Add initial public code

microsoft · May 23, 2023 · 17fede7 · 17fede7
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diff --git a/.coveragerc b/.coveragerc
@@ -0,0 +1,22 @@
+[run]
+
+branch = True
+include = syntheseus/*
+omit = syntheseus/tests/*
+
+[report]
+# Regexes for lines to exclude from consideration
+exclude_lines =
+    # Have to re-enable the standard pragma
+    pragma: no cover
+
+    # Don't complain about missing debug-only code:
+    def __repr__
+    if self\.debug
+
+    # Don't complain if tests don't hit defensive assertion code:
+    raise AssertionError
+    raise NotImplementedError
+
+    # Don't complain about abstract methods, they aren't run:
+    @(abc\.)?abstractmethod
diff --git a/.github/azure_pipelines/code-security-analysis.yml b/.github/azure_pipelines/code-security-analysis.yml
@@ -0,0 +1,33 @@
+schedules:
+- cron: '0 4 * * 0'
+  displayName: Weekly build
+  branches:
+    include:
+    - main
+
+pool:
+ vmImage: 'windows-latest'
+
+steps:
+- task: CredScan@2
+  inputs:
+    toolMajorVersion: 'V2'
+- task: Semmle@1
+  inputs:
+    sourceCodeDirectory: '$(Build.SourcesDirectory)'
+    language: 'python'
+    querySuite: 'Recommended'
+    timeout: '1800'
+    ram: '16384'
+    addProjectDirToScanningExclusionList: true
+- task: ComponentGovernanceComponentDetection@0
+  inputs:
+    scanType: 'Register'
+    verbosity: 'Verbose'
+    alertWarningLevel: 'High'
+- task: PublishSecurityAnalysisLogs@2
+  inputs:
+    ArtifactName: 'CodeAnalysisLogs'
+    ArtifactType: 'Container'
+    AllTools: true
+    ToolLogsNotFoundAction: 'Standard'
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -0,0 +1,35 @@
+name: CI
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+  workflow_dispatch:
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.7", "3.9"]
+    defaults:
+      run:
+        shell: bash -l {0}
+    name: build (Python ${{ matrix.python-version }})
+    steps:
+    - uses: actions/checkout@v3
+    - uses: conda-incubator/setup-miniconda@v2
+      with:
+        mamba-version: "*"
+        channels: conda-forge,defaults
+        channel-priority: true
+        python-version: ${{ matrix.python-version }}
+        environment-file: environment.yml
+    - name: Run pre-commit
+      run: |
+        pre-commit run --verbose --all-files
+    - name: Run unit tests and generate coverage report
+      run: |
+        python -m pytest --cov --cov-config=.coveragerc ./syntheseus/tests/
diff --git a/.gitignore b/.gitignore
@@ -0,0 +1,34 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$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
+
+# Notebook checkpoints:
+.ipynb_checkpoints
+
+# Unit test / coverage reports
+.coverage
+.coverage.*
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -0,0 +1,46 @@
+repos:
+  # Generally useful pre-commit hooks
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.3.0  # Use the ref you want to point at
+    hooks:
+    -   id: check-added-large-files
+    -   id: check-case-conflict
+    -   id: check-docstring-first
+    -   id: check-executables-have-shebangs
+    -   id: check-json
+    -   id: check-merge-conflict
+    -   id: check-symlinks
+    -   id: check-toml
+    -   id: check-yaml
+    -   id: debug-statements
+    -   id: destroyed-symlinks
+    -   id: detect-private-key
+    -   id: end-of-file-fixer
+    -   id: name-tests-test
+        args: ["--pytest-test-first"]
+    -   id: trailing-whitespace
+        args: [--markdown-linebreak-ext=md]
+
+  # latest version of black when this pre-commit config is being set up
+  - repo: https://github.com/psf/black
+    rev: 23.3.0
+    hooks:
+      - id: black
+        name: "black"
+        args: ["--config=pyproject.toml"]
+
+  # latest version of mypy at time pre-commit config is being set up
+  # NOTE: only checks code in "syntheseus" directory.
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.2.0
+    hooks:
+      - id: mypy
+        name: "mypy"
+        files: "syntheseus/"
+
+  # Latest ruff (does linting + more)
+  - repo: https://github.com/charliermarsh/ruff-pre-commit
+    rev: 'v0.0.263'
+    hooks:
+      - id: ruff
+        args: [--fix]
diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md
@@ -0,0 +1,9 @@
+# Microsoft Open Source Code of Conduct
+
+This project has adopted the [Microsoft Open Source Code of Conduct](https://opensource.microsoft.com/codeofconduct/).
+
+Resources:
+
+- [Microsoft Open Source Code of Conduct](https://opensource.microsoft.com/codeofconduct/)
+- [Microsoft Code of Conduct FAQ](https://opensource.microsoft.com/codeofconduct/faq/)
+- Contact [[email protected]](mailto:[email protected]) with questions or concerns
diff --git a/LICENSE b/LICENSE
@@ -0,0 +1,21 @@
+    MIT License
+
+    Copyright (c) Microsoft Corporation.
+
+    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
diff --git a/README.md b/README.md
@@ -0,0 +1,78 @@
+# Syntheseus
+
+[![CI](https://github.com/microsoft/syntheseus/actions/workflows/ci.yml/badge.svg?branch=main)](https://github.com/microsoft/syntheseus/actions/workflows/ci.yml)
+[![Python Version](https://img.shields.io/badge/python-3.7+-blue.svg)](https://www.python.org/downloads/)
+[![code style](https://img.shields.io/badge/code%20style-black-202020.svg)](https://github.com/ambv/black)
+[![License](https://img.shields.io/badge/license-MIT-green.svg)](LICENSE)
+
+Syntheseus is a package for retrosynthetic planning.
+It contains implementations of common search algorithms
+and a simple API to wrap custom reaction models and write
+custom algorithms.
+It is meant to allow for simple benchmarking of the components
+of retrosynthesis algorithms.
+
+## Installation
+
+Syntheseus is designed to have very few dependencies to allow it to
+be run in a wide range of environments.
+At the moment the only hard dependencies are `numpy`, `rdkit`, and `networkx`.
+It should be easy to install syntheseus into any environment which has these packages.
+
+Currently `syntheseus` is not hosted on `pypi`
+(although this will likely change in the future).
+To install, please run:
+
+```bash
+# Clone and cd into repo
+git clone https://github.com/microsoft/syntheseus.git
+cd syntheseus
+
+# Option 1: minimal install into current environment.
+# Assumes dependencies are already present in your environment.
+pip install .  --no-dependencies
+
+# Option 2: pip install with dependencies into current environment.
+pip install .
+
+# Option 3: create new conda environment and then install.
+conda env create -f environment.yml  # creates env named syntheseus
+conda activate syntheseus
+pip install .
+```
+
+## Development
+
+Syntheseus is currently under active development and does not have a fixed API
+(but we will fix it very soon).
+If you want to help us develop syntheseus please install and run `pre-commit`
+checks before committing code.
+
+We use `pytest` for testing. Please make sure tests pass on your branch before
+submitting a PR (and try to maintain high test coverage).
+
+```bash
+python -m pytest --cov syntheseus/tests
+```
+
+## Contributing
+
+This project welcomes contributions and suggestions.  Most contributions require you to agree to a
+Contributor License Agreement (CLA) declaring that you have the right to, and actually do, grant us
+the rights to use your contribution. For details, visit https://cla.opensource.microsoft.com.
+
+When you submit a pull request, a CLA bot will automatically determine whether you need to provide
+a CLA and decorate the PR appropriately (e.g., status check, comment). Simply follow the instructions
+provided by the bot. You will only need to do this once across all repos using our CLA.
+
+This project has adopted the [Microsoft Open Source Code of Conduct](https://opensource.microsoft.com/codeofconduct/).
+For more information see the [Code of Conduct FAQ](https://opensource.microsoft.com/codeofconduct/faq/) or
+contact [[email protected]](mailto:[email protected]) with any additional questions or comments.
+
+## Trademarks
+
+This project may contain trademarks or logos for projects, products, or services. Authorized use of Microsoft
+trademarks or logos is subject to and must follow
+[Microsoft's Trademark & Brand Guidelines](https://www.microsoft.com/en-us/legal/intellectualproperty/trademarks/usage/general).
+Use of Microsoft trademarks or logos in modified versions of this project must not cause confusion or imply Microsoft sponsorship.
+Any use of third-party trademarks or logos are subject to those third-party's policies.
diff --git a/SECURITY.md b/SECURITY.md
@@ -0,0 +1,41 @@
+<!-- BEGIN MICROSOFT SECURITY.MD V0.0.8 BLOCK -->
+
+## Security
+
+Microsoft takes the security of our software products and services seriously, which includes all source code repositories managed through our GitHub organizations, which include [Microsoft](https://github.com/microsoft), [Azure](https://github.com/Azure), [DotNet](https://github.com/dotnet), [AspNet](https://github.com/aspnet), [Xamarin](https://github.com/xamarin), and [our GitHub organizations](https://opensource.microsoft.com/).
+
+If you believe you have found a security vulnerability in any Microsoft-owned repository that meets [Microsoft's definition of a security vulnerability](https://aka.ms/opensource/security/definition), please report it to us as described below.
+
+## Reporting Security Issues
+
+**Please do not report security vulnerabilities through public GitHub issues.**
+
+Instead, please report them to the Microsoft Security Response Center (MSRC) at [https://msrc.microsoft.com/create-report](https://aka.ms/opensource/security/create-report).
+
+If you prefer to submit without logging in, send email to [[email protected]](mailto:[email protected]).  If possible, encrypt your message with our PGP key; please download it from the [Microsoft Security Response Center PGP Key page](https://aka.ms/opensource/security/pgpkey).
+
+You should receive a response within 24 hours. If for some reason you do not, please follow up via email to ensure we received your original message. Additional information can be found at [microsoft.com/msrc](https://aka.ms/opensource/security/msrc).
+
+Please include the requested information listed below (as much as you can provide) to help us better understand the nature and scope of the possible issue:
+
+  * Type of issue (e.g. buffer overflow, SQL injection, cross-site scripting, etc.)
+  * Full paths of source file(s) related to the manifestation of the issue
+  * The location of the affected source code (tag/branch/commit or direct URL)
+  * Any special configuration required to reproduce the issue
+  * Step-by-step instructions to reproduce the issue
+  * Proof-of-concept or exploit code (if possible)
+  * Impact of the issue, including how an attacker might exploit the issue
+
+This information will help us triage your report more quickly.
+
+If you are reporting for a bug bounty, more complete reports can contribute to a higher bounty award. Please visit our [Microsoft Bug Bounty Program](https://aka.ms/opensource/security/bounty) page for more details about our active programs.
+
+## Preferred Languages
+
+We prefer all communications to be in English.
+
+## Policy
+
+Microsoft follows the principle of [Coordinated Vulnerability Disclosure](https://aka.ms/opensource/security/cvd).
+
+<!-- END MICROSOFT SECURITY.MD BLOCK -->
diff --git a/SUPPORT.md b/SUPPORT.md
@@ -0,0 +1,14 @@
+# Support
+
+## How to file issues and get help  
+
+This project uses GitHub Issues to track bugs and feature requests. Please search the existing
+issues before filing new issues to avoid duplicates.  For new issues, file your bug or
+feature request as a new Issue.
+
+For help and questions about using this project, please file a GitHub Issue or email us.
+We will try to respond to all issues.
+
+## Microsoft Support Policy  
+
+Support for this project is limited to the resources listed above.
diff --git a/environment.yml b/environment.yml
@@ -0,0 +1,19 @@
+# Minimal environment for syntheseus
+name: syntheseus
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  # Core dependencies
+  - python>=3.7  # ideally 3.9+
+  - pip
+  - numpy  # required for some array computing
+  - rdkit  # required for molecule objects
+  - networkx
+  # Optional dependencies for visuzalization
+  - pillow
+  - python-graphviz
+  # For development
+  - pytest
+  - pytest-cov
+  - pre-commit