CI-CD

.github/workflows/python-app.yml

@@ -5,9 +5,9 @@ name: Python application
 
 on:
   push:
-    branches: [ "master", "develop"]
+    branches: [ "main", "develop", "CI-CD"]
   pull_request:
-    branches: [ "master", "develop"]
+    branches: [ "main", "develop"]
 
 permissions:
   contents: read
@@ -19,22 +19,27 @@ jobs:
 
     steps:
     - uses: actions/checkout@v4
+
     - name: Set up Python 3.11
       uses: actions/setup-python@v3
       with:
         python-version: "3.11"
+
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install flake8 pytest
-        # if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
-        pip install .
-    - name: Lint with flake8
-      run: |
-        # stop the build if there are Python syntax errors or undefined names
-        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+        pip install .[test] ruff
+
+    - name: Lint - fail on real issues
+      run: ruff check . --select F,E9
+
+    - name: Lint - style (non-blocking)
+      run: ruff check . --select E,B,I || true
+
+    ## ADD LATER
+    # - name: Format check
+    #   run: ruff format --check .
+
     - name: Test with pytest
       run: |
         pytest

.gitignore

@@ -28,6 +28,17 @@ build/
 *.tar
 *.zip
 
+# Unit test / coverage reports #
+################################
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.*
+*,cover
+
 # Logs and databases #
 ######################
 *.ipynb_checkpoints

.pre-commit-config.yaml

@@ -0,0 +1,25 @@
+
+default_language_version:
+  python: python3.11
+
+repos:
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.4.4
+    hooks:
+      - id: ruff
+        args: [--fix]
+      - id: ruff-format
+
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.6.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml
+      - id: check-toml
+      - id: debug-statements
+
+  - repo: https://github.com/rhysd/actionlint
+    rev: v1.7.0
+    hooks:
+      - id: actionlint

docs/source/conf.py

@@ -7,8 +7,6 @@
 import sys
 sys.path.insert(0, os.path.abspath('../../src/perpl'))  # Adjust to include your package
 
-import sphinx_rtd_theme
-
 # -- Project information -----------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
 

notebooks/make_ACTN2_Affimer_PERPL_plots.py

@@ -6,7 +6,7 @@
 #       extension: .py
 #       format_name: light
 #       format_version: '1.5'
-#       jupytext_version: 1.19.2
+#       jupytext_version: 1.19.3
 #   kernelspec:
 #     display_name: Python 3 (ipykernel)
 #     language: python
@@ -24,9 +24,10 @@
 # ## Imports
 
 import numpy as np
-import pandas as pd
+# import pandas as pd
 import matplotlib.pyplot as plt
-from perpl.modelling import modelling_general, zdisk_modelling, zdisk_plots
+from perpl.modelling import zdisk_modelling, zdisk_plots
+# from perpl.modelling import modelling_general
 from perpl.io import plotting
 
 # ## Set average estimated localisation precision for Affimer and PALM data.

notebooks/make_Nup107_Z_PERPL_plots.py

@@ -6,7 +6,7 @@
 #       extension: .py
 #       format_name: light
 #       format_version: '1.5'
-#       jupytext_version: 1.17.1
+#       jupytext_version: 1.19.3
 #   kernelspec:
 #     display_name: Python 3 (ipykernel)
 #     language: python
@@ -29,7 +29,6 @@
 import matplotlib.pyplot as plt
 
 from perpl.modelling import modelling_general, two_layer_fitting, background_models
-from perpl.statistics import modelstats
 from perpl.statistics.modelstats import akaike_weights
 # -
 
@@ -165,7 +164,6 @@
 weights = akaike_weights([1.])
 print(weights)
 
-# + [markdown] jp-MarkdownHeadingCollapsed=true
 # ## Plot model components
 
 # +

notebooks/make_mEos_LASP2andMYPN_PERPL_plots.py

@@ -6,7 +6,7 @@
 #       extension: .py
 #       format_name: light
 #       format_version: '1.5'
-#       jupytext_version: 1.17.1
+#       jupytext_version: 1.19.3
 #   kernelspec:
 #     display_name: Python 3 (ipykernel)
 #     language: python
@@ -27,7 +27,7 @@
 import numpy as np
 import matplotlib.pyplot as plt
 
-from perpl.modelling import modelling_general, zdisk_modelling, zdisk_plots
+from perpl.modelling import zdisk_modelling, zdisk_plots
 from perpl.io import plotting
 # -
 

pyproject.toml

@@ -2,12 +2,9 @@
 requires = ["setuptools>=64.0", "setuptools-scm>=8.0"]
 build-backend = "setuptools.build_meta"
 
-[tool.setuptools_scm]
-
 [project]
 name = "perpl"
 version = "1.3.0"
-# dynamic = ["version"]
 authors = [
     { name="Alistair Curd", email="[email protected]" }
 ]
@@ -41,4 +38,28 @@ modeldistances = "perpl.run_distance_modelling:main"
 Homepage = "https://github.com/AlistairCurd/PERPL-Python3"
 Issues = "https://github.com/AlistairCurd/PERPL-Python3/issues"
 
-# [tool.tox], [tox] ?
+
+[project.optional-dependencies]
+test = [
+    "pytest~=8.0",
+    "pytest-cov~=5.0"
+]
+
+dev = [
+    "perpl[test]",
+    "ruff~=0.4",
+    "pre-commit~=3.7"
+]
+
+[tool.pytest.ini_options]
+addopts = "-v --color=yes --cov=perpl --cov-report=term --cov-report=xml --cov-report=html"
+
+[tool.ruff]
+line-length = 88
+target-version = "py311"
+
+[tool.ruff.lint]
+select = ["E", "F", "B", "I"]
+
+[tool.ruff.format]
+quote-style = "double"

src/perpl/modelling/centriole_analysis.py

@@ -24,16 +24,17 @@
 """
 
 import time
-from scipy.ndimage.filters import gaussian_filter
-from scipy.io import loadmat
-import numpy as np
+
 import matplotlib.pyplot as plt
+import numpy as np
 import pandas as pd
+from scipy.io import loadmat
+from scipy.ndimage.filters import gaussian_filter
 
 import perpl.modelling.modelling_general as models
-from perpl.modelling.modelling_general import ModelWithFitSettings
-from relative_positions import getdistances
 from perpl.modelling.background_models import pair_correlation_disk
+from perpl.modelling.modelling_general import ModelWithFitSettings
+from perpl.relative_positions import getdistances
 
 
 def get_input_data(
@@ -1030,7 +1031,7 @@ def make_fit_results_table_variable_vertices_model_9fold_no_bg(
     # Populate the tables
     max_fit_distance = len(distance_histograms_list[0])
 
-    for i, histogram in enumerate(distance_histograms_list):
+    for i, _ in enumerate(distance_histograms_list):
         # Do the fit
         (params_optimised, params_covar, params_1sd_error) = (
             models.fit_model_to_experiment(
@@ -1158,7 +1159,8 @@ def main():
     np.save(outfile_dist_hist_list, distance_histograms_list)
 
     # Choose model
-    # model_with_info = set_up_variable_vertices_model_9fold_internal_bg_with_fit_settings()
+    # model_with_info = \
+    #   set_up_variable_vertices_model_9fold_internal_bg_with_fit_settings()
     model_with_info = set_up_variable_vertices_model_9fold_no_bg_with_fit_settings()
 
     # Could modify the fit parameter settings here
@@ -1217,7 +1219,8 @@ def main():
         )
     )
     #     estimated_params_df.to_csv(
-    #         'C:/Temp/Centriole/5nm_precision_distance_histograms_normalised_parameter_estimates.csv',
+    #         "C:/Temp/Centriole/"
+    #         + "5nm_precision_distance_histograms_normalised_parameter_estimates.csv",
     #         index=False
     #         )
 
@@ -1258,14 +1261,14 @@ def main():
         #                       model_with_info.vector_input_model)
 
         # For model without internal background
-        stdev = plot_95_ci(
-            axes,
-            x_values,
-            model_with_info.model_rpd,
-            params_optimised,
-            params_covar,
-            model_with_info.vector_input_model,
-        )
+        # stdev = plot_95_ci(
+        #    axes,
+        #    x_values,
+        #    model_with_info.model_rpd,
+        #    params_optimised,
+        #    params_covar,
+        #    model_with_info.vector_input_model,
+        #)
         axes.set_title(
             "Centriole "
             + repr(i)
@@ -1309,14 +1312,14 @@ def main():
     fitted_curve_values = model_with_info.model_rpd(x_values, *params_optimised)
     axes.plot(x_values, fitted_curve_values, color="xkcd:red", lw=0.5)
 
-    stdev = plot_95_ci(
-        axes,
-        x_values,
-        model_with_info.model_rpd,
-        params_optimised,
-        params_covar,
-        model_with_info.vector_input_model,
-    )
+    # stdev = plot_95_ci(
+    #    axes,
+    #    x_values,
+    #    model_with_info.model_rpd,
+    #    params_optimised,
+    #    params_covar,
+    #    model_with_info.vector_input_model,
+    #)
     axes.set_title("All centrioles")
 
 

src/perpl/modelling/dna_paint_data_fitting.py

@@ -32,14 +32,17 @@
 
 """
 
-from scipy.optimize import curve_fit
-import numpy as np
 import matplotlib.pyplot as plt
+import numpy as np
+from scipy.optimize import curve_fit
+
+import perpl.modelling.modelling_general as models
 import perpl.modelling.polyhedramodelling as poly
 import perpl.statistics.modelstats as stats
-import perpl.modelling.modelling_general as models
-from perpl.modelling.modelling_general import ModelWithFitSettings
-from perpl.modelling.modelling_general import stdev_of_model
+from perpl.modelling.modelling_general import (
+    ModelWithFitSettings,
+    stdev_of_model,
+)
 
 
 def create_default_fitting_params_dicts():
@@ -937,7 +940,7 @@ def plot_model_components_tri_prism(
     """
     distance_values = np.arange(0, fitlength + 1, 1)
 
-    fig = plt.figure()
+    fig = plt.figure()  # noqa: F841  # Prefer OO style, but not worth changing atm.
     axes = plt.subplot(111)
     axes.set_xlim([0, fitlength])
     axes.set_xlabel(r"$\Delta$XYZ (nm)")

src/perpl/modelling/zdisk_plots.py

@@ -22,27 +22,27 @@
 specific language governing permissions and limitations under the License.
 """
 
+import matplotlib.pyplot as plt
 import numpy as np
 import pandas as pd
-import matplotlib.pyplot as plt
 from scipy.signal import find_peaks
 
 import perpl.modelling.linearrepeatmodels as linmods
 import perpl.modelling.zdisk_modelling as zdisk_modelling
-from perpl.modelling.modelling_general import kde_1nm
-from perpl.modelling.modelling_general import pairwise_correlation_1d
-from perpl.modelling.modelling_general import stdev_of_model
 from perpl.io.plotting import estimate_rpd_churchman_1d
-from perpl.modelling.zdisk_modelling import read_relpos_from_pickles
-from perpl.modelling.zdisk_modelling import getaxialseparations_no_smoothing
-from perpl.modelling.zdisk_modelling import remove_duplicates
-from perpl.modelling.zdisk_modelling import (
-    set_up_model_4_variable_peaks_with_fit_settings,
+from perpl.modelling.modelling_general import (
+    kde_1nm,
+    pairwise_correlation_1d,
+    stdev_of_model,
 )
 from perpl.modelling.zdisk_modelling import (
+    fitmodel_to_hist,
+    getaxialseparations_no_smoothing,
+    # read_relpos_from_pickles,
+    remove_duplicates,
+    # set_up_model_4_variable_peaks_with_fit_settings,
     set_up_model_5_variable_peaks_with_fit_settings,
 )
-from perpl.modelling.zdisk_modelling import fitmodel_to_hist
 
 
 def plot_distance_hist(
@@ -80,7 +80,7 @@ def plot_distance_hist(
     histaxes.set_ylim(bottom=0)
     histaxes.set_title("Histogram")
     histaxes.set_xlabel(
-        f"$\Delta$Axial (nm) ($\Delta$Transverse < {transverse_limit} nm)"
+        rf"$\Delta$Axial (nm) ($\Delta$Transverse < {transverse_limit} nm)"
     )
     histaxes.set_ylabel("Counts")
     if close_plots: