Merge #177

177: Resolve scikit-learn conflict r=tsj5 a=tsj5

# PULL REQUEST

## Purpose and Content
This PR fixes the problems encountered by `@szy21` in #175. The purpose of that PR was to update the Manifest for the examples (Project/Manifest for CES itself is unchanged). This PR uses `@szy21` 's updates and in addition pins the versions of scipy and scikit-learn installed through Conda.jl to avoid an incompatibility in libstdc++ (documented in #176).

## Benefits and Risks

**Benefits**: Resolves #176. `@szy21's` original PR resolves #174.

**Risks**: Introduces maintenance requirement of having to remember we've pinned the versions of some dependencies going forward; since these are python dependencies this information isn't in Project.toml, so we might forget about this in the future when we want/need to update scikit-learn. This is a very minor risk, as the functionality from sk-learn that we currently use is mature.

## Linked Issues
- Closes #174, #176 

## PR Checklist
- [X] This PR has a corresponding issue OR is linked to an SDI.
- [X] I have followed CliMA's codebase [contribution](https://clima.github.io/ClimateMachine.jl/latest/Contributing/) and [style](https://clima.github.io/ClimateMachine.jl/latest/DevDocs/CodeStyle/) guidelines OR N/A.
- [X] I have followed CliMA's [documentation policy](https://github.com/CliMA/policies/wiki/Documentation-Policy).
- [X] I have checked all issues and PRs and I certify that this PR does not duplicate an open PR.
- [X] I linted my code on my local machine prior to submission: N/A.
- [X] Unit tests: N/A.
- [X] Code used in an integration test.
- [X] All tests ran successfully on my local machine.
- [X] All classes, modules, and function contain docstrings: N/A.
- [X] Documentation has been added/updated: N/A.


Co-authored-by: szy21 <[email protected]>

.buildkite/pipeline.yml

@@ -9,7 +9,8 @@ steps:
     command:
       - "echo $$JULIA_DEPOT_PATH"
       - "julia --project -e 'using Pkg; Pkg.instantiate(;verbose=true)'"
-      - "julia --project -e 'using Conda; Conda.add(\"scikit-learn\")'"
+      - "julia --project -e 'using Conda; Conda.add(\"scipy=1.8.1\")'"
+      - "julia --project -e 'using Conda; Conda.add(\"scikit-learn=1.1.1\")'"
       - "julia --project -e 'using Conda; Conda.add(\"matplotlib\")'"
     env:
       PYTHON: ""

.github/workflows/Docs.yml

@@ -43,7 +43,8 @@ jobs:
           PYTHON: ""
         run: |
           julia --color=yes --project -e 'using Pkg; Pkg.instantiate()'
-          julia --color=yes --project -e 'using Conda; Conda.add("scikit-learn")'
+          julia --project -e 'using Conda; Conda.add("scipy=1.8.1")'
+          julia --color=yes --project -e 'using Conda; Conda.add("scikit-learn=1.1.1")'
           julia --color=yes --project=docs/ -e 'using Pkg; Pkg.instantiate()'
           julia --color=yes --project=docs/ -e 'using Pkg; Pkg.precompile()'
       - name: Build and deploy

.github/workflows/Tests.yml

@@ -40,7 +40,8 @@ jobs:
       env:
         PYTHON: ""
       run: |
-        julia --project -e 'using Conda; Conda.add("scikit-learn")'
+        julia --project -e 'using Conda; Conda.add("scipy=1.8.1")'
+        julia --project -e 'using Conda; Conda.add("scikit-learn=1.1.1")'
 
     - name: Run Unit Tests
       env:
@@ -92,7 +93,8 @@ jobs:
       env:
         PYTHON: ""
       run: |
-        julia --project -e 'using Conda; Conda.add("scikit-learn")'
+        julia --project -e 'using Conda; Conda.add("scipy=1.8.1")'
+        julia --project -e 'using Conda; Conda.add("scikit-learn=1.1.1")'
 
     - name: Run Unit Tests
       env:
@@ -131,7 +133,8 @@ jobs:
       env:
         PYTHON: ""
       run: |
-        julia --project -e 'using Conda; Conda.add(\"scikit-learn\")'
+        julia --project -e 'using Conda; Conda.add("scipy=1.8.1")'
+        julia --project -e 'using Conda; Conda.add(\"scikit-learn=1.1.1\")'
 
     - name: Run Unit Tests
       env:

deps/build.jl

@@ -7,4 +7,5 @@ if lowercase(get(ENV, "CI", "false")) == "true"
     Pkg.build("PyCall")
 end
 
-Conda.add("scikit-learn")
+Conda.add("scipy=1.8.1")
+Conda.add("scikit-learn=1.1.1")

docs/src/installation_instructions.md

@@ -23,11 +23,11 @@ it is easiest to set the project to use its own
 ```
 
 
-The `scikit-learn` package then has to be installed if using a Julia project-specific 
-Conda environment:
+The `scikit-learn` package (along with `scipy`) then has to be installed if using a Julia project-specific Conda environment:
 
 ```
-> PYTHON="" julia --project -e 'using Conda; Conda.add("scikit-learn")'
+> PYTHON="" julia --project -e 'using Conda; Conda.add("scipy=1.8.1")'
+> PYTHON="" julia --project -e 'using Conda; Conda.add("scikit-learn=1.1.1")'
 
 ```