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run: Round 2 of py2 unicode #3046

merged 4 commits into from Dec 3, 2018


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@kyleam kyleam commented Dec 2, 2018

  • Fix an issue not caught by #3035.
  • Apply patch similar to @mih's #3031, but avoid py2-compatibility issue describe here.
Thanks to Yarik for pointing this out.
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@yarikoptic yarikoptic commented Dec 3, 2018

note: current buildbot failures seems to be some connectivity issue

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@yarikoptic yarikoptic left a comment

looks good but I have a confusion on double use of assure_unicode

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kyleam added 3 commits Dec 3, 2018
run calls map() in several places.  Use for

Re: datalad#3046 (review)
The tests added in dataladgh-3035 tested the Python API case, where the run
caller passes in unicode strings.  But when called from the command
line, the command will be a byte-string in Python 2.  Ensure that it's
unicode.  Do this in normalize_command() because otherwise we need to
repeat the list/string test elsewhere and outside callers (like
containers-run) would need to apply a similar py2-compatibility fix.
This is like the patch from dataladgh-3031 except that it still encodes the
message before writing it for py2 compatibility.  This approach should
still address the failure on windows (dataladgh-3030).

Remove the assure_bytes() call not only because it is causing issues
on windows but also because conceptually there isn't a reason to
encode the message here.  It will ultimately be passed to GitRepo or
AnnexRepo's commit(), which shouldn't and don't require a byte-string
message.  Current tests indicate there is no issue, and, if one
arises, it should be fixed in {GitRepo,AnnexRepo}.commit().
@kyleam kyleam force-pushed the run-py2-unicode-round2 branch from ce9c5e1 to f7c2751 Dec 3, 2018
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@codecov codecov bot commented Dec 3, 2018

Codecov Report

Merging #3046 into master will increase coverage by <.01%.
The diff coverage is 100%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master    #3046      +/-   ##
+ Coverage   90.23%   90.23%   +<.01%     
  Files         246      246              
  Lines       32502    32506       +4     
+ Hits        29328    29332       +4     
  Misses       3174     3174
Impacted Files Coverage Δ
datalad/interface/ 100% <100%> (ø) ⬆️
datalad/interface/tests/ 99.84% <100%> (ø) ⬆️

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@kyleam kyleam commented Dec 3, 2018

looks good but I have a confusion on double use of assure_unicode

Thanks for the review. Update pushed.

1:  85b14e498 = 1:  85b14e498 DOC: run: Document a normalize_command() limitation
-:  --------- > 2:  40d306828 RF(py2): run: Use
2:  0b8a152b0 ! 3:  31b249a67 BF(py2): run: Ensure that the command is unicode
    @@ -29,15 +29,6 @@
          return command

    -                          'cannot detect changes by command'))
    -             return
    --    cmd = normalize_command(cmd)
    -+    cmd = assure_unicode(normalize_command(cmd))
    -     inputs = GlobbedPaths(inputs, pwd=pwd,
    -                           expand=expand in ["inputs", "both"])

     diff --git a/datalad/interface/tests/ b/datalad/interface/tests/
     --- a/datalad/interface/tests/
3:  ce9c5e1f4 = 4:  f7c2751d2 RF: run: Do not force byte-encoding of commit message

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@yarikoptic yarikoptic commented Dec 3, 2018


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@kyleam kyleam commented Dec 3, 2018

OK, Travis all green, buildbot failures seem to be a connectivity issue, and the appveyor failure is known.

@kyleam kyleam merged commit c2b3ce1 into datalad:master Dec 3, 2018
4 of 7 checks passed
@kyleam kyleam deleted the run-py2-unicode-round2 branch Dec 3, 2018
yarikoptic added a commit that referenced this issue Feb 8, 2019
 A variety of bugfixes and enhancements

 ### Major refactoring and deprecations

 - All extracted metadata is now placed under git-annex by default.
   Previously files smaller than 20 kb were stored in git. ([#3109])
 - TODO: get_runner #3104 and pending #3131

 ### Fixes

 - Improved handling of long commands:
   - The code that inspected `SC_ARG_MAX` didn't check that the
     reported value was a sensible, positive number. ([#3025])
   - More commands that invoke `git` and `git-annex` with file
     arguments learned to split up the command calls when it is likely
     that the command would fail due to exceeding the maximum supported
     length. ([#3138])
 - The `setup_yoda_dataset` procedure created a malformed
   .gitattributes line. ([#3057])
 - [download-url] unnecessarily tried to infer the dataset when
   `--no-save` was given. ([#3029])
 - [rerun] aborted too late and with a confusing message when a ref
   specified via `--onto` didn't exist. ([#3019])
 - [run]:
   - `run` didn't preserve the current directory prefix ("./") on
      inputs and outputs, which is problematic if the caller relies on
      this representation when formatting the command. ([#3037])
   - Fixed a number of unicode py2-compatibility issues. ([#3035]) ([#3046])
   - To proceed with a failed command, the user was confusingly
     instructed to use `save` instead of `add` even though `run` uses
     `add` underneath. ([#3080])
 - Fixed a case where the helper class for checking external modules
   incorrectly reported a module as unknown. ([#3051])
 - [add-archive-content] mishandled the archive path when the leading
   path contained a symlink. ([#3058])
 - Following denied access, the credential code failed to consider a
   scenario, leading to a type error rather than an appropriate error
   message. ([#3091])
 - Some tests failed when executed from a `git worktree` checkout of the
   source repository. ([#3129])
 - During metadata extraction, batched annex processes weren't properly
   terminated, leading to issues on Windows. ([#3137])
 - [add] incorrectly handled an "invalid repository" exception when
   trying to add a submodule. ([#3141])
 - Pass `GIT_SSH_VARIANT=ssh` to git processes to be able to specify
   alternative ports in SSH urls

 ### Enhancements and new features

 - [search] learned to suggest closely matching keys if there are no
   hits. ([#3089])
 - [create-sibling] gained a `--group` option so that the caller can
   specify the file system group for the repository. ([#3098])
 - Interface classes can now override the default renderer for
   summarizing results. ([#3061])
 - [run]:
   - `--input` and `--output` can now be shortened to `-i` and `-o`.
   - Placeholders such as "{inputs}" are now expanded in the command
     that is shown in the commit message subject. ([#3065])
   - `` gained an `extra_inputs` argument so
     that wrappers like [datalad-container] can specify additional inputs
     that aren't considered when formatting the command string. ([#3038])
   - "--" can now be used to separate options for `run` and those for
     the command in ambiguous cases. ([#3119])
 - The utilities `create_tree` and `ok_file_has_content` now support
   ".gz" files. ([#3049])
 - The Singularity container for 0.11.1 now uses [nd_freeze] to make
   its builds reproducible.
 - A [publications] page has been added to the documentation. ([#3099])
 - `GitRepo.set_gitattributes` now accepts a `mode` argument that
   controls whether the .gitattributes file is appended to (default) or
   overwritten. ([#3115])
 - `datalad --help` now avoids using `man` so that the list of
   subcommands is shown.  ([#3124])

* tag '0.11.2': (124 commits)
  Changelog entry for GIT_SSH_VARIANT change
  BF: sshconnector: Don't use ssh's port flag as scp's
  RF: sshconnector: Simplify shlex quote import
  CHANGELOG(0.11.2): Fix some typos
  [DATALAD RUNCMD] CHANGELOG: Linkify 0.11.2 entries
  CHANGELOG: Do first pass for 0.11.2
  CHANGELOG: Add missing link target for download-url
  Start cooking the 0.11.2 release
  RF: appveyor - move test_install tests to be ran the last
  RF: text_type instead of str
  ENH(TST): provide my timing for the slow test
  BF(TST): adjust the test for the fact that AnnexRepo.add does not blow on nonexisting files
  ENH(TST): two tests which test quick or thorough for add failing with too long list of files
  BF: get stderr if present, otherwise just use str(e)
  BF: append out/err only if not empty/None
  Centrlize handling running commands with long files list in _run_command_files_split
  RF: remove minor duplication of -- handling, place all files handling closer to the call
  RF: move unrelated to try/except handling outside
  ENH+DOC: Report actual process handle, not just PID
@yarikoptic yarikoptic added this to the Release 0.11.2 milestone Feb 10, 2019
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