Updating to uv

Author: apmoore1

.devcontainer/Dockerfile

@@ -0,0 +1,48 @@
+FROM ubuntu:latest
+
+
+RUN apt-get -y update \
+    && apt-get install -y --no-install-recommends \
+    python3.12 \
+    python3.12-dev \
+    git \
+    make \
+    wget \
+    vim \
+    build-essential \
+    openssh-client \
+    ca-certificates \
+    gnupg2 \
+    && rm -rf /var/lib/apt/lists/*
+
+ARG USERNAME=ubuntu
+
+USER $USERNAME
+WORKDIR /home/$USERNAME
+
+
+SHELL ["/bin/bash", "-c"]
+RUN set -o pipefail \
+    && wget -qO- https://astral.sh/uv/install.sh \
+    | sh
+RUN set -o pipefail \
+    && wget -qO- https://raw.githubusercontent.com/nvm-sh/nvm/v0.40.3/install.sh \
+    | bash
+# Required as when using a mount with write permissions in a RUN command 
+# it fails because of permission reasons.
+COPY --chown=ubuntu:ubuntu docs docs
+RUN source .nvm/nvm.sh \
+    && nvm install 24 \
+    && corepack enable yarn \
+    && cd docs \
+    && corepack use yarn \
+    && cd .. \
+    && rm -rf docs
+
+ENV PATH="/home/$USERNAME/.local/bin/:$PATH"
+
+RUN uv python install 3.11
+
+RUN --mount=type=bind,source=uv.lock,target=uv.lock \
+    --mount=type=bind,source=pyproject.toml,target=pyproject.toml \
+    uv sync --no-install-project --no-install-workspace

.devcontainer/devcontainer.json

@@ -0,0 +1,31 @@
+// For format details, see https://aka.ms/devcontainer.json. For config options, see the
+// README at: https://github.com/devcontainers/templates/tree/main/src/python
+{
+	"name": "Node+Python",
+	"remoteUser": "ubuntu",
+	"updateRemoteUserUID": true,
+	// Or use a Dockerfile or Docker Compose file. More info: https://containers.dev/guide/dockerfile
+	"build": {
+		"dockerfile": "Dockerfile",
+		"context": ".."
+	},
+	"customizations": {
+		// Configure properties specific to VS Code.
+		"vscode": {
+		// Add the IDs of extensions you want installed when the container is created.
+		"extensions": ["streetsidesoftware.code-spell-checker",
+	                   "ms-toolsai.jupyter",
+					   "ms-toolsai.jupyter-renderers",
+					   "ms-python.python",
+					   "ms-python.vscode-pylance",
+					   "ms-python.vscode-python-envs",
+					   "ms-vscode.makefile-tools",
+					   "redhat.vscode-yaml",
+					   "tamasfe.even-better-toml"],
+		"settings": {
+			"python-envs.defaultEnvManager": "ms-python.python:venv"
+		}
+		}
+  	},
+	"postStartCommand": "uv sync"
+}

.dockerignore

@@ -1,4 +1,6 @@
 *
 ! docs/yarn.lock
 ! docs/package.json
-! docs/.yarnrc.yml
+! docs/.yarnrc.yml
+! uv.lock
+! pyproject.toml

.flake8

@@ -0,0 +1,7 @@
+[flake8]
+ignore = E266, E501, W503, W293
+max-line-length = 200
+select = B,C,E,F,W,T4,B9
+statistics = true
+count = true
+show_source = true

.python-version

@@ -0,0 +1 @@
+3.12

CHANGELOG.md

@@ -11,17 +11,21 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - The documentation now has a `How-to` guide on `Tag CoNLL-U Files`.
 - The documentation now has a `How-to Tag Text` guide for Finnish and English.
+- Using [developer/dev containers](https://containers.dev/) of which the files for this can be found in the [.devcontainer folder](./.devcontainer). This will allow for easier on boarding and development consistency.
 
 ## Changed
 
 - [./scripts/py2md.py](./scripts/py2md.py) script has been updated so that it works with the newest version of Python that [pydoc_markdown](https://github.com/NiklasRosenstein/pydoc-markdown) supports, which is version 3.11. This required upgrading `pydoc_markdown` from version `4.6.0` to `>=4.7` which did come with some breaking changes for this repository hence the updates to the script. With the release of [uv](https://docs.astral.sh/uv/) the Python package manager we have made use of it's ability to have script level isolated virtual environments therefore removing any `py2md` script specific requirements from the dev/tests requirements that this package requires, e.g. `pydoc_markdown` requirement has been removed and is `py2md` script specific requirement. This also means that the [makefile](./makefile) has been changed to reflect this through the command `create-api-docs` which has been changed but it's functionility and use is the same.
 - [github/workflows/documentation_check_build_deploy.yml](./.github/workflows/documentation_check_build_deploy.yml) has been added but this is a change to the original documentation build and deploy workflow. This workflow now uses [uv](https://docs.astral.sh/uv/) for managing Python as it runs the `py2md.py` script. It only deploys the documentation website when there are push events to the `main` branch rather than pull requests. In addition during the build test we save the build artifact, when we want to deploy we use that build artifact to save processing time.
 - Removed the `Docs_Docker.dockerfile` as we have setup a DevContainer that encompasses all of the requirements that this Dockerfile provides. Therefore the [makefile](./makefile) commands that correspond to building/serving the documentation have been updated, along with the [documentation](./CONTRIBUTING.md).
 - Removed the requirement for a docker container to validate the [CITATION.cff file](./CITATION.cff), now we use `uv tool run`, of which this has been documentated in [RELEASE_PROCESS.md](./RELEASE_PROCESS.md).
+- Using [uv](https://docs.astral.sh/uv/) as the Python package manager and the package build front and back end replacing setup tools for the build backend.
+- Setting the new version of PyMUSAS is through the [uv tool](https://docs.astral.sh/uv/guides/package/#updating-your-version) and this uses the version set in [./pyproject.toml](./pyproject.toml) rather than [./pymusas/__init__.py](./pymusas/__init__.py)
 
 ## Removed
 
 - `Docs_Docker.dockerfile` - see the Changed section above for the reason.
+- `requirements.txt`, `dev_requirements.txt`, and `setup.cfg`. These files are no longer needed as we have moved to using [uv](https://docs.astral.sh/uv/) as the Python package manager, and using [./pyproject.toml](./pyproject.toml) to store all of the packages's requirements and build dependencies.
 
 ## [v0.3.0](https://github.com/UCREL/pymusas/releases/tag/v0.3.0) - 2022-05-04
 

CONTRIBUTING.md

@@ -21,18 +21,24 @@ The last part of any pull request is to update the [CHANGELOG](./CHANGELOG.md) w
 
 ### Changing / Updating Python requirements
 
-If you are changing the Python requirements, this needs to be done in a few different places:
-
-1. If it is a development only requirement, not required to run the core code base within [./pymusas](./pymusas), then update:
-    * [./dev_requirements.txt](./dev_requirements.txt)
-    * [./binder/environment.yml](./binder/environment.yml)
-    * [The `tests` section of ./setup.cfg](./setup.cfg)
-2. If it is a requirement that is needed to run the core code base within [./pymusas](./pymusas), then update:
-    * [./requirements.txt](./requirements.txt)
-    * [./binder/environment.yml](./binder/environment.yml)
-    * [The `install_requires` section of ./setup.cfg](./setup.cfg)
-
-In all cases you may need to add this requirement to the `tool.isort` section `known_third_party` list of the [./pyproject.toml file.](./pyproject.toml) 
+If you are changing/updating a core requirement i.e. a requirement needed to run `pymusas` see [#core](#core) else if it is only for development of the project see [#development](#development).
+
+**Note**:
+
+1. In all cases you may need to add this requirement to the `tool.isort` section `known_third_party` list of the [./pyproject.toml file.](./pyproject.toml).
+2. Add the requirement to [./binder/environment.yml](./binder/environment.yml)
+
+#### Core
+
+``` bash
+uv add REQUIREMENT
+```
+
+#### Development
+
+``` bash
+uv add --dev REQUIREMENT
+```
 
 ### Writing docstrings
 [A lot of this has been copied from the AllenNLP CONTRIBUTING guidelines, which I think are really great!](https://github.com/allenai/allennlp/blob/main/CONTRIBUTING.md)

README.md

@@ -104,37 +104,27 @@ To run locally first ensure you have the following tools installted locally:
 When developing on the project you will want to install the Python package locally in editable format with all the extra requirements, this can be done like so:
 
 ```bash
-pip install -e .[tests]
-```
-
-For a `zsh` shell, which is the default shell for the new Macs you will need to escape with `\` the brackets:
-
-```zsh
-pip install -e .\[tests\]
+uv sync
 ```
 
 ### Running linters and tests
 
-This code base uses flake8 and mypy to ensure that the format of the code is consistent and contain type hints. The flake8 settings can be found in [./setup.cfg](./setup.cfg) and the mypy settings within [./pyproject.toml](./pyproject.toml). To run these linters:
+This code base uses isort, flake8 and mypy to ensure that the format of the code is consistent and contain type hints. ISort and mypy settings can be found within [./pyproject.toml](./pyproject.toml) and the flake8 settings can be found in [./.flake8](./.flake8). To run these linters:
 
 ``` bash
-isort pymusas tests scripts
-flake8
-mypy
+make lint
 ```
 
 To run the tests with code coverage (**NOTE** these are the code coverage tests that the Continuos Integration (CI) reports at the top of this README, the doc tests are not part of this report):
 
 ``` bash
-coverage run # Runs the tests (uses pytest)
-coverage report # Produces a report on the test coverage
+make tests
 ```
 
 To run the [doc tests](https://docs.python.org/3/library/doctest.html), these are tests to ensure that examples within the documentation run as expected:
 
 ``` bash
-coverage run -m pytest --doctest-modules pymusas/ # Runs the doc tests
-coverage report # Produces a report on the doc tests coverage
+make doc-tests
 ```
 
 ### Setting a different default python version

RELEASE_PROCESS.md

@@ -23,7 +23,7 @@ to `git@github.com:UCREL/pymusas.git` (or the `HTTPS` equivalent).
     set -x TAG 'v1.0.0'
     ```
 
-2. Update `pymusas/__init__.py` with the correct version and check that it matches the `TAG` environment variable you created in the first step.
+2. Use the uv tool to update the version within [./pyproject.toml](./pyproject.toml) and check that it matches the `TAG` environment variable you created in the first step. `uv version ${TAG}`
 
 3. Update the `CHANGELOG.md` so that everything under the "Unreleased" section is now under a section corresponding to this release.
 

binder/environment.yml

@@ -1,21 +1,19 @@
 name: pymusas
 channels:
-  - defaults
+  - conda-forge
 dependencies:
-  - python=3.9
+  - python=3.11
   - pip
   - pip:
     - nbgitpuller # This is a special Binder requirement
     - "spacy>=3.1.4"
-    - "srsly>=2.4.1,<3.0.0"
-    - "tqdm>=4.50.0,<5.0.0"
-    - "requests>=2.13.0,<3.0.0"
-    - "pytest>=6.0.0,!=7.1.0"
+    - "srsly>=2.4.1,<3.0"
+    - "tqdm>=4.50.0,<5.0"
+    - "requests>=2.13.0,<3.0"
+    - "pytest>=6.0,!=7.1.0,!=8.1.0"
     - "coverage[toml]>=6.0.0"
-    - "responses>=0.16.0"
-    - mypy==0.910
-    - types-requests
-    - "flake8>=3.8.0,<3.10.0"
-    - "pydoc-markdown>=4.0.0,<4.6.0"
-    - "isort>=5.5.4"
-    - "click<8.1.0"
+    - "responses>=0.25.7"
+    - "mypy>=1.12"
+    - "types-requests>=2.32.4.20250913"
+    - "flake8>=3.8"
+    - "isort>=6.0"