Merge pull request #82 from ken-lauer/cleanup

REF/CLN: switch to pyproject.toml, setuptools-scm and clean codebase

.git_archival.txt

@@ -0,0 +1,4 @@
+node: $Format:%H$
+node-date: $Format:%cI$
+describe-name: $Format:%(describe:tags=true,match=*[0-9]*)$
+ref-names: $Format:%D$

.gitattributes

@@ -1 +1 @@
-pytao/_version.py export-subst
+.git_archival.txt  export-subst

.github/workflows/lint.yml

@@ -0,0 +1,29 @@
+name: Lint
+on:
+  pull_request:
+  workflow_dispatch:
+  push:
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 1
+
+      - name: Install pre-commit
+        run: python -m pip install pre-commit
+
+      - name: List Python package versions
+        run: python -m pip freeze --local
+
+      - name: Run pre-commit on all files
+        shell: bash -l {0}
+        env:
+          RUFF_OUTPUT_FORMAT: github
+        run: |
+          pre-commit run \
+            --show-diff-on-failure \
+            --color=always \
+            --all-files

.github/workflows/pypi_upload.yml

@@ -11,25 +11,21 @@ jobs:
       - uses: actions/checkout@master
         with:
           fetch-depth: 0
-      - name: Set up Python 3.7
-        uses: actions/setup-python@v1
+      - name: Set up Python
+        uses: actions/setup-python@v5
         with:
-          python-version: 3.7
+          python-version: "3.9"
+      - name: Update pip
+        run: >-
+          python -m pip install --upgrade pip
       - name: Install pypa/build
         run: >-
-          python -m
-          pip install
-          build
-          --user
+          python -m pip install --upgrade build
       - name: Build a source tarball
         run: >-
-          python -m
-          build
-          --sdist
-          --outdir dist/
-          .
+          python -m build --sdist --outdir dist/ .
       - name: Publish distribution to PyPI
         if: startsWith(github.ref, 'refs/tags')
-        uses: pypa/gh-action-pypi-publish@master
+        uses: pypa/gh-action-pypi-publish@release/v1
         with:
           password: ${{ secrets.PYPI_API_TOKEN }}

.gitignore

@@ -114,3 +114,5 @@ ENV/
 
 # vim
 *.swp
+
+pytao/_version.py

.pre-commit-config.yaml

@@ -31,9 +31,13 @@ repos:
         args: ["--maxkb=100000"]
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.4.8
+    rev: v0.5.0
     hooks:
       - id: ruff
-        args: ["--config", "python/pyproject.toml"]
+        args: ["--config", "pyproject.toml"]
+        types_or: [python]
+        exclude: "^(pytao/_version.py)$"
+      - id: ruff-format
+        args: ["--config", "pyproject.toml"]
         types_or: [python]
         exclude: "^(pytao/_version.py)$"

MANIFEST.in

@@ -1,4 +1 @@
-include requirements.txt
 include LICENSE
-include versioneer.py
-include pytao/_version.py

README.md

@@ -1,27 +1,23 @@
 # PyTao
 
-[PyTao]((https://bmad-sim.github.io/pytao/index.html)) is Python interface for [Tao](https://www.classe.cornell.edu/bmad/tao.html), which is based on the Bmad subroutine library for relativistic charged–particle and X-ray simulations in accelerators and storage rings.
+[PyTao](<(https://bmad-sim.github.io/pytao/index.html)>) is Python interface for [Tao](https://www.classe.cornell.edu/bmad/tao.html), which is based on the Bmad subroutine library for relativistic charged–particle and X-ray simulations in accelerators and storage rings.
 
 Documentation for Bmad and Tao, as well as information for downloading the code if needed is given on the [Bmad website](https://www.classe.cornell.edu/bmad).
 
-
-**`Documentation`** |
-------------------- |
-[![Documentation](https://img.shields.io/badge/pytao-examples-green.svg)](https://bmad-sim.github.io/pytao/examples/basic.html#)  |
-[![Documentation](https://img.shields.io/badge/api-reference-blue.svg)](https://bmad-sim.github.io/pytao/dev_docs/api/index.html)  |
-
-
+| **`Documentation`**                                                                                                         |
+| --------------------------------------------------------------------------------------------------------------------------- |
+| [![Documentation](https://img.shields.io/badge/pytao-examples-green.svg)](https://bmad-sim.github.io/pytao/examples/basic/) |
+| [![Documentation](https://img.shields.io/badge/api-reference-blue.svg)](https://bmad-sim.github.io/pytao/api/pytao/)        |
 
 ## Installation
 
 See the [PyTao installation instructions](https://bmad-sim.github.io/pytao/user_docs/index.html) for details. The preferred installation method is using conda:
 
 ```
-$ conda install -c conda-forge pytao
+conda install -c conda-forge pytao
 ```
 
-Currently PyTao requires an installed Bmad distribution compiled with the `ACC_ENABLE_SHARED="Y"` flag. This can be set in the `bmad_dist/util/dist_prefs` file. 
-
+Currently PyTao requires an installed Bmad distribution compiled with the `ACC_ENABLE_SHARED="Y"` flag. This can be set in the `bmad_dist/util/dist_prefs` file.
 
 ## Current Build status and Release Info
 
@@ -34,18 +30,38 @@ Currently PyTao requires an installed Bmad distribution compiled with the `ACC_E
   </tr>
 </table>
 
-
-| Name | Downloads | Version | Platforms |
-| --- | --- | --- | --- |
+| Name                                                                                                           | Downloads                                                                                                           | Version                                                                                                           | Platforms                                                                                                           |
+| -------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------- | ----------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------- |
 | [![Conda Recipe](https://img.shields.io/badge/recipe-pytao-green.svg)](https://anaconda.org/conda-forge/pytao) | [![Conda Downloads](https://img.shields.io/conda/dn/conda-forge/pytao.svg)](https://anaconda.org/conda-forge/pytao) | [![Conda Version](https://img.shields.io/conda/vn/conda-forge/pytao.svg)](https://anaconda.org/conda-forge/pytao) | [![Conda Platforms](https://img.shields.io/conda/pn/conda-forge/pytao.svg)](https://anaconda.org/conda-forge/pytao) |
 
 ## Resources
 
 [Bmad website](https://www.classe.cornell.edu/bmad)
 
+## Quickstart
 
+Start a quick pytao session with IPython using:
 
+```
+$ pytao -init tao.init
+------------------------------------------------------------
+Initializing `tao` object with the following: -init tao.init
+Type`tao.` and hit tab to see available commands.
+------------------------------------------------------------
+
+Python 3.12.0 | packaged by conda-forge | (main, Oct  3 2023, 08:36:57) [Clang 15.0.7 ]
+Type 'copyright', 'credits' or 'license' for more information
+IPython 8.18.1 -- An enhanced Interactive Python. Type '?' for help.
+
+In [1]: tao
+Out[1]: <pytao.interface_commands.Tao at 0x13c43d4f0>
+```
+
+Start pytao's GUI from the command-line with:
 
+```
+pytao-gui -init tao.init
+```
 
 ## License
 

dev-environment.yml

@@ -6,7 +6,7 @@ dependencies:
   - python >=3.9
   - openPMD-beamphysics
   - numpydoc
-  - bmad >=20240626
+  - bmad >=20240628.2
   - bokeh
   - jupyterlab>3
   - ipywidgets

overrides/main.html → docs/overrides/main.html

@@ -2,10 +2,10 @@
 
 {% block content %}
 {% if page.nb_url %}
-    <a href="{{ page.nb_url }}" title="Download Notebook" class="md-content__button md-icon">
+    <a href="{{ page.nb_url }}" title="Download Notebook" class="md-content__button md-icon" style="float: inherit;">
         <img src="https://img.shields.io/badge/download-notebook-blue.svg" alt="Download Notebook"/>
     </a>
 {% endif %}
 
 {{ super() }}
-{% endblock content %}
+{% endblock content %}

environment.yml

@@ -7,7 +7,7 @@ dependencies:
   - ipykernel
   - ipywidgets
   - jupyterlab
-  - bmad >=20240626
+  - bmad >=20240628.2
   - openPMD-beamphysics
   - numpy
   - h5py