Enable pure pip/uv installations

.gitignore

@@ -92,3 +92,6 @@ venv/
 
 # pre-commit and pytest cache
 .*_cache/
+
+# uv related
+uv.lock

CONTRIBUTING.md

@@ -25,36 +25,67 @@ These are especially suitable if you're new to the project, and we recommend sta
 
 ## Contributing code
 
-
 ### Creating a development environment
-It is recommended to use [conda](conda:)
-or [mamba](mamba:) to create a
-development environment for `movement`. In the following we assume you have
-`conda` installed, but the same commands will also work with `mamba`/`micromamba`.
 
-First, create and activate a `conda` environment with some prerequisites:
+In order to make changes to `movement`, you will need to fork the [repository](movement-github:).
+If you are not familiar with `git`, we recommend reading up on [this guide](https://docs.github.com/en/get-started/using-git/about-git#basic-git-commands).
 
-```sh
-conda create -n movement-dev -c conda-forge python=3.13 pytables
-conda activate movement-dev
-```
+1. Clone the forked repository to your local machine and change directory:
 
-To install `movement` for development, clone the [GitHub repository](movement-github:),
-and then run from within the repository:
+    ```sh
+    git clone https://github.com/<your-github-username>/movement.git
+    cd movement
+    ```
 
-```sh
-pip install -e .[dev]  # works on most shells
-pip install -e '.[dev]'  # works on zsh (the default shell on macOS)
-```
+2. Set the upstream remote to the base `movement` repository:
 
-This will install the package in editable mode, including all dependencies
-required for development.
+    ```sh
+    git remote add upstream https://github.com/neuroinformatics-unit/movement.git
+    ```
 
-Finally, initialise the [pre-commit hooks](#formatting-and-pre-commit-hooks):
+3. Create an environment using [conda](conda:) or [uv](uv:getting-started/installation/) and install `movement` in editable mode, including development dependencies.
 
-```bash
-pre-commit install
-```
+    ::::{tab-set}
+
+    :::{tab-item} conda
+    First, create and activate a `conda` environment:
+
+    ```sh
+    conda create -n movement-dev -c conda-forge python=3.13
+    conda activate movement-dev
+    ```
+
+    Then, install the package in editable mode with development dependencies:
+
+    ```sh
+    pip install -e ".[dev]"
+    ```
+    :::
+
+    :::{tab-item} uv
+
+    First, create and activate a [virtual environment](uv:pip/environments/):
+
+    ```sh
+    uv venv --python=3.13
+    source .venv/bin/activate  # On macOS and Linux
+    .venv\Scripts\activate     # On Windows PowerShell
+    ```
+
+    Then, install the package in editable mode with development dependencies:
+
+    ```sh
+    uv pip install -e ".[dev]"
+    ```
+    :::
+
+    ::::
+
+4. Finally, initialise the [pre-commit hooks](#formatting-and-pre-commit-hooks):
+
+    ```sh
+    pre-commit install
+    ```
 
 ### Pull requests
 In all cases, please submit code to the main repository via a pull request (PR).
@@ -212,12 +243,12 @@ The deployment job runs on tag pushes (for PyPI releases) or manual triggers on
 This keeps the documentation aligned with releases, while allowing manual redeployment when necessary.
 
 ### Editing the documentation
-To edit the documentation, first clone the repository, and install `movement` in a
-[development environment](#creating-a-development-environment).
+To edit the documentation, ensure you have already set up a [development environment](#creating-a-development-environment).
 
-Then, install a few additional dependencies in your development environment to be able to build the documentation locally. To do this, run the following command from the root of the repository:
+To build the documentation locally, install the extra dependencies by running the following command from the repository root:
 ```sh
-pip install -r ./docs/requirements.txt
+pip install -r ./docs/requirements.txt      # conda env
+uv pip install -r ./docs/requirements.txt   # uv env
 ```
 
 Now create a new branch, edit the documentation source files (`.md` or `.rst` in the `docs` folder),

docs/requirements.txt

@@ -11,4 +11,3 @@ sphinx-design
 sphinx-gallery
 sphinx-notfound-page
 sphinx-sitemap
-tables

docs/source/conf.py

@@ -191,7 +191,6 @@
     "https://opensource.org/license/bsd-3-clause/",  # to avoid odd 403 error
     "https://www.sainsburywellcome.org/",  # Occasional ConnectTimeoutError
     "https://www.robots.ox.ac.uk/",  # occasional 404s
-    "https://silvalab.codeberg.page/BraiAn/",  # SSLError despite working link
 ]
 
 
@@ -203,11 +202,10 @@
     "movement-github": "https://github.com/neuroinformatics-unit/movement/{{path}}",
     "movement-zulip": "https://neuroinformatics.zulipchat.com/#narrow/stream/406001-Movement",
     "movement-community-calls": "https://neuroinformatics.zulipchat.com/#narrow/channel/406001-Movement/topic/Community.20Calls",
-    "conda": "https://docs.conda.io/en/latest/",
+    "conda": "https://docs.conda.io/projects/conda/en/latest/{{path}}#{{fragment}}",
     "dlc": "https://www.mackenziemathislab.org/deeplabcut/",
     "gin": "https://gin.g-node.org/{{path}}#{{fragment}}",
     "github-docs": "https://docs.github.com/en/{{path}}#{{fragment}}",
-    "mamba": "https://mamba.readthedocs.io/en/latest/",
     "myst-parser": "https://myst-parser.readthedocs.io/en/latest/{{path}}#{{fragment}}",
     "napari": "https://napari.org/dev/{{path}}",
     "setuptools-scm": "https://setuptools-scm.readthedocs.io/en/latest/{{path}}#{{fragment}}",
@@ -220,6 +218,7 @@
     "via": "https://www.robots.ox.ac.uk/~vgg/software/via/{{path}}#{{fragment}}",
     "anipose": "https://anipose.readthedocs.io/en/latest/",
     "TRex": "https://trex.run/docs/",
+    "uv": "https://docs.astral.sh/uv/{{path}}#{{fragment}}",
 }
 
 intersphinx_mapping = {

docs/source/user_guide/installation.md

@@ -1,79 +1,104 @@
 (target-installation)=
 # Installation
 
-## Install the package
-:::{admonition} Use a conda environment
-:class: note
-To avoid dependency conflicts with other packages, it is best practice to install Python packages within a virtual environment.
-We recommend using [conda](conda:) or [mamba](mamba:) to create and manage this environment, as they simplify the installation process.
-The following instructions assume that you have conda installed, but the same commands will also work with `mamba`/`micromamba`.
-:::
+## Create a virtual environment
 
-### Users
-To install movement in a new environment, follow one of the options below.
-We will use `movement-env` as the environment name, but you can choose any name you prefer.
+While not strictly required, we strongly recommended installing `movement` in a
+clean virtual environment, using tools such as
+[conda](conda:) or [uv](uv:getting-started/installation/).
 
 ::::{tab-set}
-:::{tab-item} Conda
-To create an environment with the core package only:
+:::{tab-item} conda
+Create and activate a new [conda environment](conda:user-guide/tasks/manage-environments.html):
 ```sh
-conda create -n movement-env -c conda-forge movement
+conda create -y -n movement-env -c conda-forge python=3.13
+conda activate movement-env
 ```
 
-If you wish to use the GUI, which additionally requires [napari](napari:),
-you should instead run:
+We used `movement-env` as the environment name, but you can choose any name you prefer.
+:::
+
+:::{tab-item} uv
+Create and activate a new [virtual environment](uv:pip/environments/) inside your project directory:
+
 ```sh
-conda create -n movement-env -c conda-forge movement napari pyqt
+uv venv --python=3.13
+
+source .venv/bin/activate  # On macOS and Linux
+.venv\Scripts\activate     # On Windows PowerShell
 ```
-You may exchange `pyqt` for `pyside2` if you prefer.
-See [napari's installation guide](napari:tutorials/fundamentals/installation.html)
-for more information on the backends.
+:::
+::::
 
-To activate the environment:
+## Install the package
+With your environment activated, install `movement` using one of the methods below.
+
+::::{tab-set}
+:::{tab-item} From conda-forge using conda
+Install the core package:
 ```sh
-conda activate movement-env
+conda install -c conda-forge movement
 ```
-:::
 
-:::{tab-item} Pip
-Create and activate an environment with some prerequisites:
+If you wish to use the GUI, which requires [napari](napari:), run instead:
 ```sh
-conda create -n movement-env -c conda-forge python=3.12 pytables
-conda activate movement-env
+conda install -c conda-forge movement napari pyqt
 ```
-Install the core package from the latest release on PyPI:
+You may exchange `pyqt` for `pyside6` if you prefer a different Qt backend.
+See [napari's installation guide](napari:tutorials/fundamentals/installation.html)
+for more details on available backends.
+
+:::
+
+:::{tab-item} From PyPI using pip
+Install the core package:
 ```sh
 pip install movement
 ```
-If you wish to use the GUI, which additionally requires [napari](napari:),
-you should instead run:
+If you wish to use the GUI, which requires [napari](napari:), run instead:
+```sh
+pip install "movement[napari]"
+```
+:::
+
+:::{tab-item} From PyPI using uv
+Install the core package:
+```sh
+uv pip install movement
+```
+If you wish to use the GUI, which requires [napari](napari:), run instead:
 ```sh
-pip install movement[napari]   # works on most shells
-pip install 'movement[napari]' # works on zsh (default shell on macOS)
+uv pip install "movement[napari]"
 ```
 :::
+
 ::::
 
 :::{dropdown} Note for Apple Silicon users with macOS 13 or earlier
 :color: info
 :icon: info
 
-We recommend installing `movement` following the `Conda` instructions above, as the `pip` method will likely fail for you.
-Alternatively, updating your macOS to version 14 or later will allow `pip` installations to work as expected.
+If you are using macOS 13 or earlier on Apple Silicon (M-series),
+we recommend installing `movement` via `conda-forge`.
+Alternatively, upgrade to macOS 14 to use any of the installation methods above.
 :::
 
-### Developers
-If you are a developer looking to contribute to movement, please refer to our [contributing guide](target-contributing) for detailed setup instructions and guidelines.
+:::{admonition} For developers
+:class: tip
+
+If you would like to contribute to `movement`, see our [contributing guide](target-contributing)
+for detailed developer setup instructions and coding guidelines.
+:::
 
-## Check the installation
-To verify that the installation was successful, run (with `movement-env` activated):
+## Verify the installation
+With your virtual environment activated, run:
 ```sh
 movement info
 ```
-You should see a printout including the version numbers of movement
+You should see a printout including the version numbers of `movement`
 and some of its dependencies.
 
-To test the GUI installation, you can run:
+To test the GUI installation:
 
 ```sh
 movement launch
@@ -83,37 +108,68 @@ This is equivalent to running `napari -w movement` and should open the `napari`
 window with the `movement` widget docked on the right-hand side.
 
 ## Update the package
-To update `movement` to the latest version, you need to use the same package manager you used to install it (either `conda` or `pip`). If you are not sure which one you used, you can run from your active environment:
+
+:::{dropdown} Always update using the same package manager used for installation
+:icon: info
+:color: info
+
+If your environment was created with `conda`, first check which channel `movement` was installed from before updating.
+Run `conda list movement` in your active `conda` environment and look at the **Channel** column:
+- If the channel is `conda-forge`, update using `conda`.
+- If the channel is `pypi`, update using `pip`.
+
+:::
+
+
+::::{tab-set}
+:::{tab-item} conda
 ```sh
-conda list movement
+conda update -c conda-forge movement -y
 ```
-If the output shows `conda-forge` as the channel, you used `conda` to install it. If it shows `pypi`, you used `pip`.
+:::
 
-Once this is clear, you can update `movement` by running the relevant command from below:
-::::{tab-set}
-:::{tab-item} Conda
+:::{tab-item} pip
 ```sh
-conda update movement -y
+pip install -U movement
 ```
 :::
 
-:::{tab-item} Pip
+:::{tab-item} uv
 ```sh
-pip install movement -U
+uv pip install -U movement
 ```
 :::
 ::::
 
 
-If the above fails, try installing it in a fresh new environment instead. This should prevent potential compatibility issues caused by changes in dependency versions. You can first uninstall the existing environment named `movement-env`:
+If the above fails, try installing `movement` in a fresh new environment to avoid dependency conflicts.
+
+First remove the existing environment:
+
+::::{tab-set}
+:::{tab-item} conda
 ```sh
 conda env remove -n movement-env
 ```
-Once the environment has been removed, you can create a new one following the [installation instructions](#install-the-package) above.
 
-:::{tip}
-If you are unsure about the environment name, you can get a list of the environments on your system with:
+This command assumes your environment is named `movement-env`.
+If you are unsure about the name, you can get a list of the environments
+on your system with `conda env list`.
+:::
+
+:::{tab-item} uv
+Delete the `.venv` folder in your project directory.
+
+```powershell
+rm -rf .venv       # On macOS and Linux
+rmdir /s /q .venv  # On Windows PowerShell
+```
+
+Optionally, you can clean the `uv` cache for unused packages:
 ```sh
-conda env list
+uv cache prune
 ```
 :::
+::::
+
+Once the environment has been removed, you can create a new one following the [instructions](#create-a-virtual-environment) above.