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Merge pull request #1139 from stevenhua0320/c16
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add doc/source files, change regolith.rst to index.rst in doc/source/api
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sbillinge committed Jul 20, 2024
2 parents 464e965 + 0138425 commit 0e4d74a
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70 changes: 32 additions & 38 deletions doc/source/api/regolith.rst → doc/source/api/index.rst
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:tocdepth: -1
.. _api:

regolith package
================

.. automodule:: regolith
:members:
:undoc-members:
:show-inheritance:

Subpackages
-----------
=================
Regolith API
=================
For those of you who want the gritty details.

.. toctree::
:titlesonly:
:maxdepth: 1

regolith.builders
regolith.static
regolith.templates
regolith.helpers

Submodules
Other API usage
----------

regolith.fsclient module
regolith.fsclient
^^^^^^^^^^^^^^^^^^^^^^^^

.. automodule:: regolith.fsclient
:members:
:undoc-members:
:show-inheritance:

regolith.helper_connect_main module
regolith.helper_connect_main
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

.. automodule:: regolith.helper_connect_main
:members:
:undoc-members:
:show-inheritance:

regolith.stylers module
regolith.stylers
^^^^^^^^^^^^^^^^^^^^^^^

.. automodule:: regolith.stylers
:members:
:undoc-members:
:show-inheritance:

regolith.sorters module
regolith.sorters
^^^^^^^^^^^^^^^^^^^^^^^

.. automodule:: regolith.sorters
:members:
:undoc-members:
:show-inheritance:

regolith.helper_gui_main module
regolith.helper_gui_main
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

.. automodule:: regolith.helper_gui_main
:members:
:undoc-members:
:show-inheritance:

regolith.deploy module
regolith.deploy
^^^^^^^^^^^^^^^^^^^^^^

.. automodule:: regolith.deploy
:members:
:undoc-members:
:show-inheritance:

regolith.grader module
regolith.grader
^^^^^^^^^^^^^^^^^^^^^^

.. automodule:: regolith.grader
:members:
:undoc-members:
:show-inheritance:

regolith.validators module
regolith.validators
^^^^^^^^^^^^^^^^^^^^^^^^^^

.. automodule:: regolith.validators
:members:
:undoc-members:
:show-inheritance:

regolith.runcontrol module
regolith.runcontrol
^^^^^^^^^^^^^^^^^^^^^^^^^^

.. automodule:: regolith.runcontrol
:members:
:undoc-members:
:show-inheritance:

regolith.tools module
regolith.tools
^^^^^^^^^^^^^^^^^^^^^

.. automodule:: regolith.tools
:members:
:undoc-members:
:show-inheritance:

regolith.client_manager module
regolith.client_manager
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

.. automodule:: regolith.client_manager
:members:
:undoc-members:
:show-inheritance:

regolith.builder module
regolith.builder
^^^^^^^^^^^^^^^^^^^^^^^

.. automodule:: regolith.builder
:members:
:undoc-members:
:show-inheritance:

regolith.classlist module
regolith.classlist
^^^^^^^^^^^^^^^^^^^^^^^^^

.. automodule:: regolith.classlist
:members:
:undoc-members:
:show-inheritance:

regolith.schemas module
regolith.schemas
^^^^^^^^^^^^^^^^^^^^^^^

.. automodule:: regolith.schemas
:members:
:undoc-members:
:show-inheritance:

regolith.storage module
regolith.storage
^^^^^^^^^^^^^^^^^^^^^^^

.. automodule:: regolith.storage
:members:
:undoc-members:
:show-inheritance:

regolith.helper module
regolith.helper
^^^^^^^^^^^^^^^^^^^^^^

.. automodule:: regolith.helper
:members:
:undoc-members:
:show-inheritance:

regolith.emailer module
regolith.emailer
^^^^^^^^^^^^^^^^^^^^^^^

.. automodule:: regolith.emailer
:members:
:undoc-members:
:show-inheritance:

regolith.app module
regolith.app
^^^^^^^^^^^^^^^^^^^

.. automodule:: regolith.app
:members:
:undoc-members:
:show-inheritance:

regolith.dates module
regolith.dates
^^^^^^^^^^^^^^^^^^^^^

.. automodule:: regolith.dates
:members:
:undoc-members:
:show-inheritance:

regolith.broker module
regolith.broker
^^^^^^^^^^^^^^^^^^^^^^

.. automodule:: regolith.broker
:members:
:undoc-members:
:show-inheritance:

regolith.main module
regolith.main
^^^^^^^^^^^^^^^^^^^^

.. automodule:: regolith.main
:members:
:undoc-members:
:show-inheritance:

regolith.chained_db module
regolith.chained_db
^^^^^^^^^^^^^^^^^^^^^^^^^^

.. automodule:: regolith.chained_db
:members:
:undoc-members:
:show-inheritance:

regolith.interact module
regolith.interact
^^^^^^^^^^^^^^^^^^^^^^^^

.. automodule:: regolith.interact
:members:
:undoc-members:
:show-inheritance:

regolith.commands module
regolith.commands
^^^^^^^^^^^^^^^^^^^^^^^^

.. automodule:: regolith.commands
:members:
:undoc-members:
:show-inheritance:

regolith.mongoclient module
regolith.mongoclient
^^^^^^^^^^^^^^^^^^^^^^^^^^^

.. automodule:: regolith.mongoclient
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2 changes: 1 addition & 1 deletion doc/source/collections/abstracts.rst
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Expand Up @@ -10,7 +10,7 @@ The following lists key names mapped to its type and meaning for each entry.
:coauthors: string, names of coauthors, optional
:email: string, contact email for the author., required
:firstname: string, first name of the author., required
:institution: string, name of the inistitution, required
:institution: string, name of the institution, required
:lastname: string, last name of the author., required
:references: string, HTML string of reference for the abstract itself, optional
:text: string, HTML string of the abstract., required
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128 changes: 128 additions & 0 deletions doc/source/collections/beamplan.rst
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Beamplan
========
Information about the experiment plan for the beamtime.

Schema
------
The following lists key names mapped to its type and meaning for each entry.

:_id: string, Unique identifier for the experiment plan. It should have a format '{year:2d}{month:2d}{people_id:s}_{plan_name:s}', required
:beamtime: string, The id for the beamtime. Check the Airtable., required
:begin_date: ['string', 'datetime', 'date'], The begin date of the beam time., required
:devices: list, The dictionary of devices used in the measurement e. g. , required

:type: string, optional
:end_date: ['string', 'datetime', 'date'], The end date of the beam time., required
:exp_plan: list, Steps to carry out the experiments at BNL. Need details, required

:type: string, optional
:holder: string, Sample holder used during the measurement, e. g. 3 mm OD tubes holder., required
:measurement: string, What data to be measured, e. g. PDF, XRD, SAXS. This will determine the setup., required
:notes: ['list', 'string'], Notes of the plan, e. g. the preferred time., optional

:type: string, optional
:objective: string, What to study in the experiments. What goal to achieve., required
:pipeline: string, The analysis pipeline for the experiment. If no new pipeline is needed, use 'usual'., required
:prep_plan: list, Steps to prepare the samples. Do NOT need details., required

:type: string, optional
:project: string, The id for the project which the plan belongs to. It should be on airtable., required
:project_lead: string, The id for person who put out this plan. It should be inside the people.yml., required
:samples: list, The list of samples to be measured., required

:type: string, optional
:scanplan: list, The scanplan for the experiment, e. g. tseries, Tramp, ct., required

:type: string, optional
:ship_plan: list, Steps to carry the samples from the producer to the BNL. Do NOT need details., required

:type: string, optional
:time: integer, The total time of executing the exp_plan. Unit: min., required
:todo: list, The TODO list before the beamtime., required

:type: string, optional


YAML Example
------------

.. code-block:: yaml
test:
beamtime: 2020-1-XPD
begin_date: '2020-01-01'
devices:
- cryostream
end_date: '2020-01-02'
exp_plan:
- load samples on the holder
- scan the holder to locate the samples
- take room temperature measurement of sample and the subtrate
- ramp down temperature to 100K
- ramp up, measure PDF at temperature 100K ~ 300K, 10K stepsize, 1 min exposure
holder: film holder (1 cm * 1 cm * 1 mm)
measurement: Tramp
objective: temperature ramping PDF of one WO3 film (100, 300K, 10K)
pipeline: usual
prep_plan:
- films will be made by kriti
project: 20ks_wo3
project_lead: kseth
samples:
- WO3 film
- glass subtrate
scanplan:
- Scanplan(bt, Tramp, 30, 80, 500, 10)
ship_plan:
- seal and ship to CU
- carry to the beamline
time: 190
todo:
- todo something
JSON/Mongo Example
------------------

.. code-block:: json
{
"_id": "test",
"beamtime": "2020-1-XPD",
"begin_date": "2020-01-01",
"devices": [
"cryostream"
],
"end_date": "2020-01-02",
"exp_plan": [
"load samples on the holder",
"scan the holder to locate the samples",
"take room temperature measurement of sample and the subtrate",
"ramp down temperature to 100K",
"ramp up, measure PDF at temperature 100K ~ 300K, 10K stepsize, 1 min exposure"
],
"holder": "film holder (1 cm * 1 cm * 1 mm)",
"measurement": "Tramp",
"objective": "temperature ramping PDF of one WO3 film (100, 300K, 10K)",
"pipeline": "usual",
"prep_plan": [
"films will be made by kriti"
],
"project": "20ks_wo3",
"project_lead": "kseth",
"samples": [
"WO3 film",
"glass subtrate"
],
"scanplan": [
"Scanplan(bt, Tramp, 30, 80, 500, 10)"
],
"ship_plan": [
"seal and ship to CU",
"carry to the beamline"
],
"time": 190,
"todo": [
"todo something"
]
}
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