Release 1.0.0

.coveragerc

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+[run]
+source =
+    scine_puffin
+[report]
+omit =
+    */python?.?/*
+    */site-packages/nose/*
+    # ignore _version.py and versioneer.py
+    .*version.*
+    *_version.py
+    */tests/*
+
+exclude_lines =
+    if __name__ == '__main__':

.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# Distribution / packaging
+venv/
+*.egg-info/
+*.egg
+
+# Unit test / coverage reports
+.coverage
+.coverage.*
+.cache
+coverage.xml
+
+# Sphinx documentation
+docs/build/
+docs/source/generated/
+
+# pytest
+.pytest_cache/
+
+# Editor files
+#mac
+.DS_Store
+*~
+
+#vim
+*.swp
+*.swo
+
+#pycharm
+.idea/
+
+#VSCode
+.vscode/

.gitmodules

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+[submodule "dev"]
+	path = dev
+	url = https://github.com/qcscine/development-utils.git

CHANGELOG.rst

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+Changelog
+=========
+
+Release 1.0.0
+-------------
+
+Initial Features:
+ - Runs as a daemon
+    - With possible graceful timeout/shutdown after a user-defined time
+    - With automatic cleaning of failed jobs
+    - With a tolerance for database disconnects at the end of jobs
+ - Provides a containerized version
+    - Usable with Docker, Podman, and Singularity
+    - Includes/installs all open source programs
+
+Initial Jobs:
+ - Open source (SCINE-based) jobs
+    - Conformer generation
+    - Artificial force induced reactions (AFIR) optimization
+    - Bond order generation
+    - Geometry optimization
+    - Hessian generation incl. thermo chemistry
+    - IRC scan
+    - Reactive complex reaction probing (using AFIR, NT1, NT2)
+    - Single point calculations
+    - Transition state optimization
+
+ - Specialized jobs:
+    - Gaussian: partial charges - charge model 5 (CM5)
+    - Orca: geometry optimization
+    - Turbomole: geometry optimization
+    - Turbomole: single point
+    - Turbomole: Hessian 
+    - RDKit: conformer generation
+
+Initially interfaced programs used in calculations:
+ - SCINE Molassembler
+ - SCINE Readuct
+ - SCINE Sparrow
+ - Serenity (v1.4, via SCINE Serenity Wrapper)
+ - XTB (v6.4.1, via SCINE XTB Wrapper)
+ - Orca (v4.1.X, v4.2.X)
+ - Turbomole (v7.x.x)
+ - Gaussian (g09 Rev. D.01)
+
+

CONTRIBUTING.rst

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+Contributing to SCINE Puffin
+============================
+
+Contribution Process
+--------------------
+
+The development for this code is done in a private repository maintained by the 
+Reiher Research Group. GitHub is only used for the official releases.
+
+If you would like to contribute a larger change, please write to [email protected].
+For smaller changes, you can create a pull request on GitHub. If we agree with
+the changes, a member of the Reiher Research Group will include them in our
+development code. Of course, we will give proper acknowledgment for any external
+contribution (see below for a list of all contributors). As soon as these changes 
+are available in an official release, we will close the corresponding pull requests 
+and/or issues on GitHub.
+
+Please note that contributing a small change does in no way mean that you will
+be added to the author list of a future paper and/or Zenodo entry!
+
+Main Contributors
+-----------------
+
+Almost all contributions to SCINE in general and this repository in specific come 
+from members of the Reiher research group.
+
+Further Contributors
+--------------------
+
+So far, no one else has contributed to this repository.

LICENSE.txt

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+Copyright ETH Zurich, Laboratory of Physical Chemistry, Reiher Group
+
+Redistribution and use in source and binary forms, with or without modification,
+are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+this list of conditions and the following disclaimer in the documentation and/or
+other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its contributors
+may be used to endorse or promote products derived from this software without
+specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
+IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
+INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
+BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
+OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED
+OF THE POSSIBILITY OF SUCH DAMAGE.

MANIFEST.in

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+include LICENSE
+include README.rst
+include CHANGELOG.rst
+include requirements.txt
+
+recursive-exclude * __pycache__
+recursive-exclude * *.py[co]
+
+recursive-include docs *.rst conf.py Makefile make.bat
+
+include versioneer.py
+include scine_puffin/_version.py
+
+# If including data files in the package, add them like:
+include scine_puffin/tests/resources