vz update conda yml

[vickimzhang]

Update conda yml file to include specific versions that work for Linux and windows.

Summary by CodeRabbit

• Chores

  • Package version bumped to 2.1.2.
  • Defaults channel added to environment sources.
  • Environment dependencies trimmed to three core packages.
  • .gitignore updated and internal metadata cleared.

• Removed

  • Example spatial packages, manifests, scripts, datasheets and layouts deleted.

• Bug Fixes

  • Raster input loading adjusted to use the consolidated datasheet access method.

[coderabbitai]

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ℹ️ Recent review info

⚙️ Run configuration

Configuration used: Organization UI

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Run ID: 1be0cbc6-f94c-4980-a5ab-e0b53846f4f6

📥 Commits

Reviewing files that changed from the base of the PR and between 5bc3b66 and 63f7d19.

📒 Files selected for processing (1)

• src/package.xml

🚧 Files skipped from review as they are similar to previous changes (1)

• src/package.xml

---

Walkthrough

Updated root package version and transformer attributes; simplified conda environment and added defaults channel. Removed two spatial example packages (manifests and R scripts). Cleared src/.metadata, updated .gitignore, and adjusted raster loading in src/model.R.

Changes

Cohort / File(s)	Summary
Conda environment src/helloworldR.yml	Added defaults channel; drastically reduced dependencies to three packages: r-base=4.1.3, r-rsyncrosim=2.1.7, r-terra=1.5_21 (removed previous extensive list).
Root package manifest src/package.xml	Bumped package version to 2.1.2; added isStochasticTime="True" to both transformers (firstModel, secondModel); increased condaEnvVersion from 2 to 3 for both transformers while keeping condaEnv="helloworldR.yml".
Removed Spatial1 helloworldSpatial1/package.xml, helloworldSpatial1/model.R	Deleted package manifest and R transformation script that defined RunControl/Input/Intermediate datasheets, transformer, and layouts.
Removed Spatial2 helloworldSpatial2/package.xml, helloworldSpatial2/model2.R	Deleted package manifest and R transformation script that defined OutputDatasheet, transformer, and layouts.
Repository metadata & ignore src/.metadata, .gitignore	Cleared XML content from src/.metadata. Updated .gitignore to add *.metadata and *.ssimpkg and retained *.vs/.
Model loader change src/model.R	Replaced raster loader call using datasheetSpatRaster(...) with datasheet(..., name = "helloworldSpatial_InputDatasheet", column = "InterceptRasterFile") to load raster input.

🚥 Pre-merge checks | ✅ 2 | ❌ 1

❌ Failed checks (1 inconclusive)

Check name	Status	Explanation	Resolution
Title check	❓ Inconclusive	The title 'vz update conda yml' is partially related to the changeset; it describes the conda environment file update in src/helloworldR.yml, but fails to capture the main objective of removing deprecated functions and updating transformer configurations.	Consider a more descriptive title that encompasses the primary changes, such as 'Remove spatial packages and update conda environment configuration' or 'Refactor to remove deprecated spatial transformers and update conda yml'.

✅ Passed checks (2 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.

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✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch vz-update-conda-yml

---

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[katieb1]

Would you also be able to remove the following folders from this repo:

The example library used to be the template library, but now we store these on S3.

[katieb1]

Remove datasheetSpatRaster() function from model scripts in anticipation of removing function from rsyncrosim

[coderabbitai]

Actionable comments posted: 1

🤖 Fix all issues with AI agents

In `@src/package.xml`:
- Around line 29-30: The two <transformer> entries use the same
condaEnv="helloworldR.yml" but different condaEnvVersion values (one is 3 and
the other 2); update the condaEnvVersion attribute on the transformer named
"firstModel" (and the other transformer) so both specify the same version (e.g.,
change the one set to "2" to "3"), or add a clear comment/documentation adjacent
to the transformer entries explaining why different versions are intentionally
required; ensure you update the condaEnvVersion attribute values for the
relevant <transformer> elements to keep them consistent or document the reason
for divergence.

[coderabbitai]

Actionable comments posted: 1

🤖 Fix all issues with AI agents

In `@src/model.R`:
- Around line 25-27: The call to datasheet() is invalid: datasheet() does not
accept column nor datasheet parameters and returns a data.frame (not a
SpatRaster), so replace this with either a call to
datasheetSpatRaster(myScenario, name = "helloworldSpatial_InputDatasheet",
column = "InterceptRasterFile") to directly obtain a SpatRaster, or call
datasheet(myScenario, name = "helloworldSpatial_InputDatasheet") to get the file
path column and then pass that path into terra::rast() before calling
app(rasterMap, ...). Ensure you use name = "helloworldSpatial_InputDatasheet"
(not datasheet=) and reference datasheetSpatRaster(), datasheet(),
terra::rast(), and app() when making the fix.