Add a docker/dagger-based testing workflow, adopt PEP 517/621

.github/workflows/dagger-docker.yml

@@ -0,0 +1,59 @@
+name: Dagger/Docker Testing Suite
+
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+  workflow_dispatch:
+    inputs:
+      image_tag:
+        description: 'Image tag to use for the Docker image'
+        required: true
+        default: 'latest'
+
+jobs:
+  lint:
+    name: Linting
+    runs-on: ubuntu-latest
+    steps:
+      - name: Cancel previous runs
+        uses: styfle/[email protected]
+        with:
+            access_token: ${{ github.token }}
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: Setup Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.8
+      - name: Install dependencies
+        run: |
+          python -m pip install pre-commit
+          pre-commit install
+      - name: Run pre-commit
+        run: |
+          pre-commit run --all-files --show-diff-on-failure
+
+  integration:
+    name: Integration Tests
+    needs: lint
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
+    strategy:
+        matrix:
+            python-version: ["3.10"]
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: Setup Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Dagger testing
+        run: |
+          export BASE_IMAGE_TAG=${{ github.event.inputs.image_tag }}
+          pip install .[dagger]
+          python ./ci/dagger-pipeline.py

.pre-commit-config.yaml

@@ -6,7 +6,7 @@ repos:
     rev: v3.8.0
     hooks:
       - id: pyupgrade
-        args: [ '--py37-plus' ]
+        args: [ '--py38-plus' ]
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.4.0
     hooks:
@@ -15,6 +15,19 @@ repos:
       - id: end-of-file-fixer
         exclude: .ipynb|.po|.xml
       - id: debug-statements
+        exclude: .ipynb
+      - id: check-toml
+      - id: check-yaml
+        args: [ '--allow-multiple-documents' ]
+  - repo: https://github.com/pappasam/toml-sort
+    rev: v0.23.1
+    hooks:
+      - id: toml-sort-fix
+  - repo: https://github.com/adrienverge/yamllint.git
+    rev: v1.32.0
+    hooks:
+      - id: yamllint
+        args: [ '--config-file=.yamllint.yaml' ]
   - repo: https://github.com/psf/black
     rev: 23.3.0
     hooks:
@@ -28,10 +41,10 @@ repos:
     rev: 1.7.0
     hooks:
       - id: nbqa-black
-        args: [ '--target-version=py37' ]
+        args: [ '--target-version=py38' ]
         additional_dependencies: [ black==23.3.0 ]
       - id: nbqa-pyupgrade
-        args: [ '--py37-plus' ]
+        args: [ '--py38-plus' ]
         additional_dependencies: [ pyupgrade==v3.3.1 ]
       - id: nbqa-isort
         args: [ '--profile=black' ]
@@ -42,6 +55,11 @@ repos:
       - id: nbstripout
         files: ".ipynb"
         args: [ '--keep-output', '--keep-count' ]
+  - repo: https://github.com/keewis/blackdoc
+    rev: v0.3.8
+    hooks:
+    - id: blackdoc
+      additional_dependencies: ['black==23.3.0']
   - repo: meta
     hooks:
       - id: check-hooks-apply

.yamllint.yaml

@@ -0,0 +1,8 @@
+---
+
+rules:
+  document-start: disable
+  line-length:
+    max: 120
+    level: warning
+  truthy: disable

Dockerfile

@@ -0,0 +1,33 @@
+# vim:set ft=dockerfile:
+ARG BASE_IMAGE_TAG
+FROM pavics/workflow-tests:${BASE_IMAGE_TAG:-latest}
+ARG DEBIAN_FRONTEND=noninteractive
+ENV PIP_ROOT_USER_ACTION=ignore
+LABEL org.opencontainers.image.authors="https://github.com/ouranosinc/pavics-sdi"
+LABEL Description="PAVICS-SDI-TESTING-IMAGE" Vendor="Birdhouse" Version="1.3.0"
+
+# root-level commands
+USER root
+
+# Install build tools
+RUN apt-get install --yes build-essential \
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/*
+
+# Switch to /code directory
+WORKDIR /code
+
+# Build finch environment
+COPY environment-dev.yml /code
+RUN mamba install -n birdy python=3.8 --yes \
+    && mamba env update -n birdy -f environment-dev.yml \
+    && mamba clean --all --yes
+
+# Add the finch conda environment to the path
+ENV PATH /opt/conda/envs/birdy/bin:$PATH
+
+# Copy finch source code
+COPY . /code
+
+# Build the documentation
+CMD ["make", "--directory=/code/docs", "html"]

LICENSE

@@ -0,0 +1,28 @@
+BSD 3-Clause License
+
+Copyright (c) 2017, Ouranos, CRIM
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

ci/dagger-pipeline.py

@@ -0,0 +1,49 @@
+"""Build the documentation within a docker pipeline to test integration and notebooks."""
+
+import os
+import sys
+from pathlib import Path
+
+try:
+    import anyio
+    import dagger
+    from dagger import BuildArg
+    from dagger.engine._version import CLI_VERSION as __dagger_version__  # noqa
+except ImportError:
+    raise ImportError(
+        "Dagger is not installed. Please install it with `pip install dagger-io` first."
+    )
+
+
+async def main():
+    async with dagger.Connection(dagger.Config(log_output=sys.stderr)) as client:
+        top_level_dir = client.host().directory(Path(__file__).parent.parent.as_posix())
+
+        # build container
+        sources = await top_level_dir.docker_build(
+            build_args=BuildArg("BASE_IMAGE_TAG", os.getenv("BASE_IMAGE_TAG"))
+            if os.getenv("BASE_IMAGE_TAG")
+            else None,
+        )
+
+        # smoke tests
+        python_version = sources.with_exec(["python", "-V"])
+        username = sources.with_exec(["whoami"])
+
+        # build docs
+        docs = sources.with_exec(["make", "--directory=/code/docs", "html"])
+
+        # execute
+        user = await username.stdout()
+        version = await python_version.stdout()
+        docs_built = await docs.stdout()
+
+    print("\n")
+    print(
+        f"Hello from Dagger {__dagger_version__} and {'.'.join([str(v) for v in sys.version_info[0:3]])}\n"
+    )
+    print(f"Running commands as `{user.strip()}` user in {version.strip()}.\n")
+    print(docs_built)
+
+
+anyio.run(main)

docs/source/index.rst

@@ -41,13 +41,10 @@ Contents
    arch/index
    provenance/index
    support
-   releasenotes
+   release_notes
    license
    todo
 
-
-
-
 Indices and tables
 ==================
 

docs/source/license.rst

@@ -2,18 +2,4 @@
 License
 =======
 
-
-Copyright (c) 2017, Ouranos, CRIM
-All rights reserved.
-
-Permission to use, copy, modify, and/or distribute this software for any
-purpose with or without fee is hereby granted, provided that the above
-copyright notice and this permission notice appear in all copies.
-
-THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
-WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
-MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
-ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
-WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
-ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
-OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
+.. include:: ../../LICENSE

environment-dev.yml

@@ -4,11 +4,12 @@ channels:
   - defaults
 dependencies:
   - python >=3.8,<3.12
+  - flit  # solely needed for installing pavics-sdi
   - jinja2 <=3.0.3
   - jupyter
   - myst-nb
   - nbval
   - pytest
   - sphinx
   - sphinx-intl
-  - sphinx_rtd_theme >=1.0
+  - sphinx-rtd-theme >=1.0

pavics_sdi/__init__.py

@@ -0,0 +1,4 @@
+"""PAVICS SDI package."""
+
+
+__version__ = "1.3.0"

pyproject.toml

@@ -0,0 +1,58 @@
+[build-system]
+requires = ["flit_core >=3.8,<4"]
+build-backend = "flit_core.buildapi"
+
+[project]
+name = "pavics_sdi"
+requires-python = ">=3.8"
+authors = [
+  {name = "CRIM/Ouranos", email = "[email protected]"}
+]
+maintainers = [
+  {name = "Tuan Long Vu", email = "[email protected]"},
+  {name = "David Huard", email = "[email protected]"},
+  {name = "Trevor James Smith", email = "[email protected]"},
+  {name = "Francis Charette-Migneault", email = "[email protected]"}
+]
+readme = {file = "README.rst", content-type = "text/x-rst"}
+description = "Scientific gateway for climate data analytics."
+license = {file = "LICENSE"}
+classifiers = [
+  "Intended Audience :: Science/Research",
+  "License :: OSI Approved :: BSD License",
+  "Operating System :: OS Independent",
+  "Programming Language :: Python",
+  "Programming Language :: Python :: 3",
+  "Programming Language :: Python :: 3.8",
+  "Programming Language :: Python :: 3.9",
+  "Programming Language :: Python :: 3.10",
+  "Programming Language :: Python :: 3.11",
+  "Topic :: Scientific/Engineering :: Atmospheric Science"
+]
+dynamic = ["version"]
+dependencies = []
+
+[project.optional-dependencies]
+docs = [
+  "jinja2",
+  "jupyter",
+  "jupytext",
+  "myst-nb",
+  "requests",
+  "sphinx-intl",
+  "sphinx-jsonschema",
+  "sphinx-rtd-theme>=1.0",
+  "sphinx>=1.4"
+]
+dagger = [
+  "anyio",
+  "dagger-io"
+]
+
+[project.urls]
+"Homepage" = "https://pavics-sdi.readthedocs.io"
+"Source" = "https://github.com/Ouranosinc/pavics-sdi/"
+"Changelog" = "https://pavics-sdi.readthedocs.io/en/latest/release_notes.html"
+"Issue tracker" = "https://github.com/Ouranosinc/pavics-sdi/issues"
+"About CRIM" = "https://www.crim.ca/en/"
+"About Ouranos" = "https://www.ouranos.ca/en/"