Add a serial plot for the residuals

.github/workflows/commenting_artifacts.yml

@@ -0,0 +1,50 @@
+name: Bind Reports to Pull-Request
+
+# Triggered by the name of the previos
+on:
+  workflow_run:
+    workflows: ["Notebook Pipeline (Ubuntu)"]
+    types: [completed]
+
+# Enable the option to post a comment
+permissions:
+  pull-requests: write
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    # Check that the previos workflow succeeded
+    if: ${{ github.event.workflow_run.conclusion == 'success' }}
+    steps:
+      - name: Get Artifacts Link
+        env:
+          WORKFLOW_RUN_EVENT_OBJ: ${{ toJSON(github.event.workflow_run) }}
+          GH_TOKEN: ${{ github.token }}
+        run: |
+          PREVIOUS_JOB_ID=$(jq -r '.id' <<< "$WORKFLOW_RUN_EVENT_OBJ")
+          SUITE_ID=$(jq -r '.check_suite_id' <<< "$WORKFLOW_RUN_EVENT_OBJ")
+          # Sample for a single artifact, can be improved for a multiple artifacts
+          ARTIFACT_ID=$(gh api "/repos/${{ github.repository }}/actions/artifacts" \
+            --jq ".artifacts.[] |
+            select(.workflow_run.id==${PREVIOUS_JOB_ID}) |
+            .id")
+          echo "ARTIFACT_URL=https://github.com/${{ github.repository }}/suites/${SUITE_ID}/artifacts/${ARTIFACT_ID}" >> $GITHUB_ENV
+          PR_NUMBER=$(jq -r '.pull_requests[0].number' <<< "$WORKFLOW_RUN_EVENT_OBJ")
+          echo "PR_NUMBER=${PR_NUMBER}" >> $GITHUB_ENV
+
+      - uses: actions/github-script@v6
+        env:
+          PR_NUMBER: ${{ env.PR_NUMBER }}
+          PR_NOTES: |
+            Build artifacts:
+            | Name | Link |
+            |------|------|
+            | NB/WB Pipeline | [Archived ZIP](${{ env.ARTIFACT_URL }}) |
+        with:
+          script: |
+            github.rest.issues.createComment({
+              issue_number: process.env.PR_NUMBER,
+              owner: context.repo.owner,
+              repo: context.repo.repo,
+              body: process.env.PR_NOTES
+            })

.github/workflows/test_notebook.yml

@@ -10,45 +10,64 @@ on:
 
 jobs:
   build:
-
-    runs-on: ubuntu-latest
+    runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.8", "3.9", "3.10"]
+        os: [ubuntu-latest] # Once we get the tex packages changed, we should include "macos-13"
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
 
     steps:
-    - name: Install pdflatex
+    - name: Install Required Ubuntu Packages
       run: |
         sudo apt-get update
         sudo apt-get install texlive-latex-base cm-super-minimal pdftk latex2html
-    - uses: actions/checkout@v3
-    - uses: conda-incubator/setup-miniconda@v2
+    - uses: actions/checkout@v4
+    - uses: mamba-org/setup-micromamba@v1
       with:
-          python-version: ${{ matrix.python-version }}
-          mamba-version: "*"
-          channels: conda-forge,defaults
-          channel-priority: true
-    - name: Conda info
-      shell: bash -el {0}
-      run: conda info
-    - name: Install Dependencies & Main Code
+          init-shell: bash
+          environment-name: pulsar
+          cache-environment: true
+          cache-downloads: true
+          create-args: >-
+            -c conda-forge
+            python=${{ matrix.python-version }}
+            pytest
+            cython
+            pint-pulsar
+            tempo2
+            libstempo
+            enterprise-pulsar
+            enterprise_extensions
+            scikit-sparse
+            scikit-learn
+            ruamel.yaml
+            nbconvert
+            ipywidgets>=7.6.3
+            weasyprint
+            pytest-xdist>=2.3.0
+            jupyter
+            seaborn
+            gitpython
+    - name: Install Main Code
       shell: bash -el {0}
       run: |
-        mamba install -c conda-forge python=${{ matrix.python-version }} pytest cython=0.29.36 tempo2 enterprise-pulsar enterprise_extensions scikit-sparse
         pip install -e .
     - name: Test with Standard Pulsar
       shell: bash -el {0}
       run: |
         export PULSAR_NAME='J0605+3757'
-        export JUPYTER_PLATFORM_DIRS=1 && jupyter --paths
-        tree tests
-        pytest tests/test_run_notebook.py -n auto -k $PULSAR_NAME
-        mv tmp-* nb_outputs
+        export JUPYTER_PLATFORM_DIRS=1
+        pytest tests/test_run_notebook.py -k $PULSAR_NAME
+        ls -lah
+        mv tmp* nb_outputs
     - name: Archive Notebook Output Files
-      uses: actions/upload-artifact@v3
+      uses: actions/upload-artifact@v4
       with:
-        name: TestNB-OutputFiles
+        name: TestNB-OutputFiles_${{ matrix.python-version }}_${{ matrix.os }}_${{ steps.date.outputs.date }}
         path: |
-          nb_outputs
+          nb_outputs/*/*.pdf
+          nb_outputs/*/*.tim
+          nb_outputs/*/*.par
+        compression-level: 6