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aitech-ium/IUM_10.DVC.ipynb
Tomasz Ziętkiewicz 67e14528bb Zmiana punktów
2022-05-23 10:01:41 +02:00

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{
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"source": [
"![Logo 1](https://git.wmi.amu.edu.pl/AITech/Szablon/raw/branch/master/Logotyp_AITech1.jpg)\n",
"<div class=\"alert alert-block alert-info\">\n",
"<h1> Inżynieria uczenia maszynowego </h1>\n",
"<h2> 10. <i>DVC</i> [laboratoria]</h2> \n",
"<h3> Tomasz Ziętkiewicz (2022)</h3>\n",
"</div>\n",
"\n",
"![Logo 2](https://git.wmi.amu.edu.pl/AITech/Szablon/raw/branch/master/Logotyp_AITech2.jpg)"
]
},
{
"cell_type": "markdown",
"id": "0c6f27a5",
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"source": [
"<img src=\"img/expcontrol/dvc-logo.png\">"
]
},
{
"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"
]
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{
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"source": [
"## Instalacja i inicjalizacja\n",
" - https://dvc.org/doc/install\n",
" - ```pip(x) install dvc``` albo:\n",
" - ```conda install dvc```"
]
},
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"Collecting urllib3>=1.24.1 (from dulwich>=0.20.23->dvc)\n",
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"Collecting mailchecker<5.0.0,>=4.1.0 (from python-benedict>=0.24.2->dvc)\n",
" Downloading https://files.pythonhosted.org/packages/1a/11/49e85a526dd3f2cb6bdf1dc519d64395bd56a88d9b2a5f6f3acd1f8c3f51/mailchecker-4.1.17.tar.gz (232kB)\n",
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"\u001b[?25hCollecting xmltodict<1.0.0,>=0.12.0 (from python-benedict>=0.24.2->dvc)\n",
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"Collecting phonenumbers<9.0.0,>=8.12.0 (from python-benedict>=0.24.2->dvc)\n",
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"\u001b[?25hCollecting ftfy<7.0.0,>=6.0.0 (from python-benedict>=0.24.2->dvc)\n",
" Downloading https://files.pythonhosted.org/packages/af/da/d215a091986e5f01b80f5145cff6f22e2dc57c6b048aab2e882a07018473/ftfy-6.0.3.tar.gz (64kB)\n"
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" Using cached https://files.pythonhosted.org/packages/36/7a/87837f39d0296e723bb9b62bbb257d0355c7f6128853c78955f57342a56d/python_dateutil-2.8.2-py2.py3-none-any.whl\n",
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"\u001b[?25hCollecting cffi>=1.4.0 (from pygit2<1.7,>=1.5.0; python_version < \"3.7\"->dvc)\n",
" Using cached https://files.pythonhosted.org/packages/49/7b/449daf9cacfd7355cea1b4106d2be614315c29ac16567e01756167f6daab/cffi-1.15.0-cp36-cp36m-manylinux_2_5_x86_64.manylinux1_x86_64.whl\n",
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" Downloading https://files.pythonhosted.org/packages/48/19/f2090f7dad41e225c7f2326e4cfe6fff49e57dedb5b53636c9551f86b069/cached_property-1.5.2-py2.py3-none-any.whl\n",
"Collecting immutables>=0.9 (from contextvars>=2.1; python_version < \"3.7\"->dvc)\n",
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"Collecting idna<4,>=2.5; python_version >= \"3\" (from requests>=2.22.0->dvc)\n",
" Downloading https://files.pythonhosted.org/packages/04/a2/d918dcd22354d8958fe113e1a3630137e0fc8b44859ade3063982eacd2a4/idna-3.3-py3-none-any.whl (61kB)\n",
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"Collecting yarl<2.0,>=1.0 (from aiohttp; extra == \"http\"->fsspec[http]>=2021.10.0->dvc)\n",
" Downloading https://files.pythonhosted.org/packages/fa/cb/8791922f5ec97b9ebec516d062c0e113da963568ffe2c7c04d8187ab7cc3/yarl-1.7.2-cp36-cp36m-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.whl (270kB)\n",
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"\u001b[?25hCollecting idna-ssl>=1.0; python_version < \"3.7\" (from aiohttp; extra == \"http\"->fsspec[http]>=2021.10.0->dvc)\n",
" Downloading https://files.pythonhosted.org/packages/46/03/07c4894aae38b0de52b52586b24bf189bb83e4ddabfe2e2c8f2419eec6f4/idna-ssl-1.1.0.tar.gz\n",
"Collecting frozenlist>=1.1.1 (from aiohttp; extra == \"http\"->fsspec[http]>=2021.10.0->dvc)\n",
" 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)\n",
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"\u001b[?25hCollecting async-timeout<5.0,>=4.0.0a3 (from aiohttp; extra == \"http\"->fsspec[http]>=2021.10.0->dvc)\n",
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"Collecting aiosignal>=1.1.2 (from aiohttp; extra == \"http\"->fsspec[http]>=2021.10.0->dvc)\n",
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"Collecting attrs>=17.3.0 (from aiohttp; extra == \"http\"->fsspec[http]>=2021.10.0->dvc)\n",
" Using cached https://files.pythonhosted.org/packages/be/be/7abce643bfdf8ca01c48afa2ddf8308c2308b0c3b239a44e57d020afa0ef/attrs-21.4.0-py2.py3-none-any.whl\n",
"Collecting multidict<7.0,>=4.5 (from aiohttp; extra == \"http\"->fsspec[http]>=2021.10.0->dvc)\n",
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"\u001b[?25hCollecting smmap<6,>=3.0.1 (from gitdb<5,>=4.0.1->gitpython>3->dvc)\n",
" Using cached https://files.pythonhosted.org/packages/6d/01/7caa71608bc29952ae09b0be63a539e50d2484bc37747797a66a60679856/smmap-5.0.0-py3-none-any.whl\n",
"Collecting text-unidecode>=1.3 (from python-slugify<7.0.0,>=6.0.1->python-benedict>=0.24.2->dvc)\n",
" Downloading https://files.pythonhosted.org/packages/a6/a5/c0b6468d3824fe3fde30dbb5e1f687b291608f9473681bbf7dabbf5a87d7/text_unidecode-1.3-py2.py3-none-any.whl (78kB)\n",
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"\u001b[?25hCollecting wcwidth (from ftfy<7.0.0,>=6.0.0->python-benedict>=0.24.2->dvc)\n",
" Using cached https://files.pythonhosted.org/packages/59/7c/e39aca596badaf1b78e8f547c807b04dae603a433d3e7a7e04d67f2ef3e5/wcwidth-0.2.5-py2.py3-none-any.whl\n",
"Collecting pycparser (from cffi>=1.4.0->pygit2<1.7,>=1.5.0; python_version < \"3.7\"->dvc)\n",
" Using cached https://files.pythonhosted.org/packages/62/d5/5f610ebe421e85889f2e55e33b7f9a6795bd982198517d912eb1c76e1a53/pycparser-2.21-py2.py3-none-any.whl\n",
"Building wheels for collected packages: nanotime, flufl.lock, psutil, configobj, pygtrie, dulwich, pygit2, contextvars, atpublic, mailchecker, ftfy, future, idna-ssl\n",
" Running setup.py bdist_wheel for nanotime ... \u001b[?25ldone\n",
"\u001b[?25h Stored in directory: /home/tomek/.cache/pip/wheels/41/99/17/7135f635215e1f61e906295afd11f4f791cfe4ab45f3bfdca2\n",
" Running setup.py bdist_wheel for flufl.lock ... \u001b[?25ldone\n",
"\u001b[?25h Stored in directory: /home/tomek/.cache/pip/wheels/4f/51/d7/f65a7b7f37da7594f7021b122fe677187667ad21f1171d2514\n",
" Running setup.py bdist_wheel for psutil ... \u001b[?25ldone\n",
"\u001b[?25h Stored in directory: /home/tomek/.cache/pip/wheels/6e/94/8f/ef906811f8dcf6824a9747df0381615be48d723073fb59a317\n",
" Running setup.py bdist_wheel for configobj ... \u001b[?25ldone\n",
"\u001b[?25h Stored in directory: /home/tomek/.cache/pip/wheels/f1/e4/16/4981ca97c2d65106b49861e0b35e2660695be7219a2d351ee0\n",
" Running setup.py bdist_wheel for pygtrie ... \u001b[?25ldone\n",
"\u001b[?25h Stored in directory: /home/tomek/.cache/pip/wheels/db/57/91/73782136379fe419036c5ec0e4070d8b3a35f2a36bd6a94ed8\n",
" Running setup.py bdist_wheel for dulwich ... \u001b[?25ldone\n",
"\u001b[?25h Stored in directory: /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 <git2.h>\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 <git2.h>\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 <file>...\" 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<?, ?B/s]\n",
"100%|██████████████████████████████████████| 3.60k/3.60k [00:00<00:00, 2.63MB/s]\n",
"Archive: iris.zip\n",
" inflating: Iris.csv \n",
" inflating: database.sqlite \n"
]
}
],
"source": [
"!kaggle datasets download -d uciml/iris\n",
"!unzip -o iris.zip\n",
"!rm database.sqlite iris.zip\n",
"!mkdir -p data\n",
"!mv Iris.csv data/"
]
},
{
"cell_type": "markdown",
"id": "adb9a522",
"metadata": {
"slideshow": {
"slide_type": "slide"
}
},
"source": [
"Teraz dodamy plik(i) z danymi do DVC:"
]
},
{
"cell_type": "code",
"execution_count": 14,
"id": "74d182c7",
"metadata": {
"slideshow": {
"slide_type": "slide"
}
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Adding... \n",
"!\u001b[A\n",
" 0%| |.E8dZEGBYoRayYsJLdesNS4.tmp 0.00/5.11k [00:00<?, ?it/s]\u001b[A\n",
"100% Add|██████████████████████████████████████████████|1/1 [00:04, 4.71s/file]\u001b[A\n",
"\n",
"To track the changes with git, run:\n",
"\n",
"\tgit add data/Iris.csv.dvc data/.gitignore\n",
"\u001b[0m"
]
}
],
"source": [
"!dvc add data/Iris.csv"
]
},
{
"cell_type": "markdown",
"id": "72c6b5d0",
"metadata": {
"slideshow": {
"slide_type": "slide"
}
},
"source": [
" - DVC utworzył plik `data/Iris.csv.dvc` i dadał oryginalny plik do `.gitignore`\n",
" - W repozytorium będzie obecny tylko plik `*.dvc`, zawierający odnośnik do prawdziwego pliku"
]
},
{
"cell_type": "code",
"execution_count": 16,
"id": "74d54652",
"metadata": {
"slideshow": {
"slide_type": "slide"
}
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"On branch master\r\n",
"Untracked files:\r\n",
" (use \"git add <file>...\" 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 <file>...\" to update what will be committed)\r\n",
" (use \"git restore <file>...\" 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<?, ?it/s]\u001b[A\n",
"100% Add|██████████████████████████████████████████████|1/1 [00:00, 2.68file/s]\u001b[A\n",
"\n",
"To track the changes with git, run:\n",
"\n",
"\tgit add data/Iris.csv.dvc\n",
"\u001b[0m"
]
}
],
"source": [
"!dvc add data/Iris.csv"
]
},
{
"cell_type": "code",
"execution_count": 46,
"id": "4a4865c9",
"metadata": {
"slideshow": {
"slide_type": "slide"
}
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"[master e38c244] Removed last line from Iris dataset\r\n",
" 1 file changed, 2 insertions(+), 2 deletions(-)\r\n"
]
}
],
"source": [
"!git add data/Iris.csv.dvc\n",
"!git commit -m \"Removed last line from Iris dataset\"\n"
]
},
{
"cell_type": "markdown",
"id": "d710977c",
"metadata": {
"slideshow": {
"slide_type": "slide"
}
},
"source": [
"### dvc checkout\n",
" - Polecenia `dvc checkout` używamy razem z `git checkout`, żeby zmienić branch, na którym pracujemy.\n",
" - DVC podmieni wersje plików śledzonych przez siebie na pochodzące z innego brancha (o ile pliki te się różnią i różnią się pliki `*.dvc` w odpowiednich branchach\n",
" - zmiana brancha przez git powoduje (ewentualną) zmianę plików `*.dvc` a `dvc checkout` kopiuje/linkuje pliki z katalogu `.dvc/cache` o wartościach hash odpowiadających tym z plików `*.dvc`"
]
},
{
"cell_type": "markdown",
"id": "5897e8eb",
"metadata": {
"slideshow": {
"slide_type": "slide"
}
},
"source": [
"## Wymiana danych między projektami\n",
" - za pomocą poleceń `dvc import` i `dvc update` możemy dodać i później aktualizować pliki śledzone przez DVC w innym repozytorium"
]
},
{
"cell_type": "code",
"execution_count": 48,
"id": "9b018146",
"metadata": {
"slideshow": {
"slide_type": "slide"
}
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Importing 'get-started/data.xml (https://github.com/iterative/dataset-registry)' -> 'data/data.xml'\n",
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" 60%|██████ |get-started/data.xml 21.8M/36.1M [00:13<00:02, 5.66MB/s]\u001b[A\n",
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" 93%|█████████▎|get-started/data.xml 33.5M/36.1M [00:17<00:00, 2.87MB/s]\u001b[A\n",
" 94%|█████████▎|get-started/data.xml 33.8M/36.1M [00:17<00:00, 2.87MB/s]\u001b[A\n",
" 94%|█████████▍|get-started/data.xml 34.1M/36.1M [00:17<00:00, 2.87MB/s]\u001b[A\n",
" 95%|█████████▌|get-started/data.xml 34.4M/36.1M [00:17<00:00, 2.87MB/s]\u001b[A\n",
" 96%|█████████▌|get-started/data.xml 34.8M/36.1M [00:17<00:00, 2.87MB/s]\u001b[A\n",
" 97%|█████████▋|get-started/data.xml 35.1M/36.1M [00:17<00:00, 2.87MB/s]\u001b[A\n",
" 98%|█████████▊|get-started/data.xml 35.4M/36.1M [00:18<00:00, 2.87MB/s]\u001b[A\n",
" 99%|█████████▉|get-started/data.xml 35.7M/36.1M [00:18<00:00, 2.88MB/s]\u001b[A\n",
"100%|█████████▉|get-started/data.xml 36.0M/36.1M [00:18<00:00, 2.87MB/s]\u001b[A\n",
" \u001b[A\n",
"To track the changes with git, run:\n",
"\n",
"\tgit add data/.gitignore data/data.xml.dvc\n",
"\u001b[0m"
]
}
],
"source": [
"!dvc import https://github.com/iterative/dataset-registry \\\n",
" get-started/data.xml -o data/data.xml"
]
},
{
"cell_type": "code",
"execution_count": 49,
"id": "be2c1a37",
"metadata": {
"slideshow": {
"slide_type": "slide"
}
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Data and pipelines are up to date. \n",
"\u001b[0m"
]
}
],
"source": [
"!dvc status"
]
},
{
"cell_type": "code",
"execution_count": 50,
"id": "3306c5b7",
"metadata": {
"slideshow": {
"slide_type": "slide"
}
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"total 37020\r\n",
"-rw-rw-r-- 1 tomek tomek 37891850 maj 31 11:10 data.xml\r\n",
"-rw-rw-r-- 1 tomek tomek 284 maj 31 11:10 data.xml.dvc\r\n",
"-rw-rw-r-- 1 tomek tomek 5072 maj 31 11:01 Iris.csv\r\n",
"-rw-rw-r-- 1 tomek tomek 76 maj 31 11:01 Iris.csv.dvc\r\n"
]
}
],
"source": [
"ls -l data"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "b73c56ea",
"metadata": {
"slideshow": {
"slide_type": "slide"
}
},
"outputs": [],
"source": [
"# %load data/data.xml.dvc\n",
"md5: a7cd139231cc35ed63541ce3829b96db\n",
"frozen: true\n",
"deps:\n",
"- path: get-started/data.xml\n",
" repo:\n",
" url: https://github.com/iterative/dataset-registry\n",
" rev_lock: ba014f40e29670421a67cb1c47543f402348aa13\n",
"outs:\n",
"- md5: a304afb96060aad90176268345e10355\n",
" size: 37891850\n",
" path: data.xml\n"
]
},
{
"cell_type": "markdown",
"id": "db1063ac",
"metadata": {
"slideshow": {
"slide_type": "slide"
}
},
"source": [
"## DVC pipelines\n",
" - wprowadzenie: https://youtu.be/71IGzyH95UY\n",
" - Getting started: https://dvc.org/doc/start/data-pipelines\n",
" - dvc pipelines pozwala nam zbudować (za pomocą polecenie `dvc run`) lub zdefiniować (edytując plik `dvc.yaml`) graf zależności między krokami wykonywanymi w naszym projekcie (takimi jak \"przygotowanie danych\", \"trenowanie\", \"ewaluacja\")\n",
" - tak zdefiniowany pipeline można potem uruchomić za pomocą polecenia `dvc reproduce`"
]
},
{
"cell_type": "markdown",
"id": "e2939867",
"metadata": {
"slideshow": {
"slide_type": "slide"
}
},
"source": [
"## Zadania [15pkt]\n",
"1. Zainicjalizuj repozytorium DVC wewnątrz Twojego repozytorium z projektem [1pkt]\n",
"2. Dodaj plik(i) z danymi w Twoim projekcie do DVC [1pkt]\n",
"3. Skonfiguruj remote (dane do konfiguracji podane poniżej) [3pkt]\n",
"4. Stwórz/zdefiniuj i dodaj do repozytorium plik `dvc.yaml` opisujący kroki wykonywane w Twoim projekcie. Wydziel przynajmniej 2 kroki (np. przygotowanie danych/trenowanie) powiązane ze sobą za pomocą zależności (skorzystaj z \n",
"materiałów \"Getting started\", link powyżej) [6pkt]\n",
"5. Stwórz projekt na Jenkinsie (`s1233456-dvc`), w którym sklonujesz repozytorium, ściągniesz pliki dvc (za pomocą `dvc pull`) i uruchomisz pipeline (za pomocą `dvc reproduce`) [4pkt]"
]
},
{
"cell_type": "markdown",
"id": "2f5a8590",
"metadata": {
"slideshow": {
"slide_type": "slide"
}
},
"source": [
"## SSH remote\n",
"Jednym z remote obsługiwanych przez DVC jest SFTP/SSH.\n",
"W celu jego wykorzystania na serwerze tzietkiewicz.vm.wmi.amu.edu.pl utworzony został użytkownik `ium-sftp` i skonfigurowany serwer SFTP.\n",
"Został też dla niego wygenerowany klucz ssh, który został dodany jako \"Jenkins credential\" (patrz opis konfiguracji na Jenkins poniżej)"
]
},
{
"cell_type": "markdown",
"id": "82a61107",
"metadata": {
"slideshow": {
"slide_type": "slide"
}
},
"source": [
"### Lokalnie\n",
"Będziemy potrzebować zależności :\n",
" \n",
" `conda install dvc-ssh` \n",
"\n",
"albo\n",
"\n",
"`pip install dvc[ssh] paramiko`"
]
},
{
"cell_type": "code",
"execution_count": 15,
"id": "c48c5b8e",
"metadata": {
"slideshow": {
"slide_type": "slide"
}
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Collecting package metadata (current_repodata.json): done\n",
"Solving environment: done\n",
"\n",
"## Package Plan ##\n",
"\n",
" environment location: /home/tomek/miniconda3\n",
"\n",
" added / updated specs:\n",
" - dvc-ssh\n",
"\n",
"\n",
"The following packages will be downloaded:\n",
"\n",
" package | build\n",
" ---------------------------|-----------------\n",
" bcrypt-3.2.0 | py39h3811e60_1 44 KB conda-forge\n",
" ca-certificates-2021.5.30 | ha878542_0 136 KB conda-forge\n",
" certifi-2021.5.30 | py39hf3d152e_0 141 KB conda-forge\n",
" dvc-2.3.0 | py39hf3d152e_0 542 KB conda-forge\n",
" dvc-ssh-2.3.0 | py39hf3d152e_0 9 KB conda-forge\n",
" fsspec-2021.5.0 | pyhd8ed1ab_0 77 KB conda-forge\n",
" invoke-1.5.0 | pyhd3deb0d_0 137 KB conda-forge\n",
" paramiko-2.7.2 | pyh9f0ad1d_0 135 KB conda-forge\n",
" pynacl-1.4.0 | py39h3811e60_2 1.3 MB conda-forge\n",
" ------------------------------------------------------------\n",
" Total: 2.5 MB\n",
"\n",
"The following NEW packages will be INSTALLED:\n",
"\n",
" bcrypt conda-forge/linux-64::bcrypt-3.2.0-py39h3811e60_1\n",
" dvc-ssh conda-forge/linux-64::dvc-ssh-2.3.0-py39hf3d152e_0\n",
" invoke conda-forge/noarch::invoke-1.5.0-pyhd3deb0d_0\n",
" paramiko conda-forge/noarch::paramiko-2.7.2-pyh9f0ad1d_0\n",
" pynacl conda-forge/linux-64::pynacl-1.4.0-py39h3811e60_2\n",
"\n",
"The following packages will be UPDATED:\n",
"\n",
" ca-certificates 2020.12.5-ha878542_0 --> 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<?, ?file/s]\n",
"!\u001b[A\n",
" 0%| |data/Iris.csv 0.00/4.95k [00:00<?, ?B/s]\u001b[A\n",
"1 file pushed \u001b[A\n",
"\u001b[0m"
]
}
],
"source": [
"!dvc push"
]
},
{
"cell_type": "markdown",
"id": "1468c44c",
"metadata": {
"slideshow": {
"slide_type": "slide"
}
},
"source": [
"### Jenkins\n",
"\n",
"W Jenkins można użyć mechanizmu \"Credentials\", żeby w bezpieczny sposób przekazać hasło albo klucz prywatny.\n",
"\n",
"Takie dane dla użytkownika ium-sftp zostały stworzone na Jenkinsie:\n",
"\n",
" - typu ssh key: https://tzietkiewicz.vm.wmi.amu.edu.pl:8080/credentials/store/system/domain/_/credential/48ac7004-216e-4260-abba-1fe5db753e18/\n",
" - typu \"secret text\" - zawierający hasło użytkownika ium-shftp: https://tzietkiewicz.vm.wmi.amu.edu.pl:8080/credentials/store/system/domain/_/credential/ium-sftp-password/\n",
"\n",
"Opis używania \"Credentials\" w Jenkinsfile: https://www.jenkins.io/doc/book/pipeline/jenkinsfile/#for-other-credential-types\n",
"\n",
"Klucza ssh można użyć tak: \n",
"\n",
"```Jenkinsfile\n",
"withCredentials(\n",
" [sshUserPrivateKey(credentialsId: '48ac7004-216e-4260-abba-1fe5db753e18', keyFileVariable: 'IUM_SFTP_KEY', passphraseVariable: '', usernameVariable: '')]) {\n",
" sh 'dvc remote add -d ium_ssh_remote ssh://ium-sftp@tzietkiewicz.vm.wmi.amu.edu.pl/ium-sftp'\n",
" sh 'dvc remote modify --local ium_ssh_remote keyfile $IUM_SFTP_KEY'\n",
" sh 'dvc pull'}\n",
"```\n",
"\n",
"Secret text tak:\n",
"\n",
"```Jenkinsfile\n",
" withCredentials([string(credentialsId: 'ium-sftp-password', variable: 'IUM_SFTP_PASS')]) {\n",
" sh 'dvc remote add -d ium_ssh_remote ssh://ium-sftp@tzietkiewicz.vm.wmi.amu.edu.pl/ium-sftp'\n",
" sh 'dvc remote modify --local ium_ssh_remote password $IUM_SFTP_KEY'\n",
" sh 'dvc pull'\n",
" }\n",
"```\n",
"\n",
"Przykład kongiguracji: \n",
" - https://tzietkiewicz.vm.wmi.amu.edu.pl:8080/job/docker-test-mount/ \n",
" - https://git.wmi.amu.edu.pl/tzietkiewicz/ium-helloworld"
]
}
],
"metadata": {
"author": "Tomasz Ziętkiewicz",
"celltoolbar": "Slideshow",
"email": "tomasz.zietkiewicz@amu.edu.pl",
"kernelspec": {
"display_name": "Python 3",
"language": "python",
"name": "python3"
},
"lang": "pl",
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.6.9"
},
"slideshow": {
"slide_type": "slide"
},
"subtitle": "10.DVC[laboratoria]",
"title": "Inżynieria uczenia maszynowego",
"year": "2021"
},
"nbformat": 4,
"nbformat_minor": 5
}
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