Merge branch 'main' into 247-howto-busy-taxi-fly

.github/dependabot.yml

@@ -0,0 +1,12 @@
+# Set update schedule for GitHub Actions
+# https://docs.github.com/en/code-security/dependabot/working-with-dependabot/keeping-your-actions-up-to-date-with-dependabot
+# https://docs.github.com/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file
+
+version: 2
+updates:
+
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      # Check for updates to GitHub Actions every week
+      interval: "weekly"

.github/workflows/unit-tests-pytest.yml → .github/workflows/code.yml

@@ -1,4 +1,4 @@
-name: Unit Tests
+name: CI
 
 on:
   # Triggers the workflow on push or pull request events but only for the main branch
@@ -17,29 +17,36 @@ defaults:
 jobs:
 
   lint:
-    name: Code style
+    name: Linting & Code style
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: "3.11"
 
-      - name: Install Dependencies
+      - name: Install package
         run: |
-          which python
-          which pip
+          set -vxeuo pipefail
           python -m pip install --upgrade pip
-          pip install flake8
+          pip install ruff flake8
 
       - name: Run flake8
-        run: |
-          flake8
-
-  test-matrix:
-    name: Python ${{ matrix.python-version }}
+        run: flake8
+
+      # # TODO: will replace flake8
+      # - name: Run ruff
+      #   uses: davidslusser/actions_python_ruff@v1.0.0
+      #   with:
+      #     # src: "."
+      #     # options: "--cov=src"
+      #     pip_install_command: "pip install -e .[dev]"
+      #     python_version: "3.11"
+
+  tests:
+    name: CI py${{ matrix.python-version }}
     runs-on: ubuntu-latest
     needs: lint
     strategy:
@@ -49,14 +56,17 @@ jobs:
           - "3.9"
           - "3.10"
           - "3.11"
+          # - "3.12"  # 2023-Q4  wait for upstreams to be ready
       max-parallel: 5
 
     steps:
     - name: Set time zone
       run: echo "TZ=America/Chicago" >> "$GITHUB_ENV"
 
     - name: Checkout the project from GitHub
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
 
     - name: Diagnostics
       run: |
@@ -129,6 +139,7 @@ jobs:
 
     - name: Run Bluesky queueserver
       run: |
+        set -vxeuo pipefail
         conda env list
         pushd ./bluesky/
         bash ./qserver.sh run &
@@ -140,37 +151,44 @@ jobs:
 
     - name: Run tests with pytest & coverage
       run: |
+        set -vxeuo pipefail
         coverage run --concurrency=thread --parallel-mode -m pytest -vvv .
         coverage combine
-        coverage report --precision 3
-
-  #   - name: Gather coverage data from matrix run
-  #     shell: bash -l {0}
-  #     run: |
-  #       micromamba list coveralls
-  #       which coveralls
-  #       coveralls debug
-  #       coveralls --service=github
-  #     env:
-  #       GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-  #       COVERALLS_FLAG_NAME: ${{ matrix.test-name }}
-  #       COVERALLS_PARALLEL: true
-
-  # # https://coveralls-python.readthedocs.io/en/latest/usage/configuration.html#github-actions-support
-  # coveralls:
-  #   name: Report unit test coverage to coveralls
-  #   needs: test-matrix
-  #   runs-on: ubuntu-latest
-  #   container: python:3-slim
-
-  #   steps:
-  #     - name: Gather coverage and report to Coveralls
-  #       run: |
-  #         echo "Finally!"
-  #         pip3 install --upgrade coveralls
-  #         # debug mode: output prepared json and reported files list to stdout
-  #         # https://coveralls-python.readthedocs.io/en/latest/troubleshooting.html
-  #         # coveralls debug
-  #         coveralls --service=github --finish
-  #       env:
-  #         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        python -m coverage report --precision 3
+
+    - name: Force Install coveralls by pip
+      shell: bash -l {0}
+      run: |
+        python -m pip install --force-reinstall coveralls
+  
+    - name: Upload coverage data to coveralls.io
+      shell: bash -l {0}
+      run: |
+        set -vxeuo pipefail
+        python -m coveralls debug
+        python -m coveralls --service=github
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        COVERALLS_FLAG_NAME: ${{ matrix.python-version }}
+        COVERALLS_PARALLEL: true
+
+  # https://coveralls-python.readthedocs.io/en/latest/usage/configuration.html#github-actions-support
+  coveralls:
+    name: Report unit test coverage to coveralls
+    needs: tests
+    runs-on: ubuntu-latest
+    container: python:3-slim
+
+    steps:
+      - name: Gather coverage and report to Coveralls
+        run: |
+          set -vxeuo pipefail
+          echo "Finally!"
+          pip3 install --upgrade coveralls
+          # debug mode: output prepared json and reported files list to stdout
+          # https://coveralls-python.readthedocs.io/en/latest/troubleshooting.html
+          coveralls debug
+          coveralls --service=github --finish
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+

.github/workflows/pages.yml → .github/workflows/docs.yml

@@ -27,8 +27,8 @@ defaults:
 jobs:
 
   pages:
-
-    runs-on: ubuntu-20.04
+    name: Publish documentation
+    runs-on: ubuntu-latest
 
     steps:
 
@@ -45,13 +45,23 @@ jobs:
     - name: Set time zone
       run: echo "TZ=America/Chicago" >> "$GITHUB_ENV"
 
-    - id: deployment
+    - name: Sphinx build
+      id: deployment
       uses: sphinx-notes/pages@v3
       with:
         documentation_path: ./docs/source
         publish: false
         requirements_path: ./docs/requirements.txt
 
+    - name: Diagnostic
+      run: ls -lAFgh ${{ steps.deployment.outputs.artifact }}
+
+    - name: Upload Docs ZIP file as artifact
+      uses: actions/upload-artifact@v4
+      with:
+        name: bluesky_training-docs
+        path: ${{ steps.deployment.outputs.artifact }}
+
     - uses: peaceiris/actions-gh-pages@v3
       if: ${{ github.event.inputs.deploy }}
       with:

CHANGES.rst

@@ -24,12 +24,12 @@ describe future plans.
    1.0.3
    ******
 
-   release expected by 2024-02-01
+   release expected by 2024-04-01
 
 1.0.2
 ******
 
-release expected by 2023-12-31
+release expected by 2024-03-01
 
 New Features
 ------------
@@ -38,9 +38,12 @@ New Features
 
   * ophyd-registry
 
+* Build ``registry`` of all ophyd objects.
+
 Maintenance
 ------------
 
+* Drop the (unused now) *stdlogpj* package for configuring Python's *logging*.
 * Environment for bluesky_2024_1.
 
 

LICENSE.txt

@@ -1,4 +1,4 @@
-Copyright (c) 2017-2021, UChicago Argonne, LLC
+Copyright (c) 2017-2024, UChicago Argonne, LLC
 
 All Rights Reserved
 

bluesky/environments/README.md

@@ -11,8 +11,9 @@ The repository is: https://github.com/BCDA-APS/bluesky_training/
 
 version | file
 --- | ---
-2023-3 (latest) | [`environment_2023_3.yml`](./environment_2023_3.yml)
-2023-2 | [`environment_2023_2.yml`](./environment_2023_2.yml)
+2024-1 (latest) | [`environment_2024_1.yml`](.//environment_2024_1.yml)
+2023-3 | [`environment_2023_3.yml`](./environment_2023_3.yml)
+2023-2 | [`environment_2023_2.yml`](./archive/environment_2023_2.yml)
 2023-1 | [`environment_2023_1.yml`](./archive/environment_2023_1.yml)
 2022_3 | [`environment_2022_3.yml`](./archive/environment_2022_3.yml)
 2022_2 | [`environment_2022_2.yml`](./archive/environment_2022_2.yml)

bluesky/environments/environment_2024_1.yml

@@ -47,6 +47,7 @@ dependencies:
   - qt =5
 
   # --- general support packages
+  - apischema
   - bitshuffle
   - epics-base >=7.0.5
   - h5py
@@ -91,7 +92,6 @@ dependencies:
   - pymca
   - pyRestTable
   - spec2nexus
-  - stdlogpj
   - xrayutilities
 
   # --- packaging and publishing

bluesky/instrument/framework/initialize.py

@@ -7,6 +7,7 @@
     bp  bps  bpp
     summarize_plan
     np
+    registry
     """.split()
 
 import logging
@@ -31,6 +32,7 @@
 from bluesky.utils import ts_msg_hook
 from IPython import get_ipython
 from ophyd.signal import EpicsSignalBase
+from ophydregistry import Registry
 import databroker
 import ophyd
 import warnings
@@ -117,6 +119,9 @@ def get_md_path():
         connection_timeout=iconfig.get("PV_CONNECTION_TIMEOUT", TIMEOUT),
     )
 
+# Create a registry of ophyd devices
+registry = Registry(auto_register=True)
+
 _pv = iconfig.get("RUN_ENGINE_SCAN_ID_PV")
 if _pv is None:
     logger.info("Using RunEngine metadata for scan_id")

bluesky/qserver.sh

@@ -184,7 +184,7 @@ esac
 # -----------------------------------------------------------------------------
 # :author:    Pete R. Jemian
 # :email:     jemian@anl.gov
-# :copyright: (c) 2017-2022, UChicago Argonne, LLC
+# :copyright: (c) 2017-2024, UChicago Argonne, LLC
 #
 # Distributed under the terms of the Creative Commons Attribution 4.0 International Public License.
 #

docs/source/howto/bluesky_cheat_sheet.md

@@ -452,9 +452,8 @@ If you are translating PyEpics code to Bluesky plans, consult this
 
 In the working directory, the log files are written to a `./.logs` subdirectory.
 There are two kinds of file, one that records user commands and the python
-result, the other records items sent to the
-[customized](https://github.com/prjemian/stdlogpj#example-directing-logs-to-a-specific-directory)
-Python [logging](https://docs.python.org/3/library/logging.html) package.
+result, the other records items sent to the Python
+[logging](https://docs.python.org/3/library/logging.html) package.
 
 In the IPython session, use the `!` to run a linux command:
 

docs/source/instrument/describe_instrument.ipynb

@@ -900,9 +900,8 @@
     "For diagnostic and general support, log files are created to record activity.  In the working directory, the log files are written to a `./.logs` subdirectory.\n",
     "\n",
     "There are two kinds of file, one that records user commands and the python\n",
-    "result, the other records items sent to the\n",
-    "[customized](https://github.com/prjemian/stdlogpj#example-directing-logs-to-a-specific-directory)\n",
-    "Python [logging](https://docs.python.org/3/library/logging.html) package.\n",
+    "result, the other records items sent to the Python\n",
+    "[logging](https://docs.python.org/3/library/logging.html) package.\n",
     "\n",
     "In the IPython session, use the `!` to run a linux command:"
    ]