pychemstation 0.9.0__tar.gz → 0.9.1__tar.gz

{pychemstation-0.9.0 → pychemstation-0.9.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pychemstation
-Version: 0.9.0
+Version: 0.9.1
 Summary: Library to interact with Chemstation software, primarily used in Hein lab
 Project-URL: Documentation, https://pychemstation-e5a086.gitlab.io/pychemstation.html
 Project-URL: Repository, https://gitlab.com/heingroup/device-api/pychemstation
@@ -8,10 +8,11 @@ Author-email: lucyhao <hao.lucyy@gmail.com>
 License-File: LICENSE
 Classifier: License :: OSI Approved :: MIT License
 Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
-Requires-Python: >=3.9
+Requires-Python: ~=3.9
 Requires-Dist: aghplctools==4.8.6
 Requires-Dist: coverage>=7.6.1
 Requires-Dist: matplotlib>=3.7.5

{pychemstation-0.9.0 → pychemstation-0.9.1}/pychemstation/analysis/process_report.py

@@ -15,6 +15,7 @@ from aghplctools.ingestion.text import (
     _signal_table_re,
     chunk_string,
 )
+from pandas._libs.parsers import EmptyDataError
 from result import Err, Ok, Result
 
 from ..analysis.chromatogram import AgilentHPLCChromatogram
@@ -69,6 +70,16 @@ class CSVProcessor(ReportProcessor):
         """
         super().__init__(path)
 
+    def find_csv_prefix(self) -> str:
+        files = [f for f in os.listdir(self.path) if os.path.isfile(os.path.join(self.path, f))]
+        for file in files:
+            if "00" in file:
+                name, _, file_extension = file.partition(".")
+                if "00" in name and file_extension.lower() == "csv":
+                    prefix, _, _ = name.partition("00")
+                    return prefix
+        raise FileNotFoundError("Couldn't find the prefix for CSV")
+
     def process_report(self) -> Result[AgilentReport, AnyStr]:
         """
         Method to parse details from CSV report.
@@ -76,8 +87,11 @@ class CSVProcessor(ReportProcessor):
         :return: subset of complete report details, specifically the sample location, solvents in pumps,
          and list of peaks at each wavelength channel.
         """
-        labels = os.path.join(self.path, "REPORT00.CSV")
-        if os.path.exists(labels):
+        prefix = self.find_csv_prefix()
+        labels = os.path.join(self.path, f"{prefix}00.CSV")
+        if not os.path.exists(labels):
+            raise ValueError("CSV reports do not exist, make sure to turn on the post run CSV report option!")
+        elif os.path.exists(labels):
             df_labels: Dict[int, Dict[int:AnyStr]] = pd.read_csv(
                 labels, encoding="utf-16", header=None
             ).to_dict()
@@ -93,12 +107,15 @@ class CSVProcessor(ReportProcessor):
                 elif val == "Number of Signals":
                     num_signals = int(df_labels[1][pos])
                     for s in range(1, num_signals + 1):
-                        df = pd.read_csv(
-                            os.path.join(self.path, f"REPORT0{s}.CSV"),
-                            encoding="utf-16",
-                            header=None,
-                        )
-                        peaks = df.apply(lambda row: AgilentPeak(*row), axis=1)
+                        try:
+                            df = pd.read_csv(
+                                os.path.join(self.path, f"{prefix}0{s}.CSV"),
+                                encoding="utf-16",
+                                header=None,
+                            )
+                            peaks = df.apply(lambda row: AgilentPeak(*row), axis=1)
+                        except EmptyDataError:
+                            peaks = []
                         try:
                             wavelength = df_labels[1][pos + s].partition(",4 Ref=off")[0][
                                 -3:

{pychemstation-0.9.0 → pychemstation-0.9.1}/pyproject.toml

@@ -4,10 +4,10 @@ build-backend = "hatchling.build"
 
 [project]
 name = "pychemstation"
-version = "0.9.0"
+version = "0.9.1"
 description = "Library to interact with Chemstation software, primarily used in Hein lab"
 authors = [{ name = "lucyhao", email = "hao.lucyy@gmail.com" }]
-requires-python = ">=3.9"
+requires-python = "~=3.9"
 readme = "README.md"
 dependencies = [
     "aghplctools==4.8.6",
@@ -27,6 +27,7 @@ dependencies = [
     "xsdata>=24.9",
 ]
 classifiers=[
+    "Programming Language :: Python :: 3.9",
         "Programming Language :: Python :: 3.10",
         "Programming Language :: Python :: 3.11",
         "Programming Language :: Python :: 3.12",

pychemstation-0.9.1/tests/10 IS 2025-02-10 23-41-33_10_2025-02-11 02-21-44.D/CSlbk.ini

@@ -0,0 +1,5 @@
+[RUN.LOG]
+MDT=310031002F0032002F003200300032003500200032003A00330037003A00350000000000FEFFFFFF1B
+CS=49289336
+[CSlbk.ini]
+CS=461895

pychemstation-0.9.1/tests/10 IS 2025-02-10 23-41-33_10_2025-02-11 02-21-44.D/PMP1.AnalyticalResults.drvml

@@ -0,0 +1,15 @@
+<?xml version="1.0"?>
+<AnalyticalResultsModuleData xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:xsd="http://www.w3.org/2001/XMLSchema" ModuleId="PMP1" SchemaVersion="1.0.0" xmlns="file://GenericAnalyticalResultData.xsd">
+  <ModuleInfo>
+    <SerialNumber>DEBAA04191</SerialNumber>
+    <PartNumber>G4220A</PartNumber>
+    <FirmwareRevision>B.07.38 [0002]</FirmwareRevision>
+    <Vendor>Agilent</Vendor>
+    <DisplayName>Binary Pump</DisplayName>
+  </ModuleInfo>
+  <DataChannels>
+    <AnalyticalResultsDataChannel Id="Generic" Name="G4220A:Generic file data" Description="Generic file data">
+      <DataRecords />
+    </AnalyticalResultsDataChannel>
+  </DataChannels>
+</AnalyticalResultsModuleData>

pychemstation-0.9.1/tests/10 IS 2025-02-10 23-41-33_10_2025-02-11 02-21-44.D/WLS1.Sampler.scml

@@ -0,0 +1,22 @@
+<?xml version="1.0"?>
+<SampleContainerInfo xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:xsd="http://www.w3.org/2001/XMLSchema" SchemaVersion="1.0.0" xmlns="file://SampleContainerInfo.xsd">
+  <ActiveSampleContainer ContainerId="{CCED90BB-0208-427E-EB73-D3378CD6639A}" ContainerName="*54VialPlate*" />
+  <ActiveSampleLocation LocationString="P1-F2" LocationId="P1" />
+  <ContainerDeviceInfo ModuleId="WLS1">
+    <SerialNumber>DEBAP02845</SerialNumber>
+    <PartNumber>G4226A</PartNumber>
+    <Vendor>Agilent</Vendor>
+    <DisplayName>HiP Sampler</DisplayName>
+    <SampleContainerDevice ContentType="GZipCompressedBase64Xml" Id="{AB0E860B-D6E0-4B33-9FF0-98DC7E874822}" Name="2 Plates 10 Vials">
+      <XmlContent>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</XmlContent>
+    </SampleContainerDevice>
+  </ContainerDeviceInfo>
+  <SampleContainerCatalog>
+    <SampleContainer ContentType="GZipCompressedBase64Xml" Id="{CCED90BB-0208-427E-EB73-D3378CD6639A}" Name="*54VialPlate*">
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