update docs and tests (#8)

* update all refs to Bloom lab webpage to go to new lab website

* test w GitHub Actions rather than Travis

* lint w `ruff` rather than `flake8`

* format w black

* increment version and CHANGELOG

* fix bug introduced when linting

.github/workflows/test.yml

@@ -0,0 +1,35 @@
+name: Run tests
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  test:
+    name: Run tests
+    runs-on: ubuntu-latest
+    timeout-minutes: 60
+    steps:
+      - name: checkout
+        uses: actions/checkout@v4
+
+      - name: install python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: install package and dependencies
+        run: pip install -e . && pip install -r test_requirements.txt
+
+      - name: lint code with ruff
+        run: ruff check .
+
+      - name: check code format with black
+        run: black --check .
+
+      - name: test code with `pytest`
+        run: pytest

.gitignore

@@ -1,8 +1,8 @@
 .*
 ~*
 
-!.gitignore
-!.travis.yml
+!.git*
+
 !.flake8
 !.nojekyll
 

CHANGELOG.rst

@@ -6,6 +6,10 @@ All notable changes to this project will be documented in this file.
 
 The format is based on `Keep a Changelog <https://keepachangelog.com>`_.
 
+0.7
+---
+- Test with GitHub Actions rather than Travis, lint with ``ruff`` rather than ``flake8``.
+
 0.6
 ---
 - Allow negative site numbers.

CONTRIBUTING.rst

@@ -79,29 +79,19 @@ If these are not installed, install them with::
 
     pip install -r test_requirements.txt
 
-Then use flake8_ to `lint the code <https://en.wikipedia.org/wiki/Lint_%28software%29>`_ by running::
+Then use `ruff <https://github.com/astral-sh/ruff>`_ to `lint the code <https://en.wikipedia.org/wiki/Lint_%28software%29>`_ by running::
 
-    flake8
-
-If you need to change the flake8_ configuration, edit the `.flake8 <.flake8>`_ file.
+    ruff check .    
 
 Then run the tests with pytest_ by running::
 
     pytest
 
 If you need to change the pytest_ configuration, edit the `pytest.ini <pytest.ini>`_ file.
 
-Automated testing on Travis
-+++++++++++++++++++++++++++
-The aforementioned flake8_ and pytest_ tests will be run automatically by the Travis_ continuous integration system as specified in the `.travis.yml <.travis.yml>`_ file.
-Note that running the Travis_ tests requires you to register the project with Travis_.
-
-If the tests are passing, you will see this on the Travis_ badge on GitHub repo main page.
-
-Slack notifications of test results
-+++++++++++++++++++++++++++++++++++++
-You can configure Travis_ to provide automatic Slack notifications of the test results.
-To do that, follow the `instructions here <https://docs.travis-ci.com/user/notifications/#configuring-slack-notifications>`_.
+Automated testing Github Actions
++++++++++++++++++++++++++++++++++
+The aforementioned tests are run automatically by Github actions as specified in `.github/workflows/test.yml <.github/workflows/test.yml>`_.
 
 
 Building documentation
@@ -125,8 +115,6 @@ Finally, upload to PyPI_ with twine_ as `described here <https://github.com/pypa
 Note that this requires you to have registered the package on PyPI_ if this is the first version of the package there.
 
 .. _pytest: https://docs.pytest.org
-.. _flake8: http://flake8.pycqa.org
-.. _Travis: https://docs.travis-ci.com
 .. _PyPI: https://pypi.org/
 .. _pip: https://pip.pypa.io
 .. _sphinx: https://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_google.html

LICENSE.txt

@@ -2,7 +2,7 @@ GNU GENERAL PUBLIC LICENSE
                       Version 3, 29 June 2007
 
     binary representation of protein or nucleotide sequences
-    Copyright (C) 2021  `the Bloom lab <https://research.fhcrc.org/bloom/en.html>`_
+    Copyright (C) 2021  `the Bloom lab <https://jbloomlab.org/>`_
 
     This program is free software: you can redistribute it and/or modify
     it under the terms of the GNU General Public License as published by

README.rst

@@ -4,13 +4,16 @@ binarymap
 
 .. image:: https://img.shields.io/pypi/v/binarymap.svg
         :target: https://pypi.python.org/pypi/binarymap
-
-.. image:: https://app.travis-ci.com/jbloomlab/binarymap.svg
-        :target: https://app.travis-ci.com/github/jbloomlab/binarymap
+.. image:: https://github.com/jbloomlab/binarymap/actions/workflows/test.yml/badge.svg
+        :target: https://github.com/jbloomlab/binarymap/actions/workflows/test.yml
+.. image:: https://img.shields.io/badge/code%20style-black-000000.svg
+        :target: https://github.com/psf/black
+.. image:: https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/charliermarsh/ruff/main/assets/badge/v2.json
+        :target: https://github.com/astral-sh/ruff
 
 Bbinary representation of protein or nucleotide sequences.
 
-``binarymap`` is a Python package written by `the Bloom lab <https://research.fhcrc.org/bloom/en.html>`_.
+``binarymap`` is a Python package written by `the Bloom lab <https://jbloomlab.org>`_.
 
 The source code is `on GitHub <https://github.com/jbloomlab/binarymap>`_.
 

binarymap/__init__.py

@@ -12,9 +12,9 @@
 
 """
 
-__author__ = "`the Bloom lab <https://research.fhcrc.org/bloom/en.html>`_"
+__author__ = "`the Bloom lab <https://jbloomlab.org>`_"
 __email__ = "[email protected]"
-__version__ = "0.6"
+__version__ = "0.7"
 __url__ = "https://github.com/jbloomlab/binarymap"
 
 from binarymap.binarymap import BinaryMap  # noqa: F401

binarymap/binarymap.py

@@ -17,7 +17,6 @@
 
 """
 
-
 import collections
 import re
 
@@ -383,14 +382,14 @@ def __eq__(self, other):
 
         """
         # following here: https://stackoverflow.com/a/390640
-        if type(other) != type(self):
+        if type(other) is not type(self):
             return False
         elif self.__dict__.keys() != other.__dict__.keys():
             return False
         else:
             for key, val in self.__dict__.items():
                 val2 = getattr(other, key)
-                if type(val) != type(val2):
+                if type(val) is not type(val2):
                     return False
                 elif isinstance(val, numpy.ndarray):
                     if not numpy.array_equal(val, val2):

docs/acknowledgments.rst

@@ -1,5 +1,5 @@
 Acknowledgements
 -----------------
-``binarymap`` is written by `the Bloom lab <https://research.fhcrc.org/bloom/en.html>`_.
+``binarymap`` is written by `the Bloom lab <https://jbloomlab.org>`_.
 
 See https://github.com/jbloomlab/binarymap/graphs/contributors for the full list of contributors.

docs/conf.py

@@ -69,7 +69,7 @@
 # General information about the project.
 project = "binarymap"
 copyright = f"2019--{datetime.datetime.now().year}"  # noqa: A001
-author = "`the Bloom lab <https://research.fhcrc.org/bloom/en.html>`_"
+author = "`the Bloom lab <https://jbloomlab.org>`_"
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
@@ -193,7 +193,7 @@
         master_doc,
         "binarymap.tex",
         "binarymap Documentation",
-        "`the Bloom lab <https://research.fhcrc.org/bloom/en.html>`_",
+        "`the Bloom lab <https://jbloomlab.org/>`_",
         "manual",
     ),
 ]

docs/index.rst

@@ -1,7 +1,7 @@
 ``binarymap`` documentation
 ===================================================
 
-``binarymap`` is a Python package written by `the Bloom lab <https://research.fhcrc.org/bloom/en.html>`_.
+``binarymap`` is a Python package written by `the Bloom lab <https://jbloomlab.org>`_.
 
 The package is designed to convert protein / nucleotide sequences into binary representations.
 

pytest.ini

@@ -1,2 +1,8 @@
 [pytest]
-addopts = binarymap docs --nbval --ignore setup.py --ignore docs/_build --doctest-modules
+addopts =
+  binarymap
+  docs
+  --nbval
+  --ignore setup.py
+  --ignore docs/_build
+  --doctest-modules

setup.py

@@ -1,6 +1,5 @@
 """Setup script for ``binarymap``."""
 
-
 import re
 import sys
 

test_requirements.txt

@@ -1,11 +1,4 @@
 pytest
-flake8
 black
-flake8-docstrings
-flake8-rst-docstrings
-flake8-builtins
-flake8-import-order
-flake8-comprehensions
-flake8-bugbear
-flake8-print
+ruff
 nbval