Commit 07c002b9 authored by Daniel Scheffler's avatar Daniel Scheffler
Browse files

Merged master into spectral_homogenization.


Former-commit-id: 36b7aab6
parents b3e3f112 bcab6f5b
......@@ -10,8 +10,8 @@ stages:
test_gms_preprocessing:
stage: test
script:
- source /root/anaconda3/bin/activate
- export GDAL_DATA=/root/anaconda3/share/gdal
- source /root/miniconda3/bin/activate
- export GDAL_DATA=/root/miniconda3/share/gdal
- export PYTHONPATH=$PYTHONPATH:/root # /root <- directory needed later
# update sicor
# - conda install -y -q -c conda-forge basemap
......@@ -36,8 +36,8 @@ test_gms_preprocessing:
test_styles:
stage: test
script:
- source /root/anaconda3/bin/activate
- export GDAL_DATA=/root/anaconda3/share/gdal
- source /root/miniconda3/bin/activate
- export GDAL_DATA=/root/miniconda3/share/gdal
- export PYTHONPATH=$PYTHONPATH:/root # /root <- directory needed later
- make lint
artifacts:
......
......@@ -13,8 +13,8 @@ from .processing.process_controller import process_controller # noqa: E402
__author__ = """Daniel Scheffler"""
__email__ = 'daniel.scheffler@gfz-potsdam.de'
__version__ = '0.9.8'
__versionalias__ = '20171104.01'
__version__ = '0.9.9'
__versionalias__ = '20171120.01'
__all__ = ['algorithms',
'io',
'misc',
......
py_tools_ds>=0.10.0
py_tools_ds>=0.12.4
geoarray>=0.7.1
arosics>=0.6.6
git+https://gitext.gfz-potsdam.de/EnMAP/sicor.git
......
......@@ -14,7 +14,7 @@ with open('HISTORY.rst') as history_file:
requirements = [
'matplotlib', 'numpy', 'scikit-learn', 'scipy', 'gdal', 'pyproj', 'shapely', 'ephem', 'pyorbital', 'dill', 'pytz',
'pandas', 'numba', 'spectral>=0.16', 'geopandas', 'iso8601', 'pyinstrument', 'geoalchemy2', 'sqlalchemy',
'psycopg2', 'py_tools_ds>=0.10.0', 'geoarray>=0.7.1', 'arosics>=0.6.6', 'six', 'tqdm'
'psycopg2', 'py_tools_ds>=0.12.4', 'geoarray>=0.7.1', 'arosics>=0.6.6', 'six', 'tqdm'
# spectral<0.16 has some problems with writing signed integer 8bit data
# fmask # conda install -c conda-forge python-fmask
# 'pyhdf', # conda install --yes -c conda-forge pyhdf
......@@ -25,7 +25,7 @@ test_requirements = requirements + ['coverage', 'nose', 'nose2', 'nose-htmloutpu
setup(
name='gms_preprocessing',
version='0.9.8',
version='0.9.9',
description="GeoMultiSens - Scalable Multi-Sensor Analysis of Remote Sensing Data",
long_description=readme + '\n\n' + history,
author="Daniel Scheffler",
......
......@@ -2,10 +2,10 @@
context_dir="./context"
dockerfile="gms_preprocessing_ci.docker"
tag="gms_preprocessing_ci:0.9.7"
tag="gms_preprocessing_ci:0.9.9"
gitlab_runner="gms_preprocessing_gitlab_CI_runner"
# get sicor project # TODO move this to setup.py as soon as package is public
# get sicor project
rm -rf context/sicor
git clone https://gitext.gfz-potsdam.de/EnMAP/sicor.git ./context/sicor
......
name: gms_preprocessing
channels: &id1
- http://conda.anaconda.org/ioam # only for holoviews
- http://conda.anaconda.org/conda-forge
dependencies:
- python=3.*.*
- pyqt
- numpy
- gdal
- scikit-image
- rasterio
- pyproj
- lxml
- geopandas
- ipython
- matplotlib
- basemap
- scikit-learn
- shapely
- pyhdf
- python-fmask
- holoviews
- bokeh
# arosics
- pyfftw
- pykrige
# sicor
- glymur
- pygrib
- cachetools
- pyhdf
- h5py
- pytables
- pip:
- dicttoxml
- jsmin
- cerberus
- pyprind
- pint
- iso8601
- tqdm
- mpld3
- sphinx-argparse
- six
- spectral
- flake8
- pycodestyle
- pylint
- pydocstyle
- nose
- nose2
- nose-htmloutput
- coverage
- rednose
- scipy
- ephem
- pyorbital
- dill
- pytz
- numba
- pyinstrument
- geoalchemy2
- sqlalchemy
- psycopg2
- pandas
- py_tools_ds>=0.12.4
- geoarray>=0.7.0
- arosics>=0.6.6
FROM centos:7
RUN yum update -y && \
yum install -y wget vim bzip2 gcc gcc-c++ make libgl1-mesa-glx mesa-libGL qt5-qtbase-gui git gdb
ENV anaconda_dl 'Anaconda3-5.0.0-Linux-x86_64.sh'
RUN /bin/bash -i -c "cd /root; wget https://repo.continuum.io/archive/$anaconda_dl ; \
bash -i /root/$anaconda_dl -b ; \
rm -f /root/$anaconda_dl"
# 'conda install --yes -c conda-forge 'icu=58.*' lxml' fixing a bug for conda-forge gdal build, as of 06/2017
# holoviews and bokeh is only needed for geoarray because its not installable via pip during geoarray.setup.py
RUN /bin/bash -i -c "source /root/anaconda3/bin/activate ; \
conda install --yes pyqt numba; \
conda install --yes -c conda-forge pyfftw=0.10.4 ; \
conda install --yes -c ioam holoviews bokeh ; \
conda install --yes -c conda-forge numpy gdal scikit-image scikit-learn matplotlib pyproj rasterio shapely basemap \
pykrige glymur pygrib pyproj cachetools pyhdf ephem python-fmask scipy ; \
conda install --yes -c conda-forge 'icu=58.*' lxml ; \
pip install pandas geopandas dicttoxml jsmin cerberus pyprind pint iso8601 mpld3 sphinx-argparse dill pytz \
spectral>0.16 psycopg2 pyorbital pyinstrument geoalchemy2 sqlalchemy py_tools_ds>=0.10.0 \
geoarray>=0.7.1 arosics>=0.6.6 flake8 pycodestyle pylint pydocstyle nose nose2 nose-htmloutput \
coverage rednose six tqdm" # must include all the requirements needed to build the docs!
FROM gms_base_centos:pinned_v0.1
# copy some needed stuff to /root
#COPY *.pkl /root/ # EXAMPLE
#COPY *.h5 /root/ # EXAMPLE
COPY *.yml /root/
RUN /bin/bash -i -c "\
source /root/miniconda3/bin/activate ; \
conda env update -n root -f /root/environment_gms_preprocessing.yml"
# copy sicor code to /tmp
COPY sicor /tmp/sicor
# install git lfs
RUN /bin/bash -i -c "curl -s https://packagecloud.io/install/repositories/github/git-lfs/script.rpm.sh | bash"
# installing git large file support, see here: https://git-lfs.github.com/ , change version number below for future upgrades
ENV git_lfs_v='2.1.1'
RUN /bin/bash -i -c "wget https://github.com/git-lfs/git-lfs/releases/download/v${git_lfs_v}/git-lfs-linux-amd64-${git_lfs_v}.tar.gz; \
tar -zxvf git-lfs-linux-amd64-${git_lfs_v}.tar.gz; \
cd git-lfs-${git_lfs_v}; \
bash ./install.sh"
# set matplotlib backend to Agg as default, Qt won't work in headless docker containers
RUN bash -i -c 'source /root/anaconda3/bin/activate; \
sed -i "/backend : tkagg/c\backend : Agg" $(python -c "import matplotlib; print(matplotlib.matplotlib_fname())"); \
sed -i "/backend : Qt4Agg/c\backend : Agg" $(python -c "import matplotlib; print(matplotlib.matplotlib_fname())"); \
sed -i "/backend : qt5agg/c\backend : Agg" $(python -c "import matplotlib; print(matplotlib.matplotlib_fname())")'
RUN bash -i -c "source /root/anaconda3/bin/activate; \
cd /tmp/sicor/; make install; \
" # TODO move this to setup.py as soon as package is public
RUN bash -i -c "source /root/miniconda3/bin/activate; \
cd /tmp/sicor/; make install; "
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment