pytables -> tables

versioning from setup.py instead of yml-file

.gitlab-ci.yml

@@ -44,7 +44,6 @@ pypi_linux:
   script:
     - apt-get update
     - pip install -e . --upgrade
-    - python3 -c 'from git_utils import write_vers; write_vers()'
     - python3 -m pip install -U setuptools wheel
     - python3 setup.py sdist bdist_wheel
     - python3 -m pip install -U twine
@@ -62,7 +61,6 @@ pypi_windows:
     - tags
     - test_pypi
   script:
-    - c:/Anaconda3/envs/WindEnergyToolbox/python.exe -c "from git_utils import write_vers; write_vers()"
     - 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

.pypirc

@@ -4,6 +4,6 @@ index-servers=
     #testpypi # include this line for testing
 
 [testpypi]
-repository: https://test.pypi.org/legacy/ # use this line when testing
-#repository: https://upload.pypi.org/legacy/
+#repository: https://test.pypi.org/legacy/ # use this line when testing
+repository: https://upload.pypi.org/legacy/
 username: DTUWindEnergy

README.md

 
 [![build status](https://gitlab.windenergy.dtu.dk/toolbox/WindEnergyToolbox/badges/master/build.svg)](https://gitlab.windenergy.dtu.dk/toolbox/WindEnergyToolbox/commits/master)
 [![coverage report](https://gitlab.windenergy.dtu.dk/toolbox/WindEnergyToolbox/badges/master/coverage.svg)](https://gitlab.windenergy.dtu.dk/toolbox/WindEnergyToolbox/commits/master)
+[![pypi status](https://img.shields.io/pypi/v/wetb.png)](https://pypi.python.org/pypi/wetb)
 
 # Introduction
 

docs/developer-guide.md

@@ -139,7 +139,6 @@ use ```deactivate``` to deactivate the environment.
 - [h5py](http://www.h5py.org/)
 - [matplotlib](http://matplotlib.org/)
 - [pytables](http://www.pytables.org/)
-- [pyscaffold](http://pyscaffold.readthedocs.org/en/)
 - [pytest](https://pypi.python.org/pypi/pytest)
 - [pytest-cov](https://pypi.python.org/pypi/pytest-cov/)
 - six, [future](http://python-future.org/index.html)
@@ -159,7 +158,7 @@ Install the necessary Python dependencies using the conda package manager:
 ```
 >> conda install setuptools_scm future h5py pytables pytest pytest-cov nose sphinx blosc pbr paramiko
 >> conda install scipy pandas matplotlib cython xlrd coverage xlwt openpyxl psutil pandoc twine pypandoc
->> conda install -c conda-forge pyscaffold sshtunnel --no-deps
+>> conda install -c conda-forge sshtunnel --no-deps
 ```
 
 Note that ```--no-deps``` avoids that newer packages from the channel

docs/install.md

@@ -7,9 +7,7 @@
 Install the necessary Python dependencies using the ```conda``` package manager:
 
 ```
->> conda install setuptools_scm future h5py pytables pytest pytest-cov nose sphinx blosc pbr paramiko
->> conda install scipy pandas matplotlib cython xlrd coverage xlwt openpyxl psutil
->> conda install -c conda-forge pyscaffold sshtunnel --no-deps
+>> conda install blosc
 ```
 
 Now you can install ```wetb``` with ```pip``` (there is no ```conda``` package
@@ -58,8 +56,4 @@ in Python 2.7 by default. You can also write code that is compatible with both
 [issue 1](https://gitlab.windenergy.dtu.dk/toolbox/WindEnergyToolbox/issues/1)).
 
 
-# Note
-
-This project has been set up using PyScaffold 2.5. For details and usage
-information on PyScaffold see http://pyscaffold.readthedocs.org/.
 

git_utils.py

@@ -14,11 +14,12 @@ def _run_git_cmd(cmd, git_repo_path=None):
     try:
         process = subprocess.Popen(cmd,
                                    stdout=subprocess.PIPE,
+                                   stderr=subprocess.PIPE,
                                    universal_newlines=True,
                                    cwd=os.path.abspath(git_repo_path))
-        stdout = process.communicate()[0]
+        stdout,stderr = process.communicate()
         if process.returncode != 0:
-            raise EnvironmentError()
+            raise EnvironmentError("%s\n%s"%(stdout, stderr))
         return stdout.strip()
 
     except EnvironmentError as e:
@@ -26,13 +27,22 @@ def _run_git_cmd(cmd, git_repo_path=None):
         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"]
     return _run_git_cmd(cmd, git_repo_path)
 
 
-def get_tag(git_repo_path=None):
-    return _run_git_cmd(['git', 'describe', '--tags', '--abbrev=0'], git_repo_path)
+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):
@@ -55,41 +65,69 @@ def update_git_version(version_module, git_repo_path=None):
         fid.read()
     return version_str
 
-def write_vers(vers_file='wetb/__init__.py'):
-    version = get_tag(os.getcwd())
+
+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:]
+
+    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):
+    for n, l in enumerate(lines):
         if l.startswith('__version__'):
-            lines[n] = "__version__ = '{}'\n".format(version[1:])
+            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)
+            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
-#        import version
-#        import app_utils
-#        git_path = os.path.dirname(app_utils.__file__) + "/../"
-#        update_git_version(version, git_path)
-#        tag = get_tag(os.getcwd())
-#        print(tag)
-#        version = get_git_version(os.getcwd())
-#        print(version)
-#        rename_dist_file()
-        write_vers()
+        pass
 
 
 main()

setup.py

@@ -5,10 +5,12 @@
 """
 
 import os
+from git_utils import write_vers
 import sys
 from setuptools import setup, find_packages
-import wetb
-__version__ = wetb.__version__
+
+repo = os.path.dirname(__file__)
+version = write_vers(vers_file='wetb/__init__.py', repo=repo, skip_chars=1)
 
 try:
     from pypandoc import convert_file
@@ -25,18 +27,38 @@ from Cython.Distutils import build_ext
 def setup_package():
 
     ex_info = [('wetb.fatigue_tools.rainflowcounting', ['pair_range', 'peak_trough', 'rainflowcount_astm']),
-			   ('wetb.signal.filters', ['cy_filters'])]
+               ('wetb.signal.filters', ['cy_filters'])]
     extlist = [Extension('%s.%s' % (module, n),
-                         [os.path.join(module.replace(".","/"), n)+'.pyx'],
+                         [os.path.join(module.replace(".", "/"), n) + '.pyx'],
                          include_dirs=[np.get_include()]) for module, names in ex_info for n in names]
-
     needs_sphinx = {'build_sphinx', 'upload_docs'}.intersection(sys.argv)
     sphinx = ['sphinx'] if needs_sphinx else []
-    setup(setup_requires=['six'] + sphinx,
-          cmdclass = {'build_ext': build_ext},
-          ext_modules = extlist,
+    install_requires = ['future',
+                        'h5py',
+                        'tables',
+                        'pytest',
+                        'pytest-cov',
+#                        'blosc', # gives an error - has to be pre-installed
+                        'pbr',
+                        'paramiko',
+                        'scipy',
+                        'pandas',
+                        'matplotlib',
+                        'cython',
+                        'xlrd',
+                        'coverage',
+                        'xlwt',
+                        'openpyxl',
+                        'psutil',
+                        'six',
+                        'sshtunnel']
+    build_requires = ['cython']
+    setup(install_requires=install_requires,
+          setup_requires=install_requires + build_requires + sphinx,
+          cmdclass={'build_ext': build_ext},
+          ext_modules=extlist,
           long_description=read_md('README.md'),
-          version=__version__,
+          version=version,
           packages=find_packages(),
           )