Merge branch 'feature/add_urlchecker' into 'master'

Feature/add urlchecker

See merge request !27

.gitlab-ci.yml

@@ -13,7 +13,6 @@ stages:
   - test
   - deploy_pages
   - deploy_pypi
-  - deploy_conda
   - cleanup
 
 
@@ -45,6 +44,15 @@ test_styles:
     when: always
 
 
+test_urls:
+  stage: test
+  script:
+    - source /root/miniconda3/bin/activate ci_env
+    - pip install -U urlchecker
+    - make urlcheck
+  when: always
+
+
 test_py_tools_ds_install:
   stage: test
   script:

.travis.yml

-# Config file for automatic testing at travis-ci.org
-# This file will be regenerated if you run travis_pypi_setup.py
-
-language: python
-python: 3.5
-
-env:
-  - TOXENV=py35
-  - TOXENV=py34
-  - TOXENV=py33
-  - TOXENV=py27
-  - TOXENV=py26
-  - TOXENV=pypy
-
-# command to install dependencies, e.g. pip install -r requirements.txt --use-mirrors
-install: pip install -U tox
-
-# command to run tests, e.g. python setup.py test
-script: tox -e ${TOXENV}
-
-# After you create the Github repo and add it to Travis, run the
-# travis_pypi_setup.py script to finish PyPI deployment setup
-deploy:
-  provider: pypi
-  distributions: sdist bdist_wheel
-  user: danschef
-  password:
-    secure: PLEASE_REPLACE_ME
-  on:
-    tags: true
-    repo: danschef/py_tools_ds
-    condition: $TOXENV == py27

HISTORY.rst

@@ -2,6 +2,15 @@
 History
 =======
 
+0.16.5 (2020-12-09)
+-------------------
+
+* Added URL checker CI job and fixed all dead URLs.
+* Removed travis related files.
+* Re-ordered dependencies.
+* Added Python 3.9 classifier to setup.py and removed those for <3.6.
+
+
 0.16.4 (2020-12-07)
 -------------------
 

Makefile

@@ -56,6 +56,9 @@ lint: ## check style with flake8
 	pycodestyle py_tools_ds --exclude="*.ipynb,*.ipynb*" --max-line-length=120 > ./tests/linting/pycodestyle.log
 	-pydocstyle py_tools_ds > ./tests/linting/pydocstyle.log
 
+urlcheck: ## check for dead URLs
+	urlchecker check . --file-types .py,.rst,.md,.json
+
 test: ## run tests quickly with the default Python
 	python setup.py test
 

README.rst

@@ -12,17 +12,6 @@ A collection of Python tools by Daniel Scheffler.
 Status
 ------
 
-.. .. image:: https://img.shields.io/travis/danschef/py_tools_ds.svg
-        :target: https://travis-ci.org/danschef/py_tools_ds
-
-.. .. image:: https://readthedocs.org/projects/py-tools-ds/badge/?version=latest
-        :target: https://py-tools-ds.readthedocs.io/en/latest/?badge=latest
-        :alt: Documentation Status
-
-.. .. image:: https://pyup.io/repos/github/danschef/py_tools_ds/shield.svg
-     :target: https://pyup.io/repos/github/danschef/py_tools_ds/
-     :alt: Updates
-
 .. image:: https://gitext.gfz-potsdam.de/danschef/py_tools_ds/badges/master/pipeline.svg
         :target: https://gitext.gfz-potsdam.de/danschef/py_tools_ds/commits/master
 .. image:: https://gitext.gfz-potsdam.de/danschef/py_tools_ds/badges/master/coverage.svg

py_tools_ds/geo/coord_trafo.py

@@ -63,13 +63,13 @@ def transform_wgs84_to_utm(lon, lat, zone=None):
 
 
 def transform_any_prj(prj_src, prj_tgt, x, y):
-    # type: (Union[str, int], Union[str, int], float, float) -> (float, float)
+    # type: (Union[str, int], Union[str, int], Union[float, np.ndarray], Union[float, np.ndarray]) -> (Union[float, np.ndarray], Union[float, np.ndarray])  # noqa
     """Transform X/Y data from any source projection to any target projection.
 
     :param prj_src:     GDAL projection as WKT string or EPSG code ('epsg:1234' or <EPSG_int>)
     :param prj_tgt:     GDAL projection as WKT string or EPSG code ('epsg:1234' or <EPSG_int>)
-    :param x:
-    :param y:
+    :param x:           X-coordinate(s) to be transformed (either <float> or 1D-<np.ndarray>)
+    :param y:           X-coordinate(s) to be transformed (either <float> or 1D-<np.ndarray>)
     :return:
     """
     transformer = pyproj.Transformer.from_crs(pyproj.CRS.from_user_input(prj_src),

py_tools_ds/geo/raster/reproject.py

@@ -284,7 +284,7 @@ def warp_ndarray(ndarray, in_gt, in_prj=None, out_prj=None, out_dtype=None,
     :param options:             <str> additional GDAL options as string, e.g. '-nosrcalpha' or '-order'
     :param transformerOptions:  <list> list of transformer options, e.g.  ['SRC_SRS=invalid']
     :param warpOptions:         <list> list of warp options, e.g.  ['CUTLINE_ALL_TOUCHED=TRUE'],
-                                find available options here: http://www.gdal.org/structGDALWarpOptions.html
+                                find available options here: http://www.gdal.org/doxygen/structGDALWarpOptions.html
     :param CPUs:                <int> number of CPUs to use (default: None, which means 'all CPUs available')
     :param warpMemoryLimit:     <int> size of working buffer in bytes (default: 0)
     :param progress:            <bool> show progress bar (default: True)

requirements.txt

 gdal
+geopandas
 numpy
+pandas
+pyproj>=2.1.0
 shapely
 six
 scikit-image
-pandas
-geopandas
-pyproj>=2.1.0
 spectral

setup.py

@@ -48,7 +48,7 @@ requirements = [
     'spectral'
 ]
 setup_requirements = ['setuptools']
-test_requirements = requirements + ["coverage", "nose", "nose2", "nose-htmloutput", "rednose", "shapely"]
+test_requirements = requirements + ["coverage", "nose", "nose2", "nose-htmloutput", "rednose", "shapely", "urlchecker"]
 
 setup(
     name='py_tools_ds',
@@ -72,12 +72,10 @@ setup(
         'Natural Language :: English',
         'Programming Language :: Python :: 2.7',
         'Programming Language :: Python :: 3',
-        'Programming Language :: Python :: 3.3',
-        'Programming Language :: Python :: 3.4',
-        'Programming Language :: Python :: 3.5',
         'Programming Language :: Python :: 3.6',
         'Programming Language :: Python :: 3.7',
         'Programming Language :: Python :: 3.8',
+        'Programming Language :: Python :: 3.9',
     ],
     test_suite='tests',
     tests_require=test_requirements,

tests/CI_docker/context/environment_py_tools_ds.yml

@@ -6,21 +6,24 @@ channels: &id1
 dependencies:
   - python=3.*.*
   - pip  # avoids that conda uses the wrong pip
-  - numpy
   - gdal>=2.1.0
+  - geopandas
+  - numpy
   - pyproj>=2.2.0
   - scikit-image
-  - geopandas
+
   - pip:
-    - sphinx-argparse
     - six
     - spectral
+
+    - coverage
     - flake8
-    - pycodestyle
-    - pylint
-    - pydocstyle
     - nose
     - nose2
     - nose-htmloutput
-    - coverage
+    - pycodestyle
+    - pydocstyle
+    - pylint
     - rednose
+    - sphinx-argparse
+    - urlchecker

travis_pypi_setup.py

-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-# py_tools_ds
-#
-# Copyright (C) 2019  Daniel Scheffler (GFZ Potsdam, daniel.scheffler@gfz-potsdam.de)
-#
-# This software was developed within the context of the GeoMultiSens project funded
-# by the German Federal Ministry of Education and Research
-# (project grant code: 01 IS 14 010 A-C).
-#
-# This program is free software: you can redistribute it and/or modify it under
-# the terms of the GNU Lesser General Public License as published by the Free
-# Software Foundation, either version 3 of the License, or (at your option) any
-# later version.
-#
-# This program is distributed in the hope that it will be useful, but WITHOUT
-# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-# FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
-# details.
-#
-# You should have received a copy of the GNU Lesser General Public License along
-# with this program.  If not, see <http://www.gnu.org/licenses/>.
-
-"""Update encrypted deploy password in Travis config file
-"""
-
-
-from __future__ import print_function
-import base64
-import json
-import os
-from getpass import getpass
-import yaml
-from cryptography.hazmat.primitives.serialization import load_pem_public_key
-from cryptography.hazmat.backends import default_backend
-from cryptography.hazmat.primitives.asymmetric.padding import PKCS1v15
-
-
-try:
-    from urllib import urlopen
-except ImportError:
-    from urllib.request import urlopen
-
-
-GITHUB_REPO = 'danschef/py_tools_ds'
-TRAVIS_CONFIG_FILE = os.path.join(
-    os.path.dirname(os.path.abspath(__file__)), '.travis.yml')
-
-
-def load_key(pubkey):
-    """Load public RSA key, with work-around for keys using
-    incorrect header/footer format.
-
-    Read more about RSA encryption with cryptography:
-    https://cryptography.io/latest/hazmat/primitives/asymmetric/rsa/
-    """
-    try:
-        return load_pem_public_key(pubkey.encode(), default_backend())
-    except ValueError:
-        # workaround for https://github.com/travis-ci/travis-api/issues/196
-        pubkey = pubkey.replace('BEGIN RSA', 'BEGIN').replace('END RSA', 'END')
-        return load_pem_public_key(pubkey.encode(), default_backend())
-
-
-def encrypt(pubkey, password):
-    """Encrypt password using given RSA public key and encode it with base64.
-
-    The encrypted password can only be decrypted by someone with the
-    private key (in this case, only Travis).
-    """
-    key = load_key(pubkey)
-    encrypted_password = key.encrypt(password, PKCS1v15())
-    return base64.b64encode(encrypted_password)
-
-
-def fetch_public_key(repo):
-    """Download RSA public key Travis will use for this repo.
-
-    Travis API docs: http://docs.travis-ci.com/api/#repository-keys
-    """
-    keyurl = 'https://api.travis-ci.org/repos/{0}/key'.format(repo)
-    data = json.loads(urlopen(keyurl).read().decode())
-    if 'key' not in data:
-        errmsg = "Could not find public key for repo: {}.\n".format(repo)
-        errmsg += "Have you already added your GitHub repo to Travis?"
-        raise ValueError(errmsg)
-    return data['key']
-
-
-def prepend_line(filepath, line):
-    """Rewrite a file adding a line to its beginning.
-    """
-    with open(filepath) as f:
-        lines = f.readlines()
-
-    lines.insert(0, line)
-
-    with open(filepath, 'w') as f:
-        f.writelines(lines)
-
-
-def load_yaml_config(filepath):
-    with open(filepath) as f:
-        return yaml.load(f)
-
-
-def save_yaml_config(filepath, config):
-    with open(filepath, 'w') as f:
-        yaml.dump(config, f, default_flow_style=False)
-
-
-def update_travis_deploy_password(encrypted_password):
-    """Update the deploy section of the .travis.yml file
-    to use the given encrypted password.
-    """
-    config = load_yaml_config(TRAVIS_CONFIG_FILE)
-
-    config['deploy']['password'] = dict(secure=encrypted_password)
-
-    save_yaml_config(TRAVIS_CONFIG_FILE, config)
-
-    line = ('# This file was autogenerated and will overwrite'
-            ' each time you run travis_pypi_setup.py\n')
-    prepend_line(TRAVIS_CONFIG_FILE, line)
-
-
-def main(args):
-    public_key = fetch_public_key(args.repo)
-    password = args.password or getpass('PyPI password: ')
-    update_travis_deploy_password(encrypt(public_key, password.encode()))
-    print("Wrote encrypted password to .travis.yml -- you're ready to deploy")
-
-
-if '__main__' == __name__:
-    import argparse
-    parser = argparse.ArgumentParser(description=__doc__)
-    parser.add_argument('--repo', default=GITHUB_REPO,
-                        help='GitHub repo (default: %s)' % GITHUB_REPO)
-    parser.add_argument('--password',
-                        help='PyPI password (will prompt if not provided)')
-
-    args = parser.parse_args()
-    main(args)