Address reviewers' comments

.github/workflows/check-for-syntax-errors.yml

@@ -0,0 +1,8 @@
+on: push
+name: Check for syntax errors
+jobs:
+  check-for-syntax-errors:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: cclauss/Find-Python-syntax-errors-action@master

.github/workflows/run-black-formatter.yml

@@ -0,0 +1,11 @@
+on: push
+name: Run Black formatter
+jobs:
+    run-black-formatter:
+        runs-on: ubuntu-latest
+        steps:
+            - uses: actions/checkout@v3
+            - uses: psf/black@stable
+              with:
+                  options: "--check --verbose"
+                  jupyter: true

.gitignore

@@ -0,0 +1,192 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+# Large data
+*.gb
+*.fasta
+*.ffn
+*.tar.gz
+*.tab
+experiments/data/GenomesDB/
+experiments/data/inphared/
+experiments/data/output_struct_align/
+rbp_dataset/
+rbp_dataset.zip
+phistruct_dataset.csv
+experiments/temp/feature_impt_*
+
+# Trained models
+experiments/models/
+*.joblib
+*.joblib.gz
+
+# Scratch
+experiments/scratch/
+dump/
+*scratch*
+table-*.py
+*_genus_sim.pickle
+protein_pairs.pickle
+figures/
+experiments/temp/results-*
+
+# External dependencies
+SaProt/

LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2023 Mark Edward M. Gonzales, Jennifer C. Ureta, and Anish M.S. Shrestha
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

environment.yaml

@@ -0,0 +1,27 @@
+name: PHIStruct
+channels:
+    - conda-forge
+dependencies:
+    - python=3.10
+    - pandas=1.5.1
+    - imbalanced-learn=0.11.0
+    - scikit-learn=1.2.2
+    - joblib=1.2.0
+    - pip=24.0
+    - git
+    - git-lfs
+    - wget
+    - pip:
+          - --extra-index-url https://download.pytorch.org/whl/cu117
+          - torch==1.13.1+cu117
+          - torchvision==0.14.1+cu117
+          - torchaudio==0.13.1
+          - pytorch-lightning==1.8.3
+          - wandb
+          - transformers==4.28.0
+          - easydict
+          - scipy
+          - peft
+          - lmdb
+          - torchmetrics==0.9.3
+          - fair-esm

environment_experiments.yaml

@@ -0,0 +1,23 @@
+name: PHIStruct-experiments
+channels:
+    - conda-forge
+dependencies:
+    - python=3.10
+    - tqdm=4.65.0
+    - regex=2022.7.9
+    - nltk=3.8.1
+    - biopython=1.78
+    - ete3=3.1.3
+    - pandas=1.5.3
+    - numpy=1.24.3
+    - scipy=1.9.3
+    - h5py=3.10.0
+    - scikit-learn=1.2.0
+    - imbalanced-learn=0.11.0
+    - xgboost=1.7.6
+    - matplotlib=3.7.1
+    - seaborn=0.12.2
+    - pip=24.0
+    - pip:
+          - --extra-index-url https://download.pytorch.org/whl/cu117
+          - torch==1.13.1+cu117