release 0.4.0

CHANGELOG.md

@@ -2,14 +2,16 @@
 
 ## Version 0.4.0
 
-- Much faster `Experiment.sync_from_machine`, only transferring additional log entries rather than the entire log.
+- Much faster `Experiment.sync_from_machine`, only transferring additional log 
+  entries rather than the entire log.
 - Common plotting routines for fluorescence data.
 - More reliable monitoring.
 - More reliable connections, and testing.
 - `Stage.stepped_ramp` convenience function.
 - Fixes to bugs inhibiting exposure setting, and some basic
   implementations for this.
-- Fixes to qs-monitor for cycle counts > 999 (and other large stage / step / cycle counts).
+- Fixes to qs-monitor for cycle counts > 999 (and other large stage / step / 
+  cycle counts).
 
 ## Version 0.3.1
 

README.md

@@ -4,7 +4,6 @@
 Status](https://img.shields.io/github/workflow/status/cgevans/qslib/Python%20tests)
 ![PyPI](https://img.shields.io/pypi/v/qslib)
 
-
 # qslib
 
 QSLib is a package for interacting with Applied Biosystems' QuantStudio
@@ -15,16 +14,15 @@ machines through their network connection and SCPI interface. It currently
 functions only with QuantStudio 5 machines using a 96-well block, but
 could be made to support others as well.
 
-Amongst other features that :
+Amongst other features that it has:
 
 -   Direct fluorescence data ("filter data") as Pandas dataframes, with
     times and temperature readings.
 
 -   Running-experiment data access, status information, and control.
 
 -   Protocol creation and manipulation, allowing functions outside of
-    AB's software. The ability to update protocols and add stages
-    mid-run is feasible and planned.
+    AB's software. Protocols can be modified and updated mid-run.
 
 -   Temperature data at one-second resolution during experiments.
 
@@ -48,7 +46,6 @@ It requires at least version 3.9 of Python. While it uses async code at
 its core for communication, it can be used conveniently in Jupyter or
 IPython.
 
-
 To use the library for communication with machines, you'll need a
 machine access password with Observer (for reading data and statuses)
 and/or Controller (for running experiments and controlling the machine)
@@ -57,7 +54,6 @@ recommend against having the machines be accessible online: use a
 restricted VPN connection or port forwarding. See the documentation for
 more information.
 
-
 ## Disclaimer
 
 This package was developed for my own use. It may break your machine or
@@ -67,7 +63,5 @@ render your machine unusable or be used to send commands that would
 physically/electrically damage the machine or potentially be hazardous
 to you or others.
 
-I am in no way connected with Applied Biosystems, and have developed
-this package using the machine's documentation system and standard file
-formats.
-
+I am not any way connected with Applied Biosystems.  I have developed this 
+package using the machine's documentation system and standard file formats.

docs/conf.py

@@ -79,13 +79,13 @@
     "sphinx.ext.ifconfig",
     "sphinx.ext.mathjax",
     "sphinx.ext.napoleon",
-    "myst_parser"
+    "myst_parser",
 ]
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ["_templates"]
 
-#extensions.append("recommonmark")
+# extensions.append("recommonmark")
 
 # The suffix of source filenames.
 source_suffix = [".rst", ".md"]

tests/test_accesslevel.py

@@ -39,4 +39,4 @@ def test_access():
             AccessLevel(l1) <= invalid  # type: ignore
         with pytest.raises(ValueError):
             AccessLevel(l1) == invalid  # type: ignore
-        assert str(AccessLevel(l1)) == l1
+        assert str(AccessLevel(l1)) == l1

tests/test_experiment_run.py

@@ -10,25 +10,42 @@ def patchrun(self, value: str) -> str:
         else:
             raise ValueError
 
-    monkeypatch.setattr(Machine, 'run_command', patchrun)
-    
-    m = Machine('none')
-    
+    monkeypatch.setattr(Machine, "run_command", patchrun)
+
+    m = Machine("none")
+
     m.drawer_close()
-
-@pytest.mark.parametrize("function", [("drawer_position", ()),
-                                      ("machine_status", ()),
-                                      ("run_status", ()),
-                                      ("get_running_protocol", ()),
-                                      ("list_runs_in_storage", ())])
+
+
+@pytest.mark.parametrize(
+    "function",
+    [
+        ("drawer_position", ()),
+        ("machine_status", ()),
+        ("run_status", ()),
+        ("get_running_protocol", ()),
+        ("list_runs_in_storage", ()),
+    ],
+)
 def test_mach_not_connected(function: tuple[str, tuple[Any]]) -> None:
-    m = Machine('none')
+    m = Machine("none")
     with pytest.raises(ConnectionError):
         getattr(m, function[0]).__call__(*function[1])
 
 
-@pytest.mark.parametrize("function", [("from_running", (Machine('none'),)),
-                                      ("from_machine_storage", (Machine('none'), "filename",))])
+@pytest.mark.parametrize(
+    "function",
+    [
+        ("from_running", (Machine("none"),)),
+        (
+            "from_machine_storage",
+            (
+                Machine("none"),
+                "filename",
+            ),
+        ),
+    ],
+)
 def test_expload_not_connected(function: str) -> None:
     with pytest.raises(ConnectionError):
         getattr(Experiment, function[0]).__call__(*function[1])

tests/test_protocol.py

@@ -133,6 +133,7 @@ def test_proto() -> None:
 
     assert prot_explicitfilter == prot_fromstring
 
+
 def test_exp_saveload_proto(tmp_path: pathlib.Path):
     temperatures = list(np.linspace(51.2, 49.4, num=6))
     prot = Protocol(
@@ -168,26 +169,28 @@ def test_exp_saveload_proto(tmp_path: pathlib.Path):
     # FIXME: for now, we don't do a great job with save/load for default filters
     assert exp.protocol.to_command() == exp2.protocol.to_command()
 
+
 def test_stepped_ramp_down():
-    srstage = Stage.stepped_ramp(60.0, 40.0, 60*21, 21)
+    srstage = Stage.stepped_ramp(60.0, 40.0, 60 * 21, 21)
 
     df = srstage.dataframe()
 
     assert len(df) == 21
-    assert df.iloc[-1, :]['temperature_1'] == 40.0
-    assert df.iloc[0, :]['temperature_1'] == 60.0
-    assert df.iloc[1, :]['temperature_1'] == 59.0
+    assert df.iloc[-1, :]["temperature_1"] == 40.0
+    assert df.iloc[0, :]["temperature_1"] == 60.0
+    assert df.iloc[1, :]["temperature_1"] == 59.0
 
     assert srstage == Stage(Step(60, 60.0, temp_increment=-1.0), 21)
 
+
 def test_stepped_ramp_up():
-    srstage = Stage.stepped_ramp(40.0, 60.0, 60*41, 41)
+    srstage = Stage.stepped_ramp(40.0, 60.0, 60 * 41, 41)
 
     df = srstage.dataframe()
 
     assert len(df) == 41
-    assert df.iloc[-1, :]['temperature_1'] == 60.0
-    assert df.iloc[0, :]['temperature_1'] == 40.0
-    assert df.iloc[1, :]['temperature_1'] == 40.5
+    assert df.iloc[-1, :]["temperature_1"] == 60.0
+    assert df.iloc[0, :]["temperature_1"] == 40.0
+    assert df.iloc[1, :]["temperature_1"] == 40.5
 
     assert srstage == Stage(Step(60, 40.0, temp_increment=0.5), 41)