env capture and travis

Author: bkatiemills

.travis.yml

@@ -6,7 +6,7 @@ services:
   - docker
 
 before_install:
-- docker image pull iquod/autoqc:ubuntu-16.04
+- docker image pull iquod/autoqc:ubuntu-18.04
 
 script:
-- docker container run -v $PWD:/AutoQC_latest iquod/autoqc:ubuntu-16.04 bash -c "cp /AutoQC/data/* /AutoQC_latest/data/.; cd /AutoQC_latest; /usr/local/bin/nosetests tests/*.py"
+- docker container run -v $PWD:/AutoQC_latest iquod/autoqc:ubuntu-18.04 bash -c "cp /AutoQC/data/* /AutoQC_latest/data/.; cd /AutoQC_latest; /usr/local/bin/nosetests tests/*.py"

install.sh

@@ -2,49 +2,51 @@
 # from inside AutoQC, run `bash install.sh`
 
 # install apt-get packages
-sudo apt-get update -y
-sudo apt-get install -y nano bzip2 wget unzip \
-    python2.7=2.7.12-1ubuntu0~16.04.3 \
-    python-pip \
-    libhdf5-serial-dev=1.8.16+docs-4ubuntu1 \
-    libnetcdf-dev=1:4.4.0-2 \
-    python-dev=2.7.12-1~16.04 \
-    libgl1-mesa-glx=18.0.5-0ubuntu0~16.04.1 \
-    python-qt4=4.11.4+dfsg-1build4 \
-    python-tk=2.7.12-1~16.04
+apt-get update -y
+apt-get install -y nano bzip2 wget unzip \
+    python3.6 \
+    python3-pip \
+    libhdf5-serial-dev \
+    libnetcdf-dev \
+    python3-dev \
+    libgl1-mesa-glx
+    #python-qt4=4.12.1+dfsg-2 \
+    #python-tk=2.7.12-1~16.04
 
 # install python packages
-pip install Shapely==1.6.2 \
-            netCDF4==1.3.1 \
-            matplotlib==2.1.1 \
-            pyproj==1.9.5.1 \
+pip3 install Shapely==1.6.4.post2 \
+            netCDF4==1.5.1.2 \
+            matplotlib==3.1.0 \
+            pyproj==2.1.3 \
             pandas==0.21.1 \
-            scipy==0.18.0 \
-            numpy==1.11.1 \
-            mkl==2018.0.3
-pip install seabird==0.8.0 \
+            scipy==0.18.1 \
+            mkl==2019.0
+pip3 install seabird==0.11.0 \
             gsw==3.0.3 \
-            scikit-fuzzy==0.3 \
-            oceansdb==0.6.0 \
-            cotede==0.18.0 \
-            wodpy==1.5.0
+            scikit-fuzzy==0.4.1 \
+            oceansdb==0.8.6 \
+            cotede==0.19.2 \
+            wodpy==1.6.1 \
+            numpy==1.11.3
 
 # Add AutoQC parameter files
-cd data
-wget http://www.metoffice.gov.uk/hadobs/en4/data/EN_bgcheck_info.nc
-wget http://data.nodc.noaa.gov/thredds/fileServer/woa/WOA09/NetCDFdata/temperature_seasonal_5deg.nc
-wget "http://oos.soest.hawaii.edu/thredds/ncss/etopo5?var=ROSE&disableLLSubset=on&disableProjSubset=on&horizStride=1&addLatLon=true" -O etopo5.nc 
-wget http://data.nodc.noaa.gov/thredds/fileServer/woa/WOA13/DATAv2/temperature/netcdf/decav/5deg/woa13_decav_t13_5dv2.nc
-wget http://data.nodc.noaa.gov/thredds/fileServer/woa/WOA13/DATAv2/temperature/netcdf/decav/5deg/woa13_decav_t14_5dv2.nc
-wget http://data.nodc.noaa.gov/thredds/fileServer/woa/WOA13/DATAv2/temperature/netcdf/decav/5deg/woa13_decav_t15_5dv2.nc
-wget http://data.nodc.noaa.gov/thredds/fileServer/woa/WOA13/DATAv2/temperature/netcdf/decav/5deg/woa13_decav_t16_5dv2.nc
-wget https://data.nodc.noaa.gov/thredds/fileServer/woa/WOA13/DATAv2/salinity/netcdf/decav/5deg/woa13_decav_s13_5dv2.nc
-wget https://data.nodc.noaa.gov/thredds/fileServer/woa/WOA13/DATAv2/salinity/netcdf/decav/5deg/woa13_decav_s14_5dv2.nc
-wget https://data.nodc.noaa.gov/thredds/fileServer/woa/WOA13/DATAv2/salinity/netcdf/decav/5deg/woa13_decav_s15_5dv2.nc
-wget https://data.nodc.noaa.gov/thredds/fileServer/woa/WOA13/DATAv2/salinity/netcdf/decav/5deg/woa13_decav_s16_5dv2.nc
-wget ftp://ftp.aoml.noaa.gov/phod/pub/bringas/XBT/AQC/AOML_AQC_2018/data_center/woa13_00_025.nc
-wget https://s3-us-west-2.amazonaws.com/autoqc/climatological_t_median_and_amd_for_aqc.nc
-cd ..
+# note many of these links are broken; we leave them here until replacements are found,
+# and bake the corresponding data files into the containerized environment for posterity.
+#cd data
+#wget http://www.metoffice.gov.uk/hadobs/en4/data/EN_bgcheck_info.nc
+#wget http://data.nodc.noaa.gov/thredds/fileServer/woa/WOA09/NetCDFdata/temperature_seasonal_5deg.nc
+#wget "http://oos.soest.hawaii.edu/thredds/ncss/etopo5?var=ROSE&disableLLSubset=on&disableProjSubset=on&horizStride=1&addLatLon=true" -O etopo5.nc 
+#wget http://data.nodc.noaa.gov/thredds/fileServer/woa/WOA13/DATAv2/temperature/netcdf/decav/5deg/woa13_decav_t13_5dv2.nc
+#wget http://data.nodc.noaa.gov/thredds/fileServer/woa/WOA13/DATAv2/temperature/netcdf/decav/5deg/woa13_decav_t14_5dv2.nc
+#wget http://data.nodc.noaa.gov/thredds/fileServer/woa/WOA13/DATAv2/temperature/netcdf/decav/5deg/woa13_decav_t15_5dv2.nc
+#wget http://data.nodc.noaa.gov/thredds/fileServer/woa/WOA13/DATAv2/temperature/netcdf/decav/5deg/woa13_decav_t16_5dv2.nc
+#wget https://data.nodc.noaa.gov/thredds/fileServer/woa/WOA13/DATAv2/salinity/netcdf/decav/5deg/woa13_decav_s13_5dv2.nc
+#wget https://data.nodc.noaa.gov/thredds/fileServer/woa/WOA13/DATAv2/salinity/netcdf/decav/5deg/woa13_decav_s14_5dv2.nc
+#wget https://data.nodc.noaa.gov/thredds/fileServer/woa/WOA13/DATAv2/salinity/netcdf/decav/5deg/woa13_decav_s15_5dv2.nc
+#wget https://data.nodc.noaa.gov/thredds/fileServer/woa/WOA13/DATAv2/salinity/netcdf/decav/5deg/woa13_decav_s16_5dv2.nc
+#wget ftp://ftp.aoml.noaa.gov/phod/pub/bringas/XBT/AQC/AOML_AQC_2018/data_center/woa13_00_025.nc
+#wget https://s3-us-west-2.amazonaws.com/autoqc/climatological_t_median_and_amd_for_aqc.nc
+#cd ..
 
 export OCEANSDB_DIR=$PWD/data/
-echo export 'OCEANSDB_DIR='$PWD'/data/' >> $HOME/.bashrc
+echo export 'OCEANSDB_DIR='$PWD'/data/' >> $HOME/.bashrc