Merge branch 'master' into parse_data_d_array_bug

bmad-sim · Jun 25, 2024 · 592ee4c · 592ee4c
2 parents c5b4efe + 5e9f02f
commit 592ee4c
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Showing 5 changed files with 71 additions and 62 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -4,64 +4,58 @@ on:
   push:
   pull_request:
   schedule:
-    - cron: '0 0 * * *'  # every day at midnight
+    - cron: "0 0 * * *" # every day at midnight
 
 jobs:
   build:
+    name: ${{ matrix.os }} Python ${{ matrix.python-version }}
     runs-on: ${{ matrix.os }}
     defaults:
-        run:
-          shell: bash
+      run:
+        shell: bash
     strategy:
+      fail-fast: false
       matrix:
         os: [ubuntu-latest]
-        python-version: [3.7]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
     steps:
-      - uses: actions/checkout@v2
-
-      - name: Install System Dependencies
-        run: |
-          sudo apt-get install build-essential curl wget cmake gfortran automake \
-          autoconf libtool m4 libgomp1 libreadline-dev libncurses-dev pkg-config \
-          libcairo2-dev libpango1.0-dev libxt-dev libx11-dev -y
-
-      - name: Check Latest Bmad Release
-        run: |
-          echo "Latest release is: $(curl https://www.classe.cornell.edu/~cesrulib/downloads/latest_distribution_file_prefix)"
-          # Set Environment variable for further steps
-          echo "BMADDIST=$(curl https://www.classe.cornell.edu/~cesrulib/downloads/latest_distribution_file_prefix)" >> $GITHUB_ENV
-
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+      - uses: actions/checkout@v4
         with:
-          python-version: ${{ matrix.python-version }}
+          fetch-depth: 1
 
-      - uses: actions/cache@v2
-        id: cache
+      - uses: actions/checkout@v4
         with:
-          path: ~/bmad
-          key: ${{ runner.os }}-${{ env.BMADDIST }}
+          repository: bmad-sim/bmad-ecosystem
+          fetch-depth: 1
+          path: bmad
 
-      - name: Install Bmad - ${{ env.BMADDIST }}
-        if: steps.cache.outputs.cache-hit != 'true'
-        run: .github/scripts/install_bmad.sh
+      - uses: conda-incubator/setup-miniconda@v3
+        with:
+          python-version: ${{ matrix.python-version }}
+          mamba-version: "*"
+          channels: conda-forge
+          activate-environment: pytao-dev
+          environment-file: dev-environment.yml
 
       - name: Setup Bmad
         run: |
-          echo "ACC_ROOT_DIR=/home/runner/bmad/bmad_dist" >> $GITHUB_ENV
-          echo "ACC_EXE=/home/runner/bmad/bmad_dist/production/bin" >> $GITHUB_ENV
-          echo "TAO_DIR=/home/runner/bmad/bmad_dist/tao" >> $GITHUB_ENV
-          echo "/home/runner/bmad/bmad_dist/production/bin/" >> $GITHUB_PATH
+          PYTAO_ROOT=/home/runner/work/pytao/pytao
+          echo "ACC_ROOT_DIR=$PYTAO_ROOT/bmad" >> $GITHUB_ENV
 
-      - name: Install Python Dependencies
+      - name: Show conda environment packages
+        shell: bash -l {0}
         run: |
-          pip install -r requirements.txt
-          pip install -r test-requirements.txt
+          conda list
 
-      - name: Install PyTao
+      - name: Ensure importability
+        shell: bash -l {0}
         run: |
-          pip install .
+          cd /
+          python -c "import pytao"
 
       - name: Run Tests
+        shell: bash -l {0}
         run: |
-          python run_tests.py
+          echo -e '## Test results\n\n```' >> "$GITHUB_STEP_SUMMARY"
+          pytest -v --cov=pytao/ pytao/tests 2>&1 | tee -a "$GITHUB_STEP_SUMMARY"
+          echo '```' >> "$GITHUB_STEP_SUMMARY"
diff --git a/dev-environment.yml b/dev-environment.yml
@@ -3,20 +3,27 @@ name: pytao-dev
 channels:
   - conda-forge
 dependencies:
-  - python==3.12
-# Developer
+  - python >=3.9
   - openPMD-beamphysics
   - numpydoc
+  - bmad
   - bokeh
-  - pytest
-  - pytest-cov
   - jupyterlab>3
   - ipywidgets
   - matplotlib
+  - numpy
+  - h5py
+  - pexpect
+  # Developer
   - pygments
-  - mkdocs==1.5.2
+  - pytest
+  - pytest-cov
+  - mkdocs
   - mkdocstrings
   - mkdocs-material
-  - mkdocs-jupyter==0.24.6
+  - mkdocs-jupyter
   - mkdocstrings-python
-
+  - pip
+  - pip:
+      # Install pytao from here.
+      - .
diff --git a/environment.yml b/environment.yml
@@ -1,16 +1,18 @@
 # conda env create -f environment.yml
-name: pytao-dev
+name: pytao
 channels:
   - conda-forge
 dependencies:
-  - python >= 3.9
+  - python >=3.9
   - ipykernel
   - ipywidgets
   - jupyterlab
   - bmad
   - openPMD-beamphysics
-  # PyTao release:
-  - pytao
-  # or PytTao Developer:
-#  - pip:
-#    - git+git://github.com/bmad-sim/pytao
+  - numpy
+  - h5py
+  - pexpect
+  - pip
+  - pip:
+      # Install pytao from here.
+      - .
diff --git a/pytao/interface_commands.py b/pytao/interface_commands.py
@@ -2,7 +2,7 @@
 # AUTOGENERATED FILE - DO NOT MODIFY
 # This file was generated by the script `generate_interface_commands.py`.
 # Any modifications may be overwritten.
-# Generated on: 2024-06-04 10:44:04
+# Generated on: 2024-06-24 14:25:18
 # ==============================================================================
 
 from pytao.tao_ctypes.util import parse_tao_python_data
@@ -62,14 +62,15 @@ def __execute(tao, cmd, as_dict=True, raises=True, method_name=None, cmd_type="s
     return ret
 
 
-def beam(tao, *, ix_uni='', verbose=False, as_dict=True, raises=True):
+def beam(tao, ix_branch, *, ix_uni='', verbose=False, as_dict=True, raises=True):
     """
     
     Output beam parameters that are not in the beam_init structure.
     
     Parameters
     ----------
     ix_uni : optional
+    ix_branch : ""
     
     Returns
     -------
@@ -78,10 +79,11 @@ def beam(tao, *, ix_uni='', verbose=False, as_dict=True, raises=True):
     Notes
     -----
     Command syntax:
-      python beam {ix_uni}
+      python beam {ix_uni}@{ix_branch}
     
     Where:
       {ix_uni} is a universe index. Defaults to s%global%default_universe.
+      {ix_branch} is a lattice branch index. Defaults to s%global%default_branch.
     
     Note: To set beam_init parameters use the "set beam" command.
     
@@ -91,21 +93,23 @@ def beam(tao, *, ix_uni='', verbose=False, as_dict=True, raises=True):
      init: -init $ACC_ROOT_DIR/regression_tests/python_test/csr_beam_tracking/tao.init
      args:
        ix_uni: 1
+       ix_branch: 0
     
     """
-    cmd = f'python beam {ix_uni}'
+    cmd = f'python beam {ix_uni}@{ix_branch}'
     if verbose: print(cmd)
     return __execute(tao, cmd, as_dict, raises, method_name='beam', cmd_type='string_list')
 
 
-def beam_init(tao, *, ix_uni='', verbose=False, as_dict=True, raises=True):
+def beam_init(tao, ix_branch, *, ix_uni='', verbose=False, as_dict=True, raises=True):
     """
     
     Output beam_init parameters.
     
     Parameters
     ----------
     ix_uni : optional
+    ix_branch : ""
     
     Returns
     -------
@@ -114,10 +118,11 @@ def beam_init(tao, *, ix_uni='', verbose=False, as_dict=True, raises=True):
     Notes
     -----
     Command syntax:
-      python beam_init {ix_uni}
+      python beam_init {ix_uni}@{ix_branch}
     
     Where:
       {ix_uni} is a universe index. Defaults to s%global%default_universe.
+      {ix_branch} is a lattice branch index. Defaults to s%global%default_branch.
     
     Note: To set beam_init parameters use the "set beam_init" command
     
@@ -127,9 +132,10 @@ def beam_init(tao, *, ix_uni='', verbose=False, as_dict=True, raises=True):
      init: -init $ACC_ROOT_DIR/regression_tests/python_test/csr_beam_tracking/tao.init
      args:
        ix_uni: 1
+       ix_branch: 0
     
     """
-    cmd = f'python beam_init {ix_uni}'
+    cmd = f'python beam_init {ix_uni}@{ix_branch}'
     if verbose: print(cmd)
     return __execute(tao, cmd, as_dict, raises, method_name='beam_init', cmd_type='string_list')
 

diff --git a/pytao/tests/test_interface_commands.py b/pytao/tests/test_interface_commands.py
@@ -2,7 +2,7 @@
 # AUTOGENERATED FILE - DO NOT MODIFY
 # This file was generated by the script `generate_interface_commands.py`.
 # Any modifications may be overwritten.
-# Generated on: 2024-06-04 10:44:04
+# Generated on: 2024-06-24 14:25:18
 # ==============================================================================
 
 import os
@@ -13,13 +13,13 @@
 def test_beam_1():
 
     tao = Tao(os.path.expandvars('-init $ACC_ROOT_DIR/regression_tests/python_test/csr_beam_tracking/tao.init -noplot'))
-    ret = interface_commands.beam(tao, ix_uni='1')
+    ret = interface_commands.beam(tao, ix_uni='1', ix_branch='0')
 
 
 def test_beam_init_1():
 
     tao = Tao(os.path.expandvars('-init $ACC_ROOT_DIR/regression_tests/python_test/csr_beam_tracking/tao.init -noplot'))
-    ret = interface_commands.beam_init(tao, ix_uni='1')
+    ret = interface_commands.beam_init(tao, ix_uni='1', ix_branch='0')
 
 
 def test_bmad_com_1():