pychemstation 0.8.4__tar.gz → 0.9.1__tar.gz

{pychemstation-0.8.4 → pychemstation-0.9.1}/.gitignore

@@ -4,4 +4,6 @@
 .venv
 **/__pycache__/
 target
-.DS_Store
+.DS_Store
+env
+venv

{pychemstation-0.8.4 → pychemstation-0.9.1}/.gitlab-ci.yml

@@ -13,6 +13,4 @@ pages:
     - mv doc/ ./public/
   artifacts:
     paths:
-    - public
-  rules:
-    - if: $CI_COMMIT_REF_NAME == $CI_DEFAULT_BRANCH
+    - public

pychemstation-0.9.1/.pre-commit-config.yaml

@@ -0,0 +1,10 @@
+repos:
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  # Ruff version.
+  rev: v0.11.2
+  hooks:
+    # Run the linter.
+    - id: ruff
+      args: [ --fix ]
+    # Run the formatter.
+    - id: ruff-format

pychemstation-0.9.1/PKG-INFO

@@ -0,0 +1,155 @@
+Metadata-Version: 2.4
+Name: pychemstation
+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
+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-Dist: aghplctools==4.8.6
+Requires-Dist: coverage>=7.6.1
+Requires-Dist: matplotlib>=3.7.5
+Requires-Dist: pandas>=2.0.3
+Requires-Dist: pdoc>=14.7.0
+Requires-Dist: polling>=0.3.2
+Requires-Dist: pre-commit>=4.2.0
+Requires-Dist: pytest>=7.3.5
+Requires-Dist: rainbow-api>=1.0.10
+Requires-Dist: result>=0.17.0
+Requires-Dist: scipy>=1.10.1
+Requires-Dist: seabreeze>=2.9.2
+Requires-Dist: setuptools>=75.3.2
+Requires-Dist: twine>=6.1.0
+Requires-Dist: xsdata>=24.9
+Description-Content-Type: text/markdown
+
+# Agilent HPLC Macro Control
+
+![PyPI - Downloads](https://img.shields.io/pypi/dm/pychemstation)
+
+[![PyPI Latest Release](https://img.shields.io/pypi/v/pychemstation.svg)](https://pypi.org/project/pychemstation/)
+
+> **_NOTE:_** If you are running Python **3.8**, use versions 0.**8**.x. If you are running Python **3.9** use versions 0.**8**.x.
+> If you are running Python **>=3.10**, use version 0.**10**.x. You are welcome to use newer pychemstation versions with older Python versions, but functionality
+> is not guaranteed!
+
+Unofficial Python package to control Agilent Chemstation; we are not affiliated with Agilent.
+Check out the [docs](https://pychemstation-e5a086.gitlab.io/pychemstation.html) for usage instructions. This project is under
+active development, and breaking changes may occur at any moment.
+
+## Getting started
+
+Before running this library, these are the steps you need to complete.
+
+### Add python package
+
+```bash
+pip install pychemstation
+```
+
+### Add required MACRO script
+
+1. Open ChemStation
+2. Run this in the ChemStation command line: ``Print _AutoPath$``. Go to this path in your file navigator, as this is
+   where you will put your
+   MACRO file(s).
+3. Download the [
+   `hplc_talk.mac`](https://gitlab.com/heingroup/device-api/pychemstation/-/blob/main/tests/hplc_talk.mac).
+    - On line 69, change the path name up to `\cmd` and `\reply`. For instance, you should have:
+      `MonitorFile "[my path]\cmd", "[my path]\reply"`
+    - and then add this file to the folder from the previous step.
+4. To have these MACRO files be read by ChemStation, you must either:
+    - Open ChemStation and run:
+
+```MACRO
+macro hplc_talk.mac
+HPLCTalk_Run
+```
+
+- OR add the above lines to a MACRO file named: `user.mac`, and then put `user.mac` in the same folder from step 3.
+    - ChemStation will automatically load these MACRO files for you. However, sometimes this does not work, and if it
+      does not, you will have to run the lines in the `user.mac` manually.
+
+## Example Usage
+
+```python
+from pychemstation.control import HPLCController
+from pychemstation.utils.method_types import *
+import pandas as pd
+
+DEFAULT_METHOD_DIR = "C:\\ChemStation\\1\\Methods\\"
+SEQUENCE_DIR = "C:\\USERS\\PUBLIC\\DOCUMENTS\\CHEMSTATION\\3\\Sequence"
+DEFAULT_COMMAND_PATH = "C:\\Users\\User\\Desktop\\Lucy\\"
+DATA_DIR_2 = "C:\\Users\\Public\\Documents\\ChemStation\\2\\Data"
+DATA_DIR_3 = "C:\\Users\\Public\\Documents\\ChemStation\\3\\Data"
+
+# Initialize HPLC Controller
+hplc_controller = HPLCController(data_dirs=[DATA_DIR_2, DATA_DIR_3],
+                                 comm_dir=DEFAULT_COMMAND_PATH,
+                                 method_dir=DEFAULT_METHOD_DIR,
+                                 sequence_dir=SEQUENCE_DIR)
+
+# Switching a method
+hplc_controller.switch_method("General-Poroshell")
+
+# Editing a method
+new_method = MethodDetails(
+    name="General-Poroshell",
+    params=HPLCMethodParams(
+        organic_modifier=7,
+        flow=0.44),
+    timetable=[
+        TimeTableEntry(
+            start_time=0.10,
+            organic_modifer=7,
+            flow=0.34
+        ),
+        TimeTableEntry(
+            start_time=4,
+            organic_modifer=99,
+            flow=0.55
+        )
+    ],
+    stop_time=5,
+    post_time=2
+)
+hplc_controller.edit_method(new_method)
+
+# Run a method and get a report or data from last run method
+hplc_controller.run_method(experiment_name="test_experiment")
+report = hplc_controller.get_last_run_method_report()
+vial_location = report.vial_location
+
+# Save, analyze or plot the data!
+chrom = hplc_controller.get_last_run_method_data()
+chromatogram_data = pd.DataFrame.from_dict({"x": chrom.A.x, "y": chrom.A.y})
+chromatogram_data.to_csv("Run 10.csv", index=False) 
+```
+
+## Adding your own MACROs
+
+If you wish to add your own MACRO functions, then all you need to do is write you MACRO (using Agilent's) MACRO guide,
+put the file in the `user.mac` file and then list the function you want to use.
+
+## Developing
+
+If you would like to contribute to this project, check out
+our [GitLab](https://gitlab.com/heingroup/device-api/pychemstation)!
+
+## Authors and Acknowledgements
+
+Lucy Hao, Maria Politi
+
+- Adapted from [**AnalyticalLabware**](https://github.com/croningp/analyticallabware), created by members in the Cronin
+  Group. Copyright © Cronin Group, used under the [CC-BY-4.0](https://creativecommons.org/licenses/by/4.0/) license.
+- Adapted from the [MACROS](https://github.com/Bourne-Group/HPLCMethodOptimisationGUI) used in [**Operator-free HPLC
+  automated method development guided by Bayesian optimization**](https://pubs.rsc.org/en/content/articlelanding/2024/dd/d4dd00062e),
+  created by members in the Bourne Group. Copyright © Bourne Group, used under
+  the [MIT](https://opensource.org/license/mit) license.

{pychemstation-0.8.4 → pychemstation-0.9.1}/README.md

@@ -4,8 +4,12 @@
 
 [![PyPI Latest Release](https://img.shields.io/pypi/v/pychemstation.svg)](https://pypi.org/project/pychemstation/)
 
+> **_NOTE:_** If you are running Python **3.8**, use versions 0.**8**.x. If you are running Python **3.9** use versions 0.**8**.x.
+> If you are running Python **>=3.10**, use version 0.**10**.x. You are welcome to use newer pychemstation versions with older Python versions, but functionality
+> is not guaranteed!
+
 Unofficial Python package to control Agilent Chemstation; we are not affiliated with Agilent.
-Check out the [docs](https://hein-analytical-control-5e6e85.gitlab.io/) for usage instructions. This project is under
+Check out the [docs](https://pychemstation-e5a086.gitlab.io/pychemstation.html) for usage instructions. This project is under
 active development, and breaking changes may occur at any moment.
 
 ## Getting started
@@ -45,29 +49,55 @@ HPLCTalk_Run
 
 ```python
 from pychemstation.control import HPLCController
+from pychemstation.utils.method_types import *
 import pandas as pd
 
-# these paths will be unique to your Chemstation setup
-DEFAULT_METHOD = "GENERAL-POROSHELL"
-DEFAULT_COMMAND_PATH = "C:\\Users\\User\\Desktop\\Lucy\\"
 DEFAULT_METHOD_DIR = "C:\\ChemStation\\1\\Methods\\"
-DATA_DIR_2 = "C:\\Users\\Public\\Documents\\ChemStation\\2\\Data\\"
-DATA_DIR_3 = "C:\\Users\\Public\\Documents\\ChemStation\\3\\Data\\"
-SEQUENCE_DIR = "C:\\USERS\\PUBLIC\\DOCUMENTS\\CHEMSTATION\\2\\Sequence\\"
+SEQUENCE_DIR = "C:\\USERS\\PUBLIC\\DOCUMENTS\\CHEMSTATION\\3\\Sequence"
+DEFAULT_COMMAND_PATH = "C:\\Users\\User\\Desktop\\Lucy\\"
+DATA_DIR_2 = "C:\\Users\\Public\\Documents\\ChemStation\\2\\Data"
+DATA_DIR_3 = "C:\\Users\\Public\\Documents\\ChemStation\\3\\Data"
 
+# Initialize HPLC Controller
 hplc_controller = HPLCController(data_dirs=[DATA_DIR_2, DATA_DIR_3],
                                  comm_dir=DEFAULT_COMMAND_PATH,
-                                 sequence_dir=SEQUENCE_DIR,
-                                 method_dir=DEFAULT_METHOD_DIR)
-
-hplc_controller.preprun()
-hplc_controller.switch_method(method_name=DEFAULT_METHOD)
-hplc_controller.run_method(experiment_name="Run 10")
+                                 method_dir=DEFAULT_METHOD_DIR,
+                                 sequence_dir=SEQUENCE_DIR)
+
+# Switching a method
+hplc_controller.switch_method("General-Poroshell")
+
+# Editing a method
+new_method = MethodDetails(
+    name="General-Poroshell",
+    params=HPLCMethodParams(
+        organic_modifier=7,
+        flow=0.44),
+    timetable=[
+        TimeTableEntry(
+            start_time=0.10,
+            organic_modifer=7,
+            flow=0.34
+        ),
+        TimeTableEntry(
+            start_time=4,
+            organic_modifer=99,
+            flow=0.55
+        )
+    ],
+    stop_time=5,
+    post_time=2
+)
+hplc_controller.edit_method(new_method)
+
+# Run a method and get a report or data from last run method
+hplc_controller.run_method(experiment_name="test_experiment")
+report = hplc_controller.get_last_run_method_report()
+vial_location = report.vial_location
+
+# Save, analyze or plot the data!
 chrom = hplc_controller.get_last_run_method_data()
-
-# afterwards, save, analyze or plot the data!
-values = {"x": chrom.A.x, "y": chrom.A.y}
-chromatogram_data = pd.DataFrame.from_dict(values)
+chromatogram_data = pd.DataFrame.from_dict({"x": chrom.A.x, "y": chrom.A.y})
 chromatogram_data.to_csv("Run 10.csv", index=False) 
 ```
 
@@ -87,6 +117,7 @@ Lucy Hao, Maria Politi
 
 - Adapted from [**AnalyticalLabware**](https://github.com/croningp/analyticallabware), created by members in the Cronin
   Group. Copyright © Cronin Group, used under the [CC-BY-4.0](https://creativecommons.org/licenses/by/4.0/) license.
-- Adapted from the [MACROS](https://github.com/Bourne-Group/HPLCMethodOptimisationGUI)
-  used in [**Operator-free HPLC automated method development guided by Bayesian optimization**](https://pubs.rsc.org/en/content/articlelanding/2024/dd/d4dd00062e),
-  created by members in the Bourne Group.  Copyright © Bourne Group, used under the [MIT](https://opensource.org/license/mit) license.
+- Adapted from the [MACROS](https://github.com/Bourne-Group/HPLCMethodOptimisationGUI) used in [**Operator-free HPLC
+  automated method development guided by Bayesian optimization**](https://pubs.rsc.org/en/content/articlelanding/2024/dd/d4dd00062e),
+  created by members in the Bourne Group. Copyright © Bourne Group, used under
+  the [MIT](https://opensource.org/license/mit) license.

{pychemstation-0.8.4/build/lib → pychemstation-0.9.1}/pychemstation/__init__.py

@@ -1,3 +1,3 @@
 """
 .. include:: ../README.md
-"""
+"""

pychemstation-0.9.1/pychemstation/analysis/__init__.py

@@ -0,0 +1,4 @@
+from .process_report import CSVProcessor
+from .process_report import TXTProcessor
+
+__all__ = ["CSVProcessor", "TXTProcessor"]

{pychemstation-0.8.4 → pychemstation-0.9.1}/pychemstation/analysis/base_spectrum.py

@@ -6,12 +6,12 @@ from abc import ABC, abstractmethod
 import matplotlib.pyplot as plt
 import numpy as np
 from scipy import (
-    sparse,
-    signal,
     integrate,
+    signal,
+    sparse,
 )
 
-from .utils import interpolate_to_index, find_nearest_value_index
+from ..utils.num_utils import find_nearest_value_index, interpolate_to_index
 
 
 class AbstractSpectrum(ABC):
@@ -249,7 +249,7 @@ class AbstractSpectrum(ABC):
             os.makedirs(path, exist_ok=True)
             fig.savefig(os.path.join(path, f"{filename}.png"), dpi=150)
 
-    def find_peaks(self, threshold=1, min_width=.1, min_dist=None, area=None):
+    def find_peaks(self, threshold=1, min_width=0.1, min_dist=None, area=None):
         """Finds all peaks above the threshold with at least min_width width.
 
         Args:

{pychemstation-0.8.4/pychemstation/utils → pychemstation-0.9.1/pychemstation/analysis}/chromatogram.py

@@ -6,16 +6,14 @@ from dataclasses import dataclass
 
 import numpy as np
 
-from .parsing import CHFile
-from ..analysis import AbstractSpectrum
 
-# standard filenames for spectral data
-CHANNELS = {"A": "01", "B": "02", "C": "03", "D": "04"}
+from ..utils.parsing import CHFile
+from ..analysis.base_spectrum import AbstractSpectrum
 
 ACQUISITION_PARAMETERS = "acq.txt"
 
 # format used in acquisition parameters
-TIME_FORMAT = "%Y-%m-%d-%H-%M-%S"
+TIME_FORMAT = "%Y-%m-%d %H-%M-%S"
 SEQUENCE_TIME_FORMAT = "%Y-%m-%d %H-%M"
 
 
@@ -39,12 +37,11 @@ class AgilentHPLCChromatogram(AbstractSpectrum):
     }
 
     def __init__(self, path=None, autosaving=False):
-
         if path is not None:
             os.makedirs(path, exist_ok=True)
             self.path = path
         else:
-            self.path = os.path.join(".", "hplc_data")
+            self.path = os.path.join("../utils", "hplc_data")
             os.makedirs(self.path, exist_ok=True)
 
         super().__init__(path=path, autosaving=autosaving)