Merge pull request #53 from RMeli/develop

Version 0.5.0

.github/ISSUE_TEMPLATE/bug-report.md

@@ -0,0 +1,37 @@
+---
+name: Bug Report
+about: Bug Report
+title: ''
+labels: bug
+assignees: ''
+
+---
+
+**Describe the bug**
+<!--
+A clear and concise description of what the bug is.
+-->
+
+**To Reproduce**
+<!--
+Steps to reproduce the behavior:
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error
+-->
+
+**Expected behavior**
+<!--
+A clear and concise description of what you expected to happen.
+-->
+
+**Environment**
+ - OS:
+ - Python:
+ - Package Manager [e.g. `pip`, `conda`]: 
+
+**Additional Context**
+<!--
+Add any other context about the problem here.
+-->

.github/ISSUE_TEMPLATE/empty-issue.md

@@ -0,0 +1,10 @@
+---
+name: Empty Issue
+about: Empty Issue
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+

.github/PULL_REQUEST_TEMPLATE.md

@@ -5,4 +5,5 @@
 ## Checklist
 
 - [ ] Tests
-- [ ] Documentation
+- [ ] Documentation
+- [ ] Changelog

.github/workflows/mypy.yml

@@ -25,6 +25,9 @@ jobs:
       run: |
         python -m pip install --upgrade pip
         pip install mypy
+    - name: Install Types
+      run: |
+        python -m pip install types-requests
     - name: Install  package
       run: |
         python setup.py develop --no-deps

.github/workflows/pytest.yml

@@ -0,0 +1,68 @@
+name: pytest
+
+on:
+  push:
+    branches:
+      - "develop"
+      - "master"
+  pull_request:
+    branches:
+      - "*"
+  schedule:
+    # Nightly tests (on master)
+    - cron: "0 0 * * *"
+
+defaults:
+  run:
+    # conda setup requires this special shell
+    shell: bash -l {0}
+
+jobs:
+  test:
+    name: Test ${{ matrix.os }}-${{ matrix.python-version }}-${{ matrix.chemlib }}-${{ matrix.graphlib }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [macOS-latest, ubuntu-latest, windows-latest]
+        python-version: [3.7, 3.8, 3.9]
+        chemlib: [obabel, rdkit]
+        graphlib: [nx, gt]
+        # graph-tools does not work on Windows
+        exclude:
+        - {os: "windows-latest", graphlib: "gt"}
+
+    steps:
+    - uses: actions/checkout@v1
+
+    - name: Info
+      shell: bash
+      run: |
+        uname -a
+        df -h
+        ulimit -a
+
+    - uses: conda-incubator/setup-miniconda@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+        environment-file: devtools/conda-envs/spyrmsd-test-${{ matrix.chemlib }}-${{ matrix.graphlib }}.yaml
+        channels: conda-forge,defaults
+        activate-environment: spyrmsd
+        auto-update-conda: true
+        auto-activate-base: false
+        show-channel-urls: true
+
+    - name: Install
+      run: |
+        python -m pip install . --no-deps
+        conda list
+
+    - name: Test
+      run: |
+        pytest -v --benchmark --cov=spyrmsd --cov-report=xml --color=yes tests/
+
+    - name: CodeCov
+      uses: codecov/codecov-action@v1
+      with:
+        file: ./coverage.xml
+        flags: unittests
+        name: codecov-${{ matrix.os }}-py${{ matrix.python-version }}-${{ matrix.chemlib }}-${{ matrix.graphlib }}

CHANGELOG.md

@@ -0,0 +1,36 @@
+
+# `spyrmsd` CHANGELOG
+
+------------------------------------------------------------------------------
+
+## Version 0.5.0
+
+Date:            21/06/2021
+Contributors:    @RMeli
+
+### Added
+
+* Added `molecule.Molecule` constructor from RDKit molecule [PR #50 | @RMeli]
+* Added `molecule.Molecule` constructor from Open Babel molecule [PR #50 | @RMeli]
+* Added `--n-tests` option for `pytest` [PR #44 | @RMeli]
+
+### Improved
+
+* Improved `spyrmsd.rmsdwrapper` to deal with single molecule [PR #51 | @RMeli]
+* Improved issue template [PR #46 | @RMeli]
+* Improved speed of computation of squared pairwise distances [PR #45 | @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.rmsdwrapper` to `rmsd` module [PR #52 | @RMeli]
+* Long tests no longer run in CI [PR #44 | @RMeli]
+
+### Removed
+
+* Removed `spyrmsd` module [PR #52 | @RMeli]
+* Removed Travis CI and AppVeyor bindings [PR #44 | @RMeli]
+* Removed `--long` option for `pytest` [PR #44 | @RMeli]
+
+------------------------------------------------------------------------------

LICENSE

@@ -1,7 +1,7 @@
 
 MIT License
 
-Copyright (c) 2019-2020 Rocco Meli
+Copyright (c) 2019-2021 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