feat: scaffolding, caching, EGFR

.devcontainer/Dockerfile

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+FROM mcr.microsoft.com/devcontainers/anaconda:1-3

.devcontainer/devcontainer.json

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+// Small devcontainer which loads anaconda. All postinstallation steps have to be done manually.
+// This comes with snakemake and docker-in-docker.
+
+// For format details, see https://aka.ms/devcontainer.json. For config options, see the
+// README at: https://github.com/devcontainers/templates/tree/main/src/anaconda
+{
+	"name": "Anaconda (Python 3)",
+	"build": { 
+		"context": "..",
+		"dockerfile": "Dockerfile"
+	},
+	"features": {
+		"ghcr.io/devcontainers/features/docker-in-docker:2": {},
+		// For yamlfmt
+		"ghcr.io/devcontainers/features/go:1": {},
+		// For web display
+		"ghcr.io/devcontainers/features/node:1": {},
+		// For scripting
+		"ghcr.io/va-h/devcontainers-features/uv:1": {},
+		// For paxtools
+		"ghcr.io/devcontainers/features/java:1": {}
+	}
+}

.github/workflows/publish.yml

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+name: Test SPRAS
+
+on:
+  pull_request:
+    branches: [main]
+  push:
+    branches: [main]
+
+# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+jobs:
+  pre-commit:
+    name: Run pre-commit checks
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+      - name: Setup Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.11'
+      - name: Run pre-commit checks
+        uses: pre-commit/action@v3.0.0
+  checks:
+    name: Run workflow
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+        with:
+          submodules: true
+      - name: Install uv for scripting
+        uses: astral-sh/setup-uv@v6.1.0
+        with:
+          version: "0.7.13"
+      - name: Setup conda
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          activate-environment: spras
+          environment-file: spras/environment.yml
+          auto-activate-base: false
+          miniconda-version: 'latest'
+      # Install spras in the environment using pip
+      - name: Install spras in conda env
+        shell: bash --login {0}
+        run: pip install ./spras
+      # Log conda environment contents
+      - name: Log conda environment
+        shell: bash --login {0}
+        run: conda list
+      - name: Fetch Artifact Cache
+        id: fetch-cache
+        uses: actions/cache/restore@v4
+        with:
+          path: cache/artifacts
+          key: cache-artifacts
+      - name: Process raw data through Snakemake
+        run: sh run_snakemake.sh
+      - name: Cache Artifact Cache
+        id: cache-cache
+        uses: actions/cache/save@v4
+        with:
+          path: cache/artifacts
+          key: cache-artifacts
+      - name: Run Snakemake workflow for score-based datasets
+        shell: bash --login {0}
+        run: snakemake --cores 4 --configfile configs/scores.yaml --show-failed-logs -s spras/Snakefile

.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/
+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/latest/usage/project/#working-with-version-control
+.pdm.toml
+.pdm-python
+.pdm-build/
+
+# 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
+.idea/
+
+# Snakemake
+.snakemake
+
+# Output
+/output
+/web/output
+
+# pnpm
+.pnpm-store
+
+# mac
+.DS_Store

.gitmodules

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+[submodule "spras"]
+	path = spras
+	url = https://github.com/Reed-CompBio/spras

.pre-commit-config.yaml

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+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+default_language_version:
+  # Match this to the version specified in environment.yml
+  python: python3.11
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0 # Use the ref you want to point at
+    hooks:
+      # Attempts to load all yaml files to verify syntax.
+      - id: check-yaml
+        # Attempts to load all TOML files to verify syntax.
+      - id: check-toml
+        # Trims trailing whitespace.
+      - id: trailing-whitespace
+        # Preserves Markdown hard linebreaks.
+        args: [--markdown-linebreak-ext=md]
+        # Do not trim whitespace from all files, input files may need trailing whitespace for empty values in columns.
+        types_or: [markdown, python, yaml]
+        # Skip this Markdown file, which has an example of an input text file within it.
+        exclude: input/README.md
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: 'v0.15.4'
+    hooks:
+      - id: ruff
+  - repo: https://github.com/google/yamlfmt
+    rev: v0.17.0
+    hooks:
+      - id: yamlfmt
+  - repo: https://github.com/crate-ci/typos
+    rev: v1.34.0
+    hooks:
+      - id: typos

.python-version

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+3.13

.vscode/settings.json

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+{
+    "editor.rulers": [
+        150 // enforced by ruff
+    ]
+}

.yamlfmt.yaml

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+formatter:
+  retain_line_breaks_single: true

LICENSE

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+MIT License
+
+Copyright (c) 2024 Reed College Computational Biology
+
+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.