* repro: accept multiple targets (#5111)
Currently, we iterate over targets manually in CLI, which results in a
complicated code and a DAG collection/check overhead. With this PR we
collect the DAG once, figure out all the needed targets within it and
just reproduce them in one pass.
(cherry picked from commit aec8d65791)
# Conflicts:
# dvc/command/base.py
# dvc/command/experiments.py
# dvc/command/repro.py
# tests/func/test_repro_multistage.py
* resolve conflicts
* resolve test conflicts
Co-authored-by: Ruslan Kuprieiev <[email protected]>
Co-authored-by: Ruslan Kuprieiev <[email protected]>
Currently we don't handle bad name well:
```
(dvc-3.8.3) ➜ dvc git:(config-bug) ✗ dvc config section
ERROR: unexpected error - not enough values to unpack (expected 2, got 1)
```
With this PR, we check name to conform to either `remote.name.option` or
`section.option`, so we'll give a more friendly:
```
(dvc-3.8.3) ➜ dvc git:(config-bug) ✗ dvc config section
ERROR: argument name: name argument should look like remote.name.option or section.option
usage: dvc config [-h] [--global | --system | --local] [-q | -v] [-u] [-l] [name] [value]
Get or set config options.
Documentation: <https://man.dvc.org/config>
positional arguments:
name Option name (remote.name.option or section.option).
value Option value.
optional arguments:
-h, --help show this help message and exit
--global Use global config.
--system Use system config.
--local Use local config.
-q, --quiet Be quiet.
-v, --verbose Be verbose.
-u, --unset Unset option.
-l, --list List all defined config values.
```
* experiments: commit to refs/exps/... instead of branch heads
* update exp show
* restore checkpoint_resume kwarg
* refactor new() to use experiments stash
* experiments: use refspecs to populate and collect executors
* experiments: use new stash and merge on exp checkout
* experiments: fix executor chdir
* experiments: update run and show
* skip checkout after reproduce
* checkpoints: use experiments refspecs
* check if workspace was stashed before applying
* exp show: unify checkpoint/standalone experiment collection
* git: move iter_refs to backend
* update for scm changes
* experiments: replace exp checkout in favor of exp apply
* git: handle rev_parse errors in resolve_commit
* update refs containing and baseline check
* fix sigint handling for checkpoints
* update checkpoint exists behavior
* fix checkpoint baseline behavior
* update tests
* experiments: update gc
* update show tests
* fix type checking errors
* update diff
* scm: add diff, describe
* experiments: generate human readable names
* exp run/resume: allow user specified exp name with -n/--name
* update tests
* experiments: add `exp branch` for promoting experiment to full branch
* fix test
* fix missing file
* experiments: explicitly close scm instances before cleaning up tmp dir
* repro: support regex/foreach-group to run at once
Fixes#4912Fixes#4886Fixes#4958
* Use `tree.isdir` rather than `os.path.isdir`
* Use glob rather than regex
* Update dvc/command/repro.py
* s/regex/glob
* disable glob on `collect_granular`
There's no need for a glob here
* add tests for `collect` and `collect_granular`
Outs desc will be used by viewer right away. Stage desc is for people to
start using now, but we won't be using it it viewer until DAG support is
added there.
* experiments: refactor regular/checkpoint experiment separation
* fix scm_checkout pull bug
* experiments: return stages from executor.reproduce
* since executor has to move to threadpool execution anyways, we no
longer have to work around the pickle repro result limitation
* refactor new/resume behavior
* refactor checkpoints tests
* use -f to force checkpoints reset/restart
* checkpoints: use 'exp run' and 'exp res[ume]' commands
* stage: all outs can be missing for checkpoint stages
* regular outputs may not be written at the time a checkpoint is
generated, but subsequent checkouts of that stage should not fail due
to the missing outs
* commit stage on checkpoint generation otherwise non-persist cached outs
are lost
* checkpoints: wait for stage proc to end after killing via terminate()
* stage: fix issues with killing checkpoint stage
* refactor signaling (use threading.Event instead of Condition)
* fix windows bug (kill all child processes via taskkill)
* experiments: refactor executor collection
* tests: move checkpoint tests into separate module
* refactor experiment tests to use stage fixture
* stage: make runs checkpointable
* api: add make_checkpoint API call
* tests: add test for checkpointed stage
* experiments: implement checkpoints callback chain
* initial working state
* use .dvc/tmp for checkpoint signal file location
* force repro for checkpoint experiments
* checkout: add flag to allow missing persistent outputs
(i.e. not yet created)
* use allow_persist_missing on checkpoint experiment repro
* executor: force checkout before checkpoints experiment repro
* move checkpoint commands to `dvc exp run`
* support resuming checkpoint runs with --continue
* fix git bugs
* experiments: include checkpoint commits in `exp show`
* use 1sec sleep timers
* fix apply_workspace test conflict
* tests: add test for `dvc exp run`
* cleanup signal file behavior
* fix bool conversion
* tests: add tests for checkpoint and checkpoint_continue
* fix styling
* fix checkpoint stage test
* fix checkpoint monitor thread condition/notification
* repro: support --pull
This option allows run-cache to pull the cache for the outputs
when restoring a stage instead of pulling everything at once during
`dvc pull --run-cache`.
Fixes#4223
* repro: adjust --pull help
* metrics: diff: make table more intuitive
Currently we have a "diff not supported" marker in the table, that is
used whenever dvc is not able to diff the values (e.g. no old one, no
new one or format error). It is quite ugly and it is much more intuitive
to just show both old and new values and now show that marker at all, as
if there is no old/new value it is intuitive that we can't calculate the
change. Next step is to add old/new "bad format"/etc markers for
unsupported types or malformed/missing metric files.
E.g., before:
```
Path Metric Value Change
metrics.json foo 1.2 diff not supported
```
after this PR:
```
Path Metric Old New Change
metrics.json foo None 1.2
```
* metrics/params: use em dash in diff table
* diff: support missing cache status for workspace diff
* diff: add --hide-missing option to hide cache missing status
* update command tests
* update diff func tests
* only show missing cache status when diffing local workspace
* suppress all output if no changes and --hide-missing
* use hide_missing instead of show_missing
* use is_dvc
* experiments: cleanup show UI
* show git tag/branch names instead of SHAs by default
* make timestamp formatting more like the viewer
* update tests
* place timestamps in their own column
* update command test
* exp: remove unused regex
Co-authored-by: Ruslan Kuprieiev <[email protected]>
* plots: add -e/--experiment option for plots diff
* experiments: add method to get baseline for a given experiment
* plots: default to diff against baseline instead of workspace/head for experiments
* use exact match for experiments RE since name-rev may return relative
commits
* diff: Add sort logic to sort diff ouput irrespective of output format(default/json/md)
* diff: test stub using actual value, not pass by reference for (dict)
* experiments: add initial local tmpdir executor
* fix detached head pull
* experiments: include unchanged (unrepro'd) stages in experiment hash
* experiments: repro single experiment using tmpdir executor by default
* stage experiments as stash commits before running
* include repro args/kwargs in stashed experiments
* support running arbitrary experiment commits (including stash commits)
* experiments: use ProcessPoolExecutor
* experiments: add `dvc exp` alias for `dvc experiments`
* experiments: add `dvc repro --experiment --queue`
* `--queue` can be used to stage an experiment for future execution
* experiments: show queued (unexecuted) experiments in `dvc exp show`
* revert ProcessPoolExecutor change
* experiments: add `dvc repro --run-all [--jobs]`
* `--run-all` can be used to run all queued experiments in parallel
* cleanup output
* experiments: use ProcessPoolExecutor
* fix returning unpicklable objects error
* update tests
* fix windows cleanup issue
* on windows tempdir cannot be removed if we are chdir'd into that
directory
* experiments: add initial experiments.show
* only includes metrics + params (no code/data information)
* experiments: basic `dvc experiments show` functionality
* experiments: clone and run repro inside clone workspace
* repro: add -e/--experiment option
* experiments: hash experiments to identify duplicates
* experiments: update show
* experiments: checkout experiment after running repro
* experiments: add `dvc experiments checkout`
* experiments: add simple `dvc experiments diff` command
* just shows combined output from `metrics diff` and `plots diff` for
now
* add very simple tests
* add some useful output messages
* experiments: suppress help messages while feature is in development
* experiment related commands will be accessible but hidden from the
default command help messages
* add simple experiments command tests
* experiments: disable feature by default
* experiments only enabled in test environment (DVC_TEST) or when
core.experiments config option is true
* use fetch on checkout missing revs
Also, makes fixes for `--overwrite` rename to `--force`
and also remove `remove_with_prompt` which was only being
used with `force\=True` anyway.
Fix#4003
`pipeline list` is no more, it had some very questionable applications
(none to be precise) and was duplicating old `pipeline show` functionality.
We might introduce a different command to assist in listing (e.g. for
shell completion) in the future.
New `dvc dag` replaces `dvc pipeline show` and by-default will show
all pipelines in the project in ASCII (so there is no more --ascii)
and also `--dot` support, just like before. When given a target,
`dvc dag` (in any mode) will show DAG that leads to the target,
skipping the descendants, unless `--full` is specified.
This should allow us to be able to remove a stage from a dvcfile,
(if it's a single stage file, it removes it), and make us able to
delete the overwrite the stage on run as well.
This commit:
* changes `run` `--overwrite-dvcfile` flag to `--overwrite`
* removes prompt in `run` for overwrite and fails hard
* changes `remove`: now it by default removes stage entry and unprotect outs
* `remove` has `--outs` to remove outputs instead of unprotecting them
* plots: remove --select from CLI
It needs reconsideration, we can't release it as is right now. E.g. it
expects xpath to start with `$`, but that will get interpreted by your
shell, which is bad.
* completion: update plots
* Renamed --outs-only to --dvc-only
* Changed outs_only to dvc_only
* replace output_only with dvc_only
* Restyled by black
Co-authored-by: Restyled.io <[email protected]>
* run: add --plot/--plot-no-cache
Part of #3409
* plot: move show/diff to API
* plots: show marked plots by default
Involves some refactoring to make plots comply with the rest of the code
base.
* dvc.yaml: use top-level metrics and plots
* dvc.yaml: add support for plot template
* plots: add support for templates in dvc.yaml
* dvc.yaml: allow metrics/plots to have persist/cache
* plots: render single page by-default and introduce --show-json
* plot: use "working tree" instead of "workspace"
Just to sync this with the rest of the codebase. We should consider
renaming it to "workspace" everywhere, but for now I opt to not touch
it to not break something that depends on it.
* plots: rename -f|--file to -o|--out
Better corresponds to other commands like `import`.
* plots: use RepoTree and brancher instead of api
* stage: get rid of OutputParams
* tests: plots: add simple diff test
* plots: use `--targets` instead of `--datafile`
Makes it comply with `dvc metrics/params` CLI options.
* tests: unit: plots: add --show-json test
* stage: cleanup exception for format error
Based on feedback from the users.
* lockfile: use relpath in corruption error
* dvc: rename plot to plots
Follows `dvc params/metrics` convention and is needed in preparation for new
commands and some refactoring.
Part of #3409
* completion: rename plot -> plots
* params/metrics: diff: implement tabulated markdown output
Via `--show-md` on `diff`s.
* table: show None on missing val
* tests: use `dedent`, add tests for markdown
* diff: add --show-md
Co-authored-by: Ruslan Kuprieiev <[email protected]>
Peter Rowlands (변기호)
Saugat Pachhai
Guro Bokum
Kevin Lloyd Bernal
Tomás Farías Santana
Raymond GasperandRuslan Kuprieiev
Pavel DitenbirandRuslan Kuprieiev
Puneetha Pai
karajan1001andRuslan Kuprieiev
Alexander Schepanovski
Shankho Boron GhoshandRestyled.io
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