From 0b2c7f7fbb1aff50cc1126e7a92abbc62d73ed72 Mon Sep 17 00:00:00 2001
From: "Jose M. Pizarro" <112697669+JosePizarro3@users.noreply.github.com>
Date: Mon, 10 Jun 2024 11:18:37 +0200
Subject: [PATCH] Hotfixes coverage (#18)

* Fixing pipeline and README

* Moved utils to its own folder

Fixed imports
---
 .github/workflows/actions.yml   |  1 +
 README.md                       |  2 +-
 src/pyssmf/hopping_pruning.py   |  2 +-
 src/pyssmf/parsing.py           |  4 ++--
 src/pyssmf/runner.py            | 12 ++++++------
 src/pyssmf/tb_hamiltonian.py    |  3 ++-
 src/pyssmf/utils/__init__.py    | 17 +++++++++++++++++
 src/pyssmf/{ => utils}/utils.py |  0
 src/pyssmf/visualization.py     |  1 -
 9 files changed, 30 insertions(+), 12 deletions(-)
 create mode 100644 src/pyssmf/utils/__init__.py
 rename src/pyssmf/{ => utils}/utils.py (100%)

diff --git a/.github/workflows/actions.yml b/.github/workflows/actions.yml
index eec681a..1aea2b6 100644
--- a/.github/workflows/actions.yml
+++ b/.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: |
diff --git a/README.md b/README.md
index 5006e71..bfd96d2 100644
--- a/README.md
+++ b/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
diff --git a/src/pyssmf/hopping_pruning.py b/src/pyssmf/hopping_pruning.py
index 51486c2..52dc715 100644
--- a/src/pyssmf/hopping_pruning.py
+++ b/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:
diff --git a/src/pyssmf/parsing.py b/src/pyssmf/parsing.py
index f70fda2..caba1ac 100644
--- a/src/pyssmf/parsing.py
+++ b/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]'
 
diff --git a/src/pyssmf/runner.py b/src/pyssmf/runner.py
index 2036442..bb75baf 100644
--- a/src/pyssmf/runner.py
+++ b/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):
diff --git a/src/pyssmf/tb_hamiltonian.py b/src/pyssmf/tb_hamiltonian.py
index f9b8191..fd703e8 100644
--- a/src/pyssmf/tb_hamiltonian.py
+++ b/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:
diff --git a/src/pyssmf/utils/__init__.py b/src/pyssmf/utils/__init__.py
new file mode 100644
index 0000000..b9bdc0e
--- /dev/null
+++ b/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
diff --git a/src/pyssmf/utils.py b/src/pyssmf/utils/utils.py
similarity index 100%
rename from src/pyssmf/utils.py
rename to src/pyssmf/utils/utils.py
diff --git a/src/pyssmf/visualization.py b/src/pyssmf/visualization.py
index f6e58c8..e7b4782 100644
--- a/src/pyssmf/visualization.py
+++ b/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