Merge pull request #4 from ecmwf-projects/COPDS-1893

COPDS-1893: Cookiecutter

.cruft.json

@@ -0,0 +1,19 @@
+{
+  "template": "https://github.com/ecmwf-projects/cookiecutter-conda-package",
+  "commit": "3b34cec552be24da244f3ec6133685c83a4e9f6c",
+  "checkout": null,
+  "context": {
+    "cookiecutter": {
+      "project_name": "cads-mars-server",
+      "project_slug": "cads_mars_server",
+      "project_short_description": "A proxy MARS server and client designed for CADS",
+      "copyright_holder": "European Union",
+      "copyright_year": "2024",
+      "mypy_strict": false,
+      "integration_tests": "true",
+      "pypi": true,
+      "_template": "https://github.com/ecmwf-projects/cookiecutter-conda-package"
+    }
+  },
+  "directory": null
+}

.github/workflows/on-push.yml

@@ -0,0 +1,235 @@
+name: on-push
+
+on:
+  push:
+    branches:
+    - main
+    tags:
+    - '*'
+  pull_request:
+    branches:
+    - main
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+defaults:
+  run:
+    shell: bash -l {0}
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - uses: actions/setup-python@v5
+      with:
+        python-version: 3.x
+    - uses: pre-commit/action@v3.0.1
+
+  combine-environments:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+    - uses: actions/setup-python@v5
+      with:
+        python-version: 3.x
+    - name: Install conda-merge
+      run: |
+        python -m pip install conda-merge
+    - name: Combine environments
+      run: |
+        for SUFFIX in ci integration; do
+        conda-merge ci/environment-$SUFFIX.yml environment.yml > ci/combined-environment-$SUFFIX.yml || exit
+        done
+    - uses: actions/upload-artifact@v4
+      with:
+        name: combined-environments
+        path: ci/combined-environment-*.yml
+
+  unit-tests:
+    name: unit-tests
+    needs: combine-environments
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.11']
+
+    steps:
+    - uses: actions/checkout@v4
+    - uses: actions/download-artifact@v4
+      with:
+        name: combined-environments
+        path: ci
+    - name: Get current date
+      id: date
+      run: echo "date=$(date +%Y-%m-%d)" >> "${GITHUB_OUTPUT}"
+    - uses: mamba-org/setup-micromamba@v1
+      with:
+        environment-file: ci/combined-environment-ci.yml
+        environment-name: DEVELOP
+        cache-environment: true
+        cache-environment-key: environment-${{ steps.date.outputs.date }}
+        cache-downloads-key: downloads-${{ steps.date.outputs.date }}
+        create-args: >-
+          python=${{ matrix.python-version }}
+    - name: Install package
+      run: |
+        python -m pip install --no-deps -e .
+    - name: Run tests
+      run: |
+        make unit-tests COV_REPORT=xml
+
+  type-check:
+    needs: [combine-environments, unit-tests]
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+    - uses: actions/download-artifact@v4
+      with:
+        name: combined-environments
+        path: ci
+    - name: Get current date
+      id: date
+      run: echo "date=$(date +%Y-%m-%d)" >> "${GITHUB_OUTPUT}"
+    - uses: mamba-org/setup-micromamba@v1
+      with:
+        environment-file: ci/combined-environment-ci.yml
+        environment-name: DEVELOP
+        cache-environment: true
+        cache-environment-key: environment-${{ steps.date.outputs.date }}
+        cache-downloads-key: downloads-${{ steps.date.outputs.date }}
+        create-args: >-
+          python=3.11
+    - name: Install package
+      run: |
+        python -m pip install --no-deps -e .
+    - name: Run code quality checks
+      run: |
+        make type-check
+
+  docs-build:
+    needs: [combine-environments, unit-tests]
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+    - uses: actions/download-artifact@v4
+      with:
+        name: combined-environments
+        path: ci
+    - name: Get current date
+      id: date
+      run: echo "date=$(date +%Y-%m-%d)" >> "${GITHUB_OUTPUT}"
+    - uses: mamba-org/setup-micromamba@v1
+      with:
+        environment-file: ci/combined-environment-ci.yml
+        environment-name: DEVELOP
+        cache-environment: true
+        cache-environment-key: environment-${{ steps.date.outputs.date }}
+        cache-downloads-key: downloads-${{ steps.date.outputs.date }}
+        create-args: >-
+          python=3.11
+    - name: Install package
+      run: |
+        python -m pip install --no-deps -e .
+    - name: Build documentation
+      run: |
+        make docs-build
+
+  integration-tests:
+    needs: [combine-environments, unit-tests]
+    if: |
+      success() && true
+    runs-on: ubuntu-latest
+
+    strategy:
+      matrix:
+        include:
+        - python-version: '3.6'
+          extra: -integration
+
+    steps:
+    - uses: actions/checkout@v4
+    - uses: actions/download-artifact@v4
+      with:
+        name: combined-environments
+        path: ci
+    - name: Get current date
+      id: date
+      run: echo "date=$(date +%Y-%m-%d)" >> "${GITHUB_OUTPUT}"
+    - uses: mamba-org/setup-micromamba@v1
+      with:
+        environment-file: ci/combined-environment${{ matrix.extra }}.yml
+        environment-name: DEVELOP${{ matrix.extra }}
+        cache-environment: true
+        cache-environment-key: environment-${{ steps.date.outputs.date }}
+        cache-downloads-key: downloads-${{ steps.date.outputs.date }}
+        create-args: >-
+          python=${{ matrix.python-version }}
+    - name: Install package
+      run: |
+        python -m pip install --no-deps -e .
+    - name: Run tests
+      run: |
+        make unit-tests COV_REPORT=xml
+
+  distribution:
+    runs-on: ubuntu-latest
+    needs: [unit-tests, type-check, docs-build, integration-tests]
+    if: |
+      always() &&
+      needs.unit-tests.result == 'success' &&
+      needs.type-check.result == 'success' &&
+      needs.docs-build.result == 'success' &&
+      (needs.integration-tests.result == 'success' || needs.integration-tests.result == 'skipped')
+
+    steps:
+    - uses: actions/checkout@v4
+    - uses: actions/setup-python@v5
+      with:
+        python-version: '3.11'
+    - name: Install package
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install build twine
+    - name: Build distribution
+      run: |
+        python -m build
+    - name: Check wheels
+      run: |
+        cd dist || exit
+        python -m pip install cads_mars_server*.whl || exit
+        python -m twine check --strict * || exit
+        python -c "import cads_mars_server" || exit
+        cd ..
+    - uses: actions/upload-artifact@v4
+      with:
+        name: distribution
+        path: dist
+
+  upload-to-pypi:
+    runs-on: ubuntu-latest
+    needs: distribution
+    if: |
+      always() && false &&
+      needs.distribution.result == 'success' &&
+      github.event_name == 'push' &&
+      startsWith(github.ref, 'refs/tags')
+    environment:
+      name: pypi
+      url: https://pypi.org/p/cads-mars-server
+    permissions:
+      id-token: write  # IMPORTANT: this permission is mandatory for trusted publish
+
+    steps:
+    - uses: actions/download-artifact@v4
+      with:
+        name: distribution
+        path: dist
+    - uses: pypa/gh-action-pypi-publish@v1.9.0
+      with:
+        verbose: true

.gitignore

@@ -1,6 +1,5 @@
 # setuptools-scm
 version.py
-test.ipynb
 
 # Sphinx automatic generation of API
 docs/_api/
@@ -132,7 +131,7 @@ Temporary Items
 .idea/**/usage.statistics.xml
 .idea/**/dictionaries
 .idea/**/shelf
-.idea/
+
 # AWS User-specific
 .idea/**/aws.xml
 
@@ -200,7 +199,7 @@ fabric.properties
 
 # Android studio 3.1+ serialized cache file
 .idea/caches/build_file_checksums.ser
-.idea/
+
 ### PyCharm Patch ###
 # Comment Reason: https://github.com/joeblau/gitignore.io/issues/186#issuecomment-215987721
 
@@ -470,5 +469,3 @@ $RECYCLE.BIN/
 *.lnk
 
 # End of https://www.toptal.com/developers/gitignore/api/python,jupyternotebooks,vim,visualstudiocode,pycharm,emacs,linux,macos,windows
-test.ipynb
-*.sh

.pre-commit-config-cruft.yaml

@@ -0,0 +1,7 @@
+repos:
+- repo: https://github.com/cruft/cruft
+  rev: 2.15.0
+  hooks:
+  - id: cruft
+    entry: cruft update -y
+    additional_dependencies: [toml]

.pre-commit-config.yaml

@@ -1,26 +1,39 @@
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.4.0
+  rev: v4.6.0
   hooks:
   - id: trailing-whitespace
   - id: end-of-file-fixer
   - id: check-json
   - id: check-yaml
+  - id: check-toml
+  - id: check-added-large-files
+  - id: check-merge-conflict
   - id: debug-statements
-- repo: https://github.com/PyCQA/isort
-  rev: 5.12.0
-  hooks:
-  - id: isort
-- repo: https://github.com/psf/black
-  rev: 22.10.0
-  hooks:
-  - id: black
+  - id: mixed-line-ending
 - repo: https://github.com/keewis/blackdoc
-  rev: v0.3.8
+  rev: v0.3.9
   hooks:
   - id: blackdoc
-    additional_dependencies: [black==22.3.0]
+    additional_dependencies: [black==23.11.0]
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.5.2
+  hooks:
+  - id: ruff
+    args: [--fix, --show-fixes]
+  - id: ruff-format
 - repo: https://github.com/executablebooks/mdformat
-  rev: 0.7.16
+  rev: 0.7.17
   hooks:
   - id: mdformat
+- repo: https://github.com/macisamuele/language-formatters-pre-commit-hooks
+  rev: v2.14.0
+  hooks:
+  - id: pretty-format-yaml
+    args: [--autofix, --preserve-quotes]
+  - id: pretty-format-toml
+    args: [--autofix]
+- repo: https://github.com/gitleaks/gitleaks
+  rev: v8.18.4
+  hooks:
+  - id: gitleaks

Dockerfile

@@ -0,0 +1,12 @@
+FROM continuumio/miniconda3
+
+WORKDIR /src/cads-mars-server
+
+COPY environment.yml /src/cads-mars-server/
+
+RUN conda install -c conda-forge gcc python=3.11 \
+    && conda env update -n base -f environment.yml
+
+COPY . /src/cads-mars-server
+
+RUN pip install --no-deps -e .

LICENSE

@@ -186,7 +186,7 @@
       same "printed page" as the copyright notice for easier
       identification within third-party archives.
 
-   Copyright [yyyy] [name of copyright owner]
+   Copyright 2024, European Union.
 
    Licensed under the Apache License, Version 2.0 (the "License");
    you may not use this file except in compliance with the License.

Makefile

@@ -1,4 +1,6 @@
 PROJECT := cads_mars_server
+CONDA := conda
+CONDAFLAGS :=
 COV_REPORT := html
 
 default: qa unit-tests type-check
@@ -12,4 +14,21 @@ unit-tests:
 type-check:
 	python -m mypy .
 
+conda-env-update:
+	$(CONDA) install -y -c conda-forge conda-merge
+	$(CONDA) run conda-merge environment.yml ci/environment-ci.yml > ci/combined-environment-ci.yml
+	$(CONDA) env update $(CONDAFLAGS) -f ci/combined-environment-ci.yml
+
+docker-build:
+	docker build -t $(PROJECT) .
+
+docker-run:
+	docker run --rm -ti -v $(PWD):/srv $(PROJECT)
+
+template-update:
+	pre-commit run --all-files cruft -c .pre-commit-config-cruft.yaml
+
+docs-build:
+	cd docs && rm -fr _api && make clean && make html
+
 # DO NOT EDIT ABOVE THIS LINE, ADD COMMANDS BELOW