Clean Repo

.deepsource.toml

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+version = 1
+
+[[analyzers]]
+name = "python"
+enabled = true
+
+  [analyzers.meta]
+  runtime_version = "3.x.x"
+  additional_builtins = ["_", "pretty_output"]
+
+[[transformers]]
+name = "prettier"
+enabled = true
+
+[[transformers]]
+name = "isort"
+enabled = true
+
+[[transformers]]
+name = "black"
+enabled = true

.github/.codecov.yml

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+codecov:
+  notify:
+    require_ci_to_pass: no
+
+coverage:
+  precision: 2
+  round: down
+  range: "50...100"
+
+  status:
+    project:
+      default:
+        target: auto
+        threshold: 2%
+    patch:
+      default:
+        enabled: no
+        if_not_found: success
+
+comment: false

.github/ISSUE_TEMPLATE/config.yml

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+blank_issues_enabled: false
+contact_links:
+  - name: Quacc Discussion Forum
+    url: https://github.com/arosen93/quacc/discussions
+    about: Please ask and answer questions here.

.github/ISSUE_TEMPLATE/docs.md

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+---
+name: Documentation
+about: Help improve the documentation
+title: ""
+---
+
+# Proposed change to documentation

.github/ISSUE_TEMPLATE/idea.md

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+---
+name: Idea
+about: Propose a new feature to improve Quacc
+title: ""
+---
+
+# What is the proposed feature?
+
+# Any alternatives considered?

.github/ISSUE_TEMPLATE/issue.md

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+---
+name: Issue Report
+about: Raise an issue to help improve Quacc
+title: ""
+---
+
+# What is the Issue?
+
+# Steps to Reproduce the Issue
+
+# Environment
+
+- Quacc version:
+- Python version:
+- Operating system:

.github/PULL_REQUEST_TEMPLATE.md

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+<!--
+⚠️ Your pull request title should be short, detailed, and understandable to all.
+⚠️ If your pull request fixes an open issue, please link to the issue.
+⚠️ Add a note to CHANGELOG.md with summarizing the changes under the [UNRELEASED] section.
+⚠️ Make sure to add unit tests to cover any changes.
+-->
+
+- [ ] I have added unit tests to cover my changes.
+- [ ] I have updated the documentation and `CHANGELOG.md` file accordingly.

.github/dependabot.yml

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+# To get started with Dependabot version updates, you'll need to specify which
+# package ecosystems to update and where the package manifests are located.
+# Please see the documentation for all configuration options:
+# https://help.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+
+version: 2
+updates:
+  - package-ecosystem: "pip" # See documentation for possible values
+    directory: "/" # Location of package manifests
+    schedule:
+      interval: "weekly"

.github/workflows/docs.yaml

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+name: docs
+on:
+  push:
+    branches:
+      - main
+    paths:
+      - docs/**
+  pull_request:
+  release:
+    types: [published]
+
+jobs:
+  docs:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Check out repo
+        uses: actions/checkout@v3
+
+      - name: Install pandoc
+        run: sudo apt-get install pandoc
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.9'
+          cache: pip
+          cache-dependency-path: setup.py
+
+      - name: Install pip packages
+        run: |
+          pip install .[strict,docs]
+
+      - name: Build docs
+        run: sphinx-build docs/src docs_build
+        id: build_docs
+
+      - name: Deploy docs
+        uses: peaceiris/actions-gh-pages@v3
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: ./docs_build
+        if: github.ref == 'refs/heads/main' && steps.build_docs.outcome == 'success'

.github/workflows/tests.yaml

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+name: tests
+on:
+  push:
+    branches: [main]
+    paths-ignore:
+      - CHANGELOG.md
+      - .gitignore
+      - CODE_OF_CONDUCT.md
+      - LICENSE.md
+      - README.md
+      - .deepsource.toml
+      - docs/**
+  pull_request:
+  release:
+    types: [published]
+
+jobs:
+  tests:
+    strategy:
+      fail-fast: true
+      matrix:
+        python-version: ['3.8', '3.9']
+    runs-on: ubuntu-latest
+
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    steps:
+      - name: Check out repo
+        uses: actions/checkout@v3
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: pip
+          cache-dependency-path: setup.py
+
+      - name: Set up conda
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+          activate-environment: quacc-env
+
+      - name: Install pip packages
+        run: |
+          pip install .[strict,dev]
+          pip install chardet
+          pip install pytest-cov
+
+      - name: Install conda packages
+        run: |
+          conda install -c psi4 psi4
+          conda install -c conda-forge dftbplus==22.2
+      
+      - name: Set up Covalent server
+        run: |
+          echo "y" | covalent purge
+          covalent start
+
+      - name: Run tests with pytest
+        run: pytest --cov=quacc --cov-report=xml
+
+      - name: Stop Covalent server
+        run: |
+          covalent stop
+
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v3
+        if: github.repository == 'arosen93/quacc'
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          files: ./coverage.xml
+
+  release:
+    runs-on: ubuntu-latest
+    needs: tests
+    if: github.event_name == 'release' && needs.tests.result == 'success'
+    steps:
+      - name: Check out repo
+        uses: actions/checkout@v3
+
+      - name: Build and upload dist
+        run: |
+          pip install setuptools setuptools_scm wheel
+          python setup.py sdist bdist_wheel
+          twine upload --skip-existing dist/*.tar.gz
+        env:
+          TWINE_USERNAME: __token __
+          TWINE_PASSWORD: ${{ secrets.PYPI_API_TOKEN }}

.gitignore

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+*.pyc
+*.egg*
+__pycache__
+POTCAR*
+docs_build
+docs/src/reference/*
+scratch_path.txt
+build
+dist
+tmp_path.txt
+quacc-*
+tmp*
+timer.dat
+.mypy_cache*
+.DS_Store
+.ipynb_checkpoints
+ipython_config.py

CHANGELOG.md

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+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [UNRELEASED]
+
+### Added
+
+- Added optional support for Covalent as the workflow manager.
+- Improved documentation.
+- Automatic formatting of files during PRs.
+- This `CHANGELOG.md` file.
+- The `BulkToSlabsFlow` in the EMT calculator for both Covalent and Jobflow.
+- The `BulkToSlabsFlow` in the VASP calculator for Covalent.
+- `LennardJones` demonstration recipes.
+
+### Changed
+
+- Individual compute jobs are now functions instead of classes.
+- All compute jobs are wrapped by `@ct.electron` instead of `@job`.
+- Use of Jobflow is now optional.
+- Use of a MongoDB is now optional.
+- Split `quacc.util.basics` and its associated functions into `quacc.util.dicts` and `quacc.util.files`.
+- Changed the `extras` names in `setup.py`.
+- Updated the dependencies.
+- Increased default for `max_steps` in `run_ase_opt` from 100 to 500.
+- Renamed `prerelax` kwarg in `qmof_relax_job` was changed to `run_prerelax` to reflect that it is a boolean.
+- Renamed `volume_relax` kwarg in VASP recipes to `relax_volume` to reflect that it is a boolean.
+- Renamed `molden` to `write_molden` in Gaussian recipes to reflect that it is a boolean.
+- Switch license to standard BSD-3.
+- Simplified output schema for VASP slab workflows.
+- Fixed type hinting.
+
+### Fixed
+
+- If the user-specified `scratch_dir` does not exist on the filesystem when using `run_calc`, `run_ase_opt`, or `run_ase_vib`, it will be created.
+
+### Removed
+
+- Removed the `xtb` recipes in favor of the `tblite` recipes following deprecation warning.
+- Removed the `requirements.txt` file in favor of the `setup.py` file.
+
+## [0.0.6]
+
+See https://github.com/arosen93/quacc/releases/tag/v0.0.6 for more details.
+
+## [0.0.5]
+
+See https://github.com/arosen93/quacc/releases/tag/v0.0.5 for more details.
+
+## [0.0.5]
+
+See https://github.com/arosen93/quacc/releases/tag/v0.0.5 for more details.
+
+## [0.0.4]
+
+See https://github.com/arosen93/quacc/releases/tag/v0.0.4 for more details.
+
+## [0.0.3]
+
+See https://github.com/arosen93/quacc/releases/tag/v0.0.3 for more details.
+
+## [0.0.2]
+
+See https://github.com/arosen93/quacc/releases/tag/v0.0.2 for more details.
+
+## [0.0.1]
+
+See https://github.com/arosen93/quacc/releases/tag/v0.0.1 for more details.