Switch from pipenv to uv

* Remove pipenv * Add pre-commit-uv * Add CI/CD-Pipelines * Add dependency bot * Update security
cusyio · Oct 22, 2024 · 4ac6f03 · 4ac6f03
1 parent 705f923
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diff --git a/docs/clean-prep/bulwark.ipynb b/docs/clean-prep/bulwark.ipynb
@@ -18,7 +18,7 @@
     "## 1. Installation\n",
     "\n",
     "``` console\n",
-    "$ pipenv install bulwark\n",
+    "$ uv add bulwark\n",
     "Installing bulwark…\n",
     "Adding bulwark to Pipfile's [packages]…\n",
     "✔ Installation Succeeded\n",

diff --git a/docs/clean-prep/string-matching.ipynb b/docs/clean-prep/string-matching.ipynb
@@ -32,7 +32,7 @@
     "Alternatively, you can install the two libraries with other package managers, for example\n",
     "\n",
     "``` bash\n",
-    "$ pipenv install fuzzywuzzy[speedup]\n",
+    "$ uv add fuzzywuzzy[speedup]\n",
     "```"
    ]
   },

diff --git a/docs/conf.py b/docs/conf.py
@@ -168,7 +168,6 @@
     ),
     "sphinx": ("https://www.sphinx-doc.org/en/master", None),
     "nbsphinx": ("https://nbsphinx.readthedocs.io/en/0.4.2", None),
-    "pipenv": ("https://pipenv.pypa.io/en/latest", None),
     "spack": ("https://spack-tutorial.readthedocs.io/en/latest", None),
     "ipyparallel": ("https://ipyparallel.readthedocs.io/en/latest", None),
     "bokeh": ("https://docs.bokeh.org/en/latest", None),

diff --git a/docs/data-processing/apis/fastapi/example.rst b/docs/data-processing/apis/fastapi/example.rst
@@ -36,7 +36,7 @@ Run the server with:
 
 .. code-block:: console
 
-    $ pipenv run uvicorn main:app --reload
+    $ uv run uvicorn main:app --reload
     INFO:     Uvicorn running on http://127.0.0.1:8000 (Press CTRL+C to quit)
     INFO:     Started reloader process [89155] using statreload
     INFO:     Started server process [89164]

diff --git a/docs/data-processing/apis/fastapi/install.rst b/docs/data-processing/apis/fastapi/install.rst
@@ -10,7 +10,7 @@ Requirements
 
 .. code-block:: console
 
-    $ pipenv install fastapi
+    $ uv add fastapi
     Adding fastapi to Pipfile's [packages]…
     ✔ Installation Succeeded
     Locking [dev-packages] dependencies…
@@ -27,7 +27,7 @@ server, such as `uvicorn <http://www.uvicorn.org/>`_:
 
 .. code-block:: console
 
-    $ pipenv install uvicorn
+    $ uv add uvicorn
     Adding uvicorn to Pipfile's [packages]…
     ✔ Installation Succeeded
     Locking [dev-packages] dependencies…
@@ -69,10 +69,10 @@ They can be installed, e.g. with:
 
 .. code-block:: console
 
-    $ pipenv install fastapi[ujson]
+    $ uv add fastapi[ujson]
 
 Alternatively you can install all of these with:
 
 .. code-block:: console
 
-    $ pipenv install fastapi[all]
+    $ uv add fastapi[all]
diff --git a/docs/data-processing/apis/grpc/example.rst b/docs/data-processing/apis/grpc/example.rst
@@ -49,8 +49,8 @@ Generate the gRPC Code
 
 .. code-block:: console
 
-    $ pipenv install grpcio grpcio-tools
-    $ pipenv run python -m grpc_tools.protoc --python_out=. --grpc_python_out=. accounts.proto
+    $ uv add grpcio grpcio-tools
+    $ uv run python -m grpc_tools.protoc --python_out=. --grpc_python_out=. accounts.proto
 
 This generates two files:
 
@@ -88,11 +88,11 @@ Run client and server
 
    .. code-block:: console
 
-        $ pipenv run python accounts_server.py
+        $ uv run python accounts_server.py
 
 #. Starting the client from another terminal:
 
    .. code-block:: console
 
-    $ pipenv run python accounts_client.py
+    $ uv run python accounts_client.py
     Account created: tom
diff --git a/docs/data-processing/apis/grpc/test.rst b/docs/data-processing/apis/grpc/test.rst
@@ -15,7 +15,7 @@ gRPC can be tested automatically with `pytest-grpc
 
    .. code-block:: console
 
-    $ pipenv install pytest-grpc
+    $ uv add pytest-grpc
     Installing pytest-grpc…
     Adding pytest-grpc to Pipfile's [packages]…
     ✔ Installation Succeeded
@@ -48,13 +48,13 @@ gRPC can be tested automatically with `pytest-grpc
 
    .. code-block:: console
 
-    $ pipenv run pytest --fixtures tests/
+    $ uv run pytest --fixtures tests/
 
    or directly against the Python code:
 
    .. code-block:: console
 
-    $ pipenv run pytest --fixtures tests/ --grpc-fake-server
+    $ uv run pytest --fixtures tests/ --grpc-fake-server
     ============================= test session starts ==============================
     platform darwin -- Python 3.7.3, pytest-6.2.2, py-1.10.0, pluggy-0.13.1
     rootdir: /Users/veit/cusy/trn/Python4DataScience/docs/data/grpc

diff --git a/docs/data-processing/httpx/install-example.ipynb b/docs/data-processing/httpx/install-example.ipynb
@@ -23,7 +23,7 @@
     "Alternatively, you can install httpx with other package managers, for example\n",
     "\n",
     "``` bash\n",
-    "$ pipenv install httpx\n",
+    "$ uv add httpx\n",
     "```"
    ]
   },

diff --git a/docs/data-processing/intake/install.rst b/docs/data-processing/intake/install.rst
@@ -18,7 +18,7 @@ Intake can be easily installed for your Jupyter kernel with:
 
 .. code-block:: console
 
-    $ pipenv install intake
+    $ uv add intake
 
 Create a catalog with sample data
 ---------------------------------
@@ -27,7 +27,7 @@ For the following examples we need some data sets that we create with:
 
 .. code-block:: console
 
-    $ pipenv run intake example
+    $ uv run intake example
     Creating example catalog...
       Writing us_states.yml
       Writing states_1.csv

diff --git a/docs/data-processing/postgresql/ipython-sql.rst b/docs/data-processing/postgresql/ipython-sql.rst
@@ -15,7 +15,7 @@ You can easily install ipython-sql in your Jupyter kernel with:
 
 .. code-block:: console
 
-    $ pipenv install ipython-sql
+    $ uv add ipython-sql
 
 First steps
 -----------

diff --git a/docs/data-processing/serialisation-formats/excel.ipynb b/docs/data-processing/serialisation-formats/excel.ipynb
@@ -7,7 +7,7 @@
    "source": [
     "# Excel\n",
     "\n",
-    "pandas also supports reading table data stored in Excel 2003 (and higher) files, either with the `ExcelFile` class or the `pandas.read_excel` function. Internally, these tools use the add-on packages [xlrd](https://xlrd.readthedocs.io/en/latest/) and [openpyxl](https://openpyxl.readthedocs.io/en/stable/) to read XLS and XLSX files respectively. These must be installed separately from pandas with pipenv.\n",
+    "pandas also supports reading table data stored in Excel 2003 (and higher) files, either with the `ExcelFile` class or the `pandas.read_excel` function. Internally, these tools use the add-on packages [xlrd](https://xlrd.readthedocs.io/en/latest/) and [openpyxl](https://openpyxl.readthedocs.io/en/stable/) to read XLS and XLSX files respectively. These must be installed separately from pandas with uv.\n",
     "\n",
     "To use `ExcelFile`, create an instance by passing a path to an xls or xlsx file:"
    ]

diff --git a/docs/data-processing/serialisation-formats/xml-html/beautifulsoup.ipynb b/docs/data-processing/serialisation-formats/xml-html/beautifulsoup.ipynb
@@ -36,7 +36,7 @@
     "   Alternatively, you can install BeautifulSoup with other package managers, for example\n",
     "\n",
     "   ``` console\n",
-    "   $ pipenv install beautifulsoup4\n",
+    "   $ uv add beautifulsoup4\n",
     "   ```"
    ]
   },

diff --git a/docs/data-processing/serialisation-formats/xml-html/xml-html-examples.ipynb b/docs/data-processing/serialisation-formats/xml-html/xml-html-examples.ipynb
@@ -27,7 +27,7 @@
     "Alternatively, you can install BeautifulSoup with other package managers, for example\n",
     "\n",
     "```console\n",
-    "$ pipenv install lxml beautifulsoup4 html5lib\n",
+    "$ uv add lxml beautifulsoup4 html5lib\n",
     "```"
    ]
   },

diff --git a/docs/performance/asyncio-example.ipynb b/docs/performance/asyncio-example.ipynb
@@ -21,7 +21,7 @@
     "You can install the package with\n",
     "\n",
     "``` bash\n",
-    "$ pipenv install nest-asyncio\n",
+    "$ uv add nest-asyncio\n",
     "```\n",
     "\n",
     "You can then import it into your notebook and use it with:"

diff --git a/docs/performance/dask.ipynb b/docs/performance/dask.ipynb
@@ -19,7 +19,7 @@
    "source": [
     "## Scales from laptops to clusters\n",
     "\n",
-    "Dask can be easily installed on a laptop with pipenv and expands the size of the datasets from *fits in memory* to *fits on disk*. Dask can also scale to a cluster of hundreds of machines. It is resilient, elastic, data-local and has low latency. For more information, see the [distributed scheduler](https://distributed.dask.org/en/latest/) documentation. This simple transition between a single machine and a cluster allows users to both start easily and grow as needed."
+    "Dask can be installed on a laptop with uv and expands the size of the datasets from *fits in memory* to *fits on disk*. Dask can also scale to a cluster of hundreds of machines. It is resilient, elastic, data-local and has low latency. For more information, see the [distributed scheduler](https://distributed.dask.org/en/latest/) documentation. This simple transition between a single machine and a cluster allows users to both start easily and grow as needed."
    ]
   },
   {
@@ -32,16 +32,16 @@
     "You can install everything that is required for most common applications of Dask (arrays, dataframes, …). This installs both Dask and dependencies such as NumPy, Pandas, etc. that are required for various workloads:\n",
     "\n",
     "``` bash\n",
-    "$ pipenv install \"dask[complete]\"\n",
+    "$ uv add \"dask[complete]\"\n",
     "```\n",
     "\n",
     "However, only individual subsets can be installed with:\n",
     "\n",
     "``` bash\n",
-    "$ pipenv install \"dask[array]\"\n",
-    "$ pipenv install \"dask[dataframe]\"\n",
-    "$ pipenv install \"dask[diagnostics]\"\n",
-    "$ pipenv install \"dask[distributed]\"\n",
+    "$ uv add \"dask[array]\"\n",
+    "$ uv add \"dask[dataframe]\"\n",
+    "$ uv add \"dask[diagnostics]\"\n",
+    "$ uv add \"dask[distributed]\"\n",
     "```"
    ]
   },
@@ -313,7 +313,7 @@
     "For the following example, Dask must be installed with the `distributed` option, e.g.\n",
     "\n",
     "``` bash\n",
-    "$ pipenv install dask[distributed]\n",
+    "$ uv add dask[distributed]\n",
     "```\n",
     "</div>"
    ]

diff --git a/docs/performance/ipython-profiler.ipynb b/docs/performance/ipython-profiler.ipynb
@@ -256,7 +256,7 @@
     "Alternatively, you can install `line-profiler` with other package managers, for example\n",
     "\n",
     "``` bash\n",
-    "$ pipenv install line_profiler\n",
+    "$ uv add line_profiler\n",
     "```\n",
     "\n",
     "Now you can load IPython with the `line_profiler` extension:"
@@ -336,7 +336,7 @@
     "Alternatively you can install `memory-profiler` with other package managers, for example\n",
     "\n",
     "``` bash\n",
-    "$ pipenv install memory_profiler\n",
+    "$ uv add memory_profiler\n",
     "```"
    ]
   },
@@ -450,7 +450,7 @@
     "It can be easily installed in the kernel with\n",
     "\n",
     "```\n",
-    "$ pipenv install py-heat-magic\n",
+    "$ uv add py-heat-magic\n",
     "Installing py-heat-magic…\n",
     "…```"
    ]

diff --git a/docs/performance/scalene.ipynb b/docs/performance/scalene.ipynb
@@ -27,7 +27,7 @@
     "Linux, MacOS and WSL:\n",
     "\n",
     "``` bash\n",
-    "$ pipenv install scalene\n",
+    "$ uv add scalene\n",
     "```"
    ]
   },

diff --git a/docs/productive/dvc/fds.rst b/docs/productive/dvc/fds.rst
@@ -16,7 +16,7 @@ FastDS can be easily installed with:
 
 .. code-block:: console
 
-    $ pipenv install fastds
+    $ uv add fastds
 
 Introduction
 ------------

diff --git a/docs/productive/dvc/index.rst b/docs/productive/dvc/index.rst
@@ -57,7 +57,7 @@ Finally, external dependencies can also be specified with Pipenv.
 
    .. code-block:: console
 
-        $ pipenv install dvc[ssh]
+        $ uv add dvc[ssh]
 
 Alternatively, DVC can also be installed via other package managers:
 
@@ -75,16 +75,6 @@ Alternatively, DVC can also be installed via other package managers:
 
       $ brew install iterative/homebrew-dvc/dvc
 
-.. note::
-
-   The following example was created with a current DVC version (1.0.0a9),
-   which partly uses a different syntax than earlier versions. You can
-   currently (8th June 2020) only install this with pip:
-
-    .. code-block:: console
-
-       $ pipenv install dvc[all]==1.0.0a9
-
 .. toctree::
     :hidden:
 

diff --git a/docs/productive/dvc/pipeline.rst b/docs/productive/dvc/pipeline.rst
@@ -65,7 +65,7 @@ The generated ``dvc.yaml`` file looks like this, for example:
 
     stages:
       split:
-        cmd: pipenv run python src/split.py data/data.xml
+        cmd: uv run python src/split.py data/data.xml
         deps:
         - data/data.xml
         - src/split.py

diff --git a/docs/productive/envs/index.rst b/docs/productive/envs/index.rst
@@ -2,24 +2,25 @@
 ..
 .. SPDX-License-Identifier: BSD-3-Clause
 
-Reproduce environments
-======================
+Python environments
+===================
 
-Reproducible and secure Python environments are difficult to ensure. With
-the Python package manager :term:`pip`, the call would look like this:
+The Python Basics tutorial already describes how you can create a Python
+environment with :ref:`python-basics:venv`. However, creating this reproducibly
+and securely is much more complex. With the Python package manager :term:`pip`,
+it could look like this, for example:
 
 .. code-block:: console
 
     $ python -m pip install --no-deps --require-hashes ----only-binary=:all:
 
-Dedicated environments (for example with :doc:`pipenv/index`, :term:`devpi` and
-:doc:`Spack <spack/index>` simplify this if you save the file with their
-specifications, for example ``Pipfile``, ``Pipfile.lock``, ``package-lock.json``
-:abbr:`etc (et cetera)`. In this way, you and others can reproduce the
-environments.
+Dedicated environments (for example with :term:`uv` or :doc:`Spack
+<spack/index>` simplify this if you save the files with the specifications, for
+example with :file:`uv.lock` or or :file:`spack.lock`. This way you and others
+can reproduce your environments.
 
 .. toctree::
     :hidden:
 
+    uv/index
     spack/index
-    pipenv/index