Doc sphinx

.github/workflows/ci.yml

@@ -0,0 +1,196 @@
+name: CI Pipeline
+
+on:
+  push:
+    branches:
+      - main
+      - develop
+  pull_request:
+    branches:
+      - '**'
+
+jobs:
+  build-env:
+    name: Build Conda Environment
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Set up Miniconda
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          activate-environment: lenapy_env
+          environment-file: environment.yml
+          auto-activate-base: false
+
+      - name: Cache Conda environment
+        uses: actions/cache@v4
+        with:
+          path: /usr/share/miniconda/envs/lenapy_env
+          key: conda-${{ runner.os }}-${{ hashFiles('environment.yml') }}
+          restore-keys: |
+            conda-${{ runner.os }}-
+
+  formater:
+    name: Code Formatting Check
+    runs-on: ubuntu-latest
+    needs: build-env
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Install Dependencies
+        shell: bash -l {0}
+        run: pip install -e .[formatter]
+
+      - name: Run Black & Isort
+        run: |
+          black --check --diff lenapy
+          isort lenapy --check --diff
+
+  pytest:
+    name: Run Pytest
+    runs-on: ubuntu-latest
+    needs: build-env
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Set up Miniconda
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          auto-update-conda: false
+          activate-environment: lenapy_env
+
+      - name: Restore Conda environment
+        uses: actions/cache@v4
+        with:
+          path: /usr/share/miniconda/envs/lenapy_env
+          key: conda-${{ runner.os }}-${{ hashFiles('environment.yml') }}
+
+      - name: Run Pytest with Coverage
+        shell: bash -l {0}
+        run: |
+          pip install -e .[test]
+          pytest -s tests --cov=lenapy --cov-report=xml:.ci-reports/coverage.xml --cov-report html:cov_html --cov-report=term --junitxml=pytest-results.xml
+
+      - name: Upload Coverage Report
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-report
+          path: |
+            .ci-reports/
+            cov_html/
+            pytest-results.xml
+      - name: Publish test results
+        uses: EnricoMi/publish-unit-test-result-action@v2
+        with:
+          files: pytest-results.xml
+
+  test_notebooks:
+    name: Test Jupyter Notebooks
+    runs-on: ubuntu-latest
+    needs: build-env
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Set up Miniconda
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          auto-update-conda: false
+          activate-environment: lenapy_env
+
+      - name: Restore Conda environment
+        uses: actions/cache@v4
+        with:
+          path: /usr/share/miniconda/envs/lenapy_env
+          key: conda-${{ runner.os }}-${{ hashFiles('environment.yml') }}
+
+      - name: Install Notebook Dependencies
+        shell: bash -l {0}
+        run: |
+          pip install -e .[test]
+          pip install -e .[notebook]
+
+      - name: Run Pytest on Notebooks
+        shell: bash -l {0}
+        run: |
+          pytest --nbmake --nbmake-kernel=python3 doc/tutorials/
+
+  pylint_analysis:
+    name: Pylint Code Analysis
+    runs-on: ubuntu-latest
+    needs: build-env
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Install Dependencies
+        shell: bash -l {0}
+        run: pip install -e .[quality]
+
+      - name: Run Pylint
+        shell: bash -l {0}
+        run: |
+          pylint --recursive=y --disable=all --fail-under=10 --enable=too-many-statements,too-many-nested-blocks lenapy
+
+  mccabe_analysis:
+    name: McCabe Complexity Analysis
+    runs-on: ubuntu-latest
+    needs: build-env
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Set up Conda
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          activate-environment: lenapy
+          auto-activate-base: false
+
+      - name: Install Quality Tools
+        shell: bash -l {0}
+        run: pip install .[quality]
+
+      - name: Run McCabe Complexity Check
+        shell: bash -l {0}
+        run: ./continuous_integration/scripts/check_mccabe_complexity.sh 25 lenapy lenapy/readers/ocean.py lenapy/plots/plotting.py
+
+  build_doc:
+    name: Build sphinx documentation
+    runs-on: ubuntu-latest
+    needs: build-env
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Set up Miniconda
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          auto-update-conda: false
+          activate-environment: lenapy_env
+
+      - name: Restore Conda environment
+        uses: actions/cache@v4
+        with:
+          path: /usr/share/miniconda/envs/lenapy_env
+          key: conda-${{ runner.os }}-${{ hashFiles('environment.yml') }}
+
+      - name: Install documentation dependencies
+        shell: bash -l {0}
+        run: pip install .[doc]
+      - name: Build doc
+        shell: bash -l {0}
+        run: |
+          conda install pandoc
+          sphinx-build -b html doc doc/build
+
+      - name: Upload doc as artefact
+        uses: actions/upload-artifact@v4
+        with:
+          name: doc-build
+          path: |
+            doc/build
+          retention-days: 7

.gitlab-ci.yml

@@ -0,0 +1,133 @@
+workflow:
+  rules:
+    - if: $CI_PIPELINE_SOURCE == "merge_request_event"
+    - if: $CI_PIPELINE_SOURCE == "web"
+    - if: $CI_PIPELINE_SOURCE == "schedule"
+    - if: $CI_COMMIT_BRANCH && $CI_OPEN_MERGE_REQUESTS
+      when: never
+    - if: $CI_COMMIT_BRANCH
+
+stages:
+  - init
+  - quality
+  - documentation
+
+# Default configuration for all jobs
+default:
+  tags:
+    - Usine_Logicielle
+  timeout: 30 minutes
+
+variables:
+  DEBUG:
+    value: 'false'
+    description: "Afficher des logs supplémentaires"
+
+  TAG_IMAGE_CONDA: "publicremotes-docker/continuumio/miniconda3:23.5.2-0"
+  TAG_IMAGE_SONAR: "publicremotes-docker/sonarsource/sonar-scanner-cli:4.5"
+  CI: "true"
+  JFROG_CLI_HOME_DIR: ".jfrog/"
+  JFROG_CLI_TEMP_DIR: ".jfrog_tmp"
+  JFROG_VERSION: "v2/2.14.0"
+  JFROG_OS: "jfrog-cli-linux-amd64"
+  JFROG_CLI_BUILD_NAME: "${CI_PROJECT_PATH}_${CI_COMMIT_REF_SLUG}_gitlab-ci"
+  JFROG_CLI_BUILD_NUMBER: "${CI_PIPELINE_ID}"
+
+  ARTIFACTORY_BUILD_URL: "https://${artifactory_host}/artifactory/webapp/#/builds/${JFROG_CLI_BUILD_NAME}/${JFROG_CLI_BUILD_NUMBER}"
+  CI_TEMPLATE_REGISTRY_HOST: "${ARTIFACTORY_HOST}/publicremotes-docker"
+  PIP_INDEX_URL: "https://${ARTIFACTORY_USER}:${ARTIFACTORY_TOKEN}@${ARTIFACTORY_HOST}/artifactory/api/pypi/pypi/simple"
+  PIP_CERT: "${CNES_CERTIFICATE}"
+  PIP_CACHE_DIR: ".pip-cache/"
+  CONDA_ENVS_DIRS: ".conda/envs"
+  CONDA_SSL_VERIFY: "${CNES_CERTIFICATE}"
+  PIP_SSL_VERIFY: "${CNES_CERTIFICATE}"
+  REQUESTS_CA_BUNDLE: "${CNES_CERTIFICATE}"
+
+build-env:
+  stage: init
+  image: ${ARTIFACTORY_HOST}/${TAG_IMAGE_CONDA}
+  before_script:
+    - export no_proxy=$NO_PROXY
+    - export http_proxy=$HTTP_PROXY
+    - export https_proxy=$HTTP_PROXY
+    - mkdir -p ${CONDA_ENVS_DIRS}
+    - pip install conda-lock
+  script:
+    - conda-lock install --name lenapy_env conda-lock.yml
+  timeout: 15 minutes
+  artifacts:
+    untracked: true
+    expire_in: 1 day
+
+formater:
+  stage: quality
+  image: ${ARTIFACTORY_HOST}/${TAG_IMAGE_CONDA}
+  before_script:
+  - source activate lenapy_env
+  - pip install .[formatter]
+  script:
+  - python -m black --check --diff lenapy
+  - python -m isort lenapy --check --diff
+
+pytest:
+  stage: quality
+  image: ${ARTIFACTORY_HOST}/${TAG_IMAGE_CONDA}
+  before_script:
+    - export no_proxy=$NO_PROXY
+    - export http_proxy=$HTTP_PROXY
+    - export https_proxy=$HTTP_PROXY
+  script:
+    - source activate lenapy_env
+    - pip install -e .[test]
+    - pytest -s tests --cov=lenapy --cov-report=xml:.ci-reports/coverage.xml --cov-report html:cov_html --cov-report=term --junitxml=.ci-reports/junit-report.xml
+  artifacts:
+    when: always
+    paths:
+      - ./.ci-reports/
+      - ./cov_html/
+    expire_in: 1 day
+
+test_notebooks:
+  stage: quality
+  image: ${ARTIFACTORY_HOST}/${TAG_IMAGE_CONDA}
+  script:
+    - source activate lenapy_env
+    - pip install -e .[test]
+    - pip install -e .[notebook]
+    - pytest --nbmake --nbmake-kernel=python3 doc/tutorials/
+
+pylint_analysis:
+  stage: quality
+  image: ${ARTIFACTORY_HOST}/${TAG_IMAGE_CONDA}
+  script:
+    - source activate lenapy_env
+    - pip install .[quality]
+    - pylint --recursive=y --disable=all --fail-under=10 --enable=too-many-statements,too-many-nested-blocks lenapy | tee pylint_report.txt
+  artifacts:
+    when: always
+    paths:
+      - pylint_report.txt
+    expire_in: 1 day
+
+mccabe_analysis:
+  stage: quality
+  image: ${ARTIFACTORY_HOST}/${TAG_IMAGE_CONDA}
+  script:
+    - source activate lenapy_env
+    - pip install .[quality]
+    - ./continuous_integration/scripts/check_mccabe_complexity.sh 25 lenapy lenapy/readers/ocean.py lenapy/plots/plotting.py
+
+build_doc:
+  stage: documentation
+  image: ${ARTIFACTORY_HOST}/${TAG_IMAGE_CONDA}
+  before_script:
+    - source activate lenapy_env
+    - pip install .[doc]
+  script:
+    - conda install pandoc
+    - sphinx-build -b html doc doc/build
+  artifacts:
+    when: always
+    paths:
+      - doc/build
+    expire_in: 7 day

.readthedocs.yaml

@@ -30,9 +30,9 @@ sphinx:
 # Optional but recommended, declare the Python requirements required
 # to build your documentation
 # See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
-python:
-   install:
-     - requirements: doc/requirements.txt
-
 conda:
   environment: doc/environment.yml
+python:
+  install:
+    - method: pip
+      path: .