Merge remote-tracking branch 'origin/master'

Jhsmit · Jan 23, 2024 · 4524214 · 4524214
2 parents 79ee198 + 14ef19e
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diff --git a/README.md b/README.md
@@ -10,9 +10,9 @@
 
 PyHDX is python project which can be used to derive Gibbs free energy from HDX-MS data.
 
+[PyHDX web](http://pyhdx.jhsmit.org)
 
-
-[PyHDX stable documentation](https://pyhdx.readthedocs.io/en/stable/)
+[PyHDX latest documentation](https://pyhdx.readthedocs.io/en/latest/)
 
 [PyHDX on YouTube](https://www.youtube.com/channel/UCTro6Iv1BhvjUPYZNu5TJWg)
 
@@ -60,8 +60,6 @@ A test file can be downloaded from [here](https://raw.githubusercontent.com/Jhsm
 A beta version might be available at:
 http://pyhdx-beta.jhsmit.org
 
-The latest beta docs are found [here](https://pyhdx.readthedocs.io/en/latest/)
-
 
 ## Publication
 
@@ -73,7 +71,7 @@ Python code for analysis and generation the figures in the paper are here: https
 
 ## Other
 
-HDX MS datasets repository and format (alpha):
+HDX MS datasets repository and format:
 https://github.com/Jhsmit/HDX-MS-datasets
 
 HDXMS datasets python bindings:

diff --git a/pyhdx/models.py b/pyhdx/models.py
@@ -286,7 +286,7 @@ def __init__(self, data: pd.DataFrame, **metadata: Any):
         )
 
     @classmethod
-    def from_dataset(cls, dataset: HDXDataSet, state: str | int, **metadata) -> HDXMeasurement:
+    def from_dataset(cls, dataset: HDXDataSet, state: str | int, drop_first=cfg.analysis.drop_first, **metadata) -> HDXMeasurement:
         """Create an HDXMeasurement object from a HDXDataSet object.
 
         Args:
@@ -318,7 +318,7 @@ def from_dataset(cls, dataset: HDXDataSet, state: str | int, **metadata) -> HDXM
         peptides = apply_control(peptides, fd_peptides, nd_peptides)
         peptides = correct_d_uptake(
             peptides,
-            drop_first=cfg.analysis.drop_first,
+            drop_first=drop_first,
             d_percentage=metadata.get("d_percentage", 100.0),
         )
 

diff --git a/pyhdx/web/controllers.py b/pyhdx/web/controllers.py
@@ -229,17 +229,17 @@ class GlobalSettingsControl(ControlPanel):
         doc="Select the number of N-terminal residues to ignore.",
     )
 
-    weight_exponent = param.Number(
-        default=cfg.analysis.weight_exponent,
-        bounds=(0, None),
-        doc="Value of the exponent use for weighted averaging of RFU values",
-    )
+    # weight_exponent = param.Number(
+    #     default=cfg.analysis.weight_exponent,
+    #     bounds=(0, None),
+    #     doc="Value of the exponent use for weighted averaging of RFU values",
+    # )
 
     def make_dict(self):
         widgets = self.generate_widgets()
-        widgets["config_download"] = pn.widgets.FileDownload(
-            label="Download config file", callback=self.config_download_callback
-        )
+        # widgets["config_download"] = pn.widgets.FileDownload(
+        #     label="Download config file", callback=self.config_download_callback
+        # )
 
         return widgets
 
@@ -258,13 +258,13 @@ def config_download_callback(self) -> StringIO:
 
         return sio
 
-    @param.depends("drop_first", watch=True)
-    def _update_drop_first(self):
-        cfg.analysis.drop_first = self.drop_first
+    # @param.depends("drop_first", watch=True)
+    # def _update_drop_first(self):
+    #     cfg.analysis.drop_first = self.drop_first
 
-    @param.depends("weight_exponent", watch=True)
-    def _update_weight_exponent(self):
-        cfg.analysis.weight_exponent = self.weight_exponent
+    # @param.depends("weight_exponent", watch=True)
+    # def _update_weight_exponent(self):
+    #     cfg.analysis.weight_exponent = self.weight_exponent
 
 
 class PeptideFileInputControl(PyHDXControlPanel):
@@ -857,13 +857,14 @@ def _action_load_datasets(self) -> None:
         self.widgets["load_dataset_button"].disabled = True
         try:
             config_ctrl = self.parent.control_panels["GlobalSettingsControl"]
+            drop_first = config_ctrl.drop_first
             config_ctrl.widgets["drop_first"].disabled = True
-            config_ctrl.widgets["weight_exponent"].disabled = True
+            # config_ctrl.widgets["weight_exponent"].disabled = True
         except KeyError:
-            pass
+            drop_first = 2
 
         for state in dataset.states:
-            hdxm = HDXMeasurement.from_dataset(dataset, state)
+            hdxm = HDXMeasurement.from_dataset(dataset, state, drop_first=drop_first)
             self.src.add(hdxm, state)
             self.parent.logger.info(
                 f"Loaded experiment peptides state {hdxm.state} "

diff --git a/requirements/requirements-macOS-latest-3.9.txt b/requirements/requirements-macOS-latest-3.9.txt
@@ -61,7 +61,7 @@ importlib-metadata==6.8.0
     # via
     #   dask
     #   markdown
-jinja2==3.1.2
+jinja2==3.1.3
     # via
     #   bokeh
     #   distributed

diff --git a/requirements/requirements-ubuntu-latest-3.9.txt b/requirements/requirements-ubuntu-latest-3.9.txt
@@ -65,7 +65,7 @@ importlib-metadata==6.8.0
     # via
     #   dask
     #   markdown
-jinja2==3.1.2
+jinja2==3.1.3
     # via
     #   bokeh
     #   distributed

diff --git a/requirements/requirements-windows-latest-3.9.txt b/requirements/requirements-windows-latest-3.9.txt
@@ -65,7 +65,7 @@ importlib-metadata==6.8.0
     # via
     #   dask
     #   markdown
-jinja2==3.1.2
+jinja2==3.1.3
     # via
     #   bokeh
     #   distributed