easydev 0.13.3__tar.gz → 0.15.0__tar.gz

easydev-0.15.0/PKG-INFO

@@ -0,0 +1,222 @@
+Metadata-Version: 2.4
+Name: easydev
+Version: 0.15.0
+Summary: Common utilities to ease development of Python packages
+License-Expression: BSD-3-Clause
+License-File: COPYING
+Keywords: config,decorators,development
+Author: Thomas Cokelaer
+Author-email: thomas.cokelaer@pasteur.fr
+Requires-Python: >=3.9,<4.0
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Intended Audience :: Education
+Classifier: Intended Audience :: End Users/Desktop
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Operating System :: POSIX :: Linux
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Classifier: Topic :: Software Development :: Libraries :: Python Modules
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Scientific/Engineering :: Information Analysis
+Requires-Dist: colorama (>=0.4.6,<0.5.0)
+Requires-Dist: colorlog (>=6.8.2,<7.0.0)
+Requires-Dist: line-profiler (>=5.0.0,<6.0.0)
+Requires-Dist: pexpect (>=4.9.0,<5.0.0)
+Requires-Dist: platformdirs (>=4.2.0,<5.0.0)
+Project-URL: Documentation, https://easydev.readthedocs.io
+Project-URL: Homepage, https://easydev.readthedocs.io
+Project-URL: Issues, https://github.com/cokelaer/easydev/issues
+Project-URL: Repository, https://github.com/cokelaer/easydev
+Description-Content-Type: text/x-rst
+
+easydev
+##########
+
+.. image:: https://badge.fury.io/py/easydev.svg
+    :target: https://pypi.python.org/pypi/easydev
+
+.. image:: https://github.com/cokelaer/easydev/actions/workflows/main.yml/badge.svg
+    :target: https://github.com/cokelaer/easydev/actions/workflows/main.yml
+
+.. image:: https://coveralls.io/repos/cokelaer/easydev/badge.svg?branch=main
+   :target: https://coveralls.io/r/cokelaer/easydev?branch=main
+
+.. image:: https://static.pepy.tech/personalized-badge/easydev?period=total&units=INTERNATIONAL_SYSTEM&left_color=BLACK&right_color=GREEN&left_text=downloads
+    :target: https://pepy.tech/projects/easydev
+
+:documentation: http://easydev-python.readthedocs.io/en/latest/
+:contributions: Please join https://github.com/cokelaer/easydev
+:source: Please use https://github.com/cokelaer/easydev
+:issues: Please use https://github.com/cokelaer/easydev/issues
+:Python version supported: 3.9, 3.10, 3.11, 3.12, 3.13, 3.14
+
+Overview
+--------
+
+The `easydev <http://pypi.python.org/pypi/easydev/>`_ package provides
+miscellaneous utility functions and classes that are repeatedly useful during
+the development of Python packages. The goal is to help developers speed up
+their work by providing ready-to-use tools for common tasks such as parameter
+validation, logging, progress bars, configuration files, multiprocessing, and
+more.
+
+It has been used as an incubator for other packages (e.g.,
+`colormap <http://pypi.python.org/pypi/colormap>`_) and is used in projects
+such as `bioservices <https://pypi.python.org/pypi/bioservices>`_,
+`sequana <https://sequana.readthedocs.io>`_, and
+`GDSCTools <https://gdsctools.readthedocs.io>`_.
+
+Installation
+------------
+
+Install the latest release from PyPI::
+
+    pip install easydev
+
+Features
+--------
+
+- **Parameter validation** – ``check_param_in_list``, ``check_range``
+- **Dictionary utilities** – ``swapdict``, ``AttrDict`` (access dict keys as attributes, supports nested dicts)
+- **Logging** – coloured logging via ``Logging`` class
+- **Progress bar** – ``Progress`` works in Python, IPython, and Jupyter notebooks
+- **Timer** – measure elapsed time with the ``Timer`` context manager
+- **Profiling** – ``do_profile`` decorator using ``line_profiler``
+- **Configuration files** – ``CustomConfig`` and ``DynamicConfigParser`` for INI-style config management
+- **Shell commands** – ``shellcmd`` and ``execute`` wrappers around subprocess/pexpect
+- **File utilities** – ``touch``, ``mkdirs``, ``md5``
+- **Multiprocessing** – ``MultiProcessing`` class for easy parallel job execution
+- **Codecs** – ``to_list``, ``list2string`` and other conversion helpers
+- **URL utilities** – ``isurl_reachable`` and related helpers
+- **Sphinx integration** – bundled Sphinx theme and ``copybutton`` extension
+
+Quick Start
+-----------
+
+Parameter validation::
+
+    from easydev import check_param_in_list, check_range
+
+    check_param_in_list("on", ["on", "off"])   # passes silently
+    check_range(0.5, 0, 1)                     # passes silently
+
+AttrDict – access nested dictionary keys as attributes::
+
+    from easydev import AttrDict
+
+    d = AttrDict(**{"server": {"host": "localhost", "port": 8080}})
+    print(d.server.host)   # localhost
+    d.server.port = 9090
+
+Coloured logging::
+
+    from easydev import Logging
+
+    logger = Logging("myapp", "WARNING")
+    logger.warning("something went wrong")
+    logger.debug("not shown at WARNING level")
+    logger.level = "DEBUG"
+    logger.debug("now it is shown")
+
+Progress bar::
+
+    from easydev import Progress
+
+    pb = Progress(100)
+    for i in range(100):
+        # do work here
+        pb.animate(i + 1)
+
+Timer::
+
+    from easydev import Timer
+    import time
+
+    times = []
+    with Timer(times):
+        time.sleep(0.1)
+    print(f"elapsed: {times[0]:.2f}s")
+
+Multiprocessing::
+
+    from easydev.multicore import MultiProcessing
+
+    def square(n):
+        return n * n
+
+    t = MultiProcessing(maxcpu=4)
+    for i in range(10):
+        t.add_job(square, i)
+    t.run()
+    print(t.results)
+
+Moving away from easydev
+------------------------
+
+easydev dates from a time when Python lacked many small conveniences. Most of
+its tools now have a standard-library or well-maintained third-party
+replacement, and new projects should not depend on easydev. The full
+module-by-module guide is in the
+`documentation <https://easydev.readthedocs.io/en/latest/migration.html>`_
+(``doc/source/migration.rst``). Main replacements:
+
+========================================= ======================================================
+easydev                                   Use instead
+========================================= ======================================================
+``CustomConfig``, ``AppDirs``             ``platformdirs``
+``DynamicConfigParser``                   ``configparser``
+``AttrDict``                              ``types.SimpleNamespace`` / ``dataclasses``
+``Logging``                               ``logging`` (+ ``colorlog``)
+``Progress``                              ``tqdm``
+``MultiProcessing``                       ``concurrent.futures.ProcessPoolExecutor``
+``shellcmd``, ``execute``                 ``subprocess.run``
+``mkdirs``, ``touch``, ``get_home``       ``pathlib`` / ``os.makedirs(exist_ok=True)``
+``cmd_exists``                            ``shutil.which``
+``md5``                                   ``hashlib.file_digest`` (Python 3.11+)
+``browse``                                ``webbrowser.open``
+``get_dependencies``                      ``importlib.metadata.requires``
+``get_share_file``                        ``importlib.resources.files``
+========================================= ======================================================
+
+For example, replacing ``CustomConfig``::
+
+    # before
+    from easydev import CustomConfig
+    config_dir = CustomConfig("myapp").user_config_dir
+
+    # after
+    from pathlib import Path
+    from platformdirs import user_config_dir
+
+    config_dir = Path(user_config_dir("myapp"))
+    config_dir.mkdir(parents=True, exist_ok=True)
+
+Changelog
+---------
+
+========= ==========================================================================
+Version   Description
+========= ==========================================================================
+0.15.0    * fix ``is_mac`` (always returned False)
+          * ``assert_list_almost_equal`` now warns (FutureWarning) when called without
+            ``places``/``deltas`` (nothing is compared); raises ``ListMismatchError``
+            (both ValueError and AssertionError)
+          * add a migration guide (README and documentation) explaining how to
+            replace easydev tools with the standard library, platformdirs, etc.
+          * require Python >= 3.9
+0.13.3    * update pyproject with contribs from @s-t-e-v-e-n-k see PR37
+0.13.2    * replace mock with unittest.mock (fixes
+            https://github.com/cokelaer/easydev/issues/20)
+0.13.1    * fix get_dependencies
+0.13.0    * fix requirements (line_profiler) and CI
+0.12.2    * For developers: move to pyproject. add precommit
+          * replace pkg_resources (deprecated) with importlib
+          * replace appdirs with more generic platformdirs
+========= ==========================================================================
+

easydev-0.15.0/README.rst

@@ -0,0 +1,184 @@
+easydev
+##########
+
+.. image:: https://badge.fury.io/py/easydev.svg
+    :target: https://pypi.python.org/pypi/easydev
+
+.. image:: https://github.com/cokelaer/easydev/actions/workflows/main.yml/badge.svg
+    :target: https://github.com/cokelaer/easydev/actions/workflows/main.yml
+
+.. image:: https://coveralls.io/repos/cokelaer/easydev/badge.svg?branch=main
+   :target: https://coveralls.io/r/cokelaer/easydev?branch=main
+
+.. image:: https://static.pepy.tech/personalized-badge/easydev?period=total&units=INTERNATIONAL_SYSTEM&left_color=BLACK&right_color=GREEN&left_text=downloads
+    :target: https://pepy.tech/projects/easydev
+
+:documentation: http://easydev-python.readthedocs.io/en/latest/
+:contributions: Please join https://github.com/cokelaer/easydev
+:source: Please use https://github.com/cokelaer/easydev
+:issues: Please use https://github.com/cokelaer/easydev/issues
+:Python version supported: 3.9, 3.10, 3.11, 3.12, 3.13, 3.14
+
+Overview
+--------
+
+The `easydev <http://pypi.python.org/pypi/easydev/>`_ package provides
+miscellaneous utility functions and classes that are repeatedly useful during
+the development of Python packages. The goal is to help developers speed up
+their work by providing ready-to-use tools for common tasks such as parameter
+validation, logging, progress bars, configuration files, multiprocessing, and
+more.
+
+It has been used as an incubator for other packages (e.g.,
+`colormap <http://pypi.python.org/pypi/colormap>`_) and is used in projects
+such as `bioservices <https://pypi.python.org/pypi/bioservices>`_,
+`sequana <https://sequana.readthedocs.io>`_, and
+`GDSCTools <https://gdsctools.readthedocs.io>`_.
+
+Installation
+------------
+
+Install the latest release from PyPI::
+
+    pip install easydev
+
+Features
+--------
+
+- **Parameter validation** – ``check_param_in_list``, ``check_range``
+- **Dictionary utilities** – ``swapdict``, ``AttrDict`` (access dict keys as attributes, supports nested dicts)
+- **Logging** – coloured logging via ``Logging`` class
+- **Progress bar** – ``Progress`` works in Python, IPython, and Jupyter notebooks
+- **Timer** – measure elapsed time with the ``Timer`` context manager
+- **Profiling** – ``do_profile`` decorator using ``line_profiler``
+- **Configuration files** – ``CustomConfig`` and ``DynamicConfigParser`` for INI-style config management
+- **Shell commands** – ``shellcmd`` and ``execute`` wrappers around subprocess/pexpect
+- **File utilities** – ``touch``, ``mkdirs``, ``md5``
+- **Multiprocessing** – ``MultiProcessing`` class for easy parallel job execution
+- **Codecs** – ``to_list``, ``list2string`` and other conversion helpers
+- **URL utilities** – ``isurl_reachable`` and related helpers
+- **Sphinx integration** – bundled Sphinx theme and ``copybutton`` extension
+
+Quick Start
+-----------
+
+Parameter validation::
+
+    from easydev import check_param_in_list, check_range
+
+    check_param_in_list("on", ["on", "off"])   # passes silently
+    check_range(0.5, 0, 1)                     # passes silently
+
+AttrDict – access nested dictionary keys as attributes::
+
+    from easydev import AttrDict
+
+    d = AttrDict(**{"server": {"host": "localhost", "port": 8080}})
+    print(d.server.host)   # localhost
+    d.server.port = 9090
+
+Coloured logging::
+
+    from easydev import Logging
+
+    logger = Logging("myapp", "WARNING")
+    logger.warning("something went wrong")
+    logger.debug("not shown at WARNING level")
+    logger.level = "DEBUG"
+    logger.debug("now it is shown")
+
+Progress bar::
+
+    from easydev import Progress
+
+    pb = Progress(100)
+    for i in range(100):
+        # do work here
+        pb.animate(i + 1)
+
+Timer::
+
+    from easydev import Timer
+    import time
+
+    times = []
+    with Timer(times):
+        time.sleep(0.1)
+    print(f"elapsed: {times[0]:.2f}s")
+
+Multiprocessing::
+
+    from easydev.multicore import MultiProcessing
+
+    def square(n):
+        return n * n
+
+    t = MultiProcessing(maxcpu=4)
+    for i in range(10):
+        t.add_job(square, i)
+    t.run()
+    print(t.results)
+
+Moving away from easydev
+------------------------
+
+easydev dates from a time when Python lacked many small conveniences. Most of
+its tools now have a standard-library or well-maintained third-party
+replacement, and new projects should not depend on easydev. The full
+module-by-module guide is in the
+`documentation <https://easydev.readthedocs.io/en/latest/migration.html>`_
+(``doc/source/migration.rst``). Main replacements:
+
+========================================= ======================================================
+easydev                                   Use instead
+========================================= ======================================================
+``CustomConfig``, ``AppDirs``             ``platformdirs``
+``DynamicConfigParser``                   ``configparser``
+``AttrDict``                              ``types.SimpleNamespace`` / ``dataclasses``
+``Logging``                               ``logging`` (+ ``colorlog``)
+``Progress``                              ``tqdm``
+``MultiProcessing``                       ``concurrent.futures.ProcessPoolExecutor``
+``shellcmd``, ``execute``                 ``subprocess.run``
+``mkdirs``, ``touch``, ``get_home``       ``pathlib`` / ``os.makedirs(exist_ok=True)``
+``cmd_exists``                            ``shutil.which``
+``md5``                                   ``hashlib.file_digest`` (Python 3.11+)
+``browse``                                ``webbrowser.open``
+``get_dependencies``                      ``importlib.metadata.requires``
+``get_share_file``                        ``importlib.resources.files``
+========================================= ======================================================
+
+For example, replacing ``CustomConfig``::
+
+    # before
+    from easydev import CustomConfig
+    config_dir = CustomConfig("myapp").user_config_dir
+
+    # after
+    from pathlib import Path
+    from platformdirs import user_config_dir
+
+    config_dir = Path(user_config_dir("myapp"))
+    config_dir.mkdir(parents=True, exist_ok=True)
+
+Changelog
+---------
+
+========= ==========================================================================
+Version   Description
+========= ==========================================================================
+0.15.0    * fix ``is_mac`` (always returned False)
+          * ``assert_list_almost_equal`` now warns (FutureWarning) when called without
+            ``places``/``deltas`` (nothing is compared); raises ``ListMismatchError``
+            (both ValueError and AssertionError)
+          * add a migration guide (README and documentation) explaining how to
+            replace easydev tools with the standard library, platformdirs, etc.
+          * require Python >= 3.9
+0.13.3    * update pyproject with contribs from @s-t-e-v-e-n-k see PR37
+0.13.2    * replace mock with unittest.mock (fixes
+            https://github.com/cokelaer/easydev/issues/20)
+0.13.1    * fix get_dependencies
+0.13.0    * fix requirements (line_profiler) and CI
+0.12.2    * For developers: move to pyproject. add precommit
+          * replace pkg_resources (deprecated) with importlib
+          * replace appdirs with more generic platformdirs
+========= ==========================================================================

{easydev-0.13.3 → easydev-0.15.0}/easydev/appdirs.py

@@ -1,6 +1,3 @@
-import os
-import sys
-
 from platformdirs import (
     site_config_dir,
     site_data_dir,

{easydev-0.13.3 → easydev-0.15.0}/easydev/browser.py

@@ -61,11 +61,9 @@ There is also an alias **onweb**::
     from easydev import onweb
 
 """
-import argparse
 import os
 import sys
 import webbrowser
-from optparse import OptionParser
 
 
 def browse(url, verbose=True):
@@ -93,23 +91,23 @@ def _browse_mac(url, verbose=True):  # pragma: no cover
     try:
         os.system("open /Applications/Safari.app {}".format(url))
         return
-    except:
+    except Exception:
         pass
 
     try:
         os.system("open /Applications/Safari.app {}".format("http://" + url))
         return
-    except:
+    except Exception:
         pass
 
     try:
         webbrowser.open_new(url)
-    except:
+    except Exception:
         if verbose:
             print("Could not open %s. Trying to append http://" % url)
         try:
             webbrowser.open_new("open http://{}".format(url))
-        except:
+        except Exception:
             print("Could not open http://%s" % url)
             raise Exception
 
@@ -120,7 +118,7 @@ def _browse_linux(url, verbose=True):  # pragma: no cover
     try:
         webbrowser.open(url)
         return
-    except:
+    except Exception:
         pass
 
     try:
@@ -128,7 +126,7 @@ def _browse_linux(url, verbose=True):  # pragma: no cover
             print("Could not open %s" % url)
         webbrowser.open("http://" + url)
         return
-    except:
+    except Exception:
         pass
 
     raise Exception("Could not open http://{}".format(url))
@@ -172,6 +170,4 @@ def main(args=None):  # pragma: no cover
 
 
 if __name__ == "__main__":  # pragma: no cover
-    import sys
-
     main(sys.argv)

{easydev-0.13.3 → easydev-0.15.0}/easydev/chunks.py

@@ -29,12 +29,6 @@
 __all__ = ["split_into_chunks"]
 
 
-try:
-    range = xrange  # py2
-except:
-    pass  # py3
-
-
 def split_into_chunks(items, maxchunks=10):
     """Split a list evenly into N chunks
 

{easydev-0.13.3 → easydev-0.15.0}/easydev/codecs.py

@@ -56,7 +56,7 @@ def to_list(data, verbose=True):
         try:
             data = data.tolist()
             return data
-        except:
+        except Exception:
             if verbose:
                 print("not known type. Trying to cast into a list")
             return list(data)

{easydev-0.13.3 → easydev-0.15.0}/easydev/config_tools.py

@@ -125,14 +125,14 @@ class DynamicConfigParser(ConfigParser):
             self.read(self._filename)
         elif isinstance(config_or_filename, ConfigParser):
             self._replace_config(config_or_filename)
-        elif config_or_filename == None:
+        elif config_or_filename is None:
             pass
         else:
             raise TypeError("config_or_filename must be a valid filename or valid ConfigParser instance")
 
     def read(self, filename):
         """Load a new config from a filename (remove all previous sections)"""
-        if os.path.isfile(filename) == False:
+        if not os.path.isfile(filename):
             raise IOError("filename {0} not found".format(filename))
 
         config = ConfigParser()
@@ -220,9 +220,9 @@ class DynamicConfigParser(ConfigParser):
                 try:  # numbers
                     try:
                         options[option] = self.getint(section, option)
-                    except:
+                    except Exception:
                         options[option] = self.getfloat(section, option)
-                except:  # string
+                except Exception:  # string
                     options[option] = self.get(section, option, raw=True)
         return options
 
@@ -238,7 +238,7 @@ class DynamicConfigParser(ConfigParser):
 
         """
         try:
-            if os.path.exists(filename) == True:
+            if os.path.exists(filename):
                 print("Warning: over-writing %s " % filename)
             fp = open(filename, "w")
         except Exception as err:  # pragma: no cover
@@ -311,7 +311,7 @@ class DynamicConfigParser(ConfigParser):
                     if str(self.get(section, option, raw=True)) != str(data.get(section, option, raw=True)):
                         print("option %s in section %s differ" % (option, section))
                         return False
-                except:  # pragma: no cover
+                except Exception:  # pragma: no cover
                     return False
         return True
 

{easydev-0.13.3 → easydev-0.15.0}/easydev/console.py

@@ -48,7 +48,7 @@ def get_terminal_width():
         terminal_width = width
     except (SystemExit, KeyboardInterrupt):  # pragma: no cover
         raise
-    except:
+    except Exception:
         # FALLBACK
         terminal_width = int(os.environ.get("COLUMNS", 80)) - 1
     return terminal_width

{easydev-0.13.3 → easydev-0.15.0}/easydev/copybutton.py

@@ -91,7 +91,7 @@ def get_copybutton_path():
         try:
             packagedir = easydev.__path__[0]
             packagedir = os.path.realpath(pj(packagedir, "..", "share"))
-        except:
+        except Exception:
             raise IOError("could not find data directory")
     return pj(packagedir, "copybutton.js")
 

{easydev-0.13.3 → easydev-0.15.0}/easydev/decorators.py

@@ -14,7 +14,6 @@
 #
 ##############################################################################
 """Handy decorators"""
-import threading
 from functools import wraps
 
 __all__ = ["ifpylab", "requires", "ifpandas"]
@@ -100,6 +99,7 @@ def _blocking(not_avail):
     return blocking
 """
 
+
 # same as require decorator but works with list of stirngs of
 # single string and uses the functools utilities
 def requires(requires, msg=""):
@@ -122,7 +122,7 @@ def requires(requires, msg=""):
     """
     if isinstance(requires, str):
         requires = [requires]
-    elif isinstance(requires, list) == False:
+    elif not isinstance(requires, list):
         raise TypeError(
             "First argument of the /requires/ decorator must be a"
             + "string or list of string representing the required attributes"
@@ -134,7 +134,7 @@ def requires(requires, msg=""):
         @wraps(f)
         def wrapper(*args, **kwds):
             for require in requires:
-                if hasattr(args[0], require) == False:
+                if not hasattr(args[0], require):
                     raise AttributeError("{} not found in {}. ".format(require, args[0]) + msg)
             return f(*args, **kwds)
 
@@ -157,7 +157,7 @@ def ifpandas(func):
         return func(*args, **kwds)
 
     try:
-        import pandas
+        import pandas  # noqa: F401
 
         return wrapper
     except Exception:  # pragma: no cover
@@ -179,7 +179,7 @@ def ifpylab(func):
 
     # for methods
     try:
-        import pylab
+        import pylab  # noqa: F401
 
         return wrapper
     except Exception:  # pragma: no cover

{easydev-0.13.3 → easydev-0.15.0}/easydev/easytest.py

@@ -16,14 +16,22 @@
 # $:Id $
 
 import tempfile
+import warnings
 
 __all__ = ["assert_list_almost_equal", "trysetattr", "TempFile"]
 
 
+class ListMismatchError(ValueError, AssertionError):
+    """Raised by :func:`assert_list_almost_equal` (ValueError kept for backward compatibility)"""
+
+
 def assert_list_almost_equal(first, second, places=None, deltas=None):
     """Combined version nose.tools.assert_almost_equal and assert_list_equal
 
     This function checks that 2 lists contain identical items.
+    Without *places* or *deltas* nothing is compared and a FutureWarning is
+    issued. On mismatch, :class:`ListMismatchError` is raised (it derives from
+    both ValueError, for backward compatibility, and AssertionError).
     The equality between pair of items is checked with assert_almost_equal
     function, which means you can check for the places argument
 
@@ -44,7 +52,14 @@ def assert_list_almost_equal(first, second, places=None, deltas=None):
     if deltas:
         for x, y in zip(first, second):
             if abs(x - y) > deltas:
-                raise ValueError
+                raise ListMismatchError("{} != {} within tolerance {}".format(x, y, deltas))
+    else:
+        warnings.warn(
+            "assert_list_almost_equal called without places or deltas: nothing is compared. "
+            "This will become a strict comparison in a future release.",
+            FutureWarning,
+            stacklevel=2,
+        )
 
 
 def trysetattr(this, attrname, value, possible):
@@ -71,7 +86,7 @@ def trysetattr(this, attrname, value, possible):
         AssertionError
 
     """
-    if possible == True:
+    if possible is True:
         a1 = True
         a2 = False
     else:
@@ -102,7 +117,7 @@ class TempFile(object):
     def delete(self):
         try:
             self.temp._closer.delete = True
-        except:  # pragma: no cover
+        except AttributeError:  # pragma: no cover
             self.temp.delete = True
         self.temp.close()
 

{easydev-0.13.3 → easydev-0.15.0}/easydev/logging_tools.py

@@ -59,7 +59,6 @@ class Logging(object):
     def _set_name(self, name):
         level = self.level
         self._name = name
-        logger = colorlog.getLogger(self._name)
         if level == 0:
             self._set_level("WARNING")
         else:

{easydev-0.13.3 → easydev-0.15.0}/easydev/misc.py

@@ -20,16 +20,10 @@ __all__ = ["get_home", "cmd_exists"]
 
 def get_home():
     """Return path of the HOME"""
-    # This function should be robust
     # First, let us try with expanduser
-    try:
-        homedir = os.path.expanduser("~")
-    except ImportError:  # pragma: no cover
-        # This may happen.
-        pass
-    else:
-        if os.path.isdir(homedir):
-            return homedir
+    homedir = os.path.expanduser("~")
+    if os.path.isdir(homedir):
+        return homedir
     # Then, with getenv
     for this in ("HOME", "USERPROFILE", "TMP"):  # pragma: no cover
         # getenv is same as os.environ.get

{easydev-0.13.3 → easydev-0.15.0}/easydev/multicore.py

@@ -19,6 +19,12 @@ from multiprocessing import Pool, Process, Queue, cpu_count
 __all__ = ["MultiProcessing"]
 
 
+def _init_worker():
+    import signal
+
+    signal.signal(signal.SIGINT, signal.SIG_IGN)
+
+
 class MultiProcessing(object):
     """Class to run jobs in an asynchronous manner.
 
@@ -53,7 +59,7 @@ class MultiProcessing(object):
 
 
         """
-        if maxcpu == None:
+        if maxcpu is None:
             maxcpu = cpu_count()
 
         self.maxcpu = maxcpu
@@ -102,13 +108,8 @@ class MultiProcessing(object):
             self.pb = Progress(len(self.jobs), 1)
             self.pb.animate(0)
 
-        def init_worker():
-            import signal
-
-            signal.signal(signal.SIGINT, signal.SIG_IGN)
-
         self.results = []
-        self.pool = Pool(self.maxcpu, init_worker)
+        self.pool = Pool(self.maxcpu, _init_worker)
 
         for process in self.jobs:
             self.pool.apply_async(process._target, process._args, process._kwargs, callback=self._cb)

{easydev-0.13.3 → easydev-0.15.0}/easydev/paths.py

@@ -18,7 +18,6 @@
 import importlib
 import os
 from os.path import join as pj
-from pathlib import Path
 
 __all__ = [
     "get_shared_directory_path",
@@ -53,7 +52,7 @@ def get_shared_directory_path(package):
 
     # print("install  mode ? ")
     sharedir = os.path.realpath(pj(location, package, "share"))
-    if os.path.isdir(sharedir) == True:
+    if os.path.isdir(sharedir):
         # looks like we have found the share directory so it is an install mode
         # print ("yes")
         return sharedir
@@ -63,13 +62,13 @@ def get_shared_directory_path(package):
         # FIXME: do we need the 3 cases ??
         # probably just 2 are required, one for develop and one for install mode
         sharedir = os.path.realpath(pj(location, "..", "share"))
-        if os.path.isdir(sharedir) == True:
+        if os.path.isdir(sharedir):
             return sharedir
         sharedir = os.path.realpath(pj(location, "..", "..", "share"))
-        if os.path.isdir(sharedir) == True:
+        if os.path.isdir(sharedir):
             return sharedir
         sharedir = os.path.realpath(pj(location, "..", "..", "..", "share"))
-        if os.path.isdir(sharedir) == True:
+        if os.path.isdir(sharedir):
             return sharedir
         # could not be found,
         sharedir = []
@@ -117,10 +116,10 @@ def get_share_file(package, datadir, filename):
     packagedir = get_shared_directory_path(package)
     fullpath = os.path.join(packagedir, datadir)
     # check that it exists
-    if os.path.isdir(fullpath) == False:  # pragma: no cover
+    if not os.path.isdir(fullpath):  # pragma: no cover
         raise ValueError("The directory %s in package %s does not seem to exist" % (packagedir, fullpath))
     filename_path = os.path.join(fullpath, filename)
-    if os.path.isfile(filename_path) == False:
+    if not os.path.isfile(filename_path):
         correct_files = [x for x in os.listdir(fullpath) if os.path.isfile(x)]
         msg = "The file %s does not exists. Correct filenames found in %s/%s are:\n" % (
             filename_path,

{easydev-0.13.3 → easydev-0.15.0}/easydev/platform.py

@@ -14,7 +14,6 @@
 #
 ##############################################################################
 
-import os
 import sys
 
 __all__ = ["get_platform"]
@@ -36,24 +35,17 @@ def get_platform():  # pragma: no cover
 
     """
     print("//easydev.get_platform() Will be deprecated in future version of easydev")
-    try:
-        platform = plf.system()
-        return platform
-    except:
-        # platform is not available under all systems (e.g., WLST tool
-        # see http://stackoverflow.com/questions/1854/python-what-os-am-i-running-on
-        # so, let us try sys.platform
-        platform = sys.platform
-        if platform.startswith("linux"):
-            platform = "Linux"
-        elif platform.startswith("java"):
-            platform = "Java"
-        elif platform.startswith("win"):
-            platform = "Windows"
-        elif platform.startswith("darwin"):
-            platform = "Darwin"
-        else:
-            print("platform not parsed. Return raw value of sys.platform.")
+    platform = sys.platform
+    if platform.startswith("linux"):
+        platform = "Linux"
+    elif platform.startswith("java"):
+        platform = "Java"
+    elif platform.startswith("win"):
+        platform = "Windows"
+    elif platform.startswith("darwin"):
+        platform = "Darwin"
+    else:
+        print("platform not parsed. Return raw value of sys.platform.")
     return platform
 
 
@@ -72,7 +64,7 @@ def is_linux():
 
 
 def is_mac():
-    if get_platform() == "Mac":
+    if get_platform() in ("Darwin", "Mac"):
         return True
     else:
         return False

{easydev-0.13.3 → easydev-0.15.0}/easydev/sphinx_themes.py

@@ -51,5 +51,5 @@ def get_sphinx_themes():
 
     sharedir = get_shared_directory_path("easydev")
     sharedir = pj(sharedir, "themes")
-    themes = [x for x in os.listdir(sharedir) if x.startswith(".") == False]
+    themes = [x for x in os.listdir(sharedir) if not x.startswith(".")]
     return themes

{easydev-0.13.3 → easydev-0.15.0}/easydev/tools.py

@@ -33,7 +33,7 @@ __all__ = [
 
 
 def precision(data, digit=2):
-    """Round values in a list keeping only N digits precision
+    """Truncate a value (not round) keeping only N digits precision
 
     ::
 
@@ -116,24 +116,26 @@ def shellcmd(cmd, show=False, verbose=False, ignore_errors=False):
     :param str cmd: the command to call
     :param bool show: print the command
     :param bool verbose: print the output
+    :param bool ignore_errors: do not raise when the command writes to stderr
 
-    :return: the output as a string
+    :return: the output as bytes (stripped)
     """
     if show:
         print(cmd)
     try:
         ret = subprocess.Popen([cmd], stdout=subprocess.PIPE, stderr=subprocess.PIPE, shell=True)
 
-        output = ret.stdout.read().strip()
-        error = ret.stderr.read().strip()
-        ret.wait()
+        output, error = ret.communicate()
+        output = output.strip()
+        error = error.strip()
 
+        # Legacy behaviour kept on purpose (many packages rely on it): any
+        # output on stderr is an error, the exit status is not checked.
         if len(error) > 0:
             if ignore_errors is False:
                 raise Exception(error)
-            else:
-                if verbose is True:
-                    print("Errors/Warning" + str(error))
+            elif verbose is True:
+                print("Errors/Warning" + str(error))
 
         if verbose is True:
             print(output)
@@ -161,7 +163,7 @@ def execute(cmd, showcmd=True, verbose=True):
         if verbose:
             try:
                 sys.stdout.write(line.decode())
-            except:
+            except Exception:
                 sys.stdout.write(line)
 
             sys.stdout.flush()
@@ -279,12 +281,9 @@ class AttrDict(dict):
 
         :param dict content: a valid dictionary
         """
-        # accepts dict and attrdict classes
-        try:
-            from collections import OrderedDict
-        except:
-            OrderedDict = AttrDict
+        from collections import OrderedDict
 
+        # accepts dict and attrdict classes
         if content.__class__ not in [dict, OrderedDict, AttrDict]:
             raise TypeError
 

{easydev-0.13.3 → easydev-0.15.0}/easydev/url.py

@@ -14,10 +14,7 @@
 #
 ##############################################################################
 """Utilities related to the web"""
-try:
-    import httplib
-except ImportError:
-    import http.client as httplib
+import http.client as httplib
 
 __all__ = ["isurl_reachable"]
 
@@ -39,13 +36,13 @@ def isurl_reachable(url, timeout=10, path="/"):  # pragma: no cover
     conn = httplib.HTTPConnection(url, timeout=timeout)
     try:
         conn.request("HEAD", path)
-    except:
+    except Exception:
         return False
     # 302 is a redirection
     # 200 is okay
     try:
         response = conn.getresponse()
-    except:
+    except Exception:
         return False
 
     if response.status in [200, 302]:

{easydev-0.13.3 → easydev-0.15.0}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "poetry.core.masonry.api"
 
 [project]
 name = "easydev"
-version = "0.13.3"
+version = "0.15.0"
 description = "Common utilities to ease development of Python packages"
 authors = [
     { "name" = "Thomas Cokelaer", "email" = "thomas.cokelaer@pasteur.fr" },
@@ -21,10 +21,12 @@ classifiers = [
         "Intended Audience :: Science/Research",
         "License :: OSI Approved :: BSD License",
         "Operating System :: POSIX :: Linux",
-        "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",
+        "Programming Language :: Python :: 3.14",
         "Topic :: Software Development :: Libraries :: Python Modules",
         "Topic :: Scientific/Engineering :: Bio-Informatics",
         "Topic :: Scientific/Engineering :: Information Analysis",
@@ -46,12 +48,12 @@ Documentation =  "https://easydev.readthedocs.io"
 
 
 [tool.poetry.dependencies]
-python = "^3.8"
+python = "^3.9"
 colorama = "^0.4.6"
 colorlog = "^6.8.2"
 pexpect = "^4.9.0"
 platformdirs = "^4.2.0"
-line-profiler = "^4.1.2"
+line-profiler = "^5.0.0"
 
 
 

easydev-0.13.3/PKG-INFO

@@ -1,92 +0,0 @@
-Metadata-Version: 2.3
-Name: easydev
-Version: 0.13.3
-Summary: Common utilities to ease development of Python packages
-Home-page: https://easydev.readthedocs.io
-License: BSD-3-Clause
-Keywords: config,decorators,development
-Author: Thomas Cokelaer
-Author-email: thomas.cokelaer@pasteur.fr
-Requires-Python: >=3.8,<4.0
-Classifier: Development Status :: 5 - Production/Stable
-Classifier: Intended Audience :: Education
-Classifier: Intended Audience :: End Users/Desktop
-Classifier: Intended Audience :: Developers
-Classifier: Intended Audience :: Science/Research
-Classifier: License :: OSI Approved :: BSD License
-Classifier: Operating System :: POSIX :: Linux
-Classifier: Programming Language :: Python :: 3.8
-Classifier: Programming Language :: Python :: 3.9
-Classifier: Programming Language :: Python :: 3.10
-Classifier: Programming Language :: Python :: 3.11
-Classifier: Topic :: Software Development :: Libraries :: Python Modules
-Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
-Classifier: Topic :: Scientific/Engineering :: Information Analysis
-Requires-Dist: colorama (>=0.4.6,<0.5.0)
-Requires-Dist: colorlog (>=6.8.2,<7.0.0)
-Requires-Dist: line-profiler (>=4.1.2,<5.0.0)
-Requires-Dist: pexpect (>=4.9.0,<5.0.0)
-Requires-Dist: platformdirs (>=4.2.0,<5.0.0)
-Project-URL: Documentation, https://easydev.readthedocs.io
-Project-URL: Issues, https://github.com/cokelaer/easydev/issues
-Project-URL: Repository, https://github.com/cokelaer/easydev
-Description-Content-Type: text/x-rst
-
-easydev
-##########
-
-.. image:: https://badge.fury.io/py/easydev.svg
-    :target: https://pypi.python.org/pypi/easydev
-
-.. image:: https://github.com/cokelaer/easydev/actions/workflows/main.yml/badge.svg
-    :target: https://github.com/cokelaer/easydev/actions/workflows/main.yml
-
-
-.. image:: https://coveralls.io/repos/cokelaer/easydev/badge.svg?branch=main
-   :target: https://coveralls.io/r/cokelaer/easydev?branch=main
-
-
-
-
-:documentation: http://easydev-python.readthedocs.io/en/latest/
-:contributions: Please join https://github.com/cokelaer/easydev
-:source: Please use https://github.com/cokelaer/easydev
-:issues: Please use https://github.com/cokelaer/easydev/issues
-:Python version supported: 3.9, 3.10, 3.11, 3.12
-
-
-The  `easydev <http://pypi.python.org/pypi/easydev/>`_ package
-provides miscellaneous functions that are repeatidly used during
-the development of Python packages. The goal is to help developers on
-speeding up their own dev. It has been used also as an incubator for other
-packages (e.g., http://pypi.python.org/pypi/colormap) and is stable.
-
-.. warning:: I'm not pretending to provide universal and bug-free tools. The
-    tools provided may also change. However, **easydev** is used
-    in a few other packages such as
-    `bioservices <https://pypi.python.org/pypi/bioservices>`_,
-    `sequana <https://sequana.readthedocs.io>`_ or
-    `GDSCTools <https://sequana.readthedocs.io>`_ to give a few
-    examples.
-
-
-Note 10/01/2025: Although I tried to keep back-compatibility as much as possible, test can be done only on newest version. support for python 3.7 and 3.8 were droppe because the continuous integration does not support it. However,  easydev may still be python3.7 and 3.8 compatible. Have a try.
-
-
-
-Changelog
-~~~~~~~~~
-
-========= ==========================================================================
-Version   Description
-========= ==========================================================================
-0.13.3    * update pyproject with contribs from @s-t-e-v-e-n-k see PR37
-0.13.2    * replace mock with unittest.mock (fixes
-            https://github.com/cokelaer/easydev/issues/20)
-0.13.1    * fix get_dependencies
-0.13.0    * fix requirements (line_profiler) and CI
-0.12.2    * For developers: move to pyprojet. add precomit
-          * replace pkg_resources (deprecated) with importlib
-          * replace appdirs with more generic platformdirs
-========= ==========================================================================
-

easydev-0.13.3/README.rst

@@ -1,57 +0,0 @@
-easydev
-##########
-
-.. image:: https://badge.fury.io/py/easydev.svg
-    :target: https://pypi.python.org/pypi/easydev
-
-.. image:: https://github.com/cokelaer/easydev/actions/workflows/main.yml/badge.svg
-    :target: https://github.com/cokelaer/easydev/actions/workflows/main.yml
-
-
-.. image:: https://coveralls.io/repos/cokelaer/easydev/badge.svg?branch=main
-   :target: https://coveralls.io/r/cokelaer/easydev?branch=main
-
-
-
-
-:documentation: http://easydev-python.readthedocs.io/en/latest/
-:contributions: Please join https://github.com/cokelaer/easydev
-:source: Please use https://github.com/cokelaer/easydev
-:issues: Please use https://github.com/cokelaer/easydev/issues
-:Python version supported: 3.9, 3.10, 3.11, 3.12
-
-
-The  `easydev <http://pypi.python.org/pypi/easydev/>`_ package
-provides miscellaneous functions that are repeatidly used during
-the development of Python packages. The goal is to help developers on
-speeding up their own dev. It has been used also as an incubator for other
-packages (e.g., http://pypi.python.org/pypi/colormap) and is stable.
-
-.. warning:: I'm not pretending to provide universal and bug-free tools. The
-    tools provided may also change. However, **easydev** is used
-    in a few other packages such as
-    `bioservices <https://pypi.python.org/pypi/bioservices>`_,
-    `sequana <https://sequana.readthedocs.io>`_ or
-    `GDSCTools <https://sequana.readthedocs.io>`_ to give a few
-    examples.
-
-
-Note 10/01/2025: Although I tried to keep back-compatibility as much as possible, test can be done only on newest version. support for python 3.7 and 3.8 were droppe because the continuous integration does not support it. However,  easydev may still be python3.7 and 3.8 compatible. Have a try.
-
-
-
-Changelog
-~~~~~~~~~
-
-========= ==========================================================================
-Version   Description
-========= ==========================================================================
-0.13.3    * update pyproject with contribs from @s-t-e-v-e-n-k see PR37
-0.13.2    * replace mock with unittest.mock (fixes
-            https://github.com/cokelaer/easydev/issues/20)
-0.13.1    * fix get_dependencies
-0.13.0    * fix requirements (line_profiler) and CI
-0.12.2    * For developers: move to pyprojet. add precomit
-          * replace pkg_resources (deprecated) with importlib
-          * replace appdirs with more generic platformdirs
-========= ==========================================================================