Merge remote-tracking branch 'conda/master'

# Conflicts:
#	appveyor.yml
#	utils/travis-run-install.sh

Conflicts were minor and blamable on how code has moved to new files.

CHANGELOG.md

@@ -3,22 +3,32 @@
 ### Deprecations/Breaking Changes
 * the 'r' channel is now part of defaults (#3677)
 * remove dead install_tar function (#3641)
+* no longer symlinking conda for activated envs (#3712)
 
 ### Improvements
+* noarch python packages (#3712)
 * cache VersionOrder objects to improve performance (#3596)
 * fix documentation and typos (#3526, #3572, #3627)
 * imporoved solver hint detection, simplified filtering (#3597)
 * add multikey configuration validation (#3432)
 * some Fish autocompletions (#2519)
 * reduce priority for packages removed from the index (#3703)
 * add user-agent, uid, gid to conda info (#3671)
+* make http timeouts configurable (#3832)
+* add a pkgs_dirs config parameter (#3691)
+* Add an 'always_softlink' option (#3870, #3876)
 
 ### Bug Fixes
 * account for the Windows Python 2.7 os.environ unicode aversion (#3363)
 * fix link field in record object (#3424)
 * anaconda api token bug fix; additional tests (#3673)
 * fix #3667 unicode literals and unicode decode (#3682)
 * add conda-env entrypoint (#3743)
+* fix #3807 json dump on conda config --show --json (#3811)
+* fix #3801 location of temporary hard links of index.json (#3813)
+* fix invalid yml example (#3849)
+* add arm platforms back to subdirs (#3852)
+* fix #3771 better error message for assertion errors (#3802)
 
 ### Non-User-Facing Changes
 * remove unnecessary eval (#3428)
@@ -31,24 +41,52 @@
 * integration tests for conda clean (#3695, #3699)
 * disable coverage on s3 and ftp requests adapaters (#3696, #3701)
 * github repo hygiene (#3705, #3706)
+* major install refactor (#3712)
+
+
+## 4.2.13 (unreleased)
+
+### Improvements
+* double/extend http timeouts (#3831)
+* let descriptive http errors cover more http exceptions (#3834)
+* backport some conda-build configuration (#3875)
+
+### Non-User-Facing Changes
+* flake8 E116, E121, & E123 enabled (#3883)
 
 
 ## 4.1.13 (unreleased)
 
+### Deprecations/Breaking Changes
+* show warning message for pre-link scripts (#3727)
+* error and exit for install of packages that require conda minimum version 4.3 (#3726)
+
 ### Improvements
 * use install.rm_rf for TemporaryDirectory cleanup (#3425)
+* improve handling of local dependency information (#2107)
 
 ### Bug Fixes
 * fix the api->conda substitution (#3456)
+* fix conda/install.py single-file behavior (#3854)
 
 
 ## 3.19.4 (unreleased)
 
+### Deprecations/Breaking Changes
+* show warning message for pre-link scripts (#3727)
+* error and exit for install of packages that require conda minimum version 4.3 (#3726)
+
 ### Improvements
 * improve handling of local dependency information (#2107)
+* use install.rm_rf for TemporaryDirectory cleanup (#3425)
+
+### Bug Fixes
+* fix conda/install.py single-file behavior (#3854)
+* fix the api->conda substitution (#3456)
+* fix silent directory removal (#3730)
 
 
-## 4.2.12 (unreleased)
+## 4.2.12 (2016-11-02)
 
 ### Bug Fixes
 

conda/base/context.py

@@ -69,7 +69,8 @@ class Context(Configuration):
     use_pip = PrimitiveParameter(True)
 
     _root_dir = PrimitiveParameter(sys.prefix, aliases=('root_dir',))
-    _envs_dirs = SequenceParameter(string_types, aliases=('envs_dirs',))
+    _envs_dirs = SequenceParameter(string_types, aliases=('envs_dirs', 'envs_path'),
+                                   string_delimiter=os.pathsep)
     _pkgs_dirs = SequenceParameter(string_types, aliases=('pkgs_dirs',))
 
     # connection details
@@ -96,6 +97,7 @@ class Context(Configuration):
     _custom_multichannels = MapParameter(Sequence, aliases=('custom_multichannels',))
 
     # command line
+    always_softlink = PrimitiveParameter(False, aliases=('softlink',))
     always_copy = PrimitiveParameter(False, aliases=('copy',))
     always_yes = PrimitiveParameter(False, aliases=('yes',))
     channel_priority = PrimitiveParameter(True)
@@ -116,6 +118,20 @@ class Context(Configuration):
     _croot = PrimitiveParameter('', aliases=('croot',))
     conda_build = MapParameter(string_types, aliases=('conda-build',))
 
+    def post_build_validation(self):
+        errors = []
+        if self.client_ssl_cert_key and not self.client_ssl_cert:
+            error = ValidationError('client_ssl_cert', self.client_ssl_cert, "<<merged>>",
+                                    "'client_ssl_cert' is required when 'client_ssl_cert_key' "
+                                    "is defined")
+            errors.append(error)
+        if self.always_copy and self.always_softlink:
+            error = ValidationError('always_copy', self.always_copy, "<<merged>>",
+                                    "'always_copy' and 'always_softlink' are mutually exclusive. "
+                                    "Only one can be set to 'True'.")
+            errors.append(error)
+        return errors
+
     @property
     def croot(self):
         """This is where source caches and work folders live"""
@@ -154,18 +170,6 @@ def svn_cache(self):
         conda_bld_ensure_dir(path)
         return path
 
-    def post_build_validation(self):
-        errors = []
-        if self.client_ssl_cert_key and not self.client_ssl_cert:
-            error = ValidationError('client_ssl_cert', self.client_ssl_cert, "<<merged>>",
-                                    "'client_ssl_cert' is required when 'client_ssl_cert_key' "
-                                    "is defined")
-            errors.append(error)
-        return errors
-
-    _envs_dirs = SequenceParameter(string_types, aliases=('envs_dirs', 'envs_path'),
-                                   string_delimiter=os.pathsep)
-
     @property
     def default_python(self):
         ver = sys.version_info
@@ -357,6 +361,8 @@ def get_help_dict():
             """),
         'always_copy': dals("""
             """),
+        'always_softlink': dals("""
+            """),
         'changeps1': dals("""
             """),
         'use_pip': dals("""
@@ -478,6 +484,7 @@ def inroot_notwritable(prefix):
     return (abspath(prefix).startswith(context.root_dir) and
             not context.root_writable)
 
+
 try:
     context = Context(SEARCH_PATH, conda, None)
 except LoadError as e:

conda/cli/common.py

@@ -229,7 +229,7 @@ def add_parser_copy(p):
         action="store_true",
         default=NULL,
         help="Install all packages using copies instead of hard- or soft-linking."
-        )
+    )
 
 def add_parser_pscheck(p):
     p.add_argument(

conda/cli/conda_argparse.py

@@ -30,6 +30,7 @@ def debug_argcomplete(msg):
         f.write("\n%s\n" % msg)
         f.flush()
 
+
 try:
     import argcomplete
     argcomplete.CompletionFinder

conda/cli/main_config.py

@@ -277,6 +277,7 @@ def execute_config(args, parser):
                                            'add_pip_as_python_dependency',
                                            'allow_softlinks',
                                            'always_copy',
+                                           'always_softlink',
                                            'always_yes',
                                            'auto_update_conda',
                                            'binstar_upload',

conda/cli/main_info.py

@@ -127,7 +127,7 @@ def pretty_package(pkg):
         ('build string', pkg.build),
         ('channel', Channel(pkg.channel).canonical_name),
         ('size', human_bytes(pkg.info['size'])),
-        ])
+    ])
     rest = pkg.info
     for key in sorted(rest):
         if key in {'build', 'depends', 'requires', 'channel', 'name',

conda/cli/main_remove.py

@@ -8,6 +8,7 @@
 
 import errno
 import logging
+import sys
 from argparse import RawDescriptionHelpFormatter
 from os.path import join
 
@@ -160,8 +161,7 @@ def execute(args, parser):
 
     if plan.nothing_to_do(actions):
         if args.all:
-            print()
-            print("Remove all packages in environment %s:\n" % prefix)
+            print("\nRemove all packages in environment %s:\n" % prefix, file=sys.stderr)
             if not context.json:
                 confirm_yn(args)
             rm_rf(prefix)

conda/cli/main_search.py

@@ -92,7 +92,7 @@ def configure_parser(sub_parsers):
         'win-64', and so on. The default is to search the current platform.""",
         choices=Platforms(),
         default=None,
-        )
+    )
     p.add_argument(
         "--spec",
         action="store_true",
@@ -268,7 +268,7 @@ def execute_search(args, parser):
                     pkg.build,
                     pkg.schannel,
                     disp_features(features),
-                    ))
+                ))
                 disp_name = ''
             else:
                 data = {}

conda/config.py

@@ -9,7 +9,7 @@
 import sys
 from os.path import abspath, expanduser, isfile, join
 
-from conda.base.context import context, non_x86_linux_machines  # NOQA
+from conda.base.context import context, non_x86_linux_machines
 non_x86_linux_machines = non_x86_linux_machines
 
 
@@ -38,6 +38,7 @@
     'always_yes',
     'always_copy',
     'allow_softlinks',
+    'always_softlink',
     'auto_update_conda',
     'changeps1',
     'use_pip',
@@ -81,12 +82,14 @@ def get_local_urls():
 class RC(object):
 
     def get(self, key, default=None):
+        key = key.replace('-', '_')
         return getattr(context, key, default)
 
 
 rc = RC()
 envs_dirs = context.envs_dirs
 
+
 def get_rc_path():
     path = os.getenv('CONDARC')
     if path == ' ':
@@ -98,6 +101,7 @@ def get_rc_path():
             return path
     return None
 
+
 rc_path = get_rc_path()
 
 pkgs_dirs = context.pkgs_dirs

conda/console.py

@@ -165,6 +165,7 @@ def emit(self, record):
         except IOError:
             pass
 
+
 _fetch_prog_handler = FetchProgressHandler()
 _prog_handler = ProgressHandler()
 

conda/core/index.py

@@ -4,12 +4,12 @@
 import bz2
 import hashlib
 import json
-import requests
 import warnings
 from functools import wraps
 from logging import DEBUG, getLogger
 from os import makedirs
 from os.path import dirname, join
+from requests.exceptions import ConnectionError, HTTPError, SSLError
 from requests.packages.urllib3.exceptions import InsecureRequestWarning
 
 from .linked_data import linked_data
@@ -158,8 +158,10 @@ def get_json_str(filename, resp_content):
     except ValueError as e:
         raise CondaRuntimeError("Invalid index file: {0}: {1}".format(join_url(url, filename), e))
 
-    except requests.exceptions.HTTPError as e:
-        if e.response.status_code == 404:
+    except (ConnectionError, HTTPError, SSLError) as e:
+        # status_code might not exist on SSLError
+        status_code = getattr(e.response, 'status_code', None)
+        if status_code == 404:
             if url.endswith('/noarch'):  # noarch directory might not exist
                 return None
 
@@ -171,7 +173,7 @@ def get_json_str(filename, resp_content):
             Further configuration help can be found at <%s>.
             """ % join_url(CONDA_HOMEPAGE_URL, 'docs/config.html'))
 
-        elif e.response.status_code == 403:
+        elif status_code == 403:
             if url.endswith('/noarch'):
                 return None
             else:
@@ -183,7 +185,7 @@ def get_json_str(filename, resp_content):
                 Further configuration help can be found at <%s>.
                 """ % join_url(CONDA_HOMEPAGE_URL, 'docs/config.html'))
 
-        elif e.response.status_code == 401:
+        elif status_code == 401:
             channel = Channel(url)
             if channel.token:
                 help_message = dals("""
@@ -222,7 +224,7 @@ def get_json_str(filename, resp_content):
                 Further configuration help can be found at <%s>.
                 """ % join_url(CONDA_HOMEPAGE_URL, 'docs/config.html'))
 
-        elif 500 <= e.response.status_code < 600:
+        elif status_code is not None and 500 <= status_code < 600:
             help_message = dals("""
             An remote server error occurred when trying to retrieve this URL.
 
@@ -233,24 +235,11 @@ def get_json_str(filename, resp_content):
             """)
 
         else:
-            help_message = "An HTTP error occurred when trying to retrieve this URL."
+            help_message = "An HTTP error occurred when trying to retrieve this URL.\n%r" % e
 
-        raise CondaHTTPError(help_message, e.response.url, e.response.status_code,
-                             e.response.reason)
+        raise CondaHTTPError(help_message, e.response.url if e.response else None, status_code,
+                             e.response.reason if e.response else None)
 
-    except requests.exceptions.SSLError as e:
-        msg = "SSL Error: %s\n" % e
-        stderrlog.info("SSL verification error: %s\n" % e)
-        log.debug(msg)
-
-    except requests.exceptions.ConnectionError as e:
-        msg = "Connection error: %s: %s\n" % (e, url)
-        stderrlog.info('Could not connect to %s\n' % url)
-        log.debug(msg)
-        if fail_unknown_host:
-            raise CondaRuntimeError(msg)
-
-        raise CondaRuntimeError(msg)
     cache['_url'] = url
     try:
         with open(cache_path, 'w') as fo:

conda/core/install.py

@@ -6,6 +6,7 @@
 import sys
 import warnings
 from collections import namedtuple
+from conda._vendor.auxlib.ish import dals
 from logging import getLogger
 from os import listdir
 from os.path import dirname, isdir, isfile, join
@@ -282,8 +283,13 @@ def run_script(prefix, dist, action='post-link', env_prefix=None):
     False on failure
     """
     if action == 'pre-link':
-        warnings.warn("The package %s uses a pre-link script.\n"
-                      "Pre-link scripts may be deprecated in the near future.")
+        warnings.warn(dals("""
+        Package %s uses a pre-link script. Pre-link scripts are potentially dangerous.
+        This is because pre-link scripts have the ability to change the package contents in the
+        package cache, and therefore modify the underlying files for already-created conda
+        environments.  Future versions of conda may deprecate and ignore pre-link scripts.
+        """ % dist))
+
     path = join(prefix, 'Scripts' if on_win else 'bin', '.%s-%s.%s' % (
             dist.dist_name,
             action,