Merge pull request #210 from AlexandrovLab/pandas2-up

.gitignore

@@ -9,6 +9,7 @@
 
 # Hidden files and directories
 *.DS_Store
+.vscode/
 
 # pypi build folder
 /build/

.travis.yml

@@ -1,9 +1,9 @@
-dist: xenial
+dist: focal
 language: python
 
 python:
-  - '3.8'
   - '3.9'
+  - '3.12'
 
 before_install:
   - pip install --upgrade pip setuptools packaging

CHANGELOG.md

@@ -6,6 +6,12 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 
 ## [Unreleased]
 
+## [1.3.0] - 2025-02-11
+
+### Changed
+- Updated dependencies: Now requires **Pandas >= 2.0.0**, **NumPy >= 2.0.0**, and **Python >= 3.9**.
+- Dropped support for **Python 3.8**
+
 ## [1.2.31] - 2024-11-6
 
 ### Fixed

SigProfilerMatrixGenerator/controllers/cli_controller.py

@@ -208,8 +208,12 @@ def dispatch_install(self, user_args: List[str]) -> None:
 
     def dispatch_test(self, user_args: List[str]) -> None:
         parsed_args = parse_arguments_test(user_args)
-        test_helpers.install_genomes(parsed_args.download_genomes)
-        test_helpers.test_genomes(parsed_args.test_genome, parsed_args.volume)
+
+        if parsed_args.download_genomes:
+            test_helpers.install_genomes(parsed_args.download_genomes)
+        if parsed_args.test_genome:
+            test_helpers.test_genomes(parsed_args.test_genome, parsed_args.volume)
+
 
     def dispatch_matrix_generator(self, user_args: List[str]) -> None:
         parsed_args = parse_arguments_matrix_generator(user_args)

SigProfilerMatrixGenerator/scripts/MutationMatrixGenerator.py

@@ -3108,11 +3108,10 @@ def matrix_generator(
     nontrans = mut_count_all["6144"][mut_count_all["6144"].index.str.contains("N:")]
     a = bitrans // 2
     b = bitrans % 2
-    trans = trans.append(a)
-    trans = trans.append(b)
+    trans = pd.concat([trans, a, b])
     trans = trans.groupby(trans.index.str[2:]).sum()
     trans = trans.rename(index=lambda s: "T:" + s)
-    untrans = untrans.append(a)
+    untrans = pd.concat([untrans, a])
     untrans = untrans.groupby(untrans.index.str[2:]).sum()
     untrans = untrans.rename(index=lambda s: "U:" + s)
     mut_count_all["4608"] = pd.concat([trans, untrans, nontrans])
@@ -3127,11 +3126,10 @@ def matrix_generator(
     nontrans = mut_count_all["384"][mut_count_all["384"].index.str.contains("N:")]
     a = bitrans // 2
     b = bitrans % 2
-    trans = trans.append(a)
-    trans = trans.append(b)
+    trans = pd.concat([trans, a, b])
     trans = trans.groupby(trans.index.str[2:]).sum()
     trans = trans.rename(index=lambda s: "T:" + s)
-    untrans = untrans.append(a)
+    untrans = pd.concat([untrans, a])
     untrans = untrans.groupby(untrans.index.str[2:]).sum()
     untrans = untrans.rename(index=lambda s: "U:" + s)
     mut_count_all["288"] = pd.concat([trans, untrans, nontrans])
@@ -3143,11 +3141,10 @@ def matrix_generator(
     nontrans = mut_count_all["24"][mut_count_all["24"].index.str.contains("N:")]
     a = bitrans // 2
     b = bitrans % 2
-    trans = trans.append(a)
-    trans = trans.append(b)
+    trans = pd.concat([trans, a, b])
     trans = trans.groupby(trans.index.str[2:]).sum()
     trans = trans.rename(index=lambda s: "T:" + s)
-    untrans = untrans.append(a)
+    untrans = pd.concat([untrans, a])
     untrans = untrans.groupby(untrans.index.str[2:]).sum()
     untrans = untrans.rename(index=lambda s: "U:" + s)
     mut_count_all["18"] = pd.concat([trans, untrans, nontrans])
@@ -3739,11 +3736,10 @@ def matrix_generator_INDEL(
         questionable = indel_tsb_dict[indel_tsb_dict.index.str.contains("Q:")]
         a = bitrans // 2
         b = bitrans % 2
-        trans = trans.append(a)
-        trans = trans.append(b)
+        trans = pd.concat([trans, a, b])
         trans = trans.groupby(trans.index.str[2:]).sum()
         trans = trans.rename(index=lambda s: "T:" + s)
-        untrans = untrans.append(a)
+        untrans = pd.concat([untrans, a])
         untrans = untrans.groupby(untrans.index.str[2:]).sum()
         untrans = untrans.rename(index=lambda s: "U:" + s)
         indel_tsb_dict_abbrev = pd.concat([trans, untrans, nontrans, questionable])
@@ -3954,11 +3950,10 @@ def matrix_generator_DINUC(
     questionable = mut_count_all["186"][mut_count_all["186"].index.str.contains("Q:")]
     a = bitrans // 2
     b = bitrans % 2
-    trans = trans.append(a)
-    trans = trans.append(b)
+    trans = pd.concat([trans, a, b])
     trans = trans.groupby(trans.index.str[2:]).sum()
     trans = trans.rename(index=lambda s: "T:" + s)
-    untrans = untrans.append(a)
+    untrans = pd.concat([untrans, a])
     untrans = untrans.groupby(untrans.index.str[2:]).sum()
     untrans = untrans.rename(index=lambda s: "U:" + s)
     mut_count_all["150"] = pd.concat([trans, untrans, nontrans, questionable])
@@ -3971,11 +3966,10 @@ def matrix_generator_DINUC(
     questionable = mut_4992[mut_4992.index.str.contains("Q:")]
     a = bitrans // 2
     b = bitrans % 2
-    trans = trans.append(a)
-    trans = trans.append(b)
+    trans = pd.concat([trans, a, b])
     trans = trans.groupby(trans.index.str[2:]).sum()
     trans = trans.rename(index=lambda s: "T:" + s)
-    untrans = untrans.append(a)
+    untrans = pd.concat([untrans, a])
     untrans = untrans.groupby(untrans.index.str[2:]).sum()
     untrans = untrans.rename(index=lambda s: "U:" + s)
     mut_count_all["2400"] = pd.concat([trans, untrans, nontrans, questionable])

SigProfilerMatrixGenerator/scripts/ref_install.py

@@ -3,8 +3,6 @@
 from importlib import resources
 from typing import Optional, Union
 
-import pkg_resources
-
 import SigProfilerMatrixGenerator
 
 
@@ -58,12 +56,4 @@ def get_chromosomes_dir(self) -> pathlib.Path:
         return result
 
     def _get_package_installation_folder(self):
-        try:
-            # python >= 3.9
-            result = resources.files(SigProfilerMatrixGenerator)
-        except AttributeError:
-            # python 3.8, deprecated
-            result = pathlib.Path(
-                pkg_resources.resource_filename(SigProfilerMatrixGenerator.__name__, "")
-            )
-        return result
+        return resources.files(SigProfilerMatrixGenerator)

SigProfilerMatrixGenerator/test_helpers.py

@@ -27,10 +27,6 @@
 
 def load_and_compare(matrices, solution_dir, exome=False, bed_file=True):
     for key in matrices:
-        # Only process keys that start with "SBS"
-        if not key.startswith("SBS"):
-            continue  # Skip non-SBS matrices
-
         # Determine the solution file path based on the exome flag
         if exome:
             solution_file = os.path.join(
@@ -101,7 +97,6 @@ def test_one_genome(genome, volume, exome=False, bed_file=True):
     # load the results from the solution directory and compare them to the dataframes in matrices
     if exome:
         solution_dir = os.path.join(TEST_INPUT_DIR, f"WES/solutions/{genome}/")
-        print("solution_dir", solution_dir)
     elif bed_file:
         solution_dir = os.path.join(TEST_INPUT_DIR, f"bed_file/solutions/{genome}/")
     else:

setup.py

@@ -3,7 +3,7 @@
 
 from setuptools import setup
 
-VERSION = "1.2.31"
+VERSION = "1.3.0"
 
 # remove the dist folder first if exists
 if os.path.exists("dist"):
@@ -23,7 +23,7 @@ def write_version_py(filename="SigProfilerMatrixGenerator/version.py"):
 # THIS FILE IS GENERATED FROM SIGPROFILEMATRIXGENERATOR SETUP.PY
 short_version = '%(version)s'
 version = '%(version)s'
-Update = 'v1.2.31: Resolve issue of ID and DBS matrices not being returned in the output matrices when chrom_based is set to True.'
+Update = 'v1.3.0: Require Pandas and Numpy >= 2.0.0 and Python >= 3.9'
 
 	"""
     fh = open(filename, "w")
@@ -49,15 +49,14 @@ def write_version_py(filename="SigProfilerMatrixGenerator/version.py"):
     author_email="[email protected]",
     license="UCSD",
     packages=["SigProfilerMatrixGenerator"],
-    python_requires=">=3.8",
+    python_requires=">=3.9",
     install_requires=[
         "matplotlib>=2.2.2",
-        "sigProfilerPlotting>=1.3.24",
+        "sigProfilerPlotting>=1.4.0",
         "statsmodels>=0.9.0",
-        "numpy>=1.18.5,<2.0.0",
-        "pandas>=0.23.4,<2.0.0",
-        "scipy>=1.12.0; python_version>='3.9'",
-        "scipy>=1.1.0, <1.12.0; python_version=='3.8'",
+        "numpy>=2.0.0",
+        "pandas>=2.0.0",
+        "scipy>=1.12.0",
     ],
     entry_points={
         "console_scripts": [