initial commit

MANIFEST.in

+include versioneer.py
+include bessyii_devices/_version.py
+include beamlinetools/_version.py

README.md

-# vanilla_beamlinetools
+**beamlinetools** 
 
+Python library of tools used at BESSY II BEAMLINES
 
+This is a vanilla beamlinetools that can be used to customize a beamline.
 
-## Getting started
+**Installation**
 
-To make it easy for you to get started with GitLab, here's a list of recommended next steps.
+To install pull this repository and then run 
 
-Already a pro? Just edit this README.md and make it your own. Want to make it easy? [Use the template at the bottom](#editing-this-readme)!
+`python3 setup.py .`
 
-## Add your files
 
-- [ ] [Create](https://docs.gitlab.com/ee/user/project/repository/web_editor.html#create-a-file) or [upload](https://docs.gitlab.com/ee/user/project/repository/web_editor.html#upload-a-file) files
-- [ ] [Add files using the command line](https://docs.gitlab.com/ee/gitlab-basics/add-file.html#add-a-file-using-the-command-line) or push an existing Git repository with the following command:
-
-```
-cd existing_repo
-git remote add origin https://codebase.helmholtz.cloud/hzb/bluesky/beamlines_endstations/vanilla_beamlinetools.git
-git branch -M main
-git push -uf origin main
-```
-
-## Integrate with your tools
-
-- [ ] [Set up project integrations](https://codebase.helmholtz.cloud/hzb/bluesky/beamlines_endstations/vanilla_beamlinetools/-/settings/integrations)
-
-## Collaborate with your team
-
-- [ ] [Invite team members and collaborators](https://docs.gitlab.com/ee/user/project/members/)
-- [ ] [Create a new merge request](https://docs.gitlab.com/ee/user/project/merge_requests/creating_merge_requests.html)
-- [ ] [Automatically close issues from merge requests](https://docs.gitlab.com/ee/user/project/issues/managing_issues.html#closing-issues-automatically)
-- [ ] [Enable merge request approvals](https://docs.gitlab.com/ee/user/project/merge_requests/approvals/)
-- [ ] [Set auto-merge](https://docs.gitlab.com/ee/user/project/merge_requests/merge_when_pipeline_succeeds.html)
-
-## Test and Deploy
-
-Use the built-in continuous integration in GitLab.
-
-- [ ] [Get started with GitLab CI/CD](https://docs.gitlab.com/ee/ci/quick_start/index.html)
-- [ ] [Analyze your code for known vulnerabilities with Static Application Security Testing (SAST)](https://docs.gitlab.com/ee/user/application_security/sast/)
-- [ ] [Deploy to Kubernetes, Amazon EC2, or Amazon ECS using Auto Deploy](https://docs.gitlab.com/ee/topics/autodevops/requirements.html)
-- [ ] [Use pull-based deployments for improved Kubernetes management](https://docs.gitlab.com/ee/user/clusters/agent/)
-- [ ] [Set up protected environments](https://docs.gitlab.com/ee/ci/environments/protected_environments.html)
-
-***
-
-# Editing this README
-
-When you're ready to make this README your own, just edit this file and use the handy template below (or feel free to structure it however you want - this is just a starting point!). Thanks to [makeareadme.com](https://www.makeareadme.com/) for this template.
-
-## Suggestions for a good README
-
-Every project is different, so consider which of these sections apply to yours. The sections used in the template are suggestions for most open source projects. Also keep in mind that while a README can be too long and detailed, too long is better than too short. If you think your README is too long, consider utilizing another form of documentation rather than cutting out information.
-
-## Name
-Choose a self-explaining name for your project.
-
-## Description
-Let people know what your project can do specifically. Provide context and add a link to any reference visitors might be unfamiliar with. A list of Features or a Background subsection can also be added here. If there are alternatives to your project, this is a good place to list differentiating factors.
-
-## Badges
-On some READMEs, you may see small images that convey metadata, such as whether or not all the tests are passing for the project. You can use Shields to add some to your README. Many services also have instructions for adding a badge.
-
-## Visuals
-Depending on what you are making, it can be a good idea to include screenshots or even a video (you'll frequently see GIFs rather than actual videos). Tools like ttygif can help, but check out Asciinema for a more sophisticated method.
-
-## Installation
-Within a particular ecosystem, there may be a common way of installing things, such as using Yarn, NuGet, or Homebrew. However, consider the possibility that whoever is reading your README is a novice and would like more guidance. Listing specific steps helps remove ambiguity and gets people to using your project as quickly as possible. If it only runs in a specific context like a particular programming language version or operating system or has dependencies that have to be installed manually, also add a Requirements subsection.
-
-## Usage
-Use examples liberally, and show the expected output if you can. It's helpful to have inline the smallest example of usage that you can demonstrate, while providing links to more sophisticated examples if they are too long to reasonably include in the README.
-
-## Support
-Tell people where they can go to for help. It can be any combination of an issue tracker, a chat room, an email address, etc.
-
-## Roadmap
-If you have ideas for releases in the future, it is a good idea to list them in the README.
-
-## Contributing
-State if you are open to contributions and what your requirements are for accepting them.
-
-For people who want to make changes to your project, it's helpful to have some documentation on how to get started. Perhaps there is a script that they should run or some environment variables that they need to set. Make these steps explicit. These instructions could also be useful to your future self.
-
-You can also document commands to lint the code or run tests. These steps help to ensure high code quality and reduce the likelihood that the changes inadvertently break something. Having instructions for running tests is especially helpful if it requires external setup, such as starting a Selenium server for testing in a browser.
-
-## Authors and acknowledgment
-Show your appreciation to those who have contributed to the project.
-
-## License
-For open source projects, say how it is licensed.
-
-## Project status
-If you have run out of energy or time for your project, put a note at the top of the README saying that development has slowed down or stopped completely. Someone may choose to fork your project or volunteer to step in as a maintainer or owner, allowing your project to keep going. You can also make an explicit request for maintainers.

beamlinetools.egg-info/PKG-INFO

+Metadata-Version: 2.1
+Name: beamlinetools
+Version: 0+unknown
+Summary: A collection of tools and plans specific to BEAMLINE_name 
+Home-page: https://gitlab.helmholtz-berlin.de/bessyII/bluesky/INSERT_URL
+Author: Will Smith, Simone Vadilonga, Sebastian Kazarski
+Author-email: simone.vadilonga@helmholtz-berlin.de

beamlinetools.egg-info/SOURCES.txt

+MANIFEST.in
+README.md
+setup.cfg
+setup.py
+versioneer.py
+beamlinetools/__init__.py
+beamlinetools/_version.py
+beamlinetools.egg-info/PKG-INFO
+beamlinetools.egg-info/SOURCES.txt
+beamlinetools.egg-info/dependency_links.txt
+beamlinetools.egg-info/requires.txt
+beamlinetools.egg-info/top_level.txt
+beamlinetools/BEAMLINE_CONFIG/__init__.py
+beamlinetools/BEAMLINE_CONFIG/base.py
+beamlinetools/BEAMLINE_CONFIG/baseline.py
+beamlinetools/BEAMLINE_CONFIG/beamline.py
+beamlinetools/BEAMLINE_CONFIG/data_callbacks.py
+beamlinetools/BEAMLINE_CONFIG/magics.py
+beamlinetools/BEAMLINE_CONFIG/plans.py
+beamlinetools/BEAMLINE_CONFIG/tools.py
+beamlinetools/callbacks/__init__.py
+beamlinetools/callbacks/file_exporter.py
+beamlinetools/devices/__init__.py
+beamlinetools/devices/adsimdetector.py
+beamlinetools/devices/genNodeClass.py
+beamlinetools/magics/__init__.py
+beamlinetools/magics/base.py
+beamlinetools/magics/peakinfo.py
+beamlinetools/magics/simplify_syntax.py
+beamlinetools/magics/standard_magics.py
+beamlinetools/magics/standard_magics_utils.py
+beamlinetools/utils/__init__.py
+beamlinetools/utils/pbar_bessy.py
+beamlinetools/utils/publisher.py
+beamlinetools/utils/resolve.py
+beamlinetools/utils/script_load_helper.py
\ No newline at end of file

beamlinetools.egg-info/dependency_links.txt

+

beamlinetools.egg-info/requires.txt

+ophyd
+numpy

beamlinetools.egg-info/top_level.txt

+beamlinetools

beamlinetools/BEAMLINE_CONFIG/__init__.py

+from .base import *
+from .beamline import *
+from .plans import *
+from .tools import *
+from .baseline import *
+# from .authentication_and_metadata import *
+from .magics import *
+from .data_callbacks import *

beamlinetools/BEAMLINE_CONFIG/base.py

+from bluesky import RunEngine
+from os.path import expanduser
+from tiled.client import from_uri
+from IPython import get_ipython
+
+# Check if we are in ipython shell
+is_ipython = get_ipython()
+
+RE = RunEngine({})
+
+from bluesky.callbacks.best_effort import BestEffortCallback
+bec = BestEffortCallback()
+
+# Send all metadata/data captured to the BestEffortCallback.
+RE.subscribe(bec)
+
+# Database definition, change catalog_name for the actual
+# name of the database
+# import databroker
+# db = databroker.catalog["myspot2"]
+# RE.subscribe(db.v1.insert)
+
+from os import environ
+if environ.get('TILED_URL') is not None and environ.get('TILED_API_KEY') is not None:
+    if "http" in environ.get('TILED_URL'):
+        db = from_uri(environ.get('TILED_URL'), api_key=environ.get('TILED_API_KEY'))
+
+        def post_document(name,doc):
+            db.post_document(name,doc)
+
+        RE.subscribe(post_document)
+
+# If we are in ipython shell, we can use the magics
+if is_ipython == None:
+    #define ip and port for the publisher
+    _host = environ.get('ZMQ_URL')
+
+    #create publisher to broadcast documents via 0mq
+    publisher = Publisher(_host) 
+
+    #subscribe the publisher to the document stream
+    RE.subscribe(publisher)
+
+# Temporary database, once mongo is installed and a database created use
+ # comment the following lines 
+#from databroker import Broker
+#db = Broker.named('temp')
+#RE.subscribe(db.insert)
+
+
+# If you need debug messages from the RE then uncomment this
+#from bluesky.utils import ts_msg_hook
+#RE.msg_hook = ts_msg_hook
+
+
+
+# Configure persistence between sessions of metadata
+# change beamline_name to the name of the beamline
+from bluesky.utils import PersistentDict
+import os
+cwd = os.getcwd()
+RE.md = PersistentDict(expanduser('/opt/bluesky/data/persistence/beamline/'))
+
+
+# import databroker.core
+# handler_registry = databroker.core.discover_handlers()
+
+# import matplotlib
+import matplotlib.pyplot as plt

beamlinetools/BEAMLINE_CONFIG/baseline.py

+from bluesky.preprocessors import SupplementalData
+from bessyii.default_detectors import SupplementalDataSilentDets, init_silent, close_silent
+from .base import *
+from .beamline import *
+
+
+
+# here the devices that will be read before and after a scan
+baseline = [det1]
+
+# here the devices to be read during each scan, 
+# but not plotted unless explicitly set in the plan
+silent_devices = []
+
+sd = SupplementalDataSilentDets(baseline=baseline, silent_devices=silent_devices)
+
+#add the functions to the RunEngine library so you can call them via Msg
+RE.register_command('init_silent', init_silent)
+RE.register_command('close_silent', close_silent)
+
+RE.preprocessors.append(sd)
\ No newline at end of file

beamlinetools/BEAMLINE_CONFIG/beamline.py

+# Workarounds/patches
+from ophyd.signal import EpicsSignalBase
+EpicsSignalBase.set_defaults(connection_timeout= 5, timeout=200)
+
+from ophyd import EpicsMotor
+
+# standard magics
+from bluesky.magics import BlueskyMagics
+get_ipython().register_magics(BlueskyMagics)
+
+# simulated devices
+from ophyd.sim import det1, det2, det3, det4, motor1, motor2, motor, noisy_det   # two simulated detectors
+