Migrate to Travis com

Edinburgh-Genome-Foundry · Oct 26, 2021 · 68a38c5 · 68a38c5
1 parent 14f694d
commit 68a38c5
Show file tree

Hide file tree

Showing 5 changed files with 82 additions and 58 deletions.
diff --git a/.travis.yml b/.travis.yml
@@ -3,7 +3,7 @@ python:
   - "3.6"
 # command to install dependencies
 install:
-  - pip install coveralls pytest-cov==2.6 pytest==3.2.3
+  - pip install coveralls pytest-cov pytest
   - pip install -e .
 # command to run tests
 script:

diff --git a/README.rst b/README.rst
@@ -1,12 +1,12 @@
 easy_dna
 ========
 
-.. image:: https://travis-ci.org/Edinburgh-Genome-Foundry/easy_dna.svg?branch=master
-   :target: https://travis-ci.org/Edinburgh-Genome-Foundry/easy_dna
-   :alt: Travis CI build status
+.. image:: https://app.travis-ci.com/Edinburgh-Genome-Foundry/easy_dna.svg?branch=master
+    :target: https://app.travis-ci.com/Edinburgh-Genome-Foundry/easy_dna
+    :alt: Travis CI build status
 
 .. image:: https://coveralls.io/repos/github/Edinburgh-Genome-Foundry/easy_dna/badge.svg?branch=master
-   :target: https://coveralls.io/github/Edinburgh-Genome-Foundry/easy_dna?branch=master
+    :target: https://coveralls.io/github/Edinburgh-Genome-Foundry/easy_dna?branch=master
 
 Easy_dna is a Python library implementing useful routines for manipulating DNA
 sequences, either as "ATGC" strings or Biopython records. It aims at providing
@@ -15,24 +15,26 @@ design and genbank generation.
 
 Easy_dna was originally created to gather useful methods repeatedly used in the
 different software projects of the Edinburgh Genome Foundry for DNA design and
-manufacturing. 
+manufacturing.
 
 See the API reference `here <https://edinburgh-genome-foundry.github.io/easy_dna/>`_.
 
+
 Installation
 ------------
 
 You can install easy_dna through PIP:
 
 .. code::
 
-    sudo pip install easy_dna
+    pip install easy_dna
 
 Alternatively, you can unzip the sources in a folder and type:
 
 .. code::
 
-    sudo python setup.py install
+    python setup.py install
+
 
 License = MIT
 -------------
@@ -41,6 +43,7 @@ Easy_dna is an open-source software originally written at the `Edinburgh Genome
 <http://edinburgh-genome-foundry.github.io/home.html>`_ by `Zulko <https://github.com/Zulko>`_
 and `released on Github <https://github.com/Edinburgh-Genome-Foundry/easy_dna>`_ under the MIT licence (Copyright 2019 Edinburgh Genome Foundry). Everyone is welcome to contribute!
 
+
 More biology software
 ---------------------
 

diff --git a/ez_setup.py b/ez_setup.py
@@ -1,4 +1,3 @@
-
 #!python
 """Bootstrap setuptools installation
 
@@ -32,14 +31,16 @@
 DEFAULT_VERSION = "0.9.6"
 DEFAULT_URL = "https://pypi.python.org/packages/source/s/setuptools/"
 
+
 def _python_cmd(*args):
     args = (sys.executable,) + args
     return subprocess.call(args) == 0
 
+
 def _install(tarball, install_args=()):
     # extracting the tarball
     tmpdir = tempfile.mkdtemp()
-    log.warn('Extracting in %s', tmpdir)
+    log.warn("Extracting in %s", tmpdir)
     old_wd = os.getcwd()
     try:
         os.chdir(tmpdir)
@@ -50,13 +51,13 @@ def _install(tarball, install_args=()):
         # going in the directory
         subdir = os.path.join(tmpdir, os.listdir(tmpdir)[0])
         os.chdir(subdir)
-        log.warn('Now working in %s', subdir)
+        log.warn("Now working in %s", subdir)
 
         # installing
-        log.warn('Installing Setuptools')
-        if not _python_cmd('setup.py', 'install', *install_args):
-            log.warn('Something went wrong during the installation.')
-            log.warn('See the error message above.')
+        log.warn("Installing Setuptools")
+        if not _python_cmd("setup.py", "install", *install_args):
+            log.warn("Something went wrong during the installation.")
+            log.warn("See the error message above.")
             # exitcode will be 2
             return 2
     finally:
@@ -67,7 +68,7 @@ def _install(tarball, install_args=()):
 def _build_egg(egg, tarball, to_dir):
     # extracting the tarball
     tmpdir = tempfile.mkdtemp()
-    log.warn('Extracting in %s', tmpdir)
+    log.warn("Extracting in %s", tmpdir)
     old_wd = os.getcwd()
     try:
         os.chdir(tmpdir)
@@ -78,39 +79,45 @@ def _build_egg(egg, tarball, to_dir):
         # going in the directory
         subdir = os.path.join(tmpdir, os.listdir(tmpdir)[0])
         os.chdir(subdir)
-        log.warn('Now working in %s', subdir)
+        log.warn("Now working in %s", subdir)
 
         # building an egg
-        log.warn('Building a Setuptools egg in %s', to_dir)
-        _python_cmd('setup.py', '-q', 'bdist_egg', '--dist-dir', to_dir)
+        log.warn("Building a Setuptools egg in %s", to_dir)
+        _python_cmd("setup.py", "-q", "bdist_egg", "--dist-dir", to_dir)
 
     finally:
         os.chdir(old_wd)
         shutil.rmtree(tmpdir)
     # returning the result
     log.warn(egg)
     if not os.path.exists(egg):
-        raise IOError('Could not build the egg.')
+        raise IOError("Could not build the egg.")
 
 
 def _do_download(version, download_base, to_dir, download_delay):
-    egg = os.path.join(to_dir, 'setuptools-%s-py%d.%d.egg'
-                       % (version, sys.version_info[0], sys.version_info[1]))
+    egg = os.path.join(
+        to_dir,
+        "setuptools-%s-py%d.%d.egg"
+        % (version, sys.version_info[0], sys.version_info[1]),
+    )
     if not os.path.exists(egg):
-        tarball = download_setuptools(version, download_base,
-                                      to_dir, download_delay)
+        tarball = download_setuptools(version, download_base, to_dir, download_delay)
         _build_egg(egg, tarball, to_dir)
     sys.path.insert(0, egg)
     import setuptools
+
     setuptools.bootstrap_install_from = egg
 
 
-def use_setuptools(version=DEFAULT_VERSION, download_base=DEFAULT_URL,
-                   to_dir=os.curdir, download_delay=15):
+def use_setuptools(
+    version=DEFAULT_VERSION,
+    download_base=DEFAULT_URL,
+    to_dir=os.curdir,
+    download_delay=15,
+):
     # making sure we use the absolute path
     to_dir = os.path.abspath(to_dir)
-    was_imported = 'pkg_resources' in sys.modules or \
-        'setuptools' in sys.modules
+    was_imported = "pkg_resources" in sys.modules or "setuptools" in sys.modules
     try:
         import pkg_resources
     except ImportError:
@@ -122,23 +129,23 @@ def use_setuptools(version=DEFAULT_VERSION, download_base=DEFAULT_URL,
         e = sys.exc_info()[1]
         if was_imported:
             sys.stderr.write(
-            "The required version of setuptools (>=%s) is not available,\n"
-            "and can't be installed while this script is running. Please\n"
-            "install a more recent version first, using\n"
-            "'easy_install -U setuptools'."
-            "\n\n(Currently using %r)\n" % (version, e.args[0]))
+                "The required version of setuptools (>=%s) is not available,\n"
+                "and can't be installed while this script is running. Please\n"
+                "install a more recent version first, using\n"
+                "'easy_install -U setuptools'."
+                "\n\n(Currently using %r)\n" % (version, e.args[0])
+            )
             sys.exit(2)
         else:
-            del pkg_resources, sys.modules['pkg_resources'] # reload ok
-            return _do_download(version, download_base, to_dir,
-                                download_delay)
+            del pkg_resources, sys.modules["pkg_resources"]  # reload ok
+            return _do_download(version, download_base, to_dir, download_delay)
     except pkg_resources.DistributionNotFound:
-        return _do_download(version, download_base, to_dir,
-                            download_delay)
+        return _do_download(version, download_base, to_dir, download_delay)
 
 
-def download_setuptools(version=DEFAULT_VERSION, download_base=DEFAULT_URL,
-                        to_dir=os.curdir, delay=15):
+def download_setuptools(
+    version=DEFAULT_VERSION, download_base=DEFAULT_URL, to_dir=os.curdir, delay=15
+):
     """Download setuptools from a specified location and return its filename
 
 `version` should be a valid setuptools version number that is available
@@ -157,7 +164,7 @@ def download_setuptools(version=DEFAULT_VERSION, download_base=DEFAULT_URL,
     url = download_base + tgz_name
     saveto = os.path.join(to_dir, tgz_name)
     src = dst = None
-    if not os.path.exists(saveto): # Avoid repeated downloads
+    if not os.path.exists(saveto):  # Avoid repeated downloads
         try:
             log.warn("Downloading %s", url)
             src = urlopen(url)
@@ -184,6 +191,7 @@ def _extractall(self, path=".", members=None):
     import copy
     import operator
     from tarfile import ExtractError
+
     directories = []
 
     if members is None:
@@ -194,17 +202,19 @@ def _extractall(self, path=".", members=None):
             # Extract directories with a safe mode.
             directories.append(tarinfo)
             tarinfo = copy.copy(tarinfo)
-            tarinfo.mode = 448 # decimal for oct 0700
+            tarinfo.mode = 448  # decimal for oct 0700
         self.extract(tarinfo, path)
 
     # Reverse sort directories.
     if sys.version_info < (2, 4):
+
         def sorter(dir1, dir2):
             return cmp(dir1.name, dir2.name)
+
         directories.sort(sorter)
         directories.reverse()
     else:
-        directories.sort(key=operator.attrgetter('name'), reverse=True)
+        directories.sort(key=operator.attrgetter("name"), reverse=True)
 
     # Set correct owner, mtime and filemode on directories.
     for tarinfo in directories:
@@ -230,30 +240,40 @@ def _build_install_args(options):
         if sys.version_info < (2, 6):
             log.warn("--user requires Python 2.6 or later")
             raise SystemExit(1)
-        install_args.append('--user')
+        install_args.append("--user")
     return install_args
 
+
 def _parse_args():
     """
 Parse the command line for options
 """
     parser = optparse.OptionParser()
     parser.add_option(
-        '--user', dest='user_install', action='store_true', default=False,
-        help='install in user site package (requires Python 2.6 or later)')
+        "--user",
+        dest="user_install",
+        action="store_true",
+        default=False,
+        help="install in user site package (requires Python 2.6 or later)",
+    )
     parser.add_option(
-        '--download-base', dest='download_base', metavar="URL",
+        "--download-base",
+        dest="download_base",
+        metavar="URL",
         default=DEFAULT_URL,
-        help='alternative URL from where to download the setuptools package')
+        help="alternative URL from where to download the setuptools package",
+    )
     options, args = parser.parse_args()
     # positional arguments are ignored
     return options
 
+
 def main(version=DEFAULT_VERSION):
     """Install or upgrade setuptools and EasyInstall"""
     options = _parse_args()
     tarball = download_setuptools(download_base=options.download_base)
     return _install(tarball, _build_install_args(options))
 
-if __name__ == '__main__':
+
+if __name__ == "__main__":
     sys.exit(main())
diff --git a/pypi-readme.rst b/pypi-readme.rst
@@ -1,5 +1,5 @@
 Easy DNA
-==========
+========
 
 Easy_dna is a Python library implementing useful routines for manipulating DNA
 sequences, either as "ATGC" strings or Biopython records. It aims at providing
@@ -12,8 +12,9 @@ design and genbank generation.
 
 **License:** MIT, Copyright Edinburgh Genome Foundry
 
+
 More biology software
------------------------
+---------------------
 
 .. image:: https://raw.githubusercontent.com/Edinburgh-Genome-Foundry/Edinburgh-Genome-Foundry.github.io/master/static/imgs/logos/egf-codon-horizontal.png
   :target: https://edinburgh-genome-foundry.github.io/

diff --git a/setup.py b/setup.py
@@ -1,7 +1,7 @@
 # This will try to import setuptools. If not here, it will reach for the embedded
 # ez_setup (or the ez_setup package). If none, it fails with a message
 try:
-    from setuptools import setup
+    from setuptools import setup, find_packages
 except ImportError:
     try:
         import ez_setup
@@ -15,13 +15,13 @@
             "([sudo] pip install ez_setup) and try again."
         )
 
-from setuptools import setup, find_packages
-
-exec(open("easy_dna/version.py").read())  # loads __version__
+version = {}
+with open("easy_dna/version.py") as fp:
+    exec(fp.read(), version)
 
 setup(
     name="easy_dna",
-    version=__version__,
+    version=version["__version__"],
     author="Zulko",
     description="Methods for DNA sequence reading, writing and editing.",
     long_description=open("pypi-readme.rst").read(),
@@ -36,6 +36,6 @@
         "snapgene_reader",
         "flametree",
         "pandas",
-        "crazydoc"
-    ]
+        "crazydoc",
+    ],
 )