Merge pull request #23 from RMeli/develop

graph-tool Support and General Refactoring
RMeli · Feb 25, 2020 · 1c0d03a · 1c0d03a
2 parents 4970dff + e981043
commit 1c0d03a
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diff --git a/.appveyor.yml b/.appveyor.yml
@@ -3,22 +3,28 @@ environment:
     - PYTHON: "C:\\Miniconda36-x64"
       PYTHON_VERSION: "3.6"
       CHEM: "obabel"
+      GRAPH: "nx"
       PYTHON_ARCH: "64"
 
     - PYTHON: "C:\\Miniconda36-x64"
       PYTHON_VERSION: "3.6"
       CHEM: "rdkit"
+      GRAPH: "nx"
       PYTHON_ARCH: "64"
 
     - PYTHON: "C:\\Miniconda37-x64"
       PYTHON_VERSION: "3.7"
       CHEM: "obabel"
+      GRAPH: "nx"
       PYTHON_ARCH: "64"
 
     - PYTHON: "C:\\Miniconda37-x64"
       PYTHON_VERSION: "3.7"
       CHEM: "rdkit"
+      GRAPH: "nx"
       PYTHON_ARCH: "64"
+
+    # graph-tool not supported on Windows
 
 install:
     # Make sure pip is around
@@ -35,7 +41,7 @@ install:
   - conda update --all
 
     # Create test environment for package
-  - python devtools\\scripts\\create_conda_env.py -n=test -p=%PYTHON_VERSION% devtools\\conda-envs\\spyrmsd-test-%CHEM%.yaml
+  - python devtools\\scripts\\create_conda_env.py -n=test -p=%PYTHON_VERSION% devtools\\conda-envs\\spyrmsd-test-%CHEM%-%GRAPH%.yaml
 
     # Activate the test environment
   - activate test
@@ -47,10 +53,9 @@ build: false
 
 test_script:
     # Run test and get coverage report
-  - pytest -v --cov=spyrmsd tests
+  - pytest -v --cov=spyrmsd tests --runslow
 
     # Run checks
-  - black .
   - flake8
   - mypy
 

diff --git a/.travis.yml b/.travis.yml
@@ -7,43 +7,98 @@ matrix:
       env: 
         - PYTHON_VER=3.6
         - CHEM=obabel
+        - GRAPH=nx
     - os: osx
       language: generic
       env: 
         - PYTHON_VER=3.6
         - CHEM=rdkit
+        - GRAPH=nx
     - os: osx
       language: generic
       env: 
         - PYTHON_VER=3.7
         - CHEM=obabel
+        - GRAPH=nx
     - os: osx
       language: generic
       env: 
         - PYTHON_VER=3.7
         - CHEM=rdkit
+        - GRAPH=nx
+    - os: osx
+      language: generic
+      env: 
+        - PYTHON_VER=3.6
+        - CHEM=obabel
+        - GRAPH=gt
+    - os: osx
+      language: generic
+      env: 
+        - PYTHON_VER=3.6
+        - CHEM=rdkit
+        - GRAPH=gt
+    - os: osx
+      language: generic
+      env: 
+        - PYTHON_VER=3.7
+        - CHEM=obabel
+        - GRAPH=gt
+    - os: osx
+      language: generic
+      env: 
+        - PYTHON_VER=3.7
+        - CHEM=rdkit
+        - GRAPH=gt
 
-
     - os: linux
       language: generic
       env: 
         - PYTHON_VER=3.6
         - CHEM=obabel
+        - GRAPH=nx
+    - os: linux
+      language: generic
+      env: 
+        - PYTHON_VER=3.6
+        - CHEM=rdkit
+        - GRAPH=nx
+    - os: linux
+      language: generic
+      env: 
+        - PYTHON_VER=3.7
+        - CHEM=obabel
+        - GRAPH=nx
+    - os: linux
+      language: generic
+      env: 
+        - PYTHON_VER=3.7
+        - CHEM=rdkit
+        - GRAPH=nx
+    - os: linux
+      language: generic
+      env: 
+        - PYTHON_VER=3.6
+        - CHEM=obabel
+        - GRAPH=gt
     - os: linux
       language: generic
       env: 
         - PYTHON_VER=3.6
         - CHEM=rdkit
+        - GRAPH=gt
     - os: linux
       language: generic
       env: 
         - PYTHON_VER=3.7
         - CHEM=obabel
+        - GRAPH=gt
     - os: linux
       language: generic
       env: 
         - PYTHON_VER=3.7
         - CHEM=rdkit
+        - GRAPH=gt
 
 before_install:
     # Additional info about the build
@@ -57,18 +112,17 @@ before_install:
 
 install:
     # Create test environment for package
-  - python devtools/scripts/create_conda_env.py -n=test -p=${PYTHON_VER} devtools/conda-envs/spyrmsd-test-${CHEM}.yaml
+  - python devtools/scripts/create_conda_env.py -n=test -p=${PYTHON_VER} devtools/conda-envs/spyrmsd-test-${CHEM}-${GRAPH}.yaml
     # Activate the test environment
   - conda activate test
     # Build and install package
   - python setup.py develop --no-deps
 
 script:
     # Run test and get coverage report
-  - pytest -v --cov=spyrmsd tests/
+  - pytest -v --cov=spyrmsd tests/ --runslow
 
     # Run checks
-  - black .
   - flake8
   - mypy
 

diff --git a/LICENSE b/LICENSE
@@ -1,7 +1,7 @@
 
 MIT License
 
-Copyright (c) 2019 Rocco Meli
+Copyright (c) 2019-2020 Rocco Meli
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/README.md b/README.md
@@ -7,11 +7,11 @@
 [![Documentation Status](https://readthedocs.org/projects/spyrmsd/badge/?version=develop)](https://spyrmsd.readthedocs.io/en/develop/?badge=develop)
 
 [![DOI](https://zenodo.org/badge/214157073.svg)](https://zenodo.org/badge/latestdoi/214157073)
-[![Docs](https://img.shields.io/badge/docs-pyrmsd.readthedocs.io-blueviolet)](https://pyrmsd.readthedocs.io)
-[![PyPI](https://img.shields.io/badge/PyPI-0.2.1%20-ff69b4)](https://pypi.org/project/spyrmsd/)
+[![Docs](https://img.shields.io/badge/docs-spyrmsd.readthedocs.io-blueviolet)](https://spyrmsd.readthedocs.io)
+[![PyPI](https://img.shields.io/badge/PyPI-0.3.0%20-ff69b4)](https://pypi.org/project/spyrmsd/)
 [![License](https://img.shields.io/github/license/RMeli/pyrmsd?color=%2333BBFF)](https://opensource.org/licenses/MIT)
 
-Python-first tool for symmetry-corrected RMSD calculations.
+Python tool for symmetry-corrected RMSD calculations.
 
 ## Installation
 
@@ -21,8 +21,6 @@ Python-first tool for symmetry-corrected RMSD calculations.
 pip install spyrmsd
 ```
 
-This install `spyrmsd` as a library. In order to use the standalone RMSD calculation tool, you will need to install [Open Babel](http://openbabel.org/) or [RDKit](https://rdkit.org/).
-
 ### GitHub
 
 ```bash
@@ -33,6 +31,26 @@ pip install .
 
 ### conda
 
+### Dependencies
+
+`spyrmsd` can be used both as a module or a standalone tool.
+
+#### Module
+
+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/)
+
+#### Standalone Tool
+
+Additionally, one of the following packages are required to use `spyrmsd` as a standalone tool:
+
+* [Open Babel](http://openbabel.org/)
+* [RDKit](https://rdkit.org/)
+
 ## Usage
 
 ### Standalone
@@ -67,45 +85,21 @@ from spyrmsd import rmsd
 
 #### RMSD
 
-The function  `rmsd.rmsd` computes RMSD without symmetry correction. The atoms are expected to be in the same order for both molecule being compared (no atom matching is performed).
-
-#### Symmetric RMSD
-
-The function `rmsd.rmsd_isomorphic` computes symmetry-corrected RMSD, using molecular graph isomorphisms. Symmetry correction requires molecular adjacency matrices but needs not the atoms to be in the same order.
-
-## Contributions
+The function  `rmsd.rmsd` computes RMSD without symmetry correction. The atoms are expected to be in the same order for both molecules being compared (no atom matching is performed).
 
-### List of Contributors
+#### Symmetry-Corrected RMSD
 
-| Name               | GitHub          |
-| :----------------: | :-------------: |
-| Rocco Meli         | @RMeli          | 
+The function `rmsd.symmrmsd` computes symmetry-corrected RMSD using molecular graph isomorphisms. Symmetry correction requires molecular adjacency matrices describing the connectivity but needs not the atoms to be in the same order.
 
-### Tools
+Atom matching is performed according to the molecular graph. Therefore, this function should be used when atoms in the molecules being compared are not in the same order (even if there is not symmetry).
 
-#### Formatting
+## Development
 
-The code is automatically formatted using [black](https://black.readthedocs.io/en/stable/):
+To ensure code quality and consistency the following tools are used during development:
 
-```bash
-black .
-```
-
-#### Style
-
-Code style is enforced using [Flake 8](http://flake8.pycqa.org/en/latest/)
-
-```bash
-flake8
-```
-
-#### Static Checks
-
-Static checks are performed using [mypy](http://mypy-lang.org/)
-
-```bash
-mypy
-```
+* [black](https://black.readthedocs.io/en/stable/)
+* [Flake 8](http://flake8.pycqa.org/en/latest/) (CI)
+* [mypy](http://mypy-lang.org/) (CI)
 
 ## Deployment
 

diff --git a/devtools/conda-envs/spyrmsd-all.yaml b/devtools/conda-envs/spyrmsd-all.yaml
@@ -16,6 +16,7 @@ dependencies:
   - pandas
   - scipy
   - networkx
+  - graph-tool
   - scikit-learn
 
   # Chemistry
@@ -29,6 +30,7 @@ dependencies:
   # Testing
   - pytest
   - pytest-cov
+  - pytest-benchmark
   - codecov
 
   # Doc

diff --git a/devtools/conda-envs/spyrmsd-docs.yaml b/devtools/conda-envs/spyrmsd-docs.yaml
@@ -5,13 +5,12 @@ channels:
 dependencies:
   # Base
   - python
-  - pip
-  - ipython
 
   # Maths
   - numpy
   - scipy
   - networkx
+  - graph-tool
 
   # Chemistry
   - openbabel 

diff --git a/devtools/conda-envs/spyrmsd-test-obabel-gt.yaml b/devtools/conda-envs/spyrmsd-test-obabel-gt.yaml
@@ -0,0 +1,26 @@
+name: spyrmsd
+channels:
+  - conda-forge
+dependencies:
+  # Base
+  - python
+
+  # Maths
+  - numpy
+  - scipy
+  - graph-tool
+
+  # Chemistry
+  - openbabel
+  - qcelemental
+
+  # Testing
+  - pytest
+  - pytest-cov
+  - pytest-benchmark
+
+  # Dev
+  - mypy
+  - flake8
+  - black
+  - codecov
diff --git a/devtools/conda-envs/spyrmsd-test-obabel.yaml → ...ls/conda-envs/spyrmsd-test-obabel-nx.yaml b/devtools/conda-envs/spyrmsd-test-obabel.yaml → ...ls/conda-envs/spyrmsd-test-obabel-nx.yaml
@@ -17,6 +17,7 @@ dependencies:
   # Testing
   - pytest
   - pytest-cov
+  - pytest-benchmark
 
   # Dev
   - mypy

diff --git a/devtools/conda-envs/spyrmsd-test-rdkit-gt.yaml b/devtools/conda-envs/spyrmsd-test-rdkit-gt.yaml
@@ -0,0 +1,27 @@
+name: spyrmsd
+channels:
+  - conda-forge
+  - rdkit
+dependencies:
+  # Base
+  - python
+
+  # Maths
+  - numpy
+  - scipy
+  - graph-tool
+
+  # Chemistry
+  - rdkit
+  - qcelemental
+
+  # Testing
+  - pytest
+  - pytest-cov
+  - pytest-benchmark
+
+  # Dev
+  - mypy
+  - flake8
+  - black
+  - codecov
diff --git a/devtools/conda-envs/spyrmsd-test-rdkit.yaml → ...ols/conda-envs/spyrmsd-test-rdkit-nx.yaml b/devtools/conda-envs/spyrmsd-test-rdkit.yaml → ...ols/conda-envs/spyrmsd-test-rdkit-nx.yaml
@@ -18,6 +18,7 @@ dependencies:
   # Testing
   - pytest
   - pytest-cov
+  - pytest-benchmark
 
   # Dev
   - mypy

diff --git a/devtools/conda-envs/spyrmsd.yaml b/devtools/conda-envs/spyrmsd.yaml
@@ -8,7 +8,7 @@ dependencies:
   # Maths
   - numpy
   - scipy
-  - networkx
+  - graph-tool
 
   # Chemistry
   - qcelemental
-Original file line number
+Diff line change
@@ Expand Up / @@ -17,6 +17,7 @@ dependencies: @@
       # Testing
       - pytest
       - pytest-cov
+      - pytest-benchmark
       # Dev
       - mypy
@@ Expand Down @@