93 KiB
93 KiB
Inżynieria uczenia maszynowego
10. DVC [laboratoria]
Tomasz Ziętkiewicz (2022)
DVC - Data Version Control
- dvc.org
- "Version Control System for Machine Learning Projects" (System kontroli wersji dla projektów uczenia maszynowego)
- Open Source
- Umożliwia:
- wersjonowanie danych i modeli. "Git dla danych i modeli"
- budowanie potoków ("pipeline") definiujących jak budować/trenować/ewaluować modele. "Makefile dla uczenia maszynowego"
- śledzenie, porównywanie metryk i parametrów
- ściśle zintegowany z gitem
- działa niezależnie od używanego języka/bibliotek i systemu operacyjnego
- 5-minutowe wprowadzenie: https://www.youtube.com/watch?v=UbL7VUpv1Bs&t=197s
Instalacja i inicjalizacja
- https://dvc.org/doc/install
pip(x) install dvcalbo:conda install dvc
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idna-ssl>=1.0; python_version < "3.7" (from aiohttp; extra == "http"->fsspec[http]>=2021.10.0->dvc) Downloading https://files.pythonhosted.org/packages/46/03/07c4894aae38b0de52b52586b24bf189bb83e4ddabfe2e2c8f2419eec6f4/idna-ssl-1.1.0.tar.gz Collecting frozenlist>=1.1.1 (from aiohttp; extra == "http"->fsspec[http]>=2021.10.0->dvc) Downloading https://files.pythonhosted.org/packages/51/3f/f67395ff0090b9f2835838a1f61c3e840baac70fd65bae762095dead48b2/frozenlist-1.2.0-cp36-cp36m-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.whl (191kB) [K 100% |████████████████████████████████| 194kB 1.2MB/s ta 0:00:01 [?25hCollecting async-timeout<5.0,>=4.0.0a3 (from aiohttp; extra == "http"->fsspec[http]>=2021.10.0->dvc) Downloading https://files.pythonhosted.org/packages/d6/c1/8991e7c5385b897b8c020cdaad718c5b087a6626d1d11a23e1ea87e325a7/async_timeout-4.0.2-py3-none-any.whl Collecting aiosignal>=1.1.2 (from aiohttp; extra == "http"->fsspec[http]>=2021.10.0->dvc) Downloading https://files.pythonhosted.org/packages/3b/87/fe94898f2d44a93a35d5aa74671ed28094d80753a1113d68b799fab6dc22/aiosignal-1.2.0-py3-none-any.whl Collecting attrs>=17.3.0 (from aiohttp; extra == "http"->fsspec[http]>=2021.10.0->dvc) Using cached https://files.pythonhosted.org/packages/be/be/7abce643bfdf8ca01c48afa2ddf8308c2308b0c3b239a44e57d020afa0ef/attrs-21.4.0-py2.py3-none-any.whl Collecting multidict<7.0,>=4.5 (from aiohttp; extra == "http"->fsspec[http]>=2021.10.0->dvc) Downloading https://files.pythonhosted.org/packages/82/43/81ddfbcfbdfaeaa0624f36dcb715dc8135562377b3292e93b0315a861e92/multidict-5.2.0-cp36-cp36m-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.whl (159kB) [K 100% |████████████████████████████████| 163kB 2.0MB/s ta 0:00:01 [?25hCollecting smmap<6,>=3.0.1 (from gitdb<5,>=4.0.1->gitpython>3->dvc) Using cached 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flufl.lock, psutil, configobj, pygtrie, dulwich, pygit2, contextvars, atpublic, mailchecker, ftfy, future, idna-ssl Running setup.py bdist_wheel for nanotime ... [?25ldone [?25h Stored in directory: /home/tomek/.cache/pip/wheels/41/99/17/7135f635215e1f61e906295afd11f4f791cfe4ab45f3bfdca2 Running setup.py bdist_wheel for flufl.lock ... [?25ldone [?25h Stored in directory: /home/tomek/.cache/pip/wheels/4f/51/d7/f65a7b7f37da7594f7021b122fe677187667ad21f1171d2514 Running setup.py bdist_wheel for psutil ... [?25ldone [?25h Stored in directory: /home/tomek/.cache/pip/wheels/6e/94/8f/ef906811f8dcf6824a9747df0381615be48d723073fb59a317 Running setup.py bdist_wheel for configobj ... [?25ldone [?25h Stored in directory: /home/tomek/.cache/pip/wheels/f1/e4/16/4981ca97c2d65106b49861e0b35e2660695be7219a2d351ee0 Running setup.py bdist_wheel for pygtrie ... [?25ldone [?25h Stored in directory: /home/tomek/.cache/pip/wheels/db/57/91/73782136379fe419036c5ec0e4070d8b3a35f2a36bd6a94ed8 Running setup.py bdist_wheel for dulwich ... [?25ldone [?25h Stored in directory: /home/tomek/.cache/pip/wheels/63/28/8c/0bbff7d6e30f3fc523639b000b33aba9155152e9eb23689ba0 Running setup.py bdist_wheel for pygit2 ... [?25lerror Complete output from command /usr/bin/python3 -u -c "import setuptools, tokenize;__file__='/tmp/pip-build-hr8mtrcf/pygit2/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" bdist_wheel -d /tmp/tmp4kyicel3pip-wheel- --python-tag cp36: running bdist_wheel running build running build_py creating build creating build/lib.linux-x86_64-3.6 creating build/lib.linux-x86_64-3.6/pygit2 copying pygit2/__init__.py -> build/lib.linux-x86_64-3.6/pygit2 copying pygit2/_build.py -> build/lib.linux-x86_64-3.6/pygit2 copying pygit2/_run.py -> build/lib.linux-x86_64-3.6/pygit2 copying pygit2/blame.py -> build/lib.linux-x86_64-3.6/pygit2 copying pygit2/callbacks.py -> build/lib.linux-x86_64-3.6/pygit2 copying pygit2/config.py -> build/lib.linux-x86_64-3.6/pygit2 copying pygit2/credentials.py -> build/lib.linux-x86_64-3.6/pygit2 copying pygit2/errors.py -> build/lib.linux-x86_64-3.6/pygit2 copying pygit2/ffi.py -> build/lib.linux-x86_64-3.6/pygit2 copying pygit2/index.py -> build/lib.linux-x86_64-3.6/pygit2 copying pygit2/packbuilder.py -> build/lib.linux-x86_64-3.6/pygit2 copying pygit2/refspec.py -> build/lib.linux-x86_64-3.6/pygit2 copying pygit2/remote.py -> build/lib.linux-x86_64-3.6/pygit2 copying pygit2/repository.py -> build/lib.linux-x86_64-3.6/pygit2 copying pygit2/settings.py -> build/lib.linux-x86_64-3.6/pygit2 copying pygit2/submodule.py -> build/lib.linux-x86_64-3.6/pygit2 copying pygit2/utils.py -> build/lib.linux-x86_64-3.6/pygit2 creating build/lib.linux-x86_64-3.6/pygit2/decl copying pygit2/decl/attr.h -> build/lib.linux-x86_64-3.6/pygit2/decl copying pygit2/decl/blame.h -> build/lib.linux-x86_64-3.6/pygit2/decl copying pygit2/decl/buffer.h -> build/lib.linux-x86_64-3.6/pygit2/decl copying pygit2/decl/callbacks.h -> build/lib.linux-x86_64-3.6/pygit2/decl copying pygit2/decl/checkout.h -> build/lib.linux-x86_64-3.6/pygit2/decl copying pygit2/decl/clone.h -> build/lib.linux-x86_64-3.6/pygit2/decl copying pygit2/decl/common.h -> build/lib.linux-x86_64-3.6/pygit2/decl copying pygit2/decl/config.h -> build/lib.linux-x86_64-3.6/pygit2/decl copying pygit2/decl/describe.h -> build/lib.linux-x86_64-3.6/pygit2/decl copying pygit2/decl/diff.h -> build/lib.linux-x86_64-3.6/pygit2/decl copying pygit2/decl/errors.h -> build/lib.linux-x86_64-3.6/pygit2/decl copying pygit2/decl/graph.h -> build/lib.linux-x86_64-3.6/pygit2/decl copying pygit2/decl/index.h -> build/lib.linux-x86_64-3.6/pygit2/decl copying pygit2/decl/indexer.h -> build/lib.linux-x86_64-3.6/pygit2/decl copying pygit2/decl/merge.h -> build/lib.linux-x86_64-3.6/pygit2/decl copying pygit2/decl/net.h -> build/lib.linux-x86_64-3.6/pygit2/decl copying pygit2/decl/oid.h -> build/lib.linux-x86_64-3.6/pygit2/decl copying pygit2/decl/pack.h -> build/lib.linux-x86_64-3.6/pygit2/decl copying pygit2/decl/proxy.h -> build/lib.linux-x86_64-3.6/pygit2/decl copying pygit2/decl/refspec.h -> build/lib.linux-x86_64-3.6/pygit2/decl copying pygit2/decl/remote.h -> build/lib.linux-x86_64-3.6/pygit2/decl copying pygit2/decl/repository.h -> build/lib.linux-x86_64-3.6/pygit2/decl copying pygit2/decl/revert.h -> build/lib.linux-x86_64-3.6/pygit2/decl copying pygit2/decl/stash.h -> build/lib.linux-x86_64-3.6/pygit2/decl copying pygit2/decl/strarray.h -> build/lib.linux-x86_64-3.6/pygit2/decl copying pygit2/decl/submodule.h -> build/lib.linux-x86_64-3.6/pygit2/decl copying pygit2/decl/transport.h -> build/lib.linux-x86_64-3.6/pygit2/decl copying pygit2/decl/types.h -> build/lib.linux-x86_64-3.6/pygit2/decl running build_ext generating cffi module 'build/temp.linux-x86_64-3.6/pygit2._libgit2.c' creating build/temp.linux-x86_64-3.6 building 'pygit2._pygit2' extension creating build/temp.linux-x86_64-3.6/src x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/local/include -I/usr/include/python3.6m -c src/blob.c -o build/temp.linux-x86_64-3.6/src/blob.o In file included from src/blob.c:30:0: src/blob.h:33:10: fatal error: git2.h: No such file or directory #include <git2.h> ^~~~~~~~ compilation terminated. error: command 'x86_64-linux-gnu-gcc' failed with exit status 1 ---------------------------------------- [31m Failed building wheel for pygit2[0m [?25h Running setup.py clean for pygit2 Running setup.py bdist_wheel for contextvars ... [?25ldone [?25h Stored in directory: /home/tomek/.cache/pip/wheels/a5/7d/68/1ebae2668bda2228686e3c1cf16f2c2384cea6e9334ad5f6de Running setup.py bdist_wheel for atpublic ... [?25ldone [?25h Stored in directory: /home/tomek/.cache/pip/wheels/33/25/82/57d46b60a048f8e30b31f10497539498a3b826c78e2433c2d4 Running setup.py bdist_wheel for mailchecker ... [?25ldone [?25h Stored in directory: /home/tomek/.cache/pip/wheels/fd/e1/e7/804e77a70eac7103bdba2f4b3e1eba36840b38554a4b8152c8 Running setup.py bdist_wheel for ftfy ... [?25ldone [?25h Stored in directory: /home/tomek/.cache/pip/wheels/99/2c/e6/109c8a28fef7a443f67ba58df21fe1d0067ac3322e75e6b0b7 Running setup.py bdist_wheel for future ... [?25ldone [?25h Stored in directory: /home/tomek/.cache/pip/wheels/8b/99/a0/81daf51dcd359a9377b110a8a886b3895921802d2fc1b2397e Running setup.py bdist_wheel for idna-ssl ... [?25ldone [?25h Stored in directory: /home/tomek/.cache/pip/wheels/d3/00/b3/32d613e19e08a739751dd6bf998cfed277728f8b2127ad4eb7 Successfully built nanotime flufl.lock psutil configobj pygtrie dulwich contextvars atpublic mailchecker ftfy future idna-ssl Failed to build pygit2 Installing collected packages: setuptools, colorama, dictdiffer, ply, nanotime, asynctest, idna, multidict, typing-extensions, yarl, idna-ssl, frozenlist, async-timeout, aiosignal, charset-normalizer, attrs, aiohttp, certifi, urllib3, requests, fsspec, decorator, networkx, atpublic, flufl.lock, shtab, shortuuid, smmap, gitdb, gitpython, zipp, importlib-resources, tqdm, zc.lockfile, dataclasses, commonmark, pygments, rich, aiohttp-retry, voluptuous, psutil, six, importlib-metadata, flatten-dict, configobj, pygtrie, tabulate, dulwich, appdirs, ruamel.yaml.clib, ruamel.yaml, text-unidecode, python-slugify, python-fsutil, mailchecker, pyyaml, toml, xmltodict, phonenumbers, wcwidth, ftfy, python-dateutil, python-benedict, future, pyparsing, grandalf, dpath, pycparser, cffi, cached-property, pygit2, pyasn1, pathspec, immutables, contextvars, distro, packaging, diskcache, pydot, funcy, dvc Running setup.py install for pygit2 ... [?25lerror Complete output from command /usr/bin/python3 -u -c "import setuptools, tokenize;__file__='/tmp/pip-build-hr8mtrcf/pygit2/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-6tml5js1-record/install-record.txt --single-version-externally-managed --compile --user --prefix=: running install /home/tomek/.local/lib/python3.6/site-packages/setuptools/command/install.py:37: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. setuptools.SetuptoolsDeprecationWarning, running build running build_py creating build creating build/lib.linux-x86_64-3.6 creating build/lib.linux-x86_64-3.6/pygit2 copying pygit2/__init__.py -> build/lib.linux-x86_64-3.6/pygit2 copying pygit2/_build.py -> build/lib.linux-x86_64-3.6/pygit2 copying pygit2/_run.py -> build/lib.linux-x86_64-3.6/pygit2 copying pygit2/blame.py -> build/lib.linux-x86_64-3.6/pygit2 copying pygit2/callbacks.py -> build/lib.linux-x86_64-3.6/pygit2 copying pygit2/config.py -> build/lib.linux-x86_64-3.6/pygit2 copying pygit2/credentials.py -> build/lib.linux-x86_64-3.6/pygit2 copying pygit2/errors.py -> build/lib.linux-x86_64-3.6/pygit2 copying pygit2/ffi.py -> build/lib.linux-x86_64-3.6/pygit2 copying pygit2/index.py -> build/lib.linux-x86_64-3.6/pygit2 copying pygit2/packbuilder.py -> build/lib.linux-x86_64-3.6/pygit2 copying pygit2/refspec.py -> build/lib.linux-x86_64-3.6/pygit2 copying pygit2/remote.py -> build/lib.linux-x86_64-3.6/pygit2 copying pygit2/repository.py -> build/lib.linux-x86_64-3.6/pygit2 copying pygit2/settings.py -> build/lib.linux-x86_64-3.6/pygit2 copying pygit2/submodule.py -> build/lib.linux-x86_64-3.6/pygit2 copying pygit2/utils.py -> build/lib.linux-x86_64-3.6/pygit2 creating build/lib.linux-x86_64-3.6/pygit2/decl copying pygit2/decl/attr.h -> build/lib.linux-x86_64-3.6/pygit2/decl copying pygit2/decl/blame.h -> build/lib.linux-x86_64-3.6/pygit2/decl copying pygit2/decl/buffer.h -> build/lib.linux-x86_64-3.6/pygit2/decl copying pygit2/decl/callbacks.h -> build/lib.linux-x86_64-3.6/pygit2/decl copying pygit2/decl/checkout.h -> build/lib.linux-x86_64-3.6/pygit2/decl copying pygit2/decl/clone.h -> build/lib.linux-x86_64-3.6/pygit2/decl copying pygit2/decl/common.h -> build/lib.linux-x86_64-3.6/pygit2/decl copying pygit2/decl/config.h -> build/lib.linux-x86_64-3.6/pygit2/decl copying pygit2/decl/describe.h -> build/lib.linux-x86_64-3.6/pygit2/decl copying pygit2/decl/diff.h -> build/lib.linux-x86_64-3.6/pygit2/decl copying pygit2/decl/errors.h -> build/lib.linux-x86_64-3.6/pygit2/decl copying pygit2/decl/graph.h -> build/lib.linux-x86_64-3.6/pygit2/decl copying pygit2/decl/index.h -> build/lib.linux-x86_64-3.6/pygit2/decl copying pygit2/decl/indexer.h -> build/lib.linux-x86_64-3.6/pygit2/decl copying pygit2/decl/merge.h -> build/lib.linux-x86_64-3.6/pygit2/decl copying pygit2/decl/net.h -> build/lib.linux-x86_64-3.6/pygit2/decl copying pygit2/decl/oid.h -> build/lib.linux-x86_64-3.6/pygit2/decl copying pygit2/decl/pack.h -> build/lib.linux-x86_64-3.6/pygit2/decl copying pygit2/decl/proxy.h -> build/lib.linux-x86_64-3.6/pygit2/decl copying pygit2/decl/refspec.h -> build/lib.linux-x86_64-3.6/pygit2/decl copying pygit2/decl/remote.h -> build/lib.linux-x86_64-3.6/pygit2/decl copying pygit2/decl/repository.h -> build/lib.linux-x86_64-3.6/pygit2/decl copying pygit2/decl/revert.h -> build/lib.linux-x86_64-3.6/pygit2/decl copying pygit2/decl/stash.h -> build/lib.linux-x86_64-3.6/pygit2/decl copying pygit2/decl/strarray.h -> build/lib.linux-x86_64-3.6/pygit2/decl copying pygit2/decl/submodule.h -> build/lib.linux-x86_64-3.6/pygit2/decl copying pygit2/decl/transport.h -> build/lib.linux-x86_64-3.6/pygit2/decl copying pygit2/decl/types.h -> build/lib.linux-x86_64-3.6/pygit2/decl running build_ext generating cffi module 'build/temp.linux-x86_64-3.6/pygit2._libgit2.c' creating build/temp.linux-x86_64-3.6 building 'pygit2._pygit2' extension creating build/temp.linux-x86_64-3.6/src x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/local/include -I/usr/include/python3.6m -c src/blob.c -o build/temp.linux-x86_64-3.6/src/blob.o In file included from src/blob.c:30:0: src/blob.h:33:10: fatal error: git2.h: No such file or directory #include <git2.h> ^~~~~~~~ compilation terminated. error: command 'x86_64-linux-gnu-gcc' failed with exit status 1 ---------------------------------------- [31mCommand "/usr/bin/python3 -u -c "import setuptools, tokenize;__file__='/tmp/pip-build-hr8mtrcf/pygit2/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-6tml5js1-record/install-record.txt --single-version-externally-managed --compile --user --prefix=" failed with error code 1 in /tmp/pip-build-hr8mtrcf/pygit2/[0m [?25h
Stwórzmy katalog, w którym będziemy przechowywać nasz projekt:
!mkdir -p IUM_10/sample-ml-project#Jupyter notebook magic https://ipython.readthedocs.io/en/stable/interactive/magics.html#magic-cd
%cd "IUM_10/sample-ml-project"/home/tomek/AITech/repo/aitech-ium-private/IUM_10/sample-ml-project
Inicjalizujemy puste repozytorium Git (możemy też pominąć ten krok i działać w istniejącym już repozytorium)
!git initInitialized empty Git repository in /home/tomek/AITech/repo/aitech-ium-private/IUM_10/sample-ml-project/.git/
Teraz inicjalizujemy repozytorium DVC:
!dvc initInitialized DVC repository. You can now commit the changes to git. [31m+---------------------------------------------------------------------+ [0m[31m|[0m [31m|[0m [31m|[0m DVC has enabled anonymous aggregate usage analytics. [31m|[0m [31m|[0m Read the analytics documentation (and how to opt-out) here: [31m|[0m [31m|[0m <[36mhttps://dvc.org/doc/user-guide/analytics[39m> [31m|[0m [31m|[0m [31m|[0m [31m+---------------------------------------------------------------------+ [0m [33mWhat's next?[39m [33m------------[39m - Check out the documentation: <[36mhttps://dvc.org/doc[39m> - Get help and share ideas: <[36mhttps://dvc.org/chat[39m> - Star us on GitHub: <[36mhttps://github.com/iterative/dvc[39m> [0m
Zobaczmy jakie pliki dodał (również do repozytorium git) DVC. Ich opis znajdziemy tutaj: https://dvc.org/doc/user-guide/project-structure/internal-files
!git statusOn branch master No commits yet Changes to be committed: (use "git rm --cached <file>..." to unstage) [32mnew file: .dvc/.gitignore[m [32mnew file: .dvc/config[m [32mnew file: .dvc/plots/confusion.json[m [32mnew file: .dvc/plots/confusion_normalized.json[m [32mnew file: .dvc/plots/default.json[m [32mnew file: .dvc/plots/linear.json[m [32mnew file: .dvc/plots/scatter.json[m [32mnew file: .dvc/plots/smooth.json[m [32mnew file: .dvcignore[m
Możemy teraz zacommitować zmiany w git:
!git commit -m "Initial commit"On branch master nothing to commit, working tree clean
Śledzenie plików za pomocą DVC
- dużymi plikami, takimi jak plikami z danymi wejściowymi czy plikami modeli, trudno zarządza się za pomocą gita, ze względu na problemy z:
- wydajnością
- przestrzenią w repozytorium
- ograniczenia ze strony serwisu (np. limit 100 MB na plik w Github)
- Git posiada rozszerzenie lfs(Large File Storage), które stanowi pewne rozwiązanie tego problemu. Same pliki przechowywane są na specjalnym zdalnym serwerze, w repozytorium przechowywane są jedynie odnośniki do tych plików i pewne metadane
- DVC proponuje podobne podejście, ale:
Przygotujmy przykładowe dane, pobierając je z Kaggle:
!kaggle datasets download -d uciml/iris
!unzip -o iris.zip
!rm database.sqlite iris.zip
!mkdir -p data
!mv Iris.csv data/Downloading iris.zip to /home/tomek/AITech/repo/aitech-ium-private/IUM_10/sample-ml-project 0%| | 0.00/3.60k [00:00<?, ?B/s] 100%|██████████████████████████████████████| 3.60k/3.60k [00:00<00:00, 2.63MB/s] Archive: iris.zip inflating: Iris.csv inflating: database.sqlite
Teraz dodamy plik(i) z danymi do DVC:
!dvc add data/Iris.csvAdding... ![A 0%| |.E8dZEGBYoRayYsJLdesNS4.tmp 0.00/5.11k [00:00<?, ?it/s][A 100% Add|██████████████████████████████████████████████|1/1 [00:04, 4.71s/file][A To track the changes with git, run: git add data/Iris.csv.dvc data/.gitignore [0m
- DVC utworzył plik
data/Iris.csv.dvci dadał oryginalny plik do.gitignore - W repozytorium będzie obecny tylko plik
*.dvc, zawierający odnośnik do prawdziwego pliku
!git status -uOn branch master Untracked files: (use "git add <file>..." to include in what will be committed) [31mdata/.gitignore[m [31mdata/Iris.csv.dvc[m [31miris.zip[m nothing added to commit but untracked files present (use "git add" to track)
Dodajmy pliki data/Iris.csv.dvc data/.gitignore do repozytorium git, zgodnie z sugestią DVC:
!git add data/Iris.csv.dvc data/.gitignore!git commit -m "Dodano dane IRIS (DVC)"[master cc0821a] Dodano dane IRIS (DVC) 2 files changed, 5 insertions(+) create mode 100644 data/.gitignore create mode 100644 data/Iris.csv.dvc
Plik *.dvc zawiera m.in. hash pliku. Więcej o plikach *.dvc: link
# %load data/Iris.csv.dvc
outs:
- md5: 717820ef0af287ff346c5cabfb4c612c
size: 5107
path: Iris.csv
Oryginalny plik Iris.csv został przeniesiony do katalogu ./dvc/cache/{wartość hash pliku) i podlinkowany z powrotem do oryginalnej lokalizacji. Sposób tworzenia linków może być różny w zależności od systemu plików.
!ls -l .dvc/cache/71total 8 -r--r--r-- 1 tomek tomek 5107 wrz 19 2019 7820ef0af287ff346c5cabfb4c612c
!ls -l ./datals: cannot access './data': No such file or directory
dvc remote
- żeby wysłać właściwe pliki śledzone przez DVC do zdalnej lokalizacji (z której będą mogłby być pobrane np. przez system CI albo innych użytkowników) musimy mieć skonfigurowaną taką lokazliację
- służy do tego polecenie
dvc remote add - użyjemy lokalnego "remote". Tutaj będzie to po prostu utworzony wcześniej katalog
/dvcstore. Taki katalog istnieje też na naszym Jenkinsie, oczywiście należy go podmontować w Dockerze - w realnych zastosowaniach podalibyśmy tutaj ścieżkę do jakiegoś zasobu dostępnego przez inernet jak np. serwer SFTP, ścieżka do AWS S3 itp.
Obsługiwane typy zdalnych lokalizacji (remotes): https://dvc.org/doc/command-reference/remote/add#supported-storage-types
- Amazon S3
- S3-compatible storage
- Microsoft Azure Blob Storage
- Google Drive
- Google Cloud Storage
- Aliyun OSS
- SSH
- HDFS
- WebHDFS
- HTTP
- WebDAV
- local remote
!dvc remote add -d my_local_remote /dvcstoreSetting 'my_local_remote' as a default remote.
[0m!git statusOn branch master Changes not staged for commit: (use "git add <file>..." to update what will be committed) (use "git restore <file>..." to discard changes in working directory) [31mmodified: .dvc/config[m no changes added to commit (use "git add" and/or "git commit -a")
!git add .dvc/config
!git commit -m "Added DVC remote"[master 3ff62b6] Added DVC remote 1 file changed, 4 insertions(+)
dvc push
Kiedy mamy już skonfigurowany "remote" możemy wypchnąć do niego pliki korzystając z polecenia dvc push:
!dvc push!tree /dvcstore[34;42m/dvcstore[00m └── [01;34m71[00m └── 7820ef0af287ff346c5cabfb4c612c 1 directory, 1 file
dvc pull
Żeby pobrać dane z DVC (np. w innej lokalizacji, przez innego użytkownika), musimy:
- sklonować repozytorium git (żeby m.in. pobrać pliki
*.dvc - wykonać
dvc pull
Dodawanie nowych plików i modyfikacja istniejących wygląda podobnie jak przy zwykłych plikach śledzonych przez git, tylko zamiast git używamy polecenia dvc a dodatkowo pamiętamy o zarządzaniu plikami *.dvc za pomocą gita:
!head -n -1 data/Iris.csv | sponge data/Iris.csv!git statusOn branch master nothing to commit, working tree clean
!dvc statusdata/Iris.csv.dvc: core[39m> changed outs: modified: data/Iris.csv [0m
!dvc add data/Iris.csvAdding... ![A 0%| |.TatTHknArFHCT9iDCtxHzh.tmp 0.00/5.07k [00:00<?, ?it/s][A 100% Add|██████████████████████████████████████████████|1/1 [00:00, 2.68file/s][A To track the changes with git, run: git add data/Iris.csv.dvc [0m
!git add data/Iris.csv.dvc
!git commit -m "Removed last line from Iris dataset"
[master e38c244] Removed last line from Iris dataset 1 file changed, 2 insertions(+), 2 deletions(-)
dvc checkout
- Polecenia
dvc checkoutużywamy razem zgit checkout, żeby zmienić branch, na którym pracujemy. - DVC podmieni wersje plików śledzonych przez siebie na pochodzące z innego brancha (o ile pliki te się różnią i różnią się pliki
*.dvcw odpowiednich branchach - zmiana brancha przez git powoduje (ewentualną) zmianę plików
*.dvcadvc checkoutkopiuje/linkuje pliki z katalogu.dvc/cacheo wartościach hash odpowiadających tym z plików*.dvc
Wymiana danych między projektami
- za pomocą poleceń
dvc importidvc updatemożemy dodać i później aktualizować pliki śledzone przez DVC w innym repozytorium
!dvc import https://github.com/iterative/dataset-registry \
get-started/data.xml -o data/data.xmlImporting 'get-started/data.xml (https://github.com/iterative/dataset-registry)' -> 'data/data.xml' 0% Downloading| |0/1 [00:00<?, ?file/s] ![A 0%| |get-started/data.xml 0.00/37.9M [00:00<?, ?it/s][A 0%| |get-started/data.xml 64.0k/36.1M [00:00<02:12, 286kB/s][A 0%| |get-started/data.xml 128k/36.1M [00:00<01:33, 403kB/s][A 1%| |get-started/data.xml 256k/36.1M [00:00<00:57, 658kB/s][A 1%| |get-started/data.xml 384k/36.1M [00:00<00:45, 818kB/s][A 1%|▏ |get-started/data.xml 512k/36.1M [00:00<00:53, 693kB/s][A 2%|▏ |get-started/data.xml 640k/36.1M [00:01<00:57, 644kB/s][A 2%|▏ |get-started/data.xml 768k/36.1M [00:01<00:59, 619kB/s][A 2%|▏ |get-started/data.xml 896k/36.1M [00:01<00:51, 718kB/s][A 3%|▎ |get-started/data.xml 1.00M/36.1M [00:01<00:55, 666kB/s][A 3%|▎ |get-started/data.xml 1.12M/36.1M [00:01<00:57, 633kB/s][A 3%|▎ |get-started/data.xml 1.25M/36.1M [00:02<00:57, 638kB/s][A 4%|▍ |get-started/data.xml 1.38M/36.1M [00:02<00:52, 698kB/s][A 4%|▍ 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!dvc statusData and pipelines are up to date.
[0mls -l datatotal 37020 -rw-rw-r-- 1 tomek tomek 37891850 maj 31 11:10 data.xml -rw-rw-r-- 1 tomek tomek 284 maj 31 11:10 data.xml.dvc -rw-rw-r-- 1 tomek tomek 5072 maj 31 11:01 Iris.csv -rw-rw-r-- 1 tomek tomek 76 maj 31 11:01 Iris.csv.dvc
# %load data/data.xml.dvc
md5: a7cd139231cc35ed63541ce3829b96db
frozen: true
deps:
- path: get-started/data.xml
repo:
url: https://github.com/iterative/dataset-registry
rev_lock: ba014f40e29670421a67cb1c47543f402348aa13
outs:
- md5: a304afb96060aad90176268345e10355
size: 37891850
path: data.xml
DVC pipelines
- wprowadzenie: https://youtu.be/71IGzyH95UY
- Getting started: https://dvc.org/doc/start/data-pipelines
- dvc pipelines pozwala nam zbudować (za pomocą polecenie
dvc run) lub zdefiniować (edytując plikdvc.yaml) graf zależności między krokami wykonywanymi w naszym projekcie (takimi jak "przygotowanie danych", "trenowanie", "ewaluacja") - tak zdefiniowany pipeline można potem uruchomić za pomocą polecenia
dvc reproduce
Zadania [15pkt]
- Zainicjalizuj repozytorium DVC wewnątrz Twojego repozytorium z projektem [1pkt]
- Dodaj plik(i) z danymi w Twoim projekcie do DVC [1pkt]
- Skonfiguruj remote (dane do konfiguracji podane poniżej) [1pkt]
- Stwórz/zdefiniuj i dodaj do repozytorium plik
dvc.yamlopisujący kroki wykonywane w Twoim projekcie. Wydziel przynajmniej 2 kroki (np. przygotowanie danych/trenowanie) powiązane ze sobą za pomocą zależności (skorzystaj z materiałów "Getting started", link powyżej) [6pkt] - Stwórz projekt na Jenkinsie (
s1233456-dvc), w którym sklonujesz repozytorium, ściągniesz pliki dvc (za pomocądvc pull) i uruchomisz pipeline (za pomocądvc reproduce) [6pkt]
SSH remote
Jednym z remote obsługiwanych przez DVC jest SFTP/SSH.
W celu jego wykorzystania na serwerze tzietkiewicz.vm.wmi.amu.edu.pl utworzony został użytkownik ium-sftp i skonfigurowany serwer SFTP.
Został też dla niego wygenerowany klucz ssh, który został dodany jako "Jenkins credential" (patrz opis konfiguracji na Jenkins poniżej)
Lokalnie
Będziemy potrzebować zależności :
conda install dvc-ssh
albo
pip install dvc[ssh] paramiko
conda install -c conda-forge dvc-sshCollecting package metadata (current_repodata.json): done
Solving environment: done
## Package Plan ##
environment location: /home/tomek/miniconda3
added / updated specs:
- dvc-ssh
The following packages will be downloaded:
package | build
---------------------------|-----------------
bcrypt-3.2.0 | py39h3811e60_1 44 KB conda-forge
ca-certificates-2021.5.30 | ha878542_0 136 KB conda-forge
certifi-2021.5.30 | py39hf3d152e_0 141 KB conda-forge
dvc-2.3.0 | py39hf3d152e_0 542 KB conda-forge
dvc-ssh-2.3.0 | py39hf3d152e_0 9 KB conda-forge
fsspec-2021.5.0 | pyhd8ed1ab_0 77 KB conda-forge
invoke-1.5.0 | pyhd3deb0d_0 137 KB conda-forge
paramiko-2.7.2 | pyh9f0ad1d_0 135 KB conda-forge
pynacl-1.4.0 | py39h3811e60_2 1.3 MB conda-forge
------------------------------------------------------------
Total: 2.5 MB
The following NEW packages will be INSTALLED:
bcrypt conda-forge/linux-64::bcrypt-3.2.0-py39h3811e60_1
dvc-ssh conda-forge/linux-64::dvc-ssh-2.3.0-py39hf3d152e_0
invoke conda-forge/noarch::invoke-1.5.0-pyhd3deb0d_0
paramiko conda-forge/noarch::paramiko-2.7.2-pyh9f0ad1d_0
pynacl conda-forge/linux-64::pynacl-1.4.0-py39h3811e60_2
The following packages will be UPDATED:
ca-certificates 2020.12.5-ha878542_0 --> 2021.5.30-ha878542_0
certifi 2020.12.5-py39hf3d152e_1 --> 2021.5.30-py39hf3d152e_0
dvc 2.1.0-py39hf3d152e_0 --> 2.3.0-py39hf3d152e_0
fsspec 0.9.0-pyhd8ed1ab_2 --> 2021.5.0-pyhd8ed1ab_0
Downloading and Extracting Packages
certifi-2021.5.30 | 141 KB | ##################################### | 100%
fsspec-2021.5.0 | 77 KB | ##################################### | 100%
dvc-2.3.0 | 542 KB | ##################################### | 100%
invoke-1.5.0 | 137 KB | ##################################### | 100%
paramiko-2.7.2 | 135 KB | ##################################### | 100%
bcrypt-3.2.0 | 44 KB | ##################################### | 100%
pynacl-1.4.0 | 1.3 MB | ##################################### | 100%
dvc-ssh-2.3.0 | 9 KB | ##################################### | 100%
ca-certificates-2021 | 136 KB | ##################################### | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
Note: you may need to restart the kernel to use updated packages.
!dvc remote add -f -d ium_ssh_remote ssh://ium-sftp@tzietkiewicz.vm.wmi.amu.edu.pl/ium-sftpSetting 'ium_ssh_remote' as a default remote.
[0m!dvc remote listmy_local_remote /dvcstore
ium_ssh_remote ssh://ium-sftp@tzietkiewicz.vm.wmi.amu.edu.pl/ium-sftp
[0m!dvc remote modify --local ium_ssh_remote password [hasło takie jak do serwera MLflow (patrz MSTeams)][0m!dvc push0% Uploading| |0/1 [00:00<?, ?file/s] ![A 0%| |data/Iris.csv 0.00/4.95k [00:00<?, ?B/s][A 1 file pushed [A [0m
Jenkins
W Jenkins można użyć mechanizmu "Credentials", żeby w bezpieczny sposób przekazać hasło albo klucz prywatny.
Takie dane dla użytkownika ium-sftp zostały stworzone na Jenkinsie:
- typu ssh key: https://tzietkiewicz.vm.wmi.amu.edu.pl:8080/credentials/store/system/domain/_/credential/48ac7004-216e-4260-abba-1fe5db753e18/
- typu "secret text" - zawierający hasło użytkownika ium-shftp: https://tzietkiewicz.vm.wmi.amu.edu.pl:8080/credentials/store/system/domain/_/credential/ium-sftp-password/
Opis używania "Credentials" w Jenkinsfile: https://www.jenkins.io/doc/book/pipeline/jenkinsfile/#for-other-credential-types
Klucza ssh można użyć tak:
withCredentials(
[sshUserPrivateKey(credentialsId: '48ac7004-216e-4260-abba-1fe5db753e18', keyFileVariable: 'IUM_SFTP_KEY', passphraseVariable: '', usernameVariable: '')]) {
sh 'dvc remote add -d ium_ssh_remote ssh://ium-sftp@tzietkiewicz.vm.wmi.amu.edu.pl/ium-sftp'
sh 'dvc remote modify --local ium_ssh_remote keyfile $IUM_SFTP_KEY'
sh 'dvc pull'}
Secret text tak:
withCredentials([string(credentialsId: 'ium-sftp-password', variable: 'IUM_SFTP_PASS')]) {
sh 'dvc remote add -d ium_ssh_remote ssh://ium-sftp@tzietkiewicz.vm.wmi.amu.edu.pl/ium-sftp'
sh 'dvc remote modify --local ium_ssh_remote password $IUM_SFTP_KEY'
sh 'dvc pull'
}
Przykład kongiguracji: