Merge pull request #54 from nmfs-opensci/eeholmes-patch-2

edit test
nmfs-opensci · Nov 5, 2024 · 10dd452 · 10dd452
2 parents 8e92cfb + df47799
commit 10dd452
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diff --git a/draft_images/test/Desktop/cdat.desktop b/draft_images/test/Desktop/cdat.desktop
@@ -0,0 +1,11 @@
+[Desktop Entry]
+Type=Application
+Name=CWUtils
+GenericName=CoastWatch Data Analysis Tool
+Icon=cdat
+TryExec=cdat
+Exec=cdat %F
+Terminal=false
+StartupNotify=false
+Categories=Qt;Education;Science;Geography;
+Keywords=map;globe;
diff --git a/draft_images/test/Desktop/cdat.png b/draft_images/test/Desktop/cdat.png
diff --git a/draft_images/test/Desktop/panoply.desktop b/draft_images/test/Desktop/panoply.desktop
@@ -0,0 +1,10 @@
+[Desktop Entry]
+Type=Application
+Name=Panoply
+GenericName=Panoply netCDF, HDF and GRIB Data Viewer
+Icon=panoply
+Exec=/tmp/PanoplyJ/panoply.sh %F
+Terminal=false
+StartupNotify=false
+Categories=Qt;Education;Science;Geography;
+Keywords=map;
diff --git a/draft_images/test/Desktop/panoply.png b/draft_images/test/Desktop/panoply.png
diff --git a/draft_images/test/Desktop/qgis.desktop b/draft_images/test/Desktop/qgis.desktop
@@ -0,0 +1,14 @@
+# From: https://github.com/qgis/QGIS/blob/ltr-3_28/linux/org.qgis.qgis.desktop.in
+[Desktop Entry]
+Type=Application
+Name=QGIS Desktop
+GenericName=Geographic Information System
+Icon=/srv/conda/envs/notebook/share/qgis/images/icons/qgis-icon-512x512.png
+TryExec=qgis
+Exec=qgis %F
+Terminal=false
+StartupNotify=false
+Categories=Qt;Education;Science;Geography;
+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;
+Keywords=map;globe;postgis;wms;wfs;ogc;osgeo;
+StartupWMClass=QGIS3
diff --git a/draft_images/test/Desktop/qgis.xml b/draft_images/test/Desktop/qgis.xml
@@ -0,0 +1,212 @@
+<?xml version="1.0"?>
+<!-- From: https://raw.githubusercontent.com/qgis/QGIS/ltr-3_28/debian/qgis.xml -->
+<mime-info xmlns='http://www.freedesktop.org/standards/shared-mime-info'>
+
+  <mime-type type="application/x-qgis-project">
+    <comment>QGIS Project</comment>
+    <comment xml:lang="de">QGIS-Projekt</comment>
+    <sub-class-of type="application/xml"/>
+    <alias type="application/x-qgis"/>
+    <icon name="qgis-qgs"/>
+    <magic priority="50">
+      <match type="string" offset="0" value="&lt;!DOCTYPE qgis"/>
+    </magic>
+    <glob pattern="*.qgs"/>
+  </mime-type>
+
+  <mime-type type="application/x-qgis-project-container">
+    <comment>QGIS Project</comment>
+    <comment xml:lang="de">QGIS-Projekt</comment>
+    <sub-class-of type="application/zip"/>
+    <alias type="application/x-qgis"/>
+    <icon name="qgis-qgs"/>
+    <glob pattern="*.qgz"/>
+  </mime-type>
+
+  <mime-type type="application/x-qgis-layer-settings">
+    <comment>QGIS layer settings</comment>
+    <comment xml:lang="de">QGIS-Layereinstellungen</comment>
+    <sub-class-of type="application/xml"/>
+    <icon name="qgis-qml"/>
+    <magic priority="80">
+      <match type="string" offset="0" value="&lt;!DOCTYPE qgis"/>
+    </magic>
+    <glob pattern="*.qml"/>
+  </mime-type>
+
+  <mime-type type="application/x-qgis-layer-definition">
+    <comment>QGIS layer definition</comment>
+    <comment xml:lang="de">QGIS-Layerdefinition</comment>
+    <sub-class-of type="application/xml"/>
+    <icon name="qgis-qlr"/>
+    <magic priority="50">
+      <match type="string" offset="0" value="&lt;!DOCTYPE qgis-layer-definition"/>
+    </magic>
+    <glob pattern="*.qlr"/>
+  </mime-type>
+
+  <mime-type type="application/x-qgis-composer-template">
+    <comment>QGIS composer template</comment>
+    <comment xml:lang="de">QGIS-Druckzusammenstellungsvorlage</comment>
+    <sub-class-of type="application/xml"/>
+    <icon name="qgis-qpt"/>
+    <magic priority="50">
+      <match type="string" offset="0" value="&lt;!DOCTYPE qgis"/>
+    </magic>
+    <glob pattern="*.qpt"/>
+  </mime-type>
+
+  <mime-type type="application/x-esri-shape">
+    <comment>ESRI shape file</comment>
+    <comment xml:lang="de">ESRI-Shapedatei</comment>
+    <icon name="qgis-mime"/>
+    <magic priority="100">
+      <match type="big32" offset="0" value="9994">
+        <match type="big32" offset="4" value="0">
+          <match type="big32" offset="8" value="0">
+            <match type="big32" offset="12" value="0">
+              <match type="big32" offset="16" value="0">
+                <match type="big32" offset="20" value="0">
+                  <match type="big32" offset="28" value="1000"/>
+                </match>
+              </match>
+            </match>
+          </match>
+        </match>
+      </match>
+    </magic>
+    <glob pattern="*.shp"/>
+    <glob pattern="*.shx"/>
+  </mime-type>
+
+  <mime-type type="application/x-esri-crs">
+    <comment>ESRI coordinate reference system</comment>
+    <comment xml:lang="de">ESRI-Koordinatenreferenzsystem</comment>
+    <icon name="qgis-mime"/>
+    <magic>
+      <match type="string" offset="0" value="GEOGCS["/>
+      <match type="string" offset="0" value="PROJCS["/>
+      <match type="string" offset="0" value="LOCAL_CS["/>
+    </magic>
+    <glob pattern="*.prj"/>
+  </mime-type>
+
+  <mime-type type="image/tiff">
+    <comment>TIFF raster data</comment>
+    <comment xml:lang="de">TIFF-Rasterdaten</comment>
+    <icon name="qgis-mime"/>
+    <magic priority="50">
+      <match type="string" offset="0" value="MM">
+        <match type="little16" offset="2" value="42"/>
+      </match>
+      <match type="string" offset="0" value="MM">
+        <match type="big16" offset="2" value="42"/>
+      </match>
+    </magic>
+    <glob pattern="*.tiff"/>
+    <glob pattern="*.tif"/>
+  </mime-type>
+
+  <mime-type type="image/jpeg">
+    <comment>JPEG raster data</comment>
+    <comment xml:lang="de">JPEG-Rasterdaten</comment>
+    <icon name="qgis-mime"/>
+    <magic priority="50">
+       <match type="big16" offset="0" value="65496"/>
+    </magic>
+    <glob pattern="*.jpeg"/>
+    <glob pattern="*.jpg"/>
+  </mime-type>
+
+  <mime-type type="image/jp2">
+    <comment>JPEG2000 raster data</comment>
+    <comment xml:lang="de">JPEG2000-Rasterdaten</comment>
+    <icon name="qgis-mime"/>
+    <magic priority="50">
+      <match type="little32" offset="0" value="12">
+        <match type="string" offset="8" value="jP">
+          <match type="byte" offset="10" value="32">
+            <match type="byte" offset="11" value="32">
+              <match type="byte" offset="12" value="13">
+                <match type="byte" offset="13" value="10">
+                  <match type="byte" offset="14" value="135">
+                    <match type="byte" offset="13" value="10"/>
+                  </match>
+                </match>
+              </match>
+            </match>
+          </match>
+        </match>
+      </match>
+    </magic>
+    <glob pattern="*.jp2"/>
+    <glob pattern="*.j2k"/>
+  </mime-type>
+
+  <mime-type type="application/x-raster-aig">
+    <comment>AIG raster data</comment>
+    <comment xml:lang="de">AIG-Rasterdaten</comment>
+    <icon name="qgis-mime"/>
+    <glob pattern="*.aig"/>
+  </mime-type>
+
+  <mime-type type="application/x-raster-ecw">
+    <comment>ECW raster data</comment>
+    <comment xml:lang="de">ECW-Rasterdaten</comment>
+    <icon name="qgis-mime"/>
+    <glob pattern="*.ecw"/>
+  </mime-type>
+
+  <mime-type type="application/x-raster-mrsid">
+    <comment>MrSID raster data</comment>
+    <comment xml:lang="de">MrSID-Rasterdaten</comment>
+    <icon name="qgis-mime"/>
+    <glob pattern="*.sid"/>
+  </mime-type>
+
+  <mime-type type="application/x-mapinfo-mif">
+    <comment>MapInfo file</comment>
+    <comment xml:lang="de">MapInfo-Datei</comment>
+    <icon name="qgis-mime"/>
+    <magic priority="51">
+      <match type="string" offset="0" value="VERSION">
+        <match type="string" offset="0:512" value="COLUMNS"/>
+          <match type="string" offset="0:512" value="DATA">
+        </match>
+      </match>
+    </magic>
+    <glob weight="60" pattern="*.mif"/>
+  </mime-type>
+
+  <!-- .mif is just not good enough -->
+  <mime-type type="application/x-adobe-mif">
+    <alias type="application/x-mif"/>
+    <comment>Adobe FrameMaker MIF file</comment>
+    <magic priority="100">
+      <match type="string" offset="0" value="&lt;MIFFile"/>
+    </magic>
+    <glob weight="51" pattern="*.mif"/>
+  </mime-type>
+
+  <mime-type type="application/vnd.google-earth.kml+xml">
+    <comment>Keyhole Markup Language data</comment>
+    <sub-class-of type="application/xml"/>
+    <icon name="qgis-mime"/>
+    <glob pattern="*.kml"/>
+  </mime-type>
+
+  <mime-type type="application/vnd.google-earth.kmz">
+    <comment>Zipped Keyhole Markup Language data</comment>
+    <sub-class-of type="application/zip"/>
+    <icon name="qgis-mime"/>
+    <glob pattern="*.kmz"/>
+  </mime-type>
+
+  <mime-type type="application/geopackage+sqlite3">
+    <comment>GeoPackage data</comment>
+    <sub-class-of type="application/vnd.sqlite3"/>
+    <icon name="qgis-mime"/>
+    <glob pattern="*.gpkg"/>
+  </mime-type>
+
+</mime-info>
diff --git a/draft_images/test/Dockerfile b/draft_images/test/Dockerfile
@@ -4,12 +4,35 @@ RUN echo ${PATH}
 
 USER root
 RUN echo ${PATH}
-RUN /pyrocket_scripts/install-conda-packages.sh || echo "install-conda-packages.sh failed" || true
-RUN /pyrocket_scripts/install-r-package.sh || echo "install-r-package.sh failed" || true
-RUN /pyrocket_scripts/install-pip-packages.sh || echo "install-pip-packages.sh failed" || true
-RUN /pyrocket_scripts/install-apt-packages.sh || echo "install-apt-packages.sh failed" || true
+RUN /pyrocket_scripts/install-conda-packages.sh environment.yml || echo "install-conda-packages.sh failed" || true
+RUN /pyrocket_scripts/install-r-packages.sh install.R || echo "install-r-package.sh failed" || true
+RUN /pyrocket_scripts/install-pip-packages.sh requirements.txt || echo "install-pip-packages.sh failed" || true
+RUN /pyrocket_scripts/install-apt-packages.sh apt.txt || echo "install-apt-packages.sh failed" || true
+RUN /pyrocket_scripts/install-desktop.sh || echo "setup-desktop.sh failed" || true
 RUN /pyrocket_scripts/run-postbuild.sh || echo "run-postbuild.sh failed" || true
 RUN /pyrocket_scripts/setup-start.sh || echo "setup-start.sh failed" || true
-RUN /pyrocket_scripts/setup-desktop.sh || echo "setup-desktop.sh failed" || true
 USER ${NB_USER}
 
+USER root
+# install the geospatial libraries and R spatial; the rocket script are part of py-rocket-base
+RUN PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin && \
+    /rocker_scripts/install_geospatial.sh
+
+# Install cwutils
+RUN cd /tmp && \
+    wget https://www.star.nesdis.noaa.gov/socd/coastwatch/cwf/cwutils-4_0_0_198-linux-x86_64.tar.gz && \
+    tar -zxf cwutils-4_0_0_198-linux-x86_64.tar.gz && \
+    rm -rf cwutils-4_0_0_198-linux-x86_64.tar.gz
+ENV PATH=${PATH}:/tmp/cwutils_4.0.0.198/bin
+ENV MANPATH=${MANPATH}:/tmp/cwutils_4.0.0.198/doc/man
+ENV INSTALL4J ADD VM PARAMS=-Dsun.java2d.uiScale=2.0
+
+# Install panoply
+RUN cd /tmp && \
+  wget --user-agent="Mozilla/5.0" https://www.giss.nasa.gov/tools/panoply/download/PanoplyJ-5.5.4.tgz && \
+  tar -zxf PanoplyJ-5.5.4.tgz && \
+  rm -rf PanoplyJ-5.5.4.tgz
+ENV PATH=${PATH}:/tmp/PanoplyJ
+
+USER ${NB_USER}
+WORKDIR ${HOME}
diff --git a/draft_images/test/apt.txt b/draft_images/test/apt.txt
@@ -1,5 +1,3 @@
-# Some useful stuff
+# for qgis
 libgl1-mesa-glx
 
-# Add some more
-# or not
diff --git a/draft_images/test/environment.yml b/draft_images/test/environment.yml
@@ -114,8 +114,7 @@ dependencies:
   - xmip
   - spectral # pure Python module for processing hyperspectral image data
 
-
-  # Desktop tools whose versions are more recent on conda-forge than ubuntu
+  # Desktop tools
   - qgis 
   - pyopencl  # Maybe needed for qgis? https://github.com/conda-forge/qgis-feedstock/issues/263
   # Resolves warning "No ICDs were found": https://github.com/CryoInTheCloud/hub-image/issues/50

diff --git a/draft_images/test/requirements,txt → draft_images/test/requirements.txt b/draft_images/test/requirements,txt → draft_images/test/requirements.txt
diff --git a/draft_images/test/start b/draft_images/test/start
@@ -0,0 +1,6 @@
+#!/bin/bash
+set -e
+
+export TEST=abc
+
+exec "$@"