Release 0.4.0

.github/pull_request_template.md

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+### Description
+
+### Checklist
+If you're providing a new node for maize, please make sure of the following:
+- [ ] My node has been placed in an appropriate subfolder, and exposed in the corresponding `__init__.py` file
+- [ ] My node has tests (using `TestRig`, and testing a variety of inputs and parameters)
+- [ ] My node is fully documented using [ReST syntax](https://www.sphinx-doc.org/en/master/usage/restructuredtext/basics.html) and references if neccessary
+- [ ] My code passes type-checking using `mypy --strict --explicit-package-bases`
+- [ ] My code lints correctly
+- [ ] My code has been formatted with `black`, using a `line-length` of 100

.github/workflows/mypy.yml

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+name: Mypy
+
+on: [push, workflow_dispatch]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.10"]
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v3
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh |
+            bash -s -- --batch
+        conda env create -f env-dev.yml
+        conda run --name maize-dev pip install --no-deps .
+        conda run --name maize-dev pip install types-PyYAML types-toml
+    - name: Analysing the code with mypy
+      run: |
+        conda run --name maize-dev mypy --strict --explicit-package-bases maize/steps maize/utilities

.github/workflows/pylint.yml

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+name: Pylint
+
+on: [push, workflow_dispatch]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.10"]
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v3
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh |
+            bash -s -- --batch
+        conda env create -f env-dev.yml
+        conda run --name maize-dev pip install --no-deps .
+    - name: Analysing the code with pylint
+      run: |
+        conda run --name maize-dev pylint --exit-zero maize/steps maize/utilities

.github/workflows/test-docking.yml

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+# This workflow will install Python dependencies, run tests and lint with a single version of Python
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
+
+name: Test-docking
+
+on:
+  push:
+    branches: [ "master" ]
+  pull_request:
+    branches: [ "master" ]
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.10"]
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v3
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh |
+            bash -s -- --batch
+        conda env create -f env-dev.yml
+        conda run --name maize-dev pip install --no-deps .
+        conda run --name maize-dev ./devtools/install_test_deps.sh
+    - name: Run docking test with pytest
+      run: |
+        conda run --name maize-dev pytest tests/test_docking.py

.gitignore

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+.ipynb_checkpoints
+.VSCodeCounter
+__pycache__
+*.egg-info
+.coverage
+.vscode
+.pylintrc
+.*_cache
+*_autosummary
+coverage
+docs/_build
+docs/_static
+docs/autosummary
+docs/Makefile
+docs/make.bat
+/test-config.toml
+test
+testing.ipynb
+deplicenses.txt

AUTHORS.md

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+Primary Authors
+===============
+- [Thomas Löhr](https://github.com/tlhr)
+- Marco Klähn
+
+Contributing Authors
+====================
+- Michele Assante
+- Lili Cao
+- Michael Dodds
+- Jon Paul Janet
+- Mikhail Kabeshov
+- Alessandro Tibo

CHANGELOG.md

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+# CHANGELOG
+
+## Version 0.4.0
+### Features
+- Added Gromacs module (Lily)
+- Added flexible docking with Vina
+- Added additional tag handling utilities
+- Added explicit prior and agent parameters to Reinvent
+- Added `IsomerCollection` tagging system
+- Added active learning module, subgraph, and example notebook
+
+### Changes
+- Reorganised cheminformatics
+
+### Fixes
+- Fixed relative-absolute conversion of BFEs not using reference correctly
+- Fixed `MakeAbsolute` not handling disconnected subgraphs
+- Fixed `SaveLibrary` not saving all conformers
+- Fixed `AutoDockGPU` not detecting tarred grids as inputs
+- Fixed OpenFE dumping failing on existing dump
+
+## Version 0.3.2
+### Features
+- Tests can now be skipped automatically based on available config options
+- Added absolute free energy conversion for `OpenRFE`
+
+### Changes
+- Updated REINVENT implementation
+- Updated bundled maize
+
+## Version 0.3.1
+### Changes
+- Updated bundled maize
+
+### Fixes
+- Fixed SaveCSV not using the correct tag order
+- Various type fixes
+
+## Version 0.3.0
+### Features
+- Several new filters
+- More subgraphs
+- OpenFE node
+- Constraints for AutoDockGPU and Glide
+- Nodes for reaction prediction
+- Batched CSV saving
+- Flexible docking with Vina
+
+### Changes
+- Various improvements to RMSD filtering
+- Performance improvements for `Isomer` tag handling
+- Allowed certain RDKit ops to timeout
+- More robust Schrodinger job handling
+- Integration tests
+- Maize core wheel for automated builds
+
+### Fixes
+- Fix for zombie threads when using REINVENT
+- Fix for installation only being possible using `-e`
+- Cleaned up typing
+
+## Version 0.2.3
+### Changes
+- Removed interface for REINVENT 3.2
+
+### Fixes
+- Cleanup of package structure
+- Updated dependencies
+- Added explicit check for Schrodinger license
+
+## Version 0.2.2
+### Features
+- Added Schrodinger grid preparation tools
+
+### Changes
+- Adjusted timeout for Gypsum-DL
+- Various enhancements for GLIDE
+
+### Fixes
+- Fixed `Vina` command validation for newer `Vina` versions
+- Fixed parsing issues for `Vina`
+
+
+## Version 0.2.1
+### Features
+- Improved REINVENT interface, using `ReinventEntry` and `ReinventExit`
+
+### Changes
+- Timeouts for conformer / isomer generation
+- Improved logging
+
+### Fixes
+- Check for zero bytes for `Vina` output
+
+## Version 0.2.0
+
+Updated for public release.
+
+## Version 0.1
+
+Initial release.

CONTRIBUTING.md

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+Contributing
+============
+This is a summary of code conventions and contributing guidelines for *maize-contrib*.
+
+Issues & Pull requests
+----------------------
+To report bugs or suggest new features, open an issue, or submit a pull request with your changes.
+
+Installation
+------------
+If you will be working on both *maize* and *maize-contrib* it will be easiest to install the environment for *maize-contrib* first, as it encompasses all dependencies for maize and domain-specific extensions. You can then install both packages using editable installs.
+
+Code style
+----------
+We use the [PEP8](https://peps.python.org/pep-0008/) convention with a 100 character line length - you can use `black` as a formatter with the `--line-length=100` argument. The code base features full static typing, use the following [mypy](https://mypy.readthedocs.io/en/stable/) command to check it:
+
+```shell
+mypy --follow-imports=silent --ignore-missing-imports --strict maize
+```
+
+Type hints should only be omitted when either mypy or typing doesn't yet fully support the required feature, such as [higher-kinded types](https://github.com/python/typing/issues/548) or type-tuples ([PEP646](https://peps.python.org/pep-0646/)).
+
+> [!IMPORTANT]
+> If you installed the maize core in editable mode you may need to specify its location with `$MYPYPATH` to ensure `mypy` can find it. See this [setuptools issue](https://github.com/pypa/setuptools/issues/3518).
+
+Documentation
+-------------
+Every public class or function should feature a full docstring with a full description of parameters / attributes. Custom nodes should follow the example node in `maize/steps/mai/example/step.py`, default values will be detected and added to the documentation automatically. We follow the [numpy docstring](https://numpydoc.readthedocs.io/en/latest/format.html) standard for readability reasons. Docs are built using [sphinx](https://www.sphinx-doc.org/en/master/) in the `docs` folder:
+
+```shell
+make html
+```
+
+There will be some warnings from `autosummary` that can be ignored. The built docs can then be found in `docs/_build/html`. To preview them locally you can start a local webserver running the following command in the `docs/_build/html` folder:
+
+```shell
+python -m http.server 8000
+```
+
+The docs are then available at `http://localhost:8000/index.html`.
+
+Testing
+-------
+Tests are written using [pytest](https://docs.pytest.org/en/7.2.x/contents.html), located together with the node, and can be run with:
+
+```shell
+pytest --log-cli-level=DEBUG maize/steps/mai/example/step.py
+```
+
+Any custom nodes should be covered by suitable tests in a `TestSuite<node-name>` class. To make testing the nodes a bit easier, you can use the `maize.utilities.testing.TestRig` class together with `maize.utilities.testing.MockChannel` if required.
+
+Coverage can be reported using:
+
+```shell
+pytest tests/ -v --cov maize --cov-report html:coverage
+```
+
+New versions
+------------
+To release a new version of maize, perform the following steps:
+
+1. Create a new branch titled `release-x.x.x`
+2. Add your changes to `CHANGELOG.md`
+3. Increment version in `pyproject.toml`
+4. Commit your changes
+5. Rebuild and update the remote documentation (see above)
+6. Create a tag using `git tag vx.x.x`
+7. Push your changes with `git push` and `git push --tags`
+8. Update `master`:
+    1. `git checkout master`
+    2. `git pull origin master`
+    3. `git merge release-x.x.x`
+    4. `git push origin master`