Merge pull request #87 from ken-lauer/enh_plot

ENH: matplotlib and bokeh plotting tools

.github/workflows/gh-pages.yml

@@ -1,10 +1,9 @@
-
 name: Publish Documentation
 
 on:
   push:
     branches:
-      - '**'
+      - "**"
 
 jobs:
   deploy:
@@ -27,15 +26,18 @@ jobs:
         shell: bash -l {0}
         run: |
           mamba list
+      - name: Execute notebooks
+        shell: bash -l {0}
+        run: |
+          bash scripts/execute_notebooks.bash
       - name: Build Docs
         shell: bash -l {0}
         run: |
           mkdocs build
           zip -r pytao-examples.zip docs/examples/
-          mv pytao-examples.zip ./site/assets/.
-          
+          mv pytao-examples.zip ./site/assets/
       - name: Deploy to gh-pages
         uses: peaceiris/actions-gh-pages@v3
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}
-          publish_dir: ./site/
+          publish_dir: ./site/

.github/workflows/lint.yml

@@ -12,6 +12,14 @@ jobs:
         with:
           fetch-depth: 1
 
+      - uses: conda-incubator/setup-miniconda@v3
+        with:
+          python-version: 3.12
+          mamba-version: "*"
+          channels: conda-forge
+          activate-environment: pytao-dev
+          environment-file: dev-environment.yml
+
       - name: Install pre-commit
         run: python -m pip install pre-commit
 

.gitignore

@@ -116,3 +116,10 @@ ENV/
 *.swp
 
 pytao/_version.py
+pytao/tests/artifacts
+docs/examples/alpha*.html
+docs/examples/beta*.html
+docs/examples/beta*.png
+docs/examples/fodo10.bmad 
+docs/examples/markers.bmad 
+docs/examples/wake.dat

.pre-commit-config.yaml

@@ -31,7 +31,7 @@ repos:
         args: ["--maxkb=100000"]
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.5.0
+    rev: v0.6.1
     hooks:
       - id: ruff
         args: ["--config", "pyproject.toml"]
@@ -41,3 +41,13 @@ repos:
         args: ["--config", "pyproject.toml"]
         types_or: [python]
         exclude: "^(pytao/_version.py)$"
+
+  - repo: local
+    hooks:
+      - id: jupyter-notebook-clear-output
+        name: jupyter-notebook-jupyter-clear
+        files: \.ipynb$
+        stages: [commit]
+        language: system
+        entry: jupyter nbconvert --ClearOutputPreprocessor.enabled=True --inplace
+        # exclude: "^.*().ipynb$"

dev-environment.yml

@@ -6,14 +6,15 @@ dependencies:
   - python >=3.9
   - openPMD-beamphysics
   - numpydoc
-  - bmad >=20240628.2
+  - bmad >=20240809
   - bokeh
   - jupyterlab>3
   - ipywidgets
   - matplotlib
   - numpy
   - h5py
   - pexpect
+  - pydantic >=2
   # Developer
   - pygments
   - pytest

docs/api/plot-bokeh.md

@@ -0,0 +1 @@
+::: pytao.plotting.bokeh

docs/api/plot-mpl.md

@@ -0,0 +1 @@
+::: pytao.plotting.mpl

docs/api/plot.md

@@ -0,0 +1,5 @@
+::: pytao.plotting.plot
+::: pytao.plotting.curves
+::: pytao.plotting.fields
+::: pytao.plotting.pgplot
+::: pytao.plotting.settings

docs/api/subprocesstao.md

@@ -0,0 +1 @@
+::: pytao.SubprocessTao