Small changes to deployment files.

Added environment.yml and requirement.txt.
GitLab should now produce html coverage artifacts.
io_vectordata: now warns if grid spacing is not equal in all directions.

.gitlab-ci.yml

@@ -18,6 +18,9 @@ before_script:
   # Install jutil via secure ssh connection:
   - pip install git+ssh://gitlab@iffgit.fz-juelich.de/unger/jutil.git
 
+  ## Used for
+  #- pip install pytest pytest-cov
+
 stages:
   - test
 
@@ -27,5 +30,9 @@ test:
     # TODO: Different jobs with custom develop arguments? extra_requires (hyperspy, plotting)?
     # TODO: Use pip install -e .[hyperspy], etc.
     # Install requirements (-e: editable, like python setup.py develop, but pip, not easy_install):
-    - pip install -e .  # TODO: belongs here or before_script?
+    - pip install -e .['tests']  # Also installs everything for tests!
     - python setup.py test
+    - coverage html
+  artifacts:
+    paths:
+    - htmlcov/

environment.yml

+name: pyramid
+dependencies:
+- python=3.5
+- numpy
+- pip
+- pip:
+    - pypi-package-name

pyramid/file_io/io_vectordata.py

@@ -155,7 +155,7 @@ def _load_from_ovf(filename, a):
         field = np.asarray((x_mag, y_mag, z_mag)) * float(header.get('valuemultiplier', 1))
         if a is None:
             # TODO: If transferred to HyperSpy, this has to stay in Pyramid reader!
-            if header.get('xstepsize') == header.get('ystepsize') == header.get('zstepsize'):
+            if not header.get('xstepsize') == header.get('ystepsize') == header.get('zstepsize'):
                 _log.warning('Grid spacing is not equal in x, y and z (x will be used)!')
             a = float(header.get('xstepsize', 1.))
             meshunit = header.get('meshunit', 'nm')

requirements.txt

+-e .

setup.cfg

@@ -36,7 +36,7 @@ omit =
 
 [tool:pytest]
 addopts = --cov --flake8
-flake8-max-line-length = 120
+flake8-max-line-length = 100
 flake8-ignore =
     ALL  # TODO: PEP8 deactivated by this line (remove at a later point)!
     E402 E124 E125

setup.py

@@ -8,7 +8,7 @@ import subprocess
 import sys
 from distutils.command.build import build
 
-import numpy
+#import numpy
 from setuptools import setup, find_packages
 
 
@@ -19,8 +19,8 @@ MAINTAINER_EMAIL = 'j.caron@fz-juelich.de'
 URL = ''
 VERSION = '0.1.0-dev'
 PYTHON_VERSION = (2, 7)
-DEPENDENCIES = {'numpy': (1, 10)}
-LONG_DESCRIPTION = 'long description (TODO!)'  # TODO: Long description!
+DEPENDENCIES = {'numpy': (1, 10)}  # TODO: get rid off!!!
+LONG_DESCRIPTION = 'long description (TODO!)'  # TODO: Long description! put in (Readme?) file!
 
 
 def get_package_version(package):
@@ -126,6 +126,15 @@ def get_files(rootdir):
     return filepaths
 
 
+# TODO: extend extras_require for plotting and IO:
+extras_require = {
+    # TODO: Test all if really needed! don't use nose, if possible (pure pytest)!
+    "tests": ['pytest', 'pytest-runner', 'pytest-cov', 'pytest-flake8', 'coverage', 'nose']
+    # TODO: more for mayavi (plotting in general) and hyperspy, etc (see below)...
+}
+
+
+
 print('\n-------------------------------------------------------------------------------')
 print('checking requirements')
 check_requirements()
@@ -140,17 +149,17 @@ setup(name=DISTNAME,
       download_url=URL,
       version=VERSION,
       packages=find_packages(exclude=['tests', 'doc']),
-      include_dirs=[numpy.get_include()],
+      #include_dirs=[numpy.get_include()],
       # TODO: Use requirements.txt? extras_require for optional stuff (hyperspy, plotting)?
       # TODO: After split of Pyramid, comment out and see what really is used (is e.g. scipy?)!
-      # - pip install numpy scipy nose h5py matplotlib Pillow scikit-image cmocean hyperspy
-      setup_requires=['numpy>=1.6', 'pytest-runner', 'pytest'],
-      tests_require=['nose', 'pytest-cov', 'pytest-flake8', 'coverage'],
+      #setup_requires=['numpy>=1.6', 'pytest', 'pytest-runner'],
+      #tests_require=['pytest', 'pytest-cov', 'pytest-flake8'],
       install_requires=['numpy>=1.6', 'tqdm', 'scipy', 'matplotlib', 'Pillow', 'h5py',
                         'hyperspy', 'jutil', 'cmocean'],
+      extras_require=extras_require,
       # TODO: extra: 'pyfftw', 'mayavi' (not easy to install... find a way!)
       # TODO: See https://stackoverflow.com/a/28842733 for extras_require...
       # TODO: ...replace [dev] with [IO] (hyperspy) and [plotting] (separate plotting library)!
-      test_suite='nose.collector',
+      #test_suite='nose.collector',  # TODO: don't use nose!
       cmdclass={'build': build})
 print('-------------------------------------------------------------------------------\n')