Demo instrument separation for Sync template

.github/workflows/code.yml

@@ -136,7 +136,7 @@ jobs:
         shell: bash -l {0}
         run: |
           set -vxeuo pipefail
-          ipython -c "from instrument.startup import *; RE(make_devices())"
+          ipython -c "from bits.demo_instrument.startup import *; RE(make_devices())"
 
   # https://coveralls-python.readthedocs.io/en/latest/usage/configuration.html#github-actions-support
   coveralls:

.github/workflows/init_repo.sh

@@ -6,14 +6,18 @@ echo $full_name
 
 repo=$(echo $full_name | awk -F '/' '{print $2}')
 
-original_repo="BITS"
+# Sanitize the repo name to be a valid Python package name
+sanitized_repo=$(echo "$repo" | sed 's/[^a-zA-Z0-9_-]/_/g')
 
+original_repo="BITS"
 
-echo $repo
+echo $sanitized_repo
 echo $original_repo
 
-sed -i "s/$original_repo/$repo/g" README.md
+sed -i "s/$original_repo/$sanitized_repo/g" README.md
 
+# Call the create_new_instrument function
+python3 -c "from bits.utils import create_new_instrument; create_new_instrument('$sanitized_repo')"
 
 rm -rf .github/workflows/init_repo.sh
 rm -rf .github/workflows/init_repo.yml

.github/workflows/init_repo.yml

@@ -11,9 +11,19 @@ jobs:
           fetch-depth: 0
           ref: ${{ github.head_ref }}
 
-      - name: Run init_repo.sh
-        run: |
-          bash .github/workflows/init_repo.sh ${{ github.repository }}
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.x'
+
+      # - name: Install dependencies
+      #   run: |
+      #     python -m pip install --upgrade pip
+      #     pip install -e .
+
+      # - name: Run init_repo.sh
+      #   run: |
+      #     bash .github/workflows/init_repo.sh ${{ github.repository }}
 
       - uses: stefanzweifel/git-auto-commit-action@v5
         with:

.github/workflows/template-sync.yml

@@ -1,35 +1,35 @@
-name: template_sync
-
-# see: https://github.com/AndreasAugustin/actions-template-sync
-
-on:
-    # cronjob trigger
-    schedule:
-      # 12:10 AM GMT on the first day of every month
-    - cron: "10 0 1 * *"
-    # manual trigger
-    workflow_dispatch:
-
-env:
-  TEMPLATE_REPO: BCDA-APS/BITS
-
-jobs:
-  repo-sync:
-    if: ${{ github.repository != 'bcda-aps/bits' }}
-    runs-on: ubuntu-latest
-    permissions:
-      contents: write
-      pull-requests: write
-
-    steps:
-      # To use this repository's private action, you must check out the repository
-      - name: Checkout
-        uses: actions/checkout@v4
-        with:
-          token: ${{ secrets.GH_PAT }} # `GH_PAT` is a secret that contains your PAT
-
-      - name: actions-template-sync
-        uses: AndreasAugustin/actions-template-sync@v2
-        with:
-          source_repo_path: ${{ env.TEMPLATE_REPO }}
-          upstream_branch: main
+name: template_sync
+
+# see: https://github.com/AndreasAugustin/actions-template-sync
+
+on:
+    # cronjob trigger
+    schedule:
+      # 12:10 AM GMT on the first day of every month
+    - cron: "10 0 1 * *"
+    # manual trigger
+    workflow_dispatch:
+
+env:
+  TEMPLATE_REPO: BCDA-APS/BITS
+
+jobs:
+  repo-sync:
+    if: ${{ github.repository != 'bcda-aps/bits' }}
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+      pull-requests: write
+
+    steps:
+      # To use this repository's private action, you must check out the repository
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          token: ${{ secrets.GH_PAT }} # `GH_PAT` is a secret that contains your PAT
+
+      - name: actions-template-sync
+        uses: AndreasAugustin/actions-template-sync@v2
+        with:
+          source_repo_path: ${{ env.TEMPLATE_REPO }}
+          upstream_branch: main

.github/workflows/template_sync.yml

@@ -0,0 +1,35 @@
+name: template_sync
+
+# see: https://github.com/AndreasAugustin/actions-template-sync
+
+on:
+    # cronjob trigger
+    schedule:
+      # 12:10 AM GMT on the first day of every month
+    - cron: "10 0 1 * *"
+    # manual trigger
+    workflow_dispatch:
+
+env:
+  TEMPLATE_REPO: BCDA-APS/BITS
+
+jobs:
+  repo-sync:
+    if: ${{ github.repository != 'bcda-aps/bits' }}
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+      pull-requests: write
+
+    steps:
+      # To use this repository's private action, you must check out the repository
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          token: ${{ secrets.GH_PAT }} # `GH_PAT` is a secret that contains your PAT
+
+      - name: actions-template-sync
+        uses: AndreasAugustin/actions-template-sync@v2
+        with:
+          source_repo_path: ${{ env.TEMPLATE_REPO }}
+          upstream_branch: main

.templatesyncignore

@@ -0,0 +1,6 @@
+.all-contributorsrc
+.github/dependabot.yml
+README.md
+Dockerfile
+SECURITY.md
+src/new_instrument

README.md

@@ -17,37 +17,32 @@ cd BITS
 Set up the development environment.
 
 ```bash
-export ENV_NAME=bits
+export ENV_NAME=BITS_env
+
 conda create -y -n $ENV_NAME python=3.11 pyepics
 conda activate $ENV_NAME
 pip install -e ."[all]"
 ```
 
-## IPython console
+## IPython console Start
 
 To start the bluesky instrument session in a ipython execute the next command in a terminal:
 
 ```bash
 ipython
 ```
 
-Inside the ipython console execute:
-
-```py
-from instrument.startup import *
-```
-
-## Jupyter notebook
-
+## Jupyter Notebook Start
 Start JupyterLab, a Jupyter notebook server, or a notebook, VSCode.
 
-Start the data acquisition:
+## Starting the BITS Package
 
 ```py
 from instrument.startup import *
+RE(make_devices())  # create all the ophyd-style control devices
 ```
 
-## Sim Plan Demo
+## Run Sim Plan Demo
 
 To run some simulated plans that ensure the installation worked as expected
 please run the next commands inside an ipython session or a jupyter notebook

docs/source/api/configs.rst

@@ -14,7 +14,7 @@ section.
 
 Various constants and terms used to configure the instrument package.
 
-.. literalinclude:: ../../../src/instrument/configs/iconfig.yml
+.. literalinclude:: ../../../src/bits/demo_instrument/configs/iconfig.yml
     :language: yaml
     :linenos:
 
@@ -27,7 +27,7 @@ Declarations of the ophyd (and ophyd-like) devices and signals used by the
 instrument package.  Configuration is used by the guarneri package to create the
 objects.
 
-.. literalinclude:: ../../../src/instrument/configs/devices.yml
+.. literalinclude:: ../../../src/bits/demo_instrument/configs/devices.yml
     :language: yaml
     :linenos:
 
@@ -39,6 +39,6 @@ objects.
 Declarations of the ophyd (and ophyd-like) devices and signals
 only available when Bluesky is used at the APS.
 
-.. literalinclude:: ../../../src/instrument/configs/devices_aps_only.yml
+.. literalinclude:: ../../../src/bits/demo_instrument/configs/devices_aps_only.yml
     :language: yaml
     :linenos:

docs/source/conf.py

@@ -6,12 +6,12 @@
 # -- Project information -----------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
 
-import instrument
+import bits
 
-project = "instrument"
+project = "BITS"
 copyright = "2023-2025, APS BCDA"
 author = "APS BCDA"
-version = instrument.__version__
+version = bits.__version__
 release = version.split("+")[0]
 if "+" in version:
     release += "..."

docs/source/demo.ipynb

@@ -9,7 +9,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": null,
    "metadata": {},
    "outputs": [
     {
@@ -65,7 +65,7 @@
     }
    ],
    "source": [
-    "from instrument.startup import *  # noqa"
+    "from bits.demo_instrument.startup import *  # noqa"
    ]
   },
   {

docs/source/guides/index.rst

@@ -9,5 +9,5 @@ Guides show how to use certain features of this instrument.
     :maxdepth: 2
     :glob:
 
-    *dm*
+    dm
     template_sync

docs/source/guides/template_sync.rst

@@ -15,7 +15,8 @@ Overview
 --------
 
 This document describes a method to synchronize the new instrument repo
-with the template repo. The method relies on a GitHub workflow
+with the template repo. The method relies on a GitHub
+`workflow <https://docs.github.com/en/actions/writing-workflows/about-workflows>`__
 to generate a new pull request whenever the template is updated. The
 workflow can be run on demand or as a periodic task (default is once a
 month). The workflow is installed in the new instrument's
@@ -25,16 +26,16 @@ When the workflow is run, it compares the new instrument's repo with the
 template repo. If differences are identified, the workflow creates a new
 branch in the new instrument's repo and then creates a new pull request
 to merge that branch with ``main``. Additional configuration is
-necessary to grant permission for the workflow to create a branch and PR.
+necessary to grant permission for the workflow to create a branch and
+PR.
 
-Permission is provided through a GitHub Personal Access Token (PAT). [#]_
-For this purpose, the PAT settings [#settings]_ should allow ``write`` permission
+Permission is provided through a GitHub Personal Access Token
+(`PAT <https://docs.github.com/en/authentication/keeping-your-account-and-data-secure/managing-your-personal-access-tokens>`__).
+For this purpose, the PAT
+`settings <https://github.com/settings/tokens>`__ should allow ``write``
 (includes ``read``) permission for ``workflow``. It is possible to limit
 a PAT to a single GitHub repo (a good idea for this use case).
 
-.. [#] https://docs.github.com/en/authentication/keeping-your-account-and-data-secure/managing-your-personal-access-tokens
-.. [#settings] https://github.com/settings/tokens
-
 Example instrument repository
 +++++++++++++++++++++++++++++
 

pyproject.toml

@@ -6,7 +6,7 @@ build-backend = "setuptools.build_meta"
 copyright = "2014-2025, APS"
 
 [project]
-name = "instrument"
+name = "bits"
 dynamic = ["version"]
 description = "Model of a Bluesky Data Acquisition Instrument in console, notebook, & queueserver."
 authors = [
@@ -71,14 +71,12 @@ doc = [
     "sphinx",
 ]
 
-all = ["instrument[dev,doc]"]
+all = ["bits[dev,doc]"]
 
 [project.urls]
 "Homepage" = "https://BCDA-APS.github.io/BITS/"
 "Bug Tracker" = "https://github.com/BCDA-APS/BITS/issues"
 
-# [project.scripts]
-# instrument = "instrument.app:main"
 
 [tool.black]
 line-length = 115
@@ -221,10 +219,10 @@ skip-magic-trailing-comma = false
 line-ending = "auto"
 
 [tool.setuptools]
-package-dir = {"instrument" = "src/instrument"}
+package-dir = {"bits" = "src/bits"}
 
 [tool.setuptools.package-data]
 "*" = ["*.yml"]
 
 [tool.setuptools_scm]
-write_to = "src/instrument/_version.py"
+write_to = "src/bits/_version.py"

src/instrument/__init__.py → src/bits/__init__.py

@@ -6,7 +6,7 @@
 
 configure_logging()
 
-__package__ = "instrument"
+__package__ = "bits"
 try:
     from setuptools_scm import get_version
 

src/instrument/callbacks/nexus_data_file_writer.py → src/bits/callbacks/nexus_data_file_writer.py

@@ -14,9 +14,9 @@
 
 import logging
 
-from ..core.run_engine_init import RE
-from ..utils.aps_functions import host_on_aps_subnet
-from ..utils.config_loaders import iconfig
+from bits.core.run_engine_init import RE
+from bits.utils.aps_functions import host_on_aps_subnet
+from bits.utils.config_loaders import iconfig
 
 logger = logging.getLogger(__name__)
 logger.bsdev(__file__)
@@ -48,9 +48,13 @@ def get_sample_title(self):
 nxwriter = MyNXWriter()  # create the callback instance
 """The NeXus file writer object."""
 
-if "NEXUS_DATA_FILES" in iconfig:
+if iconfig.get("NEXUS_DATA_FILES", {}).get("ENABLE", False):
     RE.subscribe(nxwriter.receiver)  # write data to NeXus files
 
-nxwriter.file_extension = iconfig.get("FILE_EXTENSION", "hdf")
-warn_missing = iconfig.get("WARN_MISSING", False)
+nxwriter.file_extension = iconfig.get("NEXUS_DATA_FILES", {}).get(
+    "FILE_EXTENSION", "hdf"
+)
+print("\n\n\n")
+print(nxwriter.file_extension)
+warn_missing = iconfig.get("NEXUS_DATA_FILES", {}).get("WARN_MISSING", False)
 nxwriter.warn_on_missing_content = warn_missing