Merge branch 'develop' of git.geomar.de:python/conda_environments into develop

.gitlab-ci.yml

-image: continuumio/miniconda3:latest
+image: continuumio/miniconda3:4.3.27
 
 variables:
   DOCKER_DRIVER: overlay
@@ -9,4 +9,4 @@ test:
     - source activate root
     - target_dir=${CONDA_PREFIX}
     - shopt -s extglob
-    - ./update_anaconda.sh ${target_dir} envs/!(monitoring_gallery).yml
+    - ./update_anaconda.sh ${target_dir}  envs/!(*@(monitoring_gallery|py2_parcels)).yml

README.md

@@ -42,6 +42,17 @@ source deactivate
 
 (Nesh: `smomw122`; HLRN: `shkifmwr`; Geomar: `wrath`)
 
+## A note on stability
+
+The environments are updated frequently (but irregularly).  This comes with a
+catch:  Updating an environment potentially introduces problems that are not
+immediately visible when testing the updated installation.  To at least
+partially make up for this, the state of the environments _before_ an update is
+copied to `<willis_home_dir>/TM/software/miniconda3_previous`.  So if you
+suddenly run into problems in an environment that used to work.  Switch to
+`miniconda3_previous` and check if this helps.  If you find problems, please
+[file an issue here][issues].
+
 ## Using the environments on nb.geomar.de
 
 There is an installer which allows for adding kernels using these environments

_env_templates/monitoring.yml

@@ -20,6 +20,7 @@ dependencies:
   - numpy
   - pandas
   - seaborn
+  - widgetsnbextension=3.1.0
+  - xarray
   - pip:
-     - "git+https://github.com/willirath/xarray.git@6f5e30f3a2f8ca907f0fd91bcd571e7d98027896#egg=xarray_wrath_allow_ploting_datetime"
      - "git+{git_protocol}git.geomar.de/open-source/cartopy_offlinedata.git@master"

_env_templates/py2_parcels.yml

+name: py2_parcels
+channels:
+  - {conda-forge}
+  - {anaconda}
+dependencies:
+  - python=2.7
+  - basemap
+  - basemap-data-hires
+  - jupyter
+  - widgetsnbextension=3.1.0
+  - parcels

_env_templates/py2_pyngl.yml

-name: py2_pyngl
-channels:
-  - {conda-forge}
-  - {willirath}
-  - {anaconda}
-dependencies:
-  - python=2.7
-  - anaconda-client
-  - aospy
-  - basemap
-  - cartopy
-  - cf_units
-  - cmocean
-  - dask
-  - eofs
-  - fortran-magic
-  - git
-  - git-lfs
-  - haversine
-  - hdf5
-  - ipython
-  - jupyter
-  - line_profiler
-  - matplotlib
-  - mtspec
-  - nco
-  - netCDF4=1.2.8
-  - numpy
-  - pandas
-  - pyngl
-  - pynio
-  - pytables
-  - seaborn
-  - seawater
-  - xarray
-  - pip:
-      - pymatlab
-      - "git+{git_protocol}git.geomar.de/open-source/cartopy_offlinedata.git@master"

_env_templates/py2_std.yml

@@ -18,6 +18,7 @@ dependencies:
   - fortran-magic
   - git
   - git-lfs
+  - gsw
   - haversine
   - hdf5
   - ipython
@@ -26,6 +27,7 @@ dependencies:
   - jupyter
   - line_profiler
   - matplotlib
+  - memory_profiler
   - mtspec
   - nco
   - netCDF4=1.2.8
@@ -37,6 +39,7 @@ dependencies:
   - seawater
   - spyder
   - xarray
+  - widgetsnbextension=3.1.0
   - pip:
       - pymatlab
       - "git+{git_protocol}git.geomar.de/open-source/cartopy_offlinedata.git@master"

_env_templates/py3_std.yml

@@ -18,6 +18,7 @@ dependencies:
   - fortran-magic
   - git
   - git-lfs
+  - gsw
   - haversine
   - hdf5
   - ipython
@@ -26,6 +27,7 @@ dependencies:
   - jupyter
   - line_profiler
   - matplotlib
+  - memory_profiler
   - mtspec
   - nco
   - netCDF4=1.2.8
@@ -37,5 +39,6 @@ dependencies:
   - seawater
   - spyder
   - xarray
+  - widgetsnbextension=3.1.0
   - pip:
      - "git+{git_protocol}git.geomar.de/open-source/cartopy_offlinedata.git@master"

_env_templates/tm_deploy.yml

@@ -5,5 +5,6 @@ channels:
 dependencies:
   - python=3
   - cartopy
+  - conda-mirror
   - git
   - git-lfs

_envs_hlrn/monitoring.yml

@@ -20,6 +20,7 @@ dependencies:
   - numpy
   - pandas
   - seaborn
+  - widgetsnbextension=3.1.0
+  - xarray
   - pip:
-     - "git+https://github.com/willirath/xarray.git@6f5e30f3a2f8ca907f0fd91bcd571e7d98027896#egg=xarray_wrath_allow_ploting_datetime"
      - "git+ssh://git@git.geomar.de/open-source/cartopy_offlinedata.git@master"

_envs_hlrn/py2_parcels.yml

+name: py2_parcels
+channels:
+  - file://home/b/shkifmwr/TM/data/conda_mirror/conda-forge_local_mirror/
+  - file://home/b/shkifmwr/TM/data/conda_mirror/anaconda_local_mirror/
+dependencies:
+  - python=2.7
+  - basemap
+  - basemap-data-hires
+  - jupyter
+  - widgetsnbextension=3.1.0
+  - parcels

_envs_hlrn/py2_pyngl.yml

-name: py2_pyngl
-channels:
-  - file://home/b/shkifmwr/TM/data/conda_mirror/conda-forge_local_mirror/
-  - file://home/b/shkifmwr/TM/data/conda_mirror/willirath_local_mirror/
-  - file://home/b/shkifmwr/TM/data/conda_mirror/anaconda_local_mirror/
-dependencies:
-  - python=2.7
-  - anaconda-client
-  - aospy
-  - basemap
-  - cartopy
-  - cf_units
-  - cmocean
-  - dask
-  - eofs
-  - fortran-magic
-  - git
-  - git-lfs
-  - haversine
-  - hdf5
-  - ipython
-  - jupyter
-  - line_profiler
-  - matplotlib
-  - mtspec
-  - nco
-  - netCDF4=1.2.8
-  - numpy
-  - pandas
-  - pyngl
-  - pynio
-  - pytables
-  - seaborn
-  - seawater
-  - xarray
-  - pip:
-      - pymatlab
-      - "git+ssh://git@git.geomar.de/open-source/cartopy_offlinedata.git@master"

_envs_hlrn/py2_std.yml

@@ -18,6 +18,7 @@ dependencies:
   - fortran-magic
   - git
   - git-lfs
+  - gsw
   - haversine
   - hdf5
   - ipython
@@ -26,6 +27,7 @@ dependencies:
   - jupyter
   - line_profiler
   - matplotlib
+  - memory_profiler
   - mtspec
   - nco
   - netCDF4=1.2.8
@@ -37,6 +39,7 @@ dependencies:
   - seawater
   - spyder
   - xarray
+  - widgetsnbextension=3.1.0
   - pip:
       - pymatlab
       - "git+ssh://git@git.geomar.de/open-source/cartopy_offlinedata.git@master"

_envs_hlrn/py3_std.yml

@@ -18,6 +18,7 @@ dependencies:
   - fortran-magic
   - git
   - git-lfs
+  - gsw
   - haversine
   - hdf5
   - ipython
@@ -26,6 +27,7 @@ dependencies:
   - jupyter
   - line_profiler
   - matplotlib
+  - memory_profiler
   - mtspec
   - nco
   - netCDF4=1.2.8
@@ -37,5 +39,6 @@ dependencies:
   - seawater
   - spyder
   - xarray
+  - widgetsnbextension=3.1.0
   - pip:
      - "git+ssh://git@git.geomar.de/open-source/cartopy_offlinedata.git@master"

_envs_hlrn/tm_deploy.yml

@@ -5,5 +5,6 @@ channels:
 dependencies:
   - python=3
   - cartopy
+  - conda-mirror
   - git
   - git-lfs

_envs_nesh/monitoring.yml

@@ -20,6 +20,7 @@ dependencies:
   - numpy
   - pandas
   - seaborn
+  - widgetsnbextension=3.1.0
+  - xarray
   - pip:
-     - "git+https://github.com/willirath/xarray.git@6f5e30f3a2f8ca907f0fd91bcd571e7d98027896#egg=xarray_wrath_allow_ploting_datetime"
      - "git+ssh://git@git.geomar.de/open-source/cartopy_offlinedata.git@master"

_envs_nesh/py2_parcels.yml

+name: py2_parcels
+channels:
+  - https://conda.anaconda.org/conda-forge
+  - https://repo.continuum.io/pkgs/free
+dependencies:
+  - python=2.7
+  - basemap
+  - basemap-data-hires
+  - jupyter
+  - widgetsnbextension=3.1.0
+  - parcels

_envs_nesh/py2_pyngl.yml

-name: py2_pyngl
-channels:
-  - https://conda.anaconda.org/conda-forge
-  - https://conda.anaconda.org/willirath
-  - https://repo.continuum.io/pkgs/free
-dependencies:
-  - python=2.7
-  - anaconda-client
-  - aospy
-  - basemap
-  - cartopy
-  - cf_units
-  - cmocean
-  - dask
-  - eofs
-  - fortran-magic
-  - git
-  - git-lfs
-  - haversine
-  - hdf5
-  - ipython
-  - jupyter
-  - line_profiler
-  - matplotlib
-  - mtspec
-  - nco
-  - netCDF4=1.2.8
-  - numpy
-  - pandas
-  - pyngl
-  - pynio
-  - pytables
-  - seaborn
-  - seawater
-  - xarray
-  - pip:
-      - pymatlab
-      - "git+ssh://git@git.geomar.de/open-source/cartopy_offlinedata.git@master"

_envs_nesh/py2_std.yml

@@ -18,6 +18,7 @@ dependencies:
   - fortran-magic
   - git
   - git-lfs
+  - gsw
   - haversine
   - hdf5
   - ipython
@@ -26,6 +27,7 @@ dependencies:
   - jupyter
   - line_profiler
   - matplotlib
+  - memory_profiler
   - mtspec
   - nco
   - netCDF4=1.2.8
@@ -37,6 +39,7 @@ dependencies:
   - seawater
   - spyder
   - xarray
+  - widgetsnbextension=3.1.0
   - pip:
       - pymatlab
       - "git+ssh://git@git.geomar.de/open-source/cartopy_offlinedata.git@master"

_envs_nesh/py3_std.yml

@@ -18,6 +18,7 @@ dependencies:
   - fortran-magic
   - git
   - git-lfs
+  - gsw
   - haversine
   - hdf5
   - ipython
@@ -26,6 +27,7 @@ dependencies:
   - jupyter
   - line_profiler
   - matplotlib
+  - memory_profiler
   - mtspec
   - nco
   - netCDF4=1.2.8
@@ -37,5 +39,6 @@ dependencies:
   - seawater
   - spyder
   - xarray
+  - widgetsnbextension=3.1.0
   - pip:
      - "git+ssh://git@git.geomar.de/open-source/cartopy_offlinedata.git@master"

_envs_nesh/tm_deploy.yml

@@ -5,5 +5,6 @@ channels:
 dependencies:
   - python=3
   - cartopy
+  - conda-mirror
   - git
   - git-lfs

_envs_vulcanus/monitoring.yml

@@ -20,6 +20,7 @@ dependencies:
   - numpy
   - pandas
   - seaborn
+  - widgetsnbextension=3.1.0
+  - xarray
   - pip:
-     - "git+https://github.com/willirath/xarray.git@6f5e30f3a2f8ca907f0fd91bcd571e7d98027896#egg=xarray_wrath_allow_ploting_datetime"
      - "git+https://git.geomar.de/open-source/cartopy_offlinedata.git@master"

_envs_vulcanus/py2_parcels.yml

+name: py2_parcels
+channels:
+  - file://media/wrath/wrath_003/conda_mirror/conda-forge_local_mirror/
+  - file://media/wrath/wrath_003/conda_mirror/anaconda_local_mirror/
+dependencies:
+  - python=2.7
+  - basemap
+  - basemap-data-hires
+  - jupyter
+  - widgetsnbextension=3.1.0
+  - parcels

_envs_vulcanus/py2_pyngl.yml

-name: py2_pyngl
-channels:
-  - file://media/wrath/wrath_003/conda_mirror/conda-forge_local_mirror/
-  - file://media/wrath/wrath_003/conda_mirror/willirath_local_mirror/
-  - file://media/wrath/wrath_003/conda_mirror/anaconda_local_mirror/
-dependencies:
-  - python=2.7
-  - anaconda-client
-  - aospy
-  - basemap
-  - cartopy
-  - cf_units
-  - cmocean
-  - dask
-  - eofs
-  - fortran-magic
-  - git
-  - git-lfs
-  - haversine
-  - hdf5
-  - ipython
-  - jupyter
-  - line_profiler
-  - matplotlib
-  - mtspec
-  - nco
-  - netCDF4=1.2.8
-  - numpy
-  - pandas
-  - pyngl
-  - pynio
-  - pytables
-  - seaborn
-  - seawater
-  - xarray
-  - pip:
-      - pymatlab
-      - "git+https://git.geomar.de/open-source/cartopy_offlinedata.git@master"

_envs_vulcanus/py2_std.yml

@@ -18,6 +18,7 @@ dependencies:
   - fortran-magic
   - git
   - git-lfs
+  - gsw
   - haversine
   - hdf5
   - ipython
@@ -26,6 +27,7 @@ dependencies:
   - jupyter
   - line_profiler
   - matplotlib
+  - memory_profiler
   - mtspec
   - nco
   - netCDF4=1.2.8
@@ -37,6 +39,7 @@ dependencies:
   - seawater
   - spyder
   - xarray
+  - widgetsnbextension=3.1.0
   - pip:
       - pymatlab
       - "git+https://git.geomar.de/open-source/cartopy_offlinedata.git@master"

_envs_vulcanus/py3_std.yml

@@ -18,6 +18,7 @@ dependencies:
   - fortran-magic
   - git
   - git-lfs
+  - gsw
   - haversine
   - hdf5
   - ipython
@@ -26,6 +27,7 @@ dependencies:
   - jupyter
   - line_profiler
   - matplotlib
+  - memory_profiler
   - mtspec
   - nco
   - netCDF4=1.2.8
@@ -37,5 +39,6 @@ dependencies:
   - seawater
   - spyder
   - xarray
+  - widgetsnbextension=3.1.0
   - pip:
      - "git+https://git.geomar.de/open-source/cartopy_offlinedata.git@master"

_envs_vulcanus/tm_deploy.yml

@@ -5,5 +5,6 @@ channels:
 dependencies:
   - python=3
   - cartopy
+  - conda-mirror
   - git
   - git-lfs

envs/monitoring.yml

@@ -20,6 +20,7 @@ dependencies:
   - numpy
   - pandas
   - seaborn
+  - widgetsnbextension=3.1.0
+  - xarray
   - pip:
-     - "git+https://github.com/willirath/xarray.git@6f5e30f3a2f8ca907f0fd91bcd571e7d98027896#egg=xarray_wrath_allow_ploting_datetime"
      - "git+https://git.geomar.de/open-source/cartopy_offlinedata.git@master"

envs/py2_parcels.yml

+name: py2_parcels
+channels:
+  - https://conda.anaconda.org/conda-forge
+  - https://repo.continuum.io/pkgs/free
+dependencies:
+  - python=2.7
+  - basemap
+  - basemap-data-hires
+  - jupyter
+  - widgetsnbextension=3.1.0
+  - parcels

envs/py2_pyngl.yml

-name: py2_pyngl
-channels:
-  - https://conda.anaconda.org/conda-forge
-  - https://conda.anaconda.org/willirath
-  - https://repo.continuum.io/pkgs/free
-dependencies:
-  - python=2.7
-  - anaconda-client
-  - aospy
-  - basemap
-  - cartopy
-  - cf_units
-  - cmocean
-  - dask
-  - eofs
-  - fortran-magic
-  - git
-  - git-lfs
-  - haversine
-  - hdf5
-  - ipython
-  - jupyter
-  - line_profiler
-  - matplotlib
-  - mtspec
-  - nco
-  - netCDF4=1.2.8
-  - numpy
-  - pandas
-  - pyngl
-  - pynio
-  - pytables
-  - seaborn
-  - seawater
-  - xarray
-  - pip:
-      - pymatlab
-      - "git+https://git.geomar.de/open-source/cartopy_offlinedata.git@master"

envs/py2_std.yml

@@ -18,6 +18,7 @@ dependencies:
   - fortran-magic
   - git
   - git-lfs
+  - gsw
   - haversine
   - hdf5
   - ipython
@@ -26,6 +27,7 @@ dependencies:
   - jupyter
   - line_profiler
   - matplotlib
+  - memory_profiler
   - mtspec
   - nco
   - netCDF4=1.2.8
@@ -37,6 +39,7 @@ dependencies:
   - seawater
   - spyder
   - xarray
+  - widgetsnbextension=3.1.0
   - pip:
       - pymatlab
       - "git+https://git.geomar.de/open-source/cartopy_offlinedata.git@master"

envs/py3_std.yml

@@ -18,6 +18,7 @@ dependencies:
   - fortran-magic
   - git
   - git-lfs
+  - gsw
   - haversine
   - hdf5
   - ipython
@@ -26,6 +27,7 @@ dependencies:
   - jupyter
   - line_profiler
   - matplotlib
+  - memory_profiler
   - mtspec
   - nco
   - netCDF4=1.2.8
@@ -37,5 +39,6 @@ dependencies:
   - seawater
   - spyder
   - xarray
+  - widgetsnbextension=3.1.0
   - pip:
      - "git+https://git.geomar.de/open-source/cartopy_offlinedata.git@master"

envs/tm_deploy.yml

@@ -5,5 +5,6 @@ channels:
 dependencies:
   - python=3
   - cartopy
+  - conda-mirror
   - git
   - git-lfs