docs: populate autodock_mock_imports with all modules

anchorna/io.py

@@ -165,14 +165,12 @@ def _make_rgb_transparent(rgb, bg_rgb, alpha):
             for (c1, c2) in zip(to_rgb(rgb), to_rgb(bg_rgb))]
 
 
-cols = list(mcolors.TABLEAU_COLORS.values())
-to_hex(cols[0], 0.3)
-
 def jalview_features(anchors, mode='aa', score_use_fluke=None):
     """
     Write anchors to Jalview feature file
     """
     assert mode in ('nt', 'cds', 'aa')
+    cols = list(mcolors.TABLEAU_COLORS.values())
     anchors = sorted(anchors, key=lambda a: a.guide.start)
     content = []
     header = []

docs/conf.py

@@ -1,36 +1,44 @@
 # Configuration file for the Sphinx documentation builder.
-# Build doc locally with with
+# Build doc locally with
 # sphinx-build -anE -c . src _build
 
-import sys
-import os
-
-os.environ['SPHINX_BUILD'] = '1'
-
-
-def version():
+def parse_version():
     from pathlib import Path
     import re
     init_path = Path(__file__).parent.parent / 'anchorna/__init__.py'
     with open(init_path) as f:
         content = f.read()
-    match = re.search("""__version__\s*=\s*['"]([^\s]+)['"]""", content)
+    regex = r"""__version__\s*=\s*['"]([^\s]+)['"]"""
+    match = re.search(regex, content)
     if match:
         return match.group(1)
 
 
+def parse_imports():
+    from pathlib import Path
+    import re
+    root_path = Path(__file__).parent.parent / 'anchorna/'
+    root_path = Path('/home/gi48zar/dev/anchorna/anchorna/')
+    regex = r'^\s*import\s+(\w+)(?:.\w+)*|^\s*from\s+(\w+)(?:.\w+)*\s+import'
+    modules = set()
+    for fname in root_path.glob('**/*.py'):
+        with open(fname) as f:
+            content = f.read()
+        for match in re.finditer(regex, content, flags=re.MULTILINE):
+            modules |= set(match.groups())
+    modules -= {None, 'anchorna'}
+    return sorted(modules)
+
+
 project = 'AnchoRNA'
 copyright = '2024, Tom Eulenfeld'
 author = 'Tom Eulenfeld'
-version = version()
+version = parse_version()
 
-### General configuration
-# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
 default_role = 'py:obj'
 templates_path = ['_templates']
 exclude_patterns = ['_build']
 
-# Add any Sphinx extension module names here
 extensions = ['sphinx.ext.autodoc',
               'sphinx.ext.autosummary',
               'sphinx.ext.intersphinx',
@@ -43,11 +51,11 @@ def version():
     'private-members': True,
     'show-inheritance': True,
 }
+autodoc_mock_imports = parse_imports()
+print(f'set {autodoc_mock_imports=}')
 
-autodoc_mock_imports = ['sugar', 'tqdm']
-
-html_theme = 'furo'
 html_title = f'AnchoRNA <br>v{version} <br>documentation'
+html_theme = 'furo'
 html_theme_options = {
     'footer_icons' : [],
     'top_of_page_buttons': [],