Merge pull request #34 from BojarLab/dev

merge for version update
BojarLab · Jan 31, 2024 · d7502e9 · d7502e9
2 parents 40b04d7 + 4d5cd61
commit d7502e9
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Showing 64 changed files with 43,093 additions and 72,782 deletions.
diff --git a/00_core.ipynb b/00_core.ipynb
diff --git a/01_glycan_data.ipynb b/01_glycan_data.ipynb
diff --git a/02_ml.ipynb b/02_ml.ipynb
diff --git a/03_motif.ipynb b/03_motif.ipynb
diff --git a/04_network.ipynb b/04_network.ipynb
diff --git a/05_examples.ipynb b/05_examples.ipynb
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -36,12 +36,13 @@ nbdev_prepare
 * Docs are automatically created from the notebooks in the nbs folder.
 
 
-## Wishlist for future glycowork updates (last update: 2023-12-04)
+## Wishlist for future glycowork updates (last update: 2024-01-31)
 #### Urgent
 * more, and more informative, error messages
 
 
 #### At some point
+* any further expansion of our universal input pipeline, to cover more usecases etc.
 * split motif_list into ‘core’ motifs (occurring frequently) and ‘extended’ motifs (that are rare or niche) for performance reasons
 * characterize_monosaccharide only factors in subsequent sequence context; make it possible (as an option) to also consider upstream sequence context
 * allow users to specify their own deep learning architecture in ml.models

diff --git a/README.md b/README.md
diff --git a/_proc/.quarto/xref/INDEX b/_proc/.quarto/xref/INDEX
@@ -1,5 +1,5 @@
 {
   "index.ipynb": {
-    "README.md": "f518931d"
+    "README.md": "1bce5a52"
   }
 }
diff --git a/_proc/00_core.ipynb b/_proc/00_core.ipynb
diff --git a/_proc/01_glycan_data.ipynb b/_proc/01_glycan_data.ipynb
diff --git a/_proc/02_ml.ipynb b/_proc/02_ml.ipynb
diff --git a/_proc/03_motif.ipynb b/_proc/03_motif.ipynb
diff --git a/_proc/04_network.ipynb b/_proc/04_network.ipynb
diff --git a/_proc/05_examples.ipynb b/_proc/05_examples.ipynb
diff --git a/_proc/CONTRIBUTING.md b/_proc/CONTRIBUTING.md
@@ -36,12 +36,13 @@ nbdev_prepare
 * Docs are automatically created from the notebooks in the nbs folder.
 
 
-## Wishlist for future glycowork updates (last update: 2023-12-04)
+## Wishlist for future glycowork updates (last update: 2024-01-31)
 #### Urgent
 * more, and more informative, error messages
 
 
 #### At some point
+* any further expansion of our universal input pipeline, to cover more usecases etc.
 * split motif_list into ‘core’ motifs (occurring frequently) and ‘extended’ motifs (that are rare or niche) for performance reasons
 * characterize_monosaccharide only factors in subsequent sequence context; make it possible (as an option) to also consider upstream sequence context
 * allow users to specify their own deep learning architecture in ml.models

diff --git a/_proc/_docs/index_files/figure-commonmark/cell-3-output-1.svg b/_proc/_docs/index_files/figure-commonmark/cell-3-output-1.svg
diff --git a/_proc/index.ipynb b/_proc/index.ipynb
diff --git a/_proc/settings.ini b/_proc/settings.ini
@@ -3,7 +3,7 @@ lib_name = glycowork
 repo_name = glycowork
 host = github
 user = BojarLab
-version = 1.0.0
+version = 1.0.1
 min_python = 3.8
 audience = Developers
 custom_sidebar = False

diff --git a/_proc/setup b/_proc/setup
@@ -5,7 +5,7 @@ with open("README.md", "r", encoding="utf-8") as fh:
 
 setuptools.setup(
     name="glycowork",
-    version="1.0.0",
+    version="1.1.0",
     author="Daniel Bojar",
     author_email="daniel.bojar@gu.se",
     description="Package for processing and analyzing glycans",
@@ -27,10 +27,13 @@ setuptools.setup(
                       "pandas>=1.3", "matplotlib-inline",
                       "python-louvain"],
     extras_require={'all':["torch_geometric", "CairoSVG",
-                           "drawSvg~=2.0", "glyles", "pubchempy", "requests"],
+                           "drawSvg~=2.0", "glyles", "pubchempy", "requests",
+                           "Pillow", "openpyxl"],
                     'dev':["torch_geometric", "CairoSVG",
-                           "drawSvg~=2.0", "glyles", "pubchempy", "requests"],
+                           "drawSvg~=2.0", "glyles", "pubchempy", "requests",
+                           "Pillow", "openpyxl"],
                     'ml':["torch_geometric"],
-                    'draw':["CairoSVG", "drawSvg~=2.0"],
+                    'draw':["CairoSVG", "drawSvg~=2.0", "Pillow",
+                            "openpyxl"],
                     'chem':["glyles", "pubchempy", "requests"]},
 )
diff --git a/build/lib/glycowork/__init__.py b/build/lib/glycowork/__init__.py
@@ -1,4 +1,4 @@
-__version__ = "1.0.0"
+__version__ = "1.0.1"
 #from .glycowork import *
 
-__all__ = ['alignment', 'ml', 'motif', 'glycan_data']
+__all__ = ['ml', 'motif', 'glycan_data', 'network']
diff --git a/build/lib/glycowork/alignment/__init__.py b/build/lib/glycowork/alignment/__init__.py