pytrms 0.9.1__tar.gz → 0.9.2__tar.gz

{pytrms-0.9.1 → pytrms-0.9.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pytrms
-Version: 0.9.1
+Version: 0.9.2
 Summary: Python bundle for proton-transfer reaction mass-spectrometry (PTR-MS).
 License: GPL-2.0
 Author: Moritz Koenemann
@@ -13,7 +13,7 @@ Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Requires-Dist: h5py (>=3.12.1,<4.0.0)
 Requires-Dist: matplotlib (>=3.9.2,<4.0.0)
-Requires-Dist: paho-mqtt (>=1.6.1,<1.7.0)
+Requires-Dist: paho-mqtt (>=1.6.1,<3.0)
 Requires-Dist: pandas (>=2.2.3,<3.0.0)
 Requires-Dist: pyModbusTCP (>=0.1.9)
 Requires-Dist: requests (>=2.32.3,<3.0.0)

{pytrms-0.9.1 → pytrms-0.9.2}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pytrms"
-version = "0.9.1"
+version = "0.9.2"
 description = "Python bundle for proton-transfer reaction mass-spectrometry (PTR-MS)."
 authors = ["Moritz Koenemann <moritz.koenemann@ionicon.com>"]
 license = "GPL-2.0"
@@ -15,8 +15,10 @@ h5py = "^3.12.1"
 matplotlib = "^3.9.2"
 requests = "^2.32.3"
 pandas = "^2.2.3"
+
+# we have legacy support for Anaconda-packages!
 pyModbusTCP = ">=0.1.9"
-paho-mqtt = "~1.6.1"
+paho-mqtt = ">=1.6.1,<3.0"
 
 [tool.poetry.group.test.dependencies]
 pytest = "^8.3.0"

{pytrms-0.9.1 → pytrms-0.9.2}/pytrms/__init__.py

@@ -1,4 +1,4 @@
-_version = '0.9.1'
+_version = '0.9.2'
 
 __all__ = ['load', 'connect']
 
@@ -6,14 +6,16 @@ __all__ = ['load', 'connect']
 def load(path):
     '''Open a datafile for post-analysis or batch processing.
 
-    returns a `Measurement`.
+    `path` may be a glob-expression to collect a whole batch.
+
+    returns a `Measurement` instance.
     '''
-    from .measurement import OfflineMeasurement
-    from .readers import IoniTOFReader
+    import glob
+    from .measurement import FinishedMeasurement
 
-    reader = IoniTOFReader(path)
+    files = glob.glob(path)
 
-    return OfflineMeasurement(reader)
+    return FinishedMeasurement(*files)
 
 def connect(host=None, method='webapi'):
     '''Connect a client to a running measurement server.

{pytrms-0.9.1 → pytrms-0.9.2}/pytrms/_base/mqttclient.py

@@ -6,9 +6,8 @@ from collections import deque
 from itertools import cycle
 from threading import Condition, RLock
 from datetime import datetime as dt
-from abc import ABC, abstractmethod
 
-import paho.mqtt.client as mqtt
+import paho.mqtt.client
 
 from .ioniclient import IoniClientBase
 
@@ -39,7 +38,6 @@ def _on_publish(client, self, mid):
 class MqttClientBase(IoniClientBase):
 
     @property
-    @abstractmethod
     def is_connected(self):
         '''Returns `True` if connected to the server.
 
@@ -49,12 +47,27 @@ class MqttClientBase(IoniClientBase):
         return (True
             and self.client.is_connected())
 
-    def __init__(self, host, subscriber_functions,
+    def __init__(self, host, port, subscriber_functions,
             on_connect, on_subscribe, on_publish, 
             connect_timeout_s=10):
-        super().__init__(host, port=1883)
-        # configure connection...
-        self.client = mqtt.Client(clean_session=True)
+        assert len(subscriber_functions) > 0, "no subscribers: for some unknown reason this causes disconnects"
+        super().__init__(host, port)
+
+        # Note: Version 2.0 of paho-mqtt introduced versioning of the user-callback to fix
+        #  some inconsistency in callback arguments and to provide better support for MQTTv5.
+        #  VERSION1 of the callback is deprecated, but is still supported in version 2.x.
+        #  If you want to upgrade to the newer version of the API callback, you will need
+        #  to update your callbacks:
+        paho_version = int(paho.mqtt.__version__.split('.')[0])
+        if paho_version == 1:
+            self.client = paho.mqtt.client.Client(clean_session=True)
+        elif paho_version == 2:
+            self.client = paho.mqtt.client.Client(paho.mqtt.client.CallbackAPIVersion.VERSION1,
+                    clean_session=True)
+        else:
+            # see https://eclipse.dev/paho/files/paho.mqtt.python/html/migrations.html
+            raise NotImplementedError("API VERSION2 for MQTTv5 (use paho-mqtt 2.x or implement user callbacks)")
+
         # clean_session is a boolean that determines the client type. If True,
         # the broker will remove all information about this client when it
         # disconnects. If False, the client is a persistent client and

{pytrms-0.9.1 → pytrms-0.9.2}/pytrms/clients/__init__.py

@@ -7,7 +7,7 @@ assert os.path.exists(_par_id_file), "par-id file not found: please re-install P
 
 import logging as _logging
 
-_logging.TRACE = 0  # overwrites logging.NOTSET
+_logging.TRACE = 5  # even more verbose than logging.DEBUG
 
 def enable_extended_logging(log_level=_logging.DEBUG):
     '''make output of http-requests more talkative.
@@ -22,7 +22,7 @@ def enable_extended_logging(log_level=_logging.DEBUG):
         requests_log.setLevel(log_level)
         requests_log.propagate = True
     
-    if log_level == _logging.TRACE:
+    if log_level <= _logging.TRACE:
         # Enabling debugging at http.client level (requests->urllib3->http.client)
         # you will see the REQUEST, including HEADERS and DATA, and RESPONSE with
         # HEADERS but without DATA. the only thing missing will be the response.body,

{pytrms-0.9.1 → pytrms-0.9.2}/pytrms/clients/db_api.py

@@ -172,6 +172,11 @@ class IoniConnect(IoniClientBase):
         """Follow the server-sent-events (SSE) on the DB-API.
 
         `event_re`  a regular expression to filter events (default: matches everything)
+
+        Note: This will block until a matching event is received.
+         Especially, it cannot be cancelled by KeyboardInterrupt (due to the `requests`
+         stream-implementation), unless the server sends a keep-alive at regular
+         intervals (as every well-behaved server should be doing)!
         """
         yield from SSEventListener(event_re, host_url=self.url, endpoint="/api/events",
                 session=self.session)

{pytrms-0.9.1 → pytrms-0.9.2}/pytrms/clients/mqtt.py

@@ -361,6 +361,10 @@ def follow_act_set_values(client, self, msg):
             # Note: this topic doesn't strictly follow the convention and is handled separately
             return
 
+        if server == "Sequencer":
+            # Note: this is a separate program and will be ignored (has its own AUTO_-numbers et.c.)
+            return
+
         if parID == "PTR_CalcConzInfo":
             # another "special" topic handled in 'follow_calc_conz_info' ...
             return
@@ -497,9 +501,9 @@ class MqttClient(MqttClientBase):
             return self._overallcycle[0]
         return 0
 
-    def __init__(self, host='127.0.0.1'):
+    def __init__(self, host='127.0.0.1', port=1883):
         # this sets up the mqtt connection with default callbacks:
-        super().__init__(host, _subscriber_functions, None, None, None)
+        super().__init__(host, port, _subscriber_functions, None, None, None)
         log.debug(f"connection check ({self.is_connected}) :: {self._server_state = } / {self._sched_cmds = }");
 
     def disconnect(self):

{pytrms-0.9.1 → pytrms-0.9.2}/pytrms/clients/ssevent.py

@@ -6,7 +6,7 @@ import requests
 
 from . import _logging
 
-log = _logging.getLogger()
+log = _logging.getLogger(__name__)
 
 _event_rv = namedtuple('ssevent', ['event', 'data'])
 
@@ -19,7 +19,7 @@ class SSEventListener(Iterable):
         for bite in response.iter_content(chunk_size=1, decode_unicode=True):
             line += bite
             if bite == '\n':
-                yield line
+                yield line.strip()
                 line = ''
 
     def __init__(self, event_re=None, host_url='http://127.0.0.1:5066',
@@ -59,19 +59,24 @@ class SSEventListener(Iterable):
 
         event = msg = ''
         for line in self._line_stream(self._connect_response):  # blocks...
-            if not line.strip():
+            if not line:
+                # an empty line concludes an event
                 if event and any(re.match(sub, event) for sub in self.subscriptions):
                     yield _event_rv(event, msg)
-                    event = msg = ''
-                else:
-                    log.log(_logging.TRACE, "sse: still alive...")
+
+                # Note: any further empty lines are ignored (may be used as keep-alive),
+                #  but in either case clear event and msg to rearm for the next event:
+                event = msg = ''
                 continue
 
             key, val = line.split(':', maxsplit=1)
-            if key == 'event':
-                event = val.strip()
+            if not key:
+                # this is a comment, starting with a colon ':' ...
+                log.log(_logging.TRACE, "sse:" + val)
+            elif key == 'event':
+                event = val.lstrip()
             elif key == 'data':
-                msg += val.strip()
+                msg += val.lstrip()
             else:
                 log.warning(f"unknown SSE-key <{key}> in stream")
 

{pytrms-0.9.1 → pytrms-0.9.2}/pytrms/instrument.py

@@ -17,7 +17,6 @@ class Instrument(ABC):
     Note, that for every client PTR instrument there is only one instance of this class.
     This is to prevent different instances to be in other states than the instrument.
     '''
-
     __instance = None
 
     def _new_state(self, newstate):
@@ -69,38 +68,41 @@ class Instrument(ABC):
         """Set a variable to a new value."""
         return self.backend.set(varname, value, unit='-')
 
+    _current_sourcefile = ''
+
     def start_measurement(self, filename=''):
         # this method must be implemented by each state
         raise RuntimeError("can't start %s" % self.__class__)
 
-    start_measurement.__doc__ = Measurement.start.__doc__
-
     def stop_measurement(self):
         # this method must be implemented by each state
         raise RuntimeError("can't stop %s" % self.__class__)
 
-    stop_measurement.__doc__ = Measurement.stop.__doc__
-
 
 class IdleInstrument(Instrument):
 
     def start_measurement(self, filename=''):
-        # if we send a filepath to the server that does not exist there, the server will
-        # open a dialog and "hang" (which I'd very much like to avoid).
-        # the safest way is to not send a path at all and start a 'Quick' measurement.
-        # but if the server is the local machine, we do our best to verify the path:
-        if filename and self.is_local:
-            home = os.path.dirname(filename)
-            os.makedirs(home, exist_ok=True)
-            base = os.path.basename(filename)
-            if not base:
-                base = '%Y-%m-%d_%H-%M-%S.h5'
-            base = time.strftime(base)
-            filename = os.path.join(home, base)
+        dirname = os.path.dirname(filename)
+        if dirname and self.is_local:
+            # Note: if we send a filepath to the server that does not exist there, the
+            #  server will open a dialog and "hang" (which I'd very much like to avoid).
+            #  the safest way is to not send a path at all and start a 'Quick' measurement.
+            #  but if the server is the local machine, we do our best to verify the path:
+            os.makedirs(dirname, exist_ok=True)
+
+        if filename:
+            basename = os.path.basename(filename)
+            # this may very well be a directory to record a filename into:
+            if not basename:
+                basename = '%Y-%m-%d_%H-%M-%S.h5'
+                filename = os.path.join(dirname, basename)
+            # finally, pass everything through strftime...
+            filename = time.strftime(filename)
             if os.path.exists(filename):
                 raise RuntimeError(f'filename exists and cannot be overwritten')
 
         self.backend.start_measurement(filename)
+        self._current_sourcefile = filename
         self._new_state(RunningInstrument)
 
         return RunningMeasurement(self)
@@ -112,3 +114,6 @@ class RunningInstrument(Instrument):
         self.backend.stop_measurement()
         self._new_state(IdleInstrument)
 
+        # TODO :: this catches only one sourcefile.. it'll do for simple cases:
+        return FinishedMeasurement(_current_sourcefile)
+

{pytrms-0.9.1 → pytrms-0.9.2}/pytrms/measurement.py

@@ -1,9 +1,10 @@
 import time
-from glob import glob
 from operator import attrgetter
 from itertools import chain
 from abc import abstractmethod, ABC
 
+import pandas as pd
+
 from .readers import IoniTOFReader
 
 __all__ = ['Measurement', 'PreparingMeasurement', 'RunningMeasurement', 'FinishedMeasurement']
@@ -145,16 +146,14 @@ class FinishedMeasurement(Measurement):
     def timebin_width_ps(self):
         return next(iter(self.sourcefiles)).timebin_width_ps
 
-    def __init__(self, filenames, _reader=IoniTOFReader):
-        if isinstance(filenames, str):
-            filenames = glob(filenames)
+    def __init__(self, *filenames, _reader=IoniTOFReader):
         if not len(filenames):
-            raise ValueError("file not found or empty glob expression")
+            raise ValueError("no filename given")
 
         self.sourcefiles = sorted((_reader(f) for f in filenames), key=attrgetter('time_of_file'))
         self._check(self.sourcefiles)
 
-    def iter_traces(self, kind='raw', index='abs_cycle', force_original=False):
+    def read_traces(self, kind='conc', index='abs_cycle', force_original=False):
         """Return the timeseries ("traces") of all masses, compounds and settings.
 
         'kind' is the type of traces and must be one of 'raw', 'concentration' or
@@ -164,8 +163,11 @@ class FinishedMeasurement(Measurement):
         'abs_time' or 'rel_time'.
 
         """
-        return chain.from_iterable(sf.get_all(kind, index, force_original) for sf in self.sourcefiles)
+        return pd.concat(sf.read_all(kind, index, force_original) for sf in self.sourcefiles)
+
+    def __iter__(self):
+        return iter(self.sourcefiles)
 
     def __len__(self):
-        return sum(len(sf) for sf in self.sourcefiles)
+        return len(self.sourcefiles)
 

{pytrms-0.9.1 → pytrms-0.9.2}/pytrms/readers/ionitof_reader.py

@@ -70,7 +70,7 @@ class IoniTOFReader:
             # well it didn't work..
             pass
         finally:
-            self.hf = h5py.File(path, 'r', swmr=True)
+            self.hf = h5py.File(path, 'r', swmr=False)
 
     @property
     def number_of_timebins(self):
@@ -97,7 +97,7 @@ class IoniTOFReader:
         return float(self.hf.attrs.get('Single Spec Duration (ms)'))
 
     def __init__(self, path):
-        self.hf = h5py.File(path, 'r', swmr=True)
+        self.hf = h5py.File(path, 'r', swmr=False)
         self.filename = os.path.abspath(self.hf.filename)
 
     table_locs = {
@@ -439,14 +439,14 @@ class IoniTOFReader:
             raise ValueError(msg) from exc
 
         try:
-            data = self._read_datainfo(tracedata, prefix=prefix)  # may raise KeyError
-            pt = self._read_datainfo(tracedata, prefix='PeakTable')  # may raise KeyError
-            labels = [b.decode('latin1') for b in pt['label']]
+            data = self._read_datainfo(tracedata, prefix=prefix)
+            pt = self._read_datainfo(tracedata, prefix='PeakTable')
         except KeyError as exc:
             raise KeyError(f'unknown group {exc}. filetype is not supported yet.') from exc
 
+        labels = [b.decode('latin1') for b in pt['label']]
         mapper = dict(zip(data.columns, labels))
-        data.rename(columns=mapper)
+        data.rename(columns=mapper, inplace=True)
         data.index = list(self.iter_index(index))
         
         return data