Fixes and minor convenience improvements from an example run-through.…

… v0.1.1.

setup.cfg

@@ -13,13 +13,11 @@ long_description_content_type = text/markdown; charset=UTF-8; variant=GFM
 url = https://github.com/cgevans/qslib/
 # Add here related links, for example:
 project_urls =
-    Documentation = https://alhambra.readthedocs.org/
-    Source = https://github.com/pyscaffold/pyscaffold/
-    Changelog = pyscaffold.org/en/latest/changelog.html
+    Documentation = https://qslib.readthedocs.org/
+    Source = https://github.com/cgevans/qslib/
+    Changelog = https://github.com/cgevans/qslib/blob/main/CHANGELOG.md
     Tracker = https://github.com/cgevans/qslib/issues
-#    Conda-Forge = https://anaconda.org/conda-forge/pyscaffold
     Download = https://github.com/cgevans/qslib/releases
-#    Twitter = https://twitter.com/PyScaffold
 
 # Change if running only on Windows, Mac or Linux (comma-separated)
 platforms = any

src/qslib/common.py

@@ -1,5 +1,5 @@
-from .machine import Machine
-from .experiment import Experiment, PlateSetup, Protocol, Stage, Step, RunStatus, MachineStatus
+from .machine import Machine, MachineStatus, RunStatus
+from .experiment import Experiment, PlateSetup, Protocol, Stage, Step
 from . import tcprotocol as tc
 
 __all__ = (

src/qslib/data.py

@@ -266,7 +266,7 @@ def df_from_readings(
         columns=pd.MultiIndex.from_tuples(
             [("time", "timestamp")]
             + [
-                (f"{r}{c:02}", v)
+                (f"{r}{c}", v)
                 for v in ["fl", "rt", "st"]
                 for r in "ABCDEFGH"
                 for c in range(1, 13)
@@ -285,7 +285,7 @@ def df_from_readings(
         pd.MultiIndex.from_tuples(
             [("time", v) for v in ["seconds", "hours", "timestamp"]]
             + [
-                (f"{r}{c:02}", v)
+                (f"{r}{c}", v)
                 for r in "ABCDEFGH"
                 for c in range(1, 13)
                 for v in ["fl", "rt", "st"]

src/qslib/experiment.py

@@ -1565,7 +1565,7 @@ def data_for_sample(self, sample: str):
         pd.Dataframe
             Slice of welldata.  Will have multiple wells if sample is in multiple wells.
         """
-        wells = [f"{x[0]}{int(x[1:])}" for x in self.plate_setup.sample_wells[sample]]
+        wells = ['time'] + [f"{x[0]}{int(x[1:])}" for x in self.plate_setup.sample_wells[sample]]
         x = self.welldata.loc[:, wells]
         return x
 
@@ -1629,7 +1629,7 @@ def _update_from_log(self):
         # beginning of the log as an info command, with quote.message.  Let's
         # try to grab it!
         if m := re.match(
-            r"^Info (?:[\d.]+) (<quote.message>.*?</quote.message>)", msglog, re.DOTALL
+            r"^Info (?:[\d.]+) (<quote.message>.*?</quote.message>)", msglog, re.DOTALL | re.MULTILINE
         ):
             # We can get the prot name too, and sample volume!
             rp = re.search(

src/qslib/tcprotocol.py

@@ -28,6 +28,7 @@
 import numpy as np
 from .util import *
 import logging
+from copy import deepcopy
 
 log = logging.getLogger(__name__)
 
@@ -506,6 +507,9 @@ def all_times(self) -> np.ndarray:
         alltimes[1::2] = d["end_time"]
         return alltimes
 
+    def copy(self) -> Protocol:
+        return deepcopy(self)
+
     @property
     def all_temperatures(self) -> np.ndarray:
         "An array of temperature settings at `all_times`."
@@ -992,7 +996,10 @@ def _from_command_dict(cls, d):
                 temp_incrementcycle=1,
             )
             c.collect = True
-            c.filters = [FilterSet.fromstring(x) for x in d["body"][1]["args"]]
+            if "args" in d["body"][1].keys():
+                c.filters = [FilterSet.fromstring(x) for x in d["body"][1]["args"]]
+            else:
+                c.filters = []
             for k, v in d["body"][2]["opts"].items():
                 k = k.lower()
                 if "increment" in k: