add type hints to Experiment.py and dac.py, set up pyrefly as dev dependency

pyproject.toml

@@ -39,6 +39,9 @@ maintainers = [
 [project.scripts]
 DAMARIS3 = "damaris.__main__:main"
 
+[dependency-groups]
+dev = ["pyrefly"]
+
 [tool.setuptools.packages.find]
 where = ["src"]
 
@@ -50,6 +53,15 @@ version = {attr = "damaris.__version__"}
 
 [tool.setuptools.data-files]
 "share/python3-damaris/images" = ["src/damaris/gui/DAMARIS3.png", "src/damaris/gui/DAMARIS3.ico"]
+
+[tool.pyrefly]
+project-includes = [
+    "src/damaris/experiments/Experiment.py",
+    "src/damaris/experiments/dac.py",
+]
+search-path = ["src"]
+python-version = "3.11"
+python-platform = "linux"
 #"share/python3-damaris/doc" = ["doc/index.html"]
 #"share/python3-damaris/doc/reference-html" = ["doc/reference-html/*"]
 #"share/python3-damaris/doc/tutorial-html" = ["doc/tutorial-html/*"]

src/damaris/experiments/Experiment.py

@@ -3,20 +3,20 @@ import types
 import numpy
 
 class StateBase(object):
-    def __init__(self):
+    def __init__(self) -> None:
         pass
-    def to_xml(self, indent = ""):
+    def to_xml(self, indent: str = "") -> str:
         return indent + "<!-- " + repr(self) + " -->"
 
 class StateSimple(StateBase):
-    def __init__(self, time, content=None):
+    def __init__(self, time: float, content: object | None = None) -> None:
         super(StateSimple, self).__init__()
         if time < 0:
             raise AssertionError("time for state is negative!")
         self.time = time
         self.content = content
 
-    def to_xml(self, indent = ""):
+    def to_xml(self, indent: str = "") -> str:
         s = indent + '<state time="%s"' % repr(self.time)
         if self.content is None:
             return s + '/>\n'
@@ -24,14 +24,14 @@ class StateSimple(StateBase):
         s += indent + '  ' + str(self.content) + '\n'
         s += indent + '</state>\n'
         return s
-    def __repr__(self):
+    def __repr__(self) -> str:
         return 'StateSimple(%s, %s)' % (self.time, repr(self.content))
 
 class StateList(StateBase):
-    def __init__(self):
+    def __init__(self) -> None:
         super(StateList, self).__init__()
-        self.list = []
+        self.list: list[object] = []
-    def to_xml(self, indent = "  "):
+    def to_xml(self, indent: str = "  ") -> str:
         s = ""
         for k in self.list:
             if hasattr(k, "to_xml"):
@@ -39,21 +39,21 @@ class StateList(StateBase):
             else:
                 s += indent + str(k)
         return s
-    def append(self, val):
+    def append(self, val: object) -> None:
         self.list.append(val)
 
 
 class StateLoop(StateList):
     """Represents a loop in the state tree"""
-    def __init__(self, repeat):
+    def __init__(self, repeat: int) -> None:
         super(StateLoop, self).__init__()
         self.repeat = repeat
-    def to_xml(self, indent = ""):
+    def to_xml(self, indent: str = "") -> str:
         s = indent + ('<sequent repeat="%d">\n' % self.repeat)
         s += super(StateLoop, self).to_xml(indent + "  ")
         s += indent + '</sequent>\n'
         return s
-    def __repr__(self):
+    def __repr__(self) -> str:
         return 'StateLoop(repeat=%d, %s)' \
             % (self.repeat, repr(self.list))
 
@@ -78,32 +78,32 @@ class Experiment:
     :param list rf_gates: list of rf gates ttl channels  len(rf_gates) == len(rf_sources)
 
     """
-    job_id = 0
+    job_id: int = 0
 
-    def __init__(self, gating=None, rf_sources=[], rf_gates=[]):
+    def __init__(self, gating: float | None = None, rf_sources: list[int] = [], rf_gates: list[int] = []) -> None:
-        self.job_id = Experiment.job_id
+        self.job_id: int = Experiment.job_id
         Experiment.job_id += 1
 
-        self.state_list = StateList()
+        self.state_list: StateList = StateList()
-        self.list_stack = []
+        self.list_stack: list[StateList] = []
-        self.description = { }
+        self.description: dict[str, object] = { }
-        self.gating = gating
+        self.gating: float | None = gating
         assert type(rf_sources) == type(list()), "rf_sources needs to be a list with the channels"
         assert type(rf_gates) == type(list()), "rf_gates needs to be a list with the channels"
         assert len(rf_gates) == len(rf_sources), "rf_sources and rf_gates must have equal number of entries"
-        self.rf_sources = rf_sources
+        self.rf_sources: list[int] = rf_sources
-        self.rf_gates = rf_gates
+        self.rf_gates: list[int] = rf_gates
         
         #for tracking the experiment length:
         #because loops are possible we need to track the length for each loop level
-        self.total_time=[0.0]
+        self.total_time: list[float] = [0.0]
         
         #and we need to know the number of iterations of the loops to multiply the state.
-        self.loop_iterations=[1]
+        self.loop_iterations: list[int] = [1]
 
     # Commands -------------------------------------------------------------------------------------
 
-    def ttl_pulse(self, length, channel = None, value = None):
+    def ttl_pulse(self, length: float, channel: int | None = None, value: int | None = None) -> None:
         """
         Creates a state with length **length** and switches requested bits of the pulse programmer to HIGH.
 
@@ -151,7 +151,7 @@ class Experiment:
         self.total_time[-1] += length
 
     ## Same as ttl_pulse, but no *channel* keyword
-    def ttls(self, length = None, value = None):
+    def ttls(self, length: float | None = None, value: int | None = None) -> None:
         """
         Same as ttl_pulse, but no *channel* keyword
 
@@ -159,6 +159,7 @@ class Experiment:
         :param int value: lines to set (integer)
         :return:
         """
+        assert value is not None, "ttls needs an integer value"
         the_value=int(value)
         s_content = '<ttlout value="0x%06x"/>' % the_value
         if length is not None:
@@ -168,7 +169,7 @@ class Experiment:
             self.state_list.append(s_content)
             
 
-    def rf_pulse(self, length=None, phase=0, source=0):
+    def rf_pulse(self, length: float | None = None, phase: float = 0, source: int = 0) -> None:
         """
         Make an rf pulse, including gating and phase switching. Only possible if Experiment is configured.
 
@@ -183,7 +184,7 @@ class Experiment:
         self.ttls(length=length, value=self.rf_gates[source]+self.rf_sources[source])
 
     ## Beginning of a new state
-    def state_start(self, time):
+    def state_start(self, time: float) -> None:
         """
         Starts a state in the pulse programs with duration *time*.
         This must be closed with :func:`state_end`.
@@ -194,13 +195,13 @@ class Experiment:
         self.total_time[-1] += time
 
     ## End of *state_start*
-    def state_end(self):
+    def state_end(self) -> None:
         """
         Closes a previous :func:`state_start`
         """
         self.state_list.append('</state>\n')
 
-    def wait(self, time, ttls=None, gating=False):
+    def wait(self, time: float, ttls: int | None = None, gating: bool = False) -> None:
         """
         Waits for a specified amount of time without performing any actions.
 
@@ -241,6 +242,7 @@ class Experiment:
 
         """
         if gating:
+            assert self.gating is not None, "gating time must be set for gating=True"
             time -= self.gating
         if ttls is not None:
             s_content = '<ttlout value="0x%06x"/>' % ttls
@@ -251,7 +253,7 @@ class Experiment:
         self.total_time[-1] += time
 
 
-    def record(self, samples, frequency, timelength=None, sensitivity = None, ttls=None, channels = 3, offset = None, impedance = None):
+    def record(self, samples: int, frequency: float, timelength: float | None = None, sensitivity: float | list[float] | None = None, ttls: int | None = None, channels: int = 3, offset: int | list[int] | None = None, impedance: float | list[float] | None = None) -> None:
         """
         Records data with a given number of samples, sampling frequency, and sensitivity.
         This command starts data acquisition from the ADC (Analog-to-Digital Converter).
@@ -365,7 +367,7 @@ class Experiment:
 
     ## Create a loop on the pulse programmer. Loop contents can not change inside the loop.
     # @params iterations Number of loop iterations
-    def loop_start(self, iterations):
+    def loop_start(self, iterations: int) -> None:
         """
         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.
@@ -384,7 +386,7 @@ class Experiment:
         self.loop_iterations.append(iterations)
 
     ## End loop state
-    def loop_end(self):
+    def loop_end(self) -> None:
         """
         Closes a l:func:`loop_start` statement.
         """
@@ -396,7 +398,7 @@ class Experiment:
         self.total_time[-1] += looptime*loopiterations
 
 
-    def set_frequency(self, frequency, phase, ttls=0):
+    def set_frequency(self, frequency: float, phase: float, ttls: int = 0) -> None:
         """
         Sets the frequency and phase of the frequency source and optionally further channels.
         The state length is 2 µs. Stabilisation time depends on RF source.
@@ -412,7 +414,7 @@ class Experiment:
         
         self.total_time[-1] += 2e-6
 
-    def set_pfg(self, dac_value=None, length=None, shape=('rec', 0), trigger=4, is_seq=False):
+    def set_pfg(self, dac_value: int | None = None, length: float | None = None, shape: tuple[str, float] = ('rec', 0), trigger: int = 4, is_seq: bool = False) -> None:
         """
         This sets the value for the PFG, it also sets it back to dac_value=0 automatically.
         If you don't wish to do so (i.e. line shapes)  set is_seq=1
@@ -480,7 +482,7 @@ class Experiment:
         else: # don't know what to do
             raise SyntaxError("form is unknown: %s"%form)
 
-    def set_dac(self, dac_value, dac_id=1, length=None, is_seq=False, ttls=0):
+    def set_dac(self, dac_value: int, dac_id: int = 1, length: float | None = None, is_seq: bool = False, ttls: int = 0) -> None:
         """
         Sets the value for the DAC (Digital-to-Analog Converter) and optionally additional TTL lines.
         This command is used to control analog output signals, such as pulsed field gradients.
@@ -544,7 +546,7 @@ class Experiment:
             
             self.total_time[-1] += 42*9e-8
 
-    def set_phase(self, phase, ttls=0):
+    def set_phase(self, phase: float, ttls: int = 0) -> None:
         """
         Sets the phase of the RF source to the specified value.
 
@@ -589,7 +591,7 @@ class Experiment:
         self.total_time[-1] += 0.5e-6
 
 
-    def set_description(self, key, value):
+    def set_description(self, key: str, value: object) -> None:
         """
         Sets a description key-value pair in the experiment description dictionary.
 
@@ -629,7 +631,7 @@ class Experiment:
             print('Warning: Overwriting existing description "%s" = "%s" with "%s"' % (key, self.description[key], value))
         self.description[key] = value
 
-    def set_pts_local(self):
+    def set_pts_local(self) -> None:
         """
         Sets the PTS310/PTS500 frequency source to local mode.
         State length is 2 µs.
@@ -653,7 +655,7 @@ class Experiment:
         return self.job_id
 
 
-    def write_xml_string(self):
+    def write_xml_string(self) -> str:
         """
         Returns the current program as a string
 
@@ -706,14 +708,14 @@ class Experiment:
 
         return xml_string
 
-    def write_quit_job(self):
+    def write_quit_job(self) -> str:
         """
         Returns a xml quit-job
         :returns: XML quit-job
         """
         return '<?xml version="1.0" encoding="ISO-8859-1"?>\n<quit/>'
     
-    def get_length(self):
+    def get_length(self) -> float:
         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].
@@ -723,13 +725,13 @@ class Experiment:
         return timelength
 
 class Quit(Experiment):
-    def write_xml_string(self):
+    def write_xml_string(self) -> str:
         return '<?xml version="1.0" encoding="ISO-8859-1"?>\n<quit no="%d"/>'%self.job_id
 
 
 # /Public Methods ------------------------------------------------------------------------------
 
-def self_test():
+def self_test() -> None:
     e = Experiment()
     e.set_description("key", "value")
     e.set_frequency(85e6, 90, ttls=16)

src/damaris/experiments/dac.py

@@ -2,7 +2,7 @@
 """
 This module holds everything connected with the DAC and PFG
 """
-def conv(I_out=0):
+def conv(I_out: float = 0) -> int:
     """
     converts the demanded Output current in Integer
     """

uv.lock

@@ -938,6 +938,25 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/10/bd/c038d7cc38edc1aa5bf91ab8068b63d4308c66c4c8bb3cbba7dfbc049f9c/pyparsing-3.3.2-py3-none-any.whl", hash = "sha256:850ba148bd908d7e2411587e247a1e4f0327839c40e2e5e6d05a007ecc69911d", size = 122781, upload-time = "2026-01-21T03:57:55.912Z" },
 ]
 
+[[package]]
+name = "pyrefly"
+version = "1.4.0"
+source = { registry = "https://pypi.org/simple" }
+sdist = { url = "https://files.pythonhosted.org/packages/b3/3e/ea6893be167fa14307d7f9a924bed9ecbbbd91b01953890b9b3c58ed5359/pyrefly-1.4.0.tar.gz", hash = "sha256:bb57c004a4842cfe93f93aebb5203ca6209a5f0c8bda47e8bc289e70940fd910", size = 6962062, upload-time = "2026-10-15T16:54:11.819Z" }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/6a/17/dfce6611acc00cb26667e5e1011438cc510f3067f961e0f07f7a0c68f416/pyrefly-1.4.0-py3-none-macosx_10_12_x86_64.whl", hash = "sha256:460cec39bc8743915e9c2c8c10ba926ad0b29b099d89c1859fb97e0059f42fa7", size = 15705624, upload-time = "2026-10-15T16:53:43.412Z" },
+    { url = "https://files.pythonhosted.org/packages/a6/78/a7b96442123fa6ed733de0d1ea933e35d6fc6b7c9cf16e05279abb493493/pyrefly-1.4.0-py3-none-macosx_11_0_arm64.whl", hash = "sha256:5a6370d686b6cbbac8869832f09a52012888371956fbc68d446a349bc85ccd43", size = 14978669, upload-time = "2026-10-15T16:53:46.546Z" },
+    { url = "https://files.pythonhosted.org/packages/23/97/dfcfec6a9d8948ab4b2746f7e87558a82bffabb7a54c22e7d3ce4bdc1932/pyrefly-1.4.0-py3-none-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:8f1b16923a6583a6764e8aec07787e2ef4df644c7030294cba71339783a9451c", size = 15438858, upload-time = "2026-10-15T16:53:48.904Z" },
+    { url = "https://files.pythonhosted.org/packages/31/12/6fa414aa87e398d6ddc7145a5d993b0975fc3511198dbb72c47873653ab6/pyrefly-1.4.0-py3-none-manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:688ad4cb4d6e711d67026fdcfb37b599f86061efe11ba5704287330e7041a69e", size = 16852241, upload-time = "2026-10-15T16:53:51.496Z" },
+    { url = "https://files.pythonhosted.org/packages/a8/73/2d7312262cf6481d6ad46eed55b8f2592c3cff60f95cc2f30a114cd1484e/pyrefly-1.4.0-py3-none-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl", hash = "sha256:f5f3c9dddb6f3128beb49cf4e0f5cb88d4d17f039008d8e0c2be653966acd234", size = 16751917, upload-time = "2026-10-15T16:53:54.39Z" },
+    { url = "https://files.pythonhosted.org/packages/2c/65/b44a1cb23667bcbcdc88558cbef79fa9e07a1152c2a1da148036b1a2e0d1/pyrefly-1.4.0-py3-none-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:b6951f51687304caebfedf13dd1a943aeafdbc95abcc4e24a683b97467a77007", size = 16066345, upload-time = "2026-10-15T16:53:57.436Z" },
+    { url = "https://files.pythonhosted.org/packages/a6/07/7ca6ff0c53e3a90ecdab05790d33f430fca5c48687613a0b182744166d98/pyrefly-1.4.0-py3-none-musllinux_1_2_aarch64.whl", hash = "sha256:838de4d4a8b9b8ed39bedd0b8b55629c69661d73a6fa3a3a4adff24b9dbeb399", size = 15461223, upload-time = "2026-10-15T16:54:00.364Z" },
+    { url = "https://files.pythonhosted.org/packages/61/be/ec7b2f38a898ce5b2219dda730e87d31fc8cfb2108a3d5844f9d590f1281/pyrefly-1.4.0-py3-none-musllinux_1_2_x86_64.whl", hash = "sha256:afb9ce2e0ae3e6106fb45f6d47536ac92b6423e601e08401cdefa850066444f5", size = 16119099, upload-time = "2026-10-15T16:54:02.664Z" },
+    { url = "https://files.pythonhosted.org/packages/6e/16/1b9549168b38a575d9c168e17b4b4ee30028d602ec0f7b07c198ef265dbe/pyrefly-1.4.0-py3-none-win32.whl", hash = "sha256:839db536d0ac29f1b23e2d974fb911075c2283e3e623755c45d826aafac175bc", size = 14858880, upload-time = "2026-10-15T16:54:05.114Z" },
+    { url = "https://files.pythonhosted.org/packages/03/02/18f075d4de0e255f184f42fc28c1f0ecc9f49dd528678479fc90cf12246c/pyrefly-1.4.0-py3-none-win_amd64.whl", hash = "sha256:7aff37c2b711c8240ed650da0c6148237b327bf7e5dfacee65884f1adea22305", size = 15726220, upload-time = "2026-10-15T16:54:07.452Z" },
+    { url = "https://files.pythonhosted.org/packages/92/62/92947076681550904c72a9dd03b24e92694ede9a48548f5e487c849e66ea/pyrefly-1.4.0-py3-none-win_arm64.whl", hash = "sha256:88879f0cb749e5fea81d9ff4c2d5431a70349c458bcdf0b61de72c79214d90a5", size = 14943690, upload-time = "2026-10-15T16:54:09.689Z" },
+]
+
 [[package]]
 name = "pyserial"
 version = "3.5"
@@ -976,6 +995,11 @@ dependencies = [
     { name = "tables" },
 ]
 
+[package.dev-dependencies]
+dev = [
+    { name = "pyrefly" },
+]
+
 [package.metadata]
 requires-dist = [
     { name = "matplotlib", specifier = ">=1.4.1,<=3.6" },
@@ -990,6 +1014,9 @@ requires-dist = [
     { name = "tables", specifier = ">=3.1.1" },
 ]
 
+[package.metadata.requires-dev]
+dev = [{ name = "pyrefly" }]
+
 [[package]]
 name = "pyxdg"
 version = "0.28"