Commit 50de4305 authored by Daniel Scheffler's avatar Daniel Scheffler
Browse files

Revised dependencies. Updated minimal version of arosics and geoarray.


Signed-off-by: Daniel Scheffler's avatarDaniel Scheffler <danschef@gfz-potsdam.de>
parent 0296248e
Pipeline #13269 failed with stages
in 73 minutes and 8 seconds
...@@ -22,8 +22,11 @@ test_gms_preprocessing: ...@@ -22,8 +22,11 @@ test_gms_preprocessing:
- export GMS_index_host=${GMS_INDEX_HOST} - export GMS_index_host=${GMS_INDEX_HOST}
- export GMS_index_port=${GMS_INDEX_PORT} - export GMS_index_port=${GMS_INDEX_PORT}
- conda install -c conda-forge cartopy # TODO remove as soon as docker container is rebuilt
- pip install "geoarray>=0.9.0" # TODO remove as soon as docker container is rebuilt
- pip install "arosics>=1.0.0" # TODO remove as soon as docker container is rebuilt
# update sicor # update sicor
# - conda install -y -q -c conda-forge basemap
# - rm -rf context/sicor # - rm -rf context/sicor
# - git clone https://gitext.gfz-potsdam.de/EnMAP/sicor.git ./context/sicor # - git clone https://gitext.gfz-potsdam.de/EnMAP/sicor.git ./context/sicor
# - cd ./context/sicor # - cd ./context/sicor
...@@ -34,8 +37,7 @@ test_gms_preprocessing: ...@@ -34,8 +37,7 @@ test_gms_preprocessing:
- pip install -U sicor - pip install -U sicor
# - python -c 'from sicor.tables import get_tables; get_tables(sensor="s2"); get_tables(sensor="l8"); get_tables(sensor="enmap", optional_downloads=("ch4",))' # - python -c 'from sicor.tables import get_tables; get_tables(sensor="s2"); get_tables(sensor="l8"); get_tables(sensor="enmap", optional_downloads=("ch4",))'
- pip install 'scipy==1.1.0' # TODO remove as soon as pinning is included in SICOR requirements or SICOR issue #63 is fixed - pip check
- pip install "geoarray>=0.8.33" # TODO remove as soon as docker container is rebuilt
# run tests # run tests
- make nosetests - make nosetests
...@@ -65,7 +67,7 @@ test_gms_preprocessing_install: ...@@ -65,7 +67,7 @@ test_gms_preprocessing_install:
# - conda config --set channel_priority strict # otherwise gdal or libgdal may be installed from defaults channel # - conda config --set channel_priority strict # otherwise gdal or libgdal may be installed from defaults channel
# install some dependencies that cause trouble when installed via pip # install some dependencies that cause trouble when installed via pip
- conda install -y -c conda-forge numpy gdal scikit-image pyproj lxml geopandas ipython matplotlib basemap scikit-learn=0.23.2 shapely pyhdf python-fmask holoviews - conda install -y -c conda-forge numpy gdal scikit-image pyproj geopandas ipython matplotlib cartopy scikit-learn=0.23.2 shapely pyhdf python-fmask holoviews
# install not pip-installable deps of arosics # install not pip-installable deps of arosics
- conda install -y -c conda-forge pyfftw pykrige - conda install -y -c conda-forge pyfftw pykrige
...@@ -76,6 +78,7 @@ test_gms_preprocessing_install: ...@@ -76,6 +78,7 @@ test_gms_preprocessing_install:
# install gms_preprocessing # install gms_preprocessing
- pip install -e . - pip install -e .
- pip check
- cd .. - cd ..
- pwd - pwd
- ls - ls
......
...@@ -137,7 +137,7 @@ Using conda_, the recommended approach is: ...@@ -137,7 +137,7 @@ Using conda_, the recommended approach is:
source activate gms_preprocessing source activate gms_preprocessing
# install some dependencies that cause trouble when installed via pip # install some dependencies that cause trouble when installed via pip
conda install -c conda-forge numpy gdal scikit-image pyproj lxml geopandas ipython matplotlib basemap scikit-learn=0.23.2 shapely pyhdf python-fmask holoviews conda install -c conda-forge numpy gdal scikit-image pyproj geopandas ipython matplotlib cartopy scikit-learn=0.23.2 shapely pyhdf python-fmask holoviews
# install not pip-installable deps of arosics # install not pip-installable deps of arosics
conda install -c conda-forge pyfftw pykrige conda install -c conda-forge pyfftw pykrige
......
...@@ -9,12 +9,10 @@ iso8601 ...@@ -9,12 +9,10 @@ iso8601
pyinstrument pyinstrument
geoalchemy2 geoalchemy2
sqlalchemy sqlalchemy
six
tqdm tqdm
jsmin jsmin
cerberus cerberus
nested_dict nested_dict
openpyxl
timeout_decorator timeout_decorator
redis redis
retools retools
......
...@@ -40,15 +40,43 @@ with open("gms_preprocessing/version.py") as version_file: ...@@ -40,15 +40,43 @@ with open("gms_preprocessing/version.py") as version_file:
exec(version_file.read(), version) exec(version_file.read(), version)
requirements = [ requirements = [
'matplotlib', 'numpy', 'scikit-learn', 'scipy', 'gdal', 'pyproj', 'shapely', 'ephem', 'pyorbital', 'dill', 'pytz', 'arosics>=1.0.0',
'pandas', 'spectral>=0.16', 'geopandas', 'iso8601', 'pyinstrument', 'geoalchemy2', 'sqlalchemy', 'natsort', 'cerberus',
'psycopg2', 'py_tools_ds>=0.12.4', 'geoarray>=0.8.33', 'arosics>=0.8.7', 'six', 'tqdm', 'jsmin', 'cerberus', 'dill',
'nested_dict', 'openpyxl', 'timeout_decorator', 'redis', 'retools', 'redis-semaphore', 'psutil', 'pyrsr>=0.3.1', 'ephem',
'spechomo', 'sicor' 'gdal',
# spectral<0.16 has some problems with writing signed integer 8bit data 'geoalchemy2',
'geoarray>=0.9.0',
'geopandas',
'iso8601',
'jsmin',
'matplotlib',
'natsort',
'nested_dict',
'numpy',
'pandas',
'psutil',
'psycopg2',
'pyinstrument',
'pyorbital',
'pyproj',
'pyrsr>=0.3.1',
'py_tools_ds>=0.12.4',
'pytz',
'redis',
'redis-semaphore',
'retools',
'scikit-learn',
'scipy',
'shapely',
'sicor',
'spechomo',
'spectral>=0.16', # spectral<0.16 has some problems with writing signed integer 8bit data
'sqlalchemy',
'timeout_decorator',
'tqdm',
# fmask # conda install -c conda-forge python-fmask # fmask # conda install -c conda-forge python-fmask
# 'pyhdf', # conda install --yes -c conda-forge pyhdf # 'pyhdf', # conda install --yes -c conda-forge pyhdf
# 'sicor', # pip install git+https://gitext.gfz-potsdam.de/EnMAP/sicor.git
] ]
setup_requirements = [] # TODO(danschef): put setup requirements (distutils extensions, etc.) here setup_requirements = [] # TODO(danschef): put setup requirements (distutils extensions, etc.) here
test_requirements = requirements + ['coverage', 'nose', 'nose2', 'nose-htmloutput', 'rednose'] test_requirements = requirements + ['coverage', 'nose', 'nose2', 'nose-htmloutput', 'rednose']
......
...@@ -6,78 +6,74 @@ channels: ...@@ -6,78 +6,74 @@ channels:
dependencies: dependencies:
- python>=3.7.* - python>=3.7.*
- pip - pip
- numpy - cartopy
- gdal - gdal
- scikit-image
- pyproj
- lxml
- geopandas - geopandas
- holoviews
- ipython - ipython
- pyhdf
- python-fmask
- matplotlib - matplotlib
- basemap - numpy
- pyproj
- scikit-image
- scikit-learn=0.23.2 # pinned due to spechomo classifiers created with this version - scikit-learn=0.23.2 # pinned due to spechomo classifiers created with this version
- shapely - shapely
- pyhdf
- python-fmask
- holoviews
# arosics # arosics
- pyfftw - pyfftw
- pykrige - pykrige
# sicor # sicor
- glymur
- pygrib
- cachetools - cachetools
- pyhdf - glymur
- h5py - h5py
- pytables
- numba
- llvmlite - llvmlite
- numba
- pygrib
- pytables
- pip: - pip:
- dicttoxml - arosics>=1.0.0
- jsmin
- cerberus - cerberus
- pyprind - dill
- pint - ecmwf-api-client
- ephem
- geoalchemy2
- geoarray>=0.9.0
- jsmin
- iso8601 - iso8601
- tqdm - natsort
- mpld3 - nested_dict
- sphinx-argparse - pandas
- six - psutil
- psycopg2
- pyinstrument
- pyorbital
- pyrsr>=0.3.1
- py_tools_ds>=0.12.4
- pytz
- redis
- retools
- redis-semaphore
- scipy
- sicor
- spechomo>=0.16
- spectral - spectral
- sqlalchemy
- timeout_decorator
- tqdm
# test and docs requirements
- coverage
- flake8 - flake8
- pylint
- pydocstyle - pydocstyle
- pylint
- nose - nose
- nose2 - nose2
- nose-htmloutput - nose-htmloutput
- coverage
- rednose - rednose
- scipy - sphinx-argparse
- ephem
- pyorbital
- dill
- pytz
- pyinstrument
- geoalchemy2
- sqlalchemy - sqlalchemy
- psycopg2 - psycopg2
- pandas
- jsmin
- cerberus
- nested_dict
- openpyxl
- timeout_decorator
- redis
- retools
- redis-semaphore
- psutil
- ecmwf-api-client
- natsort
- py_tools_ds>=0.12.4
- geoarray>=0.8.33
- arosics>=0.8.7
- pyrsr>=0.3.1
- spechomo
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