v2.2.2

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",
 ]
 

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

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'),

src/sponge/config.yaml

@@ -2,17 +2,17 @@
 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}/"
   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/"

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__(

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}')

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(
@@ -106,6 +106,8 @@ def download_with_progress(
 
     if file_path is None:
         return BytesIO(stream.getvalue())
+    else:
+        stream.close()
 
 
 def create_xml_query(
@@ -179,10 +181,14 @@ 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)

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)
 

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__(

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

tests/test_sponge.py

@@ -18,6 +18,7 @@
 ### Imports ###
 import bioframe
 import datetime
+import matplotlib
 import os
 import pytest
 import subprocess
@@ -28,12 +29,16 @@
 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
 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
@@ -221,9 +226,11 @@ 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
 
@@ -249,6 +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,
@@ -436,7 +448,8 @@ 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
 
@@ -467,7 +480,8 @@ 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
 
@@ -536,6 +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})
@@ -566,6 +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
@@ -786,7 +810,8 @@ 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
 
@@ -810,6 +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,
@@ -820,6 +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,