updated build system and deprecated modules

.gitignore

@@ -8,3 +8,4 @@ polychrom/_polymer_math.cpp
 *.dat
 .idea
 dist
+polychrom/*.so

docs/conf.py

@@ -62,8 +62,7 @@ def setup(app):
     "simtk",
     "simtk.unit",
     "simtk.unit.nanometer",
-    "simtk.openmm",
-    "joblib",
+    "simtk.openmm",    
     "scipy.interpolate.fitpack2",
 ]
 for mod_name in MOCK_MODULES:

docs/index.rst

@@ -17,7 +17,7 @@ Polychrom requires OpenMM, which can be installed through conda: ``conda install
 
 CUDA is the fastest GPU-assisted backend to OpenMM. You would need to have the required version of CUDA, or install OpenMM compiled for your version of CUDA. 
 
-Other dependencies are simple, and are listed in requirements.txt. All but joblib are installable from either conda/pip, and joblib installs well with pip.
+Other dependencies are simple, and are listed in requirements.txt. All are installable through pip or conda.
 
 Installation errors and possible fixes
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

polychrom/__init__.py

@@ -1 +1,19 @@
 __version__ = "0.1.1"
+
+# Check for OpenMM installation
+try:
+    import openmm
+except ImportError:
+    import warnings
+    warnings.warn(
+        "\n"
+        "OpenMM is not installed. Polychrom requires OpenMM for molecular dynamics simulations.\n"
+        "\n"
+        "Please install OpenMM with the appropriate backend for your system:\n"
+        "  - For CUDA: pip install openmm[cuda13]\n"
+        "  - For CPU:  pip install openmm\n"
+        "\n"
+        "Visit https://openmm.org for more information.",
+        ImportWarning,
+        stacklevel=2
+    )

polychrom/__polymer_math.cpp

@@ -6,7 +6,6 @@
 #include <cmath>
 #include <vector>
 #include <ctime>
-#include <omp.h>
 
 using namespace std;
 

polychrom/cli/show

@@ -5,7 +5,6 @@ import os
 import sys
 import tempfile
 
-import joblib
 import numpy as np
 
 usage = """
@@ -43,7 +42,7 @@ start, end, step will basically select data[start:end:step]
 
 
 if len(sys.argv) < 2:
-    print(useage)
+    print(usage)
     exit()
 
 

polychrom/cli/xyz

@@ -6,7 +6,6 @@ import sys
 import tempfile
 import textwrap
 
-import joblib
 import numpy as np
 
 usage = """

polychrom/polymerutils.py

@@ -31,9 +31,7 @@
 import io
 import os
 
-import joblib
 import numpy as np
-import six
 
 from polychrom.hdf5_format import load_URI
 
@@ -49,8 +47,7 @@ def load(filename):
 
     New-style URIs (HDF5 based storage)
 
-    Text files in openmm-polymer format
-    joblib files in openmm-polymer format
+    Joblib and text files were deprecated.
 
     Parameters
     ----------
@@ -61,24 +58,10 @@ def load(filename):
     """
     if "::" in filename:
         return hdf5_format.load_URI(filename)["pos"]
+
+    raise ValueError("Only URIs are supported in this version of polychrom")
 
-    if not os.path.exists(filename):
-        raise IOError("File not found :( \n %s" % filename)
 
-    try:  # loading from a joblib file here
-        return dict(joblib.load(filename)).pop("data")
-    except Exception:  # checking for a text file
-        data_file = open(filename)
-        line0 = data_file.readline()
-        try:
-            N = int(line0)
-        except (ValueError, UnicodeDecodeError):
-            raise TypeError("Could not read the file. Not text or joblib.")
-        data = [list(map(float, i.split())) for i in data_file.readlines()]
-
-        if len(data) != N:
-            raise ValueError("N does not correspond to the number of lines!")
-        return np.array(data)
 
 
 def fetch_block(folder, ind, full_output=False):
@@ -129,45 +112,25 @@ def fetch_block(folder, ind, full_output=False):
         pos = exists.index(True)
         block = load_URI(blocksh5[pos] + f"::{ind}")
         if not full_output:
-            block = block["pos"]
+            return block["pos"]
 
     if len(blocksdat) > 0:
-        block = load(os.path.join(folder, f"block{ind}.dat"))
-    return block
+        return load(os.path.join(folder, f"block{ind}.dat"))
+    raise ValueError(f"Cannot find the block {ind} in the folder {folder}")
 
 
 def save(data, filename, mode="txt", pdbGroups=None):
     """
     Basically unchanged polymerutils.save function from openmm-polymer
 
-    It can save into txt or joblib formats used by old openmm-polymer
+
 
     It is also very useful for saving files to PDB format to make them compatible
     with nglview, pymol_show and others
     """
     data = np.asarray(data, dtype=np.float32)
 
-    if mode.lower() == "joblib":
-        joblib.dump({"data": data}, filename=filename, compress=9)
-        return
-
-    if mode.lower() == "txt":
-        lines = [str(len(data)) + "\n"]
-
-        for particle in data:
-            lines.append("{0:.3f} {1:.3f} {2:.3f}\n".format(*particle))
-        if filename is None:
-            return lines
-
-        elif isinstance(filename, six.string_types):
-            with open(filename, "w") as myfile:
-                myfile.writelines(lines)
-        elif hasattr(filename, "writelines"):
-            filename.writelines(lines)
-        else:
-            raise ValueError("Not sure what to do with filename {0}".format(filename))
-
-    elif mode == "pdb":
+    if mode == "pdb":
         data = data - np.minimum(np.min(data, axis=0), np.zeros(3, float) - 100)[None, :]
         retret = ""
 
@@ -212,7 +175,7 @@ def add(st, n):
                 filename.write("C {0} {1} {2}".format(*i))
 
     else:
-        raise ValueError("Unknown mode : %s, use h5dict, joblib, txt or pdb" % mode)
+        raise ValueError("Unknown mode : %s, use or pdb" % mode)
 
 
 def rotation_matrix(rotate):

pyproject.toml

@@ -1,9 +1,59 @@
+[build-system]
+requires = ["setuptools>=45", "wheel", "cython>=0.29", "numpy>=1.9"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "polychrom"
+version = "0.1.1"
+description = "A library for polymer simulations and their analyses."
+readme = "README.md"
+requires-python = ">=3.7"
+license = "MIT"
+authors = [
+    {name = "Mirny Lab", email = "espresso@mit.edu"}
+]
+keywords = ["genomics", "polymer", "Hi-C", "molecular dynamics", "chromosomes"]
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Intended Audience :: Science/Research",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.7",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+]
+
+dependencies = [
+    "cython>=0.29",
+    "numpy>=1.9",
+    "scipy>=0.16",
+    "h5py>=2.5",
+    "pandas>=0.19",
+]
+
+[project.optional-dependencies]
+dev = [
+    "pytest",
+    "black",
+    "isort",
+]
+
+[project.urls]
+Homepage = "https://github.com/open2c/polychrom"
+Repository = "https://github.com/open2c/polychrom"
+
+[project.scripts]
+polychrom = "polychrom.cli:cli"
+
+[tool.setuptools.packages.find]
+include = ["polychrom*"]
+exclude = ["utilities*", "build*", "docs*", "examples*"]
+
 [tool.black]
 line-length = 120
 
 [tool.isort]
 profile = "black"
-
-[build-system]
-requires = ["setuptools", "setuptools-scm", "cython"]
-build-backend = "setuptools.build_meta"

requirements.txt

@@ -1,9 +1,6 @@
-six
 cython
 numpy>=1.9
 scipy>=0.16
 h5py>=2.5
 pandas>=0.19
-joblib
-pyknotid
 pytest

setup.py

@@ -1,70 +1,16 @@
-import io
-import os
-import re
+from setuptools import setup, Extension
 from Cython.Build import cythonize
-from Cython.Distutils import build_ext
-from setuptools import find_packages
-from distutils.core import setup
-from distutils.extension import Extension
-
-cmdclass = {}
-
-
-def _read(*parts, **kwargs):
-    filepath = os.path.join(os.path.dirname(__file__), *parts)
-    encoding = kwargs.pop("encoding", "utf-8")
-    with io.open(filepath, encoding=encoding) as fh:
-        text = fh.read()
-    return text
-
-
-def get_version():
-    version = re.search(
-        r'^__version__\s*=\s*[\'"]([^\'"]*)[\'"]',
-        _read("polychrom", "__init__.py"),
-        re.MULTILINE,
-    ).group(1)
-    return version
-
-
-def get_long_description():
-    return _read("README.md")
-
-
-def get_requirements(path):
-    content = _read(path)
-    return [req for req in content.split("\n") if req != "" and not req.startswith("#")]
-
-
-cmdclass.update({"build_ext": build_ext})
-
-ext_modules = cythonize(
-    [
-        Extension(
-            "polychrom._polymer_math",
-            ["polychrom/_polymer_math.pyx", "polychrom/__polymer_math.cpp"],
-        )
-    ]
-)
+import numpy
 
+# Define Cython extensions
+ext_modules = [
+    Extension(
+        "polychrom._polymer_math",
+        ["polychrom/_polymer_math.pyx", "polychrom/__polymer_math.cpp"],
+        include_dirs=[numpy.get_include()],
+    )
+]
 
 setup(
-    name="polychrom",
-    author="Mirny Lab",
-    author_email="espresso@mit.edu",
-    version=get_version(),
-    url="http://github.com/mirnylab/polychrom",
-    description=("A library for polymer simulations and their analyses."),
-    long_description=get_long_description(),
-    long_description_content_type="text/markdown",
-    keywords=["genomics", "polymer", "Hi-C", "molecular dynamics", "chromosomes"],
-    ext_modules=ext_modules,
-    cmdclass=cmdclass,
-    packages=find_packages(),
-    setup_requires=["cython"],
-    entry_points={
-        "console_scripts": [
-            "polychrom = polychrom.cli:cli",
-        ]
-    },
+    ext_modules=cythonize(ext_modules, language_level="3"),
 )

utilities/showChainWithRasmol.py

@@ -3,8 +3,7 @@
 import sys
 import tempfile
 import textwrap
-
-import joblib
+import polychrom.polymerutils as polymerutils
 import numpy as np
 
 if len(sys.argv) < 2:
@@ -100,8 +99,6 @@ def convertData(data, colors):
 
 
 def load(filename):
-    from openmmlib import polymerutils
-
     return polymerutils.load(filename)