Merge dev with bypassed changes

.github/workflows/build.yml

@@ -2,7 +2,7 @@ name: Build and Test
 
 on:
   push:
-    branches: [main, master, develop]
+    branches: [main, master]
   pull_request:
     branches: [main, master]
 
@@ -14,7 +14,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, macos-latest]
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13", "3.14"]
 
     steps:
       - uses: actions/checkout@v4
@@ -50,13 +50,13 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-latest, macos-13, macos-14]  # macos-13=x86, macos-14=arm64
+        os: [ubuntu-latest, macos-15-intel, macos-14]  # macos-15-intel=x86, macos-14=arm64
 
     steps:
       - uses: actions/checkout@v4
 
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.21.3
+        uses: pypa/cibuildwheel@v3.3.1
         # Config is read from pyproject.toml [tool.cibuildwheel]
 
       - uses: actions/upload-artifact@v4

.github/workflows/publish.yml

@@ -10,7 +10,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-latest, macos-13, macos-14]
+        os: [ubuntu-latest, macos-15-intel, macos-14]
 
     steps:
       - uses: actions/checkout@v4
@@ -48,7 +48,9 @@ jobs:
     name: Publish to PyPI
     needs: [build-wheels, build-sdist]
     runs-on: ubuntu-latest
-    environment: pypi
+    environment: 
+      name: pypi
+      url: https://pypi.org/project/smudgeplot
     permissions:
       id-token: write  # Required for trusted publishing
 

Makefile

@@ -8,11 +8,14 @@ endif
 HET_KMERS_INST = $(INSTALL_PREFIX)/bin/hetmers $(INSTALL_PREFIX)/bin/extract_kmer_pairs
 
 .PHONY : default
-default: exec/hetmers exec/extract_kmer_pairs
+default: exec/ exec/hetmers exec/extract_kmer_pairs
 
 .PHONY : install
 install : $(HET_KMERS_INST) 
 
+exec/:
+	mkdir -p exec
+
 $(INSTALL_PREFIX)/bin/% : exec/%
 	install -C $< $(INSTALL_PREFIX)/bin
 

README.md

@@ -1,16 +1,12 @@
 # Smudgeplot 
 
-<font size ="4">**_Version: 0.5.1 Skylight_**</font>
+<font size ="4">**_Version: 0.5.3 Skylight_**</font>
 
 <font size ="4">**_Authors: Sam Ebdon, [Gene W Myers](https://github.com/thegenemyers) and [Kamil S. Jaron](https://github.com/KamilSJaron), Tianyi Ma._**</font>
 
-We keep the same pythonic interface; the interface of this and previous versions are very similar and largely compatible.
-
-Current state: RUNNING; beta-testing;
-
 ## Installation
 
-This version of smudgeplot operates on FastK k-mer databases. The smudgeplot installation consists of a python package and C-backend to search for all the k-mer pairs (hetmers) and extract sequences of k-mer pairs (extract_kmer_pairs).
+This version of smudgeplot operates on FastK k-mer databases. The smudgeplot installation consists of a python package and C-backend to search for all the k-mer pairs (smudgeplot hetmers) and extract sequences of k-mer pairs (smudgeplot extract).
 
 We recommend installing smudgeplot within a [conda](https://conda-forge.org/download/) environment.
 
@@ -19,7 +15,10 @@ We recommend installing smudgeplot within a [conda](https://conda-forge.org/down
 conda create -n smudgeplot && conda activate smudgeplot
 conda install pip
 
-#download and install
+# install via pypi
+pip install smudgeplot
+
+# or download and install directly. See below if you need to compile the C dependencies.
 git clone https://github.com/KamilSJaron/smudgeplot.git
 cd smudgeplot && pip install .
 smudgeplot -h # check installation succeeded
@@ -31,14 +30,22 @@ Note the smudgeplot version downloadable from conda itself is not currently up t
 
 ### Compiling the C code
 
-The process above install everything including compilation of the C backend. If you would like to know how to compile the code yourself you can simply run
+The process above should install everything including compilation of the C backend. If you need or would like to know how to compile the code yourself you can simply run
 
 ```
 make
 ```
 
 This will not, however, install the smudgeplot python package. 
 
+### Pypi installation [EXPERIMENTAL] 
+
+We are working on packaging smudgeplot for pypi. You are welcome to try installing from pypi if you are interested and please open an issue if you have problems. If it fails please follow the main instructions above to install for now.
+
+```
+pip install smudgeplot
+```
+
 ## Example run on Saccharomyces data
 
 Requires ~2.1GB of space and `FastK` and `smudgeplot` installed.

playground/alternative_fitting/pair_clustering.py

@@ -13,7 +13,7 @@
 ####
 
 parser = argparse.ArgumentParser()
-parser.add_argument('infile', nargs='?', help='name of the input tsv file with covarages and frequencies.')
+parser.add_argument('infile', nargs='?', help='name of the input tsv file with coverages and frequencies.')
 parser.add_argument('-nf', '-noise_filter', help='Do not agregate into smudge k-mer pairs with frequency lower than this parameter', type=int, default=50)
 parser.add_argument('-d', '-distance', help='Manthattan distance of k-mer pairs that are considered neioboring for the local agregation purposes.', type=int, default=5)
 parser.add_argument('--mask_errors', help='instead of reporting assignments to individual smudges, just remove all monotonically decreasing points from the error line', action="store_true", default = False)

pyproject.toml

@@ -1,10 +1,13 @@
 [build-system]
-requires = ["setuptools>=61.0", "wheel"]
+requires = [
+  "setuptools>=61.0",
+  "wheel",
+]
 build-backend = "setuptools.build_meta"
 
 [project]
 name = "smudgeplot"
-version = "0.5.1"
+version = "0.5.3"
 description = "Inference of ploidy and heterozygosity structure using whole genome sequencing data"
 readme = "README.md"
 license = "Apache-2.0"
@@ -38,6 +41,8 @@ classifiers = [
   "Programming Language :: Python :: 3.10",
   "Programming Language :: Python :: 3.11",
   "Programming Language :: Python :: 3.12",
+  "Programming Language :: Python :: 3.13",
+  "Programming Language :: Python :: 3.14",
   "Operating System :: POSIX :: Linux",
   "Operating System :: MacOS",
   "Intended Audience :: Science/Research",
@@ -66,7 +71,8 @@ smudgeplot = ["bin/*"]
 [tool.cibuildwheel]
 # Skip 32-bit, PyPy, musllinux, and Windows (no Windows support for now)
 skip = ["*-win32", "*-win_amd64", "*-manylinux_i686", "pp*", "*-musllinux*"]
-build = ["cp39-*", "cp310-*", "cp311-*", "cp312-*"]
+build = ["cp39-*", "cp310-*", "cp311-*", "cp312-*", "cp313-*", "cp314-*"]
+environment = { MACOSX_DEPLOYMENT_TARGET = "11.0" }
 
 # Test that the CLI works after building
 test-command = "smudgeplot --version"

setup.py

@@ -14,7 +14,7 @@
 from setuptools import setup
 from setuptools.command.build_py import build_py
 from setuptools.command.develop import develop
-
+from setuptools.dist import Distribution
 
 class CompilationError(Exception):
     """Raised when C binary compilation fails."""
@@ -132,10 +132,14 @@ def run(self):
             print("Continuing with editable install, but binaries will not work.", file=sys.stderr)
         super().run()
 
+class BinaryDistribution(Distribution):
+    def has_ext_modules(self):
+        return True
 
 setup(
     cmdclass={
         "build_py": BuildPyWithBinaries,
         "develop": DevelopWithBinaries,
-    }
+    },
+    distclass=BinaryDistribution
 )

src/lib/PloidyList.c

@@ -1222,7 +1222,7 @@ int main(int argc, char *argv[])
     int    flags[128];
     char  *eptr;
 
-    ARG_INIT("PloidyList");
+    ARG_INIT("extract_kmer_pairs");
 
     OUT      = NULL;
     ETHRESH  = 4;

src/lib/PloidyPlot.c

@@ -1247,7 +1247,7 @@ int main(int argc, char *argv[])
     int    flags[128];
     char  *eptr;
 
-    ARG_INIT("PloidyPlot");
+    ARG_INIT("hetmers");
 
     OUT      = NULL;
     ETHRESH  = 4;