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Merge pull request #85 from emiliom/ohwe-pyrgeo2
Add py-rocket image for OceanHackWeek-en-espanol based on py-rocket-geospatial-2
2 parents 9d1d1f5 + 868f8b2 commit 88ec678

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‎.github/workflows/build-and-push.yml‎

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- 'images/asar/**'
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- 'images/echopype/**'
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- 'images/coastwatch/**'
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- 'images/py-rocket-oceanhw-esp/**'
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- 'draft_images/coastwatch-qgis/**'
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- 'draft_images/test/**'
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images/asar
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images/echopype
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images/coastwatch
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images/py-rocket-oceanhw-esp
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draft_images/coastwatch-qgis
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draft_images/test
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‎.gitignore‎

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.Rhistory
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.RData
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.Ruserdata
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*.Rproj
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*.Rproj
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build_logs/

‎images/py-rocket-oceanhw-esp/Desktop/panoply.desktop‎

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[Desktop Entry]
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Type=Application
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Name=Panoply
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GenericName=Panoply netCDF, HDF and GRIB Data Viewer
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Icon=panoply
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Exec=/tmp/PanoplyJ/panoply.sh %F
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Terminal=false
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StartupNotify=false
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Categories=Qt;Education;Science;Geography;
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Keywords=map;

‎images/py-rocket-oceanhw-esp/Desktop/panoply.png‎

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‎images/py-rocket-oceanhw-esp/Desktop/qgis.desktop‎

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# From: https://github.com/qgis/QGIS/blob/ltr-3_28/linux/org.qgis.qgis.desktop.in
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[Desktop Entry]
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Type=Application
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Name=QGIS Desktop
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GenericName=Geographic Information System
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Icon=/srv/conda/envs/notebook/share/qgis/images/icons/qgis-icon-512x512.png
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TryExec=qgis
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Exec=qgis %F
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Terminal=false
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StartupNotify=false
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Categories=Qt;Education;Science;Geography;
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MimeType=application/x-qgis-project;application/x-qgis-project-container;application/x-qgis-layer-settings;application/x-qgis-layer-definition;application/x-qgis-composer-template;image/tiff;image/jpeg;image/jp2;application/x-raster-aig;application/x-raster-ecw;application/x-raster-mrsid;application/x-mapinfo-mif;application/x-esri-shape;application/vnd.google-earth.kml+xml;application/vnd.google-earth.kmz;application/geopackage+sqlite3;
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Keywords=map;globe;postgis;wms;wfs;ogc;osgeo;
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StartupWMClass=QGIS3

‎images/py-rocket-oceanhw-esp/Desktop/qgis.xml‎

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<?xml version="1.0"?>
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<!-- From: https://raw.githubusercontent.com/qgis/QGIS/ltr-3_28/debian/qgis.xml -->
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<mime-info xmlns='http://www.freedesktop.org/standards/shared-mime-info'>
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<mime-type type="application/x-qgis-project">
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<comment>QGIS Project</comment>
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<comment xml:lang="de">QGIS-Projekt</comment>
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<sub-class-of type="application/xml"/>
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<alias type="application/x-qgis"/>
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<icon name="qgis-qgs"/>
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<magic priority="50">
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<match type="string" offset="0" value="&lt;!DOCTYPE qgis"/>
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</magic>
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<glob pattern="*.qgs"/>
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</mime-type>
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<mime-type type="application/x-qgis-project-container">
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<comment>QGIS Project</comment>
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<comment xml:lang="de">QGIS-Projekt</comment>
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<sub-class-of type="application/zip"/>
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<alias type="application/x-qgis"/>
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<icon name="qgis-qgs"/>
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<glob pattern="*.qgz"/>
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</mime-type>
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<mime-type type="application/x-qgis-layer-settings">
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<comment>QGIS layer settings</comment>
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<comment xml:lang="de">QGIS-Layereinstellungen</comment>
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<sub-class-of type="application/xml"/>
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<icon name="qgis-qml"/>
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<magic priority="80">
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<match type="string" offset="0" value="&lt;!DOCTYPE qgis"/>
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</magic>
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<glob pattern="*.qml"/>
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</mime-type>
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<mime-type type="application/x-qgis-layer-definition">
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<comment>QGIS layer definition</comment>
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<comment xml:lang="de">QGIS-Layerdefinition</comment>
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<sub-class-of type="application/xml"/>
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<icon name="qgis-qlr"/>
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<magic priority="50">
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<match type="string" offset="0" value="&lt;!DOCTYPE qgis-layer-definition"/>
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</magic>
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<glob pattern="*.qlr"/>
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</mime-type>
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<mime-type type="application/x-qgis-composer-template">
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<comment>QGIS composer template</comment>
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<comment xml:lang="de">QGIS-Druckzusammenstellungsvorlage</comment>
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<sub-class-of type="application/xml"/>
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<icon name="qgis-qpt"/>
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<magic priority="50">
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<match type="string" offset="0" value="&lt;!DOCTYPE qgis"/>
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</magic>
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<glob pattern="*.qpt"/>
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</mime-type>
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<mime-type type="application/x-esri-shape">
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<comment>ESRI shape file</comment>
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<comment xml:lang="de">ESRI-Shapedatei</comment>
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<icon name="qgis-mime"/>
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<magic priority="100">
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<match type="big32" offset="0" value="9994">
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<match type="big32" offset="4" value="0">
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<match type="big32" offset="8" value="0">
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<match type="big32" offset="12" value="0">
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<match type="big32" offset="16" value="0">
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<match type="big32" offset="20" value="0">
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<match type="big32" offset="28" value="1000"/>
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</match>
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</match>
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</match>
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</match>
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</match>
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</match>
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</magic>
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<glob pattern="*.shp"/>
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<glob pattern="*.shx"/>
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</mime-type>
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<mime-type type="application/x-esri-crs">
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<comment>ESRI coordinate reference system</comment>
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<comment xml:lang="de">ESRI-Koordinatenreferenzsystem</comment>
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<icon name="qgis-mime"/>
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<magic>
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<match type="string" offset="0" value="GEOGCS["/>
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<match type="string" offset="0" value="PROJCS["/>
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<match type="string" offset="0" value="LOCAL_CS["/>
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</magic>
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<glob pattern="*.prj"/>
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</mime-type>
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<mime-type type="image/tiff">
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<comment>TIFF raster data</comment>
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<comment xml:lang="de">TIFF-Rasterdaten</comment>
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<icon name="qgis-mime"/>
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<magic priority="50">
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<match type="string" offset="0" value="MM">
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<match type="little16" offset="2" value="42"/>
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</match>
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<match type="string" offset="0" value="MM">
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<match type="big16" offset="2" value="42"/>
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</match>
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</magic>
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<glob pattern="*.tiff"/>
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<glob pattern="*.tif"/>
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</mime-type>
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<mime-type type="image/jpeg">
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<comment>JPEG raster data</comment>
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<comment xml:lang="de">JPEG-Rasterdaten</comment>
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<icon name="qgis-mime"/>
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<magic priority="50">
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<match type="big16" offset="0" value="65496"/>
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</magic>
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<glob pattern="*.jpeg"/>
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<glob pattern="*.jpg"/>
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</mime-type>
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<mime-type type="image/jp2">
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<comment>JPEG2000 raster data</comment>
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<comment xml:lang="de">JPEG2000-Rasterdaten</comment>
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<icon name="qgis-mime"/>
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<magic priority="50">
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<match type="little32" offset="0" value="12">
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<match type="string" offset="8" value="jP">
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<match type="byte" offset="10" value="32">
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<match type="byte" offset="11" value="32">
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<match type="byte" offset="12" value="13">
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<match type="byte" offset="13" value="10">
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<match type="byte" offset="14" value="135">
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<match type="byte" offset="13" value="10"/>
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</match>
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</match>
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</match>
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</match>
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</match>
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</match>
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</match>
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</magic>
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<glob pattern="*.jp2"/>
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<glob pattern="*.j2k"/>
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</mime-type>
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<mime-type type="application/x-raster-aig">
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<comment>AIG raster data</comment>
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<comment xml:lang="de">AIG-Rasterdaten</comment>
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<icon name="qgis-mime"/>
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<glob pattern="*.aig"/>
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</mime-type>
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<mime-type type="application/x-raster-ecw">
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<comment>ECW raster data</comment>
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<comment xml:lang="de">ECW-Rasterdaten</comment>
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<icon name="qgis-mime"/>
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<glob pattern="*.ecw"/>
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</mime-type>
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<mime-type type="application/x-raster-mrsid">
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<comment>MrSID raster data</comment>
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<comment xml:lang="de">MrSID-Rasterdaten</comment>
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<icon name="qgis-mime"/>
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<glob pattern="*.sid"/>
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</mime-type>
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<mime-type type="application/x-mapinfo-mif">
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<comment>MapInfo file</comment>
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<comment xml:lang="de">MapInfo-Datei</comment>
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<icon name="qgis-mime"/>
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<magic priority="51">
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<match type="string" offset="0" value="VERSION">
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<match type="string" offset="0:512" value="COLUMNS"/>
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<match type="string" offset="0:512" value="DATA">
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</match>
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</match>
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</magic>
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<glob weight="60" pattern="*.mif"/>
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</mime-type>
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<!-- .mif is just not good enough -->
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<mime-type type="application/x-adobe-mif">
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<alias type="application/x-mif"/>
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<comment>Adobe FrameMaker MIF file</comment>
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<magic priority="100">
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<match type="string" offset="0" value="&lt;MIFFile"/>
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</magic>
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<glob weight="51" pattern="*.mif"/>
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</mime-type>
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<mime-type type="application/vnd.google-earth.kml+xml">
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<comment>Keyhole Markup Language data</comment>
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<sub-class-of type="application/xml"/>
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<icon name="qgis-mime"/>
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<glob pattern="*.kml"/>
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</mime-type>
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<mime-type type="application/vnd.google-earth.kmz">
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<comment>Zipped Keyhole Markup Language data</comment>
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<sub-class-of type="application/zip"/>
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<icon name="qgis-mime"/>
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<glob pattern="*.kmz"/>
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</mime-type>
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<mime-type type="application/geopackage+sqlite3">
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<comment>GeoPackage data</comment>
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<sub-class-of type="application/vnd.sqlite3"/>
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<icon name="qgis-mime"/>
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<glob pattern="*.gpkg"/>
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</mime-type>
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</mime-info>

‎images/py-rocket-oceanhw-esp/Dockerfile‎

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FROM ghcr.io/nmfs-opensci/py-rocket-base:2025.04.26
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LABEL org.opencontainers.image.maintainers="[email protected]"
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LABEL org.opencontainers.image.author="[email protected], [email protected]"
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LABEL org.opencontainers.image.source=https://github.com/nmfs-opensci/container-images/py-rocket-2
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LABEL org.opencontainers.image.description="OceanHackWeek-en-Espan-ol Geospatial Python (3.12) and R (4.4.3) image with Desktop (QGIS, Panoply)"
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LABEL org.opencontainers.image.licenses=Apache2.0
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LABEL org.opencontainers.image.version=2025.11.09
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ENV PROJ_LIB=/srv/conda/envs/notebook/share/proj
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USER root
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COPY . /tmp2/
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RUN /pyrocket_scripts/install-apt-packages.sh /tmp2/apt.txt || echo "install-apt-packages.sh failed" || true
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RUN /pyrocket_scripts/install-conda-packages.sh /tmp2/environment.yml || echo "install-conda-packages.sh failed" || true
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RUN /pyrocket_scripts/install-r-packages.sh /tmp2/install.R || echo "install-r-package.sh failed" || true
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RUN /pyrocket_scripts/install-desktop.sh /tmp2/Desktop|| echo "setup-desktop.sh failed" || true
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RUN rm -rf /tmp2
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USER root
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# install the geospatial libraries and R spatial; the rocket script are part of py-rocket-base
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# need to ensure that it installs to the site-library (that user can control) and with a clean PATH
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# Ensure packages go to site-library whether installed via R, Rscript, or littler (r)
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RUN echo '.libPaths("/usr/local/lib/R/site-library")' > /etc/littler.r && \
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echo '.libPaths("/usr/local/lib/R/site-library")' > /tmp/rprofile.site && \
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R_PROFILE=/tmp/rprofile.site \
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PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin \
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/rocker_scripts/install_geospatial.sh && \
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rm /etc/littler.r /tmp/rprofile.site
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# --- 11/10/25: Commented out the two steps below while refining the R environment,
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# to slim down the image build time
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# Install panoply
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# 11/6/2025 16:00 PST
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# 0.336 Connecting to www.giss.nasa.gov (www.giss.nasa.gov)|129.164.141.233|:443... failed: Connection refused.
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# 0.428 Connecting to www.giss.nasa.gov (www.giss.nasa.gov)|2001:4d0:2310:151::233|:443... failed: Network is unreachable.
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# 11/8/2025: Uploaded latest Panoply tgz to Emilio's UW website, temporarily, as a stopgap
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ENV PANOPLY_VERSION=5.7.1
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RUN cd /tmp && \
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# wget --user-agent="Mozilla/5.0" https://www.giss.nasa.gov/tools/panoply/download/PanoplyJ-${PANOPLY_VERSION}.tgz && \
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wget --user-agent="Mozilla/5.0" http://staff.washington.edu/emiliom/out/PanoplyJ-${PANOPLY_VERSION}.tgz && \
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tar -zxf PanoplyJ-${PANOPLY_VERSION}.tgz && \
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rm -rf PanoplyJ-${PANOPLY_VERSION}.tgz
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ENV PATH=${PATH}:/tmp/PanoplyJ
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# Install tools for working with Google Cloud Buckets
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RUN echo "deb [signed-by=/usr/share/keyrings/cloud.google.gpg] https://packages.cloud.google.com/apt cloud-sdk main" | tee -a /etc/apt/sources.list.d/google-cloud-sdk.list && curl https://packages.cloud.google.com/apt/doc/apt-key.gpg | gpg --dearmor -o /usr/share/keyrings/cloud.google.gpg && apt-get update -y && apt-get install google-cloud-cli -y
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USER ${NB_USER}
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WORKDIR ${HOME}

‎images/py-rocket-oceanhw-esp/README.md‎

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# README
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## py-rocket-oceanhw-esp
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Python-R image for OceanHackWeek-en-Español, https://intercoonecta.github.io. Based on customizations of the `py-rocket-geospatial-2` image.
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### Emilio's notes on new Docker image
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**I'll clean this up soon**
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```bash
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docker compose build py-rocket > build_no_custom_R.log 2>&1
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docker compose build py-rocket > build_logs/build_custom-R-pckgs.log 2>&1
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docker compose up py-rocket
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# logs from docker compose up py-rocket are available via
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docker compose logs py-rocket
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# view and rm containers
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docker ps -a
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docker rm a68304072b28
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# rename and remove images
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docker rmi 0b148c9c27c9
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docker tag a65b2f13b739 py-rocket-oceanhw-esp:r-custom-3
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docker rmi py-rocket-oceanhw-esp:latest
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```
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### From py-rocket-geospatial v2.0 README
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This creates a base Python-R image with geospatial packages for Python and R. The Python environment is the Pangeo notebook environment + extra geospatial libraries (similar to CryoCloud). The R environment is Rocker geospatial plus a few other packages. The image also includes a linux Desktop with QGIS, CoastWatch Utilities, and Panoply.
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TeXLive and Quarto are installed along with MyST and JupyterBook.
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Python 3.12 is installed with a conda environment called notebook that is activated on opening the container. R 4.4.X is installed.
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See the documentation on [py-rocket-base](https://nmfs-opensci.github.io/py-rocket-base/) for information on the image structure and design.

‎images/py-rocket-oceanhw-esp/apt.txt‎

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# for qgis
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libgl1-mesa-glx
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# for install-r-packages.sh errors
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libudunits2-dev
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libgdal-dev
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libgeos-dev
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libproj-dev
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libtbb-dev
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libnetcdf-dev

‎images/py-rocket-oceanhw-esp/docker-compose.yml‎

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services:
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py-rocket:
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build: .
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image: py-rocket-oceanhw-esp
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# container_name: py-rocket-oceanhw-esp
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command: jupyter lab --port=8080 --ip=0.0.0.0
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ports:
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- "8080:8080"

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