Protein Prediction Codebase Migration

.gitattributes

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+# Juypter notebooks contains images, and tables, and parsing text
+# blowing up the total language fraction unrealistically;
+# then 'Juypter notebooks' are suddenly major part of repo language.
+
+# As they don't want to parse notebooks better
+# (wont-fix = https://github.com/github/linguist/issues/3496)
+# Simply exclude this file from counting now:
+
+notebooks/*.ipynb linguist-generated=true
+stream_viz/tutorial/*.ipynb linguist-generated=true

.github/workflows/black.yml

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+name: Lint
+
+on: [push, pull_request]
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: psf/black@stable

.github/workflows/test.yml

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+name: Unittests
+
+on: [pull_request]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install --upgrade pip setuptools wheel
+          python -m pip install torch torchvision torchaudio --index-url https://download.pytorch.org/whl/cpu
+          python -m pip install -e .
+
+      - name: Display Python & Installed Packages
+        run: |
+          python --version
+          pip freeze
+
+      - name: Run Unit Tests
+        run: python -m unittest discover -s tests/unit -v
+        env:
+          ACTIONS_STEP_DEBUG: true  # Enable debug logs
+          ACTIONS_RUNNER_DEBUG: true # Additional debug logs from Github Actions itself

.github/workflows/token_consistency.yaml

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+name: Check consistency of tokens.txt file
+
+# Define the file paths under `paths` to trigger this check only when specific files are modified.
+# This script will then execute checks only on files that have changed, rather than all files listed in `paths`.
+
+# **Note** : To add a new token file for checks, include its path in:
+# - `on` -> `push` and `pull_request` sections
+# - `jobs` -> `check_tokens` -> `steps` -> Set global variable for multiple tokens.txt paths -> `TOKENS_FILES`
+
+on:
+  push:
+    paths:
+      - "chebai/preprocessing/bin/protein_token/tokens.txt"
+      - "chebai/preprocessing/bin/protein_token_3_gram/tokens.txt"
+  pull_request:
+    paths:
+      - "chebai/preprocessing/bin/protein_token/tokens.txt"
+      - "chebai/preprocessing/bin/protein_token_3_gram/tokens.txt"
+
+jobs:
+  check_tokens:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v2
+
+      - name: Get list of changed files
+        id: changed_files
+        run: |
+          git fetch origin dev
+
+          # Get the list of changed files compared to origin/dev and save them to a file
+          git diff --name-only origin/dev > changed_files.txt
+
+          # Print the names of changed files on separate lines
+          echo "Changed files:"
+          while read -r line; do
+            echo "Changed File name : $line"
+          done < changed_files.txt
+
+      - name: Set global variable for multiple tokens.txt paths
+        run: |
+          # All token files that needs to checked must be included here too, same as in `paths`.
+          TOKENS_FILES=(
+            "chebai/preprocessing/bin/protein_token/tokens.txt"
+            "chebai/preprocessing/bin/protein_token_3_gram/tokens.txt"
+          )
+          echo "TOKENS_FILES=${TOKENS_FILES[*]}" >> $GITHUB_ENV
+
+      - name: Process only changed tokens.txt files
+        run: |
+          # Convert the TOKENS_FILES environment variable into an array
+          TOKENS_FILES=(${TOKENS_FILES})
+
+          # Iterate over each token file path
+          for TOKENS_FILE_PATH in "${TOKENS_FILES[@]}"; do
+            # Check if the current token file path is in the list of changed files
+            if grep -q "$TOKENS_FILE_PATH" changed_files.txt; then
+              echo "----------------------- Processing $TOKENS_FILE_PATH -----------------------"
+
+              # Get previous tokens.txt version
+              git fetch origin dev
+              git diff origin/dev -- $TOKENS_FILE_PATH > tokens_diff.txt || echo "No previous tokens.txt found for $TOKENS_FILE_PATH"
+
+              # Check for deleted or added lines in tokens.txt
+              if [ -f tokens_diff.txt ]; then
+
+                # Check for deleted lines (lines starting with '-')
+                deleted_lines=$(grep '^-' tokens_diff.txt | grep -v '^---' | sed 's/^-//' || true)
+                if [ -n "$deleted_lines" ]; then
+                  echo "Error: Lines have been deleted from $TOKENS_FILE_PATH."
+                  echo -e "Deleted Lines: \n$deleted_lines"
+                  exit 1
+                fi
+
+                # Check for added lines (lines starting with '+')
+                added_lines=$(grep '^+' tokens_diff.txt | grep -v '^+++' | sed 's/^+//' || true)
+                if [ -n "$added_lines" ]; then
+
+                  # Count how many lines have been added
+                  num_added_lines=$(echo "$added_lines" | wc -l)
+
+                  # Get last `n` lines (equal to num_added_lines) of tokens.txt
+                  last_lines=$(tail -n "$num_added_lines" $TOKENS_FILE_PATH)
+
+                  # Check if the added lines are at the end of the file
+                  if [ "$added_lines" != "$last_lines" ]; then
+
+                    # Find lines that were added but not appended at the end of the file
+                    non_appended_lines=$(diff <(echo "$added_lines") <(echo "$last_lines") | grep '^<' | sed 's/^< //')
+
+                    echo "Error: New lines have been added to $TOKENS_FILE_PATH, but they are not at the end of the file."
+                    echo -e "Added lines that are not at the end of the file: \n$non_appended_lines"
+                    exit 1
+                  fi
+                fi
+
+                if [ "$added_lines" == "" ]; then
+                    echo "$TOKENS_FILE_PATH validation successful: No lines were deleted, and no new lines were added."
+                else
+                    echo "$TOKENS_FILE_PATH validation successful: No lines were deleted, and new lines were correctly appended at the end."
+                fi
+              else
+                echo "No previous version of $TOKENS_FILE_PATH found."
+              fi
+            else
+              echo "$TOKENS_FILE_PATH was not changed, skipping."
+            fi
+          done

.gitignore

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+# 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/
+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/
+
+# configs/ # commented as new configs can be added as a part of a feature
+
+/.idea
+/data
+/logs
+/results_buffer
+electra_pretrained.ckpt
+.jupyter
+.virtual_documents

.pre-commit-config.yaml

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+repos:
+-   repo: https://github.com/psf/black
+    rev: "24.2.0"
+    hooks:
+    -   id: black
+    -   id: black-jupyter # for formatting jupyter-notebook
+
+-   repo: https://github.com/pycqa/isort
+    rev: 5.13.2
+    hooks:
+      - id: isort
+        name: isort (python)
+        args: ["--profile=black"]
+
+-   repo: https://github.com/asottile/seed-isort-config
+    rev: v2.2.0
+    hooks:
+    -   id: seed-isort-config
+
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.6.0
+    hooks:
+    -   id: check-yaml
+    -   id: end-of-file-fixer
+    -   id: trailing-whitespace