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‎book/061_dependencies.ipynb‎

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{
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"cells": [
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"id": "97a9ac71-a121-4b3e-bd73-a9721222d5ac",
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"metadata": {},
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"source": [
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"---\n",
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"title: Dependencies\n",
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"toc: true\n",
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"---"
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]
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},
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{
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"cell_type": "markdown",
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"id": "c79acc5e-0543-4994-b09a-1af21a509cd2",
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"metadata": {},
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"source": [
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"In contrast to our own code that we can import or to some built-in modules such as `pathlib` that we can import directly after installing python, there are third-party libraries that we want to use but need to be first installed, such as `numpy` and `pandas`.\n",
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"This libraries are also called \"packages\".\n",
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"\n",
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"There are several repositories (also called \"indexes\") where people publish python packages and from which we can download them. The official one is [PyPI](https://pypi.org) (Python Package Index).\n",
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"\n",
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"These are open-source libraries maintained mostly by voluntary contributions of people of the community – and you can also contribute to them!\n",
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"\n",
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"These packages are being actively developed and thus in permanent evolution.\n",
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"In order to avoid compatibility problems and to ensure reproducibility, we might want to specify the exact versions of the packages we use.\n",
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"It turns out that is not an easy problem and the reason why need a **package manager**.\n",
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"\n",
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"The good news is that `uv` does that for us too."
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]
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},
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{
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"cell_type": "markdown",
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"id": "127f7c9d-dccd-48bd-bc99-e1e7de44cb6c",
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"metadata": {},
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"source": [
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"## Managing dependencies"
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]
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},
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{
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"cell_type": "markdown",
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"id": "2dce4970-2fa6-43ea-958b-1ae6a379dc94",
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"metadata": {},
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"source": [
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"The standard to specify dependencies (and other things) in python projects is to use a file called [`pyproject.toml`](https://packaging.python.org/en/latest/guides/writing-pyproject-toml/) that looks like this:\n",
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"\n",
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"```yaml\n",
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"[project]\n",
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"name = \"example_package_name\"\n",
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"version = \"0.0.1\"\n",
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"authors = [\n",
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" { name=\"Example Author\", email=\"author@example.com\" },\n",
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"]\n",
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"description = \"A small example package\"\n",
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"readme = \"README.md\"\n",
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"requires-python = \">=3.10,<3.12\"\n",
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"dependencies = [\n",
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" \"numpy==1.2.0\",\n",
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" \"pandas<2.0.0\",\n",
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" \"scikit-learn>=1.0,<2.0\"\n",
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"]\n",
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"```\n",
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"\n",
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"::: {.callout-note}\n",
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"Take a look at the `pyproject.toml` file in you project, we already have one that `uv` automatically created for us!\n",
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":::\n",
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"\n",
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"The \"dependencies\" section is the one we care about here.\n",
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"There we list all the third-party libraries that our project requires.\n",
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"Notice that we can specify both exact versions (with \"==\") as well as constraints (with \"<,>,>=,<=\").\n",
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"\n",
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"In general we don't want to deal manually with those aspects – that's the job of a package manager."
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]
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},
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{
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"cell_type": "markdown",
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"id": "00421264-b754-49af-a789-dcdf3ebe6325",
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"metadata": {},
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"source": [
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"::: {.callout-note}\n",
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"The packages usually follow a so-called \"Semantic versioning\" convention on how to name the versions of the package to avoid compatibility problems.\n",
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"In short: Given a version number MAJOR.MINOR.PATCH.\n",
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"\n",
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"> MAJOR version when you make incompatible API changes \n",
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"MINOR version when you add functionality in a backward compatible manner \n",
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"PATCH version when you make backward compatible bug fixes \n",
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"\n",
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"Read more about that [here](https://semver.org).\n",
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":::"
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]
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},
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{
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"cell_type": "markdown",
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"id": "f9e9ab15-34ff-4b43-bf21-b865aaa660ac",
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"metadata": {},
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"source": [
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"We will use here the package manager [uv](https://docs.astral.sh/uv).\n",
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"You can read the docs for more details, which I strongly recommend since the documentation is pretty good and constantly being updated.\n",
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"To add a dependency we type:\n",
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"\n",
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"```bash\n",
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"uv add PACKAGE-NAME\n",
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"```\n",
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"For example:\n",
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"```bash\n",
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"uv add numpy\n",
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"```\n",
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"\n",
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"That will add the dependency to our list as well as updating the \"lock\" file.\n",
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"Read more about this workflow and managing dependencies [here](https://docs.astral.sh/uv/guides/projects/#working-on-projects).\n",
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"\n",
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"The point is that after installing the dependency we can just import it like any other module.\n",
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"\n",
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"To remove a package from the dependencies of our project we do:\n",
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"```bash\n",
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"uv remove PACKAGE-NAME\n",
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"```\n",
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"For example:\n",
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"```bash\n",
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"uv remove numpy\n",
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"```"
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]
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},
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{
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"kernelspec": {
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"display_name": "Python 3 (ipykernel)",
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"language": "python",
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"metadata": {},
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"---\n",
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"title: Dependencies\n",
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"toc: true\n",
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"output-file: dependencies.html\n",
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"---"
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]
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},
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{
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"id": "c79acc5e-0543-4994-b09a-1af21a509cd2",
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"metadata": {},
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"source": [
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"In contrast to our own code that we can import or to some built-in modules such as `pathlib` that we can import directly after installing python, there are third-party libraries that we want to use but need to be first installed, such as `numpy` and `pandas`.\n",
21+
"This libraries are also called \"packages\".\n",
22+
"\n",
23+
"There are several repositories (also called \"indexes\") where people publish python packages and from which we can download them. The official one is [PyPI](https://pypi.org) (Python Package Index).\n",
24+
"\n",
25+
"These are open-source libraries maintained mostly by voluntary contributions of people of the community – and you can also contribute to them!\n",
26+
"\n",
27+
"These packages are being actively developed and thus in permanent evolution.\n",
28+
"In order to avoid compatibility problems and to ensure reproducibility, we might want to specify the exact versions of the packages we use.\n",
29+
"It turns out that is not an easy problem and the reason why need a **package manager**.\n",
30+
"\n",
31+
"The good news is that `uv` does that for us too."
32+
]
33+
},
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{
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"cell_type": "markdown",
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"id": "127f7c9d-dccd-48bd-bc99-e1e7de44cb6c",
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"metadata": {},
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"source": [
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"## Managing dependencies"
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]
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},
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{
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"cell_type": "markdown",
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"id": "2dce4970-2fa6-43ea-958b-1ae6a379dc94",
45+
"metadata": {},
46+
"source": [
47+
"The standard to specify dependencies (and other things) in python projects is to use a file called [`pyproject.toml`](https://packaging.python.org/en/latest/guides/writing-pyproject-toml/) that looks like this:\n",
48+
"\n",
49+
"```yaml\n",
50+
"[project]\n",
51+
"name = \"example_package_name\"\n",
52+
"version = \"0.0.1\"\n",
53+
"authors = [\n",
54+
" { name=\"Example Author\", email=\"author@example.com\" },\n",
55+
"]\n",
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"description = \"A small example package\"\n",
57+
"readme = \"README.md\"\n",
58+
"requires-python = \">=3.10,<3.12\"\n",
59+
"dependencies = [\n",
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" \"numpy==1.2.0\",\n",
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" \"pandas<2.0.0\",\n",
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" \"scikit-learn>=1.0,<2.0\"\n",
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"]\n",
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"```\n",
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"\n",
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"::: {.callout-note}\n",
67+
"Take a look at the `pyproject.toml` file in you project, we already have one that `uv` automatically created for us!\n",
68+
":::\n",
69+
"\n",
70+
"The \"dependencies\" section is the one we care about here.\n",
71+
"There we list all the third-party libraries that our project requires.\n",
72+
"Notice that we can specify both exact versions (with \"==\") as well as constraints (with \"<,>,>=,<=\").\n",
73+
"\n",
74+
"In general we don't want to deal manually with those aspects – that's the job of a package manager."
75+
]
76+
},
77+
{
78+
"cell_type": "markdown",
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"id": "00421264-b754-49af-a789-dcdf3ebe6325",
80+
"metadata": {},
81+
"source": [
82+
"::: {.callout-note}\n",
83+
"The packages usually follow a so-called \"Semantic versioning\" convention on how to name the versions of the package to avoid compatibility problems.\n",
84+
"In short: Given a version number MAJOR.MINOR.PATCH.\n",
85+
"\n",
86+
"> MAJOR version when you make incompatible API changes \n",
87+
"MINOR version when you add functionality in a backward compatible manner \n",
88+
"PATCH version when you make backward compatible bug fixes \n",
89+
"\n",
90+
"Read more about that [here](https://semver.org).\n",
91+
":::"
92+
]
93+
},
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{
95+
"cell_type": "markdown",
96+
"id": "f9e9ab15-34ff-4b43-bf21-b865aaa660ac",
97+
"metadata": {},
98+
"source": [
99+
"We will use here the package manager [uv](https://docs.astral.sh/uv).\n",
100+
"You can read the docs for more details, which I strongly recommend since the documentation is pretty good and constantly being updated.\n",
101+
"To add a dependency we type:\n",
102+
"\n",
103+
"```bash\n",
104+
"uv add PACKAGE-NAME\n",
105+
"```\n",
106+
"For example:\n",
107+
"```bash\n",
108+
"uv add numpy\n",
109+
"```\n",
110+
"\n",
111+
"That will add the dependency to our list as well as updating the \"lock\" file.\n",
112+
"Read more about this workflow and managing dependencies [here](https://docs.astral.sh/uv/guides/projects/#working-on-projects).\n",
113+
"\n",
114+
"The point is that after installing the dependency we can just import it like any other module.\n",
115+
"\n",
116+
"To remove a package from the dependencies of our project we do:\n",
117+
"```bash\n",
118+
"uv remove PACKAGE-NAME\n",
119+
"```\n",
120+
"For example:\n",
121+
"```bash\n",
122+
"uv remove numpy\n",
123+
"```"
124+
]
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},
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{
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"cell_type": "markdown",
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"id": "64fc1a40-04fe-40da-8875-04e4aa5d4d46",
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}

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