Merge branch 'master' of https://github.com/Jhsmit/PyHDX

README.md

@@ -53,12 +53,12 @@ Please refer to the [docs](https://pyhdx.readthedocs.io/en/stable/) for more det
 ## Web Application
 
 The PyHDX web application is currently hosted at:
-~~http://pyhdx.jhsmit.org~~ https://gather-mega-fioricet-ruled.trycloudflare.com/
+http://pyhdx.jhsmit.org
 
 A test file can be downloaded from [here](https://github.com/raw/Jhsmit/PyHDX/master/tests/test_data/input/ecSecB_apo.csv) and [here](https://github.com/raw/Jhsmit/PyHDX/master/tests/test_data/input/ecSecB_dimer.csv>) (right click, save as).
 
 A beta version might be available at:
-~~http://pyhdx-beta.jhsmit.org~~ https://risk-percentage-hacker-birds.trycloudflare.com/
+http://pyhdx-beta.jhsmit.org
 
 The latest beta docs are found [here](https://pyhdx.readthedocs.io/en/latest/)
 

pyhdx/batch_processing.py

@@ -29,7 +29,9 @@ class DataFile(object):
     filepath_or_buffer: Union[Path, StringIO]
 
     def __post_init__(self):
-        warnings.warn("Will be removed in favour of the `hdxms-datasets` package ", DeprecationWarning)
+        warnings.warn(
+            "Will be removed in favour of the `hdxms-datasets` package ", DeprecationWarning
+        )
 
     @cached_property
     def data(self) -> pd.DataFrame:
@@ -62,8 +64,9 @@ def __init__(
         # filter_kwargs: Optional[dict[str, Any]] = None,
         # correction_kwargs: Optional[dict[str, Any]] = None,
     ) -> None:
-
-        warnings.warn("Will be removed in favour of the `hdxms-datasets` package ", DeprecationWarning)
+        warnings.warn(
+            "Will be removed in favour of the `hdxms-datasets` package ", DeprecationWarning
+        )
         self.hdx_spec = hdx_spec
         self.data_files: dict[str, DataFile] = {}
 

pyhdx/cli.py

@@ -11,6 +11,8 @@
 from pyhdx.datasets import DataVault
 
 app = typer.Typer()
+
+
 @app.command()
 def serve(
     scheduler_address: Optional[str] = typer.Option(None, help="Address for dask scheduler to use"),
@@ -61,6 +63,8 @@ def serve(
 
 
 datasets_app = typer.Typer(help="Manage HDX datasets")
+
+
 @datasets_app.command()
 def fetch(num: int = typer.Option(10, min=1, help="Maximum number of datasets to download")):
     """Update the datasets from the PyHDX repository"""
@@ -72,6 +76,7 @@ def fetch(num: int = typer.Option(10, min=1, help="Maximum number of datasets to
         for data_id in tqdm(todo):
             vault.fetch_dataset(data_id)
 
+
 @datasets_app.command()
 def clear():
     """Clear the local dataset cache"""
@@ -81,6 +86,7 @@ def clear():
 
 app.add_typer(datasets_app, name="datasets")
 
+
 @app.callback()
 def callback():
     pass

pyhdx/config.py

@@ -146,6 +146,7 @@ def context(self, settings: dict) -> Generator[PyHDXConfig, None, None]:
         finally:
             cfg.conf = original_config
 
+
 def valid_config() -> bool:
     """Checks if the current config file in the user home directory is a valid config
     file for the current pyhdx version.

pyhdx/datasets.py

@@ -1 +1 @@
-from hdxms_datasets import *
+from hdxms_datasets import *

pyhdx/fileIO.py

@@ -80,7 +80,9 @@ def read_header(file_obj: Union[TextIO, BinaryIO], comment: str = "#") -> List[s
     return header
 
 
-def parse_header(filepath_or_buffer: Union[Path[str], str, StringIO, BytesIO], comment: str = "#") -> dict:
+def parse_header(
+    filepath_or_buffer: Union[Path[str], str, StringIO, BytesIO], comment: str = "#"
+) -> dict:
     """
     Reads the header from a file and returns JSON metadata from header lines marked as comment.
 

pyhdx/plot.py

@@ -615,7 +615,6 @@ def linear_bars(
     sort=False,
     **figure_kwargs,
 ):
-
     # input data should always be 3 levels
     # grouping is done by the first level
     # second level gives each bar
@@ -1141,6 +1140,7 @@ def get(self, item, default=None):
         except KeyError:
             return default
 
+
 # should be a frozen dataclas
 CMAP_NORM_DEFAULTS = ColorTransforms()
 

pyhdx/process.py

@@ -255,7 +255,9 @@ def filter_peptides(
 
     """
 
-    warnings.warn("`filter_peptides` will be moved to the `hdxms-datasets` package", DeprecationWarning)
+    warnings.warn(
+        "`filter_peptides` will be moved to the `hdxms-datasets` package", DeprecationWarning
+    )
     if state:
         df = df[df["state"] == state]
 

pyhdx/support.py

@@ -848,6 +848,7 @@ def array_intersection(arrays: Iterable[np.ndarray], fields: Iterable[str]) -> l
 
     return selected
 
+
 # https://stackoverflow.com/questions/31174295/getattr-and-setattr-on-nested-subobjects-chained-properties
 def rsetattr(obj, attr, val):
     pre, _, post = attr.rpartition(".")

pyhdx/web/controllers.py

@@ -47,7 +47,8 @@
 from pyhdx.datasets import HDXDataSet, DataVault, DataFile
 from pyhdx.fitting_torch import TorchFitResultSet
 from pyhdx.models import (
-    PeptideUptakeModel, HDXMeasurement,
+    PeptideUptakeModel,
+    HDXMeasurement,
 )
 from pyhdx.plot import (
     dG_scatter_figure,
@@ -293,7 +294,9 @@ class PeptideFileInputControl(PyHDXControlPanel):
 
     batch_file = param.Parameter(doc="Batch file input:")
 
-    dataset_id = param.Selector(label="Dataset ID", doc="Dataset ID to load from hdxms-datasets database")
+    dataset_id = param.Selector(
+        label="Dataset ID", doc="Dataset ID to load from hdxms-datasets database"
+    )
 
     nd_control = param.Boolean(
         default=False, precedence=-1, doc="Whether to allow users to input a ND control"
@@ -410,7 +413,7 @@ def __init__(self, parent, **params):
             todo = list(missing_datasets)[:num]
             for data_id in tqdm(todo):
                 self.data_vault.fetch_dataset(data_id)
-        self.param['dataset_id'].objects = self.data_vault.datasets
+        self.param["dataset_id"].objects = self.data_vault.datasets
         if self.data_vault.datasets:
             self.dataset_id = self.data_vault.datasets[0]
 
@@ -512,19 +515,17 @@ def _update_mode(self):
                 "measurement_name",
                 "download_spec_button",
             },
-            "Batch": {
-                "input_files_label",
-                "input_files",
-                "batch_file",
-                "batch_file_label"
-            },
+            "Batch": {"input_files_label", "input_files", "batch_file", "batch_file_label"},
             "Database": {
                 "dataset_id",
-            }
+            },
         }
 
-        #widget_dict.pop(self.input_mode)
-        excluded = set.union(*(v for k, v in widget_dict.items() if k != self.input_mode)) - widget_dict[self.input_mode]
+        # widget_dict.pop(self.input_mode)
+        excluded = (
+            set.union(*(v for k, v in widget_dict.items() if k != self.input_mode))
+            - widget_dict[self.input_mode]
+        )
         #
         #
         # if self.input_mode == "Manual":
@@ -814,7 +815,9 @@ def _action_load_datasets(self) -> None:
         """Load all specified HDX measurements"""
         if self.input_mode == "Manual":
             data_src = self.data_file_history
-            dataset = HDXDataSet(data_id=uuid.uuid4().hex, data_files=data_src, hdx_spec=self.hdx_spec)
+            dataset = HDXDataSet(
+                data_id=uuid.uuid4().hex, data_files=data_src, hdx_spec=self.hdx_spec
+            )
         elif self.input_mode == "Batch":
             if self.hdxm_list:
                 self.parent.logger.info("Cannot add data in batch after manually inputting data")
@@ -831,7 +834,9 @@ def _action_load_datasets(self) -> None:
             self.state_spec = hdx_spec["states"]
             self.data_spec = hdx_spec["data_files"]
 
-            dataset = HDXDataSet(data_id=uuid.uuid4().hex, data_files=data_src, hdx_spec=self.hdx_spec)
+            dataset = HDXDataSet(
+                data_id=uuid.uuid4().hex, data_files=data_src, hdx_spec=self.hdx_spec
+            )
             self.param["hdxm_list"].objects = dataset.states
         elif self.input_mode == "Database":
             if self.dataset_id is None:
@@ -841,18 +846,18 @@ def _action_load_datasets(self) -> None:
             self.parent.logger.info(f"Loaded dataset {dataset.data_id} from hdxms database")
 
             try:
-                authors = ", ".join([author['name'] for author in dataset.metadata['authors']])
+                authors = ", ".join([author["name"] for author in dataset.metadata["authors"]])
                 self.parent.logger.info(f"Author(s): {authors}")
             except KeyError:
                 pass
 
-            publications = dataset.metadata.get('publications', [])
+            publications = dataset.metadata.get("publications", [])
             if publications:
                 for pub in publications:
-                    pub_str = pub['title']
-                    if 'DOI' in pub:
+                    pub_str = pub["title"]
+                    if "DOI" in pub:
                         pub_str += f' ([{pub["DOI"]}](https://doi.org/{pub["DOI"]}))'
-                    elif 'URL' in pub:
+                    elif "URL" in pub:
                         pub_str += f' ([URL]({pub["URL"]}))'
                     self.parent.logger.info("Publication: " + pub_str)
         else:

pyproject.toml

@@ -34,7 +34,7 @@ dependencies = [
     "param",
     "pyyaml",
     "omegaconf",
-    "hdxms-datasets>=0.1.2",
+    "hdxms-datasets>=0.1.3",
 ]
 dynamic = ["version"]
 

requirements/requirements-macOS-latest-3.9.txt

@@ -17,7 +17,7 @@ certifi==2023.7.22
     # via requests
 charset-normalizer==3.2.0
     # via requests
-click==8.1.6
+click==8.1.7
     # via
     #   dask
     #   distributed
@@ -33,21 +33,21 @@ colorcet==3.0.1
     #   pyhdx (pyproject.toml)
 cycler==0.11.0
     # via matplotlib
-dask==2023.8.0
+dask==2023.8.1
     # via
     #   distributed
     #   pyhdx (pyproject.toml)
-distributed==2023.8.0
+distributed==2023.8.1
     # via pyhdx (pyproject.toml)
 filelock==3.12.2
     # via torch
 fsspec==2023.6.0
     # via dask
-hdxms-datasets==0.1.2
+hdxms-datasets==0.1.3
     # via pyhdx (pyproject.toml)
 hdxrate==0.2.0
     # via pyhdx (pyproject.toml)
-holoviews==1.17.0
+holoviews==1.17.1
     # via
     #   hvplot
     #   pyhdx (pyproject.toml)
@@ -66,7 +66,7 @@ jinja2==3.1.2
     #   bokeh
     #   distributed
     #   torch
-kiwisolver==1.4.4
+kiwisolver==1.4.5
     # via matplotlib
 lazy-loader==0.3
     # via scikit-image
@@ -110,7 +110,7 @@ omegaconf==2.3.0
     # via
     #   hdxms-datasets
     #   pyhdx (pyproject.toml)
-packaging==22.0
+packaging==23.1
     # via
     #   bokeh
     #   dask
@@ -120,7 +120,7 @@ packaging==22.0
     #   hvplot
     #   pyhdx (pyproject.toml)
     #   scikit-image
-pandas==1.5.3
+pandas==2.0.3
     # via
     #   hdxms-datasets
     #   holoviews
@@ -163,7 +163,7 @@ python-dateutil==2.8.2
     #   pandas
 pytz==2023.3
     # via pandas
-pyviz-comms==2.3.2
+pyviz-comms==3.0.0
     # via
     #   holoviews
     #   panel
@@ -183,7 +183,7 @@ requests==2.31.0
     #   panel
 scikit-image==0.21.0
     # via pyhdx (pyproject.toml)
-scipy==1.11.1
+scipy==1.11.2
     # via
     #   pyhdx (pyproject.toml)
     #   scikit-image
@@ -202,7 +202,7 @@ sympy==1.12
     #   torch
 tblib==2.0.0
     # via distributed
-tifffile==2023.7.18
+tifffile==2023.8.12
     # via scikit-image
 toolz==0.12.0
     # via
@@ -213,11 +213,11 @@ toposort==1.10
     # via symfit
 torch==2.0.1
     # via pyhdx (pyproject.toml)
-tornado==6.3.2
+tornado==6.3.3
     # via
     #   bokeh
     #   distributed
-tqdm==4.65.0
+tqdm==4.66.1
     # via
     #   panel
     #   pyhdx (pyproject.toml)
@@ -229,6 +229,8 @@ typing-extensions==4.7.1
     #   panel
     #   torch
     #   typer
+tzdata==2023.3
+    # via pandas
 urllib3==2.0.4
     # via
     #   distributed