• Remove multi os actions
• Upgrade to 20.04
• Remove PR trigger

Using readthedocs.

Description

The analogues from the CA step of climDown are a 2 dimensional vector in R. It should be saved to an Rdata file.

Requested Action

Complex .rda file output in wps_CA.py

Alternatives

• (Current implementation) write 2 lists to text files
• Save to .rds file

Description

Some process inputs can accept the FORMATS.DODS format, but there are no test instances for that input type.

Requested Action

Add online tests with OPeNDAP from the TREDDS data server

Alternatives

None

When installing the bird using the Makefile and running make, the following incompatible dependency error occurs and should be fixed by upgrading the nbconvert version.

ERROR: jupyter-server 1.17.0 has requirement nbconvert>=6.4.4, but you'll have nbconvert 5.6.1 which is incompatible.

Description

ClimDown has several options that should be available to set with chickadee.

Requested Action

Add all the ClimDown options the same way end_date is implemented.

Alternatives

None

Description

We would like ClimDown's ci.netcdf.wrapper turned into a wps process.

Requested Action

Since we are translating between R and python we need to use rpy2. Other than that wrinkle this should follow the standard we use for other birds.

Alternatives

None.

My username will be in the place where pacificclimate should be in several places. Also the docs will still refer to conda in some places which should be removed.

Description

The container is spitting out a bunch of logs we are not interested in that are coming from sqlalchemy.

To Reproduce

Steps to reproduce the behavior:

1. docker-compose up
2. watch logs

Expected Behaviour

Only logging from the actual app should be there.

Description

Wrap rerank.netcdf.wrapper into pywps process.

Requested Action

Use rpy2 to translate between R and python.

Alternatives

None.

The imports have built up and there may be a cleaner way of importing functions. For example what we have now:

from chickadee.io import (
    gcm_file,
    obs_file,
    varname,
    out_file,
    num_cores,
    general_options_input,
    ca_options_input,
    qdm_options_input,
)

Versus what we could do instead:

import chickadee.utils as utils
import chickadee.io as cio
...
        self.handler_inputs = [
            cio.gcm_file,
            cio.obs_file,
            cio.varname,
            cio.out_file,
            cio.num_cores,
            cio.log_level,
        ]

Description

The recent change to the Dockerfile has made the rebuild process extremely inefficient.

Requested Action

Use cachable RUN commands.

Description

Each of the github action workflows are failing.

To Reproduce

Steps to reproduce the behavior:

1. Run workflow
2. See errors

Expected Behaviour

No errors.

Several steps that are attached to notebook processing and virtual environments.

Description

We're currently using wps_tools.output_handling when asobj=True is simpler and doesn't require extra imports

Requested Action

1. Use output.get(asobj=True)
2. Remove wps_tools.output_handling

Alternatives

Continue using wps_tools.output_handling

Description

We want to take advantage of the docker tools we have to make development easier. That means re configuring the docker-compose and rewriting some of the dockerfile.

Requested Action

Update dockerfile and docker-compose.

Alternatives

None.

Description

Translate ClimDown's ca.netcdf.wrapper into a wps process.

Requested Action

Use rpy2 to translate between R and python.

Alternatives

None.

Replace other forms of CI/CD.

Is your feature request related to a problem? Please describe.
The multi-stage build is a strategy to reduce image sizes and build time. Apply this strategy in the Dockerfile

Describe the solution you'd like
Separate a single stage into two stages, build and execution, by having multiple FROM statements.

Describe alternatives you've considered
None

Title.

Description

black . --check fails in actions but not locally

To Reproduce

Steps to reproduce the behavior:

1. Run black . locally
2. Push to origin
3. Run python-ci workflow
4. See check failure

Expected Behaviour

Running black . --check locally and in actions should show the same results

Description

Some of the methods the processes use can be shared.

Requested Action

Refactor the code to use methods from a common utils module

Description

A vulnerability has been detected in the dockerfile.

To Reproduce

Steps to reproduce the behavior:

1. Run anchore scan

Expected Behaviour

No vulnerabilities should be detected

Description

R objects can be stored in rda or rds files the current implementation of wps_rerank.py only accepts rda files. Adding an rds option would be more flexible for the user.

Requested Action

Add an input option with the .rds extension and handle rds or rda input in the _handler method.

Alternatives

Just accept only rdata or only RDS

Description

A gunicorn timout occurs for the bccaq wrapper process on some machines but not others. Ideally, a more secure implementation would have consistent behaviour.

To Reproduce

Steps to reproduce the behavior:

• Run the wps_bccaq_demo online with make test-notebooks-online

Expected Behaviour

No timeout error on all machines.

Description

Version 0.4.0 of wps-tools has shared chickadee and quail functions which should be implemented in chickadee

Requested Action

Use wps-tools 0.4.0 in chickadee where possible

Alternatives

None

Description

Translate ClimDown's qdm.netcdf.wrapper using rpy2.

Requested Action

Follow the standards from other birds in the project.

Alternatives

None.

Description

User errors always say "Sorry, process failed. Please check server error log." we can add some more specific error messages.

Requested Action

Add processError() to processes

Alternatives

None

Description

The main script in climdown is the bccaq.netcdf.wrapper which is a downscaling method. We want to turn this R script into a process.

Requested Action

Since we are translating between R and python we need to use rpy2. Other than that wrinkle this should follow the standard we use for other birds.

Alternatives

We may have to consider using different R translator packages if rpy2 does not provide everything we need.

Description

wps-tools 0.3.0 is released. Use the newly added functionalities.

Requested Action

• Replace chickadee's collect_args function to the wps-tools version
• Replace chickadee's common_status_percentages dictionary to the wps-tools version
• Use local_path and url_path functions for constructing test parameters

Alternatives

None

Modules were reorganized in wps-tools 1.0.1 and output handling tools were added. Imports in chickadee should reflect these changes and the output_handling methods can be added to the demos.

Description

analogues_object in wps_rerank.py should be ComplexInput with

supported_formats=[Format("application/rda", extension=".rda", encoding="base64")]

Requested Action

The process should be able to read files in the user's local directory

Alternatives

None