pychemstation 0.4.7.dev2__py3-none-any.whl → 0.5.0__py3-none-any.whl

{pychemstation-0.4.7.dev2.dist-info → pychemstation-0.5.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pychemstation
-Version: 0.4.7.dev2
+Version: 0.5.0
 Summary: Library to interact with Chemstation software, primarily used in Hein lab
 Home-page: https://gitlab.com/heingroup/pychemstation
 Author: Lucy Hao
@@ -13,6 +13,8 @@ License-File: LICENSE
 Requires-Dist: polling
 Requires-Dist: seabreeze
 
+from tests.test_chemstation_integration import SEQUENCE_DIR
+
 # Agilent HPLC Macro Control
 
 ![PyPI - Downloads](https://img.shields.io/pypi/dm/pychemstation)
@@ -59,26 +61,27 @@ HPLCTalk_Run
 ## Example Usage
 
 ```python
-from pychemstation.control import HPLCController, MethodController, SequenceController
+from pychemstation.control import HPLCController
 import pandas as pd
 
 # these paths will be unique to your Chemstation setup
+DEFAULT_COMMAND_PATH = "C:\\Users\\User\\Desktop\\Lucy\\"
+DEFAULT_METHOD = "GENERAL-POROSHELL"
 DEFAULT_METHOD_DIR = "C:\\ChemStation\\1\\Methods\\"
 DATA_DIR = "C:\\Users\\Public\\Documents\\ChemStation\\2\\Data"
-DEFAULT_COMMAND_PATH = "C:\\Users\\User\\Desktop\\Lucy\\hplc-method-optimization\\tests"
+SEQUENCE_DIR = "C:\\USERS\\PUBLIC\\DOCUMENTS\\CHEMSTATION\\2\\Sequence"
 
 hplc_controller = HPLCController(data_dir=DATA_DIR,
-                                 comm_dir=DEFAULT_COMMAND_PATH)
-method_controller = MethodController(controller=hplc_controller,
-                                     src=DEFAULT_METHOD_DIR)
+                                 comm_dir=DEFAULT_COMMAND_PATH,
+                                 sequence_dir=SEQUENCE_DIR,
+                                 method_dir=DEFAULT_METHOD_DIR)
 
 hplc_controller.preprun()
-method_controller.switch(method_name="General-Poroshell")
-method_controller.run(experiment_name="Run 10")
-data_ready = method_controller.data_ready()
+hplc_controller.switch_method(method_name=DEFAULT_METHOD)
+hplc_controller.run_method(experiment_name="Run 10")
+data_status_valid, chrom = hplc_controller.get_last_run_method_data()
 
-if data_ready:
-    chrom = method_controller.get_data()
+if data_status_valid:
     # afterwards, save, analyze or plot the data!
     values = {"x": chrom.x, "y": chrom.y}
     chromatogram_data = pd.DataFrame.from_dict(values)

pychemstation-0.5.0.dist-info/RECORD

@@ -0,0 +1,40 @@
+.DS_Store,sha256=1lFlJ5EFymdzGAUAaI30vcaaLHt3F1LwpG7xILf9jsM,6148
+pychemstation/__init__.py,sha256=SpTl-Tg1B1HTyjNOE-8ue-N2wGnXN_2zl7RFUSxlkiM,33
+pychemstation/analysis/__init__.py,sha256=EWoU47iyn9xGS-b44zK9eq50bSjOV4AC5dvt420YMI4,44
+pychemstation/analysis/base_spectrum.py,sha256=XPf9eJ72uz0CnxCY5uFOyu1MbVX-OTTXeN1tLzIMok4,16536
+pychemstation/analysis/spec_utils.py,sha256=UOo9hJR3evJfmaohEEsyb7aq6X996ofuUfu-GKjiDi8,10201
+pychemstation/analysis/utils.py,sha256=ISupAOb_yqA4_DZRK9v18UL-XjUQccAicIJKb1VMnGg,2055
+pychemstation/control/__init__.py,sha256=aH9cPf-ljrVeVhN0K3cyEcAavmPXCjhhOnpLNf8qLqE,106
+pychemstation/control/chromatogram.py,sha256=c4_RGconn4vYU9wyS0WX-GB5FlwnBf_sfVLh_GpeehE,3716
+pychemstation/control/comm.py,sha256=8hjzp-MWWDYyYsEOdlpaJeWd-8eDQw5Y84pyMToK8gE,6008
+pychemstation/control/hplc.py,sha256=xsfg0VWHSYy2f0YWxCAKxbyDla-POhp02zF5tgBPIVo,5829
+pychemstation/control/method.py,sha256=h9KcccDtqx0hQT7JaUc1TWCB8d21t0McOuzeBsEsh4c,10977
+pychemstation/control/sequence.py,sha256=ewc7l44VAtv3wHV2QgOILu5Ny3gmubHuEeHJN9N6OjQ,7511
+pychemstation/control/table_controller.py,sha256=83i1J2CvIrJ3NtAB_E46qhUe8MvXo1_GnDPmuiq-vSA,2957
+pychemstation/control/table/__init__.py,sha256=RgMN4uIWHdNUHpGRBWdzmzAbk7XEKl6Y-qtqWCxzSZU,124
+pychemstation/control/table/method.py,sha256=pywWVFXpdewA-5pXmcmvauX2WsjFQtrAiOSBFYCJfLE,11946
+pychemstation/control/table/sequence.py,sha256=x3uftd9Y-otLPdJv1Bnamcv2mWmj6mqSo5H5yfVBRiw,8510
+pychemstation/control/table/table_controller.py,sha256=g8IPKIyLbPcXfJDN2DvKtPd9sImbUdoI44qTutQzPi8,4986
+pychemstation/generated/__init__.py,sha256=GAoZFAYbPVEJDkcOw3e1rgOqd7TCW0HyKNPM8OMehMg,1005
+pychemstation/generated/dad_method.py,sha256=0W8Z5WDtF5jpIcudMqb7XrkTnR2EGg_QOCsHRFQ0rmM,8402
+pychemstation/generated/pump_method.py,sha256=sUhE2Oo00nzVcoONtq3EMWsN4wLSryXbG8f3EeViWKg,12174
+pychemstation/utils/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+pychemstation/utils/chemstation.py,sha256=bnFIsZZwFy9NKzVUf517yN-ogzQbm0hp_aho3KUD6Is,9317
+pychemstation/utils/chromatogram.py,sha256=35nvEh6prVsWO6lMHYgGuidUOFHv954_7MNf0Az3Fz4,3759
+pychemstation/utils/constants.py,sha256=jLY-NixemSofukzSXJhAIU4aO2IJmBRAhAcq5066mFI,249
+pychemstation/utils/hplc_param_types.py,sha256=xvmsbYQp3iiS1-0-9eUy--5zk_wE1bkrlHEHSm0UC18,5206
+pychemstation/utils/macro.py,sha256=ngIhLfFCRXbFzfFu5y3LbWy16W1T2CErnx1374JjG0w,2284
+pychemstation/utils/method_types.py,sha256=tVpmWKa2BdkvpaEcvVIKOTjF76ZfHGryw168GXYoKDA,868
+pychemstation/utils/parsing.py,sha256=bnFIsZZwFy9NKzVUf517yN-ogzQbm0hp_aho3KUD6Is,9317
+pychemstation/utils/sequence_types.py,sha256=7qcyCSH35KwtVXKIkTyepGxc_E_0Mc8nYpbvcawaAZA,831
+pychemstation/utils/table_types.py,sha256=BBCRoz1R6zPV1i2u2Tdku7WwIp6EDv1rUuZVPVNgO1A,2090
+tests/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+tests/constants.py,sha256=TPwdBhG9M7VIZ5sxqEfspqC2pUS9ZSQM4z7ZKiKwzSo,625
+tests/test_comm.py,sha256=SvA9xuYnyXApMN2NniEW3rDRadknjCgKwlCV4WANyfk,2460
+tests/test_method.py,sha256=DGMDGj_O-YDc4-JYVEP152DxH81qsHP3E-5ZDlaKmTQ,2203
+tests/test_sequence.py,sha256=4xQBsVtIpNAaJ9It5XIh8zSdgbH7rULTCr7MnqPJQyI,3932
+pychemstation-0.5.0.dist-info/LICENSE,sha256=9bdF75gIf1MecZ7oymqWgJREVz7McXPG-mjqrTmzzD8,18658
+pychemstation-0.5.0.dist-info/METADATA,sha256=rtbeMfqGZz7rSuFDL-ChwK7Z2jc4F12_w9qEoT5NSpw,4020
+pychemstation-0.5.0.dist-info/WHEEL,sha256=PZUExdf71Ui_so67QXpySuHtCi3-J3wvF4ORK6k_S8U,91
+pychemstation-0.5.0.dist-info/top_level.txt,sha256=zXfKu_4nYWwPHo3OsuhshMNC3SPkcoTGCyODjURaghY,20
+pychemstation-0.5.0.dist-info/RECORD,,

{pychemstation-0.4.7.dev2.dist-info → pychemstation-0.5.0.dist-info}/top_level.txt

@@ -1 +1,2 @@
 pychemstation
+tests

tests/constants.py

@@ -0,0 +1,12 @@
+
+# CONSTANTS: paths only work in Hein group HPLC machine in room 242
+DEFAULT_COMMAND_PATH = "C:\\Users\\User\\Desktop\\Lucy\\"
+DEFAULT_METHOD = "GENERAL-POROSHELL-OPT"
+DEFAULT_TESTING_METHOD = "GENERAL-POROSHELL-MIN"
+DEFAULT_METHOD_DIR = "C:\\ChemStation\\1\\Methods\\"
+DATA_DIR = "C:\\Users\\Public\\Documents\\ChemStation\\3\\Data"
+SEQUENCE_DIR = "C:\\USERS\\PUBLIC\\DOCUMENTS\\CHEMSTATION\\3\\Sequence"
+DEFAULT_SEQUENCE = "hplc_testing"
+METHOD_EXAMPLE = "/Users/lucyhao/Codes/heinanalyticalcontrol/tests/methods/General-Poroshell.M"
+
+HEIN_LAB_CONSTANTS = [DEFAULT_COMMAND_PATH, DEFAULT_METHOD_DIR, DATA_DIR, SEQUENCE_DIR]

tests/test_comm.py

@@ -0,0 +1,66 @@
+import os
+
+import unittest
+
+from pychemstation.control import HPLCController
+from pychemstation.utils.macro import *
+from tests.constants import *
+
+
+class TestComm(unittest.TestCase):
+
+    def setUp(self):
+        for path in HEIN_LAB_CONSTANTS:
+            if not os.path.exists(path):
+                self.fail(
+                    f"{path} does not exist on your system. If you would like to run tests, please change this path.")
+
+        self.hplc_controller = HPLCController(data_dir=DATA_DIR,
+                                              comm_dir=DEFAULT_COMMAND_PATH,
+                                              method_dir=DEFAULT_METHOD_DIR,
+                                              sequence_dir=SEQUENCE_DIR)
+
+    def test_status_check_standby(self):
+        self.hplc_controller.standby()
+        self.assertTrue(self.hplc_controller.status()[0] in [HPLCAvailStatus.STANDBY, HPLCRunningStatus.NOTREADY])
+
+    def test_status_check_preprun(self):
+        self.hplc_controller.preprun()
+        self.assertTrue(self.hplc_controller.status()[0] in [HPLCAvailStatus.PRERUN, HPLCAvailStatus.STANDBY,
+                                                             HPLCRunningStatus.NOTREADY])
+
+    def test_send_command(self):
+        try:
+            self.hplc_controller.send(Command.GET_METHOD_CMD)
+        except Exception as e:
+            self.fail(f"Should not throw error: {e}")
+
+    def test_send_str(self):
+        try:
+            self.hplc_controller.send("Local TestNum")
+            self.hplc_controller.send("TestNum = 0")
+        except Exception as e:
+            self.fail(f"Should not throw error: {e}")
+
+    def test_get_response(self):
+        try:
+            self.hplc_controller.switch_method(method_name=DEFAULT_METHOD)
+            self.hplc_controller.send(Command.GET_METHOD_CMD)
+            res = self.hplc_controller.receive()
+            self.assertTrue(DEFAULT_METHOD in res)
+        except Exception as e:
+            self.fail(f"Should not throw error: {e}")
+
+    def test_pump_lamp(self):
+        pump_lamp = [
+            ("response", self.hplc_controller.lamp_on),
+            ("response", self.hplc_controller.lamp_off),
+            ("response", self.hplc_controller.pump_on),
+            ("response", self.hplc_controller.pump_off),
+        ]
+
+        for operation in pump_lamp:
+            try:
+                operation[1]()
+            except Exception as e:
+                self.fail(f"Failed due to: {e}")

tests/test_method.py

@@ -0,0 +1,64 @@
+import os
+import unittest
+
+from pychemstation.control import HPLCController
+from pychemstation.utils.method_types import *
+from tests.constants import *
+
+
+class TestMethod(unittest.TestCase):
+    def setUp(self):
+        for path in HEIN_LAB_CONSTANTS:
+            if not os.path.exists(path):
+                self.fail(
+                    f"{path} does not exist on your system. If you would like to run tests, please change this path.")
+
+        self.hplc_controller = HPLCController(data_dir=DATA_DIR,
+                                              comm_dir=DEFAULT_COMMAND_PATH,
+                                              method_dir=DEFAULT_METHOD_DIR,
+                                              sequence_dir=SEQUENCE_DIR)
+
+
+
+    def test_load_method_details(self):
+        self.hplc_controller.switch_method(DEFAULT_METHOD)
+        try:
+            gp_mtd = self.hplc_controller.method_controller.load(DEFAULT_METHOD)
+            self.assertTrue(gp_mtd.first_row.organic_modifier.val == 5)
+        except Exception as e:
+            self.fail(f"Should have not failed, {e}")
+
+    def test_method_update_timetable(self):
+        self.hplc_controller.method_controller.switch(DEFAULT_METHOD)
+        new_method = MethodTimetable(
+            first_row=HPLCMethodParams(
+                organic_modifier=7,
+                flow=0.44,
+                maximum_run_time=2,
+                temperature=15),
+            subsequent_rows=[
+                TimeTableEntry(
+                    start_time=0.10,
+                    organic_modifer=7,
+                    flow=0.34),
+                TimeTableEntry(
+                    start_time=1,
+                    organic_modifer=99,
+                    flow=0.55)])
+        try:
+            self.hplc_controller.edit_method(new_method)
+        except Exception as e:
+            self.fail(f"Should have not failed: {e}")
+
+    def test_run_method(self):
+        try:
+            self.hplc_controller.run_method(experiment_name="test_experiment")
+            chrom = self.hplc_controller.get_last_run_method_data()
+        except Exception as e:
+            self.fail(f"Should have not failed: {e}")
+
+
+
+
+if __name__ == '__main__':
+    unittest.main()

tests/test_sequence.py

@@ -0,0 +1,102 @@
+import os
+import unittest
+
+from pychemstation.control import HPLCController
+from pychemstation.utils.sequence_types import *
+from tests.constants import *
+
+
+class TestSequence(unittest.TestCase):
+    def setUp(self):
+        for path in HEIN_LAB_CONSTANTS:
+            if not os.path.exists(path):
+                self.fail(
+                    f"{path} does not exist on your system. If you would like to run tests, please change this path.")
+
+        self.hplc_controller = HPLCController(data_dir=DATA_DIR,
+                                              comm_dir=DEFAULT_COMMAND_PATH,
+                                              method_dir=DEFAULT_METHOD_DIR,
+                                              sequence_dir=SEQUENCE_DIR)
+
+    def test_switch(self):
+        try:
+            self.hplc_controller.switch_sequence(sequence_name=DEFAULT_SEQUENCE)
+        except Exception as e:
+            self.fail(f"Should have not expected: {e}")
+
+    def test_edit_row(self):
+        self.hplc_controller.switch_sequence(sequence_name=DEFAULT_SEQUENCE)
+        self.hplc_controller.edit_sequence_row(SequenceEntry(
+                    vial_location=10,
+                    method="C:\\ChemStation\\1\\Methods\\General-Poroshell",
+                    num_inj=3,
+                    inj_vol=4,
+                    sample_name="Blank",
+                    sample_type=SampleType.BLANK,
+                    inj_source=InjectionSource.HIP_ALS
+                ), 1)
+
+    def test_edit_entire_table(self):
+        self.hplc_controller.switch_sequence(sequence_name=DEFAULT_SEQUENCE)
+        seq_table = SequenceTable(
+            name=DEFAULT_SEQUENCE,
+            rows=[
+                SequenceEntry(
+                    vial_location=3,
+                    method="C:\\ChemStation\\1\\Methods\\General-Poroshell",
+                    num_inj=3,
+                    inj_vol=4,
+                    sample_name="Control",
+                    sample_type=SampleType.CONTROL,
+                    inj_source=InjectionSource.MANUAL
+                ),
+                SequenceEntry(
+                    vial_location=1,
+                    method="C:\\ChemStation\\1\\Methods\\General-Poroshell",
+                    num_inj=1,
+                    inj_vol=1,
+                    sample_name="Sample",
+                    sample_type=SampleType.SAMPLE,
+                    inj_source=InjectionSource.AS_METHOD
+                ),
+                SequenceEntry(
+                    vial_location=10,
+                    method="C:\\ChemStation\\1\\Methods\\General-Poroshell",
+                    num_inj=3,
+                    inj_vol=4,
+                    sample_name="Blank",
+                    sample_type=SampleType.BLANK,
+                    inj_source=InjectionSource.HIP_ALS
+                ),
+            ]
+        )
+        self.hplc_controller.edit_sequence(seq_table)
+
+
+    def test_run(self):
+        # self.hplc_controller.switch_sequence(sequence_name=DEFAULT_SEQUENCE)
+        seq_table = SequenceTable(
+            name=DEFAULT_SEQUENCE,
+            rows=[
+                SequenceEntry(
+                    vial_location=1,
+                    method="C:\\ChemStation\\1\\Methods\\" + DEFAULT_METHOD,
+                    num_inj=1,
+                    inj_vol=1,
+                    sample_name="Test",
+                    sample_type=SampleType.BLANK
+                ),
+                SequenceEntry(
+                    vial_location=2,
+                    method="C:\\ChemStation\\1\\Methods\\" + DEFAULT_METHOD,
+                    num_inj=1,
+                    inj_vol=1,
+                    sample_name="Test2",
+                    sample_type=SampleType.BLANK
+                ),
+            ]
+        )
+        # self.hplc_controller.edit_sequence(seq_table)
+        self.hplc_controller.run_sequence(seq_table)
+        chrom = self.hplc_controller.get_last_run_sequence_data()
+        self.assertTrue(len(chrom) == 2)

pychemstation-0.4.7.dev2.dist-info/RECORD

@@ -1,30 +0,0 @@
-pychemstation/__init__.py,sha256=SpTl-Tg1B1HTyjNOE-8ue-N2wGnXN_2zl7RFUSxlkiM,33
-pychemstation/analysis/__init__.py,sha256=EWoU47iyn9xGS-b44zK9eq50bSjOV4AC5dvt420YMI4,44
-pychemstation/analysis/base_spectrum.py,sha256=FBvwzLtF9mdqW7f8ETY9G4cpfJ-SzbiSkZq9EtXcSXo,17045
-pychemstation/analysis/spec_utils.py,sha256=8NZMV0dtfxZLARjWzM5ks0tgEYQv_SKUiZzba2IoKgw,10505
-pychemstation/analysis/utils.py,sha256=ISupAOb_yqA4_DZRK9v18UL-XjUQccAicIJKb1VMnGg,2055
-pychemstation/control/__init__.py,sha256=Azsalc8Pz1PuygH7CoTzRV8xQOSfET6zd72AMAB7irE,142
-pychemstation/control/chromatogram.py,sha256=c4_RGconn4vYU9wyS0WX-GB5FlwnBf_sfVLh_GpeehE,3716
-pychemstation/control/comm.py,sha256=iuzeFLZ_BhNVJwyNJjDiUuaoQBQpFFc0rHiRk0qOgnk,9976
-pychemstation/control/hplc.py,sha256=GvEL2zxz0_V47E_JrP4ePTUc8FahDDT3PYmd7ASbobA,29746
-pychemstation/control/method.py,sha256=h9KcccDtqx0hQT7JaUc1TWCB8d21t0McOuzeBsEsh4c,10977
-pychemstation/control/sequence.py,sha256=ewc7l44VAtv3wHV2QgOILu5Ny3gmubHuEeHJN9N6OjQ,7511
-pychemstation/control/table_controller.py,sha256=83i1J2CvIrJ3NtAB_E46qhUe8MvXo1_GnDPmuiq-vSA,2957
-pychemstation/generated/__init__.py,sha256=GAoZFAYbPVEJDkcOw3e1rgOqd7TCW0HyKNPM8OMehMg,1005
-pychemstation/generated/dad_method.py,sha256=0W8Z5WDtF5jpIcudMqb7XrkTnR2EGg_QOCsHRFQ0rmM,8402
-pychemstation/generated/pump_method.py,sha256=sUhE2Oo00nzVcoONtq3EMWsN4wLSryXbG8f3EeViWKg,12174
-pychemstation/utils/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-pychemstation/utils/chemstation.py,sha256=bnFIsZZwFy9NKzVUf517yN-ogzQbm0hp_aho3KUD6Is,9317
-pychemstation/utils/chromatogram.py,sha256=X-D-FdMwHPugrqAtp5vfPPbD_aU3gor3G6WjQzvEuSk,3742
-pychemstation/utils/constants.py,sha256=jLY-NixemSofukzSXJhAIU4aO2IJmBRAhAcq5066mFI,249
-pychemstation/utils/hplc_param_types.py,sha256=xvmsbYQp3iiS1-0-9eUy--5zk_wE1bkrlHEHSm0UC18,5206
-pychemstation/utils/macro.py,sha256=y_ynL_A-FqK3v4-StTmmbUd741vWhjm6kmduVi5IUfE,2212
-pychemstation/utils/method_types.py,sha256=PSVbKq1IHL4QJNSEl0Szaymfvm3sfXy1rqjT2W_qbN0,911
-pychemstation/utils/parsing.py,sha256=bnFIsZZwFy9NKzVUf517yN-ogzQbm0hp_aho3KUD6Is,9317
-pychemstation/utils/sequence_types.py,sha256=sin3X37EQb52CAGY2MOzY4Us9tdLg7FScTGMBWAF5Fs,689
-pychemstation/utils/table_types.py,sha256=BBCRoz1R6zPV1i2u2Tdku7WwIp6EDv1rUuZVPVNgO1A,2090
-pychemstation-0.4.7.dev2.dist-info/LICENSE,sha256=9bdF75gIf1MecZ7oymqWgJREVz7McXPG-mjqrTmzzD8,18658
-pychemstation-0.4.7.dev2.dist-info/METADATA,sha256=QuJvRtOpyJboxO9qPJFi_VbuUw4JP2UTczqXWRz2iW0,3929
-pychemstation-0.4.7.dev2.dist-info/WHEEL,sha256=PZUExdf71Ui_so67QXpySuHtCi3-J3wvF4ORK6k_S8U,91
-pychemstation-0.4.7.dev2.dist-info/top_level.txt,sha256=ONCqQRPu9Z4_k7TOvj64NVTmO8CqMg_PITePUzYchdY,14
-pychemstation-0.4.7.dev2.dist-info/RECORD,,