{ "cells": [ { "cell_type": "markdown", "id": "7fe475ae", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "![Logo 1](https://git.wmi.amu.edu.pl/AITech/Szablon/raw/branch/master/Logotyp_AITech1.jpg)\n", "
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Inżynieria uczenia maszynowego

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10. DVC [laboratoria]

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Tomasz Ziętkiewicz (2022)

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\n", "\n", "![Logo 2](https://git.wmi.amu.edu.pl/AITech/Szablon/raw/branch/master/Logotyp_AITech2.jpg)" ] }, { "cell_type": "markdown", "id": "0c6f27a5", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "" ] }, { "cell_type": "markdown", "id": "560eec71", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "## DVC - Data Version Control\n", "- [dvc.org](https://dvc.org/)\n", "- \"Version Control System for Machine Learning Projects\" (System kontroli wersji dla projektów uczenia maszynowego)\n", "- Open Source\n", "- Umożliwia:\n", " - wersjonowanie danych i modeli. \"Git dla danych i modeli\"\n", " - budowanie potoków (\"pipeline\") definiujących jak budować/trenować/ewaluować modele. \"Makefile dla uczenia maszynowego\"\n", " - śledzenie, porównywanie metryk i parametrów\n", "- ściśle zintegowany z gitem\n", "- działa niezależnie od używanego języka/bibliotek i systemu operacyjnego\n", "- 5-minutowe wprowadzenie: https://www.youtube.com/watch?v=UbL7VUpv1Bs&t=197s" ] }, { "cell_type": "markdown", "id": "9bfb356e", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "## Instalacja i inicjalizacja\n", " - https://dvc.org/doc/install\n", " - ```pip(x) install dvc``` albo:\n", " - ```conda install dvc```" ] }, { "cell_type": "code", "execution_count": 7, "id": "054c7a11", "metadata": { "slideshow": { "slide_type": "slide" } }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Collecting dvc\n", "\u001b[33m Cache entry deserialization failed, entry ignored\u001b[0m\n", " Downloading https://files.pythonhosted.org/packages/96/9d/9cca62742cb99da8002c9d6ac6c7463344deb60a219ca4f3a9778b02c67b/dvc-2.8.1-py3-none-any.whl (386kB)\n", "\u001b[K 100% |████████████████████████████████| 389kB 1.4MB/s ta 0:00:01\n", "\u001b[?25hCollecting setuptools>=34.0.0 (from dvc)\n", " Using cached 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/home/tomek/.cache/pip/wheels/63/28/8c/0bbff7d6e30f3fc523639b000b33aba9155152e9eb23689ba0\n", " Running setup.py bdist_wheel for pygit2 ... \u001b[?25lerror\n", " 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:\n", " running bdist_wheel\n", " running build\n", " running build_py\n", " creating build\n", " creating build/lib.linux-x86_64-3.6\n", " creating build/lib.linux-x86_64-3.6/pygit2\n", " copying pygit2/__init__.py -> build/lib.linux-x86_64-3.6/pygit2\n", " copying pygit2/_build.py -> build/lib.linux-x86_64-3.6/pygit2\n", " copying pygit2/_run.py -> build/lib.linux-x86_64-3.6/pygit2\n", " copying pygit2/blame.py -> build/lib.linux-x86_64-3.6/pygit2\n", " copying pygit2/callbacks.py -> build/lib.linux-x86_64-3.6/pygit2\n", " copying pygit2/config.py -> build/lib.linux-x86_64-3.6/pygit2\n", " copying pygit2/credentials.py -> build/lib.linux-x86_64-3.6/pygit2\n", " copying pygit2/errors.py -> build/lib.linux-x86_64-3.6/pygit2\n", " copying pygit2/ffi.py -> build/lib.linux-x86_64-3.6/pygit2\n", " copying pygit2/index.py -> build/lib.linux-x86_64-3.6/pygit2\n", " copying pygit2/packbuilder.py -> build/lib.linux-x86_64-3.6/pygit2\n", " copying pygit2/refspec.py -> build/lib.linux-x86_64-3.6/pygit2\n", " copying pygit2/remote.py -> build/lib.linux-x86_64-3.6/pygit2\n", " copying pygit2/repository.py -> build/lib.linux-x86_64-3.6/pygit2\n", " copying pygit2/settings.py -> build/lib.linux-x86_64-3.6/pygit2\n", " copying pygit2/submodule.py -> build/lib.linux-x86_64-3.6/pygit2\n", " copying pygit2/utils.py -> build/lib.linux-x86_64-3.6/pygit2\n", " creating build/lib.linux-x86_64-3.6/pygit2/decl\n", " copying pygit2/decl/attr.h -> build/lib.linux-x86_64-3.6/pygit2/decl\n", " copying pygit2/decl/blame.h -> build/lib.linux-x86_64-3.6/pygit2/decl\n", " copying pygit2/decl/buffer.h -> build/lib.linux-x86_64-3.6/pygit2/decl\n", " copying pygit2/decl/callbacks.h -> build/lib.linux-x86_64-3.6/pygit2/decl\n", " copying pygit2/decl/checkout.h -> build/lib.linux-x86_64-3.6/pygit2/decl\n", " copying pygit2/decl/clone.h -> build/lib.linux-x86_64-3.6/pygit2/decl\n", " copying pygit2/decl/common.h -> build/lib.linux-x86_64-3.6/pygit2/decl\n", " copying pygit2/decl/config.h -> build/lib.linux-x86_64-3.6/pygit2/decl\n", " copying pygit2/decl/describe.h -> build/lib.linux-x86_64-3.6/pygit2/decl\n", " copying pygit2/decl/diff.h -> build/lib.linux-x86_64-3.6/pygit2/decl\n", " copying pygit2/decl/errors.h -> build/lib.linux-x86_64-3.6/pygit2/decl\n", " copying pygit2/decl/graph.h -> build/lib.linux-x86_64-3.6/pygit2/decl\n", " copying pygit2/decl/index.h -> build/lib.linux-x86_64-3.6/pygit2/decl\n", " copying pygit2/decl/indexer.h -> build/lib.linux-x86_64-3.6/pygit2/decl\n", " copying pygit2/decl/merge.h -> build/lib.linux-x86_64-3.6/pygit2/decl\n", " copying pygit2/decl/net.h -> build/lib.linux-x86_64-3.6/pygit2/decl\n", " copying pygit2/decl/oid.h -> build/lib.linux-x86_64-3.6/pygit2/decl\n", " copying pygit2/decl/pack.h -> build/lib.linux-x86_64-3.6/pygit2/decl\n", " copying pygit2/decl/proxy.h -> build/lib.linux-x86_64-3.6/pygit2/decl\n", " copying pygit2/decl/refspec.h -> build/lib.linux-x86_64-3.6/pygit2/decl\n", " copying pygit2/decl/remote.h -> build/lib.linux-x86_64-3.6/pygit2/decl\n", " copying pygit2/decl/repository.h -> build/lib.linux-x86_64-3.6/pygit2/decl\n", " copying pygit2/decl/revert.h -> build/lib.linux-x86_64-3.6/pygit2/decl\n", " copying pygit2/decl/stash.h -> build/lib.linux-x86_64-3.6/pygit2/decl\n", " copying pygit2/decl/strarray.h -> build/lib.linux-x86_64-3.6/pygit2/decl\n", " copying pygit2/decl/submodule.h -> build/lib.linux-x86_64-3.6/pygit2/decl\n", " copying pygit2/decl/transport.h -> build/lib.linux-x86_64-3.6/pygit2/decl\n", " copying pygit2/decl/types.h -> build/lib.linux-x86_64-3.6/pygit2/decl\n", " running build_ext\n", " generating cffi module 'build/temp.linux-x86_64-3.6/pygit2._libgit2.c'\n", " creating build/temp.linux-x86_64-3.6\n", " building 'pygit2._pygit2' extension\n", " creating build/temp.linux-x86_64-3.6/src\n", " 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\n", " In file included from src/blob.c:30:0:\n", " src/blob.h:33:10: fatal error: git2.h: No such file or directory\n", " #include \n", " ^~~~~~~~\n", " compilation terminated.\n", " error: command 'x86_64-linux-gnu-gcc' failed with exit status 1\n", " \n", " ----------------------------------------\n", "\u001b[31m Failed building wheel for pygit2\u001b[0m\n", "\u001b[?25h Running setup.py clean for pygit2\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ " Running setup.py bdist_wheel for contextvars ... \u001b[?25ldone\n", "\u001b[?25h Stored in directory: /home/tomek/.cache/pip/wheels/a5/7d/68/1ebae2668bda2228686e3c1cf16f2c2384cea6e9334ad5f6de\n", " Running setup.py bdist_wheel for atpublic ... \u001b[?25ldone\n", "\u001b[?25h Stored in directory: /home/tomek/.cache/pip/wheels/33/25/82/57d46b60a048f8e30b31f10497539498a3b826c78e2433c2d4\n", " Running setup.py bdist_wheel for mailchecker ... \u001b[?25ldone\n", "\u001b[?25h Stored in directory: /home/tomek/.cache/pip/wheels/fd/e1/e7/804e77a70eac7103bdba2f4b3e1eba36840b38554a4b8152c8\n", " Running setup.py bdist_wheel for ftfy ... \u001b[?25ldone\n", "\u001b[?25h Stored in directory: /home/tomek/.cache/pip/wheels/99/2c/e6/109c8a28fef7a443f67ba58df21fe1d0067ac3322e75e6b0b7\n", " Running setup.py bdist_wheel for future ... \u001b[?25ldone\n", "\u001b[?25h Stored in directory: /home/tomek/.cache/pip/wheels/8b/99/a0/81daf51dcd359a9377b110a8a886b3895921802d2fc1b2397e\n", " Running setup.py bdist_wheel for idna-ssl ... \u001b[?25ldone\n", "\u001b[?25h Stored in directory: /home/tomek/.cache/pip/wheels/d3/00/b3/32d613e19e08a739751dd6bf998cfed277728f8b2127ad4eb7\n", "Successfully built nanotime flufl.lock psutil configobj pygtrie dulwich contextvars atpublic mailchecker ftfy future idna-ssl\n", "Failed to build pygit2\n", "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\n", " Running setup.py install for pygit2 ... \u001b[?25lerror\n", " 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=:\n", " running install\n", " /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.\n", " setuptools.SetuptoolsDeprecationWarning,\n", " running build\n", " running build_py\n", " creating build\n", " creating build/lib.linux-x86_64-3.6\n", " creating build/lib.linux-x86_64-3.6/pygit2\n", " copying pygit2/__init__.py -> build/lib.linux-x86_64-3.6/pygit2\n", " copying pygit2/_build.py -> build/lib.linux-x86_64-3.6/pygit2\n", " copying pygit2/_run.py -> build/lib.linux-x86_64-3.6/pygit2\n", " copying pygit2/blame.py -> build/lib.linux-x86_64-3.6/pygit2\n", " copying pygit2/callbacks.py -> build/lib.linux-x86_64-3.6/pygit2\n", " copying pygit2/config.py -> build/lib.linux-x86_64-3.6/pygit2\n", " copying pygit2/credentials.py -> build/lib.linux-x86_64-3.6/pygit2\n", " copying pygit2/errors.py -> build/lib.linux-x86_64-3.6/pygit2\n", " copying pygit2/ffi.py -> build/lib.linux-x86_64-3.6/pygit2\n", " copying pygit2/index.py -> build/lib.linux-x86_64-3.6/pygit2\n", " copying pygit2/packbuilder.py -> build/lib.linux-x86_64-3.6/pygit2\n", " copying pygit2/refspec.py -> build/lib.linux-x86_64-3.6/pygit2\n", " copying pygit2/remote.py -> build/lib.linux-x86_64-3.6/pygit2\n", " copying pygit2/repository.py -> build/lib.linux-x86_64-3.6/pygit2\n", " copying pygit2/settings.py -> build/lib.linux-x86_64-3.6/pygit2\n", " copying pygit2/submodule.py -> build/lib.linux-x86_64-3.6/pygit2\n", " copying pygit2/utils.py -> build/lib.linux-x86_64-3.6/pygit2\n", " creating build/lib.linux-x86_64-3.6/pygit2/decl\n", " copying pygit2/decl/attr.h -> build/lib.linux-x86_64-3.6/pygit2/decl\n", " copying pygit2/decl/blame.h -> build/lib.linux-x86_64-3.6/pygit2/decl\n", " copying pygit2/decl/buffer.h -> build/lib.linux-x86_64-3.6/pygit2/decl\n", " copying pygit2/decl/callbacks.h -> build/lib.linux-x86_64-3.6/pygit2/decl\n", " copying pygit2/decl/checkout.h -> build/lib.linux-x86_64-3.6/pygit2/decl\n", " copying pygit2/decl/clone.h -> build/lib.linux-x86_64-3.6/pygit2/decl\n", " copying pygit2/decl/common.h -> build/lib.linux-x86_64-3.6/pygit2/decl\n", " copying pygit2/decl/config.h -> build/lib.linux-x86_64-3.6/pygit2/decl\n", " copying pygit2/decl/describe.h -> build/lib.linux-x86_64-3.6/pygit2/decl\n", " copying pygit2/decl/diff.h -> build/lib.linux-x86_64-3.6/pygit2/decl\n", " copying pygit2/decl/errors.h -> build/lib.linux-x86_64-3.6/pygit2/decl\n", " copying pygit2/decl/graph.h -> build/lib.linux-x86_64-3.6/pygit2/decl\n", " copying pygit2/decl/index.h -> build/lib.linux-x86_64-3.6/pygit2/decl\n", " copying pygit2/decl/indexer.h -> build/lib.linux-x86_64-3.6/pygit2/decl\n", " copying pygit2/decl/merge.h -> build/lib.linux-x86_64-3.6/pygit2/decl\n", " copying pygit2/decl/net.h -> build/lib.linux-x86_64-3.6/pygit2/decl\n", " copying pygit2/decl/oid.h -> build/lib.linux-x86_64-3.6/pygit2/decl\n", " copying pygit2/decl/pack.h -> build/lib.linux-x86_64-3.6/pygit2/decl\n", " copying pygit2/decl/proxy.h -> build/lib.linux-x86_64-3.6/pygit2/decl\n", " copying pygit2/decl/refspec.h -> build/lib.linux-x86_64-3.6/pygit2/decl\n", " copying pygit2/decl/remote.h -> build/lib.linux-x86_64-3.6/pygit2/decl\n", " copying pygit2/decl/repository.h -> build/lib.linux-x86_64-3.6/pygit2/decl\n", " copying pygit2/decl/revert.h -> build/lib.linux-x86_64-3.6/pygit2/decl\n", " copying pygit2/decl/stash.h -> build/lib.linux-x86_64-3.6/pygit2/decl\n", " copying pygit2/decl/strarray.h -> build/lib.linux-x86_64-3.6/pygit2/decl\n", " copying pygit2/decl/submodule.h -> build/lib.linux-x86_64-3.6/pygit2/decl\n", " copying pygit2/decl/transport.h -> build/lib.linux-x86_64-3.6/pygit2/decl\n", " copying pygit2/decl/types.h -> build/lib.linux-x86_64-3.6/pygit2/decl\n", " running build_ext\n", " generating cffi module 'build/temp.linux-x86_64-3.6/pygit2._libgit2.c'\n", " creating build/temp.linux-x86_64-3.6\n", " building 'pygit2._pygit2' extension\n", " creating build/temp.linux-x86_64-3.6/src\n", " 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\n", " In file included from src/blob.c:30:0:\n", " src/blob.h:33:10: fatal error: git2.h: No such file or directory\n", " #include \n", " ^~~~~~~~\n", " compilation terminated.\n", " error: command 'x86_64-linux-gnu-gcc' failed with exit status 1\n", " \n", " ----------------------------------------\n", "\u001b[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/\u001b[0m\n", "\u001b[?25h" ] } ], "source": [ "!pip3 install dvc" ] }, { "cell_type": "markdown", "id": "20975d62", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "Stwórzmy katalog, w którym będziemy przechowywać nasz projekt:" ] }, { "cell_type": "code", "execution_count": 12, "id": "aae59ec2", "metadata": { "slideshow": { "slide_type": "slide" } }, "outputs": [], "source": [ "!mkdir -p IUM_10/sample-ml-project" ] }, { "cell_type": "code", "execution_count": 2, "id": "1e522a93", "metadata": { "slideshow": { "slide_type": "slide" } }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "/home/tomek/AITech/repo/aitech-ium-private/IUM_10/sample-ml-project\n" ] } ], "source": [ "#Jupyter notebook magic https://ipython.readthedocs.io/en/stable/interactive/magics.html#magic-cd\n", "%cd \"IUM_10/sample-ml-project\"" ] }, { "cell_type": "markdown", "id": "199c0d92", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "Inicjalizujemy puste repozytorium Git (możemy też pominąć ten krok i działać w istniejącym już repozytorium)" ] }, { "cell_type": "code", "execution_count": 17, "id": "c13c525b", "metadata": { "slideshow": { "slide_type": "slide" } }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Initialized empty Git repository in /home/tomek/AITech/repo/aitech-ium-private/IUM_10/sample-ml-project/.git/\r\n" ] } ], "source": [ "!git init" ] }, { "cell_type": "markdown", "id": "c7155369", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "Teraz inicjalizujemy repozytorium DVC:" ] }, { "cell_type": "code", "execution_count": 18, "id": "44f28226", "metadata": { "slideshow": { "slide_type": "slide" } }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Initialized DVC repository.\n", "\n", "You can now commit the changes to git.\n", "\n", "\u001b[31m+---------------------------------------------------------------------+\n", "\u001b[0m\u001b[31m|\u001b[0m \u001b[31m|\u001b[0m\n", "\u001b[31m|\u001b[0m DVC has enabled anonymous aggregate usage analytics. \u001b[31m|\u001b[0m\n", "\u001b[31m|\u001b[0m Read the analytics documentation (and how to opt-out) here: \u001b[31m|\u001b[0m\n", "\u001b[31m|\u001b[0m <\u001b[36mhttps://dvc.org/doc/user-guide/analytics\u001b[39m> \u001b[31m|\u001b[0m\n", "\u001b[31m|\u001b[0m \u001b[31m|\u001b[0m\n", "\u001b[31m+---------------------------------------------------------------------+\n", "\u001b[0m\n", "\u001b[33mWhat's next?\u001b[39m\n", "\u001b[33m------------\u001b[39m\n", "- Check out the documentation: <\u001b[36mhttps://dvc.org/doc\u001b[39m>\n", "- Get help and share ideas: <\u001b[36mhttps://dvc.org/chat\u001b[39m>\n", "- Star us on GitHub: <\u001b[36mhttps://github.com/iterative/dvc\u001b[39m>\n", "\u001b[0m" ] } ], "source": [ "!dvc init" ] }, { "cell_type": "markdown", "id": "00bc72ed", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "Zobaczmy jakie pliki dodał (również do repozytorium git) DVC.\n", "Ich opis znajdziemy tutaj: https://dvc.org/doc/user-guide/project-structure/internal-files" ] }, { "cell_type": "code", "execution_count": 19, "id": "d1aefe16", "metadata": { "slideshow": { "slide_type": "slide" } }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "On branch master\r\n", "\r\n", "No commits yet\r\n", "\r\n", "Changes to be committed:\r\n", " (use \"git rm --cached ...\" to unstage)\r\n", "\t\u001b[32mnew file: .dvc/.gitignore\u001b[m\r\n", "\t\u001b[32mnew file: .dvc/config\u001b[m\r\n", "\t\u001b[32mnew file: .dvc/plots/confusion.json\u001b[m\r\n", "\t\u001b[32mnew file: .dvc/plots/confusion_normalized.json\u001b[m\r\n", "\t\u001b[32mnew file: .dvc/plots/default.json\u001b[m\r\n", "\t\u001b[32mnew file: .dvc/plots/linear.json\u001b[m\r\n", "\t\u001b[32mnew file: .dvc/plots/scatter.json\u001b[m\r\n", "\t\u001b[32mnew file: .dvc/plots/smooth.json\u001b[m\r\n", "\t\u001b[32mnew file: .dvcignore\u001b[m\r\n", "\r\n" ] } ], "source": [ "!git status" ] }, { "cell_type": "markdown", "id": "72e0a272", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "Możemy teraz zacommitować zmiany w git:" ] }, { "cell_type": "code", "execution_count": 5, "id": "59780e99", "metadata": { "slideshow": { "slide_type": "slide" } }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "On branch master\r\n", "nothing to commit, working tree clean\r\n" ] } ], "source": [ "!git commit -m \"Initial commit\"" ] }, { "cell_type": "markdown", "id": "dd8e529b", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "## Śledzenie plików za pomocą DVC\n", " - dużymi plikami, takimi jak plikami z danymi wejściowymi czy plikami modeli, trudno zarządza się za pomocą gita, ze względu na problemy z:\n", " - wydajnością\n", " - przestrzenią w repozytorium\n", " - ograniczenia ze strony serwisu (np. [limit 100 MB na plik w Github](https://docs.github.com/en/repositories/working-with-files/managing-large-files/about-large-files-on-github))\n", " - Git posiada rozszerzenie [lfs(Large File Storage)](https://git-lfs.github.com/), 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\n", " - DVC proponuje podobne podejście, ale:\n", " - pliki mogą być przechowywane na niemal dowolnym serwerze, również lokalnie\n", " - brak limitu wielkości plików (w Git-LFS na Github [limit 2GB](https://docs.github.com/en/repositories/working-with-files/managing-large-files/about-git-large-file-storage))\n", " - DVC zapewnia dodatkowe narzędzie umożliwiające śledzenie plików i ich powiązań z wynikami eksperymentów\n", " - więcej, patrz [tutaj](https://dvc.org/doc/user-guide/related-technologies)" ] }, { "cell_type": "markdown", "id": "a8861abe", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "Przygotujmy przykładowe dane, pobierając je z Kaggle:" ] }, { "cell_type": "code", "execution_count": 19, "id": "f05ece1b", "metadata": { "slideshow": { "slide_type": "slide" } }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Downloading iris.zip to /home/tomek/AITech/repo/aitech-ium-private/IUM_10/sample-ml-project\n", " 0%| | 0.00/3.60k [00:00...\" to include in what will be committed)\r\n", "\t\u001b[31mdata/.gitignore\u001b[m\r\n", "\t\u001b[31mdata/Iris.csv.dvc\u001b[m\r\n", "\t\u001b[31miris.zip\u001b[m\r\n", "\r\n", "nothing added to commit but untracked files present (use \"git add\" to track)\r\n" ] } ], "source": [ "!git status -u" ] }, { "cell_type": "markdown", "id": "8589fecf", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "Dodajmy pliki `data/Iris.csv.dvc data/.gitignore` do repozytorium git, zgodnie z sugestią DVC:" ] }, { "cell_type": "code", "execution_count": 21, "id": "460c4a17", "metadata": { "slideshow": { "slide_type": "slide" } }, "outputs": [], "source": [ "!git add data/Iris.csv.dvc data/.gitignore" ] }, { "cell_type": "code", "execution_count": 22, "id": "80644077", "metadata": { "slideshow": { "slide_type": "slide" } }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "[master cc0821a] Dodano dane IRIS (DVC)\r\n", " 2 files changed, 5 insertions(+)\r\n", " create mode 100644 data/.gitignore\r\n", " create mode 100644 data/Iris.csv.dvc\r\n" ] } ], "source": [ "!git commit -m \"Dodano dane IRIS (DVC)\"" ] }, { "cell_type": "markdown", "id": "03899863", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "Plik `*.dvc` zawiera m.in. hash pliku. Więcej o plikach `*.dvc`: [link](https://dvc.org/doc/user-guide/project-structure/dvc-files)" ] }, { "cell_type": "code", "execution_count": null, "id": "8cb2ba7c", "metadata": { "slideshow": { "slide_type": "slide" } }, "outputs": [], "source": [ "# %load data/Iris.csv.dvc\n", "outs:\n", "- md5: 717820ef0af287ff346c5cabfb4c612c\n", " size: 5107\n", " path: Iris.csv\n" ] }, { "cell_type": "markdown", "id": "0b421d45", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "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](https://dvc.org/doc/user-guide/large-dataset-optimization)." ] }, { "cell_type": "code", "execution_count": 27, "id": "1d471f3a", "metadata": { "slideshow": { "slide_type": "slide" } }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "total 8\r\n", "-r--r--r-- 1 tomek tomek 5107 wrz 19 2019 7820ef0af287ff346c5cabfb4c612c\r\n" ] } ], "source": [ "!ls -l .dvc/cache/71" ] }, { "cell_type": "code", "execution_count": 1, "id": "9666e0ae", "metadata": { "slideshow": { "slide_type": "slide" } }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "ls: cannot access './data': No such file or directory\r\n" ] } ], "source": [ "!ls -l ./data" ] }, { "cell_type": "markdown", "id": "901e8e90", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "## dvc remote\n", " - 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\n", " - służy do tego polecenie [`dvc remote add`](https://dvc.org/doc/command-reference/remote/add)\n", " - 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\n", " - w realnych zastosowaniach podalibyśmy tutaj ścieżkę do jakiegoś zasobu dostępnego przez inernet jak np. serwer SFTP, ścieżka do AWS S3 itp." ] }, { "cell_type": "markdown", "id": "5e47dbd3", "metadata": {}, "source": [ "Obsługiwane typy zdalnych lokalizacji (remotes): https://dvc.org/doc/command-reference/remote/add#supported-storage-types\n", " - Amazon S3\n", " - S3-compatible storage\n", " - Microsoft Azure Blob Storage\n", " - Google Drive\n", " - Google Cloud Storage\n", " - Aliyun OSS\n", " - SSH\n", " - HDFS\n", " - WebHDFS\n", " - HTTP\n", " - WebDAV\n", " - local remote" ] }, { "cell_type": "code", "execution_count": 28, "id": "731f6ea4", "metadata": { "slideshow": { "slide_type": "slide" } }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Setting 'my_local_remote' as a default remote.\r\n", "\u001b[0m" ] } ], "source": [ "!dvc remote add -d my_local_remote /dvcstore" ] }, { "cell_type": "code", "execution_count": 39, "id": "9c3deeaf", "metadata": { "slideshow": { "slide_type": "slide" } }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "On branch master\r\n", "Changes not staged for commit:\r\n", " (use \"git add ...\" to update what will be committed)\r\n", " (use \"git restore ...\" to discard changes in working directory)\r\n", "\t\u001b[31mmodified: .dvc/config\u001b[m\r\n", "\r\n", "no changes added to commit (use \"git add\" and/or \"git commit -a\")\r\n" ] } ], "source": [ "!git status" ] }, { "cell_type": "code", "execution_count": 41, "id": "899eac7d", "metadata": { "slideshow": { "slide_type": "slide" } }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "[master 3ff62b6] Added DVC remote\r\n", " 1 file changed, 4 insertions(+)\r\n" ] } ], "source": [ "!git add .dvc/config\n", "!git commit -m \"Added DVC remote\"" ] }, { "cell_type": "markdown", "id": "8c556c96", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "## dvc push\n", "Kiedy mamy już skonfigurowany \"remote\" możemy wypchnąć do niego pliki korzystając z polecenia `dvc push`:" ] }, { "cell_type": "code", "execution_count": null, "id": "c7f24f75", "metadata": { "slideshow": { "slide_type": "slide" } }, "outputs": [], "source": [ "!dvc push" ] }, { "cell_type": "code", "execution_count": 33, "id": "8a355575", "metadata": { "slideshow": { "slide_type": "slide" } }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\u001b[34;42m/dvcstore\u001b[00m\r\n", "└── \u001b[01;34m71\u001b[00m\r\n", " └── 7820ef0af287ff346c5cabfb4c612c\r\n", "\r\n", "1 directory, 1 file\r\n" ] } ], "source": [ "!tree /dvcstore" ] }, { "cell_type": "markdown", "id": "af59ecb3", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "## dvc pull\n", "Żeby pobrać dane z DVC (np. w innej lokalizacji, przez innego użytkownika), musimy:\n", " - sklonować repozytorium git (żeby m.in. pobrać pliki `*.dvc`\n", " - wykonać `dvc pull`" ] }, { "cell_type": "markdown", "id": "9fa914a7", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "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:" ] }, { "cell_type": "code", "execution_count": 37, "id": "dde39796", "metadata": { "slideshow": { "slide_type": "slide" } }, "outputs": [], "source": [ "!head -n -1 data/Iris.csv | sponge data/Iris.csv" ] }, { "cell_type": "code", "execution_count": 42, "id": "7f14ec60", "metadata": { "slideshow": { "slide_type": "slide" } }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "On branch master\r\n", "nothing to commit, working tree clean\r\n" ] } ], "source": [ "!git status" ] }, { "cell_type": "code", "execution_count": 43, "id": "8a841039", "metadata": { "slideshow": { "slide_type": "slide" } }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "data/Iris.csv.dvc: core\u001b[39m>\n", "\tchanged outs:\n", "\t\tmodified: data/Iris.csv\n", "\u001b[0m" ] } ], "source": [ "!dvc status" ] }, { "cell_type": "code", "execution_count": 44, "id": "bf6c1067", "metadata": { "slideshow": { "slide_type": "slide" } }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Adding... \n", "!\u001b[A\n", " 0%| |.TatTHknArFHCT9iDCtxHzh.tmp 0.00/5.07k [00:00 'data/data.xml'\n", " 0% Downloading| |0/1 [00:00 2021.5.30-ha878542_0\n", " certifi 2020.12.5-py39hf3d152e_1 --> 2021.5.30-py39hf3d152e_0\n", " dvc 2.1.0-py39hf3d152e_0 --> 2.3.0-py39hf3d152e_0\n", " fsspec 0.9.0-pyhd8ed1ab_2 --> 2021.5.0-pyhd8ed1ab_0\n", "\n", "\n", "\n", "Downloading and Extracting Packages\n", "certifi-2021.5.30 | 141 KB | ##################################### | 100% \n", "fsspec-2021.5.0 | 77 KB | ##################################### | 100% \n", "dvc-2.3.0 | 542 KB | ##################################### | 100% \n", "invoke-1.5.0 | 137 KB | ##################################### | 100% \n", "paramiko-2.7.2 | 135 KB | ##################################### | 100% \n", "bcrypt-3.2.0 | 44 KB | ##################################### | 100% \n", "pynacl-1.4.0 | 1.3 MB | ##################################### | 100% \n", "dvc-ssh-2.3.0 | 9 KB | ##################################### | 100% \n", "ca-certificates-2021 | 136 KB | ##################################### | 100% \n", "Preparing transaction: done\n", "Verifying transaction: done\n", "Executing transaction: done\n", "\n", "Note: you may need to restart the kernel to use updated packages.\n" ] } ], "source": [ "conda install -c conda-forge dvc-ssh" ] }, { "cell_type": "code", "execution_count": 27, "id": "e9a04876", "metadata": { "slideshow": { "slide_type": "slide" } }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Setting 'ium_ssh_remote' as a default remote.\n", "\u001b[0m" ] } ], "source": [ "!dvc remote add -f -d ium_ssh_remote ssh://ium-sftp@tzietkiewicz.vm.wmi.amu.edu.pl/ium-sftp" ] }, { "cell_type": "code", "execution_count": 28, "id": "e3f27bbb", "metadata": { "slideshow": { "slide_type": "slide" } }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "my_local_remote\t/dvcstore\n", "ium_ssh_remote\tssh://ium-sftp@tzietkiewicz.vm.wmi.amu.edu.pl/ium-sftp\n", "\u001b[0m" ] } ], "source": [ "!dvc remote list" ] }, { "cell_type": "code", "execution_count": 9, "id": "5b2fa175", "metadata": { "slideshow": { "slide_type": "slide" } }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "/bin/bash: dvc: command not found\r\n" ] } ], "source": [ "!dvc remote modify --local ium_ssh_remote password #[hasło takie jak do serwera MLflow ]" ] }, { "cell_type": "code", "execution_count": 30, "id": "ea6e16fa", "metadata": { "slideshow": { "slide_type": "slide" } }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " 0% Uploading| |0/1 [00:00