- partially refactor existing pidfile behavior into using proc manager
- old pidfiles are now json-serialized executor info files placed in
proc manager subdirs (alongside proc manager pidfile/logs/etc)
- move multiprocessing based (attached) execution into separate
execution path from future "detached" execution support
- introduce ExecutorManager classes
- move executor init + execution from experiments.__init__ into the
manager classes
- make executors serializable via ExecutorInfo
- allow mismatched RSA signature algo names in initial
SSH_MSG_USERAUTH_PK_OK response
- unit test overridden asyncssh publickey auth compatibility with
github ssh server
- vendor should use ssh-agent or default IdentityFile(s) when no SSH key
has been provided by the user
- encrypted (fallback) keys will always be passed to ssh-agent
* executor: move local specific git initialization out of base
* machine: return kwargs for executor init instead of executor object
* executor: add initial ssh executor
* ssh-executor: disable strict host checking for dvc-machine instances
* initial tests for ssh executor
* drop GIT_SSH_COMMAND usage
* push: accept destination odb as a parameter
* separate cache initialization into executor.init_cache
* add test for ssh executor cache init
* remove dead code
* machine: fixture-ize default test scenarios
* test SSHExecutor.from_machine
* tpi: return default SSH port for constructing executors
* git: support client kwargs for auth in remote methods
* tests: use docker for git/ssh server
* move dulwich backend into subdir
* add base sync<->async support
* dulwich: add initial asyncssh SSH vendor
* dulwich: use asyncssh as the default SSH vendor
* add test for git over ssh
* test read (fetch) over ssh
* ci: re-enable ssh tests
temporary workaround for #6788, #6789
* move async stubs into dvc.scm.asyn
* tests: use sshfs and not dvc.fs.ssh
* allow explicit 0-length read in asyncssh vendor
* machine: install dvc via startup_script by default
* machine: support configuring instance type and startup script
* accept startup_script as a config relpath
* use pushd/popd in default install script
* objects.status: use object IDs instead of naive objects
* objects.transfer: use object IDs instead of naive objects
* objects: add ReferenceHashFile
* odb: add ReferenceObjectDB
* repo: collect used object IDs instead of naive objs
* support basic/naive fs serialization
* objects.stage: stage file objects in addition to trees
* objects: remove save(), update transfer()
* output/dep: update for osave removal
* path_info: support both url and path attributes
* status/gc: use object IDs instead of naive objs
* diff: update staging usage
* commit: update staging usage
* tests: clean staging when needed
* tests: update for save/transfer/stage changes
* dvcfs: don't allow config serialization (repofs should be used instead)
* utils: return mtime as str, size as int
* tests: update unit tests for save/stage/transfer changes
* objects: use Repo.open when needed in ReferenceHashFile
* fix ls test staging
* objects.stage: don't skip hash check when loading from state
- individual hashes will still be loaded from state if they are still
valid
* ReferenceHashFile: serialize repo fs paths relative to repo root
* preserve state when staging
* objects.tree: skip hash computation in digest() when we have already
loaded hash from state
* always check file existence in referencehashfile
* update repofs test since stage no longer allows nonexistent files
* odb: only protect on check() if hash was verified
* staging: use unique memfs namespace for staging per dest ODB
* tests: clean full staging namespace
* refodb: preserve repofs cache dir
* repodependency: stage imports to local ODB and strict check circular
imports
* fetch: fetch staging last
* staging: make dest odb mandatory and preserve state
* refodb: cache nonlocal fs's
* fix rebase errors
* repofs: support full instantiation from fs config
* repofs: preserve subrepo factory for erepos
* tests: clarify repofs dirty file behavior
* objects: migrate remote status to objects.status
* data_cloud: use objects.status
* objects: migrate remote._process to objects.transfer
* data_cloud: use objects.transfer
* objects: handle memfs staging objects in transfer
* fetch/import: use unified transfer()
* update get_remote and transfer exception usage
* update tests
* objects.transfer: use src ODB verify rules after xfer
* odb: move index from remote into odb
* objects.transfer: skip src status check when possible
* update tests
* remove dvc.remote
* odb.index: migrate to diskcache
* objects: fix status/transfer optimization
* update index usage
* state: remove dead sqlite related code
* update cloud tests
* drop unnecessary remove in tests
* use abstract base class in odb index
* status: load trees from local cache instead of remote odb when possible
* handle status when dir cache is explicitly removed
* exp: allow fetching from arbitrary executor by git URL
* exp: write info for running executors to .dvc/tmp/exp/run
currently only includes PID and git fetch URL
* exp: refactor stash/queue cleanup
* exp: add ability to collect dict of currently running experiments
* exp show: display run/queue state in the table
* exp run: unlock main repo while running tmpdir executors
* add tests for new exp show behavior
* fix workspace checkpoint run handling
* fix issue where running stash revs were shown as queued
* use "running"/"queued"
* add executor (location) column
* compare: add TabularData.is_empty
* use td.is_empty to drop state/executor
* use "workspace" and "temp" as executor names
* fs: use fsspecwrapper in memfs
* odb: add memfs staging ODB in ODBManager
* odb: add read_only attribute for odb instances
* objects: handle memfs paths when staging trees
* odb: remove git ODB
* output: use staging ODB
* RepoDependency: use staging odb for imports
* dvcfs: handle case where dir cache is unavailable
* fix circular import check
* odb: use temp local ODB for staging
* objects: use staging ODB in stage() and tree load
* objects: add typing for add/check/load/stage
* output/dep: use new staging
* add unit tests for local odb staging
* localfs: account for string paths in move()
* include local in odb.by_scheme
* tests: count dir cache like any other object in test_pull_git_imports
* odb: clear staging on gc()
* objects: add tree.get/filter/insert
* output: use obj.filter/get for granular dir commit
* squash filter logic output
* dependency: don't filter imports at the dep level
* don't init staging ODB for external cache
* use staging ODB when computing tree hash for external outs
* remove unneeded force in test granular commit
* use unique-per-manager memfs URLs for staging
* odb: make staging per-ODBManager
* objects: move state dependent staging into ODBManager
* objects: support checking multiple odbs
- staging dependent checks can be done via ODBManager.check
* checkout: do state lookup before explicit stage() in _changed()
* output: use odbmanager based staging
* RepoDependency: use odbmanager based staging
* update obj staging unit tests
* checkout: remove check(), handle individual file exceptions on link()
* diff: use odbmanager based staging
* objects: add ObjectPermissionError for read/write perm errors
* odb: move staging out of odbmanager
* objects: handle staging ODB in objects.stage()
* objects.tree: don't stage anything in tree methods
* odb: clear staged objects on gc()
* remote: don't filter objs by scheme, objs are already grouped by ODB
* diff: update objects.stage usage
* output/dep: update stage() usage
* update ODB tests
* update func tests
* remove memfs from FS_MAP
* revert unneeded objects.check() changes
* remove unused tree.insert()
* revert unused odbmanager changes
* add separate odb error classes
* stage external outs directly in ODB
* check for obj existence in main ODB before staging
* use .dvc/tmp/staging instead of per-odb staging
* gc: only gc loal staging once
* objects: add ExternalRepoFile object type
* RepoDependency: implement get_obj (use ExternalRepoFile)
* drop distinction between used external and used objects
* update tests
* remove unneeded fetch from ExternalRepoFile
* wrap erepo errors as an object error
* update cloud/remote functions for new used_objs behavior
* fix update() rev/locked behavior
* update import tests
* remove ExternalRepoFile
* move get_obj and get_used_objs implementations back into repo dependency
* return objects plus associated ODB (remote) in get_used_objs
* odb: add tmp_dir field and support creating Remote from an odb
* return dict mapping odb -> objects in get_used_objs
* use dummy git odb for git imports
* fetch: support pulling from specific odb
* update cloud funcs for get_used_objs usage
* update tests for used_objs behavior
* use fetch in dep.download
* catch circular imports from local fs repos
* add tests for chained and circular imports
* move tmp_dir into odb config
* update return docstring for repo.used_objs
* objects: make HashInfo & HashFile hashable
* stage/output: collect objects (HashFiles) instead of NamedCache
* remote/data_cloud: use objs instead of NamedCache
* repo: use objects instead of NamedCache
* rerun black after rebase
* remove NamedCache usage from run-cache
* drop NamedCache
* update HashInfo.__hash__
* update unit tests
* revert remote_name change
* start cleaning up test failures
* fix tree obj expansion
* update missing cache logging
* fix external dict handling
* update naive odb.gc
* update state save behavior for pull
* update test_data_cloud
* update test_remote
* fix gc with multiple repos
* objects.tree: support filtering w/preserved hash_info
* fix stage cache restore
* drop fs.path_info from HashFile.__hash__
* objects: add optional name attribute
* revert missing cache logging name/suffix changes
* revert name changes in remote tests
* review fixes
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* Update dvc/remote/base.py
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
Co-authored-by: Ruslan Kuprieiev <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* dvcfile: add check for gitignored when validating filenames
* update tests
* update exception using in tests
* review fixes
- clarify method name
- use FileIsGitIgnored
* apply: allow applying exp with multiple possible branches
* default to new checkpoint branch after applying ambiguous commit
* output shas in addition to exp names by default
* update show tests
* git: allow force checkout in detach_head context
* exp run: error when trying to resume from a non-head checkpoint without
modifications
* add test for apply/resume from intermediate checkpoint
* list some possible heads when multiple matches
* stage,commit: add support for only committing data stages from
experiments
* exp run: `dvc commit` data deps when stashing exp changes
* add test for modified DVC-tracked data when generating experiment
* test with and without params change
* handle run without target
* exp: add util method for getting baseline HEAD during run
* exp: use baseline for dvc commands which compare to HEAD during exp run
* add test for new util method
* update plots diff test mock
* exp run: gracefully handle duplicate workspace runs
* exp run: fix issue where errors could be logged twice
* move ref conflict check into its own function
* pygit2: disable set_ref with reflog message
* git: implement is_dirty in dulwich
* pygit2: implement _stash_apply
* pygit: update to 1.5.0
* enable set_ref(message=...) for pygit2
* git: replace backend reflog_delete in favor of _stash_drop
* pygit: support stash_push with custom refs
* update tests for backend stash_drop behavior
* pygit: raise MergeConflictError on failed stash apply
* pygit: reload index from disk before stash apply
* update stash_apply checkout strategy
* mark flaky test
* repro: skip DVC deps in SCM track stage
(DVC deps will be tracked when their own stage is repro'd)
* scm: use git status when reminding to git-track files
* sort names in reminder instead of random set order
* update unit test
* git: return backend-agnostic object for resolve_commit
* use int timestamps instead of datetime
* make branch_revs Git method instead of backend
* pygit: implement resolve_commit
* dulwich: implement add with --update
* add git backend test for add()
* fix list comprehension in dulwich status()
* allow adding single string path instead of list
* handle windows paths in add(update=...)
* exp show: add -n/--num to display the last N commits from HEAD
* exp run: fix empty commit with no changes
* add test for exp show with multiple commits
* allow -n greater than num commits in repo
* review fix
* pygit2: implement get/set/remove refs
* pygit: implement iter_refs
* pygit: implement resolve_rev
* pygit2: implement working tree checkout
* pygit2: implement reset, explicitly read/write index when used
* pygit2: checkout does not need to reset index
* pygit2: handle "-" branch shorthand in checkout
* tests: install post-checkout hook should be run via gitpython
* exp apply: use stricter exception handling for merge conflict
* pygit: fix index read/write usage
* gitpython: handle untracked file conflicts in stash apply
* fix flaky/race index issue
* dvc repro: fail on checkpoint stages
* exp res: check for moved HEAD/baseline before resuming
* exp run/res: always consider last checkpoint as applied for workspace runs
* experiments: use relpaths when tracking changed files
* experiments: suppress SCM hints in tempdir executors
* experiments: move multiprocessing error logging into child
* exp run: clarify help text for --temp
* stage: support explicit allow_missing in checkout
* exp: explicitly clear EXEC_BRANCH and checkout with allow_missing on
starting experiment run
* git: wrap stash apply errors with SCMError
* git: add `git status` to backends
* exp: reset staged git changes before workspace exp runs to avoid merge
conflicts
* test untracked (and staged) pipeline file and deps for both workspace
and tmpdir runs
* experiments: explicitly track pipeline files and uncached deps for exp
commmits
* fix exp typing errors
* exp apply: show passed exp name in CLI output instead of resolved git sha
* exp res: warn that --name will be ignored when resuming without
modifications
* exp gc: don't re-use gc parameter check message
* exp: update help strings
* exp: warn if exp dir contains untracked files after tmpdir execution
* experiments: move executor into a module
* experiments: separate executor into base/local
* rename LocalExecutor to TempDirExecutor, run in .dvc/tmp by default
* git: restore HEAD using reset not checkout in detached_head()
* experiments: support calling BaseExecutor.reproduce directly for
workspace runs
* experiments: run single experiments in local workspace by default
* update experiments tests for workspace changes
* experiments: update checkpoints for workspace runs
* update checkpoints tests
* update test_show
* add force param for apply
* exp apply: add --force option
* exp run/res: add --temp option to force tempdir execution for single
experiments
* force apply in non-apply specific tests
* experiments: add utils.exp_commits for iterating over experiment commits
* repo: add support for all_experiments in brancher and used_cache
* git: make all_commits return commits in standard refs instead of --all
* gc: add --all-experiments to preserve cache for experiments
* update gc tests
* repo: support pushing and fetching specific revs internally
* exp push: push cache for experiment by default
* exp pull: pull cache for experiment by default
* fix empty git repo bug
* git: remove scm from backends, make backends configurable
* git: implement get/set/remove ref in gitpython
* git: support reflog --rewrite for stash
* tests: support testing individual backends in unit/scm/test_git
* stash: create reflog if it does not exist for gitpython backend
* git: fix Stash.push args typing
* experiments: handle case where args file was inadvertently committed to
git
* add test for args file being committed to git
