docs/update-conda-cluster.md

-# Update conda ```wetb_py3``` environment and ```wetb```
+# Update conda ```py36-wetb``` environment and ```wetb```
 
 There are pre-configured miniconda/anaconda python environments installed on
 Gorm and Jess at:
 
 ```
-/home/python/miniconda3/envs/wetb_py3
+/home/python/miniconda3/envs/py36-wetb
 ```
 Note that these refer to the home drives of Gorm and Jess respectively and thus
 refer to two different directories (but are named the same).
@@ -15,20 +15,20 @@ Update the root Anaconda environment:
 conda update --all
 ```
 
-Activate the ```wetb_py3``` environment:
+Activate the ```py36-wetb``` environment:
 
 ```
-source activate wetb_py3
+source activate py36-wetb
 ```
 
 
-Update the ```wetb_py3``` environment:
+Update the ```py36-wetb``` environment:
 
 ```
 conda update --all
 ```
 
-Pull latest wetb changes and create re-distributable binary wheel package for ```wetb_py3```:
+Pull latest wetb changes and create re-distributable binary wheel package for ```py36-wetb```:
 
 ```
 cd /home/MET/repositories/tooblox/WindEnergyToolbox
@@ -45,5 +45,5 @@ pip install --no-deps -U dist/wetb-X.Y.Z.post0.devXXXXXXXX-cp35m-linux_x86_64.wh
 The option ```--no-deps``` is used here to avoid pip installing possible newer
 versions of packages that should be managed by conda. This only works when all
 dependencies of ```wetb``` are met (which is assumed by default for the
-```wetb_py3``` environment).
+```py36-wetb``` environment).
 

git_utils.py

+'''
+Created on 28. jul. 2017
+
+@author: mmpe
+'''
+import os
+import subprocess
+
+
+def _run_git_cmd(cmd, git_repo_path=None):
+    git_repo_path = git_repo_path or os.getcwd()
+    if not os.path.isdir(os.path.join(git_repo_path, ".git")):
+        raise Warning("'%s' does not appear to be a Git repository." % git_repo_path)
+    try:
+        process = subprocess.Popen(cmd,
+                                   stdout=subprocess.PIPE,
+                                   stderr=subprocess.PIPE,
+                                   universal_newlines=True,
+                                   cwd=os.path.abspath(git_repo_path))
+        stdout,stderr = process.communicate()
+        if process.returncode != 0:
+            raise EnvironmentError("%s\n%s"%(stdout, stderr))
+        return stdout.strip()
+
+    except EnvironmentError as e:
+        raise e
+        raise Warning("unable to run git")
+
+
+def get_git_branch(git_repo_path=None):
+    cmd = ["git", "rev-parse", "--abbrev-ref", "HEAD"]
+    return _run_git_cmd(cmd, git_repo_path)
+
+
+def get_git_version(git_repo_path=None):
+    cmd = ["git", "describe", "--tags", "--dirty", "--always"]
+    # format it will return: 'v0.1.0-12-g22668f0'
+    v = _run_git_cmd(cmd, git_repo_path)
+    # convert to something Pypi likes: 0.1.2.dev3.123456
+    # see also https://setuptools.pypa.io/en/latest/userguide/distribution.html
+    # and/or PEP440 https://peps.python.org/pep-0440/
+    v = v.replace('-', '.post', 1)
+    return v
+
+
+def get_tag(git_repo_path=None, verbose=False):
+    tag = _run_git_cmd(['git', 'describe', '--tags', '--always', '--abbrev=0'],
+                       git_repo_path)
+    if verbose:
+        print(tag)
+    return tag
+
+
+def set_tag(tag, push, git_repo_path=None):
+    _run_git_cmd(["git", "tag", tag], git_repo_path)
+    if push:
+        _run_git_cmd(["git", "push"], git_repo_path)
+        _run_git_cmd(["git", "push", "--tags"], git_repo_path)
+
+
+def update_git_version(version_module, git_repo_path=None):
+    """Update <version_module>.__version__ to git version"""
+
+    version_str = get_git_version(git_repo_path)
+    assert os.path.isfile(version_module.__file__)
+    with open(version_module.__file__, "w") as fid:
+        fid.write("__version__ = '%s'" % version_str)
+
+    # ensure file is written, closed and ready
+    with open(version_module.__file__) as fid:
+        fid.read()
+    return version_str
+
+
+def write_vers(vers_file='wetb/__init__.py', repo=None, skip_chars=1):
+    """Writes out version string as follows:
+        "last tag"-("nr commits since tag")-("branch name")-("hash commit")
+    and where nr of commits since last tag is only included if >0,
+    branch name is only inlcuded when not on master,
+    and hash commit is only included when not at a tag (when nr of commits > 0)
+    """
+    if not repo:
+        repo = os.getcwd()
+    version_long = get_git_version(repo)
+    branch = get_git_branch(repo)
+
+    verel = version_long.split('-')
+    # tag name
+    version = verel[0][skip_chars:]
+    # number of commits since last tag, only if >0
+    nr_commits = 0
+    if len(verel) > 1:
+        try:
+            nr_commits = int(verel[1])
+        except ValueError:
+            nr_commits = -1
+        if nr_commits > 0:
+            version += '-' + verel[1]
+    # branch name, only when NOT on master
+    if branch != 'master':
+        version += '-' + branch
+    # hash commit, only if not at tag
+    if len(verel) > 2 and nr_commits > 0:
+        # first character on the hash is always a g (not part of the hash)
+        version += '-' + verel[2][1:]
+    # if "-HEAD" is added to the version, which pypi does not like:
+    if version.endswith('-HEAD'):
+        version = version[:-5]
+    print(version_long)
+    print('Writing version: {} in {}'.format(version, vers_file))
+
+    with open(vers_file, 'r') as f:
+        lines = f.readlines()
+    for n, l in enumerate(lines):
+        if l.startswith('__version__'):
+            lines[n] = "__version__ = '{}'\n".format(version)
+    for n, l in enumerate(lines):
+        if l.startswith('__release__'):
+            lines[n] = "__release__ = '{}'\n".format(version)
+    with open(vers_file, 'w') as f:
+        f.write(''.join(lines))
+    return version
+
+
+def rename_dist_file():
+    for f in os.listdir('dist'):
+        if f.endswith('whl'):
+            split = f.split('linux')
+            new_name = 'manylinux1'.join(split)
+            old_path = os.path.join('dist', f)
+            new_path = os.path.join('dist', new_name)
+            os.rename(old_path, new_path)
+
+
+def main():
+    """Example of how to run (pytest-friendly)"""
+    if __name__ == '__main__':
+        pass
+
+
+main()

pyproject.toml

+[build-system]
+requires = [
+    "setuptools>=60",
+    "setuptools-scm>=8.0"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "wetb"
+authors = [{name="DTU Wind and Energy Systems"}]
+description = "The Wind Energy Toolbox (or ```wetb```, pronounce as wee-tee-bee) is a collection of Python scripts that facilitate working with (potentially a lot) of HAWC2, HAWCStab2, FAST or other text input based simulation tools."
+dependencies = [
+    'certifi',
+    'click',
+    'Cython',
+    'h5py',
+    'Jinja2',
+    'lxml',
+    'matplotlib',
+    'pillow',
+    'mock',
+    'numpy',
+    'numba',
+    'openpyxl',
+    'pandas',
+    'paramiko',
+    'psutil',
+    'pytest',
+    'pytest-cov',
+    'scipy',
+    'sshtunnel',
+    'tables',
+    'tqdm',
+    'xarray',
+    'xlwt',
+    'XlsxWriter',
+]
+license = {text = "wetb is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License (GPL, http://www.gnu.org/copyleft/gpl.html) as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version.  wetb 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 General Public License for more details http://www.gnu.org/licenses/  We encourage you to submit new code for possible inclusion in future versions of wetb."}
+dynamic = ["version"]
+
+[project.urls]
+repository = "https://gitlab.windenergy.dtu.dk/toolbox/WindEnergyToolbox"
+documentation = "https://toolbox.pages.windenergy.dtu.dk/WindEnergyToolbox/"
+
+
+[project.optional-dependencies]
+prepost = ["openpyxl", "tables", "xlwt", "Cython"]
+all = ["openpyxl", "tables", "xlwt", "Cython", "paramiko", "sshtunnel", 'pytest', 'mock', 'click']
+
+[tool.setuptools_scm]
+version_scheme = "no-guess-dev"
+
+[tool.setuptools]
+packages = ["wetb"]

remove-py2-support.sh

+#!/bin/bash
+
+find ./ -type f -iname "*.py" -exec sed -i '/from __future__ import print_function/d' {} \;
+find ./ -type f -iname "*.py" -exec sed -i '/from __future__ import division/d' {} \;
+find ./ -type f -iname "*.py" -exec sed -i '/from __future__ import unicode_literals/d' {} \;
+find ./ -type f -iname "*.py" -exec sed -i '/from __future__ import absolute_import/d' {} \;
+find ./ -type f -iname "*.py" -exec sed -i '/from io import open/d' {} \;
+find ./ -type f -iname "*.py" -exec sed -i '/from builtins import object/d' {} \;
+find ./ -type f -iname "*.py" -exec sed -i '/from builtins import map/d' {} \;
+find ./ -type f -iname "*.py" -exec sed -i '/from builtins import chr/d' {} \;
+find ./ -type f -iname "*.py" -exec sed -i '/from builtins import dict/d' {} \;
+find ./ -type f -iname "*.py" -exec sed -i '/from builtins import super/d' {} \;
+find ./ -type f -iname "*.py" -exec sed -i '/from builtins import zip/d' {} \;
+find ./ -type f -iname "*.py" -exec sed -i '/from builtins import range/d' {} \;
+find ./ -type f -iname "*.py" -exec sed -i '/from builtins import str/d' {} \;
+find ./ -type f -iname "*.py" -exec sed -i '/from builtins import int/d' {} \;
+find ./ -type f -iname "*.py" -exec sed -i '/from future import standard_library/d' {} \;
+find ./ -type f -iname "*.py" -exec sed -i '/standard_library.install_aliases()/d' {} \;
+

requirements.txt

-# Add your requirements here like:
-six
-numpy>=1.4
-scipy>=0.9
-matplotlib
-pytest
-xlrd
-xlwt
-openpyxl
-h5py
-pandas
-tables
-future
-paramiko
-psutil
-pbr
-PyScaffold
-pytest-cov
-sshtunnel
-

setup.cfg

-[metadata]
-name = wetb
-summary = Wind Energy Toolbox
-author = DTU Wind Energy
-author-email = mmpe@dtu.dk
-license = GPLv3
-home-page = https://gitlab.windenergy.dtu.dk/toolbox/WindEnergyToolbox
-description-file = README
-# Add here all kinds of additional classifiers as defined under
-# https://pypi.python.org/pypi?%3Aaction=list_classifiers
-classifiers = Development Status :: 4 - Beta,
-              Programming Language :: Python,
-              Programming Language :: Python :: 2.7,
-              Programming Language :: Python :: 3,
-              Programming Language :: Python :: 3.3,
-              Programming Language :: Python :: 3.4,
-			  Programming Language :: Python :: 3.5,
-              Environment :: Console,
-              Intended Audience :: Education,
-              Intended Audience :: Science/Research,
-              License :: OSI Approved :: GPL License,
-              Operating System :: OS Independent,
-              Operating System :: POSIX :: Linux,
-              Operating System :: Unix,
-              Operating System :: MacOS,
-              Operating System :: Microsoft :: Windows
-              Topic :: Scientific/Engineering :: Mathematics
-
-[entry_points]
-# Add here console scripts like:
-# console_scripts =
-#     hello_world = wetb.module:function
-# as well as other entry_points.
-
-
-[files]
-# Add here 'data_files', 'packages' or 'namespace_packages'.
-# Additional data files are defined as key value pairs of source and target:
-packages =
-    wetb
-# data_files =
-#    share/wetb_docs = docs/*
-
-[extras]
-# Add here additional requirements for extra features, like:
-# PDF =
-#    ReportLab>=1.2
-#    RXP
-#ALL =
-#    django
-#    cookiecutter
-
-[test]
-# py.test options when running `python setup.py test`
-#addopts = tests
-
-[tool:pytest]
-# Options for py.test:
-# Specify command line options as you would do when invoking py.test directly.
-# e.g. --cov-report html (or xml) for html/xml output or --junitxml junit.xml
-# in order to write a coverage file that can be read by Jenkins.
-#addopts =
-#    --cov wetb --cov-report term-missing
-#    --verbose
-python_files = WindEnergyToolbox/wetb/*
-
-[aliases]
-docs = build_sphinx
-
-[bdist_wheel]
-# Use this option if your package is pure-python
-universal = 0
-
-[build_sphinx]
-# Options for Sphinx build
-source_dir = docs
-build_dir = docs/_build
-
-[pbr]
-# Let pbr run sphinx-apidoc
-autodoc_tree_index_modules = True
-# autodoc_tree_excludes = ...
-# Let pbr itself generate the apidoc
-# autodoc_index_modules = True
-# autodoc_exclude_modules = ...
-# Convert warnings to errors
-# warnerrors = True
-
-[devpi:upload]
-# Options for the devpi: PyPI serer and packaging tool
-# VCS export must be deactivated since we are using setuptools-scm
-no-vcs = 1
-formats = bdist_wheel

tests/__init__.py

+import numpy as np
+npt = np.testing
\ No newline at end of file