Merge branch 'rename_functs_2' into rename_functions

.github/workflows/pr-conventional-commit.yml

@@ -0,0 +1,15 @@
+name: PR Conventional Commit Validation
+
+on:
+  pull_request:
+    types: [opened, synchronize, reopened, edited]
+
+jobs:
+  validate-pr-title:
+    runs-on: ubuntu-latest
+    steps:
+      - name: PR Conventional Commit Validation
+        uses:  ytanikin/[email protected]
+        with:
+          task_types: '["feat","fix","docs","test","ci","refactor","perf","chore","revert"]'
+          add_label: 'false'

.github/workflows/pre-commit.yaml

@@ -25,9 +25,15 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v4
-    - uses: actions/setup-python@v5
+    - name: install the latest version uv
+      uses: astral-sh/setup-uv@v3
       with:
-        python-version: '3.10'
-    - run: pip install pre-commit
-    - run: pre-commit install
-    - run: pre-commit run --all-files
+        version: latest
+    - name: create virtual environment
+      run: uv venv --python '3.10'
+    - name: install pre-commit
+      run: uv pip install pre-commit
+    - name: install pre-commit hooks
+      run: uv run pre-commit install
+    - name: Run pre-commit hooks
+      run: uv run pre-commit run --all-files

.github/workflows/tests.yaml

@@ -16,7 +16,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.10', '3.11']
+        python-version: ['3.10', '3.11', '3.12']
         os: [ubuntu-latest, macos-latest, windows-latest]
     defaults:
       run:
@@ -25,12 +25,14 @@ jobs:
     runs-on: ${{ matrix.os }}
     steps:
       - uses: actions/checkout@v4
-      - run: pipx install poetry
-      - uses: actions/setup-python@v5
+      - name: install the latest version uv
+        uses: astral-sh/setup-uv@v3
         with:
-          python-version: ${{ matrix.python-version }}
-          cache: 'poetry'
-          cache-dependency-path: '**/pyproject.toml'
-      - run: poetry install
-      - run: poetry run pytest -m ""  # Run all markers
-
+          version: latest
+      - name: create venv
+        run: uv venv --python ${{ matrix.python-version }}
+      - name: install dependencies
+        run: uv pip install -e ".[dev]"
+      - name: run tests
+        run: uv run pytest -m ""  # Run all markers
+

.gitignore

@@ -1,6 +1,7 @@
-#False Python
+# False Python
 __pycache__
 dist
+**/*.egg-info
 
 # Log files
 *.out
@@ -19,9 +20,6 @@ site/*
 .vscode/
 .idea/
 
-# Poetry
-poetry.lock
-
 # Misc
 *.sh
 *.model

CITATION.cff

@@ -21,13 +21,9 @@ authors:
     given-names: Carl
   - family-names: Binxin
     given-names: Ru
-  - family-names: Kober
-    given-names: Nils
-  - family-names: Vallaeys
-    given-names: Théophane
   - family-names: Hutter
     given-names: Frank
 title: "Neural Pipeline Search (NePS)"
-version: 0.12.1
-date-released: 2024-07-03
+version: 0.12.2
+date-released: 2024-07-09
 url: "https://github.com/automl/neps"

CONTRIBUTING.md

@@ -16,67 +16,49 @@ Automatic checks are run on every pull request and on every commit to `master`.
 
 There are three required steps and one optional:
 
-1. Optional: Install miniconda and create an environment
-1. Install poetry
-1. Install the neps package using poetry
+1. Install uv
+1. Install the neps package using uv
 1. Activate pre-commit for the repository
 
 For instructions see below.
 
-## 1. Optional: Install miniconda and create a virtual environment
+## 1. Install uv
 
-To manage python versions install e.g., miniconda with
+First, install uv, e.g., via
 
 ```bash
-wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O install_miniconda.sh
-bash install_miniconda.sh -b -p $HOME/.conda  # Change to place of preference
-rm install_miniconda.sh
+# On macOS and Linux.
+curl -LsSf https://astral.sh/uv/install.sh | sh
 ```
 
-Consider running `~/.conda/bin/conda init` or `~/.conda/bin/conda init zsh` .
-
-Then finally create the environment and activate it
-
 ```bash
-conda create -n neps python=3.10
-conda activate neps
+# On Windows.
+powershell -ExecutionPolicy ByPass -c "irm https://astral.sh/uv/install.ps1 | iex"
 ```
 
-## 2. Install poetry
-
-First, install poetry, e.g., via
+## 2. Clone the neps repository
 
 ```bash
-curl -sSL https://install.python-poetry.org | python3 -
-# or directly into your virtual env using `pip install poetry`
+git clone https://github.com/automl/neps.git
+cd neps
 ```
 
-Then consider appending
+## 3. Create a virtual environment and install the neps package
 
 ```bash
-export PATH="$HOME/.local/bin:$PATH"
-```
-
-to your `.zshrc` / `.bashrc` or alternatively simply running the export manually.
-
-## 3. Install the neps Package Using poetry
-
-Clone the repository, e.g.,
-
-```bash
-git clone https://github.com/automl/neps.git
-cd neps
+uv venv --python 3.11
+source .venv/bin/activate
 ```
 
 Then, inside the main directory of neps run
 
 ```bash
-poetry install
+uv pip install -e ".[dev]"
 ```
 
 This will installthe neps package but also additional dev dependencies.
 
-## 4. Activate pre-commit for the repository
+### 4. Activate pre-commit for the repository
 
 With the python environment used to install the neps package run in the main directory of neps
 
@@ -93,9 +75,6 @@ your choice, e.g.
 [VSCode](https://marketplace.visualstudio.com/items?itemName=charliermarsh.ruff),
 [PyCharm](https://plugins.jetbrains.com/plugin/20574-ruff).
 
-
-# Checks and Tests
-
 We have setup checks and tests at several points in the development flow:
 
 - At every commit we automatically run a suite of [pre-commit](https://pre-commit.com/) hooks that perform static code analysis, autoformating, and sanity checks.
@@ -104,11 +83,13 @@ This is setup during our [installation process](https://automl.github.io/neps/co
 The tests correspond directly to examples in [neps_examples](https://github.com/automl/neps/tree/master/neps_examples) and only check for crash-causing errors.
 - At every push all integration tests and regression tests are run automatically using [github actions](https://github.com/automl/neps/actions).
 
-## Linting (Ruff)
+## Checks and tests
+
+### Linting (Ruff)
 For linting we use `ruff` for checking code quality. You can install it locally and use it as so:
 
 ```bash
-pip install ruff
+uv pip install ruff
 ruff check --fix neps  # the --fix flag will try to fix issues it can automatically
 ```
 
@@ -127,11 +108,11 @@ The configuration of `ruff` is in the `pyproject.toml` file and we refer you to
 
 There you can find the documentation for all of the rules employed.
 
-## Type Checking (Mypy)
+### Type Checking (Mypy)
 For type checking we use `mypy`. You can install it locally and use it as so:
 
 ```bash
-pip install mypy
+uv pip install mypy
 mypy neps
 ```
 
@@ -159,15 +140,15 @@ or types defined from NePS, there is probably a good reason for a mypy error.
 If you have issues regarding typing, please feel free to reach out for help `@eddiebergman`.
 
 
-## Examples and Integration Tests
+### Examples and Integration Tests
 
-We use examples in [neps_examples](https://github.com/automl/neps/tree/master/neps_examples) as integration tests, which we run from the main directory via
+We use some examples in [neps_examples](https://github.com/automl/neps/tree/master/neps_examples) as integration tests, which we run from the main directory via
 
 ```bash
 pytest
 ```
 
-If tests fail for you on the master, please raise an issue on github, preferabbly with some informationon the error,
+If tests fail for you on the master, please raise an issue on github, preferably with some information on the error,
 traceback and the environment in which you are running, i.e. python version, OS, etc.
 
 ## Regression Tests
@@ -212,11 +193,12 @@ In the case of regression test failure, try running it again first, if the probl
 You can also run tests locally by running:
 
 ```
-poetry run pytest -m regression_all
+uv run pytest -m regression_all
 ```
 
 ## Disabling and Skipping Checks etc.
 
+
 ### Pre-commit: How to not run hooks?
 
 To commit without running `pre-commit` use `git commit --no-verify -m <COMMIT MESSAGE>`.
@@ -231,32 +213,31 @@ There are two options:
   code = "foo"  # type: ignore
   ```
 
-## Managing Dependencies
+### Managing Dependencies
 
-To manage dependencies and for package distribution we use [poetry](https://python-poetry.org/docs/) (replaces pip).
+To manage dependencies we use [uv](https://docs.astral.sh/uv/getting-started/) (replaces pip).
 
-## Add dependencies
+#### Add dependencies
 
 To install a dependency use
 
 ```bash
-poetry add dependency
+uv add dependency
 ```
 
 and commit the updated `pyproject.toml` to git.
 
-For more advanced dependency management see examples in `pyproject.toml` or have a look at the [poetry documentation](https://python-poetry.org/).
+For more advanced dependency management see examples in `pyproject.toml` or have a look at the [uv documentation](https://docs.astral.sh/uv/getting-started/).
 
-## Install dependencies added by others
+#### Install dependencies added by others
 
 When other contributors added dependencies to `pyproject.toml`, you can install them via
 
 ```bash
-poetry lock
-poetry install
+uv pip install -e ".[dev]"
 ```
 
-# Documentation
+## Documentation
 
 We use [MkDocs](https://www.mkdocs.org/getting-started/), more specifically [Material for MkDocs](https://squidfunk.github.io/mkdocs-material/) for documentation.
 To support documentation for multiple versions, we use the plugin [mike](https://github.com/jimporter/mike).
@@ -278,7 +259,7 @@ To publish the documentation run
 mike deploy 0.5.1 latest -p
 ```
 
-# Releasing a New Version
+## Releasing a New Version
 
 There are four steps to releasing a new version of neps:
 
@@ -288,42 +269,30 @@ There are four steps to releasing a new version of neps:
 3. Update Documentation
 4. Publish on PyPI
 
-## 0. Understand Semantic Versioning
+### 0. Understand Semantic Versioning
 
 We follow the [semantic versioning](https://semver.org) scheme.
 
-## 1. Update the Package Version and CITATION.cff
+## 1. Run tests
 
 ```bash
-poetry version v0.9.0
+uv run pytest
 ```
 
-and manually change the version specified in `CITATION.cff`.
-
-## 2. Commit with a Version Tag
-
-First commit and test
+## 2. Update the Package Version and CITATION.cff
 
 ```bash
-git add pyproject.toml
-git commit -m "Bump version from v0.8.4 to v0.9.0"
-pytest
+bump-my-version bump <major | minor | patch>
 ```
 
-Then tag and push
-
-```bash
-git tag v0.9.0
-git push --tags
-git push
-```
+This will automatically update the version in `pyproject.toml` and `CITATION.cff`, tag the commit and push it to the remote repository.
 
-## 3. Update Documentation
+### 3. Update Documentation
 
 First check if the documentation has any issues via
 
 ```bash
-mike deploy 0.9.0 latest -u
+mike deploy <current version> latest -u
 mike serve
 ```
 
@@ -332,19 +301,20 @@ and then looking at it.
 Afterwards, publish it via
 
 ```bash
-mike deploy 0.9.0 latest -up
+mike deploy <current version> latest -up
 ```
 
-## 4. Publish on PyPI
+### 4. Publish on PyPI
 
 To publish to PyPI:
 
-1. Get publishing rights, e.g., asking Danny or Maciej or Neeratyoy.
+1. Get publishing rights, e.g., asking Danny or Neeratyoy.
 2. Be careful, once on PyPI we can not change things.
 3. Run
 
 ```bash
-poetry publish --build
+uv build
+uv publish
 ```
 
 This will ask for your PyPI credentials.