updates setup.cfg and docs to python 3.10 (#124)

SINTEF · Aug 25, 2023 · c3f51fa · c3f51fa
1 parent e96cc61
commit c3f51fa
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Showing 7 changed files with 10 additions and 10 deletions.
diff --git a/docs/_config.yml b/docs/_config.yml
@@ -35,7 +35,7 @@ html:
 sphinx:
   extra_extensions:
   - 'sphinx.ext.autodoc'
-  - 'sphinxcontrib.napoleon'
+  - 'sphinx.ext.napoleon'
   - 'sphinx.ext.autosummary'
   config:
     autosummary_generate: True
diff --git a/docs/conf.py b/docs/conf.py
@@ -8,7 +8,7 @@
 comments_config = {'hypothesis': False, 'utterances': False}
 copyright = '2022'
 exclude_patterns = ['**.ipynb_checkpoints', '.DS_Store', 'Thumbs.db', '_build']
-extensions = ['sphinx_togglebutton', 'sphinx_copybutton', 'myst_nb', 'jupyter_book', 'sphinx_thebe', 'sphinx_comments', 'sphinx_external_toc', 'sphinx.ext.intersphinx', 'sphinx_design', 'sphinx_book_theme', 'sphinx.ext.autodoc', 'sphinxcontrib.napoleon', 'sphinx.ext.autosummary', 'sphinx_jupyterbook_latex']
+extensions = ['sphinx_togglebutton', 'sphinx_copybutton', 'myst_nb', 'jupyter_book', 'sphinx_thebe', 'sphinx_comments', 'sphinx_external_toc', 'sphinx.ext.intersphinx', 'sphinx_design', 'sphinx_book_theme', 'sphinx.ext.autodoc', 'sphinx.ext.napoleon', 'sphinx.ext.autosummary', 'sphinx_jupyterbook_latex']
 external_toc_exclude_missing = False
 external_toc_path = '_toc.yml'
 html_baseurl = ''

diff --git a/docs/environment.yml b/docs/environment.yml
@@ -2,12 +2,12 @@ name: pyopia
 channels:
     - conda-forge
 dependencies:    # These are the conda packages
-    - python=3.8
+    - python=3.10
     - pip
     - flake8
     - numpy>=1.20.1
     - pandas
-    - h5py=2.10.0
+    - h5py
     - pytables=3.6.1
     - scipy
     - scikit-image

diff --git a/pyopia/__init__.py b/pyopia/__init__.py
@@ -1 +1 @@
-__version__ = '0.0.55'
+__version__ = '0.0.56'
diff --git a/pyopia/instrument/holo.py b/pyopia/instrument/holo.py
@@ -221,7 +221,7 @@ def create_kernel(im, pixel_size, wavelength, n, offset, minZ, maxZ, stepZ):
 
     f = (np.pi / (pixel_size / 1e6)) * (f1**2 + f2**2)**0.5
 
-    z = (np.linspace(minZ * 1e-3, maxZ * 1e-3, np.int32((maxZ - minZ)/stepZ + 1)) / n) + (offset * 1e-3)
+    z = (np.arange(minZ * 1e-3, maxZ * 1e-3, stepZ * 1e-3) / n) + (offset * 1e-3)
 
     wavelength_m = wavelength * 1e-9
     k = 2 * np.pi / wavelength_m

diff --git a/pyopia/tests/test_pipeline.py b/pyopia/tests/test_pipeline.py
@@ -83,7 +83,7 @@ def test_holo_pipeline():
         print('stats header: ', stats.columns)
         print('Total number of particles: ', len(stats))
         assert len(stats) == 42, ('Number of particles expected in this test is 42.' +
-                                  'This test counted' + len(stats) +
+                                  'This test counted' + str(len(stats)) +
                                   'Something has altered the number of particles detected')
 
 
@@ -137,7 +137,7 @@ def test_silcam_pipeline():
         assert num_images == 1, ('Number of images expected is 1.' +
                                  'This test counted' + str(num_images))
         assert len(stats) == 870, ('Number of particles expected in this test is 870.' +
-                                   'This test counted' + len(stats) +
+                                   'This test counted' + str(len(stats)) +
                                    'Something has altered the number of particles detected')
 
 

diff --git a/setup.cfg b/setup.cfg
@@ -7,11 +7,11 @@ classifiers =
     Intended Audience :: Developers,
     Natural Language :: English,
     Programming Language :: Python :: 3,
-    Programming Language :: Python :: 3.8,
+    Programming Language :: Python :: 3.10,
 
 
 [options]
 packages = find:
-python_requires = >=3.8
+python_requires = >=3.10
 setup_requires =
     setuptools_scm