87 KiB
87 KiB
Inżynieria uczenia maszynowego
22 maja 2024
10. DVC
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
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
- Github ma zintegrowany LFS z limitem 1GB dla kont bezpłatnych
- DVC proponuje podobne podejście co LFS, ale:
Instalacja i inicjalizacja
- https://dvc.org/doc/install
pip install dvcpipx install dvcconda install dvc
!pip3 install dvcRequirement already satisfied: dvc in ./venv/lib/python3.10/site-packages (3.50.2) Requirement already satisfied: attrs>=22.2.0 in ./venv/lib/python3.10/site-packages (from dvc) (23.2.0) Requirement already satisfied: psutil>=5.8 in ./venv/lib/python3.10/site-packages (from dvc) (5.9.8) Requirement already satisfied: zc.lockfile>=1.2.1 in ./venv/lib/python3.10/site-packages (from dvc) (3.0.post1) Requirement already satisfied: ruamel.yaml>=0.17.11 in ./venv/lib/python3.10/site-packages (from dvc) (0.18.6) Requirement already satisfied: dvc-http>=2.29.0 in ./venv/lib/python3.10/site-packages (from dvc) (2.32.0) Requirement already satisfied: shortuuid>=0.5 in ./venv/lib/python3.10/site-packages (from dvc) (1.0.13) Requirement already satisfied: platformdirs<4,>=3.1.1 in ./venv/lib/python3.10/site-packages (from dvc) (3.11.0) Requirement already satisfied: scmrepo<4,>=3.3.2 in ./venv/lib/python3.10/site-packages (from dvc) (3.3.5) Requirement already satisfied: pygtrie>=2.3.2 in ./venv/lib/python3.10/site-packages (from dvc) (2.5.0) Requirement already satisfied: dvc-data<3.16,>=3.15 in ./venv/lib/python3.10/site-packages (from dvc) (3.15.1) Requirement already satisfied: fsspec in ./venv/lib/python3.10/site-packages (from dvc) (2024.5.0) Requirement already satisfied: dvc-objects in ./venv/lib/python3.10/site-packages (from dvc) (5.1.0) Requirement already satisfied: grandalf<1,>=0.7 in ./venv/lib/python3.10/site-packages (from dvc) (0.8) Requirement already satisfied: hydra-core>=1.1 in ./venv/lib/python3.10/site-packages (from dvc) (1.3.2) Requirement already satisfied: tabulate>=0.8.7 in ./venv/lib/python3.10/site-packages (from dvc) (0.9.0) Requirement already satisfied: colorama>=0.3.9 in ./venv/lib/python3.10/site-packages (from dvc) (0.4.6) Requirement already satisfied: tomlkit>=0.11.1 in ./venv/lib/python3.10/site-packages (from dvc) (0.12.5) Requirement already satisfied: rich>=12 in ./venv/lib/python3.10/site-packages (from dvc) (13.7.1) Requirement already satisfied: dvc-render<2,>=1.0.1 in ./venv/lib/python3.10/site-packages (from dvc) (1.0.2) Requirement already satisfied: flufl.lock<8,>=5 in ./venv/lib/python3.10/site-packages (from dvc) (7.1.1) Requirement already satisfied: packaging>=19 in ./venv/lib/python3.10/site-packages (from dvc) (24.0) Requirement already satisfied: pyparsing>=2.4.7 in ./venv/lib/python3.10/site-packages (from dvc) (3.1.2) Requirement already satisfied: flatten-dict<1,>=0.4.1 in ./venv/lib/python3.10/site-packages (from dvc) (0.4.2) Requirement already satisfied: dulwich in ./venv/lib/python3.10/site-packages (from dvc) (0.22.1) Requirement already satisfied: configobj>=5.0.6 in ./venv/lib/python3.10/site-packages (from dvc) (5.0.8) Requirement already satisfied: dvc-studio-client<1,>=0.20 in ./venv/lib/python3.10/site-packages (from dvc) (0.20.0) Requirement already satisfied: omegaconf in ./venv/lib/python3.10/site-packages (from dvc) (2.3.0) Requirement already satisfied: distro>=1.3 in ./venv/lib/python3.10/site-packages (from dvc) (1.9.0) Requirement already satisfied: dpath<3,>=2.1.0 in ./venv/lib/python3.10/site-packages (from dvc) (2.1.6) Requirement already satisfied: funcy>=1.14 in ./venv/lib/python3.10/site-packages (from dvc) (2.0) Requirement already satisfied: dvc-task<1,>=0.3.0 in ./venv/lib/python3.10/site-packages (from dvc) (0.4.0) Requirement already satisfied: voluptuous>=0.11.7 in ./venv/lib/python3.10/site-packages (from dvc) (0.14.2) Requirement already satisfied: kombu in ./venv/lib/python3.10/site-packages (from dvc) (5.3.7) Requirement already satisfied: shtab<2,>=1.3.4 in ./venv/lib/python3.10/site-packages (from dvc) (1.7.1) Requirement already satisfied: iterative-telemetry>=0.0.7 in ./venv/lib/python3.10/site-packages (from dvc) (0.0.8) Requirement already satisfied: celery in ./venv/lib/python3.10/site-packages (from dvc) (5.4.0) Requirement already satisfied: pathspec>=0.10.3 in ./venv/lib/python3.10/site-packages (from dvc) 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markdown-it-py>=2.2.0 in ./venv/lib/python3.10/site-packages (from rich>=12->dvc) (3.0.0) Requirement already satisfied: ruamel.yaml.clib>=0.2.7 in ./venv/lib/python3.10/site-packages (from ruamel.yaml>=0.17.11->dvc) (0.2.8) Requirement already satisfied: pygit2>=1.14.0 in ./venv/lib/python3.10/site-packages (from scmrepo<4,>=3.3.2->dvc) (1.15.0) Requirement already satisfied: asyncssh<3,>=2.13.1 in ./venv/lib/python3.10/site-packages (from scmrepo<4,>=3.3.2->dvc) (2.14.2) Requirement already satisfied: gitpython>3 in ./venv/lib/python3.10/site-packages (from scmrepo<4,>=3.3.2->dvc) (3.1.43) Requirement already satisfied: setuptools in ./venv/lib/python3.10/site-packages (from zc.lockfile>=1.2.1->dvc) (59.6.0) Requirement already satisfied: aiohttp in ./venv/lib/python3.10/site-packages (from aiohttp-retry>=2.5.0->dvc-http>=2.29.0->dvc) (3.9.5) Requirement already satisfied: typing-extensions>=3.6 in ./venv/lib/python3.10/site-packages (from asyncssh<3,>=2.13.1->scmrepo<4,>=3.3.2->dvc) (4.11.0) Requirement already satisfied: cryptography>=39.0 in ./venv/lib/python3.10/site-packages (from asyncssh<3,>=2.13.1->scmrepo<4,>=3.3.2->dvc) (42.0.7) Requirement already satisfied: prompt-toolkit>=3.0.36 in ./venv/lib/python3.10/site-packages (from click-repl>=0.2.0->celery->dvc) (3.0.43) Requirement already satisfied: gitdb<5,>=4.0.1 in ./venv/lib/python3.10/site-packages (from gitpython>3->scmrepo<4,>=3.3.2->dvc) (4.0.11) Requirement already satisfied: mdurl~=0.1 in ./venv/lib/python3.10/site-packages (from markdown-it-py>=2.2.0->rich>=12->dvc) (0.1.2) Requirement already satisfied: pydantic-core==2.18.2 in ./venv/lib/python3.10/site-packages (from pydantic!=2.0.0,<3,>=1.9.0->gto<2,>=1.6.0->dvc) (2.18.2) Requirement already satisfied: annotated-types>=0.4.0 in ./venv/lib/python3.10/site-packages (from pydantic!=2.0.0,<3,>=1.9.0->gto<2,>=1.6.0->dvc) (0.7.0) Requirement already satisfied: cffi>=1.16.0 in ./venv/lib/python3.10/site-packages (from pygit2>=1.14.0->scmrepo<4,>=3.3.2->dvc) (1.16.0) Requirement already satisfied: orjson in ./venv/lib/python3.10/site-packages (from sqltrie<1,>=0.11.0->dvc-data<3.16,>=3.15->dvc) (3.10.3) Requirement already satisfied: shellingham>=1.3.0 in ./venv/lib/python3.10/site-packages (from typer>=0.4.1->gto<2,>=1.6.0->dvc) (1.5.4) Requirement already satisfied: async-timeout<5.0,>=4.0 in ./venv/lib/python3.10/site-packages (from aiohttp->aiohttp-retry>=2.5.0->dvc-http>=2.29.0->dvc) (4.0.3) Requirement already satisfied: aiosignal>=1.1.2 in ./venv/lib/python3.10/site-packages (from aiohttp->aiohttp-retry>=2.5.0->dvc-http>=2.29.0->dvc) (1.3.1) Requirement already satisfied: yarl<2.0,>=1.0 in ./venv/lib/python3.10/site-packages (from aiohttp->aiohttp-retry>=2.5.0->dvc-http>=2.29.0->dvc) (1.9.4) Requirement already satisfied: multidict<7.0,>=4.5 in ./venv/lib/python3.10/site-packages (from aiohttp->aiohttp-retry>=2.5.0->dvc-http>=2.29.0->dvc) (6.0.5) Requirement already satisfied: frozenlist>=1.1.1 in ./venv/lib/python3.10/site-packages (from aiohttp->aiohttp-retry>=2.5.0->dvc-http>=2.29.0->dvc) (1.4.1) Requirement already satisfied: pycparser in ./venv/lib/python3.10/site-packages (from cffi>=1.16.0->pygit2>=1.14.0->scmrepo<4,>=3.3.2->dvc) (2.22) Requirement already satisfied: smmap<6,>=3.0.1 in ./venv/lib/python3.10/site-packages (from gitdb<5,>=4.0.1->gitpython>3->scmrepo<4,>=3.3.2->dvc) (5.0.1) Requirement already satisfied: wcwidth in ./venv/lib/python3.10/site-packages (from prompt-toolkit>=3.0.36->click-repl>=0.2.0->celery->dvc) (0.2.13)
Stwórzmy katalog, w którym będziemy przechowywać nasz projekt:
!rm -r -f IUM_10/sample-ml-project-2024
!mkdir -p IUM_10/sample-ml-project-2024#Jupyter notebook magic https://ipython.readthedocs.io/en/stable/interactive/magics.html#magic-cd
%cd "IUM_10/sample-ml-project-2024"/home/pawel/ium/IUM_10/sample-ml-project-2024
/home/pawel/ium/venv/lib/python3.10/site-packages/IPython/core/magics/osm.py:417: UserWarning: This is now an optional IPython functionality, setting dhist requires you to install the `pickleshare` library. self.shell.db['dhist'] = compress_dhist(dhist)[-100:]
Inicjalizujemy puste repozytorium Git (możemy też pominąć ten krok i działać w istniejącym już repozytorium)
!git initReinitialized existing Git repository in /home/pawel/ium/IUM_10/sample-ml-project-2024/.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: .dvcignore[m
.dvc/config- główny plik konfiguracyjny DVC.dvc/config.local- nadpisuje wartości zconfig, do lokalnych zmian niecommitowanych do repozytorium.dvc/.gitignore- pliki DVC, które nie mają znaleźć się w repo.dvcignore- DVC pomija pliki zdefiniowane w tym pliku (np. aby poprawić wydajność)
Możemy teraz zacommitować zmiany w git:
!git commit -m "Initial commit"[master (root-commit) a9746ad] Initial commit 3 files changed, 6 insertions(+) create mode 100644 .dvc/.gitignore create mode 100644 .dvc/config create mode 100644 .dvcignore
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/pawel/ium/IUM_10/sample-ml-project-2024 0%| | 0.00/3.60k [00:00<?, ?B/s] 100%|██████████████████████████████████████| 3.60k/3.60k [00:00<00:00, 8.23MB/s] Archive: iris.zip inflating: Iris.csv inflating: database.sqlite
Teraz dodamy plik(i) z danymi do DVC:
!dvc add data/Iris.csv[?25l[32m⠋[0m Checking graph core[39m> Adding... ![A Collecting files and computing hashes in data/Iris.csv |0.00 [00:00, ?file/s[A [A ![A 0% Checking cache in '/home/pawel/ium/IUM_10/sample-ml-project-2024/.dvc/cache[A [A ![A 0%| |Adding data/Iris.csv to cache 0/1 [00:00<?, ?file/s][A [A ![A 0%| |Checking out /home/pawel/ium/IUM_10/sa0/1 [00:00<?, ?files/s][A 100% Adding...|████████████████████████████████████████|1/1 [00:00, 31.90file/s][A To track the changes with git, run: git add data/.gitignore data/Iris.csv.dvc To enable auto staging, run: dvc config core.autostage true [0m
- DVC utworzył plik
data/Iris.csv.dvci dodał 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 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 92b2c9d] Dodano dane IRIS (DVC) 2 files changed, 6 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
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/files/md5/71total 8 -r--r--r-- 1 pawel pawel 5107 Sep 19 2019 7820ef0af287ff346c5cabfb4c612c
!head -n 3 .dvc/cache/files/md5/71/7820ef0af287ff346c5cabfb4c612cId,SepalLengthCm,SepalWidthCm,PetalLengthCm,PetalWidthCm,Species 1,5.1,3.5,1.4,0.2,Iris-setosa 2,4.9,3.0,1.4,0.2,Iris-setosa
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 rzeczywistych zastosowaniach podalibyśmy tutaj ścieżkę do jakiegoś zasobu dostępnego przez internet 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
Dodawanie remote typu local
!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 7123494] Added DVC remote 1 file changed, 1 insertion(+), 1 deletion(-)
dvc push
Kiedy mamy już skonfigurowany "remote" możemy wypchnąć do niego pliki korzystając z polecenia dvc push:
!dvc pushCollecting |1.00 [00:00, 137entry/s] Pushing ![A 0% Checking cache in '/home/pawel/dvcstore/files/md5'| |0/? [00:00<?, ?file[A [A ![A 0% Checking cache in '/home/pawel/ium/IUM_10/sample-ml-project-2024/.dvc/cache[A [A ![A 0%| |Pushing to local 0/1 [00:00<?, ?file/s][A Pushing [A 1 file pushed [0m
!tree ~/dvcstore[01;34m/home/pawel/dvcstore[0m └── [01;34mfiles[0m └── [01;34mmd5[0m └── [01;34m71[0m └── 7820ef0af287ff346c5cabfb4c612c 3 directories, 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 | tee data/Iris.csvId,SepalLengthCm,SepalWidthCm,PetalLengthCm,PetalWidthCm,Species 1,5.1,3.5,1.4,0.2,Iris-setosa 2,4.9,3.0,1.4,0.2,Iris-setosa 3,4.7,3.2,1.3,0.2,Iris-setosa 4,4.6,3.1,1.5,0.2,Iris-setosa 5,5.0,3.6,1.4,0.2,Iris-setosa 6,5.4,3.9,1.7,0.4,Iris-setosa 7,4.6,3.4,1.4,0.3,Iris-setosa 8,5.0,3.4,1.5,0.2,Iris-setosa 9,4.4,2.9,1.4,0.2,Iris-setosa 10,4.9,3.1,1.5,0.1,Iris-setosa 11,5.4,3.7,1.5,0.2,Iris-setosa 12,4.8,3.4,1.6,0.2,Iris-setosa 13,4.8,3.0,1.4,0.1,Iris-setosa 14,4.3,3.0,1.1,0.1,Iris-setosa 15,5.8,4.0,1.2,0.2,Iris-setosa 16,5.7,4.4,1.5,0.4,Iris-setosa 17,5.4,3.9,1.3,0.4,Iris-setosa 18,5.1,3.5,1.4,0.3,Iris-setosa 19,5.7,3.8,1.7,0.3,Iris-setosa 20,5.1,3.8,1.5,0.3,Iris-setosa 21,5.4,3.4,1.7,0.2,Iris-setosa 22,5.1,3.7,1.5,0.4,Iris-setosa 23,4.6,3.6,1.0,0.2,Iris-setosa 24,5.1,3.3,1.7,0.5,Iris-setosa 25,4.8,3.4,1.9,0.2,Iris-setosa 26,5.0,3.0,1.6,0.2,Iris-setosa 27,5.0,3.4,1.6,0.4,Iris-setosa 28,5.2,3.5,1.5,0.2,Iris-setosa 29,5.2,3.4,1.4,0.2,Iris-setosa 30,4.7,3.2,1.6,0.2,Iris-setosa 31,4.8,3.1,1.6,0.2,Iris-setosa 32,5.4,3.4,1.5,0.4,Iris-setosa 33,5.2,4.1,1.5,0.1,Iris-setosa 34,5.5,4.2,1.4,0.2,Iris-setosa 35,4.9,3.1,1.5,0.1,Iris-setosa 36,5.0,3.2,1.2,0.2,Iris-setosa 37,5.5,3.5,1.3,0.2,Iris-setosa 38,4.9,3.1,1.5,0.1,Iris-setosa 39,4.4,3.0,1.3,0.2,Iris-setosa 40,5.1,3.4,1.5,0.2,Iris-setosa 41,5.0,3.5,1.3,0.3,Iris-setosa 42,4.5,2.3,1.3,0.3,Iris-setosa 43,4.4,3.2,1.3,0.2,Iris-setosa 44,5.0,3.5,1.6,0.6,Iris-setosa 45,5.1,3.8,1.9,0.4,Iris-setosa 46,4.8,3.0,1.4,0.3,Iris-setosa 47,5.1,3.8,1.6,0.2,Iris-setosa 48,4.6,3.2,1.4,0.2,Iris-setosa 49,5.3,3.7,1.5,0.2,Iris-setosa 50,5.0,3.3,1.4,0.2,Iris-setosa 51,7.0,3.2,4.7,1.4,Iris-versicolor 52,6.4,3.2,4.5,1.5,Iris-versicolor 53,6.9,3.1,4.9,1.5,Iris-versicolor 54,5.5,2.3,4.0,1.3,Iris-versicolor 55,6.5,2.8,4.6,1.5,Iris-versicolor 56,5.7,2.8,4.5,1.3,Iris-versicolor 57,6.3,3.3,4.7,1.6,Iris-versicolor 58,4.9,2.4,3.3,1.0,Iris-versicolor 59,6.6,2.9,4.6,1.3,Iris-versicolor 60,5.2,2.7,3.9,1.4,Iris-versicolor 61,5.0,2.0,3.5,1.0,Iris-versicolor 62,5.9,3.0,4.2,1.5,Iris-versicolor 63,6.0,2.2,4.0,1.0,Iris-versicolor 64,6.1,2.9,4.7,1.4,Iris-versicolor 65,5.6,2.9,3.6,1.3,Iris-versicolor 66,6.7,3.1,4.4,1.4,Iris-versicolor 67,5.6,3.0,4.5,1.5,Iris-versicolor 68,5.8,2.7,4.1,1.0,Iris-versicolor 69,6.2,2.2,4.5,1.5,Iris-versicolor 70,5.6,2.5,3.9,1.1,Iris-versicolor 71,5.9,3.2,4.8,1.8,Iris-versicolor 72,6.1,2.8,4.0,1.3,Iris-versicolor 73,6.3,2.5,4.9,1.5,Iris-versicolor 74,6.1,2.8,4.7,1.2,Iris-versicolor 75,6.4,2.9,4.3,1.3,Iris-versicolor 76,6.6,3.0,4.4,1.4,Iris-versicolor 77,6.8,2.8,4.8,1.4,Iris-versicolor 78,6.7,3.0,5.0,1.7,Iris-versicolor 79,6.0,2.9,4.5,1.5,Iris-versicolor 80,5.7,2.6,3.5,1.0,Iris-versicolor 81,5.5,2.4,3.8,1.1,Iris-versicolor 82,5.5,2.4,3.7,1.0,Iris-versicolor 83,5.8,2.7,3.9,1.2,Iris-versicolor 84,6.0,2.7,5.1,1.6,Iris-versicolor 85,5.4,3.0,4.5,1.5,Iris-versicolor 86,6.0,3.4,4.5,1.6,Iris-versicolor 87,6.7,3.1,4.7,1.5,Iris-versicolor 88,6.3,2.3,4.4,1.3,Iris-versicolor 89,5.6,3.0,4.1,1.3,Iris-versicolor 90,5.5,2.5,4.0,1.3,Iris-versicolor 91,5.5,2.6,4.4,1.2,Iris-versicolor 92,6.1,3.0,4.6,1.4,Iris-versicolor 93,5.8,2.6,4.0,1.2,Iris-versicolor 94,5.0,2.3,3.3,1.0,Iris-versicolor 95,5.6,2.7,4.2,1.3,Iris-versicolor 96,5.7,3.0,4.2,1.2,Iris-versicolor 97,5.7,2.9,4.2,1.3,Iris-versicolor 98,6.2,2.9,4.3,1.3,Iris-versicolor 99,5.1,2.5,3.0,1.1,Iris-versicolor 100,5.7,2.8,4.1,1.3,Iris-versicolor 101,6.3,3.3,6.0,2.5,Iris-virginica 102,5.8,2.7,5.1,1.9,Iris-virginica 103,7.1,3.0,5.9,2.1,Iris-virginica 104,6.3,2.9,5.6,1.8,Iris-virginica 105,6.5,3.0,5.8,2.2,Iris-virginica 106,7.6,3.0,6.6,2.1,Iris-virginica 107,4.9,2.5,4.5,1.7,Iris-virginica 108,7.3,2.9,6.3,1.8,Iris-virginica 109,6.7,2.5,5.8,1.8,Iris-virginica 110,7.2,3.6,6.1,2.5,Iris-virginica 111,6.5,3.2,5.1,2.0,Iris-virginica 112,6.4,2.7,5.3,1.9,Iris-virginica 113,6.8,3.0,5.5,2.1,Iris-virginica 114,5.7,2.5,5.0,2.0,Iris-virginica 115,5.8,2.8,5.1,2.4,Iris-virginica 116,6.4,3.2,5.3,2.3,Iris-virginica 117,6.5,3.0,5.5,1.8,Iris-virginica 118,7.7,3.8,6.7,2.2,Iris-virginica 119,7.7,2.6,6.9,2.3,Iris-virginica 120,6.0,2.2,5.0,1.5,Iris-virginica 121,6.9,3.2,5.7,2.3,Iris-virginica 122,5.6,2.8,4.9,2.0,Iris-virginica 123,7.7,2.8,6.7,2.0,Iris-virginica 124,6.3,2.7,4.9,1.8,Iris-virginica 125,6.7,3.3,5.7,2.1,Iris-virginica 126,7.2,3.2,6.0,1.8,Iris-virginica 127,6.2,2.8,4.8,1.8,Iris-virginica 128,6.1,3.0,4.9,1.8,Iris-virginica 129,6.4,2.8,5.6,2.1,Iris-virginica 130,7.2,3.0,5.8,1.6,Iris-virginica 131,7.4,2.8,6.1,1.9,Iris-virginica 132,7.9,3.8,6.4,2.0,Iris-virginica 133,6.4,2.8,5.6,2.2,Iris-virginica 134,6.3,2.8,5.1,1.5,Iris-virginica 135,6.1,2.6,5.6,1.4,Iris-virginica 136,7.7,3.0,6.1,2.3,Iris-virginica 137,6.3,3.4,5.6,2.4,Iris-virginica 138,6.4,3.1,5.5,1.8,Iris-virginica 139,6.0,3.0,4.8,1.8,Iris-virginica 140,6.9,3.1,5.4,2.1,Iris-virginica 141,6.7,3.1,5.6,2.4,Iris-virginica 142,6.9,3.1,5.1,2.3,Iris-virginica 143,5.8,2.7,5.1,1.9,Iris-virginica 144,6.8,3.2,5.9,2.3,Iris-virginica 145,6.7,3.3,5.7,2.5,Iris-virginica 146,6.7,3.0,5.2,2.3,Iris-virginica 147,6.3,2.5,5.0,1.9,Iris-virginica 148,6.5,3.0,5.2,2.0,Iris-virginica 149,6.2,3.4,5.4,2.3,Iris-virginica
!git statusOn branch master nothing to commit, working tree clean
!dvc statusdata/Iris.csv.dvc:
changed outs:
modified: data/Iris.csv
[0m!dvc add data/Iris.csv[?25l[32m⠋[0m Checking graph core[39m> Adding... ![A Collecting files and computing hashes in data/Iris.csv |0.00 [00:00, ?file/s[A [A ![A 0% Checking cache in '/home/pawel/ium/IUM_10/sample-ml-project-2024/.dvc/cache[A [A ![A 0%| |Adding data/Iris.csv to cache 0/1 [00:00<?, ?file/s][A [A ![A 0%| |Checking out /home/pawel/ium/IUM_10/sa0/1 [00:00<?, ?files/s][A 100% Adding...|████████████████████████████████████████|1/1 [00:00, 50.81file/s][A To track the changes with git, run: git add data/Iris.csv.dvc To enable auto staging, run: dvc config core.autostage true [0m
!git add data/Iris.csv.dvc
!git commit -m "Removed last line from Iris dataset"
[master 9de24e1] Removed last line from Iris dataset 1 file changed, 2 insertions(+), 2 deletions(-)
!wc -l .dvc/cache/files/md5/*/*151 .dvc/cache/files/md5/71/7820ef0af287ff346c5cabfb4c612c 150 .dvc/cache/files/md5/bc/cff2e578d76852294184c1dce9fdbf 301 total
dvc checkout
- Polecenia
dvc checkoutużywamy razem zgit checkout, żeby zmienić gałąź, na której pracujemy. - DVC podmieni wersje plików śledzonych przez siebie na pochodzące z innej gałęzi (o ile pliki te się różnią i różnią się pliki
*.dvcna odpowiednich gałęziach) - Zmiana gałęzi 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 data.xml| |0/1 [00:00<?, ?files/s] ![A 0%| |get-started/data.xml 0.00/13.8M [00:00<?, ?B/s][A 0%| |get-started/data.xml 16.5k/13.8M [00:00<01:47, 135kB/s][A 0%| |get-started/data.xml 66.5k/13.8M [00:00<00:48, 294kB/s][A 1%| |get-started/data.xml 102k/13.8M [00:00<00:48, 295kB/s][A 2%|▏ |get-started/data.xml 221k/13.8M [00:00<00:25, 566kB/s][A 3%|▎ |get-started/data.xml 374k/13.8M [00:00<00:17, 813kB/s][A 3%|▎ |get-started/data.xml 493k/13.8M [00:00<00:15, 873kB/s][A 5%|▍ |get-started/data.xml 697k/13.8M [00:00<00:12, 1.10MB/s][A 6%|▌ |get-started/data.xml 799k/13.8M [00:01<00:13, 1.02MB/s][A 7%|▋ |get-started/data.xml 935k/13.8M [00:01<00:12, 1.05MB/s][A 8%|▊ |get-started/data.xml 1.05M/13.8M [00:01<00:12, 1.07MB/s][A 8%|▊ |get-started/data.xml 1.10M/13.8M [00:01<00:15, 872kB/s][A 9%|▉ |get-started/data.xml 1.24M/13.8M [00:01<00:13, 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!dvc statusData and pipelines are up to date.
[0mls -l datatotal 14124 -rw-r--r-- 1 pawel pawel 5072 May 22 07:57 Iris.csv -rw-r--r-- 1 pawel pawel 88 May 22 07:57 Iris.csv.dvc -rw-r--r-- 1 pawel pawel 14445097 May 22 07:59 data.xml -rw-r--r-- 1 pawel pawel 296 May 22 07:59 data.xml.dvc
DVC pipelines
- Wprowadzenie: https://youtu.be/71IGzyH95UY
- Getting started: https://dvc.org/doc/start/data-pipelines
- DVC pipelines pozwalają zbudować (za pomocą polecenia
dvc run) lub zdefiniować (edytując plikdvc.yaml) graf zależności między krokami wykonywanymi w naszym projekcie (takimi jak "przygotowanie danych", "uczenie", "ewaluacja"). - Tak zdefiniowany pipeline można potem uruchomić za pomocą polecenia
dvc reproduce.
Zadania [5 pkt + dodatkowo 10 pkt]
Termin: 29 maja 2024
- 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) [3pkt]
- [Dodatkowo] 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) [10pkt (opcjonalne)]
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 (szczegóły)
conda install dvc-ssh
albo
pip install dvc[ssh] paramiko
# conda install -c conda-forge dvc-ssh
!pip install dvc[ssh] paramikoRequirement already satisfied: dvc[ssh] in /home/pawel/ium/venv/lib/python3.10/site-packages (3.50.2) Collecting paramiko Downloading paramiko-3.4.0-py3-none-any.whl (225 kB) [2K [90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━[0m [32m225.9/225.9 KB[0m [31m4.1 MB/s[0m eta [36m0:00:00[0ma [36m0:00:01[0m [?25hRequirement already satisfied: ruamel.yaml>=0.17.11 in /home/pawel/ium/venv/lib/python3.10/site-packages (from dvc[ssh]) (0.18.6) Requirement already satisfied: fsspec in /home/pawel/ium/venv/lib/python3.10/site-packages (from dvc[ssh]) (2024.5.0) Requirement already satisfied: dvc-studio-client<1,>=0.20 in /home/pawel/ium/venv/lib/python3.10/site-packages (from dvc[ssh]) (0.20.0) Requirement already satisfied: tomlkit>=0.11.1 in /home/pawel/ium/venv/lib/python3.10/site-packages (from dvc[ssh]) (0.12.5) Requirement already satisfied: dvc-objects in /home/pawel/ium/venv/lib/python3.10/site-packages (from dvc[ssh]) (5.1.0) Requirement already satisfied: distro>=1.3 in /home/pawel/ium/venv/lib/python3.10/site-packages (from dvc[ssh]) (1.9.0) Requirement already satisfied: pygtrie>=2.3.2 in /home/pawel/ium/venv/lib/python3.10/site-packages (from dvc[ssh]) (2.5.0) Requirement already satisfied: voluptuous>=0.11.7 in /home/pawel/ium/venv/lib/python3.10/site-packages (from dvc[ssh]) (0.14.2) Requirement already satisfied: attrs>=22.2.0 in /home/pawel/ium/venv/lib/python3.10/site-packages (from dvc[ssh]) (23.2.0) Requirement already satisfied: dvc-http>=2.29.0 in /home/pawel/ium/venv/lib/python3.10/site-packages (from dvc[ssh]) (2.32.0) Requirement already satisfied: rich>=12 in /home/pawel/ium/venv/lib/python3.10/site-packages (from dvc[ssh]) (13.7.1) Requirement already satisfied: dulwich in /home/pawel/ium/venv/lib/python3.10/site-packages (from dvc[ssh]) (0.22.1) Requirement already satisfied: pyparsing>=2.4.7 in /home/pawel/ium/venv/lib/python3.10/site-packages (from dvc[ssh]) (3.1.2) Requirement already satisfied: shortuuid>=0.5 in /home/pawel/ium/venv/lib/python3.10/site-packages (from dvc[ssh]) (1.0.13) Requirement already satisfied: flufl.lock<8,>=5 in /home/pawel/ium/venv/lib/python3.10/site-packages (from dvc[ssh]) (7.1.1) Requirement already satisfied: kombu in /home/pawel/ium/venv/lib/python3.10/site-packages (from dvc[ssh]) (5.3.7) Requirement already satisfied: iterative-telemetry>=0.0.7 in /home/pawel/ium/venv/lib/python3.10/site-packages (from dvc[ssh]) (0.0.8) Requirement already satisfied: dpath<3,>=2.1.0 in /home/pawel/ium/venv/lib/python3.10/site-packages (from dvc[ssh]) (2.1.6) Requirement already satisfied: colorama>=0.3.9 in /home/pawel/ium/venv/lib/python3.10/site-packages (from dvc[ssh]) (0.4.6) Requirement already satisfied: celery in /home/pawel/ium/venv/lib/python3.10/site-packages (from dvc[ssh]) (5.4.0) Requirement already satisfied: packaging>=19 in /home/pawel/ium/venv/lib/python3.10/site-packages (from dvc[ssh]) (24.0) Requirement already satisfied: tabulate>=0.8.7 in /home/pawel/ium/venv/lib/python3.10/site-packages (from dvc[ssh]) (0.9.0) Requirement already satisfied: shtab<2,>=1.3.4 in /home/pawel/ium/venv/lib/python3.10/site-packages (from dvc[ssh]) (1.7.1) Requirement already satisfied: scmrepo<4,>=3.3.2 in /home/pawel/ium/venv/lib/python3.10/site-packages (from dvc[ssh]) (3.3.5) Requirement already satisfied: dvc-render<2,>=1.0.1 in /home/pawel/ium/venv/lib/python3.10/site-packages (from dvc[ssh]) (1.0.2) Requirement already satisfied: gto<2,>=1.6.0 in /home/pawel/ium/venv/lib/python3.10/site-packages (from dvc[ssh]) (1.7.1) Requirement already satisfied: pydot>=1.2.4 in /home/pawel/ium/venv/lib/python3.10/site-packages (from dvc[ssh]) (2.0.0) Requirement already satisfied: psutil>=5.8 in /home/pawel/ium/venv/lib/python3.10/site-packages (from dvc[ssh]) (5.9.8) Requirement already satisfied: configobj>=5.0.6 in /home/pawel/ium/venv/lib/python3.10/site-packages (from dvc[ssh]) (5.0.8) Requirement already satisfied: funcy>=1.14 in /home/pawel/ium/venv/lib/python3.10/site-packages (from dvc[ssh]) (2.0) Requirement already satisfied: grandalf<1,>=0.7 in /home/pawel/ium/venv/lib/python3.10/site-packages (from dvc[ssh]) (0.8) Requirement already satisfied: dvc-task<1,>=0.3.0 in /home/pawel/ium/venv/lib/python3.10/site-packages (from dvc[ssh]) (0.4.0) Requirement already satisfied: requests>=2.22 in /home/pawel/ium/venv/lib/python3.10/site-packages (from dvc[ssh]) (2.31.0) Requirement already satisfied: zc.lockfile>=1.2.1 in /home/pawel/ium/venv/lib/python3.10/site-packages (from dvc[ssh]) (3.0.post1) Requirement already satisfied: flatten-dict<1,>=0.4.1 in /home/pawel/ium/venv/lib/python3.10/site-packages (from dvc[ssh]) (0.4.2) Requirement already satisfied: networkx>=2.5 in /home/pawel/ium/venv/lib/python3.10/site-packages (from dvc[ssh]) (3.3) Requirement already satisfied: pathspec>=0.10.3 in /home/pawel/ium/venv/lib/python3.10/site-packages (from dvc[ssh]) (0.12.1) Requirement already satisfied: hydra-core>=1.1 in /home/pawel/ium/venv/lib/python3.10/site-packages (from dvc[ssh]) (1.3.2) Requirement already satisfied: omegaconf in /home/pawel/ium/venv/lib/python3.10/site-packages (from dvc[ssh]) (2.3.0) Requirement already satisfied: tqdm<5,>=4.63.1 in /home/pawel/ium/venv/lib/python3.10/site-packages (from dvc[ssh]) (4.66.2) Requirement already satisfied: dvc-data<3.16,>=3.15 in /home/pawel/ium/venv/lib/python3.10/site-packages (from dvc[ssh]) (3.15.1) Requirement already satisfied: platformdirs<4,>=3.1.1 in /home/pawel/ium/venv/lib/python3.10/site-packages (from dvc[ssh]) (3.11.0) Collecting dvc-ssh<5,>=4 Downloading dvc_ssh-4.1.1-py3-none-any.whl (15 kB) Collecting bcrypt>=3.2 Downloading bcrypt-4.1.3-cp39-abi3-manylinux_2_28_x86_64.whl (283 kB) [2K [90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━[0m [32m283.7/283.7 KB[0m [31m12.6 MB/s[0m eta [36m0:00:00[0m [?25hCollecting pynacl>=1.5 Downloading PyNaCl-1.5.0-cp36-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_24_x86_64.whl (856 kB) [2K [90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━[0m [32m856.7/856.7 KB[0m [31m14.2 MB/s[0m eta [36m0:00:00[0ma [36m0:00:01[0m [?25hRequirement already satisfied: cryptography>=3.3 in /home/pawel/ium/venv/lib/python3.10/site-packages (from paramiko) (42.0.7) Requirement already satisfied: six in /home/pawel/ium/venv/lib/python3.10/site-packages (from configobj>=5.0.6->dvc[ssh]) (1.16.0) Requirement already satisfied: cffi>=1.12 in /home/pawel/ium/venv/lib/python3.10/site-packages (from cryptography>=3.3->paramiko) (1.16.0) Requirement already satisfied: diskcache>=5.2.1 in /home/pawel/ium/venv/lib/python3.10/site-packages (from dvc-data<3.16,>=3.15->dvc[ssh]) (5.6.3) Requirement already satisfied: dictdiffer>=0.8.1 in /home/pawel/ium/venv/lib/python3.10/site-packages (from dvc-data<3.16,>=3.15->dvc[ssh]) (0.9.0) Requirement already satisfied: sqltrie<1,>=0.11.0 in /home/pawel/ium/venv/lib/python3.10/site-packages (from dvc-data<3.16,>=3.15->dvc[ssh]) (0.11.0) Requirement already satisfied: aiohttp-retry>=2.5.0 in /home/pawel/ium/venv/lib/python3.10/site-packages (from dvc-http>=2.29.0->dvc[ssh]) (2.8.3) Collecting sshfs[bcrypt]>=2023.4.1 Downloading sshfs-2024.4.1-py3-none-any.whl (15 kB) Requirement already satisfied: billiard<5.0,>=4.2.0 in /home/pawel/ium/venv/lib/python3.10/site-packages (from celery->dvc[ssh]) (4.2.0) Requirement already satisfied: tzdata>=2022.7 in /home/pawel/ium/venv/lib/python3.10/site-packages (from celery->dvc[ssh]) (2024.1) Requirement already satisfied: python-dateutil>=2.8.2 in /home/pawel/ium/venv/lib/python3.10/site-packages (from celery->dvc[ssh]) (2.9.0.post0) Requirement already satisfied: vine<6.0,>=5.1.0 in /home/pawel/ium/venv/lib/python3.10/site-packages (from celery->dvc[ssh]) (5.1.0) Requirement already satisfied: click-plugins>=1.1.1 in /home/pawel/ium/venv/lib/python3.10/site-packages (from celery->dvc[ssh]) (1.1.1) Requirement already satisfied: click-repl>=0.2.0 in /home/pawel/ium/venv/lib/python3.10/site-packages (from celery->dvc[ssh]) (0.3.0) Requirement already satisfied: click<9.0,>=8.1.2 in /home/pawel/ium/venv/lib/python3.10/site-packages (from celery->dvc[ssh]) (8.1.7) Requirement already satisfied: click-didyoumean>=0.3.0 in /home/pawel/ium/venv/lib/python3.10/site-packages (from celery->dvc[ssh]) (0.3.1) Requirement already satisfied: atpublic>=2.3 in /home/pawel/ium/venv/lib/python3.10/site-packages (from flufl.lock<8,>=5->dvc[ssh]) (4.1.0) Requirement already satisfied: semver>=2.13.0 in /home/pawel/ium/venv/lib/python3.10/site-packages (from gto<2,>=1.6.0->dvc[ssh]) (3.0.2) Requirement already satisfied: pydantic!=2.0.0,<3,>=1.9.0 in /home/pawel/ium/venv/lib/python3.10/site-packages (from gto<2,>=1.6.0->dvc[ssh]) (2.7.1) Requirement already satisfied: entrypoints in /home/pawel/ium/venv/lib/python3.10/site-packages (from gto<2,>=1.6.0->dvc[ssh]) (0.4) Requirement already satisfied: typer>=0.4.1 in /home/pawel/ium/venv/lib/python3.10/site-packages (from gto<2,>=1.6.0->dvc[ssh]) (0.12.3) Requirement already satisfied: antlr4-python3-runtime==4.9.* in /home/pawel/ium/venv/lib/python3.10/site-packages (from hydra-core>=1.1->dvc[ssh]) (4.9.3) Requirement already satisfied: filelock in /home/pawel/ium/venv/lib/python3.10/site-packages (from iterative-telemetry>=0.0.7->dvc[ssh]) (3.14.0) Requirement already satisfied: appdirs in /home/pawel/ium/venv/lib/python3.10/site-packages (from iterative-telemetry>=0.0.7->dvc[ssh]) (1.4.4) Requirement already satisfied: amqp<6.0.0,>=5.1.1 in /home/pawel/ium/venv/lib/python3.10/site-packages (from kombu->dvc[ssh]) (5.2.0) Requirement already satisfied: PyYAML>=5.1.0 in /home/pawel/ium/venv/lib/python3.10/site-packages (from omegaconf->dvc[ssh]) (6.0.1) Requirement already satisfied: certifi>=2017.4.17 in /home/pawel/ium/venv/lib/python3.10/site-packages (from requests>=2.22->dvc[ssh]) (2024.2.2) Requirement already satisfied: idna<4,>=2.5 in /home/pawel/ium/venv/lib/python3.10/site-packages (from requests>=2.22->dvc[ssh]) (3.6) Requirement already satisfied: charset-normalizer<4,>=2 in /home/pawel/ium/venv/lib/python3.10/site-packages (from requests>=2.22->dvc[ssh]) (3.3.2) Requirement already satisfied: urllib3<3,>=1.21.1 in /home/pawel/ium/venv/lib/python3.10/site-packages (from requests>=2.22->dvc[ssh]) (2.2.1) Requirement already satisfied: pygments<3.0.0,>=2.13.0 in /home/pawel/ium/venv/lib/python3.10/site-packages (from rich>=12->dvc[ssh]) (2.17.2) Requirement already satisfied: markdown-it-py>=2.2.0 in /home/pawel/ium/venv/lib/python3.10/site-packages (from rich>=12->dvc[ssh]) (3.0.0) Requirement already satisfied: ruamel.yaml.clib>=0.2.7 in /home/pawel/ium/venv/lib/python3.10/site-packages (from ruamel.yaml>=0.17.11->dvc[ssh]) (0.2.8) Requirement already satisfied: pygit2>=1.14.0 in /home/pawel/ium/venv/lib/python3.10/site-packages (from scmrepo<4,>=3.3.2->dvc[ssh]) (1.15.0) Requirement already satisfied: gitpython>3 in /home/pawel/ium/venv/lib/python3.10/site-packages (from scmrepo<4,>=3.3.2->dvc[ssh]) (3.1.43) Requirement already satisfied: asyncssh<3,>=2.13.1 in /home/pawel/ium/venv/lib/python3.10/site-packages (from scmrepo<4,>=3.3.2->dvc[ssh]) (2.14.2) Requirement already satisfied: setuptools in /home/pawel/ium/venv/lib/python3.10/site-packages (from zc.lockfile>=1.2.1->dvc[ssh]) (59.6.0) Requirement already satisfied: aiohttp in /home/pawel/ium/venv/lib/python3.10/site-packages (from aiohttp-retry>=2.5.0->dvc-http>=2.29.0->dvc[ssh]) (3.9.5) Requirement already satisfied: typing-extensions>=3.6 in /home/pawel/ium/venv/lib/python3.10/site-packages (from asyncssh<3,>=2.13.1->scmrepo<4,>=3.3.2->dvc[ssh]) (4.11.0) Requirement already satisfied: pycparser in /home/pawel/ium/venv/lib/python3.10/site-packages (from cffi>=1.12->cryptography>=3.3->paramiko) (2.22) Requirement already satisfied: prompt-toolkit>=3.0.36 in /home/pawel/ium/venv/lib/python3.10/site-packages (from click-repl>=0.2.0->celery->dvc[ssh]) (3.0.43) Requirement already satisfied: gitdb<5,>=4.0.1 in /home/pawel/ium/venv/lib/python3.10/site-packages (from gitpython>3->scmrepo<4,>=3.3.2->dvc[ssh]) (4.0.11) Requirement already satisfied: mdurl~=0.1 in /home/pawel/ium/venv/lib/python3.10/site-packages (from markdown-it-py>=2.2.0->rich>=12->dvc[ssh]) (0.1.2) Requirement already satisfied: pydantic-core==2.18.2 in /home/pawel/ium/venv/lib/python3.10/site-packages (from pydantic!=2.0.0,<3,>=1.9.0->gto<2,>=1.6.0->dvc[ssh]) (2.18.2) Requirement already satisfied: annotated-types>=0.4.0 in /home/pawel/ium/venv/lib/python3.10/site-packages (from pydantic!=2.0.0,<3,>=1.9.0->gto<2,>=1.6.0->dvc[ssh]) (0.7.0) Requirement already satisfied: orjson in /home/pawel/ium/venv/lib/python3.10/site-packages (from sqltrie<1,>=0.11.0->dvc-data<3.16,>=3.15->dvc[ssh]) (3.10.3) Requirement already satisfied: shellingham>=1.3.0 in /home/pawel/ium/venv/lib/python3.10/site-packages (from typer>=0.4.1->gto<2,>=1.6.0->dvc[ssh]) (1.5.4) Requirement already satisfied: async-timeout<5.0,>=4.0 in /home/pawel/ium/venv/lib/python3.10/site-packages (from aiohttp->aiohttp-retry>=2.5.0->dvc-http>=2.29.0->dvc[ssh]) (4.0.3) Requirement already satisfied: aiosignal>=1.1.2 in /home/pawel/ium/venv/lib/python3.10/site-packages (from aiohttp->aiohttp-retry>=2.5.0->dvc-http>=2.29.0->dvc[ssh]) (1.3.1) Requirement already satisfied: multidict<7.0,>=4.5 in /home/pawel/ium/venv/lib/python3.10/site-packages (from aiohttp->aiohttp-retry>=2.5.0->dvc-http>=2.29.0->dvc[ssh]) (6.0.5) Requirement already satisfied: yarl<2.0,>=1.0 in /home/pawel/ium/venv/lib/python3.10/site-packages (from aiohttp->aiohttp-retry>=2.5.0->dvc-http>=2.29.0->dvc[ssh]) (1.9.4) Requirement already satisfied: frozenlist>=1.1.1 in /home/pawel/ium/venv/lib/python3.10/site-packages (from aiohttp->aiohttp-retry>=2.5.0->dvc-http>=2.29.0->dvc[ssh]) (1.4.1) Requirement already satisfied: smmap<6,>=3.0.1 in /home/pawel/ium/venv/lib/python3.10/site-packages (from gitdb<5,>=4.0.1->gitpython>3->scmrepo<4,>=3.3.2->dvc[ssh]) (5.0.1) Requirement already satisfied: wcwidth in /home/pawel/ium/venv/lib/python3.10/site-packages (from prompt-toolkit>=3.0.36->click-repl>=0.2.0->celery->dvc[ssh]) (0.2.13) Installing collected packages: bcrypt, pynacl, paramiko, sshfs, dvc-ssh Successfully installed bcrypt-4.1.3 dvc-ssh-4.1.1 paramiko-3.4.0 pynacl-1.5.0 sshfs-2024.4.1
## Poniższe są potrzebne, żeby polecania dvc remote działały:
!sudo apt install libssl3 libffi7[sudo] password for pawel:
Dodajemy remote:
!dvc remote add -f -d ium_ssh_remote ssh://ium-sftp@tzietkiewicz.vm.wmi.amu.edu.plSetting 'ium_ssh_remote' as a default remote.
[0m!dvc remote listmy_local_remote /home/pawel/dvcstore
ium_ssh_remote ssh://ium-sftp@tzietkiewicz.vm.wmi.amu.edu.pl
[0mZapisujemy hasło:
!dvc remote modify --local ium_ssh_remote password IUM@2021[0mPushujemy do skonfigurowanego remote:
!dvc pushCollecting |1.00 [00:00, 252entry/s] Pushing ![A 0% Checking cache in 'files/md5'| |0/? [00:00<?, ?files/s][A [A ![A 0% Checking cache in '/home/pawel/ium/IUM_10/sample-ml-project-2024/.dvc/cache[A [A ![A 0%| |Pushing to ssh 0/1 [00:00<?, ?file/s][A ![A[A 0%| |/home/pawel/ium/IUM_10/sample-m0.00/4.95k [00:00<?, ?B/s][A[A [A[A 100%|██████████|Pushing to ssh 1/1 [00:00<00:00, 8.63file/s][A Pushing [A 1 file pushed [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:8081/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:8081/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_PASS'
sh 'dvc pull'
}
Przykład konfiguracji: