Merge pull request #768 from jmchilton/py3_quick

Try enabling more Python 3 testing.

Author: jmchilton

.travis.yml

@@ -7,6 +7,7 @@ env:
   - TOX_ENV=py27-lint-readme
   - TOX_ENV=py27-lint-docs
   - TOX_ENV=py27-quick
+  - TOX_ENV=py34-quick
   - TOX_ENV=py27
   - TOX_ENV=py34
   - TOX_ENV=py27-lint-docstrings

planemo/bioconda_scripts/bioconductor_skeleton.py

@@ -3,6 +3,7 @@
 https://github.com/bioconda/bioconda-recipes/blob/master/scripts/bioconductor/bioconductor_skeleton.py
 (written by Ryan Dale github: daler)
 """
+from __future__ import print_function
 
 import configparser
 import hashlib
@@ -12,14 +13,13 @@
 import shutil
 import tarfile
 import tempfile
-import urlparse
 from collections import OrderedDict
 from textwrap import dedent
 
 import bs4
 import pyaml
 import requests
-
+from six.moves.urllib.parse import urljoin
 
 logging.basicConfig(level=logging.INFO, format='[bioconductor_skeleton.py %(asctime)s]: %(message)s')
 logger = logging.getLogger()
@@ -135,7 +135,7 @@ def f(href):
         # build the actual URL based on the identified package name and the
         # relative URL from the source. Here we're just hard-coding
         # '../src/contrib' based on the structure of the bioconductor site.
-        return os.path.join(urlparse.urljoin(self.url, '../src/contrib'), s[0])
+        return os.path.join(urljoin(self.url, '../src/contrib'), s[0])
 
     @property
     def tarball_url(self):
@@ -197,8 +197,8 @@ def description(self):
         e = c['top']
 
         # Glue together newlines
-        for k in e.keys():
-            e[k] = e[k].replace('\n', ' ')
+        for k, v in e.items():
+            e[k] = v.replace('\n', ' ')
 
         return dict(e)
 

planemo/database/postgres.py

@@ -2,6 +2,8 @@
 
 import subprocess
 
+from galaxy.util import unicodify
+
 from planemo.io import communicate
 from .interface import DatabaseSource
 
@@ -20,7 +22,7 @@ def __init__(self, **kwds):
     def list_databases(self):
         """Use `psql --list` to generate a list of identifiers."""
         command_builder = self._psql_command_builder("--list")
-        stdout = self._communicate(command_builder)
+        stdout = unicodify(self._communicate(command_builder))
         output_lines = stdout.splitlines()
         identifiers = []
         for line in output_lines:

planemo/git.py

@@ -1,8 +1,10 @@
 """Utilities for interacting with git using planemo abstractions."""
+from __future__ import absolute_import
+
 import os
 import subprocess
 
-from six import text_type
+from galaxy.util import unicodify
 
 from planemo import io
 
@@ -81,7 +83,7 @@ def diff(ctx, directory, range):
         stdout=subprocess.PIPE, stderr=subprocess.PIPE,
         universal_newlines=True
     )
-    return [l.strip() for l in text_type(stdout).splitlines() if l]
+    return [l.strip() for l in unicodify(stdout).splitlines() if l]
 
 
 def clone(*args, **kwds):
@@ -103,7 +105,7 @@ def rev(ctx, directory):
     stdout, _ = io.communicate(
         cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE
     )
-    return text_type(stdout).strip()
+    return unicodify(stdout).strip()
 
 
 def is_rev_dirty(ctx, directory):
@@ -117,8 +119,8 @@ def rev_if_git(ctx, directory):
     """Determine git revision (or ``None``)."""
     try:
         the_rev = rev(ctx, directory)
-        is_dirtry = is_rev_dirty(ctx, directory)
-        if is_dirtry:
+        is_dirty = is_rev_dirty(ctx, directory)
+        if is_dirty:
             the_rev += "-dirty"
         return the_rev
     except RuntimeError:

planemo/io.py

@@ -51,7 +51,7 @@ def shell(cmds, **kwds):
 def info(message, *args):
     if args:
         message = message % args
-    _echo(click.style(message, bold=True, fg='green'))
+    click.echo(click.style(message, bold=True, fg='green'))
 
 
 def can_write_to_path(path, **kwds):
@@ -64,20 +64,13 @@ def can_write_to_path(path, **kwds):
 def error(message, *args):
     if args:
         message = message % args
-    _echo(click.style(message, bold=True, fg='red'), err=True)
+    click.echo(click.style(message, bold=True, fg='red'), err=True)
 
 
 def warn(message, *args):
     if args:
         message = message % args
-    _echo(click.style(message, fg='red'), err=True)
-
-
-def _echo(message, err=False):
-    if sys.version_info[0] == 2:
-        click.echo(message, err=err)
-    else:
-        print(message)
+    click.echo(click.style(message, fg='red'), err=True)
 
 
 def shell_join(*args):
@@ -133,7 +126,7 @@ def find_matching_directories(path, pattern, recursive):
 
 @contextlib.contextmanager
 def real_io():
-    """Ensure stdout and stderr have ``fileno`` attributes.
+    """Ensure stdout and stderr have supported ``fileno()`` method.
 
     nosetests replaces these streams with :class:`StringIO` objects
     that may not work the same in every situtation - :func:`subprocess.Popen`
@@ -142,9 +135,8 @@ def real_io():
     original_stdout = sys.stdout
     original_stderr = sys.stderr
     try:
-        if not hasattr(sys.stdout, "fileno"):
+        if commands.redirecting_io(sys=sys):
             sys.stdout = sys.__stdout__
-        if not hasattr(sys.stderr, "fileno"):
             sys.stderr = sys.__stderr__
         yield
     finally:

planemo/reports/xunit_handler.py

@@ -5,5 +5,4 @@ def handle_report_xunit_kwd(kwds, collected_data):
     if kwds.get('report_xunit', False):
         with open(kwds['report_xunit'], 'w') as handle:
             handle.write(template_data(
-                collected_data, template_name='xunit.tpl')
-                .encode('ascii', 'xmlcharrefreplace'))
+                collected_data, template_name='xunit.tpl'))

planemo/tool_builder.py

@@ -300,7 +300,7 @@ def _build_galaxy(**kwds):
     # process raw cite urls
     cite_urls = kwds.get("cite_url", [])
     del kwds["cite_url"]
-    citations = map(UrlCitation, cite_urls)
+    citations = list(map(UrlCitation, cite_urls))
     kwds["bibtex_citations"] = citations
 
     # handle requirements and containers

requirements.txt

@@ -11,8 +11,8 @@ jinja2
 glob2
 virtualenv
 lxml
-gxformat2>=0.1.1
+gxformat2>=0.2.0
 ephemeris>=0.2.0
-galaxy-lib>=17.9.8
+galaxy-lib>=17.9.12
 html5lib>=0.9999999,!=0.99999999,!=0.999999999,!=1.0b10,!=1.0b09
 cwltool==1.0.20170828135420

tests/test_io.py

@@ -1,10 +1,8 @@
 """Test utilities from :module:`planemo.io`."""
 import tempfile
 
-from .test_utils import (
-    assert_equal,
-    io,
-)
+from planemo import io
+from .test_utils import assert_equal
 
 
 def test_io_capture():
@@ -40,7 +38,7 @@ def assert_filtered_is(paths, expected, **kwds):
     assert_filtered_is(["/a/c"], [], exclude=["/a"])
     assert_filtered_is(["/b"], ["/b"], exclude=["/a"])
     assert_filtered_is(["/a/b/c"], [], exclude=["c"])
-    with tempfile.NamedTemporaryFile() as tmp:
+    with tempfile.NamedTemporaryFile(mode='w+') as tmp:
         tmp.write("#exclude c\n\nc\n")
         tmp.flush()
         assert_filtered_is(["/a/b/c", "/a/b/d"], ["/a/b/d"], exclude_from=[tmp.name])

tests/test_shed_upload.py

@@ -138,7 +138,7 @@ def test_upload_from_git(self):
                 "git add .",
                 "git commit -m 'initial commit'"
             ]))
-            rev = git.rev(None, "single_tool").decode("UTF-8")
+            rev = git.rev(None, "single_tool")
             upload_command = [
                 "shed_update", "--force_repository_creation",
                 "git+single_tool/.git"