update docs, rework GUI, update logo

BojarLab · Feb 17, 2025 · 77bbfa3 · 77bbfa3
1 parent d1ff321
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Showing 15 changed files with 41,803 additions and 42,520 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/CHANGELOG.md b/CHANGELOG.md
@@ -9,6 +9,7 @@
 - Added setuptools to required_installs to support pip installation beyond `pip 25.0` (94646ad)
 - Added pyproject.toml to support pip installation beyond `pip 25.0` (94646ad)
 - Added CITATION.bib to allow for even easier citation of glycowork (a64f694)
+- Reworked user interface of the `glycoworkGUI`
 
 ### Changed 🔄
 - Bumped minimum supported Python version to 3.9 (3.8 is no longer supported, see https://devguide.python.org/versions/) (4960c5c)
@@ -99,7 +100,7 @@
 - Supported triple-branch reordering in `find_isomorphs` and `choose_correct_isoform` (918d18f)
 - Improved `find_isomorphs` to swap neighboring branches with different levels of nesting (41bb1a1, 034b6ad)
 - `choose_correct_isoform` can now also be used with a single glycan sequence, in which case it internally calls `find_isomorphs` to generate material for choosing (918d18f)
-- `choose_correct_isoform` can now correctly handle more complex sequences than before (41bb1a1, 034b6ad)
+- `choose_correct_isoform` can now correctly handle more complex sequences than before (41bb1a1, 034b6ad, d1ff321)
 - `canonicalize_iupac` now can handle modifications such as Neu5,9Ac2 / Neu4,5Ac2 or multiple ones like in (6S)(4S)Gal, even if in the wrong order (034b6ad)
 - `canonicalize_iupac` now can handle even more typos (e.g., 'aa1-3' in specifying a linkage) (a64f694, 241141b)
 - `canonicalize_iupac` now can handle even more inconsistencies (e.g., mix of short-hand and expanded linkages)
@@ -220,7 +221,7 @@
 
 #### models
 ##### Changed 🔄
-- In `prep_model`, the `hidden_dim` argument can now also be used to modify the protein embedding size of a newly defined LectinOracle model 
+- In `prep_model`, the `hidden_dim` argument can now also be used to modify the protein embedding size of a newly defined LectinOracle model (d1ff321) 
 
 ### network
 #### evolution

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -2,7 +2,7 @@
 
 ## How to get started
 
-Before anything else, please install the git hooks that run automatic scripts during each commit and merge to strip the notebooks of superfluous metadata (and avoid merge conflicts). After cloning the repository, run the following command inside it:
+Before anything else, please install `nbdev2` and install the git hooks that run automatic scripts during each commit and merge to strip the notebooks of superfluous metadata (and avoid merge conflicts). After cloning the repository, run the following command inside it:
 ```
 nbdev_install_hooks
 ```
@@ -21,7 +21,7 @@ nbdev_install_hooks
 
 ## PR submission guidelines
 
-* Before submitting a PR, run these commands locally, that will run all tests and return any errors that may have occurred:
+* Before submitting a PR, run these commands locally (note that you will have to have `glycowork[all]` installed, to cover all tests), that will run all tests and return any errors that may have occurred:
 
 ```
 nbdev_prepare

diff --git a/README.md b/README.md
diff --git a/bin/glycoworkGUI.py b/bin/glycoworkGUI.py
diff --git a/glycowork/ml/models.py b/glycowork/ml/models.py
@@ -311,7 +311,7 @@ def prep_model(model_type: Literal["SweetNet", "LectinOracle", "LectinOracle_fle
         model.load_state_dict(torch.load("SweetNet_v1_4.pt", map_location = device, weights_only = True))
       model = model.to(device)
     elif model_type == 'LectinOracle':
-      model = LectinOracle(len(libr), num_classes = num_classes, input_size_prot = 10*hidden_dim)
+      model = LectinOracle(len(libr), num_classes = num_classes, input_size_prot = int(10*hidden_dim))
       model = model.apply(lambda module: init_weights(module, mode = 'xavier'))
       if trained:
         if not Path("LectinOracle_v1_4.pt").exists():

diff --git a/glycowork/motif/processing.py b/glycowork/motif/processing.py
@@ -7,7 +7,7 @@
 from collections import defaultdict
 from itertools import permutations, combinations
 from typing import Dict, List, Set, Union, Optional, Callable, Tuple, Generator
-from glycowork.glycan_data.loader import (unwrap, multireplace, count_nested_brackets,
+from glycowork.glycan_data.loader import (unwrap, multireplace,
                                           find_nth, find_nth_reverse, lib, HexOS, HexNAcOS,
                                           linkages, Hex, HexNAc, dHex, Sia, HexA, Pen)
 
@@ -293,7 +293,7 @@ def kill_noncanonical(glycans):
           if current_count > paren_counts[-2]:  # Compare with parent branch
             kill_list.add(g)
           current_count = paren_counts[-2]  # Return to parent branch's count
-          paren_counts.pop()  # Remove current branch level 
+          paren_counts.pop()  # Remove current branch level
     return [g for g in glycans if g not in kill_list]
 
   # Handle neighboring branches

diff --git a/glycowork_badge_wo_bg.jpg b/glycowork_badge_wo_bg.jpg
diff --git a/index.ipynb b/index.ipynb
diff --git a/index_files/figure-commonmark/cell-3-output-1.svg b/index_files/figure-commonmark/cell-3-output-1.svg