From 618b728d261a7e335b3959960e487d38d33e45fa Mon Sep 17 00:00:00 2001
From: Jan Caron <j.caron@fz-juelich.de>
Date: Sun, 16 Jul 2017 15:43:25 +0200
Subject: [PATCH] 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 | 9 ++++++++-
environment.yml | 7 +++++++
pyramid/file_io/io_vectordata.py | 2 +-
requirements.txt | 1 +
setup.cfg | 2 +-
setup.py | 25 +++++++++++++++++--------
6 files changed, 35 insertions(+), 11 deletions(-)
create mode 100644 environment.yml
create mode 100644 requirements.txt
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 5dce810..cb95938 100644
--- a/.gitlab-ci.yml
+++ b/.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/
diff --git a/environment.yml b/environment.yml
new file mode 100644
index 0000000..c45b555
--- /dev/null
+++ b/environment.yml
@@ -0,0 +1,7 @@
+name: pyramid
+dependencies:
+- python=3.5
+- numpy
+- pip
+- pip:
+ - pypi-package-name
diff --git a/pyramid/file_io/io_vectordata.py b/pyramid/file_io/io_vectordata.py
index 6083f20..9fec4da 100644
--- a/pyramid/file_io/io_vectordata.py
+++ b/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')
diff --git a/requirements.txt b/requirements.txt
new file mode 100644
index 0000000..d6e1198
--- /dev/null
+++ b/requirements.txt
@@ -0,0 +1 @@
+-e .
diff --git a/setup.cfg b/setup.cfg
index 4588955..800d7c2 100644
--- a/setup.cfg
+++ b/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
diff --git a/setup.py b/setup.py
index e571acf..d36cd31 100644
--- a/setup.py
+++ b/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')
--
GitLab