Add optional Assimulo integration CI

[bernalde]

Summary

• Add a non-blocking Assimulo integration job to the CI workflow.
• Use conda-forge through setup-miniconda and environment.yml to install the solver stack.
• Install PharmaPy with --no-deps inside the conda environment so pip does not try to rebuild Assimulo.
• Add TESTING.md with the local core and Assimulo test commands.

Traceability

Closes #6.
Built on the merged #93 / #9 packaging and dependency-bounds work.
Refs #1, #2, CryPTSys#106, and CryPTSys#107.

Verification

• actionlint .github/workflows/ci.yml
• pytest --collect-only -q
• pytest tests/ -m "not assimulo" -q -rs
• pytest tests/ -m assimulo -q -rs (local environment without Assimulo: 6 selected, 6 skipped)
• python -m build --sdist --no-isolation
• GitHub Actions CI pull_request run 28606044218: Core tests and Assimulo integration tests passed.

Actions

GitHub Actions now runs both the core job and the informational Assimulo job. The Assimulo job remains marked continue-on-error: true until the conda solver stack is proven stable across follow-up runs.

[bernalde]

Review for b7f53d9152acb6c6ea0f05b4e50842a90497fdca.

Blocking issues:

• Blocking: Update the new Assimulo CI lane off deprecated action/runtime inputs before merge. See the inline comment on .github/workflows/ci.yml for the exact GitHub annotations and replacement inputs.

I would not merge this until the blocking issues above are addressed.

Nonblocking issues:

• None.

Questions:

• None.

Tests run and outcomes:

• Local PR-head: pytest --collect-only -q -> 12 tests collected.
• Local PR-head: pytest tests/ -m 'not assimulo' -q -rs -> 6 passed, 6 deselected.
• Local PR-head: pytest tests/ -m assimulo -q -rs -> 6 skipped, 6 deselected because Assimulo is not installed locally.
• Local PR-head: python -m build --sdist --no-isolation -> passed; the sdist included TESTING.md and environment.yml.
• GitHub PR-head checks for b7f53d9: CI pull_request run 28589354850 and push run 28589351179 both completed successfully for Core tests and Assimulo integration tests; the pull-request run has the CI annotations described in the inline finding.

Merge-readiness:

• The PR is still a draft, so this COMMENT review does not satisfy branch-protection approval. GitHub reports mergeStateStatus as CLEAN; branch protection for master returned Branch not protected; reviewDecision is empty. This account is the PR author, so it cannot provide formal approval or requested-changes review if one is needed after the draft and blocking CI issue are cleared.

[bernalde]

Blocking: This new CI lane is still using deprecated action/runtime inputs. The current PR-head run for b7f53d9 annotates actions/checkout@v4 and conda-incubator/setup-miniconda@v3 as Node.js 20 actions being forced onto Node.js 24, and it also warns that auto-activate-base is deprecated and that defaults may be added implicitly. Since #6 asks for a stable conda-forge Assimulo lane, please update this job to the current workflow conventions (actions/checkout@v5, conda-incubator/setup-miniconda@v4, the replacement activation input) and remove implicit defaults, for example with conda-remove-defaults: true, before merging. Rebasing on current master will also bring the core job back to checkout@v5/setup-python@v6 for PR-head checks.

[bernalde]

Addressed in a2f1bbc: the workflow now uses checkout@v5, setup-python@v6, setup-miniconda@v4, auto-activate, and conda-remove-defaults: true, while preserving the current master permissions/concurrency hardening. The current pull_request CI run 28606044218 passed without the prior deprecation annotations.

[bernalde]

Addressed the review feedback on the CI action/runtime deprecations.

Commits pushed:

• a2f1bbc Update CI action versions

Main changes:

• Updated the workflow hardening to match current master: push only on master, read-only contents permission, and concurrency cancellation.
• Moved CI actions to current majors: actions/checkout@v5, actions/setup-python@v6, and conda-incubator/setup-miniconda@v4.
• Replaced deprecated auto-activate-base with auto-activate and set conda-remove-defaults: true.
• Updated the PR body now that Relax dependency bounds and enable Dependabot #93 / Relax dependency pins and enable Dependabot #9 has landed, and marked the PR ready for review.

Tests and checks:

• actionlint .github/workflows/ci.yml passed.
• pytest --collect-only -q passed: 12 tests collected.
• pytest tests/ -m "not assimulo" -q -rs passed: 6 passed, 6 deselected.
• pytest tests/ -m assimulo -q -rs passed locally as expected without Assimulo: 6 skipped, 6 deselected.
• python -m build --sdist --no-isolation passed.
• GitHub Actions pull_request run 28606044218 passed on a2f1bbc: Core tests and Assimulo integration tests both succeeded.

Comments intentionally not addressed:

• None.

Remaining:

• The PR is no longer draft and GitHub reports mergeStateStatus as CLEAN. This account authored the PR, so a separate eligible maintainer approval may still be needed if the repository requires formal approval.