Merge branch 'env' into 'master'

showcase different data access options

Closes #1

See merge request !2

CHANGELOG.md

 # CHANGELOG
 
+### unreleased
+
+- Add notebooks showcasing accessing output of different models from different sources: (!2, [Aaron Spring](https://renkulab.io/gitlab/aaron.spring))
+    - S2S-Project models:
+        - from from European Weather Cloud:
+            - [`climetlab-s2s-ai-challenge`](https://github.com/ecmwf-lab/climetlab-s2s-ai-challenge/) [recommended], see [`climetlab-s2s-ai-challenge` notebooks](https://github.com/ecmwf-lab/climetlab-s2s-ai-challenge/tree/main/notebooks)
+            - `curl` & `wget`, see [wget_curl.ipynb](https://renkulab.io/gitlab/aaron.spring/s2s-ai-challenge-template/-/blob/master/notebooks/data_access/wget_curl.ipynb)
+            - `intake`, see [intake.ipynb](https://renkulab.io/gitlab/aaron.spring/s2s-ai-challenge-template/-/blob/master/notebooks/data_access/intake.ipynb)
+        - `IRIDL` including overview, see [IRIDL.ipynb](https://renkulab.io/gitlab/aaron.spring/s2s-ai-challenge-template/-/blob/master/notebooks/data_access/IRIDL.ipynb)
+    - SubX-Project models: `IRIDL` including overview, see [IRIDL.ipynb](https://renkulab.io/gitlab/aaron.spring/s2s-ai-challenge-template/-/blob/master/notebooks/data_access/IRIDL.ipynb)
+    - How to access password-protected S2S-Project output from IRIDL with xarray? see [IRIDL.ipynb](https://renkulab.io/gitlab/aaron.spring/s2s-ai-challenge-template/-/blob/master/notebooks/data_access/IRIDL.ipynb)
+- fix `netcdf4` version to `1.5.4` for `opendap` to work lazily with `xarray` (!2, [Aaron Spring](https://renkulab.io/gitlab/aaron.spring))
+
+
 ### 2021-05-31: `v0.2` *release*
 
 After this `v0.2` release, this CHANGELOG.md will describe all changes made in this template repository.
 
 - update `README` how to join competition, please `git pull` if you forked before
 - find status of your submission in `s2s-ai-competition-scoring-image` https://renkulab.io/gitlab/tasko.olevski/s2s-ai-competition-scoring-image/-/blob/master/README.md 
-- calculate `RPSS` with respect to climatology (not ECMWF anymore)
+- calculate `RPSS` with respect to climatology (not ECMWF anymore) ([Aaron Spring](https://renkulab.io/gitlab/aaron.spring))
     - update `RPSS_verification.ipynb`
-    - update `scorer`: https://renkulab.io/gitlab/tasko.olevski/s2s-ai-competition-scoring-image
+    - update `scorer`: https://renkulab.io/gitlab/tasko.olevski/s2s-ai-competition-scoring-image ([Tasko Olevski](https://renkulab.io/gitlab/tasko.olevski), [Aaron Spring](https://renkulab.io/gitlab/aaron.spring))
     - Averaged ECMWF RPSS skill value to beat at least: -0.0070
 
 
 ### 2021-05-26: `v0.1` *pre-release*
 
-- update `README` how to join competition !4
-- git lfs track zarr: `git lfs track "**/*.zarr/**"` !4
-- add notebooks: !4
+- update `README` how to join competition (!4, [Aaron Spring](https://renkulab.io/gitlab/aaron.spring))
+- git lfs track zarr: `git lfs track "**/*.zarr/**"` (!4, [Aaron Spring](https://renkulab.io/gitlab/aaron.spring))
+- add notebooks: (!4, [Aaron Spring](https://renkulab.io/gitlab/aaron.spring))
     - create renku datasets: `renku_datasets_biweekly.ipynb`
     - RPSS verification: `RPSS_verification.ipynb`
     - ML train and predict based on weatherbench: `ML_train_and_predict.ipynb`
     - mean bias reduction: `mean_bias_reduction.ipynb`
     - template for training and predictions: `ML_forecast_template.ipynb`
-- add renku dataset `s2s-ai-challenge` with files: !4
+- add renku dataset `s2s-ai-challenge` with files: (!4, [Aaron Spring](https://renkulab.io/gitlab/aaron.spring))
     - `hindcast-like-observations_2000-2019_biweekly_deterministic.zarr`
     - `forecast-like-observations_2020_biweekly_deterministic.zarr`
     - `hindcast-like-observations_2000-2019_biweekly_tercile-edges.nc`
@@ -31,10 +45,10 @@ After this `v0.2` release, this CHANGELOG.md will describe all changes made in t
     - `ecmwf_forecast-input_2020_biweekly_deterministic.zarr`
     - `ecmwf_hindcast-input_2000-2019_biweekly_deterministic.zarr`
     - `ecmwf_recalibrated_benchmark_2020_biweekly_terciled.nc`
-- add reproducibility section below in training !4
+- add reproducibility section below in training (!4, [Aaron Spring](https://renkulab.io/gitlab/aaron.spring))
 - how to deal with this dry mask? provide as renku dataset? now implicitly masked in categorized observations `obs_p`
-- justify if training takes more than a week !4
-- show RPS for all years. ToDo: take RPSS #4
+- justify if training takes more than a week (!4, [Aaron Spring](https://renkulab.io/gitlab/aaron.spring))
+- show RPS for all years. ~~ToDo: take RPSS~~ (!4, [Aaron Spring](https://renkulab.io/gitlab/aaron.spring))
 
 
 

environment.yml

@@ -5,27 +5,27 @@ dependencies:
   - xarray
   # ML
   - tensorflow
-  #- pytorch
+  - pytorch
   # viz
   - matplotlib-base
   # - cartopy
   # scoring
-  - xskillscore  # includes sklearn
+  - xskillscore>=0.0.20  # includes sklearn
   # data access
-  #- intake
-  #- fsspec
+  - intake
+  - fsspec
   - zarr
   - s3fs
-  #- intake-xarray
+  - intake-xarray
   - cfgrib
-  #- pydap
-  #- h5netcdf
-  # - netcdf4#==1.5.1  # see https://github.com/pydata/xarray/issues/4925
+  - nc-time-axis
+  - pydap
+  - h5netcdf
+  - netcdf4==1.5.3
   - pip
   - pip:
     - climetlab >= 0.7.0
     - climetlab_s2s_ai_challenge >= 0.6.3
     - configargparse # for weatherbench
-    - netcdf4 # ==1.5.1  # see https://github.com/pydata/xarray/issues/4925
-    - git+https://github.com/phausamann/sklearn-xarray.git@develop
+    - netcdf4==1.5.4
 prefix: "/opt/conda"

notebooks/data_access/EWC_catalog.yml

+plugins:
+  source:
+    - module: intake_xarray
+
+sources:
+  training-input:
+    description: climetlab name in AI/ML community naming for hindcasts as input to the ML-model in training period
+    driver: netcdf
+    parameters:
+      model:
+        description: name of the S2S model
+        type: str
+        default: ecmwf
+        allowed: [ecmwf, eccc, ncep]
+      param:
+        description: variable name
+        type: str
+        default: tp
+        allowed: [t2m, ci, gh, lsm, msl, q, rsn, sm100, sm20, sp, sst, st100, st20, t, tcc, tcw, ttr, tp, v, u]
+      date:
+        description: initialization weekly thursdays
+        type: datetime
+        default: 2020.01.02
+        min: 2020.01.02
+        max: 2020.12.31
+      version:
+        description: versioning of the data
+        type: str
+        default: 0.3.0
+      format:
+        description: data type
+        type: str
+        default: netcdf
+        allowed: [netcdf, grib]
+      ending:
+        description: data format compatible with format; netcdf -> nc, grib -> grib
+        type: str
+        default: nc
+        allowed: [nc, grib]
+    xarray_kwargs:
+        engine: h5netcdf
+    args: # add simplecache:: for caching: https://filesystem-spec.readthedocs.io/en/latest/features.html#caching-files-locally
+      urlpath: https://storage.ecmwf.europeanweather.cloud/s2s-ai-challenge/data/training-input/{{version}}/{{format}}/{{model}}-hindcast-{{param}}-{{date.strftime("%Y%m%d")}}.{{ending}}
+
+  test-input:
+    description: climetlab name in AI/ML community naming for 2020 forecasts as input to ML model in test period 2020
+    driver: netcdf
+    parameters:
+      model:
+        description: name of the S2S model
+        type: str
+        default: ecmwf
+        allowed: [ecmwf, eccc, ncep]
+      param:
+        description: variable name
+        type: str
+        default: tp
+        allowed: [t2m, ci, gh, lsm, msl, q, rsn, sm100, sm20, sp, sst, st100, st20, t, tcc, tcw, ttr, tp, v, u]
+      date:
+        description: initialization weekly thursdays
+        type: datetime
+        default: 2020.01.02
+        min: 2020.01.02
+        max: 2020.12.31
+      version:
+        description: versioning of the data
+        type: str
+        default: 0.3.0
+      format:
+        description: data type
+        type: str
+        default: netcdf
+        allowed: [netcdf, grib]
+      ending:
+        description: data format compatible with format; netcdf -> nc, grib -> grib
+        type: str
+        default: nc
+        allowed: [nc, grib]
+    xarray_kwargs:
+        engine: h5netcdf
+    args: # add simplecache:: for caching: https://filesystem-spec.readthedocs.io/en/latest/features.html#caching-files-locally
+      urlpath: https://storage.ecmwf.europeanweather.cloud/s2s-ai-challenge/data/test-input/{{version}}/{{format}}/{{model}}-forecast-{{param}}-{{date.strftime("%Y%m%d")}}.{{ending}}
+
+  training-output-reference:
+    description: climetlab name in AI/ML community naming for 2020 forecasts as output reference to compare to ML model output to in training period
+    driver: netcdf
+    parameters:
+      param:
+        description: variable name
+        type: str
+        default: tp
+        allowed: [t2m, tp]
+      date:
+        description: initialization weekly thursdays
+        type: datetime
+        default: 2020.01.02
+        min: 2020.01.02
+        max: 2020.12.31
+    xarray_kwargs:
+        engine: h5netcdf
+    args: # add simplecache:: for caching: https://filesystem-spec.readthedocs.io/en/latest/features.html#caching-files-locally
+      urlpath: https://storage.ecmwf.europeanweather.cloud/s2s-ai-challenge/data/test-output-reference/{{param}}-{{date.strftime("%Y%m%d")}}.nc
+            
+  test-output-reference:
+    description: climetlab name in AI/ML community naming for 2020 forecasts as output reference to compare to ML model output to in test period 2020
+    driver: netcdf
+    parameters:
+      param:
+        description: variable name
+        type: str
+        default: tp
+        allowed: [t2m, tp]
+      date:
+        description: initialization weekly thursdays
+        type: datetime
+        default: 2020.01.02
+        min: 2020.01.02
+        max: 2020.12.31
+    xarray_kwargs:
+        engine: h5netcdf
+    args: # add simplecache:: for caching: https://filesystem-spec.readthedocs.io/en/latest/features.html#caching-files-locally
+      urlpath: https://storage.ecmwf.europeanweather.cloud/s2s-ai-challenge/data/test-output-reference/{{param}}-{{date.strftime("%Y%m%d")}}.nc

notebooks/data_access/README.md

+# Data Access
+
+- European Weather Cloud:
+    - [`climetlab-s2s-ai-challenge`](https://github.com/ecmwf-lab/climetlab-s2s-ai-challenge)
+    - `wget`: wget_curl.ipynb
+    - `curl`: wget_curl.ipynb
+    - `mouse`: wget_curl.ipynb
+    - `intake`: intake.ipynb
+- [IRI Data Library](iridl.ldeo.columbia.edu/): IRIDL.ipynb
+    - S2S: http://iridl.ldeo.columbia.edu/SOURCES/.ECMWF/.S2S/ (restricted access explained in IRIDL.ipynb)
+    - SubX: http://iridl.ldeo.columbia.edu/SOURCES/.Models/.SubX/
+    - NMME: http://iridl.ldeo.columbia.edu/SOURCES/.Models/.NMME/
+- s2sprediction.net

notebooks/data_access/wget_curl.ipynb

+%% Cell type:markdown id: tags:
+
+# Data Access via `curl` or `wget`
+
+Data easily available via `climetlab`: https://github.com/ecmwf-lab/climetlab-s2s-ai-challenge
+
+Data holdings listed:
+
+- https://storage.ecmwf.europeanweather.cloud/s2s-ai-challenge/data/test-input/0.3.0/netcdf/index.html
+- https://storage.ecmwf.europeanweather.cloud/s2s-ai-challenge/data/training-input/0.3.0/netcdf/index.html
+- https://storage.ecmwf.europeanweather.cloud/s2s-ai-challenge/data/test-output-reference/index.html
+- https://storage.ecmwf.europeanweather.cloud/s2s-ai-challenge/data/training-output-reference/index.html
+
+Therefore, S3 data also accessible with `curl` or `wget`. Alternatively, you can click on the html links and download files by mouse click.
+
+%% Cell type:code id: tags:
+
+``` python
+import xarray as xr
+import os
+from subprocess import call
+xr.set_options(display_style='text')
+```
+
+%%%% Output: stream
+
+    /opt/conda/lib/python3.8/site-packages/xarray/backends/cfgrib_.py:27: UserWarning: Failed to load cfgrib - most likely there is a problem accessing the ecCodes library. Try `import cfgrib` to get the full error message
+      warnings.warn(
+
+%%%% Output: execute_result
+
+    <xarray.core.options.set_options at 0x7f5170570520>
+
+%% Cell type:code id: tags:
+
+``` python
+# version of the EWC data
+version = '0.3.0'
+```
+
+%% Cell type:markdown id: tags:
+
+# `hindcast-input`
+
+on-the-fly hindcasts corresponding to the 2020 forecasts
+
+%% Cell type:code id: tags:
+
+``` python
+parameter = 't2m'
+date = '20200102'
+model = 'ecmwf'
+```
+
+%% Cell type:code id: tags:
+
+``` python
+url = f'https://storage.ecmwf.europeanweather.cloud/s2s-ai-challenge/data/training-input/{version}/netcdf/{model}-hindcast-{parameter}-{date}.nc'
+os.system(f'wget {url}')
+
+assert os.path.exists(f'{model}-hindcast-{parameter}-{date}.nc')
+```
+
+%% Cell type:markdown id: tags:
+
+# `forecast-input`
+
+2020
+
+%% Cell type:code id: tags:
+
+``` python
+url = f'https://storage.ecmwf.europeanweather.cloud/s2s-ai-challenge/data/test-input/{version}/netcdf/{model}-forecast-{parameter}-{date}.nc'
+os.system(f'wget {url}')
+
+assert os.path.exists(f'{model}-forecast-{parameter}-{date}.nc')
+```
+
+%% Cell type:markdown id: tags:
+
+# `hindcast-like-observations`
+
+CPC observations formatted like training period hindcasts
+
+%% Cell type:code id: tags:
+
+``` python
+url = f'https://storage.ecmwf.europeanweather.cloud/s2s-ai-challenge/data/training-output-reference/{parameter}-{date}.nc'
+os.system(f'wget {url}')
+
+assert os.path.exists(f'{parameter}-{date}.nc')
+```
+
+%% Cell type:markdown id: tags:
+
+# `forecast-like-observations`
+
+CPC observations formatted like test period 2020 forecasts
+
+%% Cell type:code id: tags:
+
+``` python
+url = f'https://storage.ecmwf.europeanweather.cloud/s2s-ai-challenge/data/test-output-reference/{parameter}-{date}.nc'
+os.system(f'wget {url}')
+
+assert os.path.exists(f'{parameter}-{date}.nc')
+```
+
+%% Cell type:code id: tags:
+
+``` python
+```