Merge pull request #5 from GeoStat-Framework/develop

1.1.0 release

.travis.yml

@@ -1,42 +1,68 @@
 language: python
+python: 3.7
 
-matrix:
-  include:
-    # separate sdist and coverage with py36 on linux
-    - name: "sdist and coverage"
-      sudo: required
-      language: python
-      python: 3.6
-      services: docker
-      script:
-        - python -m pip install -U setuptools pytest-cov coveralls
-        - python setup.py sdist -d dist
-        - python -m pip install -r requirements.txt
-        - python -m pytest --cov ogs5py --cov-report term-missing -v tests/
-        - python -m coveralls
-    # universal wheel on 64bit Linux with py36
-    - name: "py2.py3 wheel"
-      sudo: required
-      language: python
-      python: 3.6
-      services: docker
+# setuptools-scm needs all tags in order to obtain a proper version
+git:
+  depth: false
 
 env:
   global:
+    # Note: TWINE_PASSWORD is set in Travis settings
     - TWINE_USERNAME=geostatframework
-    - CIBW_BEFORE_BUILD="pip install setuptools"
-
-script:
-  # create wheels
-  - python -m pip install cibuildwheel==1.0.0
-  - python -m cibuildwheel --output-dir dist
-
-after_success:
-  - python -m pip install twine
-  - python -m twine upload --verbose --skip-existing --repository-url https://test.pypi.org/legacy/ dist/*
-  - if [[ $TRAVIS_TAG ]]; then python -m twine upload --verbose --skip-existing dist/*; fi
 
 notifications:
   email:
     recipients:
-      - [email protected]
+    - [email protected]
+
+# before_install:
+#   - |
+#     if [[ "$TRAVIS_OS_NAME" = windows ]]; then
+#         choco install python --version 3.7.7
+#         export PATH="/c/Python37:/c/Python37/Scripts:$PATH"
+#         # make sure it's on PATH as 'python3'
+#         ln -s /c/Python37/python.exe /c/Python37/python3.exe
+#     fi
+
+install:
+  - python3 -m pip install .[test] coveralls
+
+script:
+  - python3 -m pytest --cov ogs5py --cov-report term-missing -v tests/
+
+stages:
+  - test
+  - name: deploy
+    if: (NOT type IN (pull_request)) AND (repo = GeoStat-Framework/ogs5py)
+
+jobs:
+  include:
+    - stage: test
+      name: Test on Linux
+      services: docker
+      after_success: python3 -m coveralls
+    - stage: test
+      name: Test on MacOS
+      os: osx
+      language: generic
+    # skip windows due to a VTK BUG
+    # - stage: test
+    #   name: Test on Windows
+    #   os: windows
+    #   language: shell
+
+    # Test Deploy source distribution
+    - stage: deploy
+      name: Test Deploy
+      install: python3 -m pip install -U setuptools wheel twine
+      script: python3 setup.py sdist --formats=gztar bdist_wheel
+      after_success:
+       - python3 -m twine upload --verbose --skip-existing --repository-url https://test.pypi.org/legacy/ dist/*
+
+    # Deploy source distribution
+    - stage: deploy
+      name: Deploy to PyPI
+      if: tag IS present
+      install: python3 -m pip install -U setuptools wheel twine
+      script: python3 setup.py sdist --formats=gztar bdist_wheel
+      after_success: python3 -m twine upload --verbose --skip-existing dist/*

.zenodo.json

@@ -0,0 +1,18 @@
+{
+  "contributors": [
+    {
+      "orcid": "0000-0002-2547-8102",
+      "affiliation": "Helmholtz Centre for Environmental Research - UFZ",
+      "type": "Supervisor",
+      "name": "Falk He\u00dfe"
+    }
+  ],
+  "license": "MIT",
+  "creators": [
+    {
+      "orcid": "0000-0001-9060-4008",
+      "affiliation": "Helmholtz Centre for Environmental Research - UFZ",
+      "name": "Sebastian M\u00fcller"
+    }
+  ]
+}

CHANGELOG.md

@@ -3,6 +3,17 @@
 All notable changes to **ogs5py** will be documented in this file.
 
 
+## [1.1.0] - 2020-03-22
+
+### Bugfixes
+* meshio 4 was not compatible
+* fixed integer type in exporting meshes with element/material IDs
+* better check for OGS5 success on Windows
+
+### Changes
+* drop py2.7 support
+
+
 ## [1.0.5] - 2019-11-18
 
 ### Bugfixes

MANIFEST.in

@@ -1,6 +1,7 @@
 include MANIFEST.in
 include setup.py
 recursive-include ogs5py *.py
+recursive-include tests *.py
 recursive-include docs/source *
 include docs/Makefile docs/requirements.txt
 include LICENSE

README.md

@@ -2,9 +2,9 @@
 
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.2546767.svg)](https://doi.org/10.5281/zenodo.2546767)
 [![PyPI version](https://badge.fury.io/py/ogs5py.svg)](https://badge.fury.io/py/ogs5py)
-[![Build Status](https://travis-ci.org/GeoStat-Framework/ogs5py.svg?branch=master)](https://travis-ci.org/GeoStat-Framework/ogs5py)
+[![Build Status](https://travis-ci.com/GeoStat-Framework/ogs5py.svg?branch=master)](https://travis-ci.org/GeoStat-Framework/ogs5py)
 [![Coverage Status](https://coveralls.io/repos/github/GeoStat-Framework/ogs5py/badge.svg?branch=master)](https://coveralls.io/github/GeoStat-Framework/ogs5py?branch=master)
-[![Documentation Status](https://readthedocs.org/projects/ogs5py/badge/?version=latest)](https://geostat-framework.readthedocs.io/projects/ogs5py/en/latest/?badge=latest)
+[![Documentation Status](https://readthedocs.org/projects/ogs5py/badge/?version=stable)](https://geostat-framework.readthedocs.io/projects/ogs5py/en/stable/?badge=stable)
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/ambv/black)
 
 <p align="center">
@@ -147,13 +147,12 @@ model.run_model(ogs_exe="path/to/ogs")
 
 ## Requirements:
 
-- [NumPy >= 1.13.0](https://www.numpy.org)
-- [Pandas >= 0.23.0](https://pandas.pydata.org/)
-- [whichcraft](https://github.com/pydanny/whichcraft)
-- [meshio](https://github.com/nschloe/meshio)
-- [lxml](https://github.com/lxml/lxml)
-- [vtk](https://vtk.org/)
-- [pexpect](https://github.com/pexpect/pexpect)
+- [NumPy >= 1.14.5](https://www.numpy.org)
+- [Pandas >= 0.23.2](https://pandas.pydata.org/)
+- [meshio >= 4.0.3; <5.0](https://github.com/nschloe/meshio)
+- [lxml >= 4.0; <5.0](https://github.com/lxml/lxml)
+- [pexpect >= 4.0; <5.0](https://github.com/pexpect/pexpect)
+- [vtk >= 8.1](https://vtk.org/)
 
 ## Contact
 
@@ -162,12 +161,12 @@ You can contact us via <[email protected]>.
 
 ## License
 
-[MIT][gpl_link] © 2018-2019 (inspired by Falk Hesse and Miao Jing)
+[MIT][gpl_link] © 2018-2020 (inspired by Falk Hesse and Miao Jing)
 
 This project is based on [OGSPY][ogspy_link].
 
 [ogspy_link]: https://github.com/fhesze/OGSPY
 [gpl_link]: https://github.com/GeoStat-Framework/ogs5py/blob/master/LICENSE
 [ogs5_link]: https://www.opengeosys.org/ogs-5/
-[doc_link]: https://geostat-framework.readthedocs.io/projects/ogs5py/en/latest/
-[tut1_link]: https://geostat-framework.readthedocs.io/projects/ogs5py/en/latest/tutorial_01_pump.html
+[doc_link]: https://ogs5py.readthedocs.io/
+[tut1_link]: https://geostat-framework.readthedocs.io/projects/ogs5py/en/stable/tutorial_01_pump.html

docs/requirements.txt

@@ -1,4 +1,3 @@
-# required for readthedocs.org
-numpydoc
-# https://stackoverflow.com/a/11704396/6696397
--r ../requirements.txt
+-r requirements_doc.txt
+-r ../requirements_setup.txt
+-r ../requirements.txt

docs/requirements_doc.txt

@@ -0,0 +1 @@
+numpydoc

docs/source/conf.py

@@ -20,6 +20,7 @@
 # NOTE:
 # pip install sphinx_rtd_theme
 # is needed in order to build the documentation
+import datetime
 import os
 import sys
 
@@ -95,8 +96,9 @@ def setup(app):
 master_doc = "contents"
 
 # General information about the project.
+curr_year = datetime.datetime.now().year
 project = "ogs5py"
-copyright = "2019, Sebastian Mueller"
+copyright = "2019 - {}, Sebastian Mueller".format(curr_year)
 author = "Sebastian Mueller"
 
 # The version info for the project you're documenting, acts as replacement for

docs/source/index.rst

@@ -143,16 +143,15 @@ Otherwise you need to specify the path to the executable within the run command:
 Requirements
 ============
 
-- `NumPy >= 1.13.0 <https://www.numpy.org>`_
-- `Pandas >= 0.23.0 <https://pandas.pydata.org/>`_
-- `whichcraft <https://github.com/pydanny/whichcraft>`_
-- `meshio <https://github.com/nschloe/meshio>`_
-- `lxml <https://github.com/lxml/lxml>`_
-- `vtk <https://vtk.org/>`_
-- `pexpect <https://github.com/pexpect/pexpect>`_
+- `NumPy >= 1.14.5 <https://www.numpy.org>`_
+- `Pandas >= 0.23.2 <https://pandas.pydata.org/>`_
+- `meshio >= 4.0.3; <5.0 <https://github.com/nschloe/meshio>`_
+- `lxml >= 4.0; <5.0 <https://github.com/lxml/lxml>`_
+- `pexpect >= 4.0; <5.0 <https://github.com/pexpect/pexpect>`_
+- `vtk >= 8.1 <https://vtk.org/>`_
 
 
 License
 =======
 
-`MIT <https://github.com/GeoStat-Framework/ogs5py/blob/master/LICENSE>`_ © 2019
+`MIT <https://github.com/GeoStat-Framework/ogs5py/blob/master/LICENSE>`_

ogs5py/__init__.py

@@ -125,8 +125,6 @@
    PCS_TYP
    PRIM_VAR_BY_PCS
 """
-from __future__ import absolute_import
-
 from ogs5py._version import __version__
 from ogs5py.ogs import OGS
 from ogs5py.fileclasses import (

ogs5py/_version.py

@@ -1,3 +1,3 @@
 # -*- coding: utf-8 -*-
 """Provide a central version."""
-__version__ = "1.0.5"
+__version__ = "1.0.6.dev0"

ogs5py/fileclasses/__init__.py

@@ -48,8 +48,6 @@
 
 ----
 """
-from __future__ import absolute_import
-
 from ogs5py.fileclasses.asc import ASC
 from ogs5py.fileclasses.bc import BC
 from ogs5py.fileclasses.cct import CCT

ogs5py/fileclasses/asc/__init__.py

@@ -12,8 +12,6 @@
 
 ----
 """
-from __future__ import absolute_import
-
 from ogs5py.fileclasses.asc.core import ASC
 
 __all__ = ["ASC"]

ogs5py/fileclasses/asc/core.py

@@ -1,7 +1,5 @@
 # -*- coding: utf-8 -*-
 """Class for the ogs ASC file."""
-
-from __future__ import absolute_import, division, print_function
 from ogs5py.fileclasses.base import LineFile
 
 

ogs5py/fileclasses/base.py

@@ -15,7 +15,6 @@
 
 ----
 """
-from __future__ import print_function, division, absolute_import
 import os
 import shutil
 import time

ogs5py/fileclasses/bc/__init__.py

@@ -12,8 +12,6 @@
 
 ----
 """
-from __future__ import absolute_import
-
 from ogs5py.fileclasses.bc.core import BC
 
 __all__ = ["BC"]

ogs5py/fileclasses/bc/core.py

@@ -1,7 +1,5 @@
 # -*- coding: utf-8 -*-
 """Class for the ogs BOUNDARY CONDITION file."""
-
-from __future__ import absolute_import, division, print_function
 from ogs5py.fileclasses.base import BlockFile
 
 

ogs5py/fileclasses/cct/__init__.py

@@ -12,8 +12,6 @@
 
 ----
 """
-from __future__ import absolute_import
-
 from ogs5py.fileclasses.cct.core import CCT
 
 __all__ = ["CCT"]

ogs5py/fileclasses/cct/core.py

@@ -1,7 +1,5 @@
 # -*- coding: utf-8 -*-
 """Class for the ogs COMMUNICATION TABLE file."""
-
-from __future__ import absolute_import, division, print_function
 from ogs5py.fileclasses.base import BlockFile
 
 

ogs5py/fileclasses/ddc/__init__.py

@@ -12,8 +12,6 @@
 
 ----
 """
-from __future__ import absolute_import
-
 from ogs5py.fileclasses.ddc.core import DDC
 
 __all__ = ["DDC"]

ogs5py/fileclasses/ddc/core.py

@@ -1,7 +1,5 @@
 # -*- coding: utf-8 -*-
 """Class for the ogs DOMAIN DECOMPOSITION file."""
-
-from __future__ import absolute_import, division, print_function
 from ogs5py.fileclasses.base import BlockFile
 
 

ogs5py/fileclasses/fct/__init__.py

@@ -12,8 +12,6 @@
 
 ----
 """
-from __future__ import absolute_import
-
 from ogs5py.fileclasses.fct.core import FCT
 
 __all__ = ["FCT"]

ogs5py/fileclasses/fct/core.py

@@ -1,7 +1,5 @@
 # -*- coding: utf-8 -*-
 """Class for the ogs FUNCTION file."""
-
-from __future__ import absolute_import, division, print_function
 from ogs5py.fileclasses.base import BlockFile
 
 

ogs5py/fileclasses/gem/__init__.py

@@ -13,8 +13,6 @@
 
 ----
 """
-from __future__ import absolute_import
-
 from ogs5py.fileclasses.gem.core import GEM, GEMinit
 
 __all__ = ["GEM", "GEMinit"]

ogs5py/fileclasses/gem/core.py

@@ -1,7 +1,5 @@
 # -*- coding: utf-8 -*-
 """Class for the ogs GEOCHEMICAL THERMODYNAMIC MODELING COUPLING file."""
-
-from __future__ import absolute_import, division, print_function
 import os
 from ogs5py.fileclasses.base import BlockFile, LineFile
 

ogs5py/fileclasses/gli/__init__.py

@@ -20,8 +20,6 @@
 
 ----
 """
-from __future__ import absolute_import
-
 from ogs5py.fileclasses.gli.core import GLI, GLIext
 
 __all__ = ["GLI", "GLIext"]

ogs5py/fileclasses/gli/checker.py

@@ -1,6 +1,5 @@
 # -*- coding: utf-8 -*-
 """Checking routines for the ogs5py-GLI package."""
-from __future__ import division, print_function, absolute_import
 import numpy as np
 from ogs5py.tools.types import STRTYPE, GLI_KEYS, PLY_KEYS, SRF_KEYS, VOL_KEYS