Add GitHub actions for testing (#108)

Replaces TravisCI and restores working CI.

.coveragerc

@@ -10,4 +10,5 @@ exclude_lines =
     if __name__ == .__main__.:
 ignore_errors = True
 omit =
-    tests/*
+    tests/*
+    docs/*

.github/workflows/ci.yml

@@ -0,0 +1,156 @@
+name: build
+
+on:
+  push:
+    branches: [master]
+  pull_request:
+    branches: [master]
+
+jobs:
+  lint:
+    runs-on: ${{ matrix.platform }}
+    strategy:
+      matrix:
+        platform: [ubuntu-latest]
+        python-version: [3.9]
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip setuptools wheel
+      shell: bash
+
+    - name: Linter
+      run: |
+        python -m pip install flake8
+        flake8 .
+
+  build_and_test_linux:
+    runs-on: ${{ matrix.platform }}
+    strategy:
+      matrix:
+        platform: [ubuntu-latest]
+        python-version: [3.6, 3.7, 3.8, 3.9]
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip setuptools wheel bump2version twine
+      shell: bash
+
+    - name: Linter
+      run: |
+        python -m pip install flake8
+        flake8 .
+
+    - name: Build
+      run: |
+        python --version
+        python setup.py sdist bdist_wheel
+        twine check dist/*.whl
+        twine check dist/*.tar.gz
+        bump2version --dry-run --verbose --allow-dirty patch
+        bump2version --dry-run --verbose --allow-dirty minor
+        bump2version --dry-run --verbose --allow-dirty major
+
+    - name: Test
+      run: |
+        python -m pip install .
+        script -q -e -c "python setup.py test"
+
+  test_macos:
+    runs-on: ${{ matrix.platform }}
+    strategy:
+      matrix:
+        platform: [macos-latest]
+        python-version: [3.6, 3.7, 3.8, 3.9]
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip setuptools wheel
+        brew install expect
+      shell: bash
+
+    - name: Test Linux/MacOS
+      run: |
+        python -m pip install .
+        unbuffer python setup.py test
+
+   # test_windows:
+   #   runs-on: ${{ matrix.platform }}
+   #   strategy:
+   #     matrix:
+   #       platform: [windows-latest]
+   #       python-version: [3.6, 3.7, 3.8, 3.9]
+
+   #   steps:
+   #   - uses: actions/checkout@v2
+
+   #   - name: Set up Python ${{ matrix.python-version }}
+   #     uses: actions/setup-python@v2
+   #     with:
+   #       python-version: ${{ matrix.python-version }}
+
+   #   - name: Install dependencies
+   #     run: |
+   #       python -m pip install --upgrade pip setuptools wheel
+
+   #   - name: Test Windows
+   #     run: |
+   #       python -m pip install .
+   #       Invoke-Expression 'python setup.py test'
+
+  coverage:
+    runs-on: ${{ matrix.platform }}
+    strategy:
+      matrix:
+        platform: [ubuntu-latest]
+        python-version: [3.9]
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip setuptools wheel
+        python -m pip install coverage
+
+    - name: Get Coverage
+      run: |
+        python -m pip install .
+        script -q -e -c "coverage run setup.py test"
+
+    # from https://about.codecov.io/blog/
+    # python-code-coverage-using-github-actions-and-codecov/
+    - name: Upload Coverage to Codecov
+      uses: codecov/codecov-action@v2
+      with:
+        fail_ci_if_error: true
+        verbose: true

README.md

@@ -1,8 +1,7 @@
 # pdb-tools
 
 [![PyPI version](https://badge.fury.io/py/pdb-tools.svg)](https://badge.fury.io/py/pdb-tools)
-[![Travis (.org) branch](https://img.shields.io/travis/haddocking/pdb-tools/master.svg?style=flat&label=TravisCI)](https://travis-ci.org/haddocking/pdb-tools)
-[![AppVeyor branch](https://img.shields.io/appveyor/ci/JoaoRodrigues/pdb-tools-2coq6.svg?style=flat&label=AppVeyor)](https://ci.appveyor.com/project/JoaoRodrigues/pdb-tools-2coq6)
+[![tests](https://github.com/haddocking/pdb-tools/workflows/tests/badge.svg?branch=master)](https://github.com/haddocking/pdb-tools/actions?workflow=tests)
 [![codecov](https://codecov.io/gh/haddocking/pdb-tools/branch/master/graph/badge.svg)](https://codecov.io/gh/haddocking/pdb-tools)
 [![DOI](https://zenodo.org/badge/27217350.svg)](https://doi.org/10.12688/f1000research.17456.1)
 

pdbtools/__init__.py

@@ -121,4 +121,4 @@
     'pdb_uniqname',
     'pdb_validate',
     'pdb_wc',
-    ]
+]

pdbtools/pdb_selaltloc.py

@@ -39,7 +39,6 @@
 data to another. They are based on old FORTRAN77 code that was taking too much
 effort to maintain and compile. RIP.
 """
-import operator
 import os
 import sys
 
@@ -250,8 +249,8 @@ def is_another_altloc_group(
         resname,
         prev_resname,
         altloc_lines,
-        rploc,
-        ):
+        rploc
+):
     """Detect if current line belongs to a new altloc group."""
     a0 = prev_altloc
     a1 = altloc
@@ -264,7 +263,7 @@ def is_another_altloc_group(
 
     is_another = (
         all((a0, ra0, ru0)) and (
-               (a0 != a1 and a1 == ' ' and ru1 > ru0)
+            (a0 != a1 and a1 == ' ' and ru1 > ru0)
             or (a0 == ' ' and a1 != ' ' and ru1 > ru0)
             or (a0 == ' ' and a1 == ' ' and (ru1 != ru0 or ra1 != ra0))
             or (
@@ -274,9 +273,9 @@ def is_another_altloc_group(
                 and ru1 > ru0
                 and len(rl) > 1
                 and all(len(v) == len(rv[0]) for v in rv[1:])
-                )
             )
         )
+    )
 
     return is_another
 
@@ -348,8 +347,8 @@ def flush_resloc_occ_same_residue(altloc_lines, **kw):
     for atom, linest in sorted_atoms:
         lines = linest[1]
 
-        atom_lines = [l for l in lines if l.startswith(("ATOM", "HETATM"))]
-        anisou_lines = [l for l in lines if l.startswith(("ANISOU"))]
+        atom_lines = [ln for ln in lines if ln.startswith(("ATOM", "HETATM"))]
+        anisou_lines = [ln for ln in lines if ln.startswith(("ANISOU"))]
 
         if anisou_lines:
             new = []
@@ -359,7 +358,7 @@ def flush_resloc_occ_same_residue(altloc_lines, **kw):
                     "There is an error with this PDB. "
                     "We expect one ANISOU line per ATOM/HETATM lines. "
                     "But the number of ATOM/HETATM and ANISOU lines differ."
-                    )
+                )
                 raise ValueError(emsg)
 
             for _a, _b in zip(atom_lines, anisou_lines):

pdbtools/pdb_tidy.py

@@ -223,7 +223,6 @@ def make_TER(prev_line):
                 in_model = True
                 serial_offset = 0
 
-
         if serial > 99999:
             emsg = 'ERROR!! Structure contains more than 99.999 atoms.\n'
             sys.stderr.write(emsg)

tox.ini → setup.cfg

@@ -7,13 +7,12 @@ exclude =
     tests/,
     setup.py
 
-# Ignore long lines and lambda warnings
-ignore = E501,E731
+# Ignore:
+# E501: long lines
+# E731: lambda warnings
+# W503/W504: line breaks before/after operators
+ignore = E501,E731,W503,W504
 
 # Enable statistics at the end
 statistics = True
 
-[testenv]
-passenv = TOXENV CI TRAVIS TRAVIS_*
-deps = codecov>=1.4.0
-commands = codecov -e TOXENV