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 reduced to three core packages for a much smaller spec.
  • .gitignore updated and internal metadata cleared.

• Removed

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

• Bug Fixes

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

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[coderabbitai]

Walkthrough

Updated package version and transformer attributes; conda environment simplified and defaults channel added. Removed two spatial example packages (manifests and R scripts), cleared src/.metadata, and updated .gitignore.

Changes

Cohort / File(s)	Change Summary
Conda environment src/helloworldR.yml	Added defaults channel; reduced dependencies to three packages: r-base=4.1.3, r-rsyncrosim=2.1.7, r-terra=1.5_21 (removed prior extensive deps).
Root package manifest src/package.xml	Bumped package version to 2.1.2; added isStochasticTime="True" to transformers; updated firstModel condaEnvVersion from 2 to 3 (secondModel remains 2).
Removed Spatial1 implementation helloworldSpatial1/model.R, helloworldSpatial1/package.xml	Deleted R transformation script and package manifest that defined RunControl, InputDatasheet, IntermediateDatasheet, transformer, and layouts.
Removed Spatial2 implementation helloworldSpatial2/model2.R, helloworldSpatial2/package.xml	Deleted R transformation script and package manifest 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 (retained *.vs/).

🚥 Pre-merge checks | ✅ 2 | ❌ 1

❌ Failed checks (1 warning)

Check name	Status	Explanation	Resolution
Title check	⚠️ Warning	The title 'vz update conda yml' refers to updating the conda YAML file, which is partially related to the changeset. However, the PR encompasses much more extensive changes including removal of entire packages, version bumps, and deletion of spatial model files, making the title incomplete and not representative of the main scope.	Revise the title to better reflect the full scope of changes, such as 'Remove spatial model packages and update conda dependencies' or similar, which captures the primary changes beyond just the conda YAML update.

✅ 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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[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]

⚠️ Potential issue | 🟠 Major

🧩 Analysis chain

🏁 Script executed:

cat -n src/package.xml | head -50

Repository: ApexRMS/helloworldSpatial

Length of output: 2958

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🏁 Script executed:

fd -type f \( -name "README*" -o -name "*.md" -o -name "CHANGELOG*" \) | head -20

Repository: ApexRMS/helloworldSpatial

Length of output: 239

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🏁 Script executed:

fd -type f \( -name "README*" -o -name "*.md" -o -name "CHANGELOG*" \)

Repository: ApexRMS/helloworldSpatial

Length of output: 239

---

🏁 Script executed:

find . -maxdepth 2 -iname "readme*" -o -iname "changelog*" -o -iname "*.md" | head -20

Repository: ApexRMS/helloworldSpatial

Length of output: 80

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🏁 Script executed:

cat -n README.md

Repository: ApexRMS/helloworldSpatial

Length of output: 666

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🏁 Script executed:

rg "condaEnvVersion" --no-heading

Repository: ApexRMS/helloworldSpatial

Length of output: 198

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🏁 Script executed:

find . -name "helloworldR.yml" -o -name "helloworldR*"

Repository: ApexRMS/helloworldSpatial

Length of output: 90

---

🏁 Script executed:

cat -n src/helloworldR.yml

Repository: ApexRMS/helloworldSpatial

Length of output: 254

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Align condaEnvVersion between transformers (or document why they differ).

Both transformers point to the same helloworldR.yml but specify different condaEnvVersion values (3 vs 2). If only one environment version exists, the second transformer may fail to resolve its environment. Align both to version 3, or document why the split is necessary.

🤖 Prompt for AI Agents

In `@src/package.xml` around lines 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.