diff --git a/.github/dependabot.yml b/.github/dependabot.yml new file mode 100644 index 0000000..0d08e26 --- /dev/null +++ b/.github/dependabot.yml @@ -0,0 +1,11 @@ +# To get started with Dependabot version updates, you'll need to specify which +# package ecosystems to update and where the package manifests are located. +# Please see the documentation for all configuration options: +# https://docs.github.com/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file + +version: 2 +updates: + - package-ecosystem: "github-actions" # See documentation for possible values + directory: "/" # Location of package manifests + schedule: + interval: "weekly" diff --git a/.github/workflows/build_docs.yml b/.github/workflows/build_docs.yml index f21745c..cd87bad 100644 --- a/.github/workflows/build_docs.yml +++ b/.github/workflows/build_docs.yml @@ -10,40 +10,31 @@ on: jobs: build_docs: - runs-on: ubuntu-22.04 + runs-on: ubuntu-24.04 env: - PYTHON_VERSION: "3.10" PUBLISH_DIR: ./_build/html steps: # checkout the repository - - uses: actions/checkout@v4 + - uses: actions/checkout@v5 # setup Python - - name: Install Python ${{ env.PYTHON_VERSION }} - uses: actions/setup-python@v4 + - name: Install Python + uses: actions/setup-python@v6 with: - python-version: ${{ env.PYTHON_VERSION }} + python-version-file: ".python-version" - # preserve pip cache to speed up installation - - name: Cache pip - uses: actions/cache@v3 - with: - path: ~/.cache/pip - # Look to see if there is a cache hit for the corresponding requirements file - key: ${{ runner.os }}-pip-${{ hashFiles('*requirements-docs.txt') }} - restore-keys: | - ${{ runner.os }}-pip- - - name: Install Python dependencies - run: | - python3 -m pip install --upgrade pip - python3 -m pip install -r requirements-docs.txt + - name: Install uv + uses: astral-sh/setup-uv@v6 + + - name: Install the project + run: uv sync --extra docs - name: Build docs - run: python3 -m jupyter book build . + run: uv run jupyter book build . - name: Upload artifact - uses: actions/upload-artifact@v3 + uses: actions/upload-artifact@v5 with: name: documentation path: ${{ env.PUBLISH_DIR }} diff --git a/.github/workflows/deploy_docs.yml b/.github/workflows/deploy_docs.yml index ebbaf27..aace797 100644 --- a/.github/workflows/deploy_docs.yml +++ b/.github/workflows/deploy_docs.yml @@ -1,51 +1,41 @@ -name: Github Pages +name: Publish documentation on: push: - branches: [main] # Only run on push to main + branches: [main] + workflow_dispatch: + -# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages permissions: contents: read pages: write id-token: write -# Allow one concurrent deployment concurrency: group: "pages" cancel-in-progress: true jobs: - build-docs: + + build: uses: ./.github/workflows/build_docs.yml deploy: - needs: [build-docs] - + needs: build environment: name: github-pages url: ${{ steps.deployment.outputs.page_url }} runs-on: ubuntu-latest - steps: - - name: Download docs artifact - # docs artifact is uploaded by build-docs job - uses: actions/download-artifact@v3 - with: - name: documentation - path: "./public" - - - name: Upload artifact - uses: actions/upload-pages-artifact@v2 - with: - path: "./public" + steps: - name: Checkout - uses: actions/checkout@v4 + uses: actions/checkout@v5 - name: Setup Pages - uses: actions/configure-pages@v3 + uses: actions/configure-pages@v5 + - name: Deploy to GitHub Pages id: deployment - uses: actions/deploy-pages@v2 + uses: actions/deploy-pages@v4 diff --git a/.github/workflows/pre-commit.yml b/.github/workflows/pre-commit.yml index 83e94e7..7c6df47 100644 --- a/.github/workflows/pre-commit.yml +++ b/.github/workflows/pre-commit.yml @@ -9,10 +9,13 @@ on: jobs: check-code: - runs-on: ubuntu-22.04 + runs-on: ubuntu-24.04 steps: # This action sets the current path to the root of your github repo - - uses: actions/checkout@v4 + - uses: actions/checkout@v5 + + - name: Install Python + uses: actions/setup-python@v6 - name: Install pre-commit run: python3 -m pip install pre-commit diff --git a/.github/workflows/reproduce_results.yml b/.github/workflows/reproduce_results.yml index dc82691..65ef2f5 100644 --- a/.github/workflows/reproduce_results.yml +++ b/.github/workflows/reproduce_results.yml @@ -22,38 +22,32 @@ jobs: RESULTDIR: ./artifacts/results steps: - - uses: actions/checkout@v4 + - uses: actions/checkout@v5 - - name: Setup Python - uses: actions/setup-python@v4 + # setup Python + - name: Install Python + uses: actions/setup-python@v6 with: - python-version: "3.10" + python-version-file: ".python-version" - - name: Cache - id: cache - uses: actions/cache@v3 - with: - path: | - ~/.cache/pip - key: cache_v1 - restore-keys: | - cache_v1 + - name: Install uv + uses: astral-sh/setup-uv@v6 - - name: Install dependencies - run: python3 -m pip install -r requirements.txt + - name: Install the project + run: uv sync - name: Run pre-processing - run: python3 code/pre_processing.py --datapath=${{ env.DATAPATH }} + run: uv run python3 code/pre_processing.py --datapath=${{ env.DATAPATH }} - name: Run simulation - run: python3 code/run_all.py --resultdir=${{ env.RESULTDIR }} + run: uv run python3 code/run_all.py --resultdir=${{ env.RESULTDIR }} - name: Postprocess - run: python3 code/postprocess.py --resultdir=${{ env.RESULTDIR }} --datapath=${{ env.DATAPATH }} --figdir=${{ env.FIGDIR }} + run: uv run python3 code/postprocess.py --resultdir=${{ env.RESULTDIR }} --datapath=${{ env.DATAPATH }} --figdir=${{ env.FIGDIR }} - name: Upload artifact if: always() - uses: actions/upload-artifact@v3 + uses: actions/upload-artifact@v5 with: path: ./artifacts if-no-files-found: error diff --git a/.python-version b/.python-version new file mode 100644 index 0000000..e4fba21 --- /dev/null +++ b/.python-version @@ -0,0 +1 @@ +3.12 diff --git a/README.md b/README.md index 6f0f83d..b4530c4 100644 --- a/README.md +++ b/README.md @@ -11,7 +11,19 @@ Provide the abstract of the paper ## Getting started -We provide a pre-build Docker image which can be used to run the the code in this repository. First thing you need to do is to ensure that you have [docker installed](https://docs.docker.com/get-docker/). +First install `uv` +```bash +curl -LsSf https://astral.sh/uv/install.sh | sh +``` +Then create a virtual environment and install dependencies + +```bash +uv venv +source .venv/bin/activate +uv sync --locked --all-extras --dev +``` + +We also provide a pre-build Docker image which can be used to run the the code in this repository. First thing you need to do is to ensure that you have [docker installed](https://docs.docker.com/get-docker/). To start an interactive docker container you can execute the following command diff --git a/_config.yml b/_config.yml index 0afdee5..a6be5c6 100644 --- a/_config.yml +++ b/_config.yml @@ -51,4 +51,4 @@ sphinx: - "sphinxcontrib.bibtex" -exclude_patterns: [".pytest_cache/*", ".github/*"] +exclude_patterns: [".pytest_cache/*", ".github/*", "venv/*", ".venv/*"] diff --git a/cspell.json b/cspell.json index 8d72e79..e2215ac 100644 --- a/cspell.json +++ b/cspell.json @@ -12,7 +12,8 @@ "nagumo", "postprocess", "scientificcomputing", - "zenodo" + "zenodo", + "venv" ], "ignoreWords": [], "import": [] diff --git a/pyproject.toml b/pyproject.toml index 38a03e4..69933b4 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -5,6 +5,7 @@ build-backend = "setuptools.build_meta" [project] name = "my-paper" version = "1.2.0" +requires-python = ">=3.10" dependencies = [ "ap_features", "matplotlib", diff --git a/requirements-dev.txt b/requirements-dev.txt deleted file mode 100644 index 218e400..0000000 --- a/requirements-dev.txt +++ /dev/null @@ -1,94 +0,0 @@ -# -# This file is autogenerated by pip-compile with Python 3.11 -# by the following command: -# -# pip-compile --extra=dev --output-file=requirements-dev.txt pyproject.toml -# -ap-features==2023.7.4 - # via my-paper (pyproject.toml) -attrs==23.1.0 - # via wmctrl -cfgv==3.4.0 - # via pre-commit -contourpy==1.2.0 - # via matplotlib -cycler==0.12.1 - # via matplotlib -distlib==0.3.7 - # via virtualenv -fancycompleter==0.9.1 - # via pdbpp -filelock==3.13.1 - # via virtualenv -fonttools==4.44.0 - # via matplotlib -identify==2.5.31 - # via pre-commit -jinja2==3.1.2 - # via pandas -kiwisolver==1.4.5 - # via matplotlib -llvmlite==0.40.1 - # via numba -markupsafe==2.1.3 - # via jinja2 -matplotlib==3.8.1 - # via my-paper (pyproject.toml) -nodeenv==1.8.0 - # via pre-commit -numba==0.57.1 - # via ap-features -numpy==1.24.4 - # via - # ap-features - # contourpy - # matplotlib - # my-paper (pyproject.toml) - # numba - # pandas - # scipy -packaging==23.2 - # via matplotlib -pandas[output-formatting]==2.1.2 - # via my-paper (pyproject.toml) -pdbpp==0.10.3 - # via my-paper (pyproject.toml) -pillow==10.1.0 - # via matplotlib -platformdirs==3.11.0 - # via virtualenv -pre-commit==3.5.0 - # via my-paper (pyproject.toml) -pygments==2.16.1 - # via pdbpp -pyparsing==3.1.1 - # via matplotlib -pyrepl==0.9.0 - # via fancycompleter -python-dateutil==2.8.2 - # via - # matplotlib - # pandas -pytz==2023.3.post1 - # via pandas -pyyaml==6.0.1 - # via pre-commit -scipy==1.11.3 - # via - # ap-features - # my-paper (pyproject.toml) -six==1.16.0 - # via python-dateutil -tabulate==0.9.0 - # via pandas -tqdm==4.66.1 - # via ap-features -tzdata==2023.3 - # via pandas -virtualenv==20.24.6 - # via pre-commit -wmctrl==0.5 - # via pdbpp - -# The following packages are considered to be unsafe in a requirements file: -# setuptools diff --git a/requirements-docs.txt b/requirements-docs.txt deleted file mode 100644 index 3e27fc5..0000000 --- a/requirements-docs.txt +++ /dev/null @@ -1,347 +0,0 @@ -# -# This file is autogenerated by pip-compile with Python 3.11 -# by the following command: -# -# pip-compile --extra=docs --output-file=requirements-docs.txt pyproject.toml -# -accessible-pygments==0.0.4 - # via pydata-sphinx-theme -alabaster==0.7.13 - # via sphinx -ap-features==2023.7.4 - # via my-paper (pyproject.toml) -appnope==0.1.3 - # via - # ipykernel - # ipython -asttokens==2.4.1 - # via stack-data -attrs==23.1.0 - # via - # jsonschema - # jupyter-cache - # referencing -babel==2.13.1 - # via - # pydata-sphinx-theme - # sphinx -beautifulsoup4==4.12.2 - # via pydata-sphinx-theme -certifi==2023.7.22 - # via requests -charset-normalizer==3.3.2 - # via requests -click==8.1.7 - # via - # jupyter-book - # jupyter-cache - # sphinx-external-toc -comm==0.1.4 - # via ipykernel -contourpy==1.2.0 - # via matplotlib -cycler==0.12.1 - # via matplotlib -debugpy==1.8.0 - # via ipykernel -decorator==5.1.1 - # via ipython -docutils==0.18.1 - # via - # jupyter-book - # myst-parser - # pybtex-docutils - # pydata-sphinx-theme - # sphinx - # sphinx-togglebutton - # sphinxcontrib-bibtex -executing==2.0.1 - # via stack-data -fastjsonschema==2.18.1 - # via nbformat -fonttools==4.44.0 - # via matplotlib -idna==3.4 - # via requests -imagesize==1.4.1 - # via sphinx -importlib-metadata==6.8.0 - # via - # jupyter-cache - # myst-nb -ipykernel==6.26.0 - # via myst-nb -ipython==8.17.2 - # via - # ipykernel - # myst-nb -jedi==0.19.1 - # via ipython -jinja2==3.1.2 - # via - # jupyter-book - # myst-parser - # pandas - # sphinx -jsonschema==4.19.2 - # via - # jupyter-book - # nbformat -jsonschema-specifications==2023.7.1 - # via jsonschema -jupyter-book==0.15.1 - # via my-paper (pyproject.toml) -jupyter-cache==0.6.1 - # via myst-nb -jupyter-client==8.5.0 - # via - # ipykernel - # nbclient -jupyter-core==5.5.0 - # via - # ipykernel - # jupyter-client - # nbclient - # nbformat -jupytext==1.15.2 - # via my-paper (pyproject.toml) -kiwisolver==1.4.5 - # via matplotlib -latexcodec==2.0.1 - # via pybtex -linkify-it-py==2.0.2 - # via jupyter-book -llvmlite==0.40.1 - # via numba -markdown-it-py==2.2.0 - # via - # jupytext - # mdit-py-plugins - # myst-parser -markupsafe==2.1.3 - # via jinja2 -matplotlib==3.8.1 - # via my-paper (pyproject.toml) -matplotlib-inline==0.1.6 - # via - # ipykernel - # ipython -mdit-py-plugins==0.3.5 - # via - # jupytext - # myst-parser -mdurl==0.1.2 - # via markdown-it-py -myst-nb==0.17.2 - # via jupyter-book -myst-parser==0.18.1 - # via myst-nb -nbclient==0.7.4 - # via - # jupyter-cache - # myst-nb -nbformat==5.9.2 - # via - # jupyter-cache - # jupytext - # myst-nb - # nbclient -nest-asyncio==1.5.8 - # via ipykernel -numba==0.57.1 - # via ap-features -numpy==1.24.4 - # via - # ap-features - # contourpy - # matplotlib - # my-paper (pyproject.toml) - # numba - # pandas - # scipy -packaging==23.2 - # via - # ipykernel - # matplotlib - # pydata-sphinx-theme - # sphinx 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