Merge pull request #70 from databio/dev

minor update for pypi

.gitignore

@@ -7,6 +7,7 @@
 # Ignore Python build-related directories.
 .eggs/
 build/
+dist/
 
 # Keep everything in data.
 !metadata/*
@@ -30,6 +31,7 @@ pipeline_output/
 !*README.md*
 !*.rst
 !*.xlsx
+!*.in
 
 # Make sure to track .gitignore.
 !.gitignore

MANIFEST.in

@@ -0,0 +1,3 @@
+include requirements/*
+include README.md
+include logo_pypiper.svg

doc/source/changelog.rst

@@ -1,5 +1,8 @@
 Changelog
 ******************************
+- **v0.7.1** (*2018-02-27*):
+
+    - Package cleanup for Pypi.
 
 - **v0.7.0** (*2017-12-12*):
 

pypiper/_version.py

@@ -1 +1 @@
-__version__ = "0.7.0"
+__version__ = "0.7.1"

pypiper/manager.py

@@ -749,7 +749,7 @@ def checkprint(self, cmd, shell="guess", nofail=False, errmsg=None):
 
         try:
             return subprocess.check_output(cmd, shell=shell)
-        except (OSError, subprocess.CalledProcessError) as e:
+        except Exception as e:
             self._triage_error(e, nofail, errmsg)
 
 
@@ -863,7 +863,7 @@ def callprint(self, cmd, shell="guess", nofail=False, container=None, lock_name=
             if p.returncode != 0:
                 raise OSError("Subprocess returned nonzero result.")
 
-        except (OSError, subprocess.CalledProcessError) as e:
+        except Exception as e:
             self._triage_error(e, nofail, errmsg)
 
         return [returncode, local_maxmem]

pypiper/ngstk.py

@@ -1525,7 +1525,7 @@ def macs2_call_peaks(
             cmd += " -c {0}".format(control_bams if type(control_bams) is str else " ".join(control_bams))
 
         if paired:
-            cmd += "-f BAMPE "
+            cmd += " -f BAMPE "
 
         # Additional settings based on whether the marks is associated with
         # broad peaks
@@ -1604,7 +1604,7 @@ def zinba_call_peaks(self, treatment_bed, control_bed, cpus, tagmented=False):
 
     def filter_peaks_mappability(self, peaks, alignability, filtered_peaks):
         cmd = self.tools.bedtools + " intersect -wa -u -f 1"
-        cmd += " -a {0} -b {1} > {2} ".format(peaks, alignability, filteredPeaks)
+        cmd += " -a {0} -b {1} > {2} ".format(peaks, alignability, filtered_peaks)
         return cmd
 
     def homer_find_motifs(self, peak_file, genome, output_dir, size=150, length="8,10,12,14,16", n_motifs=12):

pypiper/utils.py

@@ -16,7 +16,7 @@
 # What to export/attach to pypiper package namespace.
 # Conceptually, reserve this for functions expected to be used in other
 # packages, and import from utils within pypiper for other functions.
-__all__ = ["add_pypiper_args", "build_command"]
+__all__ = ["add_pypiper_args", "build_command", "get_parameter"]
 
 
 
@@ -259,6 +259,55 @@ def flag_name(status):
 
 
 
+def get_parameter(param, param_pools, on_missing=None, error=True):
+    """
+    Get the value for a particular parameter.
+
+    Other than the parameter name itself, the other critical
+
+    :param str param: Name of parameter for which to determine/fetch value.
+    :param Sequence[Mapping[str, object]] param_pools: Ordered (priority)
+        collection of mapping from parameter name to value; this should be
+        ordered according to descending priority.
+    :param object | function(str) -> object on_missing: default value or
+        action to take if the requested parameter is missing from all of the
+        pools. If a callable, it should return a value when passed the
+        requested parameter as the one and only argument.
+    :param bool error: Whether to raise an error if the requested parameter
+        is not mapped to a value AND there's no value or strategy provided
+        with 'on_missing' with which to handle the case of a request for an
+        unmapped parameter.
+    :return object: Value to which the requested parameter first mapped in
+        the (descending) priority collection of parameter 'pools,' or
+        a value explicitly defined or derived with 'on_missing.'
+    :raise KeyError: If the requested parameter is unmapped in all of the
+        provided pools, and the argument to the 'error' parameter evaluates
+        to True.
+    """
+
+    # Search for the requested parameter.
+    for pool in param_pools:
+        if param in pool:
+            return pool[param]
+
+    # Raise error if unfound and no strategy or value is provided or handling
+    # unmapped parameter requests.
+    if error and on_missing is None:
+        raise KeyError("Unmapped parameter: '{}'".format(param))
+
+    # Use the value or strategy for handling unmapped parameter case.
+    try:
+        return on_missing(param)
+    except TypeError:
+        if hasattr(on_missing, "__call__"):
+            raise TypeError(
+                "Any callable passed as the action to take when a requested "
+                "parameter is missing should accept that parameter and return "
+                "a value.")
+        return on_missing
+
+
+
 def is_in_file_tree(fpath, folder):
     """
     Determine whether a file is in a folder.

setup.py

@@ -43,15 +43,21 @@ def read_reqs_file(reqs_name):
 # Dev installation is full user + test.
 addl_reqs["dev"] = list(set(test_reqs + addl_reqs["all"]))
 
+# Handle the pypi README formatting.
+try:
+    import pypandoc
+    long_description = pypandoc.convert_file('README.md', 'rst')
+except(IOError, ImportError):
+    long_description = open('README.md').read()
 
 setup(
     name='pypiper',
     packages=['pypiper'],
     version=version,
-    description='A lightweight python toolkit for gluing together restartable, robust command line pipelines',
+    description=long_description,
     author='Nathan Sheffield, Johanna Klughammer, Andre Rendeiro',
     author_email='nathan@code.databio.org, jklughammer@cemm.oeaw.ac.at, arendeiro@cemm.oeaw.ac.at',
-    url='https://github.com/epigen/pypiper/',
+    url='https://github.com/databio/pypiper/',
     test_suite="tests",         # python setup.py test
     tests_require=test_reqs,    # Test-specific package dependencies
     # Extra package if doing `python setup.py test`