Merge pull request #140 from IMMM-SFA/dev

new release
IMMM-SFA · Dec 26, 2024 · 2c3cd05 · 2c3cd05
2 parents 3cb8456 + fd197b2
commit 2c3cd05
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diff --git a/.github/ISSUE_TEMPLATE/contribution_proposal.yml b/.github/ISSUE_TEMPLATE/contribution_proposal.yml
@@ -1,5 +1,5 @@
 name: Contribution Proposal
-description: 
+description:
   Want to contribute to our eBook?  Fill the following proposal form and we will review your contribution idea shortly.
 labels: ["needs triage"]
 
@@ -26,7 +26,7 @@ body:
       description: Please provide your email address
     validations:
       required: true
-        
+
   - type: textarea
     id: issue-institution
     attributes:
@@ -38,11 +38,11 @@ body:
   - type: textarea
     id: issue-source
     attributes:
-      label: Referral 
+      label: Referral
       description: How did you hear about the eBook?
     validations:
       required: true
-    
+
   - type: dropdown
     id: issue-category
     attributes:

diff --git a/.github/PULL_REQUEST_TEMPLATE/contribution_checklist.md b/.github/PULL_REQUEST_TEMPLATE/contribution_checklist.md
@@ -9,7 +9,7 @@ Please ensure that you are able to check all of the following boxes before submi
 - [ ] My contribution proposal has been approved
 - [ ] I have performed a self-review of my own code
 - [ ] All elements of my contribution are fully open-source and can be distributed with an [Open Source Initiative approved license](https://opensource.org/licenses/) with an understanding that they may be used in community demonstrations and other activities.  Author citations will be present in the notebook for any contributed work to ensure the author(s) receive full credit for their contribution.
-- [ ] Any data or code reused in your submission are correctly cited giving credit to the original authors. 
+- [ ] Any data or code reused in your submission are correctly cited giving credit to the original authors.
 - [ ] The notebook provided is written in English and able to be a stand-alone product that needs no further explanation past what is written in the notebook to make use of it.
 - [ ] The provided work is not merely a regurgitation of an existing tutorial or demonstration but represents a novel contribution.
 - [ ] All contributions and communication thereof must abide by our [code of conduct](https://uc-ebook.org/docs/html/code_of_conduct.html).

diff --git a/.github/workflows/01_test.yml b/.github/workflows/01_test.yml
@@ -1,43 +1,66 @@
-name: Build
+name: Test
 
 on:
   push:
-    branches: [ main, dev ]
+    branches:
+      - main
+      - dev
+  pull_request:
+    branches:
+      - main
+      - dev
+
+  schedule:
+    - cron: '0 8 * * 1'  # Runs every monday at 12am Pacific time
 
 jobs:
   build:
-      runs-on: ${{ matrix.os }}
-
-      strategy:
-        matrix:
-          os: [ubuntu-latest]
+    strategy:
+      matrix:
+        python-version: [ '3.9', '3.10', '3.11', '3.12' ]
+        os: [ ubuntu-latest ]
+      fail-fast: false
 
-      env:
-        OS: ${{ matrix.os }}
-        PYTHON: '3.9'
+    name: Python ${{ matrix.python-version }} on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
 
-      steps:
+    steps:
+      - uses: actions/checkout@v2
 
-        - uses: actions/checkout@v2
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@master
+        with:
+          python-version: ${{ matrix.python-version }}
 
-        - name: Set up Python
-          uses: actions/setup-python@master
-          with:
-            python-version: 3.9
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install .
 
-        - name: Install dependencies
-          run: |
-            python -m pip install --upgrade pip
-            pip install -r requirements.txt
+      - name: Install pytest-mock
+        run: |
+          pip install pytest-mock
 
-        - name: Test and generate coverage report
-          run: |
+      - name: Test and generate coverage report
+        run: |
             pip install pytest
             pip install pytest-cov
             pytest --cov=./ --cov-report=xml
 
-        # - name: Upload coverage to Codecov
-        #   uses: codecov/codecov-action@v1
-        #   with:
-        #     file: ./coverage.xml
-        #     fail_ci_if_error: true
+      - uses: codecov/codecov-action@v4
+        with:
+          files: ./coverage.xml # optional
+          name: codecov-umbrella # optional
+          token: ${{ secrets.CODECOV_TOKEN }} # required
+
+      - name: Notify on failure
+        if: failure()  # This step will only run if any previous step fails
+        run: |
+          echo "Build or tests failed. Please check the logs."
+          
+      - name: Test and generate coverage report
+        run: |
+          pip install pytest
+          pip install pytest-cov
+          pip install pytest-mock  # Ensure pytest-mock is installed before testing
+          pytest --cov=./ --cov-report=xml  # Run tests and generate a coverage report
diff --git a/.github/workflows/02_deploy.yml b/.github/workflows/02_deploy.yml
@@ -18,7 +18,7 @@ jobs:
         working-directory: 'docs/'
         run: |
           python -m pip install --upgrade pip
-          pip install -r requirements.txt
+          pip install ".[docs]"
       - name: Build html and pdf ebook
         working-directory: 'docs/'
         run: |
@@ -91,4 +91,4 @@ jobs:
           branch: gh-pages
           directory: landing/build
           force: true
-          github_token: ${{ secrets.GITHUB_TOKEN }}
+          github_token: ${{ secrets.GITHUB_TOKEN }}
diff --git a/.github/workflows/03_dev_deploy.yml b/.github/workflows/03_dev_deploy.yml
@@ -9,16 +9,15 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v2
-      - uses: actions/setup-python@v2
+      - uses: actions/setup-python@master
         with:
           python-version: '3.9'
       - name: Install latex dependencies
         run: sudo apt-get update -y && sudo apt-get install -y texlive latexmk texlive-latex-recommended texlive-latex-extra texlive-fonts-recommended ghostscript
-      - name: Update pip and install python dependencies
-        working-directory: 'docs/'
+      - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install -r requirements.txt
+          pip install ".[docs]"
       - name: Build html and pdf ebook
         working-directory: 'docs/'
         env:
@@ -48,12 +47,12 @@ jobs:
           AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY_DEV }}
           AWS_REGION: ${{ secrets.AWS_REGION_DEV }}
       - name: Log in to Docker Hub
-        uses: docker/login-action@f054a8b539a109f9f41c372932f1ae047eff08c9
+        uses: docker/login-action@v1
         with:
           username: ${{ secrets.DOCKER_USERNAME }}
           password: ${{ secrets.DOCKER_PASSWORD }}
       - name: Build and push Docker image
-        uses: docker/build-push-action@ad44023a93711e3deb337508980b4b5e9bcdc5dc
+        uses: docker/build-push-action@v2
         with:
           context: .
           file: Dockerfile_dev
@@ -86,4 +85,4 @@ jobs:
           branch: gh-pages
           directory: deploy
           force: true
-          github_token: ${{ secrets.GITHUB_TOKEN }}
+          github_token: ${{ secrets.GITHUB_TOKEN }}
diff --git a/.github/workflows/04_publish-to-pypi.yml b/.github/workflows/04_publish-to-pypi.yml
@@ -0,0 +1,125 @@
+# This GitHub Action will only push to PyPI if the branch is tagged and then merged to main.
+# Tag the branch with:
+# $ git push REMOTE-NAME TAG-NAME
+
+name: Publish Python to PyPI
+
+on:
+  push:
+    branches:
+        - main
+
+jobs:
+  build:
+    name: Build distribution
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: "3.10.x"
+    - name: Install pypa/build
+      run: >-
+        python3 -m
+        pip install
+        build
+        --user
+    - name: Build a binary wheel and a source tarball
+      run: python3 -m build
+    - name: Store the distribution packages
+      uses: actions/upload-artifact@v4
+      with:
+        name: python-package-distributions
+        path: dist/
+
+  publish-to-pypi:
+    name: >-
+      Publish Python distribution to PyPI
+    if: startsWith(github.ref, 'refs/tags/')  # only publish to PyPI on tag pushes
+    needs:
+    - build
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/msdbook
+    permissions:
+      id-token: write  # IMPORTANT: mandatory for trusted publishing
+
+    steps:
+    - name: Download all the dists
+      uses: actions/download-artifact@v4
+      with:
+        name: python-package-distributions
+        path: dist/
+    - name: Publish distribution to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+
+  github-release:
+    name: >-
+      Sign the Python distribution with Sigstore
+      and upload them to GitHub Release
+    needs:
+    - publish-to-pypi
+    runs-on: ubuntu-latest
+
+    permissions:
+      contents: write  # IMPORTANT: mandatory for making GitHub Releases
+      id-token: write  # IMPORTANT: mandatory for sigstore
+
+    steps:
+    - name: Download all the dists
+      uses: actions/download-artifact@v4
+      with:
+        name: python-package-distributions
+        path: dist/
+    - name: Sign the dists with Sigstore
+      uses: sigstore/[email protected]
+      with:
+        inputs: >-
+          ./dist/*.tar.gz
+          ./dist/*.whl
+    - name: Create GitHub Release
+      env:
+        GITHUB_TOKEN: ${{ github.token }}
+      run: >-
+        gh release create
+        '${{ github.ref_name }}'
+        --repo '${{ github.repository }}'
+        --notes ""
+    - name: Upload artifact signatures to GitHub Release
+      env:
+        GITHUB_TOKEN: ${{ github.token }}
+      # Upload to GitHub Release using the `gh` CLI.
+      # `dist/` contains the built packages, and the
+      # sigstore-produced signatures and certificates.
+      run: >-
+        gh release upload
+        '${{ github.ref_name }}' dist/**
+        --repo '${{ github.repository }}'
+
+  publish-to-testpypi:
+    name: Publish to TestPyPI
+    needs:
+    - build
+    runs-on: ubuntu-latest
+
+    environment:
+      name: testpypi
+      url: https://test.pypi.org/p/msdbook
+
+    permissions:
+      id-token: write  # IMPORTANT: mandatory for trusted publishing
+
+    steps:
+    - name: Download all the dists
+      uses: actions/download-artifact@v4
+      with:
+        name: python-package-distributions
+        path: dist/
+    - name: Publish distribution to TestPyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        repository-url: https://test.pypi.org/legacy/
+        verbose: true
diff --git a/.gitignore b/.gitignore
@@ -1,3 +1,6 @@
+# msdbook
+msdbook/data/
+
 # system
 .DS_Store
 
@@ -109,7 +112,7 @@ celerybeat.pid
 
 # Environments
 .env
-.venv
+.venv*
 env/
 venv/
 ENV/

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -0,0 +1,25 @@
+# pre-commit hooks require a user to have installed `pre-commit`:
+#   $ brew install pre-commit
+# Then install the hooks within the repo:
+#   $ cd /PATH/TO/REPO
+#   $ pre-commit install
+
+repos:
+-   repo: https://github.com/charliermarsh/ruff-pre-commit
+    rev: v0.5.5
+    hooks:
+        - id: ruff
+          args: [ --fix, --exit-non-zero-on-fix]
+          exclude: .rst
+-   repo: https://github.com/psf/black
+    rev: 24.4.2
+    hooks:
+    - id: black
+      args: [--line-length=100]
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.6.0
+    hooks:
+    -   id: check-ast
+    -   id: check-yaml
+    -   id: end-of-file-fixer
+    -   id: trailing-whitespace
diff --git a/Dockerfile b/Dockerfile
@@ -1,13 +1,10 @@
-FROM jupyter/minimal-notebook:2022-05-03
+FROM ghcr.io/msd-live/jupyter/python-notebook:latest
 
 USER root
 
-RUN git clone https://github.com/IMMM-SFA/msd_uncertainty_ebook.git msd_uncertainty_ebook
+RUN git clone --depth=1 --branch=main https://github.com/IMMM-SFA/msd_uncertainty_ebook.git msd_uncertainty_ebook
 RUN cd msd_uncertainty_ebook && pip install .
 
-# Now create a symlinked data folder inside the msdbook package that links to /home/demo/data folder
-RUN mkdir -p /bucket/data
-RUN rm -rf /opt/conda/lib/python3.9/site-packages/msdbook/data
-RUN ln -s /bucket/data /opt/conda/lib/python3.9/site-packages/msdbook/data
-
-
+# Install msdbook data
+RUN mkdir -p /opt/conda/lib/python3.11/site-packages/msdbook/data
+RUN python -c 'from msdbook.install_supplement import install_package_data; install_package_data()'
diff --git a/Dockerfile_dev b/Dockerfile_dev
@@ -1,13 +1,10 @@
-FROM jupyter/minimal-notebook:2022-05-03
+FROM ghcr.io/msd-live/jupyter/python-notebook:latest
 
 USER root
 
 RUN git clone --depth=1 --branch=dev https://github.com/IMMM-SFA/msd_uncertainty_ebook.git msd_uncertainty_ebook
 RUN cd msd_uncertainty_ebook && pip install .
 
-# Now create a symlinked data folder inside the msdbook package that links to /home/demo/data folder
-RUN mkdir -p /bucket/data
-RUN rm -rf /opt/conda/lib/python3.9/site-packages/msdbook/data
-RUN ln -s /bucket/data /opt/conda/lib/python3.9/site-packages/msdbook/data
-
-
+# Install msdbook data
+RUN mkdir -p /opt/conda/lib/python3.11/site-packages/msdbook/data
+RUN python -c 'from msdbook.install_supplement import install_package_data; install_package_data()'