remove unused dependencies and move other to extra. install via pip install...

.gitlab-ci.yml

@@ -13,10 +13,12 @@ test:
     test
 #  except:
 #    - test_pypi
+  variables:
+    GIT_SUBMODULE_STRATEGY: recursive
   before_script:
-  - git submodule sync --recursive
-  - git submodule update --init --recursive
-  - python -m pip install .
+  #- git submodule sync --recursive
+  #- git submodule update --init --recursive
+  - python -m pip install .[all]
   - pip3 install pytest mock click
   script:
   - python3 -m pytest --cov-report term-missing:skip-covered --cov-report xml:coverage.xml --cov=wetb
@@ -81,37 +83,24 @@ upload_package_local:
 
 
   # ===== BUILD WHEELS AND UPLOAD TO PYPI =====
-pypi_linux:
-  stage:
-    deploy
-  only:
-    - tags
-    - test_pypi
-  script:
-    - apt-get update
-    - pip install -e . --upgrade
-    - python3 -m pip install -U setuptools wheel
-    - python3 setup.py sdist bdist_wheel
-    - python3 -m pip install -U twine
-    - python3 -c 'from git_utils import rename_dist_file; rename_dist_file()'
-    - twine upload dist/* -u $TWINE_USERNAME -p $TWINE_PASSWORD
-    #- twine upload --repository-url https://test.pypi.org/legacy/ dist/* -u $TWINE_USERNAME -p $TWINE_PASSWORD # for testing purposes
+upload_package_pypi:
+  image: continuumio/anaconda3:latest
   tags:
-    - python
-
+    - docker, linux, shared
+  stage: deploy
+  needs:
+  - job: build_poetry_wheel
+    artifacts: true
+  - job: test
+    artifacts: false
 
-pypi_windows:
-  stage:
-    deploy
+  script:
+    - pip install twine
+    - twine upload dist/* -u $TWINE_USERNAME -p $TWINE_PASSWORD
   only:
     - tags
     - test_pypi
-  script:
-    - c:/Anaconda3/envs/WindEnergyToolbox/python.exe setup.py bdist_wheel
-    - twine upload dist/* -u %TWINE_USERNAME% -p %TWINE_PASSWORD%
-    #- twine upload --repository-url https://test.pypi.org/legacy/ dist/* -u %TWINE_USERNAME% -p %TWINE_PASSWORD% # for testing purposes
-  tags:
-    - CPAV_old
+
 
 build_poetry_wheel:
   stage: build

docs/source/installation.rst

@@ -4,21 +4,9 @@ Installation
 ===========================
 
 
-Install C++ compilers (Windows)
---------------------------------
-
-Your computer must have a C++ compiler installed in order to install
-``wetb``. Windows users can follow the instructions on 
-`this page <https://wiki.python.org/moin/WindowsCompilers>`_ under
-the section "14.2 standalone".
-
-
 Normal user
 --------------------------------
 
-You must first have installed a C++ compiler before you can use these
-commands. See section above.
-
 * Quick install::
 
     pip install wetb
@@ -30,6 +18,14 @@ commands. See section above.
 * Update an installation to the most recent version::
 
     pip install --upgrade wetb
+	
+* Install with dependencies needed by prepost
+  
+    pip install wetb[prepost]
+	
+* Install with all dependencies 
+  
+    pip install wetb[all]
 
 **NOTE**. Dependency conflicts can arise if you do not install
 ``wetb`` into a clean environment. In particular, your installation
@@ -47,5 +43,9 @@ Clone the repository and install a local editable copy::
 
   git clone https://gitlab.windenergy.dtu.dk/toolbox/WindEnergyToolbox.git
   cd WindEnergyToolbox
-  pip install -e .
+  pip install -e .[all]
+  
+  
+  
+  
 

examples/02_generate_dlc_with_definition.py

-from wetb.hawc2.hawc2_input_writer import HAWC2InputWriter
-from wetb.hawc2.tests import test_files
-import os
-
-
-def main():
-    if __name__ == '__main__':
-
-        # ======================================================================
-        # load master htc file path
-        # ======================================================================
-        path = os.path.dirname(test_files.__file__) + "/simulation_setup/DTU10MWRef6.0/"
-        htc_base_file = path + 'htc/DTU_10MW_RWT.htc'
-        
-        h2writer = HAWC2InputWriter(htc_base_file)
-
-        # ======================================================================
-        # Set DLC definition module filename
-        # ======================================================================
-        definition_file = 'dlc_definition.py'
-
-        #=======================================================================
-        # Generate htc files from definition file, and print list of simulations
-        #=======================================================================
-        df = h2writer.from_definition(definition_file)
-        print(df)
-
-main()
\ No newline at end of file

examples/dlc_definition.py

-
-constants = {'simulation.time_stop':100}
-
-variables = {'wind.wsp': [4, 6, 8],
-             'wind.tint': [0.1, 0.15, 0.2]}
-
-functions = {'Name': lambda x: 'sim_wsp' + str(x['wind.wsp']) + '_ti' + str(x['wind.tint'])}
-
-
-

pyproject.toml

@@ -8,30 +8,32 @@ readme = "README.md"
 
 [tool.poetry.dependencies]
 click = "^8.0.4"
-Cython = "^0.29.35"
+Cython = {version="^0.29.35", optional=true}
 h5py = "^3.1.0"
 Jinja2 = "^3.0.3"
 lxml = "^4.9.2"
 matplotlib = "^3.3.4"
 mock = "^5.0.2"
 numpy = ">=1.4"
-openpyxl = "^3.1.2"
+openpyxl =  { version = "^3.1.2", optional = true }
 pandas = "^1.1.5"
-paramiko = "^3.2.0"
-pbr = "^5.11.1"
+paramiko = {version="^3.2.0", optional = true}
 psutil = "^5.9.5"
 pytest = "^7.0.1"
 pytest-cov = "^4.0.0"
 python = "^3.6"
 scipy = ">=0.9.0"
-six = "^1.16.0"
-sshtunnel = "^0.4.0"
-tables = "^3.7.0"
+sshtunnel = {version="^0.4.0", optional = true}
+tables = {version="^3.7.0", optional=true}
 tqdm = "^4.64.1"
-wafo = "^0.1.2"
-xlwt = "^1.3.0"
+wafo = {version="^0.1.2", optional=true}
+xlwt = {version="^1.3.0", optional=true}
 XlsxWriter = "^3.1.2"
 
+[tool.poetry.extras]
+prepost = ["openpyxl", "tables", "wafo", "xlwt", "Cython"]
+all = ["openpyxl", "tables", "wafo", "xlwt", "Cython", "paramiko", "sshtunnel"]
+
 
 [build-system]
 requires = ["poetry-core"]

requirements.txt

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

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,
-#			  Programming Language :: Python :: 3.6,
-#              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

setup.py

@@ -4,6 +4,7 @@
     Setup file for wetb.
 """
 
+from distutils.extension import Extension
 import os
 from git_utils import write_vers
 import sys
@@ -28,9 +29,6 @@ with open("README.md", "r") as fh:
     long_description = fh.read()
 
 
-from distutils.extension import Extension
-
-
 def setup_package(build_ext_switch=True):
     # if build_ext_switch:
     #     import numpy as np
@@ -51,28 +49,30 @@ def setup_package(build_ext_switch=True):
     sphinx = ['sphinx'] if needs_sphinx else []
     install_requires = ['mock',
                         'h5py',
-                        #'tables', # Has blosc2 as requirement, fails unless C compiler is present on win32
+                        # 'tables', # Has blosc2 as requirement, fails unless C compiler is present on win32
                         'pytest',
                         'pytest-cov',
                         #                        'blosc', # gives an error - has to be pre-installed
                         'pbr',
-                        'paramiko',
                         'scipy',
                         'pandas',
                         'matplotlib',
                         'coverage',
-                        'xlwt',
-                        'openpyxl',
                         'psutil',
-                        'six',
-                        'sshtunnel',
                         'Click',
                         'jinja2', ]
-    extras_require={
-          'prepost': [
-              'tables',  # requires blosc2 and may not install on 32 bit systems without a C compiler
-              'cython',
-          ]
+    extras_require = {
+        'prepost': [
+            'tables',  # requires blosc2 and may not install on 32 bit systems without a C compiler
+            'cython',
+            'openpyxl',
+        ],
+        'all': ['tables',  # requires blosc2 and may not install on 32 bit systems without a C compiler
+                'cython',
+                'sshtunnel',
+                'openpyxl',
+                'paramiko',
+                ]
     }
 
     setup(install_requires=install_requires,

tests/test_examples.py

@@ -6,7 +6,7 @@ import mock
 import pytest
 import matplotlib.pyplot as plt
 import sys
-from examples import examples
+from wetb import examples
 from tests.run_main import run_module_main
 
 

wetb/utils/timing.py

-from six import exec_
 import time
 import inspect
 def get_time(f):