Merge pull request #141 from mrakitin/cli-prep-env

Better way to prepare bluesky environment

.github/workflows/docs.yml

@@ -44,32 +44,43 @@ jobs:
         with:
           docker-binary: ${{ env.DOCKER_BINARY }}
 
-      - name: Set up Python ${{ matrix.python-version }} with conda
-        uses: conda-incubator/setup-miniconda@v2
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
         with:
-          activate-environment: ${{ env.REPOSITORY_NAME }}-py${{ matrix.python-version }}
-          auto-update-conda: true
-          miniconda-version: "latest"
           python-version: ${{ matrix.python-version }}
-          mamba-version: "*"
-          channels: conda-forge
 
-      - name: Install documentation-building requirements
+      # - name: Set up Python ${{ matrix.python-version }}
+      #   uses: conda-incubator/setup-miniconda@v2
+      #   with:
+      #     activate-environment: ${{ env.REPOSITORY_NAME }}-py${{ matrix.python-version }}
+      #     auto-update-conda: true
+      #     miniconda-version: "latest"
+      #     python-version: ${{ matrix.python-version }}
+      #     mamba-version: "*"
+      #     channels: conda-forge
+
+      - name: Install documentation-building requirements with apt/dpkg
         run: |
-          set -vxeo pipefail
-          conda env list
-          mamba install -c conda-forge pandoc
-          pip install --upgrade pip wheel
-          pip install -v .
-          pip install -r requirements-dev.txt
-          pip list
-          conda list
+          set -vxeuo pipefail
+          wget --progress=dot:giga "https://github.com/jgm/pandoc/releases/download/3.1.6.1/pandoc-3.1.6.1-1-amd64.deb" -O /tmp/pandoc.deb
+          sudo dpkg -i /tmp/pandoc.deb
+          # conda install -c conda-forge -y pandoc
+          which pandoc
+          pandoc --version
+
+      - name: Install documentation-building requirements with pip
+        run: |
+          set -vxeuo pipefail
+          python -m pip install --upgrade pip wheel
+          python -m pip install -v .
+          python -m pip install -r requirements-dev.txt
+          python -m pip list
 
       - name: Copy databroker config file
         run: |
           set -vxeuo pipefail
           mkdir -v -p ~/.config/databroker/
-          cp examples/local.yml ~/.config/databroker/
+          cp -v examples/local.yml ~/.config/databroker/
 
       - name: Build Docs
         run: |

.github/workflows/publish-pypi.yml

@@ -30,7 +30,7 @@ jobs:
         run: |
           set -vxeuo pipefail
           python -m pip install --upgrade pip
-          pip install wheel setuptools
+          python -m pip install wheel setuptools
           python setup.py sdist bdist_wheel
 
       - name: Publish wheels to PyPI

.github/workflows/testing.yml

@@ -44,36 +44,34 @@ jobs:
         with:
           docker-binary: ${{ env.DOCKER_BINARY }}
 
-      - name: Set up Python ${{ matrix.python-version }} with conda
-        uses: conda-incubator/setup-miniconda@v2
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
         with:
-          activate-environment: ${{ env.REPOSITORY_NAME }}-py${{ matrix.python-version }}
-          auto-update-conda: true
-          miniconda-version: "latest"
           python-version: ${{ matrix.python-version }}
-          mamba-version: "*"
-          channels: conda-forge
+
+      # - name: Set up Python ${{ matrix.python-version }} with conda
+      #   uses: conda-incubator/setup-miniconda@v2
+      #   with:
+      #     activate-environment: ${{ env.REPOSITORY_NAME }}-py${{ matrix.python-version }}
+      #     auto-update-conda: true
+      #     miniconda-version: "latest"
+      #     python-version: ${{ matrix.python-version }}
+      #     mamba-version: "*"
+      #     channels: conda-forge
 
       - name: Install the package and its dependencies
         run: |
-          # set -vxeuo pipefail
-          # Do not check for unbound variables (the '-u' flag) as it fails on
-          # conda deactivate command:
-          # /usr/share/miniconda3/envs/sirepo-bluesky-py3.9/etc/conda/deactivate.d/glib_deactivate.sh:
-          # line 1: GSETTINGS_SCHEMA_DIR_CONDA_BACKUP: unbound variable
           set -vxeo pipefail
-          conda env list
-          pip install --upgrade pip wheel
-          pip install -v .
-          pip install -r requirements-dev.txt
-          pip list
-          conda list
+          python -m pip install --upgrade pip wheel
+          python -m pip install -v .
+          python -m pip install -r requirements-dev.txt
+          python -m pip list
 
       - name: Copy databroker config file
         run: |
           set -vxeuo pipefail
           mkdir -v -p ~/.config/databroker/
-          cp examples/local.yml ~/.config/databroker/
+          cp -v examples/local.yml ~/.config/databroker/
 
       - name: Test with pytest
         run: |

docs/source/notebooks/madx.ipynb

@@ -24,7 +24,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "%run -i ../../../examples/prepare_flyer_env.py\n",
+    "from sirepo_bluesky import prepare_re_env\n",
+    "\n",
+    "%run -i $prepare_re_env.__file__ -e flyer\n",
     "\n",
     "import matplotlib.pyplot as plt\n",
     "\n",

docs/source/notebooks/shadow.ipynb

@@ -36,7 +36,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "%run -i ../../../examples/prepare_det_env.py\n",
+    "from sirepo_bluesky import prepare_re_env\n",
+    "\n",
+    "%run -i $prepare_re_env.__file__\n",
     "\n",
     "from sirepo_bluesky.sirepo_bluesky import SirepoBluesky\n",
     "from sirepo_bluesky.sirepo_ophyd import BeamStatisticsReport, create_classes\n",
@@ -104,7 +106,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "%run -i ../../../examples/prepare_det_env.py\n",
+    "from sirepo_bluesky import prepare_re_env\n",
+    "\n",
+    "%run -i $prepare_re_env.__file__\n",
     "\n",
     "from sirepo_bluesky.sirepo_bluesky import SirepoBluesky\n",
     "from sirepo_bluesky.sirepo_ophyd import BeamStatisticsReport, create_classes\n",
@@ -190,7 +194,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.11"
+   "version": "3.9.13"
   }
  },
  "nbformat": 4,

docs/source/notebooks/srw.ipynb

@@ -36,7 +36,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "%run -i ../../../examples/prepare_det_env.py\n",
+    "from sirepo_bluesky import prepare_re_env\n",
+    "\n",
+    "%run -i $prepare_re_env.__file__\n",
     "\n",
     "from sirepo_bluesky.sirepo_bluesky import SirepoBluesky\n",
     "from sirepo_bluesky.sirepo_ophyd import create_classes\n",
@@ -103,7 +105,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "%run -i ../../../examples/prepare_det_env.py\n",
+    "from sirepo_bluesky import prepare_re_env\n",
+    "\n",
+    "%run -i $prepare_re_env.__file__\n",
     "\n",
     "from sirepo_bluesky.sirepo_bluesky import SirepoBluesky\n",
     "from sirepo_bluesky.sirepo_ophyd import create_classes\n",
@@ -184,7 +188,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "%run -i ../../../examples/prepare_det_env.py\n",
+    "from sirepo_bluesky import prepare_re_env\n",
+    "\n",
+    "%run -i $prepare_re_env.__file__\n",
     "\n",
     "from sirepo_bluesky.sirepo_bluesky import SirepoBluesky\n",
     "from sirepo_bluesky.sirepo_ophyd import create_classes\n",

docs/source/release-history.rst

@@ -20,11 +20,13 @@ API
   is turned into a document for SRW and Shadow apps. The beam stats show up in
   Bluesky's ``BestEffortCallback``.
 - Removed old API support and relevant tests.
+- ``create_classes`` does not need the ``data`` kwarg as it obtains it via
+  ``connection``.
 
 Documentation
 .............
 - Suppress Shadow3 code's stdout in notebooks/code.
-- Converted project's `README.rst` to `README.md` for better rendering on PyPI.
+- Converted project's ``README.rst`` to ``README.md`` for better rendering on PyPI.
 
 Examples
 ........

requirements-dev.txt

@@ -16,6 +16,6 @@ matplotlib
 nbsphinx
 numpydoc
 pandoc
-sphinx
+sphinx==7.1.2
 sphinx-copybutton
 tabulate>=0.9.0

setup.py

@@ -50,7 +50,7 @@
     entry_points={
         "console_scripts": [
             # 'command = some.module:some_function',
-            "json-yaml-converter = sirepo_bluesky.utils.json_yaml_converter:cli_converter"
+            "json-yaml-converter = sirepo_bluesky.utils.json_yaml_converter:cli_converter",
         ],
     },
     include_package_data=True,

sirepo_bluesky/__init__.py

@@ -1,6 +1,7 @@
 from ophyd import Signal
 
 from ._version import get_versions
+from .utils import prepare_re_env  # noqa: F401
 
 __version__ = get_versions()["version"]
 del get_versions

sirepo_bluesky/tests/test_sirepo_flyer.py

@@ -68,7 +68,7 @@ def _test_sirepo_flyer(RE_no_plot, db, tmpdir, sim_id, server_name):
     hdr = db[-1]
     t = hdr.table(stream_name="sirepo_flyer")
     db_means = []
-    actual_means = [
+    expected_means = [
         36779651609602.38,
         99449330615601.89,
         149289119385413.34,
@@ -78,7 +78,9 @@ def _test_sirepo_flyer(RE_no_plot, db, tmpdir, sim_id, server_name):
     for i in range(len(t)):
         db_means.append(t.iloc[i]["sirepo_flyer_mean"])
 
-    assert set(actual_means) == set(db_means), "fly scan means do not match actual means"
+    assert np.allclose(
+        sorted(expected_means), sorted(db_means), rtol=1.0e-6
+    ), "fly scan expected means do not match actual means"
 
     durations = []
     for i in range(len(t)):