_user_config,
     ({'region_file': 'LICENSE'}, 'hg38'),
     ({'chromosomes': ['chr19']}, 'random_assembly'),
 ])
+@pytest.mark.xfail(
+    reason='Ensembl server may be down, so this test can fail',
+    raises=[ConnectionError, HTTPError],
+    strict=False,
+)
 def test_region_retriever(settings, assembly, core_config, default_user_config,
     tmp_path):
     default_user_config.deep_update({'region': settings})
@@ -574,6 +585,11 @@ def test_region_retriever(settings, assembly, core_config, default_user_config,
     {'region': {'chromosomes': ['chr19']}},
     {'on_the_fly_processing': True, 'region': {'chromosomes': ['chr19']}},
 ])
+@pytest.mark.xfail(
+    reason='Ensembl server may be down, so this test can fail',
+    raises=[ConnectionError, HTTPError],
+    strict=False,
+)
 def test_data_retriever(config_update, core_config, default_user_config,
     tmp_path):
     # The full bigbed file is way too big, just a placeholder
@@ -819,6 +835,11 @@ def run_integration_test_common(
 @pytest.mark.integration
 @pytest.mark.network
 @pytest.mark.slow
+@pytest.mark.xfail(
+    reason='Ensembl server may be down, so this test can fail',
+    raises=[ConnectionError, HTTPError],
+    strict=False,
+)
 def test_full_default_workflow(tmp_path):
     _,_ = run_integration_test_common(
         tmp_path,
@@ -829,6 +850,11 @@ def test_full_default_workflow(tmp_path):
 
 @pytest.mark.integration
 @pytest.mark.network
+@pytest.mark.xfail(
+    reason='Ensembl server may be down, so this test can fail',
+    raises=[ConnectionError, HTTPError],
+    strict=False,
+)
 def test_small_workflow(tmp_path):
     motif_output,ppi_output = run_integration_test_common(
         tmp_path,

From f0dbbbacb44c67639c1389b35e257aef69f846b5 Mon Sep 17 00:00:00 2001
From: Ladislav Hovan <19410951+ladislav-hovan@users.noreply.github.com>
Date: Wed, 16 Sep 2026 15:03:37 +0200
Subject: [PATCH 8/8] Change list to tuple for exception types

---
 tests/test_sponge.py | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/tests/test_sponge.py b/tests/test_sponge.py
index acc1c96..978fc20 100644
--- a/tests/test_sponge.py
+++ b/tests/test_sponge.py
@@ -258,7 +258,7 @@ def test_create_xml_query(input):
 ])
 @pytest.mark.xfail(
     reason='Ensembl server may be down, so this test can fail',
-    raises=[ConnectionError, HTTPError],
+    raises=(ConnectionError, HTTPError),
     strict=False,
 )
 def test_retrieve_ensembl_data(dataset, fields, filters, core_config):
@@ -552,7 +552,7 @@ def test_tfbs_retriever(settings, assembly, on_the_fly, default_user_config,
 ])
 @pytest.mark.xfail(
     reason='Ensembl server may be down, so this test can fail',
-    raises=[ConnectionError, HTTPError],
+    raises=(ConnectionError, HTTPError),
     strict=False,
 )
 def test_region_retriever(settings, assembly, core_config, default_user_config,
@@ -587,7 +587,7 @@ def test_region_retriever(settings, assembly, core_config, default_user_config,
 ])
 @pytest.mark.xfail(
     reason='Ensembl server may be down, so this test can fail',
-    raises=[ConnectionError, HTTPError],
+    raises=(ConnectionError, HTTPError),
     strict=False,
 )
 def test_data_retriever(config_update, core_config, default_user_config,
@@ -837,7 +837,7 @@ def run_integration_test_common(
 @pytest.mark.slow
 @pytest.mark.xfail(
     reason='Ensembl server may be down, so this test can fail',
-    raises=[ConnectionError, HTTPError],
+    raises=(ConnectionError, HTTPError),
     strict=False,
 )
 def test_full_default_workflow(tmp_path):
@@ -852,7 +852,7 @@ def test_full_default_workflow(tmp_path):
 @pytest.mark.network
 @pytest.mark.xfail(
     reason='Ensembl server may be down, so this test can fail',
-    raises=[ConnectionError, HTTPError],
+    raises=(ConnectionError, HTTPError),
     strict=False,
 )
 def test_small_workflow(tmp_path):