feat: integrated simularium file generation in combine-api

[AlexPatrie]

What does this PR do?:

• integrates biosimulators-simularium as a dependency in apps/combine-api.
• configures combine-api/pyproject.toml accordingly for versioning.
• introduces a "standard" format for representing the output of spatial simulations with VTK (see the biosimulators-simularium tooling for more info)
• implements .simularium and .vtk file generation for Smoldyn (spatial) simulation runs via biosimulators_simularium.execute() within the body of combine_api.handlers.run.handler().
• includes aforementioned file generation in handler output for archive bundling and the creation of output.zip for all simulation runs that include Smoldyn.
• introduces appropriate testing logic for the simularium/vtk integration.
• performs minor CSS/style maintenance and adjustment for components throughout repo (fixes nav-button flicker, for example.)

How did you test the changes?:

• introduced a new unittest method for smoldyn urls only.
• pytest
• CI/CD

[nx-cloud]

☁️ Nx Cloud Report

CI is running/has finished running commands for commit f9b1ee0. As they complete they will appear below. Click to see the status, the terminal output, and the build insights.

📂 See all runs for this CI Pipeline Execution

---

✅ Successfully ran 9 targets

• nx affected --target test --parallel=false
• nx docker combine-api
• nx docker dispatch-service
• nx docker api
• nx docker mail-service
• nx docker simulators-api
• nx docker simdata-api
• nx affected --target build --prod --parallel=false
• nx affected --target lint

---

Sent with 💌 from NxCloud.

[jcschaff]

fixed my comments, looks good.

[jcschaff]

do you have to merge master in first? it seems to be using the master workflow scripts, and not finding simdata-api??

[gitguardian]

⚠️ GitGuardian has uncovered 2 secrets following the scan of your pull request.

Please consider investigating the findings and remediating the incidents. Failure to do so may lead to compromising the associated services or software components.

🔎 Detected hardcoded secrets in your pull request

GitGuardian id	GitGuardian status	Secret	Commit	Filename
9207574	Triggered	Generic CLI Secret	18ea618	apps/dispatch-service/src/app/services/sbatch/expected_sbatch.ts	View secret
9207574	Triggered	Generic CLI Secret	18ea618	apps/dispatch-service/src/app/services/sbatch/expected_sbatch.ts	View secret

🛠 Guidelines to remediate hardcoded secrets

1. Understand the implications of revoking this secret by investigating where it is used in your code.
2. Replace and store your secrets safely. Learn here the best practices.
3. Revoke and rotate these secrets.
4. If possible, rewrite git history. Rewriting git history is not a trivial act. You might completely break other contributing developers' workflow and you risk accidentally deleting legitimate data.

To avoid such incidents in the future consider

• following these best practices for managing and storing secrets including API keys and other credentials
• install secret detection on pre-commit to catch secret before it leaves your machine and ease remediation.

---

<sup>🦉 GitGuardian detects secrets in your source code to help developers and security teams secure the modern development process. You are seeing this because you or someone else with access to this repository has authorized GitGuardian to scan your pull request.

Our GitHub checks need improvements? Share your feedbacks!</sup>

[sonarcloud]

Quality Gate passed

The SonarCloud Quality Gate passed, but some issues were introduced.

6 New issues
0 Security Hotspots
No data about Coverage
0.0% Duplication on New Code

See analysis details on SonarCloud

[biosimulations-daemon]

🎉 This PR is included in version 9.56.0 🎉

The release is available on GitHub release

Your semantic-release bot 📦🚀