Hotfixes coverage (#18)

* Fixing pipeline and README

* Moved utils to its own folder

Fixed imports

.github/workflows/actions.yml

@@ -21,6 +21,7 @@ jobs:
       - name: Install dependencies
         run: |
           pip install uv
+          uv pip install coveralls --system
           uv pip install '.[dev]' --system
       - name: mypy
         run: |

README.md

@@ -49,7 +49,7 @@ Our CI/CD pipeline produces a more comprehensive test report using `coverage` an
 
 ```sh
 uv pip install coverage coveralls
-python -m pytest --cov=src  tests
+python -m pytest --cov=src tests
 ```
 
 ### Run linting and auto-formatting

src/pyssmf/hopping_pruning.py

@@ -17,7 +17,7 @@
 import numpy as np
 import logging
 
-from .schema import Model
+from pyssmf.schema import Model
 
 
 class Pruner:

src/pyssmf/parsing.py

@@ -23,8 +23,8 @@
 from nomad.units import ureg
 
 # NOMAD schema
-from .schema import System, BravaisLattice, Model
-from .utils import get_files
+from pyssmf.schema import System, BravaisLattice, Model
+from pyssmf.utils import get_files
 
 re_n = r'[\n\r]'
 

src/pyssmf/runner.py

@@ -18,12 +18,12 @@
 import os
 from scipy.stats import norm
 
-from .input import ValidLatticeModels
-from .schema import Model
-from .parsing import MinimalWannier90Parser, ToyModels
-from .hopping_pruning import Pruner
-from .tb_hamiltonian import TBHamiltonian
-from .visualization import plot_hopping_matrices, plot_band_structure, plot_dos
+from pyssmf.input import ValidLatticeModels
+from pyssmf.schema import Model
+from pyssmf.parsing import MinimalWannier90Parser, ToyModels
+from pyssmf.hopping_pruning import Pruner
+from pyssmf.tb_hamiltonian import TBHamiltonian
+from pyssmf.visualization import plot_hopping_matrices, plot_band_structure, plot_dos
 
 
 class Runner(ValidLatticeModels):

src/pyssmf/tb_hamiltonian.py

@@ -22,7 +22,8 @@
 
 from nomad.atomutils import Formula
 from nomad.units import ureg
-from .schema import Model
+
+from pyssmf.schema import Model
 
 
 class KSampling:

src/pyssmf/utils/__init__.py

@@ -0,0 +1,17 @@
+#
+# Copyright: Dr. José M. Pizarro.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+
+from .utils import get_files, extract_hdf5_dataset

src/pyssmf/visualization.py

@@ -15,7 +15,6 @@
 #
 
 import numpy as np
-import PyQt5  # noqa: F401
 
 import matplotlib.pyplot as plt
 from matplotlib.widgets import Slider