BioLizardStylePython 2.0.0__tar.gz → 2.0.1__tar.gz

{biolizardstylepython-2.0.0 → biolizardstylepython-2.0.1}/CHANGELOG.md

@@ -2,13 +2,22 @@
 
 <!--next-version-placeholder-->
 
+## v2.0.1
+big fixes issue [#34](https://github.com/lizard-bio/nature-grade-visualization-playground/issues/34) and [#33](https://github.com/lizard-bio/nature-grade-visualization-playground/issues/33)
+
+### Fix
+
+- remove matplotlib cache clearing at __init__.py, issue [#34](https://github.com/lizard-bio/nature-grade-visualization-playground/issues/34)
+- always use lato from lato-font package, instead of searcing for local lato installation 
+- Add seaborn as a dependency and define optional dev dependencies issue [#33](https://github.com/lizard-bio/nature-grade-visualization-playground/issues/33)
+
 ## v2.0.0 (2025-03-06)
 
 Plotly layout and improved color scales.
 
 ### Breaking changes
 
-- Make sure all discrete colorscales and all continuous colorscales behave the same way, i.e. calling a discrete palette returns a `matplotlib.colors.ListedColormap` object, and all continuous palettes now return a `matplotlib.colors.LinearSegmentedColormap` object.
+- Make sure all discrete colorscales and all continuous colorscales behave the same way, i.e. calling a discrete palette returns a `matplotlib.colors.ListedColormap` object, and all continuous palettes now return a `matplotlib.colors.LinearSegmentedColormap` object. issue #23 
 
 ### Feature
 
@@ -16,12 +25,12 @@ Plotly layout and improved color scales.
     - viridis-like continuous colorscale "l_viridis"
     - colorscale for paired discrete data
     - hues colorscale for discrete data with many levels
-- plotly template for interactive graphs with plotly express and plotly graph objects
+- plotly template for interactive graphs with plotly express and plotly graph objects, issue #6 
 
 ### Fix
 
-- adjust discrete palette to avoid dark colors that are hard to distinguish from each other + extend to 10 colors
-- Make sure all discrete colorscales and all continuous colorscales behave the same way, i.e. calling a discrete palette returns a `matplotlib.colors.ListedColormap` object, and all continuous palettes now return a `matplotlib.colors.LinearSegmentedColormap` object.
+- adjust discrete palette to avoid dark colors that are hard to distinguish from each other + extend to 10 colors, issue #15
+- Make sure all discrete colorscales and all continuous colorscales behave the same way, i.e. calling a discrete palette returns a `matplotlib.colors.ListedColormap` object, and all continuous palettes now return a `matplotlib.colors.LinearSegmentedColormap` object. issue #23 
 
 ### Tests
 
@@ -31,7 +40,8 @@ Plotly layout and improved color scales.
 
 - added plotly docs
 - added extra info about the colorscales and how to intereact with them
-- restructure examples notebook: separate sections for seaborn and matplotlib 
+- restructure examples notebook: separate sections for seaborn and matplotlib
+- added colorspace package to dependencies instead of manual installation through git, issue #26 
 
 
 ## v.1.0.0 (2024-09-25)

{biolizardstylepython-2.0.0 → biolizardstylepython-2.0.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: BioLizardStylePython
-Version: 2.0.0
+Version: 2.0.1
 Summary: Enhance plots with the signature Biolizard aesthetic for matplotlib and seaborn.
 Project-URL: Homepage, https://github.com/lizard-bio/nature-grade-visualization-playground/tree/main
 Author: Robbe Neirynck
@@ -17,6 +17,11 @@ Requires-Dist: fonts>=0.0.3
 Requires-Dist: matplotlib>=3.7.1
 Requires-Dist: pillow>=9.4.0
 Requires-Dist: plotly>=5.20.0
+Requires-Dist: seaborn>=0.13.2
+Requires-Dist: setuptools>=78.1.0
+Provides-Extra: dev
+Requires-Dist: numpy>=2.2.4; extra == 'dev'
+Requires-Dist: pytest>=8.3.5; extra == 'dev'
 Description-Content-Type: text/markdown
 
 # BioLizardStylePython

{biolizardstylepython-2.0.0 → biolizardstylepython-2.0.1}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "BioLizardStylePython"
-version = "2.0.0"
+version = "2.0.1"
 authors = [
   { name = "BioLizard", email = "contact@lizard.bio"},
   { name = "Aniko Meijer", email = "aniko.meijer@lizard.bio"},
@@ -28,14 +28,21 @@ classifiers = [
 
 dependencies = [
     "matplotlib>=3.7.1",
+    "seaborn>=0.13.2",
     "Pillow>=9.4.0",
     "fonts>=0.0.3",
     "font-lato>=0.1.0",
-#    "deprecated>=1.2.0",
+    #    "deprecated>=1.2.0",
     "colorspace>=0.4.0",
-    "plotly>=5.20.0"
+    "plotly>=5.20.0",
+    "setuptools>=78.1.0",
 ]
 
+[project.optional-dependencies]
+dev = [
+    "pytest>=8.3.5",
+    "numpy>=2.2.4",
+]
 
 [project.urls]
 "Homepage" = "https://github.com/lizard-bio/nature-grade-visualization-playground/tree/main"

biolizardstylepython-2.0.1/src/BioLizardStylePython/__init__.py

@@ -0,0 +1,45 @@
+# check if colorspace installed
+try:
+    import colorspace
+except ModuleNotFoundError:
+    print('Could not find colorspace module. Install with `pip install git+https://github.com/retostauffer/python-colorspace.git`')
+    raise
+
+# clear matplotlib cache to make sure lato font is recognized
+import matplotlib as mpl
+# import os
+# import glob
+# import warnings
+
+# for f in glob.glob(mpl.get_cachedir() + '/*'):
+#     try:
+#         os.remove(f)
+#     except PermissionError:
+#         warnings.warn(f"Permission denied: {f}", UserWarning)
+
+
+# # # check if lato font installed and install if needed
+# from matplotlib import font_manager
+# fonts = font_manager.fontManager.ttflist
+# font_names = [font.name for font in fonts if 'lato' in font.name.lower()]
+# font_names = set(font_names)
+
+
+# if len(font_names) == 0:
+#     from fonts.ttf import Lato, LatoBold
+#     font_manager.fontManager.addfont(Lato)  #  adds a custom font from a file without installing it into the operating system
+#     font_manager.fontManager.addfont(LatoBold)
+#     prop = font_manager.FontProperties(fname=Lato)
+#     lato_localname = prop.get_name()
+# else:
+#     lato_localname = font_names.pop()  #pick first one, usually there should only be one.. (?)
+
+from matplotlib import font_manager
+from fonts.ttf import Lato, LatoBold
+font_manager.fontManager.addfont(Lato)  #  adds a custom font from a file without installing it into the operating system
+font_manager.fontManager.addfont(LatoBold)
+# prop = font_manager.FontProperties(fname=Lato)
+# lato_localname = prop.get_name()
+
+from .utils import *
+from .plotly_template import *

{biolizardstylepython-2.0.0 → biolizardstylepython-2.0.1}/src/BioLizardStylePython/plotly_template.py

@@ -1,6 +1,7 @@
 import plotly.graph_objects as go
 import plotly.io as pio
 import matplotlib.colors
+from fonts.ttf import Lato, LatoBold
 from .utils import biolizard_qualitative_pal, biolizard_divergent_pal, l_viridis_pal, blz_blue, blz_green
 
 lizard_style_template = go.layout.Template()
@@ -16,7 +17,7 @@ lizard_style_template.layout = {
                    'sequential': [matplotlib.colors.rgb2hex(l_viridis_pal(i)) for i in range(255)],
                    'sequentialminus': [matplotlib.colors.rgb2hex(l_viridis_pal.reversed()(i)) for i in range(255)]},
     'colorway': biolizard_qualitative_pal.colors,
-    'font': {'family': 'Lato', 'size': 12},
+    'font': {'family': Lato, 'size': 12},
     'geo': {'bgcolor': blz_blue,
             'oceancolor': blz_blue,
             'lakecolor': blz_blue,
@@ -113,7 +114,7 @@ lizard_style_template.layout = {
                           'showline': True,
                           'ticks': 'outside',
                           'exponentformat': 'power'}},
-    'title': {'x': 0.05, 'font': {'family': 'Lato Black', 'size': 16, 'color': '#222222'}},
+    'title': {'x': 0.05, 'font': {'family': LatoBold, 'size': 16, 'color': '#222222'}},
     'violinmode' : 'group',
     'waterfallmode': 'group',
     'xaxis': {'automargin': True,
@@ -125,7 +126,7 @@ lizard_style_template.layout = {
               'showgrid': False,
               'showline': True,
               'ticks': 'outside',
-              'title': {'standoff': 15, 'font': {'family': 'Lato', 'size': 14, 'color': '#222222'}},
+              'title': {'standoff': 15, 'font': {'family': Lato, 'size': 14, 'color': '#222222'}},
               'zeroline': False,
               'zerolinecolor': '#808080',
               'exponentformat': 'power'},
@@ -138,7 +139,7 @@ lizard_style_template.layout = {
               'showgrid': False,
               'showline': True,
               'ticks': 'outside',
-              'title': {'standoff': 15, 'font': {'family': 'Lato', 'size': 14, 'color': '#222222'}},
+              'title': {'standoff': 15, 'font': {'family': Lato, 'size': 14, 'color': '#222222'}},
               'zeroline': False,
               'zerolinecolor': '#808080',
               'exponentformat': 'power'},

{biolizardstylepython-2.0.0 → biolizardstylepython-2.0.1}/src/BioLizardStylePython/utils.py

@@ -37,8 +37,8 @@ def lizard_style(plotly=False):
     """
     style_path = os.path.join(os.path.dirname(__file__), 'lizard_style.mplstyle')
     plt.style.use(style_path)
-    from BioLizardStylePython import lato_localname
-    plt.rcParams['font.sans-serif'] = [lato_localname]
+    # from BioLizardStylePython import lato_localname
+    # plt.rcParams['font.sans-serif'] = [lato_localname]
 
     if plotly:
         import plotly.io as pio

biolizardstylepython-2.0.0/src/BioLizardStylePython/__init__.py

@@ -1,32 +0,0 @@
-# check if colorspace installed
-try:
-    import colorspace
-except ModuleNotFoundError:
-    print('Could not find colorspace module. Install with `pip install git+https://github.com/retostauffer/python-colorspace.git`')
-    raise
-
-# clear matplotlib cache to make sure lato font is recognized
-import matplotlib as mpl
-import os, glob
-for f in glob.glob(mpl.get_cachedir() + '/*'):
-    os.remove(f)
-
-
-# # check if lato font installed and install if needed
-from matplotlib import font_manager
-fonts = font_manager.fontManager.ttflist
-font_names = [font.name for font in fonts if 'lato' in font.name.lower()]
-font_names = set(font_names)
-
-
-if len(font_names) == 0:
-    from fonts.ttf import Lato, LatoBold
-    font_manager.fontManager.addfont(Lato)  #  adds a custom font from a file without installing it into the operating system
-    font_manager.fontManager.addfont(LatoBold)
-    prop = font_manager.FontProperties(fname=Lato)
-    lato_localname = prop.get_name()
-else:
-    lato_localname = font_names.pop()  #pick first one, usually there should only be one.. (?)
-
-from .utils import *
-from .plotly_template import *