From a25981738dc78a49ec40362bba5fc390d9410bc9 Mon Sep 17 00:00:00 2001 From: "Michael J. Stealey" Date: Tue, 7 Feb 2017 11:29:19 -0500 Subject: [PATCH 01/30] iRODS 4.2.0 --- Dockerfile | 16 +++++++++------- 1 file changed, 9 insertions(+), 7 deletions(-) diff --git a/Dockerfile b/Dockerfile index 2c03731..320eedb 100644 --- a/Dockerfile +++ b/Dockerfile @@ -41,13 +41,6 @@ RUN npm install -g phantomjs-prebuilt WORKDIR / -# Install iRODS 4.1.8 packages -RUN curl ftp://ftp.renci.org/pub/irods/releases/4.1.8/ubuntu14/irods-runtime-4.1.8-ubuntu14-x86_64.deb -o irods-runtime.deb \ - && curl ftp://ftp.renci.org/pub/irods/releases/4.1.8/ubuntu14/irods-icommands-4.1.8-ubuntu14-x86_64.deb -o irods-icommands.deb \ - && sudo dpkg -i irods-runtime.deb irods-icommands.deb \ - && sudo apt-get -f install \ - && rm irods-runtime.deb irods-icommands.deb - # 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 \ @@ -68,6 +61,15 @@ RUN ./configure --with-python --with-geos=yes \ && sudo ldconfig WORKDIR / +# Install iRODS v.4.2.0 +RUN wget -qO - https://packages.irods.org/irods-signing-key.asc | sudo apt-key add - \ + && echo "deb [arch=amd64] https://packages.irods.org/apt/ trusty main" | \ + sudo tee /etc/apt/sources.list.d/renci-irods.list \ + && sudo apt-get update && sudo apt-get install -y \ + apt-transport-https \ + irods-runtime \ + irods-icommands + # Install SSH for remote PyCharm debugging RUN mkdir /var/run/sshd RUN sed -i 's/PermitRootLogin without-password/PermitRootLogin yes/' /etc/ssh/sshd_config From a4eb025ef434a8268e9dcf4820e79b59e935fbbc Mon Sep 17 00:00:00 2001 From: phuongdm Date: Thu, 12 Jul 2018 00:47:15 +0700 Subject: [PATCH 02/30] Update requirements.txt Fix numpy error --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 2e130fd..4f286c6 100644 --- a/requirements.txt +++ b/requirements.txt @@ -63,7 +63,7 @@ Mezzanine==4.1.0 mock==1.3.0 netCDF4==1.2.4 nose==1.3.7 -numpy==1.10.4 +numpy==1.14.5 oauthlib==1.0.3 OWSLib==0.10.3 pandas==0.18.0 From d8a267b206d1f33992ab2f102f749e6219bfb37c Mon Sep 17 00:00:00 2001 From: phuongdm Date: Fri, 27 Jul 2018 11:05:02 -0400 Subject: [PATCH 03/30] Update requirements.txt --- requirements.txt | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/requirements.txt b/requirements.txt index 4f286c6..d5763a6 100644 --- a/requirements.txt +++ b/requirements.txt @@ -67,7 +67,7 @@ numpy==1.14.5 oauthlib==1.0.3 OWSLib==0.10.3 pandas==0.18.0 -paramiko==1.16.0 +paramiko==2.4.1 pbr==1.10.0 pep8==1.7.0 Pillow==3.1.1 @@ -76,7 +76,6 @@ psutil==4.0.0 psycopg2==2.6.1 py2-ipaddress==3.4.1 PyCRS==0.1.3 -pycrypto==2.6.1 pyflakes==1.1.0 pylint==1.5.5 pyparsing==2.1.7 From 79d18cbd3d09abd06e8c88ae0bab9286a21e7126 Mon Sep 17 00:00:00 2001 From: Scott Black Date: Mon, 30 Jul 2018 09:12:44 -0600 Subject: [PATCH 04/30] version changes for django 1.11 upgrade --- requirements.txt | 48 ++++++++++++++++++++++++------------------------ 1 file changed, 24 insertions(+), 24 deletions(-) diff --git a/requirements.txt b/requirements.txt index d5763a6..6856970 100644 --- a/requirements.txt +++ b/requirements.txt @@ -5,49 +5,49 @@ astroid==1.4.8 autoflake==0.6.6 autopep8==1.2.2 bagit==1.5.4 -beautifulsoup4==4.4.1 +beautifulsoup4==4.5.3 billiard==3.3.0.23 -bleach==1.4.3 +bleach==2.0 celery==3.1.23 -chardet==2.3.0 +chardet==3.0.4 colorama==0.3.7 coverage==4.0.3 cycler==0.10.0 defusedexpat==0.4 defusedxml==0.4.1 -Django==1.8.14 +Django==1.11 django-appconf==1.0.2 -django-autocomplete-light==2.0.9 +django-autocomplete-light==3.2.10 django-braces==1.9.0 -django-compressor==2.0 -django-contrib-comments==1.6.2 -django-cors-headers==1.1.0 -django-crispy-forms==1.6.0 -django-debug-toolbar==1.4 -django-haystack==2.4.1 +django-compressor==2.2 +django-contrib-comments==1.8.0 +django-cors-headers==2.4.0 +django-crispy-forms==1.7.2 +django-debug-toolbar==1.9.1 +django-haystack==2.8.1 django-heartbeat==2.0.2 django-inplaceedit==1.4.1 -django-jsonfield==0.9.19 -django-modeltranslation==0.11 -django-nose==1.4.3 -django-oauth-toolkit==0.10.0 +django-jsonfield==1.0.1 +django-modeltranslation==0.12.2 +django-nose==1.4.5 +django-oauth-toolkit==1.1.0 django-robots==2.0 django-security==0.9.3 django-timedeltafield==0.7.10 django-widget-tweaks==1.4.1 -djangorestframework==3.3.3 +djangorestframework==3.8.2 docker-py==1.7.2 dominate==2.3.1 ecdsa==0.13 -filebrowser-safe==0.4.3 -flake8==2.5.4 +filebrowser-safe==0.4.6 +flake8==3.5.0 funcsigs==1.0.2 future==0.15.2 # GDAL==2.1.3 # Installed from source geojson==1.3.2 gevent==1.1.2 -google.foresite-toolkit==1.3 -grappelli-safe==0.4.2 +google.foresite-toolkit==1.3.3 +grappelli-safe==0.4.5 greenlet==0.4.10 gunicorn==19.6.0 html5lib==0.9999999 @@ -55,16 +55,16 @@ isodate==0.5.4 keepalive==0.5 kombu==3.0.35 lazy-object-proxy==1.2.2 -lxml==3.6.0 +lxml==3.7.3 mapnik==0.1 matplotlib==1.5.1 mccabe==0.4.0 -Mezzanine==4.1.0 +Mezzanine==4.3.0 mock==1.3.0 netCDF4==1.2.4 nose==1.3.7 -numpy==1.14.5 -oauthlib==1.0.3 +numpy==1.15.0 +oauthlib==2.1.0 OWSLib==0.10.3 pandas==0.18.0 paramiko==2.4.1 From c80dc14f20e4b87fbee171223d5270dccb07857d Mon Sep 17 00:00:00 2001 From: Scott Black Date: Mon, 30 Jul 2018 11:32:20 -0600 Subject: [PATCH 05/30] update aucomplete version --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 6856970..0e50c98 100644 --- a/requirements.txt +++ b/requirements.txt @@ -17,7 +17,7 @@ defusedexpat==0.4 defusedxml==0.4.1 Django==1.11 django-appconf==1.0.2 -django-autocomplete-light==3.2.10 +django-autocomplete-light==2.3.3 django-braces==1.9.0 django-compressor==2.2 django-contrib-comments==1.8.0 From ee32f9b4df93641c6d3dada5e637cf9659b90341 Mon Sep 17 00:00:00 2001 From: Scott Black Date: Mon, 30 Jul 2018 12:05:37 -0600 Subject: [PATCH 06/30] upgrade pip to get latest python modules --- Dockerfile | 2 ++ 1 file changed, 2 insertions(+) diff --git a/Dockerfile b/Dockerfile index 320eedb..e99e46f 100644 --- a/Dockerfile +++ b/Dockerfile @@ -4,6 +4,8 @@ MAINTAINER Michael J. Stealey ENV DEBIAN_FRONTEND noninteractive ENV PY_SAX_PARSER=hs_core.xmlparser +RUN pip install --upgrade pip + RUN apt-get update && apt-get install -y \ apt-transport-https \ ca-certificates \ From 62e74c6c84c032c0398a5223d69bce9b8f0da447 Mon Sep 17 00:00:00 2001 From: Scott Black Date: Mon, 30 Jul 2018 12:39:44 -0600 Subject: [PATCH 07/30] revert autcomplete version change --- Dockerfile | 2 -- requirements.txt | 2 +- 2 files changed, 1 insertion(+), 3 deletions(-) diff --git a/Dockerfile b/Dockerfile index e99e46f..320eedb 100644 --- a/Dockerfile +++ b/Dockerfile @@ -4,8 +4,6 @@ MAINTAINER Michael J. Stealey ENV DEBIAN_FRONTEND noninteractive ENV PY_SAX_PARSER=hs_core.xmlparser -RUN pip install --upgrade pip - RUN apt-get update && apt-get install -y \ apt-transport-https \ ca-certificates \ diff --git a/requirements.txt b/requirements.txt index 0e50c98..6856970 100644 --- a/requirements.txt +++ b/requirements.txt @@ -17,7 +17,7 @@ defusedexpat==0.4 defusedxml==0.4.1 Django==1.11 django-appconf==1.0.2 -django-autocomplete-light==2.3.3 +django-autocomplete-light==3.2.10 django-braces==1.9.0 django-compressor==2.2 django-contrib-comments==1.8.0 From a7d127612be9630eeefad02b763d9853aaf65171 Mon Sep 17 00:00:00 2001 From: Scott Black Date: Mon, 30 Jul 2018 13:28:51 -0600 Subject: [PATCH 08/30] add missing oauth version --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 6856970..0e50c98 100644 --- a/requirements.txt +++ b/requirements.txt @@ -17,7 +17,7 @@ defusedexpat==0.4 defusedxml==0.4.1 Django==1.11 django-appconf==1.0.2 -django-autocomplete-light==3.2.10 +django-autocomplete-light==2.3.3 django-braces==1.9.0 django-compressor==2.2 django-contrib-comments==1.8.0 From 1da4ee5e4e7ec43360cfd7bfa5e908a1bb5d8ce4 Mon Sep 17 00:00:00 2001 From: phuongdm Date: Tue, 31 Jul 2018 10:22:18 -0400 Subject: [PATCH 09/30] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 090320f..ae732a6 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,7 @@ # hs_docker_base Base image for HydroShare project. -Build information at Docker hub: [mjstealey/hs_docker_base](https://hub.docker.com/r/mjstealey/hs_docker_base/) +Build information at Docker hub: [hydroshare/hs_docker_base](https://hub.docker.com/r/hydroshare/hs_docker_base/) **requires.io** From b7aa922777cf7f8c0f36922c2e3e4323d077aa96 Mon Sep 17 00:00:00 2001 From: Scott Black Date: Tue, 31 Jul 2018 11:53:07 -0600 Subject: [PATCH 10/30] update requests version --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 0e50c98..dbbe13b 100644 --- a/requirements.txt +++ b/requirements.txt @@ -88,7 +88,7 @@ pytz==2016.3 rcssmin==1.0.6 rdflib==4.0.1 redis==2.10.5 -requests==2.9.1 +requests==2.13.0 requests-oauthlib==0.6.1 rjsmin==1.0.12 selenium==3.0.2 From bad4ed5e37921620821481714d63e701b366d81e Mon Sep 17 00:00:00 2001 From: Scott Black Date: Thu, 9 Aug 2018 15:42:17 -0600 Subject: [PATCH 11/30] update requirements from hydroshare project --- requirements.txt | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/requirements.txt b/requirements.txt index dbbe13b..ba5abb5 100644 --- a/requirements.txt +++ b/requirements.txt @@ -27,24 +27,30 @@ django-debug-toolbar==1.9.1 django-haystack==2.8.1 django-heartbeat==2.0.2 django-inplaceedit==1.4.1 +django-ipware==2.1.0 django-jsonfield==1.0.1 django-modeltranslation==0.12.2 django-nose==1.4.5 django-oauth-toolkit==1.1.0 +django-rest-swagger==2.2.0 django-robots==2.0 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 docker-py==1.7.2 dominate==2.3.1 +drf-yasg==1.9.2 ecdsa==0.13 filebrowser-safe==0.4.6 flake8==3.5.0 +flex==6.13.2 funcsigs==1.0.2 future==0.15.2 # GDAL==2.1.3 # Installed from source geojson==1.3.2 +geopy==1.16.0 gevent==1.1.2 google.foresite-toolkit==1.3.3 grappelli-safe==0.4.5 @@ -52,6 +58,7 @@ greenlet==0.4.10 gunicorn==19.6.0 html5lib==0.9999999 isodate==0.5.4 +jsonschema==2.6.0 keepalive==0.5 kombu==3.0.35 lazy-object-proxy==1.2.2 @@ -61,6 +68,7 @@ matplotlib==1.5.1 mccabe==0.4.0 Mezzanine==4.3.0 mock==1.3.0 +nameparser==0.5.7 netCDF4==1.2.4 nose==1.3.7 numpy==1.15.0 @@ -72,6 +80,7 @@ pbr==1.10.0 pep8==1.7.0 Pillow==3.1.1 prettytable==0.7.2 +probablepeople==0.5.4 psutil==4.0.0 psycopg2==2.6.1 py2-ipaddress==3.4.1 @@ -91,6 +100,7 @@ redis==2.10.5 requests==2.13.0 requests-oauthlib==0.6.1 rjsmin==1.0.12 +robot-detection==0.4 selenium==3.0.2 sh==1.11 Shapely==1.5.13 @@ -98,6 +108,7 @@ six==1.10.0 SPARQLWrapper==1.7.6 sqlparse==0.2.0 suds-jurko==0.6 +swagger-spec-validator==2.3.1 tzlocal==1.2.2 virtualenv==15.0.2 websocket-client==0.37.0 From 42f7353fc52ab14d388ceac3e42896ba9448cbe9 Mon Sep 17 00:00:00 2001 From: Scott Black Date: Fri, 10 Aug 2018 10:08:41 -0600 Subject: [PATCH 12/30] update requierment versions for upgrade --- requirements.txt | 44 +++++++++++++++++++++++++++++++++++++++----- 1 file changed, 39 insertions(+), 5 deletions(-) diff --git a/requirements.txt b/requirements.txt index ba5abb5..c4c5ef6 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,21 +1,29 @@ amqp==1.4.9 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==2.0 +bleach==2.0.0 celery==3.1.23 +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 defusedxml==0.4.1 -Django==1.11 +Django==1.11.15 django-appconf==1.0.2 django-autocomplete-light==2.3.3 django-braces==1.9.0 @@ -41,14 +49,18 @@ django-widget-tweaks==1.4.1 djangorestframework==3.8.2 docker-py==1.7.2 dominate==2.3.1 -drf-yasg==1.9.2 +DoubleMetaphone==0.1 +drf-yasg==1.10.0 ecdsa==0.13 +enum34==1.1.6 filebrowser-safe==0.4.6 flake8==3.5.0 flex==6.13.2 funcsigs==1.0.2 -future==0.15.2 -# GDAL==2.1.3 # Installed from source +functools32==3.2.3.post2 +future==0.16.0 +GDAL==2.1.3 +geographiclib==1.49 geojson==1.3.2 geopy==1.16.0 gevent==1.1.2 @@ -57,13 +69,20 @@ grappelli-safe==0.4.5 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 +MarkupSafe==1.0 matplotlib==1.5.1 mccabe==0.4.0 Mezzanine==4.3.0 @@ -73,6 +92,7 @@ netCDF4==1.2.4 nose==1.3.7 numpy==1.15.0 oauthlib==2.1.0 +openapi-codec==1.3.2 OWSLib==0.10.3 pandas==0.18.0 paramiko==2.4.1 @@ -80,36 +100,50 @@ 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 +pyasn1==0.4.4 +pycodestyle==2.3.1 +pycparser==2.18 PyCRS==0.1.3 pyflakes==1.1.0 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 +python-crfsuite==0.9.6 python-dateutil==2.5.3 -e git+https://github.com/iPlantCollaborativeOpenSource/python-irodsclient.git@dcd234c166c06bdfc40fa2ef135c2511e0a4e7ac#egg=python_irodsclient pytz==2016.3 +PyYAML==3.13 rcssmin==1.0.6 rdflib==4.0.1 redis==2.10.5 requests==2.13.0 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 +uritemplate==3.0.0 +validate-email==1.3 virtualenv==15.0.2 websocket-client==0.37.0 wrapt==1.10.8 From 1455468edb4d6d2175601fd96164d098dfacc99e Mon Sep 17 00:00:00 2001 From: Scott Black Date: Fri, 10 Aug 2018 10:29:11 -0600 Subject: [PATCH 13/30] remove GDAL from pip install --- requirements.txt | 1 - 1 file changed, 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index c4c5ef6..4fe1e1c 100644 --- a/requirements.txt +++ b/requirements.txt @@ -59,7 +59,6 @@ flex==6.13.2 funcsigs==1.0.2 functools32==3.2.3.post2 future==0.16.0 -GDAL==2.1.3 geographiclib==1.49 geojson==1.3.2 geopy==1.16.0 From ea1947f5fcc9f7e321edfc4c5f9175f295ff5d3a Mon Sep 17 00:00:00 2001 From: Scott Black Date: Tue, 14 Aug 2018 14:35:52 -0600 Subject: [PATCH 14/30] use the latest mezzanine and comments libraries --- requirements.txt | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/requirements.txt b/requirements.txt index 4fe1e1c..3ea3663 100644 --- a/requirements.txt +++ b/requirements.txt @@ -28,7 +28,7 @@ django-appconf==1.0.2 django-autocomplete-light==2.3.3 django-braces==1.9.0 django-compressor==2.2 -django-contrib-comments==1.8.0 +django-contrib-comments==1.9.0 django-cors-headers==2.4.0 django-crispy-forms==1.7.2 django-debug-toolbar==1.9.1 @@ -84,7 +84,7 @@ mapnik==0.1 MarkupSafe==1.0 matplotlib==1.5.1 mccabe==0.4.0 -Mezzanine==4.3.0 +Mezzanine==4.3.1 mock==1.3.0 nameparser==0.5.7 netCDF4==1.2.4 From 0565fad67bf573f765009453a48a2adef64f5846 Mon Sep 17 00:00:00 2001 From: Scott Black Date: Tue, 21 Aug 2018 15:22:50 -0600 Subject: [PATCH 15/30] update mccabe version for flake8 compatibility --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 3ea3663..c927abb 100644 --- a/requirements.txt +++ b/requirements.txt @@ -83,7 +83,7 @@ lxml==3.7.3 mapnik==0.1 MarkupSafe==1.0 matplotlib==1.5.1 -mccabe==0.4.0 +mccabe==0.6.1 Mezzanine==4.3.1 mock==1.3.0 nameparser==0.5.7 From fd8fa20c80e14ad01d1ada136ae93fc86395158e Mon Sep 17 00:00:00 2001 From: Scott Black Date: Thu, 23 Aug 2018 11:21:47 -0600 Subject: [PATCH 16/30] [#2863] - remove django-rest-swagger in favor of drf-yasg --- requirements.txt | 1 - 1 file changed, 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index c927abb..f84d88b 100644 --- a/requirements.txt +++ b/requirements.txt @@ -40,7 +40,6 @@ django-jsonfield==1.0.1 django-modeltranslation==0.12.2 django-nose==1.4.5 django-oauth-toolkit==1.1.0 -django-rest-swagger==2.2.0 django-robots==2.0 django-security==0.9.3 django-test-without-migrations==0.6 From c6e380f45a3d9eac77eae920fc34e03bc3ec530c Mon Sep 17 00:00:00 2001 From: Scott Black Date: Tue, 6 Nov 2018 06:37:34 -0700 Subject: [PATCH 17/30] Revert "Django 1.11" --- requirements.txt | 99 ++++++++++++++---------------------------------- 1 file changed, 28 insertions(+), 71 deletions(-) diff --git a/requirements.txt b/requirements.txt index f84d88b..d5763a6 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,96 +1,70 @@ amqp==1.4.9 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 +beautifulsoup4==4.4.1 billiard==3.3.0.23 -bleach==2.0.0 +bleach==1.4.3 celery==3.1.23 -cffi==1.11.5 -chardet==3.0.4 -click==6.7 +chardet==2.3.0 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 defusedxml==0.4.1 -Django==1.11.15 +Django==1.8.14 django-appconf==1.0.2 -django-autocomplete-light==2.3.3 +django-autocomplete-light==2.0.9 django-braces==1.9.0 -django-compressor==2.2 -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-haystack==2.8.1 +django-compressor==2.0 +django-contrib-comments==1.6.2 +django-cors-headers==1.1.0 +django-crispy-forms==1.6.0 +django-debug-toolbar==1.4 +django-haystack==2.4.1 django-heartbeat==2.0.2 django-inplaceedit==1.4.1 -django-ipware==2.1.0 -django-jsonfield==1.0.1 -django-modeltranslation==0.12.2 -django-nose==1.4.5 -django-oauth-toolkit==1.1.0 +django-jsonfield==0.9.19 +django-modeltranslation==0.11 +django-nose==1.4.3 +django-oauth-toolkit==0.10.0 django-robots==2.0 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==3.3.3 docker-py==1.7.2 dominate==2.3.1 -DoubleMetaphone==0.1 -drf-yasg==1.10.0 ecdsa==0.13 -enum34==1.1.6 -filebrowser-safe==0.4.6 -flake8==3.5.0 -flex==6.13.2 +filebrowser-safe==0.4.3 +flake8==2.5.4 funcsigs==1.0.2 -functools32==3.2.3.post2 -future==0.16.0 -geographiclib==1.49 +future==0.15.2 +# GDAL==2.1.3 # Installed from source geojson==1.3.2 -geopy==1.16.0 gevent==1.1.2 -google.foresite-toolkit==1.3.3 -grappelli-safe==0.4.5 +google.foresite-toolkit==1.3 +grappelli-safe==0.4.2 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 +lxml==3.6.0 mapnik==0.1 -MarkupSafe==1.0 matplotlib==1.5.1 -mccabe==0.6.1 -Mezzanine==4.3.1 +mccabe==0.4.0 +Mezzanine==4.1.0 mock==1.3.0 -nameparser==0.5.7 netCDF4==1.2.4 nose==1.3.7 -numpy==1.15.0 -oauthlib==2.1.0 -openapi-codec==1.3.2 +numpy==1.14.5 +oauthlib==1.0.3 OWSLib==0.10.3 pandas==0.18.0 paramiko==2.4.1 @@ -98,50 +72,33 @@ 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 -pyasn1==0.4.4 -pycodestyle==2.3.1 -pycparser==2.18 PyCRS==0.1.3 pyflakes==1.1.0 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 -python-crfsuite==0.9.6 python-dateutil==2.5.3 -e git+https://github.com/iPlantCollaborativeOpenSource/python-irodsclient.git@dcd234c166c06bdfc40fa2ef135c2511e0a4e7ac#egg=python_irodsclient pytz==2016.3 -PyYAML==3.13 rcssmin==1.0.6 rdflib==4.0.1 redis==2.10.5 -requests==2.13.0 +requests==2.9.1 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 -uritemplate==3.0.0 -validate-email==1.3 virtualenv==15.0.2 websocket-client==0.37.0 wrapt==1.10.8 From 2fa65e5506afa99497fd642db0741b31162cf6aa Mon Sep 17 00:00:00 2001 From: Scott Black Date: Tue, 6 Nov 2018 15:44:14 -0700 Subject: [PATCH 18/30] updgrade security vulnerabilities --- requirements.txt | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/requirements.txt b/requirements.txt index f84d88b..0938ad5 100644 --- a/requirements.txt +++ b/requirements.txt @@ -34,7 +34,6 @@ django-crispy-forms==1.7.2 django-debug-toolbar==1.9.1 django-haystack==2.8.1 django-heartbeat==2.0.2 -django-inplaceedit==1.4.1 django-ipware==2.1.0 django-jsonfield==1.0.1 django-modeltranslation==0.12.2 @@ -93,7 +92,7 @@ oauthlib==2.1.0 openapi-codec==1.3.2 OWSLib==0.10.3 pandas==0.18.0 -paramiko==2.4.1 +paramiko==2.4.2 pbr==1.10.0 pep8==1.7.0 Pillow==3.1.1 @@ -122,7 +121,7 @@ PyYAML==3.13 rcssmin==1.0.6 rdflib==4.0.1 redis==2.10.5 -requests==2.13.0 +requests==2.20.0 requests-oauthlib==0.6.1 rfc3987==1.3.8 rjsmin==1.0.12 From dde235f4d2f6309e7e9ab38b2cb28a857c193d44 Mon Sep 17 00:00:00 2001 From: Scott Black Date: Thu, 8 Nov 2018 11:47:12 -0700 Subject: [PATCH 19/30] Revert "Revert "Django 1.11"" --- requirements.txt | 99 ++++++++++++++++++++++++++++++++++-------------- 1 file changed, 71 insertions(+), 28 deletions(-) diff --git a/requirements.txt b/requirements.txt index d5763a6..f84d88b 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,70 +1,96 @@ amqp==1.4.9 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 -beautifulsoup4==4.4.1 +bcrypt==3.1.4 +beautifulsoup4==4.5.3 billiard==3.3.0.23 -bleach==1.4.3 +bleach==2.0.0 celery==3.1.23 -chardet==2.3.0 +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 defusedxml==0.4.1 -Django==1.8.14 +Django==1.11.15 django-appconf==1.0.2 -django-autocomplete-light==2.0.9 +django-autocomplete-light==2.3.3 django-braces==1.9.0 -django-compressor==2.0 -django-contrib-comments==1.6.2 -django-cors-headers==1.1.0 -django-crispy-forms==1.6.0 -django-debug-toolbar==1.4 -django-haystack==2.4.1 +django-compressor==2.2 +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-haystack==2.8.1 django-heartbeat==2.0.2 django-inplaceedit==1.4.1 -django-jsonfield==0.9.19 -django-modeltranslation==0.11 -django-nose==1.4.3 -django-oauth-toolkit==0.10.0 +django-ipware==2.1.0 +django-jsonfield==1.0.1 +django-modeltranslation==0.12.2 +django-nose==1.4.5 +django-oauth-toolkit==1.1.0 django-robots==2.0 django-security==0.9.3 +django-test-without-migrations==0.6 django-timedeltafield==0.7.10 django-widget-tweaks==1.4.1 -djangorestframework==3.3.3 +djangorestframework==3.8.2 docker-py==1.7.2 dominate==2.3.1 +DoubleMetaphone==0.1 +drf-yasg==1.10.0 ecdsa==0.13 -filebrowser-safe==0.4.3 -flake8==2.5.4 +enum34==1.1.6 +filebrowser-safe==0.4.6 +flake8==3.5.0 +flex==6.13.2 funcsigs==1.0.2 -future==0.15.2 -# GDAL==2.1.3 # Installed from source +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 -grappelli-safe==0.4.2 +google.foresite-toolkit==1.3.3 +grappelli-safe==0.4.5 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==3.6.0 +lxml==3.7.3 mapnik==0.1 +MarkupSafe==1.0 matplotlib==1.5.1 -mccabe==0.4.0 -Mezzanine==4.1.0 +mccabe==0.6.1 +Mezzanine==4.3.1 mock==1.3.0 +nameparser==0.5.7 netCDF4==1.2.4 nose==1.3.7 -numpy==1.14.5 -oauthlib==1.0.3 +numpy==1.15.0 +oauthlib==2.1.0 +openapi-codec==1.3.2 OWSLib==0.10.3 pandas==0.18.0 paramiko==2.4.1 @@ -72,33 +98,50 @@ 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 +pyasn1==0.4.4 +pycodestyle==2.3.1 +pycparser==2.18 PyCRS==0.1.3 pyflakes==1.1.0 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 +python-crfsuite==0.9.6 python-dateutil==2.5.3 -e git+https://github.com/iPlantCollaborativeOpenSource/python-irodsclient.git@dcd234c166c06bdfc40fa2ef135c2511e0a4e7ac#egg=python_irodsclient pytz==2016.3 +PyYAML==3.13 rcssmin==1.0.6 rdflib==4.0.1 redis==2.10.5 -requests==2.9.1 +requests==2.13.0 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 +uritemplate==3.0.0 +validate-email==1.3 virtualenv==15.0.2 websocket-client==0.37.0 wrapt==1.10.8 From 82bf23bbc02f67d0a4e7c503ed69a2e5c338e472 Mon Sep 17 00:00:00 2001 From: Scott Black Date: Fri, 30 Nov 2018 11:47:21 -0700 Subject: [PATCH 20/30] [#3025] - upgrade packages for mezzanine and django upgrade compatibility --- requirements.txt | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/requirements.txt b/requirements.txt index 0938ad5..17207d3 100644 --- a/requirements.txt +++ b/requirements.txt @@ -9,7 +9,7 @@ bagit==1.5.4 bcrypt==3.1.4 beautifulsoup4==4.5.3 billiard==3.3.0.23 -bleach==2.0.0 +bleach==3.0.2 celery==3.1.23 cffi==1.11.5 chardet==3.0.4 @@ -51,7 +51,7 @@ DoubleMetaphone==0.1 drf-yasg==1.10.0 ecdsa==0.13 enum34==1.1.6 -filebrowser-safe==0.4.6 +filebrowser-safe==0.5.0 flake8==3.5.0 flex==6.13.2 funcsigs==1.0.2 @@ -62,7 +62,7 @@ geojson==1.3.2 geopy==1.16.0 gevent==1.1.2 google.foresite-toolkit==1.3.3 -grappelli-safe==0.4.5 +grappelli-safe==0.5.1 greenlet==0.4.10 gunicorn==19.6.0 html5lib==0.9999999 From 0c4eac2e086fc4e68c37060ec1f3c2f4b8fffd99 Mon Sep 17 00:00:00 2001 From: Scott Black Date: Thu, 24 Jan 2019 16:32:24 -0700 Subject: [PATCH 21/30] [#2810] add markdown to hs_docker_base --- requirements.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/requirements.txt b/requirements.txt index 17207d3..f1282ac 100644 --- a/requirements.txt +++ b/requirements.txt @@ -79,6 +79,7 @@ kombu==3.0.35 lazy-object-proxy==1.2.2 lxml==3.7.3 mapnik==0.1 +markdown==3.0.1 MarkupSafe==1.0 matplotlib==1.5.1 mccabe==0.6.1 From db9d7f698513d7a9a66fa06b1fdfc8ae03dc9e6f Mon Sep 17 00:00:00 2001 From: Scott Black Date: Fri, 25 Jan 2019 14:35:54 -0700 Subject: [PATCH 22/30] [#2810] - upgrade numpy version --- requirements.txt | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/requirements.txt b/requirements.txt index f1282ac..f0bc01a 100644 --- a/requirements.txt +++ b/requirements.txt @@ -79,7 +79,7 @@ kombu==3.0.35 lazy-object-proxy==1.2.2 lxml==3.7.3 mapnik==0.1 -markdown==3.0.1 +Markdown==3.0.1 MarkupSafe==1.0 matplotlib==1.5.1 mccabe==0.6.1 @@ -88,7 +88,7 @@ mock==1.3.0 nameparser==0.5.7 netCDF4==1.2.4 nose==1.3.7 -numpy==1.15.0 +numpy==1.16.0 oauthlib==2.1.0 openapi-codec==1.3.2 OWSLib==0.10.3 From 0531e5bd30ae5c34c8eeafa6f5deeb75aa316b61 Mon Sep 17 00:00:00 2001 From: Mark O'Brien Date: Wed, 6 Feb 2019 14:26:25 -0500 Subject: [PATCH 23/30] Add display times to unit tests with nose timer --- requirements.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/requirements.txt b/requirements.txt index f0bc01a..2ea0315 100644 --- a/requirements.txt +++ b/requirements.txt @@ -88,6 +88,7 @@ mock==1.3.0 nameparser==0.5.7 netCDF4==1.2.4 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 From 560ea6304ba38b3a89c040a24de2e4b6d0d3939f Mon Sep 17 00:00:00 2001 From: hyi Date: Thu, 7 Feb 2019 10:10:24 -0500 Subject: [PATCH 24/30] upgraded python irods client version and django minor version --- requirements.txt | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/requirements.txt b/requirements.txt index 2ea0315..2db488e 100644 --- a/requirements.txt +++ b/requirements.txt @@ -23,7 +23,7 @@ cryptography==2.3 cycler==0.10.0 defusedexpat==0.4 defusedxml==0.4.1 -Django==1.11.15 +Django==1.11.18 django-appconf==1.0.2 django-autocomplete-light==2.3.3 django-braces==1.9.0 @@ -117,7 +117,7 @@ pysolr==3.4.0 pysqlite==2.8.1 python-crfsuite==0.9.6 python-dateutil==2.5.3 --e git+https://github.com/iPlantCollaborativeOpenSource/python-irodsclient.git@dcd234c166c06bdfc40fa2ef135c2511e0a4e7ac#egg=python_irodsclient +python-irodsclient==0.8.1 pytz==2016.3 PyYAML==3.13 rcssmin==1.0.6 From 2cb9f2a6f405889e6e21bf9ba159a78198bf121a Mon Sep 17 00:00:00 2001 From: Mark O'Brien Date: Wed, 13 Feb 2019 16:20:42 -0500 Subject: [PATCH 25/30] Add django-pytest --- requirements.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/requirements.txt b/requirements.txt index 2db488e..c89fcdb 100644 --- a/requirements.txt +++ b/requirements.txt @@ -48,6 +48,7 @@ djangorestframework==3.8.2 docker-py==1.7.2 dominate==2.3.1 DoubleMetaphone==0.1 +django-pytest>=0.2.0, <1.0.0 drf-yasg==1.10.0 ecdsa==0.13 enum34==1.1.6 From bedfd40e5dbdff94cd376e2750d8c90f27e44b89 Mon Sep 17 00:00:00 2001 From: Mark O'Brien Date: Thu, 14 Feb 2019 17:10:35 -0500 Subject: [PATCH 26/30] Fix package name --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index c89fcdb..71e33e9 100644 --- a/requirements.txt +++ b/requirements.txt @@ -48,7 +48,6 @@ djangorestframework==3.8.2 docker-py==1.7.2 dominate==2.3.1 DoubleMetaphone==0.1 -django-pytest>=0.2.0, <1.0.0 drf-yasg==1.10.0 ecdsa==0.13 enum34==1.1.6 @@ -116,6 +115,7 @@ pyparsing==2.1.7 pyproj==1.9.5.1 pysolr==3.4.0 pysqlite==2.8.1 +pytest-django>=0.2.0, <1.0.0 python-crfsuite==0.9.6 python-dateutil==2.5.3 python-irodsclient==0.8.1 From 8505345ca6cec70d1595decd8ed15c4e886a1afa Mon Sep 17 00:00:00 2001 From: Mark O'Brien Date: Thu, 14 Feb 2019 19:05:15 -0500 Subject: [PATCH 27/30] Correct version --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 71e33e9..c02a05d 100644 --- a/requirements.txt +++ b/requirements.txt @@ -115,7 +115,7 @@ pyparsing==2.1.7 pyproj==1.9.5.1 pysolr==3.4.0 pysqlite==2.8.1 -pytest-django>=0.2.0, <1.0.0 +pytest-django>=3.4.7, 4.0.0 python-crfsuite==0.9.6 python-dateutil==2.5.3 python-irodsclient==0.8.1 From d4b0bb2092fb4bed9c6362fc1c14b1ccec3aebab Mon Sep 17 00:00:00 2001 From: Mark O'Brien Date: Thu, 14 Feb 2019 19:09:06 -0500 Subject: [PATCH 28/30] Add less than for max version --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index c02a05d..73ecbac 100644 --- a/requirements.txt +++ b/requirements.txt @@ -115,7 +115,7 @@ pyparsing==2.1.7 pyproj==1.9.5.1 pysolr==3.4.0 pysqlite==2.8.1 -pytest-django>=3.4.7, 4.0.0 +pytest-django>=3.4.7, <4.0.0 python-crfsuite==0.9.6 python-dateutil==2.5.3 python-irodsclient==0.8.1 From c3df75ca4f160586ee4a36419fd9d92497615390 Mon Sep 17 00:00:00 2001 From: engineSound Date: Mon, 6 May 2019 14:26:54 -0400 Subject: [PATCH 29/30] add timeago package/fix debian error --- Dockerfile | 2 ++ requirements.txt | 1 + 2 files changed, 3 insertions(+) diff --git a/Dockerfile b/Dockerfile index 320eedb..7dbaedc 100644 --- a/Dockerfile +++ b/Dockerfile @@ -4,6 +4,8 @@ MAINTAINER Michael J. Stealey ENV DEBIAN_FRONTEND noninteractive ENV PY_SAX_PARSER=hs_core.xmlparser +RUN printf "deb http://archive.debian.org/debian/ jessie main\ndeb-src http://archive.debian.org/debian/ jessie main\ndeb http://security.debian.org jessie/updates main\ndeb-src http://security.debian.org jessie/updates main" > /etc/apt/sources.list + RUN apt-get update && apt-get install -y \ apt-transport-https \ ca-certificates \ diff --git a/requirements.txt b/requirements.txt index 73ecbac..3ddbb7e 100644 --- a/requirements.txt +++ b/requirements.txt @@ -142,6 +142,7 @@ 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 From aaa3f7ae912c2914bf4634bc69c94f9cae1fba3c Mon Sep 17 00:00:00 2001 From: engineSound Date: Mon, 6 May 2019 18:32:20 -0400 Subject: [PATCH 30/30] remve debian sources --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 7dbaedc..9ba5d89 100644 --- a/Dockerfile +++ b/Dockerfile @@ -4,7 +4,7 @@ MAINTAINER Michael J. Stealey ENV DEBIAN_FRONTEND noninteractive ENV PY_SAX_PARSER=hs_core.xmlparser -RUN printf "deb http://archive.debian.org/debian/ jessie main\ndeb-src http://archive.debian.org/debian/ jessie main\ndeb http://security.debian.org jessie/updates main\ndeb-src http://security.debian.org jessie/updates main" > /etc/apt/sources.list +RUN printf "deb http://archive.debian.org/debian/ jessie main\ndeb http://security.debian.org jessie/updates main" > /etc/apt/sources.list RUN apt-get update && apt-get install -y \ apt-transport-https \