🎨🐛 Add mock import of modules and link to contribution guidelines (fixes #22)

.readthedocs.yaml

@@ -10,11 +10,5 @@ sphinx:
 
 # Optionally build your docs in additional formats such as PDF and ePub
 formats: all
-
-python:
-  version: 3.7
-  install:
-    - requirements: docs/requirements.txt
-
-
+
 

autometa/common/markers.py

@@ -255,18 +255,18 @@ def main():
         datefmt='%m/%d/%Y %I:%M:%S %p',
         level=logger.DEBUG)
     parser = argparse.ArgumentParser(
-        description='Annotate ORFs with kingdom-marker information',
-        formatter_class=argparse.ArgumentDefaultsHelpFormatter)
+        description='Annotate ORFs with kingdom-marker information')
     parser.add_argument('orfs',
-        help='Path to a fasta file containing amino acid sequences of open reading frames')
+                        help='Path to a fasta file containing amino acid sequences of open reading frames')
     parser.add_argument('--kingdom', help='kingdom to search for markers',
-        choices=['bacteria', 'archaea'], default='bacteria')
+                        choices=['bacteria', 'archaea'], default='bacteria')
     parser.add_argument('--dbdir',
-        help='Path to directory containing the single-copy marker HMM databases.',
-        default=MARKERS_DIR)
-    args=parser.parse_args()
+                        help='Path to directory containing the single-copy marker HMM databases.',
+                        default=MARKERS_DIR)
+    args = parser.parse_args()
 
-    markers=Markers(orfs_fpath=args.orfs, kingdom=args.kingdom, dbdir=args.dbdir)
+    markers = Markers(orfs_fpath=args.orfs,
+                      kingdom=args.kingdom, dbdir=args.dbdir)
 
     markers.get()
 

docs/source/conf.py

@@ -16,8 +16,8 @@
 
 for dirpath, dirnames, filenames in os.walk('../../', topdown=True):
     sys.path.insert(0, os.path.abspath(dirpath))
-    
-#autodoc_mock_imports = ["Bio","hdbscan", "sklearn","umap", "tqdm"]
+
+autodoc_mock_imports = ["Bio", "hdbscan", "tsne", "sklearn", "umap", "tqdm"]
 
 import parse_argparse  # nopep8
 

docs/source/contribution-guidelines.rst

@@ -1,5 +1,7 @@
 =======================
-Contribution Guidelines
+Contributing Guidelines
 =======================
 
-.. todo:: Guidelines about how to contribute
+"Autometa is an open-source project developed on 
+GitHub. If you would like to help develop Autometa or 
+have ideas for new features please see our `contributing guidelines <https://github.com/KwanLab/Autometa/blob/master/.github/CONTRIBUTING.md>`__