PR for version 1.0

.github/PULL_REQUEST_TEMPLATE/detailed_pr_template.md

@@ -0,0 +1,39 @@
+# Description
+
+Please include a summary of the changes and the related issue. Please also include relevant motivation and context. 
+List any dependencies that are required for this change.
+
+## Fixes
+
+Which issues/bugs/feature requests does this PR fix/tackle?
+
+## Type of change
+
+Please check all applicable
+
+- [ ] Bug fix (non-breaking change which fixes an issue)
+- [ ] New feature (non-breaking change which adds functionality)
+- [ ] Breaking change (fix or feature that would cause existing functionality to not work as expected).
+- [ ] This change requires a documentation update
+
+If you tick the third one, please justify breaking DataSAILs current functionality.
+
+# How Has This Been Tested?
+
+Please list the added tests and what new/changed behavior they test. Please also state if you changed/added things that 
+are covered by already existing tests.
+
+# Checklist:
+
+- [ ] I have read the contribution guidelines for DataSAIL
+- [ ] My code follows the style guidelines of this project
+- [ ] I have performed a self-review of my code
+- [ ] I have commented my code including:
+  - [ ] Doc-Strings for all new methods following the 
+        [Google Guidelines](https://github.com/google/styleguide/blob/gh-pages/pyguide.md#38-comments-and-docstrings)
+  - [ ] Hard-to-understand areas, e.g., algorithmic steps 
+- [ ] I have made corresponding changes to the documentation
+- [ ] I have added tests that prove my fix is effective or that my feature works
+- [ ] New and existing pytests pass locally with my changes
+- [ ] New dependencies have been added to the recipes for conda-build (only if applicable) (check eventually for 
+      minimal and maximal version requirements)

.github/PULL_REQUEST_TEMPLATE/fast_pr_template.md

@@ -0,0 +1,16 @@
+## Description
+
+Please include a summary of the changes and the related issue. Please also include relevant motivation and context. 
+List any dependencies that are required for this change.
+
+## Issue ticket number and link
+
+Which issues/bugs/feature requests does this PR fix/tackle?
+
+# Checklist
+
+- [ ] I have read the contribution guidelines for DataSAIL
+- [ ] My code follows the style guidelines of this project
+- [ ] I have performed a self-review of my code
+- [ ] I have commented my code including Doc-Strings for all new methods following the 
+      [Google Guidelines](https://github.com/google/styleguide/blob/gh-pages/pyguide.md#38-comments-and-docstrings)

.github/workflows/publish_conda.yaml

@@ -10,19 +10,17 @@ jobs:
     runs-on: 'ubuntu-latest'
     steps:
     - uses: actions/checkout@v1
-    - name: publish-to-conda
-      uses: Old-Shatterhand/[email protected].11
+    - name: publish-full-to-conda
+      uses: Old-Shatterhand/[email protected].10
       with:
         AnacondaToken: ${{ secrets.DATASAIL_ANACONDA_TOKEN }}
         Versions: "3.8,3.9,3.10,3.11,3.12"
         Folder: "recipe"
         Platforms: "osx-64"
-        UploadOriginal: 1
-    - name: publish-to-conda-pt2
-      uses: Old-Shatterhand/[email protected]
+    - name: publish-lite-to-conda
+      uses: Old-Shatterhand/[email protected]
       with:
         AnacondaToken: ${{ secrets.DATASAIL_ANACONDA_TOKEN }}
         Versions: "3.8,3.9,3.10,3.11,3.12"
-        Folder: "recipe"
-        Platforms: "osx-arm64,win-64"
-        UploadOriginal: 0
+        Folder: "recipe_lite"
+        Platforms: "osx-64,osx-arm64,win-64"

.github/workflows/test.yaml

@@ -9,10 +9,14 @@ on:
     branches:
       - main
       - dev
+      - dev_1.0
+      - dev_1.0_weighting
   pull_request:
     branches:
       - main
       - dev
+      - dev_1.0
+      - dev_1.0_weighting
   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
@@ -21,10 +25,10 @@ jobs:
   test:
     runs-on: 'ubuntu-latest'
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Setup Mamba
-        uses: conda-incubator/setup-miniconda@v2
+        uses: conda-incubator/setup-miniconda@v3
         with:
           python-version: '3.10'
           miniforge-variant: Mambaforge
@@ -35,7 +39,7 @@ jobs:
       - name: Install environment
         shell: bash -l {0}
         run: |
-          mamba install -c conda-forge -c bioconda -y numpy pandas networkx matplotlib pytest setuptools pyscipopt"<4.0.0" foldseek mmseqs2 cd-hit mash tmalign cvxpy pytest-cov rdkit">=2022.09.1" pytest-cases scikit-learn pyyaml
+          mamba install -c conda-forge -c bioconda -y numpy pandas networkx matplotlib pytest setuptools pyscipopt"<4.0.0" foldseek mmseqs2 cd-hit mash tmalign diamond cvxpy pytest-cov rdkit">=2023.09.1" pytest-cases scikit-learn pyyaml h5py
           pip install grakel
 
       - name: Run tests

.github/workflows/test_rdkit.yaml

@@ -0,0 +1,59 @@
+# This is a basic workflow to help you get started with Actions
+
+name: Test RDKit
+
+# Controls when the workflow will run
+on:
+  # Triggers the workflow on push or pull request events but only for the main branch
+  push:
+    branches:
+      - main
+      - dev
+      - dev_1.0_rdkit
+  pull_request:
+    branches:
+      - main
+      - dev
+      - dev_1.0_rdkit
+  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:
+    strategy:
+        matrix:
+            rdkit-version:
+              - rdkit">=2022.03.1,<2022.09.1"
+              - rdkit">=2023.03.1,<2023.09.1"
+    runs-on: 'ubuntu-latest'
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Setup Mamba
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          python-version: '3.10'
+          miniforge-variant: Mambaforge
+          miniforge-version: latest
+          activate-environment: MPP
+          use-mamba: true
+
+      - name: Install environment
+        shell: bash -l {0}
+        run: |
+          mamba install -c conda-forge -c bioconda -y numpy pandas networkx matplotlib pytest setuptools pyscipopt"<4.0.0" foldseek mmseqs2 cd-hit mash tmalign diamond cvxpy pytest-cov ${{ matrix.rdkit-version }} pytest-cases scikit-learn pyyaml h5py
+          pip install grakel
+
+      - name: Run tests
+        shell: bash -l {0}
+        run: |
+          cd tests
+          pytest test_pipeline.py::test_molecule_formats
+
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v3
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          fail_ci_if_error: false
+          files: coverage.xml

.gitignore

@@ -20,27 +20,75 @@ tmp/
 log*.txt
 *.png
 *.pdf
+*.log
+*.pkl
+*.ipynb
+*.sh
 
 MoleculeNet.py
 run_moleculenet.sh
 viz_molnet.py
 /experiments/MPP/datasail/
 /experiments/MPP/deepchem/
-/experiments/PDBBind/lppdbbind/
-/experiments/PDBBind/runs/
+/experiments/DTI/runs/
 /experiments/segfault/
 /experiments/tsne/
 /experiments/umap/
-/experiments/david.py
+/experiments/ablation/david.py
 /experiments/MPP_timing.pkl
 /experiments/stiming.png
 /experiments/timing.png
 /runs/
-/experiments/PDBBind/datasail/
+/experiments/DTI/datasail/
 /experiments/MPP/lohi/
-/experiments/PDBBind/deepchem/
-/experiments/PDBBind/graphpart/
-/experiments/PDBBind/lohi/
+/experiments/DTI/deepchem/
+/experiments/DTI/graphpart/
+/experiments/DTI/lohi/
 /experiments_local/
 /mave_test/
-/tests/data/rw_data/mave_splits/
+/tests/data/rw_data/mave_splits/
+/experiments/Biogen/data/
+/experiments/Biogen/datasail/HLM/
+/experiments/Biogen/deepchem/HLM/
+/experiments/Biogen/lohi/HLM/
+/experiments/MPP/ML4Mol/
+/experiments/MPP/ML4Mol_bace/
+/experiments/MPP/ML4Mol_qm8/
+/experiments/MPP/ML4Mol_qm9/
+/experiments/MPP/tsne/
+/experiments/MPP/timing.pkl
+/experiments/MPP/train_ML4Mol.py
+/experiments/DTI/ML4Mol/
+/experiments/DTI/drug_embeds.pkl
+/experiments/DTI/ML4Mol.ipynb
+/experiments/DTI/prot_embeds.pkl
+/experiments/DTI/tsne_embeds.pkl
+/experiments/analysis/cdhit_leak/
+/experiments/analysis/backup.pkl
+/experiments/analysis/cluster_silhouette_scores.pkl
+/experiments/analysis/clusterings/
+/experiments/analysis/backup_scip2.pkl
+/experiments/analysis/cluster_tables.pkl
+/experiments/analysis/density.pkl
+/experiments/analysis/figures.ipynb
+/experiments/analysis/jaccard.pkl
+/experiments/analysis/performances.pkl
+/experiments/analysis/qm9.tar.gz
+/experiments/analysis/rna.fasta
+/experiments/analysis/save.pkl
+/experiments/analysis/save_clustering.py
+/experiments/analysis/silhouette_scores.pkl
+/experiments/analysis/Untitled.ipynb
+/ML4Mol/ML4Mol_prepare.ipynb
+/ML4Mol/ML4Mol_QM8.ipynb
+/ML4Mol/ML4Mols_split.ipynb
+/Untitled.ipynb
+/ML4Mol/
+/experiments/Biogen/datasail/
+/experiments/Biogen/deepchem/
+/experiments/Biogen/lohi/
+/experiments/MPP/datasail_old/
+/experiments/MPP/deepchem_old/
+/experiments/MPP/lohi_old/
+/experiments/time2/
+/experiments/time/

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "experiments/DTI/lppdbbind"]
+	path = experiments/DTI/lppdbbind
+	url = [email protected]:kalininalab/LP-PDBBind.git

CHANGELOG.md

@@ -1,6 +1,6 @@
 # Change Log
 
-## [Planned]
+## [Planned - Long-term project ideas]
 
 - [ ] Normalization of objectives for better comparability and better splits in solvers
 - [ ] Time-limit and solution limit for all solvers
@@ -9,7 +9,18 @@
 - [ ] Reports of results with plots and tables a PDF and or HTML
 - [ ] Generalization to R-dimensional datasets (see [paper](https://doi.org/10.1101/2023.11.15.566305))
 - [ ] Input from config files
+- [ ] Replace GraKel with something "modern" and fully "conda-installable" to make DataSAIL fully conda-installable
 - [ ] Stratified splits
+- [ ] Include [MashMap3](https://github.com/marbl/MashMap)
+- [ ] Include MASH for amino acid sequences
+
+## v0.3.0 (2024-01-??)
+
+- Stratified splits
+- Extensive checks of available solvers
+- Time and Space limits for all solvers
+- Runtime experiments and experiments on a [stratified dataset](LINK)
+- Bugs and Docu fixed
 
 ## v0.2.2 (2023-12-11)
 
@@ -28,7 +39,7 @@
 
 ## v0.2.1 (2023-10-26)
 
-- Renaming of splitting techniques to align with paper to be I1/C1/I2/C2
+- Renaming of splitting techniques to align with preprint to be I1/C1/I2/C2
 - More tests to better cover the supposed functionality
 - Now supports for Python 3.8 to Python 3.11
 - Experiments on [MoleculeNet](https://doi.org/10.1039/C7SC02664A) and [LP-PDBBind](https://doi.org/10.48550/arXiv.2308.09639)

CONTRIBUTING.md

@@ -0,0 +1,5 @@
+Contributing to DataSAIL
+========================
+
+As with every other open-source project, you can contribute to DataSAIL. For more information, we refer you to the 
+[contribution guidelines in our documentation]().