Commit c907efd9 authored by Daniel Scheffler's avatar Daniel Scheffler
Browse files

Revised environment_gms_preprocessing.yml as the inhouse libs are now on...


Revised environment_gms_preprocessing.yml as the inhouse libs are now on conda-forge. Adapted docker setup files to new installation procedure of sicor.

Signed-off-by: Daniel Scheffler's avatarDaniel Scheffler <danschef@gfz-potsdam.de>
parent 50de4305
Pipeline #14375 failed with stage
in 4 minutes and 19 seconds
......@@ -2,13 +2,9 @@
context_dir="./context"
dockerfile="gms_preprocessing_ci.docker"
tag="gms_preprocessing_ci:0.18.3"
tag="gms_preprocessing_ci:0.18.5"
gitlab_runner="gms_preprocessing_gitlab_CI_runner"
# get sicor project
rm -rf context/sicor
git clone https://gitext.gfz-potsdam.de/EnMAP/sicor.git ./context/sicor
# download sicor cache (fastens SICOR CI tests a lot, but cache needs to be updated manually using a local sicor repo:
# 1. clone a fresh copy of sicor or delete sicor/sicor/aerosol_0_ch4_34d3778719cc87188787de09bb8f870d16050078.pkl.zip
# 2. run a sicor test including sicor_ac or enmap_ac (recreates cache file) -> upload newly created cache file
......
......@@ -6,41 +6,31 @@ channels:
dependencies:
- python>=3.7.*
- pip
- cartopy
- arosics>=1.0.0
- gdal
- geoarray>=0.9.0
- geopandas
- holoviews
- ipython
- pyhdf
- python-fmask
- matplotlib
- numpy
- pyproj
- pyrsr>=0.3.1
- py_tools_ds>=0.12.4
- scikit-image
- scikit-learn=0.23.2 # pinned due to spechomo classifiers created with this version
- shapely
# arosics
- pyfftw
- pykrige
# sicor
- cachetools
- glymur
- h5py
- llvmlite
- numba
- pygrib
- pytables
- sicor
- spechomo>=0.16
- pip:
- arosics>=1.0.0
- cerberus
- dill
- ecmwf-api-client
- ecmwf-api-client # remove as soon as this is part of the sicor setup.py requirements
- ephem
- geoalchemy2
- geoarray>=0.9.0
- jsmin
- iso8601
- natsort
......@@ -50,15 +40,11 @@ dependencies:
- psycopg2
- pyinstrument
- pyorbital
- pyrsr>=0.3.1
- py_tools_ds>=0.12.4
- pytz
- redis
- retools
- redis-semaphore
- scipy
- sicor
- spechomo>=0.16
- spectral
- sqlalchemy
- timeout_decorator
......@@ -74,6 +60,3 @@ dependencies:
- nose-htmloutput
- rednose
- sphinx-argparse
- sqlalchemy
- psycopg2
......@@ -8,16 +8,13 @@ RUN /bin/bash -i -c "\
source /root/miniconda3/bin/activate; \
conda update -n base -c conda-forge conda;\
source activate ci_env; \
conda env update -n ci_env -f /root/environment_gms_preprocessing.yml"
# copy sicor code to /tmp
COPY sicor /tmp/sicor
RUN bash -i -c "\
source /root/miniconda3/bin/activate ci_env; \
cd /tmp/sicor/ ; \
make install"
conda env update -n ci_env -f /root/environment_gms_preprocessing.yml; \
python -c 'from sicor.tables import get_tables; get_tables(sensor="s2"); get_tables(sensor="l8")'"
# copy sicor cache files to sicor root directory (speeds up SICOR CI tests because table subsets dont have to be created each time)
# -> sicor root directory is the default directory of these cache files if sicor_cache_dir is not set in EnPT options
COPY *.zip /tmp/sicor/sicor/
RUN mkdir /tmp/sicor_cache
COPY *.zip /tmp/sicor_cache
RUN /bin/bash -i -c "\
SICOR_PATH=$(python -c 'from sicor import __path__; print(__path__)'); \
mv /tmp/sicor_cache/*.zip ${SICOR_PATH}"
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