Merge pull request #51 from h2020charisma/pydantic2_migration

Migrate to pydantic2

.github/dependabot.yml

@@ -0,0 +1,11 @@
+---
+version: 2
+updates:
+
+  # Maintain dependencies for GitHub Actions
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "monthly"
+    assignees:
+      - "kerberizer"

.github/workflows/publish.yml

@@ -22,10 +22,10 @@ jobs:
     steps:
 
       - name: Checkout the repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v4.1.7
 
       - name: Setup Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v5.2.0
         with:
           python-version: '3.9'
 
@@ -38,4 +38,4 @@ jobs:
         run: python -m build
 
       - name: Publish package
-        uses: pypa/gh-action-pypi-publish@release/v1
+        uses: pypa/gh-action-pypi-publish@v1.10.1

.gitignore

@@ -1,3 +1,11 @@
+# vim
+.*.un~
+.*.swp
+Session.vim
+
+# VS Code
+.vscode
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]
@@ -20,7 +28,6 @@ parts/
 sdist/
 var/
 wheels/
-pip-wheel-metadata/
 share/python-wheels/
 *.egg-info/
 .installed.cfg
@@ -50,6 +57,7 @@ coverage.xml
 *.py,cover
 .hypothesis/
 .pytest_cache/
+cover/
 
 # Translations
 *.mo
@@ -72,6 +80,7 @@ instance/
 docs/_build/
 
 # PyBuilder
+.pybuilder/
 target/
 
 # Jupyter Notebook
@@ -82,7 +91,9 @@ profile_default/
 ipython_config.py
 
 # pyenv
-.python-version
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
 
 # pipenv
 #   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
@@ -91,7 +102,24 @@ ipython_config.py
 #   install all needed dependencies.
 #Pipfile.lock
 
-# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/latest/usage/project/#working-with-version-control
+.pdm.toml
+.pdm-python
+.pdm-build/
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
 __pypackages__/
 
 # Celery stuff
@@ -128,11 +156,15 @@ dmypy.json
 # Pyre type checker
 .pyre/
 
+# pytype static type analyzer
+.pytype/
 
-# vim
-.*.un~
-.*.swp
-Session.vim
+# Cython debug symbols
+cython_debug/
 
-# VS Code
-.vscode
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/

.python-version

@@ -0,0 +1 @@
+3.9

setup.py

@@ -6,7 +6,7 @@
 
 NAME = 'oranchada'
 
-VERSION = '0.0.15'
+VERSION = '1.0.0'
 
 DESCRIPTION = 'Orange add-on for Raman spectroscopy'
 README_FILE = path.join(path.dirname(__file__), 'README.pypi')
@@ -46,7 +46,7 @@
     'orange-widget-base>=4.16.1',
     'pip>=9.0',  # same as for Orange 3.28
     'ploomber~=0.23.0',
-    'ramanchada2~=0.1.1',
+    'ramanchada2~=1.0',
     'setuptools>=36.3',  # same as for Orange 3.28
     'tables~=3.9.1',
     # 'AnyQt>=0.0.6',
@@ -101,7 +101,7 @@
 }
 
 CLASSIFIERS = [
-    'Development Status :: 4 - Beta',
+    'Development Status :: 5 - Production/Stable',
     'Environment :: Plugins',
     'Intended Audience :: Developers',
     'Intended Audience :: Education',

src/orangecontrib/oranchada/base_widget/base_widget.py

@@ -48,7 +48,7 @@ def __init__(self):
         gui.checkBox(self.optionsBox, self, "should_plot_legend", "Plot legend", callback=self.auto_process)
 
     class Outputs:
-        out_spe = Output("RC2Spectra", RC2Spectra, default=True, auto_summary = False)
+        out_spe = Output("RC2Spectra", RC2Spectra, default=True, auto_summary=False)
         data = Output("Data", Table, default=False)
 
     def force_plot(self):
@@ -91,13 +91,13 @@ def custom_plot(self, ax):
     def set_x_title(self, ax):
         xlab = ''
         for spe in reversed(self.out_spe):
-            if 'xlabel' in spe.meta.__root__:
+            if 'xlabel' in spe.meta.root:
                 xlab = spe.meta['xlabel']
         if not xlab:
             return
         should_warn = False
         for spe in self.out_spe:
-            if 'xlabel' in spe.meta.__root__:
+            if 'xlabel' in spe.meta.root:
                 if xlab != spe.meta['xlabel']:
                     should_warn = True
             else:
@@ -118,7 +118,7 @@ def send_output_table(self):
             if self.out_spe:
                 try:
                     self.Outputs.data.send(self.output_table_domain())
-                except: # just in case the new implementation breaks
+                except:  # just in case the new implementation breaks
                     self.Outputs.data.send(self.output_table_old())
 
     def output_table_domain(self):
@@ -142,16 +142,14 @@ def output_table_domain(self):
                     row_data[column_index] = y
                 meta_values = []
                 for key in all_meta_keys:
-                    if key in spe.meta.__root__:
+                    if key in spe.meta.root:
                         meta_values.append(spe.meta[key])
                     else:
                         meta_values.append(None)
                 data.append(row_data + meta_values)
 
             return Table.from_list(domain, data)
 
-
-
     def send_outputs(self):
         if self.out_spe:
             self.Outputs.out_spe.send(self.out_spe)

src/orangecontrib/oranchada/processings/add_baseline.py

@@ -1,13 +1,13 @@
 from typing import Union
 
-import pydantic
 import ramanchada2 as rc2
 from AnyQt.QtWidgets import QGroupBox
 from Orange.widgets import gui
+from pydantic import validate_call
 
 
 class AddBaseline:
-    @pydantic.validate_arguments(config=dict(arbitrary_types_allowed=True))
+    @validate_call(config=dict(arbitrary_types_allowed=True))
     def __init__(self, parent, *,
                  n_freq: tuple[str, Union[None, QGroupBox]],
                  amplitude: tuple[str, Union[None, QGroupBox]],
@@ -43,7 +43,7 @@ def __init__(self, parent, *,
             gui.doubleSpin(quadratic[1], self._parent, self._quadratic, -100, 100, decimals=7, step=.000001,
                            label='quadratic', callback=self.auto_process)
 
-    @pydantic.validate_arguments(config=dict(arbitrary_types_allowed=True))
+    @validate_call(config=dict(arbitrary_types_allowed=True))
     def __call__(self, spe: rc2.spectrum.Spectrum) -> rc2.spectrum.Spectrum:
         return spe.add_baseline(n_freq=self.n_freq,
                                 amplitude=self.amplitude,

src/orangecontrib/oranchada/processings/add_noise.py

@@ -1,13 +1,13 @@
 from typing import Union
 
-import pydantic
 import ramanchada2 as rc2
 from AnyQt.QtWidgets import QGroupBox
 from Orange.widgets import gui
+from pydantic import validate_call
 
 
 class AddNoise:
-    @pydantic.validate_arguments(config=dict(arbitrary_types_allowed=True))
+    @validate_call(config=dict(arbitrary_types_allowed=True))
     def __init__(self, parent, *,
                  noise_scale: tuple[str, Union[None, QGroupBox]],
                  ):
@@ -21,7 +21,7 @@ def __init__(self, parent, *,
     def auto_process(self):
         self._parent.auto_process()
 
-    @pydantic.validate_arguments(config=dict(arbitrary_types_allowed=True))
+    @validate_call(config=dict(arbitrary_types_allowed=True))
     def __call__(self, spe: rc2.spectrum.Spectrum) -> rc2.spectrum.Spectrum:
         return spe.add_poisson_noise(self.noise_scale)
 

src/orangecontrib/oranchada/processings/gen_spe.py

@@ -1,13 +1,14 @@
-from Orange.widgets import gui
-import ramanchada2 as rc2
+from typing import Union
+
 import numpy as np
+import ramanchada2 as rc2
 from AnyQt.QtWidgets import QGroupBox
-import pydantic
-from typing import Union
+from Orange.widgets import gui
+from pydantic import validate_call
 
 
 class GenSpe:
-    @pydantic.validate_arguments(config=dict(arbitrary_types_allowed=True))
+    @validate_call(config=dict(arbitrary_types_allowed=True))
     def __init__(self, parent, *,
                  spe_xmin: tuple[str, Union[None, QGroupBox]],
                  spe_xmax: tuple[str, Union[None, QGroupBox]],
@@ -44,7 +45,7 @@ def set_deltas(self):
             self.deltas = '620.9: 16, 795.8: 10, 1001.4: 100, 1031.8: 27, 1155.3: 13, 1450.5: 8, 1583.1: 12, 1602.3: 28, 2852.4: 9, 2904.5: 13, 3054.3: 32'  # noqa: E501
             self.deltas_edit.setReadOnly(True)
 
-    @pydantic.validate_arguments(config=dict(arbitrary_types_allowed=True))
+    @validate_call(config=dict(arbitrary_types_allowed=True))
     def __call__(self) -> rc2.spectrum.Spectrum:
         deltas_dict = dict([[float(j) for j in i.split(':')] for i in self.deltas.replace(' ', '').split(',')])
         spe1 = rc2.spectrum.Spectrum(x=np.array(list(deltas_dict.keys())), y=np.array(list(deltas_dict.values())))

src/orangecontrib/oranchada/tests/process_spectra_test.py

@@ -1,5 +1,5 @@
 import unittest
-from widgets import ProcessSpectraWidget
+from widgets_pro.process_spectra import ProcessSpectraWidget
 
 
 class TestLoadSpectraWidget(unittest.TestCase):

src/orangecontrib/oranchada/widgets_pro/load_file.py

@@ -61,12 +61,12 @@ def process(self):
         for fname in self.filenames:
             name, extension = os.path.splitext(fname)
             if extension == ".cha":
-                spe = rc2.spectrum.from_chada(fname,dataset=self.dataset)
+                spe = rc2.spectrum.from_chada(fname, dataset=self.dataset)
             else:
                 spe = rc2.spectrum.from_local_file(fname,
-                                               filetype=(self.fileformat if self.fileformat != 'Auto' else None),
-                                               )
-            meta_dct = spe.meta.dict()['__root__']
+                                                   filetype=(self.fileformat if self.fileformat != 'Auto' else None),
+                                                   )
+            meta_dct = spe.meta.model_dump()
             meta_dct['xlabel'] = 'Raman shift [cm¯¹]'
             spe.meta = meta_dct
             self.out_spe.append(spe)

src/orangecontrib/oranchada/widgets_pro/load_test_spectra.py

@@ -58,7 +58,7 @@ def process(self):
         self.out_spe = list()
         for fn in data.prepend_prefix(self.selected_filenames):
             spe = rc2.spectrum.from_local_file(fn)
-            meta_dct = spe.meta.dict()['__root__']
+            meta_dct = spe.meta.model_dump()
             meta_dct['xlabel'] = 'Raman shift [cm¯¹]'
             spe.meta = meta_dct
             self.out_spe.append(spe)

src/orangecontrib/oranchada/widgets_pro/raman_shift_to_wavelength.py

@@ -25,10 +25,10 @@ def process(self):
         self.out_spe = list()
         for inspe in self.in_spe:
             spe = inspe.shift_cm_1_to_abs_nm_filter(laser_wave_length_nm=self.laser_wl)
-            if 'xlabel' in spe.meta.__root__:
+            if 'xlabel' in spe.meta.root:
                 if spe.meta['xlabel'] != 'Raman shift [cm¯¹]':
                     self.Warning.x_label_not_ramanshift()
-                meta_dct = spe.meta.dict()['__root__']
+                meta_dct = spe.meta.model_dump()
                 meta_dct['xlabel'] = 'Wavelength [nm]'
                 spe.meta = meta_dct
             self.out_spe.append(spe)

src/orangecontrib/oranchada/widgets_pro/wavelength_to_raman_shift.py

@@ -24,10 +24,10 @@ class Warning(FilterWidget.Warning):
     def process(self):
         self.out_spe = list()
         for spe in self.in_spe:
-            if 'xlabel' in spe.meta.__root__:
+            if 'xlabel' in spe.meta.root:
                 if spe.meta['xlabel'] != 'Wavelength [nm]':
                     self.Warning.x_label_not_wavelength()
-                meta_dct = spe.meta.dict()['__root__']
+                meta_dct = spe.meta.model_dump()
                 meta_dct['xlabel'] = 'Raman shift [cm¯¹]'
                 spe.meta = meta_dct
             self.out_spe.append(