deepmedchem 0.2.0b1__tar.gz

deepmedchem-0.2.0b1/.github/workflows/ci.yml

@@ -0,0 +1,39 @@
+name: ci
+
+on:
+  push:
+    branches: [main]
+  release:
+    types: [published]
+
+concurrency:
+  group: deepmedchem-python-ci-${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  test-and-package:
+    name: Python 3.10 test and package
+    runs-on: ubuntu-latest
+    timeout-minutes: 10
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
+      - run: python -m pip install -e ".[test]"
+      - run: ruff check .
+      - run: pytest
+      - run: python -m build
+      - run: python -m twine check dist/*
+      - name: Wheel installation smoke test
+        run: |
+          python -m venv /tmp/deepmedchem-wheel-smoke
+          /tmp/deepmedchem-wheel-smoke/bin/python -m pip install dist/*.whl
+          /tmp/deepmedchem-wheel-smoke/bin/python - <<'PY'
+          from deepmedchem import AsyncClient, Client, Run, Selection
+
+          selection = Selection.from_database("example").sample(seed=42).limit(10)
+          assert Run.selection(selection).to_dict()["schema_version"] == "run/1"
+          assert Client and AsyncClient
+          print("wheel import and builder smoke passed")
+          PY

deepmedchem-0.2.0b1/.github/workflows/release.yml

@@ -0,0 +1,48 @@
+name: release
+
+on:
+  workflow_dispatch:
+    inputs:
+      publish_pypi:
+        description: Publish this build with the configured PyPI Trusted Publisher
+        type: boolean
+        required: true
+        default: false
+
+permissions:
+  contents: read
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    timeout-minutes: 10
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
+      - run: python -m pip install build twine
+      - run: python -m build
+      - run: python -m twine check dist/*
+      - uses: actions/upload-artifact@v4
+        with:
+          name: python-dist
+          path: dist/*
+          retention-days: 1
+
+  publish-pypi:
+    if: inputs.publish_pypi
+    needs: build
+    runs-on: ubuntu-latest
+    timeout-minutes: 10
+    environment: pypi
+    permissions:
+      id-token: write
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          name: python-dist
+          path: dist
+      - uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          password: ${{ secrets.PYPI_API_TOKEN }}

deepmedchem-0.2.0b1/.gitignore

@@ -0,0 +1,218 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[codz]
+*$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
+
+# UV
+#   Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+# uv.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
+# poetry.toml
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#   pdm recommends including project-wide configuration in pdm.toml, but excluding .pdm-python.
+#   https://pdm-project.org/en/latest/usage/project/#working-with-version-control
+# pdm.lock
+# pdm.toml
+.pdm-python
+.pdm-build/
+
+# pixi
+#   Similar to Pipfile.lock, it is generally recommended to include pixi.lock in version control.
+# pixi.lock
+#   Pixi creates a virtual environment in the .pixi directory, just like venv module creates one
+#   in the .venv directory. It is recommended not to include this directory in version control.
+.pixi
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# Redis
+*.rdb
+*.aof
+*.pid
+
+# RabbitMQ
+mnesia/
+rabbitmq/
+rabbitmq-data/
+
+# ActiveMQ
+activemq-data/
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.envrc
+.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/
+
+# Abstra
+#   Abstra is an AI-powered process automation framework.
+#   Ignore directories containing user credentials, local state, and settings.
+#   Learn more at https://abstra.io/docs
+.abstra/
+
+# Visual Studio Code
+#   Visual Studio Code specific template is maintained in a separate VisualStudioCode.gitignore 
+#   that can be found at https://github.com/github/gitignore/blob/main/Global/VisualStudioCode.gitignore
+#   and can be added to the global gitignore or merged into this file. However, if you prefer, 
+#   you could uncomment the following to ignore the entire vscode folder
+# .vscode/
+# Temporary file for partial code execution
+tempCodeRunnerFile.py
+
+# Ruff stuff:
+.ruff_cache/
+
+# PyPI configuration file
+.pypirc
+
+# Marimo
+marimo/_static/
+marimo/_lsp/
+__marimo__/
+
+# Streamlit
+.streamlit/secrets.toml

deepmedchem-0.2.0b1/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2026 Deep MedChem
+
+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.

deepmedchem-0.2.0b1/PKG-INFO

@@ -0,0 +1,192 @@
+Metadata-Version: 2.4
+Name: deepmedchem
+Version: 0.2.0b1
+Summary: Official Python client for the DeepMedChem chemical-space platform
+Project-URL: Homepage, https://deepmedchem.com
+Project-URL: Documentation, https://docs.deepmedchem.com/docs/python/quickstart
+Project-URL: Repository, https://github.com/Deep-MedChem/deepmedchem-python
+Project-URL: Issues, https://github.com/Deep-MedChem/deepmedchem-python/issues
+Author: Deep MedChem
+License-Expression: MIT
+License-File: LICENSE
+Keywords: api-client,chemical-space,cheminformatics,drug-discovery
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Science/Research
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Scientific/Engineering :: Chemistry
+Classifier: Typing :: Typed
+Requires-Python: >=3.10
+Requires-Dist: httpx<1,>=0.27
+Requires-Dist: keyring<27,>=25.3
+Requires-Dist: platformdirs<5,>=4.2
+Requires-Dist: pydantic<3,>=2.8
+Requires-Dist: pyyaml<7,>=6
+Requires-Dist: tomli<3,>=2; python_version < '3.11'
+Provides-Extra: auth
+Provides-Extra: test
+Requires-Dist: build<2,>=1.2; extra == 'test'
+Requires-Dist: keyring<27,>=25.3; extra == 'test'
+Requires-Dist: pytest<10,>=8.2; extra == 'test'
+Requires-Dist: ruff>=0.6; extra == 'test'
+Requires-Dist: twine<7,>=5; extra == 'test'
+Description-Content-Type: text/markdown
+
+# DeepMedChem Python SDK
+
+The official, chemistry-thin Python client for the DeepMedChem hosted chemical-space platform.
+It contains no RDKit, models, databases, or proprietary search implementation.
+
+> **Beta:** `deepmedchem` 0.2 is available for early use. APIs may still change before the
+> stable release.
+
+## Installation
+
+```bash
+pip install deepmedchem
+```
+
+Authenticate once with the OS credential store, or set `DEEPMEDCHEM_API_KEY` in automation:
+
+```bash
+deepmedchem login
+deepmedchem status
+```
+
+## Quickstart
+
+```python
+import deepmedchem as dmc
+
+result = dmc.search(
+    "CC(=O)OC1=CC=CC=C1C(=O)O",  # Aspirin
+    database="enamine-real-v5a",
+    method="shape",
+    limit=3,
+)
+
+print(repr(result))
+for hit in result.hits:
+    price = f"${hit.price}" if hit.price is not None else "unavailable"
+    print(f"{hit.rank}  score={hit.score:.4f}  price={price}  {hit.smiles}")
+```
+
+Example output (the database release and search results can change):
+
+```text
+SearchResult(3 molecules, method='shape', database='enamine-real-v5a')
+1  score=0.9726  price=$245  O=C(O)Oc1ccccc1C(=O)O
+2  score=0.9719  price=$163  COC(=O)Oc1ccccc1C(=O)O
+3  score=0.8713  price=$245  O=C(O)COc1ccccc1C(=O)O
+```
+
+Prices are whole US dollars for delivery to the United States and default to 1 mg where the
+vendor uses pack sizes. They are returned in the original search response, so both `hit.price`
+and the aligned `result.prices` list are available without another API request. An unavailable
+price is `None`.
+
+| Database | Price available | Basis |
+| --- | --- | --- |
+| Freedom Space 5 | Yes | $250 at 1 mg |
+| Enamine REAL | Yes | $163 or $245, selected by the trained factorized model |
+| eMolecules Synple | Yes | Building-block prices plus reaction price |
+| eMolecules eXplore | Yes | Building-block prices plus reaction price |
+| VAST | No | — |
+| d2b / molecule.one | No | — |
+| ChemInfinita | No | — |
+
+## SMILES and SMARTS substructure search
+
+Use `format="smiles"` for a concrete molecular graph, including the existing
+junction-spanning examples. Use `format="smarts"` for atom lists, ring constraints,
+recursive expressions, and other SMARTS query features:
+
+```python
+junction = dmc.substructure(
+    "CNC(=O)N1CCC1", format="smiles", database="enamine-real-v5a", limit=10
+)
+hydrazides = dmc.substructure(
+    "[N;R0][N;R0]C(=O)", format="smarts", database="enamine-real-v5a", limit=10
+)
+```
+
+See the runnable [substructure example](examples/docs/substructure_search.py) for several
+SQC-derived SMARTS queries. Complex recursive SMARTS can require a longer timeout.
+
+Module-level `search`, `substructure`, `sample`, and `catalog` operations create and close a small
+internal client. The explicit `Client` remains available for connection reuse and advanced
+selections/runs. Search results behave as ordered SMILES sequences (`result[0]`, `result[:3]`,
+`list(result)`) while retaining typed hits, scores, prices, metadata, warnings, and the complete raw
+response locally.
+
+Credentials resolve from an explicit `api_key`, `DEEPMEDCHEM_API_KEY`, compatibility environment
+variables, a custom credential provider, or the selected profile's OS-keyring entry. Use
+`deepmedchem login --profile dev` for the development service; profiles never share credentials.
+
+Every request identifies its source with `X-DMC-Client`, `X-DMC-Client-Version`, and
+`X-DMC-SDK-Version`. The default values attribute direct SDK use to `deepmedchem-python`; an
+application such as Navigator can override `application` and `application_version` while retaining
+the installed SDK version separately.
+
+## Selections and durable runs
+
+`Selection` and `Run` are immutable, chemistry-thin builders. They produce the public
+`molecule-selection/1` and `run/1` documents; all chemistry and capability validation remains on
+the API.
+
+```python
+from deepmedchem import Client, Run, Selection
+
+template = (
+    Selection.from_database("enamine-real-v5a")
+    .ranked()
+    .maximize_similarity("rdkit.ecfp4_tanimoto", reference="query")
+    .limit(10)
+)
+
+run_spec = Run.selection_batch(
+    template=template,
+    items={
+        "lead-001": {"query": "CCO"},
+        "lead-002": {"query": "CCN"},
+    },
+)
+
+with Client() as dmc:
+    run = dmc.runs.create(run_spec, idempotency_key="lead-set-v1")
+    terminal = dmc.runs.wait(run.id)
+    results = list(dmc.runs.iter_results(terminal.id))
+```
+
+`AsyncClient` offers matching asynchronous operations and iterators. `DMCClient` and
+`AsyncDMCClient` are compatibility aliases for code written against the pre-split Navigator SDK.
+
+## Navigator
+
+The `navigator` terminal application is distributed separately as `dmc-navigator`. It depends on
+this SDK and adds file handling, login commands, terminal presentation, and Navigator-specific
+workflows.
+
+## Development
+
+```bash
+python -m venv .venv
+. .venv/bin/activate
+python -m pip install -e ".[test]"
+ruff check .
+pytest
+python -m build
+twine check dist/*
+```
+
+API documentation: <https://docs.deepmedchem.com/docs/python/quickstart>
+
+Runnable authenticated examples using the established Enamine query panels are in
+[`examples/live`](examples/live/README.md).
+
+For interactive RDKit visualization of similarity and SMARTS substructure queries, open the
+[`Enamine search notebook`](examples/notebooks/enamine_search.ipynb).

deepmedchem-0.2.0b1/README.md

@@ -0,0 +1,154 @@
+# DeepMedChem Python SDK
+
+The official, chemistry-thin Python client for the DeepMedChem hosted chemical-space platform.
+It contains no RDKit, models, databases, or proprietary search implementation.
+
+> **Beta:** `deepmedchem` 0.2 is available for early use. APIs may still change before the
+> stable release.
+
+## Installation
+
+```bash
+pip install deepmedchem
+```
+
+Authenticate once with the OS credential store, or set `DEEPMEDCHEM_API_KEY` in automation:
+
+```bash
+deepmedchem login
+deepmedchem status
+```
+
+## Quickstart
+
+```python
+import deepmedchem as dmc
+
+result = dmc.search(
+    "CC(=O)OC1=CC=CC=C1C(=O)O",  # Aspirin
+    database="enamine-real-v5a",
+    method="shape",
+    limit=3,
+)
+
+print(repr(result))
+for hit in result.hits:
+    price = f"${hit.price}" if hit.price is not None else "unavailable"
+    print(f"{hit.rank}  score={hit.score:.4f}  price={price}  {hit.smiles}")
+```
+
+Example output (the database release and search results can change):
+
+```text
+SearchResult(3 molecules, method='shape', database='enamine-real-v5a')
+1  score=0.9726  price=$245  O=C(O)Oc1ccccc1C(=O)O
+2  score=0.9719  price=$163  COC(=O)Oc1ccccc1C(=O)O
+3  score=0.8713  price=$245  O=C(O)COc1ccccc1C(=O)O
+```
+
+Prices are whole US dollars for delivery to the United States and default to 1 mg where the
+vendor uses pack sizes. They are returned in the original search response, so both `hit.price`
+and the aligned `result.prices` list are available without another API request. An unavailable
+price is `None`.
+
+| Database | Price available | Basis |
+| --- | --- | --- |
+| Freedom Space 5 | Yes | $250 at 1 mg |
+| Enamine REAL | Yes | $163 or $245, selected by the trained factorized model |
+| eMolecules Synple | Yes | Building-block prices plus reaction price |
+| eMolecules eXplore | Yes | Building-block prices plus reaction price |
+| VAST | No | — |
+| d2b / molecule.one | No | — |
+| ChemInfinita | No | — |
+
+## SMILES and SMARTS substructure search
+
+Use `format="smiles"` for a concrete molecular graph, including the existing
+junction-spanning examples. Use `format="smarts"` for atom lists, ring constraints,
+recursive expressions, and other SMARTS query features:
+
+```python
+junction = dmc.substructure(
+    "CNC(=O)N1CCC1", format="smiles", database="enamine-real-v5a", limit=10
+)
+hydrazides = dmc.substructure(
+    "[N;R0][N;R0]C(=O)", format="smarts", database="enamine-real-v5a", limit=10
+)
+```
+
+See the runnable [substructure example](examples/docs/substructure_search.py) for several
+SQC-derived SMARTS queries. Complex recursive SMARTS can require a longer timeout.
+
+Module-level `search`, `substructure`, `sample`, and `catalog` operations create and close a small
+internal client. The explicit `Client` remains available for connection reuse and advanced
+selections/runs. Search results behave as ordered SMILES sequences (`result[0]`, `result[:3]`,
+`list(result)`) while retaining typed hits, scores, prices, metadata, warnings, and the complete raw
+response locally.
+
+Credentials resolve from an explicit `api_key`, `DEEPMEDCHEM_API_KEY`, compatibility environment
+variables, a custom credential provider, or the selected profile's OS-keyring entry. Use
+`deepmedchem login --profile dev` for the development service; profiles never share credentials.
+
+Every request identifies its source with `X-DMC-Client`, `X-DMC-Client-Version`, and
+`X-DMC-SDK-Version`. The default values attribute direct SDK use to `deepmedchem-python`; an
+application such as Navigator can override `application` and `application_version` while retaining
+the installed SDK version separately.
+
+## Selections and durable runs
+
+`Selection` and `Run` are immutable, chemistry-thin builders. They produce the public
+`molecule-selection/1` and `run/1` documents; all chemistry and capability validation remains on
+the API.
+
+```python
+from deepmedchem import Client, Run, Selection
+
+template = (
+    Selection.from_database("enamine-real-v5a")
+    .ranked()
+    .maximize_similarity("rdkit.ecfp4_tanimoto", reference="query")
+    .limit(10)
+)
+
+run_spec = Run.selection_batch(
+    template=template,
+    items={
+        "lead-001": {"query": "CCO"},
+        "lead-002": {"query": "CCN"},
+    },
+)
+
+with Client() as dmc:
+    run = dmc.runs.create(run_spec, idempotency_key="lead-set-v1")
+    terminal = dmc.runs.wait(run.id)
+    results = list(dmc.runs.iter_results(terminal.id))
+```
+
+`AsyncClient` offers matching asynchronous operations and iterators. `DMCClient` and
+`AsyncDMCClient` are compatibility aliases for code written against the pre-split Navigator SDK.
+
+## Navigator
+
+The `navigator` terminal application is distributed separately as `dmc-navigator`. It depends on
+this SDK and adds file handling, login commands, terminal presentation, and Navigator-specific
+workflows.
+
+## Development
+
+```bash
+python -m venv .venv
+. .venv/bin/activate
+python -m pip install -e ".[test]"
+ruff check .
+pytest
+python -m build
+twine check dist/*
+```
+
+API documentation: <https://docs.deepmedchem.com/docs/python/quickstart>
+
+Runnable authenticated examples using the established Enamine query panels are in
+[`examples/live`](examples/live/README.md).
+
+For interactive RDKit visualization of similarity and SMARTS substructure queries, open the
+[`Enamine search notebook`](examples/notebooks/enamine_search.ipynb).