Merge pull request BojarLab#63 from BojarLab/dev

merge for v1.4
Glycocalex · Nov 11, 2024 · f9358d4 · f9358d4
2 parents 683d731 + d5780bd
commit f9358d4
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diff --git a/.gitattributes b/.gitattributes
diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
@@ -0,0 +1,44 @@
+# This is a basic workflow to help you get started with Actions
+name: Testing
+
+# Controls when the workflow will run
+on:
+  # Triggers the workflow on push or pull request events to the main and dev branches
+  push:
+    branches:
+      - main
+      - dev
+  pull_request:
+    branches:
+      - main
+      - dev
+  workflow_dispatch:  # make is manually start-able
+
+# A workflow run is made up of one or more jobs that can run sequentially or in parallel
+jobs:
+  # This workflow contains a single job called "test"
+  test:
+    runs-on: 'ubuntu-latest'
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Setup Miniforge
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          python-version: '3.8'
+          miniforge-version: latest
+          activate-environment: MPP
+          use-mamba: true
+
+      - name: Install environment
+        shell: bash -l {0}
+        run: |
+          python -m pip install --upgrade pip
+          test -f setup.py && pip install -e ".[all]"
+          pip install pytest
+
+      - name: Run tests
+        shell: bash -l {0}
+        run: |
+          cd tests
+          pytest
diff --git a/.gitignore b/.gitignore
@@ -9,6 +9,8 @@
 _tmp*
 tmp*
 tags
+/build/
+/_proc/
 
 # Byte-compiled / optimized / DLL files
 __pycache__/

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
@@ -37,7 +37,7 @@ nbdev_prepare
 
 * Docs are automatically created from the notebooks in the nbs folder.
 
-## Wishlist for future glycowork updates (last update: 2024-01-31)
+## Wishlist for future glycowork updates (last update: 2024-07-10)
 
 ### Urgent
 
@@ -50,4 +50,5 @@ nbdev_prepare
 * 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
 * implement multiple sequence alignment and other substitution matrices
-* parallelize motif matching
+* parallelize motif matching
+* refactor glycan graphs to be directed graphs & treat linkages as edges (would mean a *lot* of downstream fixes/refactoring)
diff --git a/README.md b/README.md
diff --git a/_proc/.gitignore b/_proc/.gitignore
diff --git a/_proc/.quarto/idx/00_core.ipynb.json b/_proc/.quarto/idx/00_core.ipynb.json
diff --git a/_proc/.quarto/xref/INDEX b/_proc/.quarto/xref/INDEX
diff --git a/_proc/00_core.ipynb b/_proc/00_core.ipynb
-Original file line number
+Diff line change
@@ Expand Up / @@ -9,6 +9,8 @@ @@
     _tmp*
     tmp*
     tags
+    /build/
+    /_proc/
     # Byte-compiled / optimized / DLL files
     __pycache__/
@@ Expand Down @@