retrocast 0__tar.gz

retrocast-0/.github/release-drafter.yml

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+# .github/release-drafter.yml
+
+name-template: "v$RESOLVED_VERSION"
+tag-template: "v$RESOLVED_VERSION"
+include-pre-releases: true
+prerelease: true
+
+# automatically add a 'dependencies' label for your robot friends
+autolabeler:
+  - label: "dependencies"
+    branch:
+      - '/^dependabot\//'
+      - '/^renovate\//'
+    title:
+      - '/^build\(deps\)/' # for dependabot group updates
+
+categories:
+  - title: "🚨 BREAKING CHANGES"
+    labels:
+      - "breaking-change"
+  - title: "🛡️ Security Fixes"
+    labels:
+      - "type/security"
+  - title: "✨ New Features"
+    labels:
+      - "type/feature"
+  - title: "🐛 Bug Fixes"
+    labels:
+      - "type/bug"
+  - title: "🚀 Performance Improvements"
+    labels:
+      - "scope/performance"
+  - title: "📚 Documentation"
+    labels:
+      - "type/docs"
+  - title: "🛠️ Maintenance & Internal Improvements"
+    labels:
+      - "type/refactor"
+      - "type/chore"
+      - "scope/ci-cd"
+      - "scope/testing"
+  - title: "⬆️ Dependency Updates"
+    labels:
+      - "dependencies"
+
+change-template: "- $TITLE @$AUTHOR (#$NUMBER)"
+change-title-escapes: '\<*_&'
+
+version-resolver:
+  major:
+    labels:
+      - "breaking-change"
+  minor:
+    labels:
+      - "type/feature"
+  patch:
+    labels:
+      - "type/bug"
+      - "type/docs"
+      - "type/refactor"
+      - "type/chore"
+      - "type/security"
+      - "scope/performance"
+      - "dependencies"
+  default: patch
+
+template: |
+  ## Changes
+
+  $CHANGES

retrocast-0/.github/workflows/publish-pypi.yml

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+name: "Publish to PyPi"
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  run:
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+    permissions:
+      id-token: write
+      contents: read
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v5
+        with:
+          ref: master
+          fetch-depth: 0  # Full history needed for setuptools-scm to read git tags
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
+      - name: Install Python 3.13
+        run: uv python install 3.13
+      - name: Build
+        run: uv build
+      # Check that basic features work and we didn't miss to include crucial files
+      - name: Smoke test (wheel)
+        run: uv run --isolated --no-project --with dist/*.whl --with pytest tests/smoke_test.py
+      - name: Smoke test (source distribution)
+        run: uv run --isolated --no-project --with dist/*.tar.gz --with pytest tests/smoke_test.py
+      - name: Publish
+        run: uv publish

retrocast-0/.github/workflows/publish-release.yml

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+name: Publish Release
+on:
+  release:
+    types: [published] # Runs when a draft is published
+
+permissions:
+  contents: write
+
+jobs:
+  create_python_package:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Install uv
+        uses: astral-sh/setup-uv@v3
+        with:
+          enable-cache: true
+          cache-dependency-glob: uv.lock
+
+      - name: Set up Python
+        run: uv python install 3.13
+
+      - name: Build
+        run: uv build
+
+      - name: Upload artifacts to release
+        uses: softprops/action-gh-release@v1
+        with:
+          files: dist/*

retrocast-0/.github/workflows/release-drafter.yml

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+name: Label PR & Draft Release
+
+on:
+  push:
+    branches:
+      - main
+      - master
+  pull_request:
+    types: [opened, reopened, synchronize]
+  workflow_dispatch:
+
+permissions:
+  contents: read
+  pull-requests: write
+
+jobs:
+  process_pr:
+    permissions:
+      contents: write
+      pull-requests: write
+    runs-on: ubuntu-latest
+    steps:
+      - name: Assign labels from commits
+        if: github.event_name == 'pull_request'
+        id: assign-labels
+        uses: mauroalderete/action-assign-labels@v1
+        with:
+          pull-request-number: ${{ github.event.pull_request.number }}
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          conventional-commits: |
+            conventional-commits:
+              - type: 'feat'
+                nouns: ['FEATURE', 'Feature', 'feature', 'FEAT', 'Feat', 'feat']
+                labels: ['type/feature']
+              - type: 'fix'
+                nouns: ['FIX', 'Fix', 'fix', 'FIXED', 'Fixed', 'fixed']
+                labels: ['type/bug']
+              - type: 'refactor'
+                nouns: ['REFACTOR', 'Refactor', 'refactor', 'ref', 'REF']
+                labels: ['type/refactor']
+              - type: 'perf'
+                nouns: ['PERF', 'Perf', 'perf', 'PERFORMANCE', 'Performance', 'performance']
+                labels: ['scope/performance']
+              - type: 'docs'
+                nouns: ['DOCS', 'Docs', 'docs', 'DOC', 'Doc', 'doc']
+                labels: ['type/docs']
+              - type: 'tests'
+                nouns: ['TESTS', 'Tests', 'tests']
+                labels: ['scope/testing']
+          maintain-labels-not-matched: false
+          apply-changes: true
+
+      - uses: release-drafter/release-drafter@v6.0.0
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

retrocast-0/.github/workflows/tests.yml

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+name: Tests
+
+on:
+  push:
+    branches:
+      - main
+      - master
+  pull_request:
+    branches:
+      - main
+      - master
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      pull-requests: write
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Set up Python 3.13
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.13"
+
+      - name: Install uv
+        run: |
+          curl -LsSf https://astral.sh/uv/install.sh | sh
+          echo "$HOME/.cargo/bin" >> $GITHUB_PATH
+
+      - name: Cache dependencies
+        uses: actions/cache@v4
+        with:
+          path: |
+            ~/.cache/uv
+            ~/.uv
+            .venv
+          key: ${{ runner.os }}-uv-${{ hashFiles('pyproject.toml') }}
+          restore-keys: |
+            ${{ runner.os }}-uv-
+
+      - name: Create and activate virtual environment
+        run: |
+          uv venv
+          echo "$PWD/.venv/bin" >> $GITHUB_PATH
+
+      - name: Install dependencies
+        run: uv sync
+
+      - name: Run tests
+        run: uv run pytest -v
+
+      - name: generate coverage report
+        id: coverage
+        run: |
+          set +e  # disable exit on error temporarily
+          report=$(uv run pytest --cov=retrocast --cov-report=term-missing)
+          exit_code=$?
+          set -e  # re-enable exit on error
+
+          # this is some bash magic to make the multiline report available to next steps
+          echo "report<<EOF" >> $GITHUB_OUTPUT
+          echo "$report" >> $GITHUB_OUTPUT
+          echo "EOF" >> $GITHUB_OUTPUT
+
+          exit $exit_code  # fail the step if tests failed
+
+      - name: find changed files in src
+        id: changed-src-files
+        if: github.event_name == 'pull_request'
+        uses: tj-actions/changed-files@v46 # check for the latest version, they update a lot
+        with:
+          files: src/** # or whatever your source directory is
+
+      - name: print coverage report to logs
+        run: |
+          echo "${{ steps.coverage.outputs.report }}"
+
+      - name: add coverage report as a pr comment
+        if: github.event_name == 'pull_request' && steps.changed-src-files.outputs.any_changed == 'true'
+        uses: actions/github-script@v7
+        with:
+          script: |
+            const output = `### Pytest Coverage Report 🧪
+            \`\`\`
+            ${{ steps.coverage.outputs.report }}
+            \`\`\`
+            `;
+
+            github.rest.issues.createComment({
+              owner: context.repo.owner,
+              repo: context.repo.repo,
+              issue_number: context.issue.number,
+              body: output
+            });

retrocast-0/.github/workflows/typing.yml

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+name: Linting & Type Checking
+
+on:
+  push:
+    branches:
+      - main
+      - master
+  pull_request:
+    branches:
+      - main
+      - master
+
+jobs:
+  type-check:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.11"
+
+      - name: Install uv
+        run: |
+          curl -LsSf https://astral.sh/uv/install.sh | sh
+          echo "$HOME/.cargo/bin" >> $GITHUB_PATH
+
+      # this is the same caching logic from your tests workflow. big speed up.
+      - name: Cache dependencies
+        uses: actions/cache@v4
+        with:
+          path: |
+            ~/.cache/uv
+            .venv
+          key: ${{ runner.os }}-uv-${{ hashFiles('pyproject.toml') }}
+          restore-keys: |
+            ${{ runner.os }}-uv-
+
+      - name: Install dependencies
+        run: uv sync --extra viz
+
+      - name: Run ruff (linter)
+        run: uv run ruff check
+
+      - name: Run ruff (formatter)
+        run: uv run ruff format --check
+
+      - name: Run ty
+        run: uv run ty check .

retrocast-0/.github/workflows/update-major-minor-tags.yml

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+name: Update Major Minor Tags
+on:
+  push:
+    tags:
+      - "v[0-9]+.[0-9]+.[0-9]+"  # Only run on semantic version tags
+
+permissions:
+  contents: write
+
+jobs:
+  update_major_minor_tags:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0  # Fetch all history for all tags
+      - uses: haya14busa/action-update-semver@v1.2.1

retrocast-0/.gitignore

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+# Python-generated files
+__pycache__/
+*.py[oc]
+build/
+dist/
+wheels/
+*.egg-info
+.mypy_cache/
+.ruff_cache/
+.pytest_cache/
+
+# Other junk
+.DS_Store
+
+# Virtual environments
+.venv
+
+# Jupyter Trash
+*.ipynb
+
+# Data
+data/transfers/
+data/**/*.json.gz
+data/**/*.csv
+data/**/*.txt
+data/0-assets/*.pkl
+data/0-assets/model-configs/**/*.pickle
+data/0-assets/model-configs/**/*.pkl
+data/0-assets/model-configs/**/*.onnx
+data/0-assets/model-configs/**/*.csv*
+data/0-assets/model-configs/**/*.ckpt*
+data/0-assets/model-configs/**/*.pt*
+data/0-assets/model-configs/**/*.smi*
+data/0-assets/model-configs/**/*.sdf*
+data/0-assets/model-configs/**/*.zip*
+data/0-assets/model-configs/**/*.hdf5*
+data/0-assets/model-configs/**/*.txt*
+data/0-assets/model-configs/**/*.dat*
+data/0-assets/model-configs/**/.*
+data/0-assets/model-configs/**/*.md
+data/analysis/**/*.html
+data/analysis/**/*.json
+data/analysis/**/*.txt
+data/analysis/**/*.png
+
+data/evaluations/**/*.pkl
+data/evaluations/**/*.json.gz
+data/evaluations/**/results.json
+data/processed/**/*.json.gz
+data/scored/
+
+
+_backups/
+# AI
+_prompts/
+
+clone.sh
+
+# internal code
+scripts/dms/private/
+
+# Testing
+.coverage*
+archive
+archive-v2
+collectors/
+
+tests/testing_data/**/results.json
+docs/coding-style.md
+
+data/statistics
+data/seed-stability-archive
+
+!data/1-benchmarks/definitions/*.json.gz
+data/1-benchmarks/definitions/re-export
+data/1-benchmarks/**/*.gz
+data/1-benchmarks/**/*.hdf5
+data/2-raw
+data/3-processed/
+data/4-scored/
+data/5-results/
+data/5-results/**/*.html
+data/5-results/**/*.jpg
+data/6-comparisons
+data/7-meta-analysis
+
+docs/testing-framework.md
+.ignore
+
+.hypothesis
+AGENTS.md

retrocast-0/.pre-commit-config.yaml

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+repos:
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    # Ruff version.
+    rev: v0.14.1
+    hooks:
+      # Run the linter.
+      - id: ruff-check
+        name: ruff (linter)
+        args: [--fix]
+      # Run the formatter.
+      - id: ruff-format
+        name: ruff (formatter)
+
+  - repo: local
+    hooks:
+      - id: ty
+        name: ty check
+        entry: uv run ty check .
+        language: system
+        pass_filenames: false

retrocast-0/.python-version

@@ -0,0 +1 @@
+3.11

retrocast-0/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2025 isChemist Group (Anton Morgunov)
+
+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.