SigProfilerExtractor 1.4.0__tar.gz → 1.4.1__tar.gz

{sigprofilerextractor-1.4.0 → sigprofilerextractor-1.4.1}/.github/workflows/ci.yml

@@ -70,7 +70,11 @@ jobs:
     - name: Install genome
       run: |
         python install_genome.py ${{ github.workspace }}/src/
-    
+
+    - name: Run unit tests
+      run: |
+        python -m unittest discover -s tests -v
+
     - name: Run tests
       run: |
         python3 test.py

{sigprofilerextractor-1.4.0 → sigprofilerextractor-1.4.1}/CHANGELOG.md

@@ -7,6 +7,10 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 
 ## [Unreleased]
 
+### Changed
+- Updated the default COSMIC reference signature version from 3.5 to 3.6.
+- Updated the minimum SigProfilerAssignment version to 1.1.5 for COSMIC v3.6 support.
+
 ## [1.2.7] - 2026-01-22
 
 ### Fixed

{sigprofilerextractor-1.4.0 → sigprofilerextractor-1.4.1}/Dockerfile

@@ -9,6 +9,9 @@ RUN apt-get update && apt-get install -y \
     python3-pip python3-dev git && \
     apt-get clean && rm -rf /var/lib/apt/lists/*
 
+# Upgrade Ubuntu's packaging tools before invoking the PEP 517 build backend.
+RUN python3 -m pip install --no-cache-dir --upgrade pip setuptools wheel
+
 WORKDIR /usr/src/app
 
 # Install GPU-enabled PyTorch wheels

{sigprofilerextractor-1.4.0 → sigprofilerextractor-1.4.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SigProfilerExtractor
-Version: 1.4.0
+Version: 1.4.1
 Summary: Extracts mutational signatures from mutational catalogues
 Home-page: https://github.com/SigProfilerSuite/SigProfilerExtractor.git
 Author: S Mishu Ashiqul Islam
@@ -15,7 +15,7 @@ Requires-Dist: numpy>=2.0.0
 Requires-Dist: pandas>=2.0.0
 Requires-Dist: sigProfilerPlotting>=1.4.3
 Requires-Dist: SigProfilerMatrixGenerator>=1.3.5
-Requires-Dist: SigProfilerAssignment>=1.1.3
+Requires-Dist: SigProfilerAssignment>=1.1.5
 Requires-Dist: statsmodels>=0.9.0
 Requires-Dist: scikit-learn>=0.24.2
 Requires-Dist: psutil>=5.6.1
@@ -120,7 +120,7 @@ help(sig.importdata)
 Extracts mutational signatures from an array of samples.
 
 ```python 
-sigProfilerExtractor(input_type, out_put, input_data, reference_genome="GRCh37", opportunity_genome = "GRCh37", context_type = "default", exome = False, 
+sigProfilerExtractor(input_type, out_put, input_data, reference_genome="GRCh37", opportunity_genome = "GRCh37", cosmic_version=3.6, context_type = "default", exome = False,
                          minimum_signatures=1, maximum_signatures=10, nmf_replicates=100, resample = True, batch_size=1, cpu=-1, gpu=False, 
                          nmf_init="random", precision= "single", matrix_normalization= "gmm", seeds= "random", 
                          min_nmf_iterations= 10000, max_nmf_iterations=1000000, nmf_test_conv= 10000, nmf_tolerance= 1e-15, get_all_signature_matrices= False)
@@ -161,7 +161,7 @@ sigProfilerExtractor(input_type, out_put, input_data, reference_genome="GRCh37",
 |  | **combined_stability** | Float | The cutoff thresh-hold of the combined stability (sum of average and minimum stability) (default: `1.0`). Solutions with combined stabilities below this thresh-hold will not be considered. |
 |  | **allow_stability_drop** | Boolean | Defines if solutions with a drop in stability with respect to the highest stable number of signatures will be considered (default: `False`). |
 | **Decomposition** |  |  |  | 
-|  | **cosmic_version** | Float | Defines the version of the COSMIC reference signatures (default: `3.5`). Takes a positive float among `1`, `2`, `3`, `3.1`, `3.2`, `3.3`, `3.4`, and `3.5`.|
+|  | **cosmic_version** | Float | Defines the version of the COSMIC reference signatures (default: `3.6`). Takes a positive float among `1`, `2`, `3`, `3.1`, `3.2`, `3.3`, `3.4`, `3.5`, and `3.6`.|
 |  | **make_decomposition_plots** | Boolean | Generate de novo to COSMIC signature decomposition plots as part of the results (default: `True`). Set to `False` to skip generating these plots. |
 |  | **collapse_to_SBS96** | Boolean | If `True`, SBS288 and SBS1536 de novo signatures will be mapped to SBS96 reference signatures (default: `True`). If `False`, those will be mapped to reference signatures of the same context.
 | **Others** |  |  |  | 

{sigprofilerextractor-1.4.0 → sigprofilerextractor-1.4.1}/README.md

@@ -88,7 +88,7 @@ help(sig.importdata)
 Extracts mutational signatures from an array of samples.
 
 ```python 
-sigProfilerExtractor(input_type, out_put, input_data, reference_genome="GRCh37", opportunity_genome = "GRCh37", context_type = "default", exome = False, 
+sigProfilerExtractor(input_type, out_put, input_data, reference_genome="GRCh37", opportunity_genome = "GRCh37", cosmic_version=3.6, context_type = "default", exome = False,
                          minimum_signatures=1, maximum_signatures=10, nmf_replicates=100, resample = True, batch_size=1, cpu=-1, gpu=False, 
                          nmf_init="random", precision= "single", matrix_normalization= "gmm", seeds= "random", 
                          min_nmf_iterations= 10000, max_nmf_iterations=1000000, nmf_test_conv= 10000, nmf_tolerance= 1e-15, get_all_signature_matrices= False)
@@ -129,7 +129,7 @@ sigProfilerExtractor(input_type, out_put, input_data, reference_genome="GRCh37",
 |  | **combined_stability** | Float | The cutoff thresh-hold of the combined stability (sum of average and minimum stability) (default: `1.0`). Solutions with combined stabilities below this thresh-hold will not be considered. |
 |  | **allow_stability_drop** | Boolean | Defines if solutions with a drop in stability with respect to the highest stable number of signatures will be considered (default: `False`). |
 | **Decomposition** |  |  |  | 
-|  | **cosmic_version** | Float | Defines the version of the COSMIC reference signatures (default: `3.5`). Takes a positive float among `1`, `2`, `3`, `3.1`, `3.2`, `3.3`, `3.4`, and `3.5`.|
+|  | **cosmic_version** | Float | Defines the version of the COSMIC reference signatures (default: `3.6`). Takes a positive float among `1`, `2`, `3`, `3.1`, `3.2`, `3.3`, `3.4`, `3.5`, and `3.6`.|
 |  | **make_decomposition_plots** | Boolean | Generate de novo to COSMIC signature decomposition plots as part of the results (default: `True`). Set to `False` to skip generating these plots. |
 |  | **collapse_to_SBS96** | Boolean | If `True`, SBS288 and SBS1536 de novo signatures will be mapped to SBS96 reference signatures (default: `True`). If `False`, those will be mapped to reference signatures of the same context.
 | **Others** |  |  |  | 

sigprofilerextractor-1.4.1/SigProfilerExtractor/_version.py

@@ -0,0 +1 @@
+version = '1.4.1'

{sigprofilerextractor-1.4.0 → sigprofilerextractor-1.4.1}/SigProfilerExtractor/controllers/cli_controller.py

@@ -209,8 +209,12 @@ def parse_arguments_extractor(args: List[str], description: str) -> argparse.Nam
     parser.add_argument(
         "--cosmic_version",
         type=float,
-        default=3.5,
-        help="COSMIC version for reference signatures. Valid values are 1, 2, 3, 3.1, 3.2, 3.3, 3.4, and 3.5 (default: 3.5).",
+        default=sigpro.DEFAULT_COSMIC_VERSION,
+        help=(
+            "COSMIC version for reference signatures. Valid values are "
+            f"{', '.join(map(str, sigpro.SUPPORTED_COSMIC_VERSIONS))} "
+            f"(default: {sigpro.DEFAULT_COSMIC_VERSION})."
+        ),
     )
     parser.add_argument(
         "--make_decomposition_plots",

{sigprofilerextractor-1.4.0 → sigprofilerextractor-1.4.1}/SigProfilerExtractor/sigpro.py

@@ -55,6 +55,9 @@ from SigProfilerAssignment import decomposition as decomp
 from numpy.random import SeedSequence
 from sigProfilerPlotting import sigProfilerPlotting as sigPlot
 
+DEFAULT_COSMIC_VERSION = 3.6
+SUPPORTED_COSMIC_VERSIONS = (1, 2, 3, 3.1, 3.2, 3.3, 3.4, 3.5, 3.6)
+
 MUTTYPE = "MutationType"
 
 
@@ -240,7 +243,7 @@ def sigProfilerExtractor(
     input_data,
     reference_genome="GRCh37",
     opportunity_genome="GRCh37",
-    cosmic_version=3.5,
+    cosmic_version=DEFAULT_COSMIC_VERSION,
     context_type="default",
     exome=False,
     minimum_signatures=1,
@@ -356,6 +359,8 @@ def sigProfilerExtractor(
 
     DECOMPOSITION:-
 
+    cosmic_version: Float, optional. Defines the version of the COSMIC reference signatures. Default is 3.6.
+
     nnls_add_penalty: Float, optional. Takes any positive float. Default is 0.05. Defines the strong (add) thresh-hold cutoff to be assigned signatures to a sample.
 
     nnls_remove_penalty: Float, optional. Takes any positive float. Default is 0.01. Defines the weak (remove) thresh-hold cutoff to be assigned signatures to a sample.

{sigprofilerextractor-1.4.0 → sigprofilerextractor-1.4.1}/SigProfilerExtractor.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SigProfilerExtractor
-Version: 1.4.0
+Version: 1.4.1
 Summary: Extracts mutational signatures from mutational catalogues
 Home-page: https://github.com/SigProfilerSuite/SigProfilerExtractor.git
 Author: S Mishu Ashiqul Islam
@@ -15,7 +15,7 @@ Requires-Dist: numpy>=2.0.0
 Requires-Dist: pandas>=2.0.0
 Requires-Dist: sigProfilerPlotting>=1.4.3
 Requires-Dist: SigProfilerMatrixGenerator>=1.3.5
-Requires-Dist: SigProfilerAssignment>=1.1.3
+Requires-Dist: SigProfilerAssignment>=1.1.5
 Requires-Dist: statsmodels>=0.9.0
 Requires-Dist: scikit-learn>=0.24.2
 Requires-Dist: psutil>=5.6.1
@@ -120,7 +120,7 @@ help(sig.importdata)
 Extracts mutational signatures from an array of samples.
 
 ```python 
-sigProfilerExtractor(input_type, out_put, input_data, reference_genome="GRCh37", opportunity_genome = "GRCh37", context_type = "default", exome = False, 
+sigProfilerExtractor(input_type, out_put, input_data, reference_genome="GRCh37", opportunity_genome = "GRCh37", cosmic_version=3.6, context_type = "default", exome = False,
                          minimum_signatures=1, maximum_signatures=10, nmf_replicates=100, resample = True, batch_size=1, cpu=-1, gpu=False, 
                          nmf_init="random", precision= "single", matrix_normalization= "gmm", seeds= "random", 
                          min_nmf_iterations= 10000, max_nmf_iterations=1000000, nmf_test_conv= 10000, nmf_tolerance= 1e-15, get_all_signature_matrices= False)
@@ -161,7 +161,7 @@ sigProfilerExtractor(input_type, out_put, input_data, reference_genome="GRCh37",
 |  | **combined_stability** | Float | The cutoff thresh-hold of the combined stability (sum of average and minimum stability) (default: `1.0`). Solutions with combined stabilities below this thresh-hold will not be considered. |
 |  | **allow_stability_drop** | Boolean | Defines if solutions with a drop in stability with respect to the highest stable number of signatures will be considered (default: `False`). |
 | **Decomposition** |  |  |  | 
-|  | **cosmic_version** | Float | Defines the version of the COSMIC reference signatures (default: `3.5`). Takes a positive float among `1`, `2`, `3`, `3.1`, `3.2`, `3.3`, `3.4`, and `3.5`.|
+|  | **cosmic_version** | Float | Defines the version of the COSMIC reference signatures (default: `3.6`). Takes a positive float among `1`, `2`, `3`, `3.1`, `3.2`, `3.3`, `3.4`, `3.5`, and `3.6`.|
 |  | **make_decomposition_plots** | Boolean | Generate de novo to COSMIC signature decomposition plots as part of the results (default: `True`). Set to `False` to skip generating these plots. |
 |  | **collapse_to_SBS96** | Boolean | If `True`, SBS288 and SBS1536 de novo signatures will be mapped to SBS96 reference signatures (default: `True`). If `False`, those will be mapped to reference signatures of the same context.
 | **Others** |  |  |  | 

{sigprofilerextractor-1.4.0 → sigprofilerextractor-1.4.1}/SigProfilerExtractor.egg-info/SOURCES.txt

@@ -31,6 +31,8 @@ SigProfilerExtractor.egg-info/dependency_links.txt
 SigProfilerExtractor.egg-info/entry_points.txt
 SigProfilerExtractor.egg-info/not-zip-safe
 SigProfilerExtractor.egg-info/requires.txt
+SigProfilerExtractor.egg-info/scm_file_list.json
+SigProfilerExtractor.egg-info/scm_version.json
 SigProfilerExtractor.egg-info/top_level.txt
 SigProfilerExtractor/controllers/cli_controller.py
 SigProfilerExtractor/data/CNVInput/Battenberg_test.tsv
@@ -79,6 +81,7 @@ docs/assets/images/osf/yhqnw.png
 docs/assets/images/osf/z98fk.png
 docs/assets/images/osf/zu6sm.png
 docs/assets/stylesheets/extra.css
+tests/test_cosmic_version.py
 wikies/CLI-Usage.md
 wikies/Citation.md
 wikies/Home.md

{sigprofilerextractor-1.4.0 → sigprofilerextractor-1.4.1}/SigProfilerExtractor.egg-info/requires.txt

@@ -4,7 +4,7 @@ numpy>=2.0.0
 pandas>=2.0.0
 sigProfilerPlotting>=1.4.3
 SigProfilerMatrixGenerator>=1.3.5
-SigProfilerAssignment>=1.1.3
+SigProfilerAssignment>=1.1.5
 statsmodels>=0.9.0
 scikit-learn>=0.24.2
 psutil>=5.6.1

sigprofilerextractor-1.4.1/SigProfilerExtractor.egg-info/scm_file_list.json

@@ -0,0 +1,85 @@
+{
+  "files": [
+    "LICENSE.txt",
+    "mkdocs.yml",
+    "CHANGELOG.md",
+    "mkdocs_hooks.py",
+    "MANIFEST.in",
+    "Dockerfile",
+    "setup.py",
+    "pyproject.toml",
+    "test.py",
+    "README.md",
+    "install_genome.py",
+    ".gitignore",
+    ".github/workflows/ci.yml",
+    ".github/workflows/static.yml",
+    ".github/workflows/create-version-tag.yml",
+    ".github/workflows/release.yml",
+    ".github/workflows/docs.yml",
+    "tests/test_cosmic_version.py",
+    "SigProfilerExtractor/nmf_gpu.py",
+    "SigProfilerExtractor/subroutines.py",
+    "SigProfilerExtractor/__init__.py",
+    "SigProfilerExtractor/nmf_cpu.py",
+    "SigProfilerExtractor/version.py",
+    "SigProfilerExtractor/sigpro.py",
+    "SigProfilerExtractor/nndsvd.py",
+    "SigProfilerExtractor/estimate_best_solution.py",
+    "SigProfilerExtractor/sigprofilerextractor_cli.py",
+    "SigProfilerExtractor/data/MatObjInput/21_breast_WGS_substitutions.mat",
+    "SigProfilerExtractor/data/TextInput/Samples_SBS.txt",
+    "SigProfilerExtractor/data/TextInput/Samples_SV.txt",
+    "SigProfilerExtractor/data/TextInput/Samples_CNV.txt",
+    "SigProfilerExtractor/data/TextInput/Samples_DBS.txt",
+    "SigProfilerExtractor/data/TextInput/Samples_ID.txt",
+    "SigProfilerExtractor/data/CNVInput/Battenberg_test.tsv",
+    "SigProfilerExtractor/data/VCFInput/PD3905a.vcf",
+    "SigProfilerExtractor/data/VCFInput/PD3851a.vcf",
+    "SigProfilerExtractor/data/VCFInput/PD3890a.vcf",
+    "SigProfilerExtractor/data/VCFInput/PD3945a.vcf",
+    "SigProfilerExtractor/data/VCFInput/PD3904a.vcf",
+    "SigProfilerExtractor/data/CSVInput/csv_example.csv",
+    "SigProfilerExtractor/data/ReferenceFiles/CN_classes_dictionary.txt",
+    "SigProfilerExtractor/data/ReferenceFiles/CNV_features.tsv",
+    "SigProfilerExtractor/controllers/cli_controller.py",
+    "docs/4. Using the Tool - Output.md",
+    "docs/2. Quick Start Example.md",
+    "docs/3. Using the Tool - Input.md",
+    "docs/5. Output - All Solutions.md",
+    "docs/6. Output - Suggested Solution.md",
+    "docs/home.md",
+    "docs/1. Installation.md",
+    "docs/index.md",
+    "docs/assets/images/osf/whn8t.png",
+    "docs/assets/images/osf/h796w.png",
+    "docs/assets/images/osf/z98fk.png",
+    "docs/assets/images/osf/dahws.png",
+    "docs/assets/images/osf/xcm95.png",
+    "docs/assets/images/osf/5u7v8.png",
+    "docs/assets/images/osf/yhqnw.png",
+    "docs/assets/images/osf/5tr9y.png",
+    "docs/assets/images/osf/9uf4s.png",
+    "docs/assets/images/osf/rz3ue.png",
+    "docs/assets/images/osf/a7gkf.png",
+    "docs/assets/images/osf/4hnaj.png",
+    "docs/assets/images/osf/kb4w2.png",
+    "docs/assets/images/osf/5f8ep.png",
+    "docs/assets/images/osf/xqzfh.png",
+    "docs/assets/images/osf/p4cfj.png",
+    "docs/assets/images/osf/c5hzf.png",
+    "docs/assets/images/osf/zu6sm.png",
+    "docs/assets/images/osf/r9wcm.png",
+    "docs/assets/images/osf/akef5.png",
+    "docs/assets/images/osf/h3tvx.png",
+    "docs/assets/images/osf/ku93g.png",
+    "docs/assets/stylesheets/extra.css",
+    "wikies/Home.md",
+    "wikies/CLI-Usage.md",
+    "wikies/Citation.md",
+    "wikies/Installation.md",
+    "wikies/Python-API.md",
+    "wikies/_Sidebar.md",
+    "wikies/Output.md"
+  ]
+}

sigprofilerextractor-1.4.1/SigProfilerExtractor.egg-info/scm_version.json

@@ -0,0 +1,8 @@
+{
+  "tag": "1.4.1",
+  "distance": 0,
+  "node": "ge7e36e4fce537e598894e39eab4aaffee025c66e",
+  "dirty": false,
+  "branch": "HEAD",
+  "node_date": "2026-07-31"
+}

{sigprofilerextractor-1.4.0 → sigprofilerextractor-1.4.1}/docs/3. Using the Tool - Input.md

@@ -77,7 +77,7 @@ The full list of parameters is included in the following table:
 |  | **min_stability** | Float | Default is 0.2. The cutoff thresh-hold of the minimum stability. Solutions with minimum stabilities below this thresh-hold will not be considered.  | 
 |  | **combined_stability** | Float | Default is 1.0. The cutoff thresh-hold of the combined stability (sum of average and minimum stability). Solutions with combined stabilities below this thresh-hold will not be considered. | 
 | **Decomposition** |  |  |  | 
-|  | **cosmic_version** | Float | Takes a positive float among 1, 2, 3, 3.1, 3.2. Default is 3.1. Defines the version of COSMIC reference signatures. | 
+|  | **cosmic_version** | Float | Takes a positive float among 1, 2, 3, 3.1, 3.2, 3.3, 3.4, 3.5, and 3.6. Default is 3.6. Defines the version of COSMIC reference signatures. |
 |  | **de_novo_fit_penalty** | Float | Takes any positive float. Default is 0.02. Defines the weak (remove) thresh-hold cutoff to assign denovo signatures to a sample. | 
 |  | **nnls_add_penalty** | Float | Takes any positive float. Default is 0.05. Defines the strong (add) thresh-hold cutoff to assign COSMIC signatures to a sample. | 
 |  | **nnls_remove_penalty** | Float | Takes any positive float. Default is 0.01. Defines the weak (remove) thresh-hold cutoff to assign COSMIC signatures to a sample. | 

{sigprofilerextractor-1.4.0 → sigprofilerextractor-1.4.1}/setup.py

@@ -12,7 +12,7 @@ INSTALL_REQUIRES = [
     "pandas>=2.0.0",
     "sigProfilerPlotting>=1.4.3",  # Requires v1.4.3+ for pandas 3.12 compatibility fixes in tmbplot.py
     "SigProfilerMatrixGenerator>=1.3.5",
-    "SigProfilerAssignment>=1.1.3",
+    "SigProfilerAssignment>=1.1.5",
     "statsmodels>=0.9.0",
     "scikit-learn>=0.24.2",
     "psutil>=5.6.1",

sigprofilerextractor-1.4.1/tests/test_cosmic_version.py

@@ -0,0 +1,112 @@
+import inspect
+import unittest
+from importlib import metadata, resources
+
+import pandas as pd
+from packaging.version import Version
+from SigProfilerAssignment import decompose_subroutines
+
+from SigProfilerExtractor import sigpro
+from SigProfilerExtractor.controllers.cli_controller import parse_arguments_extractor
+
+
+class CosmicVersionDefaultsTest(unittest.TestCase):
+    def test_extractor_api_defaults_to_cosmic_v3_6(self):
+        parameters = inspect.signature(sigpro.sigProfilerExtractor).parameters
+
+        self.assertEqual(parameters["cosmic_version"].default, 3.6)
+        self.assertEqual(sigpro.DEFAULT_COSMIC_VERSION, 3.6)
+        self.assertIn(3.6, sigpro.SUPPORTED_COSMIC_VERSIONS)
+
+    def test_cli_defaults_to_cosmic_v3_6(self):
+        parsed_args = parse_arguments_extractor(
+            ["matrix", "test-output", "test-input.tsv"],
+            "Test parser",
+        )
+
+        self.assertEqual(parsed_args.cosmic_version, 3.6)
+
+    def test_cli_preserves_explicit_older_cosmic_version(self):
+        parsed_args = parse_arguments_extractor(
+            [
+                "matrix",
+                "test-output",
+                "test-input.tsv",
+                "--cosmic_version",
+                "3.5",
+            ],
+            "Test parser",
+        )
+
+        self.assertEqual(parsed_args.cosmic_version, 3.5)
+
+
+class SigProfilerAssignmentCompatibilityTest(unittest.TestCase):
+    def test_installed_assignment_version_supports_cosmic_v3_6(self):
+        self.assertGreaterEqual(
+            Version(metadata.version("SigProfilerAssignment")),
+            Version("1.1.5"),
+        )
+
+    def test_assignment_packages_cosmic_v3_6_reference_matrices(self):
+        reference_root = (
+            resources.files("SigProfilerAssignment")
+            / "data"
+            / "Reference_Signatures"
+        )
+        expected_files = (
+            ("GRCh37", "COSMIC_v3.6_SBS_GRCh37.txt"),
+            ("GRCh37", "COSMIC_v3.6_SBS_GRCh37_exome.txt"),
+            ("GRCh37", "COSMIC_v3.6_DBS_GRCh37.txt"),
+            ("GRCh37", "COSMIC_v3.6_ID_GRCh37.txt"),
+            ("GRCh37", "COSMIC_v3.6_CN_GRCh37.txt"),
+            ("GRCh37", "COSMIC_v3.6_RNA-SBS_GRCh37.txt"),
+            ("GRCh38", "COSMIC_v3.6_SBS_GRCh38.txt"),
+            ("GRCh38", "COSMIC_v3.6_DBS_GRCh38.txt"),
+            ("GRCh38", "COSMIC_v3.6_SV_GRCh38.txt"),
+            ("mm9", "COSMIC_v3.6_SBS_mm9.txt"),
+            ("mm10", "COSMIC_v3.6_SBS_mm10.txt"),
+            ("mm39", "COSMIC_v3.6_SBS_mm39.txt"),
+            ("rn6", "COSMIC_v3.6_SBS_rn6.txt"),
+            ("rn7", "COSMIC_v3.6_SBS_rn7.txt"),
+        )
+
+        for genome, filename in expected_files:
+            with self.subTest(genome=genome, filename=filename):
+                reference_file = reference_root / genome / filename
+                self.assertTrue(reference_file.is_file())
+                self.assertGreater(len(reference_file.read_bytes()), 100)
+
+    def test_assignment_loads_v3_6_references_for_supported_contexts(self):
+        genomes = ("GRCh37", "GRCh38", "mm9", "mm10", "mm39", "rn6", "rn7")
+        test_cases = [
+            (rows, genome, exome)
+            for rows in (96, 78)
+            for genome in genomes
+            for exome in (False, True)
+        ]
+        test_cases.extend(
+            (
+                (83, "GRCh37", False),
+                (48, "GRCh37", False),
+                (32, "GRCh38", False),
+            )
+        )
+
+        for rows, genome, exome in test_cases:
+            with self.subTest(rows=rows, genome=genome, exome=exome):
+                samples = pd.DataFrame(index=range(rows))
+                signatures, names, _, _ = decompose_subroutines.getProcessAvg(
+                    samples,
+                    genome_build=genome,
+                    cosmic_version=sigpro.DEFAULT_COSMIC_VERSION,
+                    exome=exome,
+                )
+
+                self.assertEqual(signatures.shape[0], rows)
+                self.assertGreater(signatures.shape[1], 0)
+                self.assertEqual(len(names), signatures.shape[1])
+
+
+if __name__ == "__main__":
+    unittest.main()

sigprofilerextractor-1.4.0/SigProfilerExtractor/_version.py

@@ -1 +0,0 @@
-version = '1.4.0'