Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

ENH: run: Support "extra inputs" #3038

Merged
merged 2 commits into from Dec 2, 2018
Merged

Conversation

@kyleam
Copy link
Contributor

@kyleam kyleam commented Nov 30, 2018

To let run interface wrappers (like containers-run) specify inputs
without surprising users (who did not explicitly specify those
inputs), add an "extra_inputs" argument to run_command().  There's no
reason we couldn't add it to Run.__call__ along with a command-line
switch and format field, but let's avoid doing so exposing another
user-facing option until a clear use case arises.

Re: datalad/datalad-container#38

Run.__call__() is a direct call to run_command() mirrors aside from
the --rerun compatibility kludge, the interface decorations, and this
empty command check.  Wrappers may want to call run_command() directly
to get access to the options not exposed in Run's interface (e.g.,
`inject` and the upcoming `extra_inputs`).

Move the empty command check to run_command() so that wrappers don't
have to do that check themselves.
kyleam added a commit to kyleam/datalad-container that referenced this issue Nov 30, 2018
`containers-run` builds on `run`, augmenting the input list with a
Singularity image.  This means that if a user then puts "{inputs}" in
their command, the image file is included too.  This is almost
certainly surprising to the user because the user has not explicitly
specified the image with --input and is probably not aware that
containers-run adds it.  Avoid this by using run_command's recently
added extra_inputs argument.

Re: datalad/datalad#3038
Closes datalad#38.
Copy link
Member

@yarikoptic yarikoptic left a comment

Little comment about testing

datalad/interface/tests/test_run.py Show resolved Hide resolved
To let run interface wrappers (like containers-run) specify inputs
without surprising users (who did not explicitly specify those
inputs), add an "extra_inputs" argument to run_command().  There's no
reason we couldn't add it to Run.__call__ along with a command-line
switch and format field, but let's avoid exposing another user-facing
option until a clear use case arises.

Re: datalad/datalad-container#38
@kyleam kyleam force-pushed the run-inputs-extra branch from 3a10059 to dd407d1 Dec 1, 2018
@codecov
Copy link

@codecov codecov bot commented Dec 1, 2018

Codecov Report

Merging #3038 into master will increase coverage by <.01%.
The diff coverage is 100%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master    #3038      +/-   ##
==========================================
+ Coverage   90.12%   90.12%   +<.01%     
==========================================
  Files         246      246              
  Lines       32462    32470       +8     
==========================================
+ Hits        29257    29265       +8     
  Misses       3205     3205
Impacted Files Coverage Δ
datalad/interface/rerun.py 96.24% <ø> (ø) ⬆️
datalad/interface/run.py 100% <100%> (ø) ⬆️
datalad/interface/tests/test_run.py 99.83% <100%> (ø) ⬆️

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update 0347878...dd407d1. Read the comment docs.

1 similar comment
@codecov
Copy link

@codecov codecov bot commented Dec 1, 2018

Codecov Report

Merging #3038 into master will increase coverage by <.01%.
The diff coverage is 100%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master    #3038      +/-   ##
==========================================
+ Coverage   90.12%   90.12%   +<.01%     
==========================================
  Files         246      246              
  Lines       32462    32470       +8     
==========================================
+ Hits        29257    29265       +8     
  Misses       3205     3205
Impacted Files Coverage Δ
datalad/interface/rerun.py 96.24% <ø> (ø) ⬆️
datalad/interface/run.py 100% <100%> (ø) ⬆️
datalad/interface/tests/test_run.py 99.83% <100%> (ø) ⬆️

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update 0347878...dd407d1. Read the comment docs.

@yarikoptic
Copy link
Member

@yarikoptic yarikoptic commented Dec 1, 2018

Looks LGTM to me. travis - should be fixed (workarounded) by #3039

@yarikoptic yarikoptic merged commit a2caa34 into datalad:master Dec 2, 2018
5 of 7 checks passed
@kyleam kyleam deleted the run-inputs-extra branch Dec 2, 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`.
     ([#3066])
   - Placeholders such as "{inputs}" are now expanded in the command
     that is shown in the commit message subject. ([#3065])
   - `interface.run.run_command` 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
  ENH: Declare our GIT_SSH_COMMAND as GIT_SSH_VARIANT=ssh
  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
kyleam added a commit to kyleam/datalad-container that referenced this issue Apr 23, 2019
`containers-run` builds on `run`, augmenting the input list with a
Singularity image.  This means that if a user then puts "{inputs}" in
their command, the image file is included too.  This is almost
certainly surprising to the user because the user has not explicitly
specified the image with --input and is probably not aware that
containers-run adds it.  Avoid this by using run_command's recently
added extra_inputs argument.

Re: datalad/datalad#3038
Closes datalad#38.
kyleam added a commit to kyleam/datalad-container that referenced this issue May 28, 2019
`containers-run` builds on `run`, augmenting the input list with a
Singularity image.  This means that if a user then puts "{inputs}" in
their command, the image file is included too.  This is almost
certainly surprising to the user because the user has not explicitly
specified the image with --input and is probably not aware that
containers-run adds it.  Avoid this by using run_command's recently
added extra_inputs argument.

Re: datalad/datalad#3038
Closes datalad#38.
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Linked issues

Successfully merging this pull request may close these issues.

None yet

2 participants