From 4e707bfb6dba22ea67d26e4b811049562eed2930 Mon Sep 17 00:00:00 2001 From: Sandro Loch Date: Tue, 5 Dec 2023 06:19:08 -0300 Subject: [PATCH] fix: Separate dependencies into groups for Poetry installation (#175) * fix: Separate dependencies into groups for Poetry installation * fix: Change setup.cfg * Update config for ci workflow * feat(makefile): Introduce new targets for conda environment setup * feat(makefile): Add optional variable to create conda env * fix(ci): Install dev dependencies * chore(ci): Add geos dependencies * Fix broken poetry install * feat(ci): update workflow to support Python 3.10 and 3.11 --- .github/workflows/python-package.yml | 41 ++- Makefile | 31 +- conda/dev.yaml | 8 +- docker/scripts/entrypoint.sh | 9 +- docker/scripts/poetry-install.sh | 2 +- docs/source/tutorials/Dengue.ipynb | 1 - poetry.lock | 474 +++++++++------------------ pyproject.toml | 21 +- setup.cfg | 13 +- 9 files changed, 246 insertions(+), 354 deletions(-) diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml index 364c9fe5..3b4ab88c 100644 --- a/.github/workflows/python-package.yml +++ b/.github/workflows/python-package.yml @@ -1,25 +1,32 @@ -name: tests +name: main on: [push, pull_request] jobs: - build: + tests: runs-on: ubuntu-latest - timeout-minutes: 60 + timeout-minutes: 10 + + defaults: + run: + shell: bash -l {0} + strategy: matrix: - python-version: ["3.9"] + python_version: ["3.10", "3.11"] + concurrency: - group: ci-${{ github.ref }} + group: ci-tests-${{ matrix.python_version }}-${{ github.ref }} cancel-in-progress: true - - defaults: - run: - shell: bash -l {0} steps: - - uses: actions/checkout@v2 - + - uses: actions/checkout@v3 + + - name: Prepare conda environment + run: | + sed -i s/python\ 3\.11/python\ ${{ matrix.python_version }}/ conda/dev.yaml + cat conda/dev.yaml + - uses: conda-incubator/setup-miniconda@v2 with: miniconda-version: "latest" @@ -30,15 +37,20 @@ jobs: use-mamba: true miniforge-variant: Mambaforge + - name: Install dependencies run: | curl -sSL https://install.python-poetry.org/ | python - export PATH="$HOME/.poetry/bin:$PATH" - poetry config virtualenvs.create false - poetry build && poetry install + poetry config virtualenvs.create false + + - name: Install main dependencies + run: | + make conda-install-main ENVCREATE=conda-env - name: Lint with flake8 run: | + make conda-install-dev make check-codestyle - name: Run jupyterlab with PySUS @@ -47,4 +59,5 @@ jobs: - name: Test with pytest run: | - make test + make conda-install-geo + make test-pysus diff --git a/Makefile b/Makefile index a9d23f96..22399545 100644 --- a/Makefile +++ b/Makefile @@ -1,6 +1,7 @@ SHELL := /usr/bin/env bash PYTHON := python PYTHONPATH := ${PWD} +ENVCREATE:= .PHONY: clean clean-test clean-pyc clean-build help @@ -36,11 +37,34 @@ SEMANTIC_RELEASE = npx --yes \ semantic-release +# Create a Conda environment and install dependencies for development. +.PHONY: conda-env +conda-env: + mamba env create -f conda/dev.yaml --force + +# Install main project dependencies using Poetry. +.PHONY: conda-install-main +conda-install-main: ${ENVCREATE} + conda run -n pysus poetry install --only main + +.PHONY: conda-install-dev +conda-install-dev: + conda run -n pysus poetry install --only dev + +.PHONY: conda-install-docs +conda-install-docs: + conda run -n pysus poetry install --only docs + +.PHONY: conda-install-geo +conda-install-geo: + conda run -n pysus pip install --no-use-pep517 shapely==1.8.5.post1 + conda run -n pysus poetry install --only geo + +# Linting .PHONY: pre-commit-install pre-commit-install: poetry run pre-commit install -#* Linting .PHONY: check-codestyle check-codestyle: ## check style with flake8 # stop the build if there are Python syntax errors or undefined names @@ -62,11 +86,10 @@ down-jupyter-pysus: ## stop and remove containers for all services test-jupyter-pysus: ## run pytest for notebooks inside jupyter container $(DOCKER) exec -T jupyter bash /test_notebooks.sh -.PHONY: test -test: ## run tests quickly with the default Python +.PHONY: test-pysus +test-pysus: ## run tests quickly with the default Python cp docs/source/**/*.ipynb pysus/Notebooks poetry run pytest -vv pysus/tests/ - poetry run pytest --nbmake --nbmake-timeout=800 pysus/Notebooks/*.ipynb coverage: ## check code coverage quickly with the default Python coverage run --source pysus/tests/ -m pytest diff --git a/conda/dev.yaml b/conda/dev.yaml index d39f4da4..98b8c5ad 100644 --- a/conda/dev.yaml +++ b/conda/dev.yaml @@ -1,12 +1,12 @@ name: pysus channels: - conda-forge - - nodefaults + - defaults dependencies: - - python >= 3.11 + - python>=3.11 + - numpy>=1.26.2 - cffi - gcc - make - - nbsphinx + - poetry>=1.3.2 - pip - - poetry >= 1.3.2 diff --git a/docker/scripts/entrypoint.sh b/docker/scripts/entrypoint.sh index 51012533..3803b594 100755 --- a/docker/scripts/entrypoint.sh +++ b/docker/scripts/entrypoint.sh @@ -1,3 +1,10 @@ #!/bin/bash -exec jupyter-lab --browser='firefox' --allow-root --NotebookApp.token='' --NotebookApp.password='' +jupyter_lab_path=$(which jupyter) + +if [ -z "$jupyter_lab_path" ]; then + echo "Jupyter not found" + exit 1 +fi + +$jupyter_lab_path lab --browser='firefox' --allow-root --NotebookApp.token='' --NotebookApp.password='' diff --git a/docker/scripts/poetry-install.sh b/docker/scripts/poetry-install.sh index 9850dd50..8f82276a 100644 --- a/docker/scripts/poetry-install.sh +++ b/docker/scripts/poetry-install.sh @@ -3,4 +3,4 @@ set -ex poetry config virtualenvs.create false -poetry install --all-extras --with docs +poetry install --without geo diff --git a/docs/source/tutorials/Dengue.ipynb b/docs/source/tutorials/Dengue.ipynb index 002a4e56..b4e85f10 100644 --- a/docs/source/tutorials/Dengue.ipynb +++ b/docs/source/tutorials/Dengue.ipynb @@ -30,7 +30,6 @@ ], "source": [ "from pysus.ftp.databases.sinan import SINAN\n", - "import keplergl\n", "import pandas as pd\n", "import geopandas as gpd\n", 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