Pypi compatible wheel builds

.gitignore

@@ -24,6 +24,7 @@ docs/_build
 
 Releases/
 dist/
+*.egg-info
 
 Tutorials/Klarner2018/jobs.py
 Tutorials/*/*.json

MANIFEST.in

@@ -1,2 +1,5 @@
 global-exclude *~
 global-exclude *.pyc
+
+recursive-include pyboolnet/binaries *
+recursive-include pyboolnet/repository *

binaries/linux64/settings.cfg → pyboolnet/binaries/linux64/settings.cfg

@@ -5,10 +5,3 @@ clasp           = ./clasp-3.1.1/clasp-3.1.1-x86-linux
 bnet2prime      = ./BNetToPrime/BNetToPrime_linux64
 espresso        = ./espresso/espresso_linux64
 eqntott         = ./eqntott/eqntott_linux64
-dot             = /usr/bin/dot
-neato           = /usr/bin/neato
-fdp             = /usr/bin/fdp
-sfdp            = /usr/bin/sfdp
-circo           = /usr/bin/circo
-twopi           = /usr/bin/twopi
-convert         = /usr/bin/convert

binaries/mac64/settings.cfg → pyboolnet/binaries/mac64/settings.cfg

@@ -5,10 +5,3 @@ clasp           = ./clasp-3.2.0/clasp-3.2.0_mac64
 bnet2prime      = ./BNetToPrime/BNetToPrime_mac64
 espresso        = ./espresso/espresso_mac64
 eqntott         = ./eqntott/eqntott_mac64
-dot             = /usr/bin/dot
-neato           = /usr/bin/neato
-fdp             = /usr/bin/fdp
-sfdp            = /usr/bin/sfdp
-circo           = /usr/bin/circo
-twopi           = /usr/bin/twopi
-convert         = /usr/bin/convert

binaries/win64/settings.cfg → pyboolnet/binaries/win64/settings.cfg

@@ -5,10 +5,3 @@ clasp           = ./clasp-3.1.1/clasp-3.1.1_win64.exe
 bnet2prime      = ./BNetToPrime/BNetToPrime_win64.exe
 espresso        = ./espresso/espresso_win64.exe
 eqntott         = ./eqntott/eqntott_win64.exe
-dot             = dot
-neato           = neato
-fdp             = fdp
-sfdp            = sfdp
-circo           = circo
-twopi           = twopi
-convert         = convert

pyboolnet/helpers.py

@@ -4,11 +4,23 @@
 import logging
 import math
 import os
+
+import platform
+from importlib.resources import files, as_file
+from pathlib import Path
+import shutil
+
 from typing import List
 from configparser import ConfigParser
 
 ROOT_DIR = os.path.join(os.path.dirname(__file__))
 
+_SUBDIR_MAP = {
+    "Linux": "linux64",
+    "Darwin": "mac64",
+    "Windows": "win64",
+}
+
 
 log = logging.getLogger(__name__)
 
@@ -17,20 +29,48 @@ def read_txt_version() -> str:
     with open(os.path.join(ROOT_DIR, "version.txt"), "r") as fp:
         return fp.read()
 
+def _get_platform_subdir() -> str:
+    system = platform.system()
+    try:
+        return _SUBDIR_MAP[system]
+    except KeyError:
+        raise RuntimeError(f"Unsupported OS: {system}")
 
 def read_executables() -> dict:
-    config_parser = ConfigParser()
-    settings_file = os.path.join(ROOT_DIR, "binaries", "settings.cfg")
-
-    if not os.path.exists(settings_file):
-        execs = dict(
-            nusmv="./NuSMV-2.6.0/bin/NuSMV",
-            gringo="./gringo-4.4.0-x86-linux/gringo",
-            clasp="./clasp-3.1.1/clasp-3.1.1-x86-linux",
-            bnet2prime="./BNetToPrime/BNetToPrime")
-    else:
-        config_parser.read(settings_file)
-        execs = {n: config_parser.get("Executables", n) for n in config_parser.options("Executables")}
+    """
+    Collects paths to executables
+    """
+
+    execs = {}
+
+    # OS-specific binaries directory within installed package
+    subdir = _get_platform_subdir()
+    binaries_dir = files("pyboolnet.binaries") / subdir
+    settings_resource = binaries_dir / "settings.cfg"
+
+    if not settings_resource.exists():
+        raise RuntimeError(f"Missing settings.cfg in {binaries_dir}")
+
+    with as_file(settings_resource) as settings_path:
+        config_parser = ConfigParser()
+        config_parser.read(settings_path)
+        for name in config_parser.options("Executables"):
+            raw_path = config_parser.get("Executables", name)
+            p = Path(raw_path)
+
+            # relative path to the settings.cfg file
+            if p.is_absolute():
+                execs[name] = str(p)
+            else:
+                execs[name] = str((binaries_dir / raw_path).resolve())
+
+    # system tools
+    for executable in ["dot", "neato", "fdp", "sfdp", "circo", "twopi", "convert"]:
+        path = shutil.which(executable)
+        if path is None:
+            log.warning("Executable %s not found in system PATH", executable)
+        else:
+            execs[executable] = path
 
     return execs
 

setup.py

@@ -9,49 +9,22 @@
 
 from pyboolnet import VERSION
 
-PACKAGE_DATA_FILES = []
-THIS_OS = platform.system()
-SUBDIR_MAP = dict(
-    Linux="linux64",
-    Darwin="mac64",
-    Windows="win64",
-)
-
-if "CONDA_BUILD" in os.environ:
-    subdir = "conda"
-else:
-    try:
-        subdir = SUBDIR_MAP[THIS_OS]
-    except KeyError:
-        print(f"the operating system is not recognized: os={THIS_OS}")
-        sys.exit(1)
-
-BINARIES_SOURCE_DIR = os.path.join("binaries", subdir)
-print(f"detected os and binaries: {THIS_OS=}, {BINARIES_SOURCE_DIR=}")
-
-BINARIES_TARGET_DIR = os.path.join("pyboolnet", "binaries")
-copy_tree(src=BINARIES_SOURCE_DIR, dst=BINARIES_TARGET_DIR)
-print(f"copy_tree: {BINARIES_SOURCE_DIR=}, {BINARIES_TARGET_DIR=}")
-
-for root, _, filenames in os.walk(BINARIES_TARGET_DIR):
-    root = root.replace(BINARIES_TARGET_DIR, "binaries")
-    PACKAGE_DATA_FILES.extend([os.path.join(root, x) for x in filenames])
-
-REPOSITORY_PATH = os.path.join("pyboolnet", "repository")
-for root, _, filenames in os.walk(REPOSITORY_PATH):
-    root = root.replace(REPOSITORY_PATH, "repository")
-    PACKAGE_DATA_FILES.extend([os.path.join(root, x) for x in filenames])
-
 setup(
     name="pyboolnet",
     version=VERSION,
     description="Python toolbox for the generation, manipulation and analysis of Boolean networks.",
     author="Hannes Klarner",
     author_email="leevilux@yahoo.de",
     url="https://github.com/hklarner/pyboolnet",
-    package_data={"pyboolnet": PACKAGE_DATA_FILES, "": ['version.txt']},
     packages=find_packages(),
     include_package_data=True,
+    package_data={
+        "pyboolnet": [
+            "binaries/*/*",
+            "binaries/*/*/*",
+            "repository/**/*"],
+        "": ['version.txt'],
+    },
     classifiers=[
         "Programming Language :: Python",
         "License :: OSI Approved :: GNU Library or Lesser General Public License (LGPL)",