Maintenance/patches for v0.3.3 (#599)

* Force recalculation of SVD attributes in scheme._prepare_data Fixes #597
* 🔨 Remove no-op code related to new_dims 
* Remove unneeded check in spectral_penalties._get_area Fixes #598
* Add python 3.9 support (#450)
* Bump numba dependencies as needed for Python 3.9

.github/workflows/CI_CD_actions.yml

@@ -24,8 +24,8 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install -U pip wheel
-          pip install .
           python -m pip install -U -r requirements_dev.txt
+          pip install .
       - name: Show installed packages
         run: pip freeze
       - name: Build docs
@@ -43,8 +43,8 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install -U pip wheel
-          pip install .
           python -m pip install -U -r requirements_dev.txt
+          pip install .
       - name: Show installed packages
         run: pip freeze
       - name: Check doc links
@@ -61,7 +61,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, windows-latest, macOS-latest]
-        python-version: [3.8]
+        python-version: [3.8, 3.9]
 
     steps:
       - uses: actions/checkout@v2

CONTRIBUTING.rst

@@ -113,7 +113,7 @@ Before you submit a pull request, check that it meets these guidelines:
 1. The pull request should include tests.
 2. If the pull request adds functionality, the docs should be updated. Put
    your new functionality into a function with a `docstring`_.
-3. The pull request should work for Python 3.8
+3. The pull request should work for Python 3.8 and 3.9
    Check your Github Actions ``https://github.com/<your_name_here>/pyglotaran/actions``
    and make sure that the tests pass for all supported Python versions.
 

glotaran/analysis/scheme.py

@@ -202,29 +202,14 @@ def _prepare_data(self, data: dict[str, xr.DataArray | xr.Dataset]):
             dataset = self._transpose_dataset(dataset)
             self._add_weight(label, dataset)
 
-            # This protects transposing when getting data with svd in it
-            if "data_singular_values" in dataset and (
-                dataset.coords["right_singular_value_index"].size
-                != dataset.coords[self.model.global_dimension].size
-            ):
-                dataset = dataset.rename(
-                    right_singular_value_index="right_singular_value_indexTMP"
-                )
-                dataset = dataset.rename(left_singular_value_index="right_singular_value_index")
-                dataset = dataset.rename(right_singular_value_indexTMP="left_singular_value_index")
-                dataset = dataset.rename(right_singular_vectors="right_singular_value_vectorsTMP")
-                dataset = dataset.rename(
-                    left_singular_value_vectors="right_singular_value_vectors"
-                )
-                dataset = dataset.rename(
-                    right_singular_value_vectorsTMP="left_singular_value_vectors"
-                )
-            new_dims = [self.model.model_dimension, self.model.global_dimension]
-            new_dims += [
-                dim
-                for dim in dataset.dims
-                if dim not in [self.model.model_dimension, self.model.global_dimension]
-            ]
+            # TODO: avoid computation if not requested
+            l, s, r = np.linalg.svd(dataset.data, full_matrices=False)
+            dataset["data_left_singular_vectors"] = (("time", "left_singular_value_index"), l)
+            dataset["data_singular_values"] = (("singular_value_index"), s)
+            dataset["data_right_singular_vectors"] = (
+                ("right_singular_value_index", "spectral"),
+                r,
+            )
 
             self._data[label] = dataset
 

glotaran/builtin/models/kinetic_spectrum/spectral_penalties.py

@@ -128,9 +128,6 @@ def _get_area(
             start_idx, end_idx = _get_idx_from_interval(interval, global_axis)
             for i in range(start_idx, end_idx + 1):
                 index_clp_labels = clp_labels[label][i] if index_dependent else clp_labels[label]
-                if area and np.any(np.isclose(area_indices, global_axis[i], atol=group_tolerance)):
-                    # already got clp for this index
-                    continue
                 if compartment in index_clp_labels:
                     area.append(clps[label][i][index_clp_labels.index(compartment)])
                     area_indices.append(global_axis[i])

requirements_dev.txt

@@ -7,7 +7,7 @@ asteval==0.9.22
 numpy==1.20.1
 scipy==1.6.1
 click==7.1.2
-numba==0.52.0
+numba==0.53.0
 pandas==1.2.2
 pyyaml==5.4.1
 xarray==0.16.2

setup.cfg

@@ -17,6 +17,7 @@ classifiers =
     Operating System :: OS Independent
     Programming Language :: Python :: 3
     Programming Language :: Python :: 3.8
+    Programming Language :: Python :: 3.9
     Topic :: Scientific/Engineering
     Topic :: Scientific/Engineering :: Chemistry
     Topic :: Scientific/Engineering :: Physics
@@ -40,7 +41,7 @@ install_requires =
     sdtfile>=2020.8.3
     setuptools>=41.2
     xarray>=0.16.2
-python_requires = >=3.8, <3.9
+python_requires = >=3.8, <3.10
 setup_requires =
     setuptools>=41.2
 tests_require = pytest