* repo: make Repo.scm a cached attribute
* checkpoints: create final checkpoint after repro when needed
* use correct exception rev in _collect_and_commit
* 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
* dvctree: use string paths for performance reasons in
_get_granular_checksum()
* dvctree: cache most recently accessed metadata
* dvctree: cache output dir cache during walk() calls
* diff: use get_file_hash directly instead of get_hash when appropriate
* dvctree: cache most recen dir_cache hashes in _get_granular_checksum
* revert metadata cache changes
- mostly unnecessary after granular checksum changes, will be better
addressed by the future exception handling updates
* fix windows path issue
* HashInfo: store HashInfo.dir_info as a dict instead of list
* DvcTree: use hash_info.dir_info for getting granular file hashes
* use str relpath
* use correct dir_info hash type
* fix windows paths
* 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
* diff: use RepoTree to get granular results for dir outs
* update tests for dir file granularity
* diff: prefer repo_tree.get_hash when possible
* DvcTree: handle extra files in dirty dvc out dirs
* 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
* executor: abstract tmpdir population using tree upload
* experiments: unmark flaky test
* fix wrong tree download
* LocalTree: use os.replace instead of os.rename in _upload
* experiments: use RepoTree for executor output collection
* experiments: use tree.download for output collection
* cleanup docstring
* use string name for tqdm
* experiments: add options to include/exclude specific metrics/params columns in
`dvc exp show`
* allow param/metric file to be provided to keep consistency with other
dvc commands
* match nested params/metrics names
* tests: add test to ensure dir hashes are not pushed for incomplete
directories
* push: do not push .dir file for directory with missing files
* update test
* tests: test importing into subdirectory
* import: fix bug when output subdir doesnt already exist
* use urlparse to determine if output path is local, not os.path.exists
* account for windows drive letters
* import: error out if output subdirectory does not exist
* restore Experiments.chdir
* used in experiments.show
* experiments: make checkout work without `git reset --hard`
* experiments: remove --force parameter
* experiments: reject checkout if current workspace commit doesnt match
expected baseline
* 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
* erepo: use shallow clones when rev is branch or tag name
* tests: test erepo shallow clone behavior
* erepo: fix detached head after shallow cloning a tag
* move unshallow logic into its own function
* erepo: default rev should be origin HEAD not local HEAD
* use functools.partial
* review fixes
* comment shallow clone behavior in erepo
* don't duplicate unnecessary fetch/pull call
* 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
* s3,gs: don't append "/" to prefixed path when listing objects
* remote: use optional prefix kwarg for walk_files
* if prefix is True, path will be walked as a prefix
* if prefix is False, path will be treated as a directory (trailing
slash will be appended for S3-like remotes)
* tests: add unit test for BaseRemoteTree.list_paths
* trees: BaseTree.walk should handle errors like os.walk
* use onerror callback if exceptions should be logged or raised
* repo.ls: use onerror for tree.walk
* remote: move constants into trees
* remote: replace Remote() Cache() helper functions
* output: update for remote changes
* cache/data_cloud: update for remote changes
* dependency: update for remote changes
* stage: update for remote changes
* remote: move remaining non-index methods into tree
* tests: update remote unit tests
* remote: LocalCache needs to lock remote index, not cache index
* fix bugs from moved PARAM_CHECKSUM/PARAM_RELPATH
* tests: repo tree open needs state context
* remote: make Remote.gc a class method
* operates on obj.tree, so that GC can be done with both remote and
cache instances
* bug fixes
* tests: update test_data_cloud
* bug fixes
* tests: update func tests
* remote: move get_file_checksum() into tree
* makes RemoteTree and RepoTree consistent with regard to checksum
calculation
* remote: save() now takes explicit tree parameter
* when tree is remote.tree, save will be a move + link operation
(same as default existing behavior)
* when saving path from a different tree, save will be a copy operation
* tests: update for moved remote/tree functions
* remote: move get_checksum into tree
* remote: separate cloud remote and cache classes
* tests: update unit tests for remote/cache separation
* remote: cloud cache should extend cloud remote
* remote: move LocalRemote.get
* tests: update func tests
* dependency: update for moved get_checksum
* remote: fix state lookup bug
* dvcignore: ignore paths outside of CleanTree root
* remote: local remote/cache should always use its own working tree
* repo tree (CleanTree) instance should not be relevant to local cache
operations. When the dvcignore CleanTree is relevant, repo.tree should
be used. For local remote/cache operations, the local remote work_tree
should be used.
* state: tie state to local cache working tree
* tests: update tests
* state: use os.path.exists instead of WorkingTree.exists in some cases
* remote: move upload()/download() into tree
* remote: move path_info/path_cls into tree
* remote.azure: finish moving methods into tree
* remote.gs: finish moving methods into tree
* remote.hdfs: finish moving methods to tree
* remote.http: finish moving methods into tree
* remote.oss: finish moving methods into tree
* remote.s3: finish moving methods into tree
* remote.ssh: finish moving methods into tree
* remote.gdrive: finish moving methods into tree
* tests: update remote unit tests
* tests: update func tests
* remote: use walk_files() for all remotes
* list_cache_paths() now uses tree.walk_files() for all remotes except
local/ssh
* fix DS warnings
* bugfixes
* BaseRemote: start moving tree functions into BaseRemoteTree
* remote: add LocalRemoteTree
* remote: add cloud remote trees
* remote: move remove(), makedirs() into tree
* remote: move move(), copy(), symlink(), hardlink(), reflink() into tree
* fix attributes for moved remote methods
* tests: update unit tests for moved remote tree methods
* tests: mv unit/remote/test_remote_dir.py unit/remote/test_remote_tree.py
* fix attributes for moved remote tree functions
* tests: update func tests for moved remote tree methods
* test fixes
* fix DS warnings
* ignore: dvcignore root is distinct from tree_root
* for subrepos, dvcignore root should be the subrepo's .dvcignore, not
host repo's .dvcignore
* tests: add test for subrepo dvcignore behavior
* tests: add test for metrics show -T with pre-existing tags
* brancher: ignore git revisions that do not contain repo
* tests: update test to include cmd
* CleanTree: tree_root for subrepos should be the repo root, not scm root
* only force subrepo root for git trees
* fix windows shell quotes
* tests: test that CleanTree works outside of walk()
* ignore: CleanTree should always check ignores, not just for walk()
* CleanTree: handle broken symlinks
* handle case for linking from shared local cache dirs
* Fix windows relpath/different drive issue
* erepo: load external repos directly from git tree
* erepo: add fetch_external
* remote/RepoTree: add callback for keeping track of download counts when
saving tree to cache
* repo: use erepo.fetch_external() in repo.fetch()
* erepo: return cache save_infos in fetch_external
* DependencyRepo: use erepo.fetch_external and cache.checkout instead of
pull_to
* erepo: remove pull_to
* DvcTree: support granularity for isdir()
* DvcTree: fix indentation bug
* RepoTree: add copytree() method
* LocalRemote: use working tree for local cache walk_files
* repo: state should be noop for GitTree based erepos
* erepo: add get_external()
* test_get: remove unneeded caplog check
* erepo: add get_rev()
* tests: fix erepo test bug
* ls: use RepoTree
* remote: support trees in _collect_dir
* remote: support trees in get_dir_checksum
* RepoTree: fix dir_cache relpaths in windows
* remote: fix duplicated fetch bug
* utils: don't skip md5 dos2unix check for git blobs
* otherwise md5 checksums will not match when comparing git version to
cached filesystem version on windows
* DvcTree: use out.dir_cache instead of out.collect_use_dir_cache
* RepoTree: support filtering out dvcfiles during walk()
* RepoTree: support recursive isdvc()
* remote: support computing checksums for tree objects
* RepoTree: pull dir contents on walk() if in `fetch` mode
* tests: add func test for DVC dir pull on RepoTree.walk()
* DvcTree: support granular open()
* RepoTree: add get_file_checksum()
* remote: revert checksum changes
* remote: add tree support for cache.save()
* tests: test saving directly to cache from RepoTree
* remote: local cache needs its own WorkingTree instance when repo.tree is
GitTree
* RepoTree: state context should be entered by open()/walk() caller
* RepoTree: only pull dir contents when cache has changed
* tree: update tree tests
* fix ds warnings, update comments
* fix windows tests
* GitTree: add stat() function
* BaseTree: make walk_files a base tree method
* WorkingTree: add stat() method (wrapper for os.stat)
* utils.fs: support non-working tree for get_mtime_and_size
* utils.fs: add copy_fobj_to_file
* utils: support using tree.open in file_md5
* DvcTree: support stream or fetch on open()
* tests: test DvcTree dir cache support for walk()
* RepoTree: finish implementation of BaseTree functions
* repo: use RepoTree/DvcTree.open() for repo.open_by_relpath
* repo: only use RepoTree when needed for now
* fix docstring
* RepoTree: only use DvcTree.open for DVC outs
* drop python 3.5 support
* dvc: remove fspath() use inside os.path calls
* dvc: replace dvc.compat.fspath with os.fspath
* tests: replace dvc.compat.fspath with os.fspath
* utils: relpath() should use fspath/str
* utils: os.readlink doesn't support path-like obj on Windows until 3.8
* tests: ensure repro --downstream preserves dependency order
* repo: use reverse post-order DFS in repro --downstream
- Fixes#3602
* make test_repro and test_repro_multistage consistent
* rebase master, update multistage test
* remote: use checksums instead of paths when filling dir statuses
* remote: prefer using str paths over PathInfo for performance reasons
* only use string paths for RemoteLOCAL
* only optimize calls made from RemoteLOCAL.cache_exists
* fix ds warning
* use os.path in local
* remote: re-add checksum_to_path() to return string paths when applicable
- cloud remotes still default to using PathInfo's
* cache fspath string
* use abspath in checksum_to_path
- if path is not relpath from cwd or abspath, posix lstat() syscall
runtime doubles (from calculating relpath from cwd)
* remote: locally index list of checksums available on cloud remotes
* fix review issues
- use pytest fixtures
- use sha256 digest
- s/fd/fobj/
- check more specific IO errors
* remote: use .dir checksums to validate index
* command: add --drop-index option for push/pull/status
* tests: --drop-index unit tests
* remote: make index threadsafe
* remote: force re-index after gc
* only save/dump index once per command
* remote: add helper index functions update_all/replace_all
* remote: store index as sqlite3 database
* fix deepsource warnings
* rename --drop-index to --clear-index
* rename index.invalidate to index.clear
* functional tests for remote.index
* fix index not being updated on status -c
* remote: add index.intersection()
* remote: use index when making assumptions about remote .dir contents
* add missing func tests
* do not index standalone files
* cleanup index test fixture
* fix deepsource warnings
* update autocompletion scripts/cli help message for --clear-index
* tests: remove unused mocker
* push: only index successfully pushed dirs
- do not index files on partial push/upload
* remote: revert behavior to trust .dir files on remote
- skip unnecessary index check for dir contents if .dir file exists on
the remote
* fix missing RemoteIndexNoop functions
* separate index validation from status dir exists query
* bugfix: include indexed checksums for all cache_exists cases
* review fix: cleanup debug messages
* tests: fix DS warning
* remove --clear-index
* remove unused index functions
* repo: separate dir cache and file cache in memory
- `used_cache()`/`get_used_cache()` in repo/stage/output now return
tuples of (dir_cache, file_cache) instead of one flat/merged cache
* update tests for new get_used_cache behavior
* remote: if .dir checksum exists on remote, assume contents also exists
- affects all commands which use `cache_exists()` (remote status)
* push: only upload .dir file after full file contents has been uploaded
* gc: always remove .dir checksums first
* functional tests for push/gc
* repo: support nesting dir caches in NamedCache
* remote: NamedCache updates
* Fix tests
* Fix deepsource warnings
* tests: use pytest mocker fixture
* Update dvc/cache.py
Co-Authored-By: Saugat Pachhai <[email protected]>
Co-authored-by: Ruslan Kuprieiev <[email protected]>
Co-authored-by: Saugat Pachhai <[email protected]>
* remote: use progress bar when paginating
- add `progress_callback` parameter to `list_cache_paths()` so that
remotes can update remote cache traverse progress bar after fetching a
page
* Show remote size estimation status as no-total progress bar
* Update pbar per item rather than per page
* make tests more explicit (don't use mock.ANY)
* Apply suggestions from code review
minor fixes/tidy
* Use progress_callback in ssh/local list_cache_paths()
- keep ssh/local consistent with other remotes (even though `dvc
gc`/`RemoteBASE.all()` do not currently use progress bars)
* Fix review issues
Co-authored-by: Casper da Costa-Luis <[email protected]>
* remote: Optimize traverse/no_traverse behavior
- estimate remote file count by fetching a single parent cache dir, then
determine whether or not to use no_traverse method for checking
remainder of cache entries in `cache_exists`
- thread requests when traversing full remote file lists (by fetching
one parent cache dir per thread)
* Use arbitrary prefix length for traverse remote cache queries
- default to 3
- for remotes that only support per-directory query use 2 (gdrive, hdfs)
* Add unit tests for new traverse/no_traverse behavior
* Fix deepsource warning
* Fix review issues
* fix CI
* Fix review issues
* obsolete no_traverse config option
- remove RemoteBASE.DEFAULT_NO_TRAVERSE and replace it with
RemoteBASE.CAN_TRAVERSE (True for all remotes except http)
* review issues - use 'object exists' instead of 'no_traverse'
* fix obsolete no_traverse test issues
* fix SSHMocked func tests
* remote.http: support _upload() via HTTP POST
- uploaded files are sent as chunked encoding POST data
Fixes#3247
* remote.http: add support for HTTP basic and digest auth
- username, password, ask_password options work the same way as for
ssh remotes
- basic_auth (bool) and digest_auth (bool) options added for http(s)
remotes
- digest_auth takes precedence over basic_auth if both are enabled
* remote.http: auth_method() unit tests
* tests: Add functional tests for HTTP remotes
- HTTP remotes now tested locally using a SimpleHTTPServer instance that
allows reading/writing to a temp directory
* tests: fix http tests on py3.5, 3.6
* remote.http: add custom auth method
* s/custom_header/custom_auth_header/
* Apply suggestions from code review
Co-Authored-By: Saugat Pachhai <[email protected]>
Co-Authored-By: Ruslan Kuprieiev <[email protected]>
Co-authored-by: Saugat Pachhai <[email protected]>
Co-authored-by: Ruslan Kuprieiev <[email protected]>
