Merge pull request #86 from RMeli/develop

Version 0.6.0
RMeli · Sep 8, 2023 · 32118ba · 32118ba
2 parents c20ace5 + b5532dd
commit 32118ba
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diff --git a/.codecov.yml b/.codecov.yml
@@ -11,4 +11,4 @@ comment:
   branches: null
   behavior: default
   flags: null
-  paths: null
+  paths: null
diff --git a/.coveragerc b/.coveragerc
@@ -1,6 +1,6 @@
 [run]
 source = spyrmsd
-omit = 
+omit =
     spyrmsd/_version.py
     spyrmsd/due.py
 
@@ -13,6 +13,3 @@ exclude_lines =
     # Don't complain if non-runnable code isn't run:
     if 0:
     if __name__ == .__main__.:
-
-    # OpenBabel2
-    except ImportError:
diff --git a/.gitattributes b/.gitattributes
@@ -0,0 +1 @@
+spyrmsd/_version.py export-subst
diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
@@ -1,7 +1,7 @@
 # How to contribute
 
 We welcome contributions from external contributors, and this document
-describes how to merge code changes into `spyrmsd`. 
+describes how to merge code changes into `spyrmsd`.
 
 ## Getting Started
 

diff --git a/.github/ISSUE_TEMPLATE/bug-report.md b/.github/ISSUE_TEMPLATE/bug-report.md
@@ -29,7 +29,7 @@ A clear and concise description of what you expected to happen.
 **Environment**
  - OS:
  - Python:
- - Package Manager [e.g. `pip`, `conda`]: 
+ - Package Manager [e.g. `pip`, `conda`]:
 
 **Additional Context**
 <!--

diff --git a/.github/ISSUE_TEMPLATE/empty-issue.md b/.github/ISSUE_TEMPLATE/empty-issue.md
@@ -6,5 +6,3 @@ labels: ''
 assignees: ''
 
 ---
-
-
diff --git a/.github/workflows/flake8.yml b/.github/workflows/flake8.yml
@@ -13,10 +13,10 @@ jobs:
 
     strategy:
       matrix:
-        python-version: [3.6, 3.7, 3.8]
+        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"]
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v1
       with:
@@ -28,6 +28,6 @@ jobs:
     - name: Install  package
       run: |
         python setup.py develop --no-deps
-    - name: Lint with flake8 
+    - name: Lint with flake8
       run: |
-        flake8 . --count --show-source --statistics
+        flake8 . --count --show-source --statistics
diff --git a/.github/workflows/mypy.yml b/.github/workflows/mypy.yml
@@ -13,10 +13,10 @@ jobs:
 
     strategy:
       matrix:
-        python-version: [3.6, 3.7, 3.8]
+        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"]
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v1
       with:
@@ -33,4 +33,4 @@ jobs:
         python setup.py develop --no-deps
     - name: Lint with mypy
       run: |
-        mypy
+        mypy
diff --git a/.github/workflows/pre-commit.yml b/.github/workflows/pre-commit.yml
@@ -0,0 +1,24 @@
+name: pre-commit
+
+on:
+  push:
+    branches: [ master, develop ]
+  pull_request:
+    branches: [ master, develop ]
+
+jobs:
+  main:
+    runs-on: ubuntu-latest
+
+    strategy:
+      matrix:
+        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"]
+
+    steps:
+    - uses: actions/checkout@v3
+    - uses: actions/setup-python@v4
+      with:
+        python-version: '3.x'
+    - uses: pre-commit/[email protected]
+    - uses: pre-commit-ci/[email protected]
+      if: always()
diff --git a/.github/workflows/pypi.yml b/.github/workflows/pypi.yml
@@ -11,9 +11,9 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - name: Set up Python
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v4
       with:
         python-version: '3.x'
     - name: Install dependencies

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
@@ -24,15 +24,17 @@ jobs:
     strategy:
       matrix:
         os: [macOS-latest, ubuntu-latest, windows-latest]
-        python-version: [3.7, 3.8, 3.9]
+        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"]
         chemlib: [obabel, rdkit]
         graphlib: [nx, gt]
-        # graph-tools does not work on Windows
         exclude:
+        # graph-tools does not work on Windows
         - {os: "windows-latest", graphlib: "gt"}
+        # FIXME: Keeps failing in CI for unknown reasons during miniconda setup
+        - {os: "ubuntu-latest", graphlib: "gt", chemlib: "rdkit", python-version: "3.7"}
 
     steps:
-    - uses: actions/checkout@v1
+    - uses: actions/checkout@v3
 
     - name: Info
       shell: bash
@@ -61,7 +63,7 @@ jobs:
         pytest -v --benchmark --cov=spyrmsd --cov-report=xml --color=yes tests/
 
     - name: CodeCov
-      uses: codecov/codecov-action@v1
+      uses: codecov/codecov-action@v3
       with:
         file: ./coverage.xml
         flags: unittests

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,6 +1,10 @@
+exclude: |
+            (?x)^(
+                docs/source/conf.py
+            )$
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.0.1
+    rev: v4.4.0
     hooks:
     - id: check-json
     - id: check-merge-conflict
@@ -10,18 +14,19 @@ repos:
     - id: end-of-file-fixer
     - id: trailing-whitespace
 -   repo: https://github.com/psf/black
-    rev: 21.7b0
+    rev: 23.7.0
     hooks:
     -   id: black
 -   repo: https://github.com/PyCQA/flake8
-    rev: 3.9.2
+    rev: 6.1.0
     hooks:
     -   id: flake8
 -   repo: https://github.com/PyCQA/isort
-    rev: 5.9.3
+    rev: 5.12.0
     hooks:
     -   id: isort
 -   repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v0.910
+    rev: v1.5.1
     hooks:
     -   id: mypy
+        additional_dependencies: [types-requests]
diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -13,4 +13,4 @@ formats:
   - pdf
 
 conda:
-  environment: devtools/conda-envs/spyrmsd-docs.yaml
+  environment: devtools/conda-envs/spyrmsd-docs.yaml
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,6 +3,39 @@
 
 ------------------------------------------------------------------------------
 
+## Version 0.6.0
+
+Date:            08/09/2023
+Contributors:    @RMeli
+
+### Improved
+
+* Documentation on loading RDKit and Open Babel molecules [PR #77 | @RMeli]
+
+### Changed
+
+* Versions of `pre-commit` hooks tools [PR #85 | @RMeli]
+* Version of several GitHub actions [PR #76 | @RMeli]
+* Versioneer to `0.28` [PR #76 | @RMeli]
+* Minimum Python version to `3.7` to match CI [PR #76 | @RMeli]
+* Code according to `black==23.3.0` [PR #76 | @RMeli]
+
+### Added
+
+* `pre-commit` CI action [PR #85 | @RMeli]
+* `extras_require` to `setup.py` for RDKit and Open Babel [PR #84 | @RMeli]
+* Error message when `spyrmsd` is used as module but neither OpenBabel nor RDKit are installed [PR #81 | @RMeli]
+* Pin to `sphinx<7` to avoid compatibility with RTD theme [PR #77 | @RMeli]
+
+### Removed
+
+* `ubuntu-latest-3.7-rdkit-gt` configuration from CI due to continuous failures [PR #84 | @RMeli]
+* Outdated information about RDKit from the documentation [PR #84 | @RMeli]
+* Support for Open Babel 2 [PR #84 | @RMeli]
+* LGTM badge and code annotations [PR #76 | @RMeli]
+
+------------------------------------------------------------------------------
+
 ## Version 0.5.2
 
 Date:            23/02/2022

diff --git a/CITATION.cff b/CITATION.cff
@@ -5,7 +5,7 @@ authors:
   given-names: "Rocco"
   orcid: "https://orcid.org/0000-0002-2845-3410"
 title: "spyrmsd"
-version: 0.5.1
+version: 0.6.0
 doi: 10.5281/zenodo.3631876
 date-released: 2021-06-21
 url: "https://github.com/RMeli/spyrmsd"

diff --git a/MANIFEST.in b/MANIFEST.in
@@ -3,4 +3,4 @@ include MANIFEST.in
 include versioneer.py
 
 graft spyrmsd
-global-exclude *.py[cod] __pycache__ *.so
+global-exclude *.py[cod] __pycache__ *.so
diff --git a/README.md b/README.md
@@ -4,13 +4,12 @@
 ![flake8](https://github.com/RMeli/spyrmsd/workflows/flake8/badge.svg)
 ![mypy](https://github.com/RMeli/spyrmsd/workflows/mypy/badge.svg)
 [![codecov](https://codecov.io/gh/RMeli/spyrmsd/branch/develop/graph/badge.svg)](https://codecov.io/gh/RMeli/spyrmsd/branch/master)
-[![Language grade: Python](https://img.shields.io/lgtm/grade/python/g/RMeli/spyrmsd.svg?logo=lgtm&logoWidth=18)](https://lgtm.com/projects/g/RMeli/spyrmsd/context:python)
 
 [![Docs](https://img.shields.io/badge/docs-spyrmsd.readthedocs.io-blueviolet)](https://spyrmsd.readthedocs.io)
 [![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-v0.5.2%20-ff69b4)](https://pypi.org/project/spyrmsd/)
+[![PyPI](https://img.shields.io/badge/PyPI-v0.6.0%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)
@@ -38,7 +37,11 @@ If you find `spyrmsd` useful, please consider citing the following paper:
 
 `spyrmsd` is available on [PyPI](https://pypi.org/project/spyrmsd/) and [conda-forge](https://github.com/conda-forge/spyrmsd-feedstock) and can be easily installed from source. See [Dependencies](###Dependencies) for a description of all the dependencies.
 
-_Note_: `spyrmsd` will install [NetworkX](https://networkx.github.io/) (multi-platform). You can install [graph-tool](https://graph-tool.skewed.de/) on macOS and Linux for higher performance.
+> [!NOTE]
+> `spyrmsd` will install [NetworkX](https://networkx.github.io/) (multi-platform). You can install [graph-tool](https://graph-tool.skewed.de/) on macOS and Linux for higher performance.
+
+> [!WARNING]
+> If `spyrmsd` is used as a standalone tool, it is required to install either [RDKit](https://rdkit.org/) or [Open Babel](http://openbabel.org/). Neither is automatically installed with `pip` nor `conda`.
 
 ### PyPI
 
@@ -72,7 +75,8 @@ The following packages are required to use `spyrmsd` as a module:
 * [numpy](https://numpy.org/)
 * [scipy](https://www.scipy.org/)
 
-_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.
+> [!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.
 
 #### Standalone Tool
 
@@ -81,8 +85,6 @@ Additionally, one of the following packages is required to use `spyrmsd` as a st
 * [Open Babel](http://openbabel.org/)
 * [RDKit](https://rdkit.org/)
 
-_Note_: [RDKit](https://rdkit.org/) is not available on PyPI ([Why the RDKit isn't available on PyPi](https://rdkit.blogspot.com/2019/11/why-rdkit-isnt-available-on-pypi.html)). See [RDKit Installation](http://www.rdkit.org/docs/Install.html) for installation instructions.
-
 ## Usage
 
 ### Standalone Tool
@@ -130,7 +132,8 @@ def rmsd(
 )
 ```
 
-Note: atomic properties (`aprops`) can be any Python object when using [NetworkX](https://networkx.github.io/), or integers, floats, or strings when using [graph-tool](https://graph-tool.skewed.de/).
+> [!NOTE]
+> Atomic properties (`aprops`) can be any Python object when using [NetworkX](https://networkx.github.io/), or integers, floats, or strings when using [graph-tool](https://graph-tool.skewed.de/).
 
 #### Symmetry-Corrected RMSD
 
@@ -153,7 +156,8 @@ def symmrmsd(
 )
 ```
 
-Note: atomic properties (`aprops`) can be any Python object when using [NetworkX](https://networkx.github.io/), or integers, floats, or strings when using [graph-tool](https://graph-tool.skewed.de/).
+> [!NOTE]
+> Atomic properties (`aprops`) can be any Python object when using [NetworkX](https://networkx.github.io/), or integers, floats, or strings when using [graph-tool](https://graph-tool.skewed.de/).
 
 ## Development
 

diff --git a/credits.sh b/credits.sh
@@ -6,4 +6,4 @@ python -m duecredit test_import.py
 
 printf "\n\nBIBTEX\n------\n\n"
 
-duecredit summary --format bibtex
+duecredit summary --format bibtex
diff --git a/devtools/README.md b/devtools/README.md
@@ -13,7 +13,7 @@ Conda is the recommended package manager for this project.
 
 * `conda-envs`: directory containing the YAML file(s) which fully describe Conda environments
   * `spyrmsd.yaml`: Full Conda environment for `spyrmsd`.
-  
+
 Channels are usually not specified here and therefore respect global Conda configuration.
 
 ## Deployment

diff --git a/devtools/conda-envs/spyrmsd-all.yaml b/devtools/conda-envs/spyrmsd-all.yaml
@@ -33,7 +33,7 @@ dependencies:
   - codecov
 
   # Doc
-  - sphinx
+  - sphinx<7
   - sphinx_rtd_theme
   - pip:
     - duecredit

diff --git a/devtools/conda-envs/spyrmsd-docs.yaml b/devtools/conda-envs/spyrmsd-docs.yaml
@@ -17,5 +17,5 @@ dependencies:
   - rdkit
 
   # Doc
-  - sphinx
+  - sphinx<7
   - sphinx_rtd_theme
diff --git a/docs/README.md b/docs/README.md
@@ -4,7 +4,7 @@ The docs for this project are built with [Sphinx](http://www.sphinx-doc.org/en/m
 
 ## Installation
 
-Ensure that Sphinx and the ReadTheDocs theme are installed:
+Ensure that Sphinx and the [Read the Docs](https://sphinx-rtd-theme.readthedocs.io/en/stable/index.html) theme are installed:
 
 ```bash
 conda install sphinx sphinx_rtd_theme
@@ -20,6 +20,15 @@ Create API documentation automatically with `sphinx-apidoc`:
 sphinx-apidoc -f -M -e  -T -o source/api ../spyrmsd
 ```
 
+### Convert Tutorial Jupyter Notebooks to HTML
+
+Jupyter Notebooks need to be converted to HTML:
+
+```bash
+pip install pandoc
+jupyter nbconvert --to rst tutorial.ipynb
+```
+
 ### Build Documentation
 
 Use the `Makefile` to compile static HTML pages:
@@ -30,4 +39,4 @@ make html
 
 ### Visualize Documentation
 
-The compiled docs will be in the `build` directory and can be viewed by opening `index.html` (which may itself be inside a directory called `html/` depending on what version of Sphinx is installed).
+The compiled docs will be in the `build` directory and can be viewed by opening `index.html` (which may itself be inside a directory called `html/` depending on what version of Sphinx is installed).
diff --git a/docs/source/api.rst b/docs/source/api.rst
@@ -5,4 +5,4 @@ API
    :maxdepth: 2
    :caption: Contents:
 
-   api/spyrmsd
+   api/spyrmsd