Merge pull request #59 from RMeli/develop

Version 0.5.1
RMeli · Sep 21, 2021 · 9e9cd9a · 9e9cd9a
2 parents c3713df + 3c11da5
commit 9e9cd9a
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diff --git a/.gitignore b/.gitignore
@@ -40,6 +40,7 @@ pip-delete-this-directory.txt
 .coverage.*
 .cache
 .pytest_cache
+.hypothesis
 
 # Sphinx documentation
 docs/_build/

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -0,0 +1,27 @@
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.0.1
+    hooks:
+    - id: check-json
+    - id: check-merge-conflict
+    - id: check-yaml
+    - id: check-toml
+    - id: debug-statements
+    - id: end-of-file-fixer
+    - id: trailing-whitespace
+-   repo: https://github.com/psf/black
+    rev: 21.7b0
+    hooks:
+    -   id: black
+-   repo: https://github.com/PyCQA/flake8
+    rev: 3.9.2
+    hooks:
+    -   id: flake8
+-   repo: https://github.com/PyCQA/isort
+    rev: 5.9.3
+    hooks:
+    -   id: isort
+-   repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v0.910
+    hooks:
+    -   id: mypy
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,9 +3,30 @@
 
 ------------------------------------------------------------------------------
 
+## Version 0.5.1
+
+Date:            21/09/2021
+Contributors:    @RMeli
+
+### Fixed
+
+* Fixed wrong covalent radius in `graph.adjacency_matrix_from_atomic_coordinates()` [PR #58 | @RMeli]
+
+### Added
+
+* Added [pre-commit](https://pre-commit.com/) configuration file [PR #57 | @RMeli]
+* Added support for gzip-compressed files (`.gz`) [PR #56 | @RMeli]
+
+### Removed
+
+* Removed dependency `QCElemental` [PR #58 | @RMeli]
+
+------------------------------------------------------------------------------
+
 ## Version 0.5.0
 
 Date:            21/06/2021
+
 Contributors:    @RMeli
 
 ### Added
@@ -23,7 +44,7 @@ Contributors:    @RMeli
 ### Changed
 
 * `spyrmsd` standalone tool now invoked with `python -m spyrmsd -h` [PR #52 | @RMeli]
-* Moved `spyrmsd.coords_to_molecule` to `molecule` module [PR #52 | @RMeli]
+* Moved `spyrmsd.coords_from_molecule` to `molecule` module [PR #52 | @RMeli]
 * Moved `spyrmsd.rmsdwrapper` to `rmsd` module [PR #52 | @RMeli]
 * Long tests no longer run in CI [PR #44 | @RMeli]
 

diff --git a/CITATION.cff b/CITATION.cff
@@ -0,0 +1,25 @@
+cff-version: 1.2.0
+message: "If you use this software, please cite it as below."
+authors:
+- family-names: "Meli"
+  given-names: "Rocco"
+  orcid: "https://orcid.org/0000-0002-2845-3410"
+title: "spyrmsd"
+version: 0.5.1
+doi: 10.5281/zenodo.3631876
+date-released: 2021-06-21
+url: "https://github.com/RMeli/spyrmsd"
+preferred-citation:
+  type: article
+  authors:
+  - family-names: "Meli"
+    given-names: "Rocco"
+    orcid: "https://orcid.org/0000-0002-2845-3410"
+  - family-names: "Biggin"
+    given-names: "Philip C."
+    orcid: "https://orcid.org/0000-0001-5100-8836"
+  doi: "10.1186/s13321-020-00455-2"
+  journal: "J. Cheminform."
+  title: "spyrmsd: symmetry-corrected RMSD calculations in Python"
+  volume: 12
+  year: 2020
diff --git a/README.md b/README.md
@@ -10,7 +10,7 @@
 [![Documentation Status](https://readthedocs.org/projects/spyrmsd/badge/?version=develop)](https://spyrmsd.readthedocs.io/en/develop/?badge=develop)
 
 [![License](https://img.shields.io/github/license/RMeli/pyrmsd?color=%2333BBFF)](https://opensource.org/licenses/MIT)
-[![PyPI](https://img.shields.io/badge/PyPI-v0.5.0%20-ff69b4)](https://pypi.org/project/spyrmsd/)
+[![PyPI](https://img.shields.io/badge/PyPI-v0.5.1%20-ff69b4)](https://pypi.org/project/spyrmsd/)
 [![Conda Version](https://img.shields.io/conda/vn/conda-forge/spyrmsd.svg)](https://anaconda.org/conda-forge/spyrmsd)
 
 [![J. Cheminform.](https://img.shields.io/badge/J.%20Cheminform.-10.1186%2Fs13321--020--00455--2-blue)](https://doi.org/10.1186/s13321-020-00455-2)
@@ -71,7 +71,6 @@ The following packages are required to use `spyrmsd` as a module:
 * [graph-tool](https://graph-tool.skewed.de/) or [NetworkX](https://networkx.github.io/)
 * [numpy](https://numpy.org/)
 * [scipy](https://www.scipy.org/)
-* [qcelemental](http://docs.qcarchive.molssi.org/projects/qcelemental/en/latest/)
 
 _Note_: `spyrmsd` uses [graph-tool](https://graph-tool.skewed.de/) by default but will fall back to [NetworkX](https://networkx.github.io/) if the former is not installed (e.g. on Windows). However, in order to support cross-platform installation [NetworkX](https://networkx.github.io/) is installed by default, and [graph-tool](https://graph-tool.skewed.de/) needs to be installed manually.
 
@@ -158,8 +157,11 @@ To ensure code quality and consistency the following tools are used during devel
 
 * [black](https://black.readthedocs.io/en/stable/)
 * [Flake 8](http://flake8.pycqa.org/en/latest/) (CI)
+* [isort]()
 * [mypy](http://mypy-lang.org/) (CI)
 
+Pre-commit `git` hooks can be installed with [pre-commit](https://pre-commit.com/).
+
 ## Copyright
 
 Copyright (c) 2019-2021, Rocco Meli.

diff --git a/devtools/conda-envs/spyrmsd-all.yaml b/devtools/conda-envs/spyrmsd-all.yaml
@@ -20,9 +20,8 @@ dependencies:
   - scikit-learn
 
   # Chemistry
-  - openbabel 
+  - openbabel
   - rdkit
-  - qcelemental
 
   # Plotting
   - matplotlib

diff --git a/devtools/conda-envs/spyrmsd-docs.yaml b/devtools/conda-envs/spyrmsd-docs.yaml
@@ -13,10 +13,9 @@ dependencies:
   - graph-tool
 
   # Chemistry
-  - openbabel 
+  - openbabel
   - rdkit
-  - qcelemental
 
   # Doc
   - sphinx
-  - sphinx_rtd_theme
+  - sphinx_rtd_theme
diff --git a/devtools/conda-envs/spyrmsd-test-obabel-gt.yaml b/devtools/conda-envs/spyrmsd-test-obabel-gt.yaml
@@ -12,7 +12,6 @@ dependencies:
 
   # Chemistry
   - openbabel
-  - qcelemental
 
   # Testing
   - pytest

diff --git a/devtools/conda-envs/spyrmsd-test-obabel-nx.yaml b/devtools/conda-envs/spyrmsd-test-obabel-nx.yaml
@@ -12,7 +12,6 @@ dependencies:
 
   # Chemistry
   - openbabel
-  - qcelemental
 
   # Testing
   - pytest

diff --git a/devtools/conda-envs/spyrmsd-test-rdkit-gt.yaml b/devtools/conda-envs/spyrmsd-test-rdkit-gt.yaml
@@ -13,7 +13,6 @@ dependencies:
 
   # Chemistry
   - rdkit
-  - qcelemental
 
   # Testing
   - pytest

diff --git a/devtools/conda-envs/spyrmsd-test-rdkit-nx.yaml b/devtools/conda-envs/spyrmsd-test-rdkit-nx.yaml
@@ -13,7 +13,6 @@ dependencies:
 
   # Chemistry
   - rdkit
-  - qcelemental
 
   # Testing
   - pytest

diff --git a/devtools/conda-envs/spyrmsd.yaml b/devtools/conda-envs/spyrmsd.yaml
@@ -9,6 +9,3 @@ dependencies:
   - numpy
   - scipy
   - graph-tool
-
-  # Chemistry
-  - qcelemental
diff --git a/docs/source/api/spyrmsd.constants.rst b/docs/source/api/spyrmsd.constants.rst
@@ -0,0 +1,7 @@
+spyrmsd.constants module
+========================
+
+.. automodule:: spyrmsd.constants
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/source/api/spyrmsd.due.rst b/docs/source/api/spyrmsd.due.rst
@@ -0,0 +1,7 @@
+spyrmsd.due module
+==================
+
+.. automodule:: spyrmsd.due
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/source/api/spyrmsd.rst b/docs/source/api/spyrmsd.rst
@@ -21,6 +21,8 @@ Submodules
 .. toctree::
    :maxdepth: 4
 
+   spyrmsd.constants
+   spyrmsd.due
    spyrmsd.graph
    spyrmsd.hungarian
    spyrmsd.io

diff --git a/docs/source/installation.rst b/docs/source/installation.rst
@@ -47,7 +47,6 @@ The following packages are required to use ``spyrmsd`` as a module:
 * graph-tool_ or NetworkX_
 * numpy_
 * scipy_
-* qcelemental_
 
 .. note::
    ``spyrmsd`` uses graph-tool_ by default but will  fall back  to NetworkX_ if the former is not installed (e.g. on Windows).
@@ -72,4 +71,3 @@ Additionally, one of the following packages is required to use ``spyrmsd`` as a
 .. _NetworkX: https://networkx.github.io/
 .. _numpy: https://numpy.org/
 .. _scipy: https://www.scipy.org/
-.. _qcelemental: http://docs.qcarchive.molssi.org/projects/qcelemental/en/latest/
diff --git a/pyproject.toml b/pyproject.toml
@@ -10,8 +10,7 @@ author = "Rocco Meli"
 author-email = "[email protected]"
 home-page = "https://spyrmsd.readthedocs.io"
 classifiers = [
-    "License :: OSI Approved :: MIT License", 
+    "License :: OSI Approved :: MIT License",
     "Programming Language :: Python :: 3",]
 requires-python = ">=3.6"
-requires = ["numpy", "scipy", "networkx>=2", "qcelemental"]
-
+requires = ["numpy", "scipy", "networkx>=2"]
diff --git a/setup.py b/setup.py
@@ -31,7 +31,7 @@
     packages=find_packages(),
     include_package_data=True,
     url="https://spyrmsd.readthedocs.io",
-    install_requires=["numpy", "scipy", "qcelemental", "networkx>=2"],
+    install_requires=["numpy", "scipy", "networkx>=2"],
     extras_require={"bib": ["duecredit"]},
     platforms=["Linux", "Mac OS-X", "Unix", "Windows"],
     python_requires=">=3.6",

diff --git a/spyrmsd/__main__.py b/spyrmsd/__main__.py
@@ -4,12 +4,11 @@
 
 if __name__ == "__main__":
 
-    from spyrmsd import io
-    from spyrmsd.rmsd import rmsdwrapper
-
+    import argparse as ap
     import sys
 
-    import argparse as ap
+    from spyrmsd import io
+    from spyrmsd.rmsd import rmsdwrapper
 
     parser = ap.ArgumentParser(
         prog="python -m spyrmsd",