Merge pull request #44 from uparma/feature/setup_cfg

Feature/setup cfg

.gitignore

@@ -1,9 +1,9 @@
 __pycache__
 *.pyc
 docs/build
-*.json
 build
 pyenv
 .idea
 .DS_Store
 .tox
+uparma/version.txt

pyproject.toml

@@ -0,0 +1,46 @@
+[dev-dependencies]
+black = { version = "^18.3-alpha.0", python = "^3.8" }
+
+[build-system]
+requires = ["setuptools>=45", "wheel", "setuptools_scm[toml]>=6.0"]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools_scm]
+write_to = "uparma/version.txt"
+
+[tool.black]
+line-length = 88
+target-version = ["py38"]
+include = '\.pyi?$'
+extend-exclude = '''
+/(
+  # The following are specific to Black, you probably don't want those.
+  | blib2to3
+  | profiling
+)/
+'''
+
+[tool.tox]
+legacy_tox_ini = """
+
+[tox]
+envlist = py38,py39
+isolated_build = True
+
+[testenv]
+passenv =
+    *
+commands =
+    pytest {posargs}
+
+[testenv:coverage]
+commands =
+    coverage erase
+    coverage run --source=ursgal {envbindir}/pytest {posargs}
+    coverage report -m
+"""
+
+[tool.pytest.ini_options]
+markers = [
+    "slow: marks tests as slow (deselect with '-m \"not slow\"')",
+]

setup.cfg

@@ -0,0 +1,36 @@
+[metadata]
+name = uparma
+description = tba
+long_description = tba
+author = tba
+author_email = [email protected]
+url = https://github.com/uparma
+license = tba
+classifier = 
+     Development Status :: 4 - Beta
+     Environment :: Console
+     Intended Audience :: Education
+     Intended Audience :: Science/Research
+     Intended Audience :: Developers
+     License :: OSI Approved :: MIT License
+     Operating System :: MacOS :: MacOS X
+     Operating System :: Microsoft :: Windows
+     Operating System :: POSIX
+     Operating System :: POSIX :: SunOS/Solaris
+     Operating System :: Unix
+     Programming Language :: Python :: 3.5
+     Topic :: Scientific/Engineering :: Bio-Informatics
+     Topic :: Scientific/Engineering :: Chemistry
+     Topic :: Scientific/Engineering :: Medical Science Apps
+
+[options]
+packages = find_namespace:
+install_requires =
+    pytest==6.2.2
+    requests==2.25.1
+
+[options.package_data]
+uparma = *.txt, *.json
+
+[egg_info]
+egg_base = .

setup.py

@@ -1,52 +1,38 @@
-#!/usr/bin/env python3
-from setuptools import setup
-import os
-
-
-# We store our version number in a simple text file:
-version_path = os.path.join(os.path.dirname(__file__), "uparma", "version.txt")
-
-with open(version_path, "r") as version_file:
-    uparma_py_version = version_file.read().strip()
-
-with open("requirements.txt") as req_file:
-    reqs = req_file.readlines()
-
-
-setup(
-    name="uparma",
-    version=uparma_py_version,
-    packages=["uparma"],
-    package_dir={"uparma": "uparma"},
-    description="uparma",
-    package_data={
-        "uparma": [
-            "version.txt",
-            "lib_version.txt",
-        ]
-    },
-    install_requires=reqs,
-    long_description="Universal Parameter Mapper for Proteomics tools",
-    author="... and Christian Fufezan",
-    author_email="[email protected]",
-    url="http://github.com/uparma/uparma-py",
-    license="Lesser GNU General Public License (LGPL)",
-    platforms="any that supports python 3.4",
-    classifiers=[
-        "Development Status :: 4 - Beta",
-        "Environment :: Console",
-        "Intended Audience :: Science/Research",
-        "Intended Audience :: Developers",
-        "Operating System :: MacOS :: MacOS X",
-        "Operating System :: Microsoft :: Windows",
-        "Operating System :: POSIX",
-        "Operating System :: POSIX :: SunOS/Solaris",
-        "Operating System :: Unix",
-        "Programming Language :: Python :: 3",
-        "Programming Language :: Python :: 3.4",
-        "Topic :: Scientific/Engineering :: Bio-Informatics",
-        "Topic :: Scientific/Engineering :: Chemistry",
-        "Topic :: Scientific/Engineering :: Medical Science Apps.",
-        "Topic :: Software Development :: Libraries :: Python Modules",
-    ],
+import setuptools
+
+
+def branch_dependent_version():
+    import setuptools_scm
+
+    def void(version):
+        return ""
+
+    def version_scheme(version):
+        if version.branch not in ["main", "master"]:
+            _v = setuptools_scm.get_version(local_scheme=void)
+        else:
+            _v = str(version.tag)
+        return _v
+
+    def local_scheme(version):
+        if version.branch not in ["main", "master"]:
+            _v = setuptools_scm.get_version(version_scheme=void)
+        else:
+            _v = ""
+        return _v
+
+    scm_version = {
+        "root": ".",
+        "relative_to": __file__,
+        "version_scheme": version_scheme,
+        "local_scheme": local_scheme
+        # >> "no-local-version" not quit good enough
+        # >> on dev "node-and-timestamp",  # version_scheme,
+    }
+    return scm_version
+
+
+setuptools.setup(
+    use_scm_version=branch_dependent_version,
+    setup_requires=["setuptools_scm"],
 )

uparma/__init__.py

@@ -1,9 +1,13 @@
 import os
+from importlib.metadata import PackageNotFoundError, version
 
-# Load version
-version_path = os.path.join(os.path.dirname(__file__), "version.txt")
-with open(version_path, "r") as version_file:
-    __version__ = version_file.read().strip()
+try:
+    __version__ = version(__name__)
+except PackageNotFoundError:
+    __version__ = None
+
+# Version
+__version_str__ = str(__version__)
 
 lib_version_path = os.path.join(os.path.dirname(__file__), "lib_version.txt")
 with open(lib_version_path, "r") as lib_version_file:

uparma/uparma.py

@@ -14,11 +14,13 @@
     (
         "general",
         "parameters",
-    ): f"https://raw.githubusercontent.com/uparma/uparma-lib/v{uparma.__lib_version__}/jsons/parameters.json",
+    ): f"https://raw.githubusercontent.com/uparma/uparma-lib/master/jsons/parameters.json",
+    # f"https://raw.githubusercontent.com/uparma/uparma-lib/v{uparma.__lib_version__}/jsons/parameters.json",
     (
         "general",
         "styles",
-    ): f"https://raw.githubusercontent.com/uparma/uparma-lib/v{uparma.__lib_version__}/jsons/styles.json",
+    ): f"https://raw.githubusercontent.com/uparma/uparma-lib/master/jsons/styles.json",
+    # f"https://raw.githubusercontent.com/uparma/uparma-lib/v{uparma.__lib_version__}/jsons/styles.json",
 }
 
 base_path = Path(__file__)
@@ -84,6 +86,13 @@ def __init__(
                 refresh_jsons = True
                 # we will have to pull
 
+            if refresh_jsons is False:
+                with open(full_path) as j:
+                    try:
+                        self.jsons[url_id] = json.load(j)
+                    except json.decoder.JSONDecodeError:
+                        refresh_jsons = True
+
             if refresh_jsons is True:
                 with requests.get(url) as req:
                     with open(full_path, "w") as j:
@@ -94,9 +103,6 @@ def __init__(
                             )
                         print(json.dumps(req.json(), indent=2, sort_keys=True), file=j)
                     self.jsons[url_id] = req.json()
-            else:
-                with open(full_path) as j:
-                    self.jsons[url_id] = json.load(j)
 
         # Let's overwrite with custom
         if parameter_data is not None: