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Add plotnine to terra-jupyter-python #126

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mbookman opened this issue May 27, 2020 · 1 comment
Closed

Add plotnine to terra-jupyter-python #126

mbookman opened this issue May 27, 2020 · 1 comment

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@mbookman
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plotnine is an implementation of a grammar of graphics in Python, it is based on ggplot2.

Having this available in terra-jupyter-python would make it such that the code for R and Python notebooks in Terra can look similar and decrease the cognitive load on researchers when going back-and-forth between the two languages.

Note that the AoU Dockerfile adds plotnine.
deflaux added a commit to deflaux/terra-docker that referenced this issue Feb 3, 2021
@deflaux
Use recent versions of Python packages in terra-jupyter-python.
5545b25 
Changes include:
* removed all version pins
* rearranged packages alphabetically into one pip install command
* removed explicit installation of redundant packages that will be installed as a side effect by higher level packages
  * google-api-core
  * matplotlib
  * numpy
  * pandas
  * protobuf
* added package plotnine per DataBiosphere#126
* added package tensorflow_cpu to get rid of the warnings about GPUs being unavailable for Terra Cloud Runtimes
* --use_rest_api flag is now needed for %%bigquery magic
  * As of release [google-cloud-bigquery 1.26.0 (2020-07-20)](https://github.com/googleapis/python-bigquery/blob/master/CHANGELOG.md#1260-2020-07-20) the BigQuery Python client uses the BigQuery Storage client by default.
  * This currently causes an error on Terra Cloud Runtimes `the user does not have 'bigquery.readsessions.create' permission for '<Terra billing project id>'`.
  * To work-around we both uninstall the dependency so that flag `--use_rest_api` can be used with `%%bigquery` to use the older, slower mechanism for data transfer.
deflaux added a commit to deflaux/terra-docker that referenced this issue Mar 1, 2021
@deflaux
Remove Python package version pins.
14e05c7 
Also:
* added package `plotnine` per DataBiosphere#126
* replaced package `tensorflow` with `tensorflow_cpu` to get rid of the warnings about GPUs being unavailable for Terra Cloud Runtimes
* added package `google-resumable-media` as an explicit dependency to ensure a more recent version of it is used, pandas-gbq depends on it for table uploads
* `--use_rest_api` flag is now needed for `%%bigquery magic`
  * As of release [google-cloud-bigquery 1.26.0 (2020-07-20)](https://github.com/googleapis/python-bigquery/blob/master/CHANGELOG.md#1260-2020-07-20) the BigQuery Python client uses the BigQuery Storage client by default.
  * This currently causes an error on Terra Cloud Runtimes `the user does not have 'bigquery.readsessions.create' permission for '<Terra billing project id>'`.
  * To work-around this must uninstall the dependency `google-cloud-bigquery-storage` so that flag `--use_rest_api` can be used with `%%bigquery` to use the older, slower mechanism for data transfer.
deflaux added a commit to deflaux/terra-docker that referenced this issue Mar 5, 2021
@deflaux
Remove Python package version pins.
47c1820 
Also:
* added package `plotnine` per DataBiosphere#126
* replaced package `tensorflow` with `tensorflow_cpu` to get rid of the warnings about GPUs being unavailable for Terra Cloud Runtimes
* added package `google-resumable-media` as an explicit dependency to ensure a more recent version of it is used, pandas-gbq depends on it for table uploads
* `--use_rest_api` flag is now needed for `%%bigquery magic`
  * As of release [google-cloud-bigquery 1.26.0 (2020-07-20)](https://github.com/googleapis/python-bigquery/blob/master/CHANGELOG.md#1260-2020-07-20) the BigQuery Python client uses the BigQuery Storage client by default.
  * This currently causes an error on Terra Cloud Runtimes `the user does not have 'bigquery.readsessions.create' permission for '<Terra billing project id>'`.
  * To work-around this must uninstall the dependency `google-cloud-bigquery-storage` so that flag `--use_rest_api` can be used with `%%bigquery` to use the older, slower mechanism for data transfer.
deflaux added a commit to deflaux/terra-docker that referenced this issue Mar 5, 2021
@deflaux
Update all Python package versions by unpinning them.
8999f74 
Also:
* added package `plotnine` per DataBiosphere#126
* replaced package `tensorflow` with `tensorflow_cpu` to get rid of the warnings about GPUs being unavailable for Terra Cloud Runtimes
* added package `google-resumable-media` as an explicit dependency to ensure a more recent version of it is used, pandas-gbq depends on it for table uploads
* `--use_rest_api` flag is now needed for `%%bigquery magic`
  * As of release [google-cloud-bigquery 1.26.0 (2020-07-20)](https://github.com/googleapis/python-bigquery/blob/master/CHANGELOG.md#1260-2020-07-20) the BigQuery Python client uses the BigQuery Storage client by default.
  * This currently causes an error on Terra Cloud Runtimes `the user does not have 'bigquery.readsessions.create' permission for '<Terra billing project id>'`.
  * To work-around this we uninstall the dependency `google-cloud-bigquery-storage` so that flag `--use_rest_api` can be used with `%%bigquery` to use the older, slower mechanism for data transfer.
* add nbstripout to terra-jupyter-aou and enable it globally
* improve test coverage by enabling tests that were intentionally commented out for the prior image
@deflaux deflaux mentioned this issue Mar 5, 2021
Closed
@deflaux deflaux mentioned this issue Mar 18, 2021
Merged
deflaux added a commit that referenced this issue Mar 23, 2021
@deflaux
Update all Python package versions by unpinning them. (#207)
2834279 
Update all Python package versions by unpinning them.

Also:
* added package `plotnine` per #126
* replaced package `tensorflow` with `tensorflow_cpu` to get rid of the warnings about GPUs being unavailable for Terra Cloud Runtimes
* added package `google-resumable-media` as an explicit dependency to ensure a more recent version of it is used, pandas-gbq depends on it for table uploads
* `--use_rest_api` flag is now needed for `%%bigquery magic`
  * As of release [google-cloud-bigquery 1.26.0 (2020-07-20)](https://github.com/googleapis/python-bigquery/blob/master/CHANGELOG.md#1260-2020-07-20) the BigQuery Python client uses the BigQuery Storage client by default.
  * This currently causes an error on Terra Cloud Runtimes `the user does not have 'bigquery.readsessions.create' permission for '<Terra billing project id>'`.
  * To work-around this we uninstall the dependency `google-cloud-bigquery-storage` so that flag `--use_rest_api` can be used with `%%bigquery` to use the older, slower mechanism for data transfer.
* add `nbstripout` to `terra-jupyter-aou` and enable it globally
* improve test coverage by
  * enabling tests that were intentionally commented out for the prior image
  * adding tests for `gcloud`, `gsutil`, and `bq` command line tools
@Qi77Qi
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Qi77Qi commented Apr 22, 2021

think @deflaux 's PR has already addressed this...

@Qi77Qi Qi77Qi closed this as completed Apr 22, 2021
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@mbookman @Qi77Qi