Merge pull request #46 from hydroshare/python-3-wip

Python 3 upgrade

Dockerfile

@@ -1,4 +1,4 @@
-FROM python:2.7.11
+FROM python:3.6-jessie
 MAINTAINER Michael J. Stealey <[email protected]>
 
 ENV DEBIAN_FRONTEND noninteractive
@@ -10,14 +10,18 @@ RUN apt-get update && apt-get install -y \
     apt-transport-https \
     ca-certificates \
     sudo \
-    && apt-key adv --keyserver hkp://p80.pool.sks-keyservers.net:80 --recv-keys 58118E89F3A912897C070ADBF76221572C52609D \
-    && curl -sL https://deb.nodesource.com/setup_7.x | sudo -E bash -
+    && apt-key adv --keyserver hkp://p80.pool.sks-keyservers.net:80 --recv-keys 58118E89F3A912897C070ADBF76221572C52609D
+
+RUN curl -sL https://deb.nodesource.com/setup_7.x | sudo -E bash -
 
 # Add docker.list and requirements.txt - using /tmp to keep hub.docker happy
 COPY . /tmp
 RUN cp /tmp/docker.list /etc/apt/sources.list.d/ \
     && cp /tmp/requirements.txt /requirements.txt
 
+RUN sudo sh -c 'echo "deb http://apt.postgresql.org/pub/repos/apt/ `lsb_release -cs`-pgdg main" >> /etc/apt/sources.list.d/pgdg.list' \
+    && wget -q https://www.postgresql.org/media/keys/ACCC4CF8.asc -O - | sudo apt-key add -
+
 RUN apt-get update && apt-get install -y --fix-missing --no-install-recommends \
     apt-utils \
     docker-engine \
@@ -43,20 +47,24 @@ RUN npm install -g phantomjs-prebuilt
 
 WORKDIR /
 
+#install numpy before matplotlib
+RUN pip install 'numpy==1.16.0'
+RUN pip install git+https://github.com/sblack-usu/defusedexpat.git
+
 # Install pip based packages (due to dependencies some packages need to come first)
-RUN export CPLUS_INCLUDE_PATH=/usr/include/gdal \
-    && export C_INCLUDE_PATH=/usr/include/gdal \
-    && export GEOS_CONFIG=/usr/bin/geos-config \
-    && HDF5_INCDIR=/usr/include/hdf5/serial \
-    && pip install --upgrade pip \
-    && pip install -r requirements.txt
-
-# Install GDAL 2.1.0 from source
-RUN wget http://download.osgeo.org/gdal/2.1.3/gdal-2.1.3.tar.gz \
-    && tar -xzf gdal-2.1.3.tar.gz \
-    && rm gdal-2.1.3.tar.gz
-
-WORKDIR /gdal-2.1.3
+RUN export CPLUS_INCLUDE_PATH=/usr/include/gdal 
+RUN export C_INCLUDE_PATH=/usr/include/gdal 
+RUN export GEOS_CONFIG=/usr/bin/geos-config 
+RUN HDF5_INCDIR=/usr/include/hdf5/serial 
+RUN pip install --upgrade pip 
+RUN pip install -r requirements.txt
+
+# Install GDAL 2.4.1 from source
+RUN wget http://download.osgeo.org/gdal/2.4.1/gdal-2.4.1.tar.gz \
+    && tar -xzf gdal-2.4.1.tar.gz \
+    && rm gdal-2.4.1.tar.gz
+
+WORKDIR /gdal-2.4.1
 RUN ./configure --with-python --with-geos=yes \
     && make \
     && sudo make install \
@@ -72,6 +80,11 @@ RUN wget -qO - https://packages.irods.org/irods-signing-key.asc | sudo apt-key a
     irods-runtime \
     irods-icommands
 
+# inplaceedit in pip doesn't seem compatible with Django 1.11 yet...
+RUN pip install git+https://github.com/theromis/django-inplaceedit.git@e6fa12355defedf769a5f06edc8fc079a6e982ec
+# foresite-toolkit in pip isn't compatible with python3
+RUN pip install git+https://github.com/sblack-usu/foresite-toolkit.git#subdirectory=foresite-python/trunk
+
 # Install SSH for remote PyCharm debugging
 RUN mkdir /var/run/sshd
 RUN sed -i 's/PermitRootLogin without-password/PermitRootLogin yes/' /etc/ssh/sshd_config
@@ -88,6 +101,8 @@ RUN groupadd --system storage-hydro --gid=10000 \
 RUN echo 'hydro-service:docker' | chpasswd
 ENV DEBIAN_FRONTEND teletype
 
+# set UTF-8 env locale
+RUN echo UTF-8/en_US.UTF-8 UTF-8 > /etc/local.gen && locale-gen
 # Cleanup
 RUN apt-get clean \
     && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*

requirements.txt

@@ -1,29 +1,17 @@
-amqp==1.4.9
+amqp==2.5.0
 anyjson==0.3.3
 arrow==0.7.0
-asn1crypto==0.24.0
-astroid==1.4.8
-autoflake==0.6.6
 autopep8==1.2.2
 bagit==1.5.4
-bcrypt==3.1.4
-beautifulsoup4==4.5.3
-billiard==3.3.0.23
-bleach==3.0.2
-celery==3.1.23
+celery==4.3.0
 cffi==1.11.5
-chardet==3.0.4
 click==6.7
-colorama==0.3.7
-configparser==3.5.0
 coreapi==2.3.3
-coreschema==0.0.4
 coverage==4.0.3
-cryptography==2.3
 cycler==0.10.0
-defusedexpat==0.4
+#defusedexpat==0.4
 defusedxml==0.4.1
-Django==1.11.18
+Django==1.11.23
 django-appconf==1.0.2
 django-autocomplete-light==2.3.3
 django-braces==1.9.0
@@ -32,6 +20,7 @@ django-contrib-comments==1.9.0
 django-cors-headers==2.4.0
 django-crispy-forms==1.7.2
 django-debug-toolbar==1.9.1
+django-freshly==0.1.2
 django-haystack==2.8.1
 django-heartbeat==2.0.2
 django-ipware==2.1.0
@@ -44,109 +33,78 @@ django-security==0.9.3
 django-test-without-migrations==0.6
 django-timedeltafield==0.7.10
 django-widget-tweaks==1.4.1
-djangorestframework==3.8.2
+djangorestframework==3.9.1
 docker-py==1.7.2
-dominate==2.3.1
+dominate==2.4.0
 DoubleMetaphone==0.1
 drf-haystack==1.8.5
 drf-yasg==1.10.0
-ecdsa==0.13
+ecdsa==0.13.3
 enum34==1.1.6
 filebrowser-safe==0.5.0
 flake8==3.5.0
-flex==6.13.2
+flex==6.14.1
+flower==0.9.3
 funcsigs==1.0.2
-functools32==3.2.3.post2
+#functools32==3.2.3.post2
 future==0.16.0
-geographiclib==1.49
 geojson==1.3.2
 geopy==1.16.0
-gevent==1.1.2
-google.foresite-toolkit==1.3.3
+gevent==1.4.0
 grappelli-safe==0.5.1
-greenlet==0.4.10
 gunicorn==19.6.0
 html5lib==0.9999999
-idna==2.7
 inflection==0.3.1
-ipaddress==1.0.22
 isodate==0.5.4
-itypes==1.1.0
 Jinja2==2.10
 jsonpointer==1.14
 jsonschema==2.6.0
 keepalive==0.5
-kombu==3.0.35
-lazy-object-proxy==1.2.2
-lxml==3.7.3
-mapnik==0.1
+kombu==4.6.3
+lxml==4.4.0
+#mapnik==0.1
 Markdown==3.0.1
 MarkupSafe==1.0
-matplotlib==1.5.1
+matplotlib==3.1.2
 mccabe==0.6.1
 Mezzanine==4.3.1
 mock==1.3.0
 nameparser==0.5.7
-netCDF4==1.2.4
+netCDF4==1.5.1.2 
 nose==1.3.7
 nose-timer>=0.7.4,<1.0.0
-numpy==1.16.0
-oauthlib==2.1.0
-openapi-codec==1.3.2
+oauthlib==3.1.0
 OWSLib==0.10.3
-pandas==0.18.0
 paramiko==2.4.2
 pbr==1.10.0
 pep8==1.7.0
-Pillow==3.1.1
 prettytable==0.7.2
-probableparsing==0.0.1
 probablepeople==0.5.4
-psutil==4.0.0
-psycopg2==2.6.1
-py2-ipaddress==3.4.1
+psycopg2==2.8.2
+ipaddress==1.0.22
 pyasn1==0.4.4
 pycodestyle==2.3.1
-pycparser==2.18
-PyCRS==0.1.3
-pyflakes==1.1.0
+PyCRS==1.0.1
+pyflakes==1.6.0
 pylint==1.5.5
-PyNaCl==1.2.1
-pyparsing==2.1.7
 pyproj==1.9.5.1
 pysolr==3.4.0
-pysqlite==2.8.1
+pysqlite3==0.2.1
 pytest-django>=3.4.7, <4.0.0
 python-crfsuite==0.9.6
 python-dateutil==2.5.3
 python-irodsclient==0.8.1 
 pytz==2016.3
-PyYAML==3.13
+PyYAML==5.1
 rcssmin==1.0.6
 rdflib==4.0.1
 redis==2.10.5
 requests==2.20.0
-requests-oauthlib==0.6.1
 rfc3987==1.3.8
-rjsmin==1.0.12
 robot-detection==0.4
-ruamel.ordereddict==0.4.13
-ruamel.yaml==0.15.52
 selenium==3.0.2
-sh==1.11
-Shapely==1.5.13
-simplejson==3.16.0
-six==1.10.0
-SPARQLWrapper==1.7.6
-sqlparse==0.2.0
-strict-rfc3339==0.7
 suds-jurko==0.6
-swagger-spec-validator==2.3.1
-tzlocal==1.2.2
 timeago==1.0.10
 uritemplate==3.0.0
-validate-email==1.3
 virtualenv==15.0.2
-websocket-client==0.37.0
-wrapt==1.10.8
 xmltodict==0.10.2