added sphinx documentation

doc/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= python -m sphinx
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

doc/conf.py

@@ -0,0 +1,36 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+import sys,os
+#sys.path.insert(0, os.path.abspath('../src'))
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+project = 'DAMARIS'
+copyright = '2026, Markus Rosenstihl'
+author = 'Markus Rosenstihl'
+
+version = '0.19'
+release = '0.19'
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = [
+    'sphinx.ext.autodoc',
+    'sphinx.ext.napoleon',
+    ]
+
+templates_path = ['_templates']
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+language = 'en'
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+#html_theme = 'alabaster'
+html_theme = 'sphinx_rtd_theme'
+html_static_path = ['_static']

doc/index.rst

@@ -0,0 +1,38 @@
+.. DAMARIS documentation master file, created by
+   sphinx-quickstart on Mon Mar 23 15:55:16 2026.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+DAMARIS documentation
+=====================
+
+Add your content using ``reStructuredText`` syntax. See the
+`reStructuredText <https://www.sphinx-doc.org/en/master/usage/restructuredtext/index.html>`_
+documentation for details.
+
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+API Reference
+-------------
+
+Experiments
+~~~~~~~~~~~
+
+.. automodule:: damaris.experiments.Experiment
+   :members:
+   :undoc-members:
+
+Data Objects
+~~~~~~~~~~~~
+
+.. automodule:: damaris.data.Accumulation
+   :members:
+   :undoc-members:
+
+.. automodule:: damaris.data.ADC_Result
+   :members:
+   :undoc-members:
+

doc/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=.
+set BUILDDIR=_build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

pyproject.toml

@@ -35,7 +35,6 @@ maintainers = [
 [project.scripts]
 DAMARIS3 = "damaris.__main__:main"
 
-
 [tool.setuptools]
 packages = [
     "damaris",

src/experiments/Experiment.py

@@ -71,10 +71,13 @@ from . import dac
 class Experiment:
     """
     Class holding the complete state tree for a single experiment. This state tree represents one
-    program on the pulse card. It is written in a single file  and  picked up by the backend.
+    program on the pulse card. It is written in a single file and picked up by the backend.
-    """
-    ## Experiment class holding the state tree
 
+    :param Gating gating: gate length in s
+    :param list rf_sources: list of rf sources ttl channels
+    :param list rf_gates: list of rf gates ttl channels  len(rf_gates) == len(rf_sources)
+
+    """
     job_id = 0
 
     def __init__(self, gating=None, rf_sources=[], rf_gates=[]):
@@ -102,14 +105,6 @@ class Experiment:
 
     # Commands -------------------------------------------------------------------------------------
 
-    ## Creates a state with ttl signals of duration *length*.
-    #
-    # **Example:**
-    # ttl_pulse(length=1e-6,value=3) 
-    # will create a ttl pulse on channels 0 and 1 (2**0 + 2**1) of duration 1us
-    # @param length time length if this state
-    # @param channel select a single channel (1...24)
-    # @param value select the channels via decimal representation (2**0 + 2**1 ...)
     def ttl_pulse(self, length, channel = None, value = None):
         """
         Creates a state with length **length** and switches
@@ -117,8 +112,7 @@ class Experiment:
 
         :param float length: pulse length in seconds
         :param int  channel: selects a single channel (No. 1 - 24)
-        :param int  value: lines to set (integer) for example value=3 selects channels 1 and 2 (2**1 + 2**2)
+        :param int  value: lines to set (integer) for example value=3 selects channels 0 and 1 (2**0 + 2**1)
-
         """
         the_value=0
         if value is not None:
@@ -150,12 +144,11 @@ class Experiment:
 
     def rf_pulse(self, length=None, phase=0, source=0):
         """
-        make an rf pulse, including gating and phase switching
+        Make an rf pulse, including gating and phase switching. Only possible if Experiment is configured.
 
         :param float length: pulse length
         :param float phase: pulse phase
         :param int source: source id
-        :return:
         """
         if not self.gating:
             raise SyntaxError("Can not use rf_pulse without configuration: Experiment(gating=None, rf_sources=[], rf_gates=[]")
@@ -167,7 +160,9 @@ class Experiment:
     def state_start(self, time):
         """
         Starts a state in the pulse programs with duration *time*.
-        This must be closed with state_end()
+        This must be closed with :func:`state_end`.
+
+        Typically only used in very special cases.
         """
         self.state_list.append('<state time="%s">\n' % repr(time))
         self.total_time[-1] += time
@@ -175,13 +170,10 @@ class Experiment:
     ## End of *state_start*
     def state_end(self):
         """
-        Closes a previous start_state()
+        Closes a previous :func:`state_start`
         """
         self.state_list.append('</state>\n')
 
-    ## An empty state doing nothing
-    # @param time Duration of this state
-    # @param ttls Additinional ttl channels
     def wait(self, time, ttls=None, gating=False):
         """
         Wait specified **time** doing nothing.
@@ -201,24 +193,19 @@ class Experiment:
             
         self.total_time[-1] += time
 
-    ## Records  data with given number of samples, sampling-frequency frequency and sensitivity
+
-    # @param samples Number of samples to record
-    # @param frequency Sampling frequency
-    # @param timelength Length of this state, per default calculated automatically
-    # @param sensitivity Sensitivity in Umax/V
-    # @param ttls Additional ttl channels
     def record(self, samples, frequency, timelength=None, sensitivity = None, ttls=None, channels = 3, offset = None, impedance = None):
         """
-        Records  data with given number of samples, sampling frequency and sensitivity.
+        Records data with a given number of samples, sampling frequency and sensitivity.
-        Optionally, the time length of this state can be specified. If not specified **timelength** is
+        Optionally, the time length of this state can be specified. If not specified, **timelength** is
         deduced from **samples**/**frequency**:
 
         :param int samples: Number of samples to record
-        :param float frequency: Sampling frequency
+        :param float frequency: Sampling frequency / Hz
         :param float timelength: Length of this state, per default calculated automatically
-        :param float sensitivity: Sensitivity in Umax/V
+        :param float sensitivity: Sensitivity in U_MAX/V
-        :param int ttls: lines to set (integer)
+        :param int ttls: additional ttl lines to set (integer)
-        :param int channels: default=3, Number of channels counting from 0
+        :param int channels: channels to activate, default=3 (0+1)
         """
         attributes='s="%d" f="%d"'%(samples,frequency)#%g
         if channels != 1 and channels != 3 and channels != 5 and channels != 15:
@@ -270,11 +257,11 @@ class Experiment:
     def loop_start(self, iterations):
         """
         creates a loop of given number of iterations and has to be closed by loop_end().
-        Commands inside the loop can not change, i.e. the parameters are the same for each loop run. 
+        Commands inside the loop can not change, i.e., the parameters are the same for each loop run.
         This loop is created on the pulse programmer, thus saving commands.
-        One must close the loop with loop_end (see below)!
+        Close the loop with :func:`loop_end`.
 
-        :param int iterations: iterations to loop
+        :param int iterations: number of iterations to loop
         """
         l = StateLoop(iterations)
         self.state_list.append(l)
@@ -288,7 +275,7 @@ class Experiment:
     ## End loop state
     def loop_end(self):
         """
-        Closes a loop_start() statement.
+        Closes a l:func:`loop_start` statement.
         """
         # (This line could probably be guarded by a mutex)
         self.state_list = self.list_stack.pop(-1)
@@ -297,11 +284,7 @@ class Experiment:
         loopiterations=self.loop_iterations.pop(-1)
         self.total_time[-1] += looptime*loopiterations
 
-    ## Set the frequency and phase of the frequency source.
+
-    ## This state needs 2us.
-    # @param frequency New frequency in Hz
-    # @param phase New phase in degrees 
-    # @param ttls Additional ttl channels
     def set_frequency(self, frequency, phase, ttls=0):
         """
         Sets the frequency and phase of the frequency source and optionally further channels.
@@ -309,7 +292,7 @@ class Experiment:
 
         :param float frequency: frequency to set in Hz
         :param float phase: phase to set
-        :param int ttls: default=0,  lines to set (integer)
+        :param int ttls: default=0, additional ttl lines to set (integer)
         """
         s_content = '<analogout id="0" f="%f" phase="%f"/>' % (frequency, phase)
         if ttls != 0:
@@ -318,16 +301,10 @@ class Experiment:
         
         self.total_time[-1] += 2e-6
 
-    ## Creates a, possibly shaped, pulsed gradient.
-    # @param dac_value DAC value to set
-    # @param length Duration of the state, minimum length is 42*90ns=3.78us (default)
-    # @param shape Tuple of (shape, resolution/seconds), shape can be one of: rec (default), sin2, sin
-    # @param is_seq If set to *True*, do NOT set DAC to zero after this state
-    # @param trigger Additional ttl channels
     def set_pfg(self, dac_value=None, length=None, shape=('rec', 0), trigger=4, is_seq=False):
         """
-        This sets the value for the PFG, it also sets it back automatically.
+        This sets the value for the PFG, it also sets it back to dac_value=0 automatically.
-        If you don't whish to do so (i.e. line shapes)  set is_seq=1
+        If you don't wish to do so (i.e. line shapes)  set is_seq=1
         If you want to set a trigger, set trigger (default=4, i.e. channel 2)
         If you want shaped gradients: shape=(ashape, resolution), ashape can be rec, sin2, sin
 
@@ -392,22 +369,15 @@ class Experiment:
         else: # don't know what to do
             raise SyntaxError("form is unknown: %s"%form)
 
-
-    ## sets the value of a DAC
-    # @param dac_value DAC value to set
-    # @param dac_id ID of the dac in case of multiple DAC(default=1)
-    # @param length Duration of the state
-    # @param is_seq If set to *True*, do NOT set DAC to zero after this state
-    # @param ttls Additional ttl channels
     def set_dac(self, dac_value, dac_id=1, length=None, is_seq=False, ttls=0):
         """
-        This sets the value for the DAC and if given the TTLs.
+        This sets the value for the DAC and if given additional ttl lines.
-        It also sets it back to zero automatically.
+        It also sets it back to zero automatically when is_seq=False.
         If you don't wish to set the value back to zero (i.e. line shapes) set is_seq=True
 
         The state length is at least 3.78 µs (is_seq=1) or 7.28µs (is_seq=0).
 
-        :param int dac_value: dac value, between -2**19-1 and +2**19
+        :param int dac_value: DAC value, between -2**19-1 and +2**19
         :param int dac_id: default=1, which DAC to control
         :param float length: default=None, length of this state in seconds. If *None* length=42*90ns=3.78µs
         :param bool is_seq: default=False, do not reset DAC to 0 (zero) if True
@@ -429,10 +399,6 @@ class Experiment:
             
             self.total_time[-1] += 42*9e-8
 
-    ## sets the phase of the frequency source.
-    ## This state needs 0.5us, though the phase switching time is dependent on the frequency source
-    # @param phase New phase to set
-    # @param ttls Additional ttl channels
     def set_phase(self, phase, ttls=0):
         """
         Sets the phase of the RF source to this value.
@@ -450,11 +416,7 @@ class Experiment:
         
         self.total_time[-1] += 0.5e-6
 
-    ## sets a description which is carried via the back end result 
+
-    ## file to the result script in the front end. In the result script 
-    ## you can extract the description with get_description(key)
-    # @param key Name of description
-    # @param value Value of description
     def set_description(self, key, value):
         """Sets a description which is carried via the back end result 
         file to the result script in the front end. In the result script 
@@ -467,7 +429,6 @@ class Experiment:
             print('Warning: Overwriting existing description "%s" = "%s" with "%s"' % (key, self.description[key], value))
         self.description[key] = value
 
-    ## set the PTS310/PTS500 frequency source to local mode
     def set_pts_local(self):
         """
         Sets the PTS310/PTS500 frequency source to local mode.
@@ -483,7 +444,7 @@ class Experiment:
 
     # Public Methods -------------------------------------------------------------------------------
 
-    def get_job_id(self):
+    def get_job_id(self) -> int:
         """
         Returns the job-id of the current experiment
 
@@ -554,13 +515,11 @@ class Experiment:
     
     def get_length(self):
         timelength = 0.0
-        
         #calculate the correct timelength also for unclosed loops, if there is no unclosed loop
         #the timelength of this experiment is self.total_time[-1].
         for i in range(len(self.total_time)):
             timelength += self.total_time[i]
             timelength *= self.loop_iterations[i]
-            
         return timelength
 
 class Quit(Experiment):
@@ -570,8 +529,6 @@ class Quit(Experiment):
 
 # /Public Methods ------------------------------------------------------------------------------
 
-
-
 def self_test():
     e = Experiment()
     e.set_description("key", "value")