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Link Checker Report

Summary

Status Count
๐Ÿ” Total 852
โœ… Successful 792
โณ Timeouts 0
๐Ÿ”€ Redirected 0
๐Ÿ‘ป Excluded 59
โ“ Unknown 0
๐Ÿšซ Errors 1

Errors per input

Errors in docs/bookmarks/research.md

  • [ERR] https://vcell.org/ | Failed: Network error: error:0A000086:SSL routines:tls_post_process_server_certificate:certificate verify failed:ssl/statem/statem_clnt.c:2092: (unable to get local issuer certificate)
    Full Github Actions output

Get the ODE Function from ODE system 

using ModelingToolkit
using DifferentialEquations
using Plots

# Independent (time) and dependent (state) variables (x and RHS)
@variables t x(t) RHS(t)

# Setting parameters in the modeling
@parameters ฯ„

# Differential operator w.r.t. time
D = Differential(t)

# Equations in MTK use the tilde character (`~`) as equality.
# Every MTK system requires a name. The `@named` macro simply ensures that the symbolic name matches the name in the REPL.

@named fol_separate = ODESystem([
    RHS  ~ (1 - x)/ฯ„,
    D(x) ~ RHS
])

model = structural_simplify(fol_separate)

f = ODEFunction(model, jac=true)

f.jac

f([0.0], [1.0], 0.0)


u0 = [x => 0.0]
tspan = (0.0, 10.0)
param = [ฯ„ => 3.0]
prob = ODEProblem(model, u0, tspan, param)
sol = solve(prob)

Dependency Dashboard

This issue lists Renovate updates and detected dependencies. Read the Dependency Dashboard docs to learn more.

This repository currently has no open or pending branches.

Detected dependencies

github-actions
.github/workflows/linkcheck.yml
  • actions/checkout v4@692973e3d937129bcbf40652eb9f2f61becf3332
  • actions/cache v4@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9
  • lycheeverse/lychee-action v1.10.0@2b973e86fc7b1f6b36a93795fe2c9c6ae1118621
  • peter-evans/create-issue-from-file v5@24452a72d85239eacf1468b0f1982a9f3fec4c94
.github/workflows/pages.yml
  • actions/checkout v4@692973e3d937129bcbf40652eb9f2f61becf3332
  • actions/setup-python v5@82c7e631bb3cdc910f68e0081d67478d79c6982d
  • actions/cache v4@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9
  • actions/configure-pages v5@983d7736d9b0ae728b81ab479565c72886d7745b
  • actions/upload-pages-artifact v3@56afc609e74202658d3ffba0e8f6dda462b719fa
  • actions/deploy-pages v4@d6db90164ac5ed86f2b6aed7e0febac5b3c0c03e
pip_requirements
requirements.txt
  • mkdocs-material ==9.5.27
  • mkdocs-git-revision-date-localized-plugin ==1.2.6
  • mkdocs-ezlinked-plugin ==0.3.3
  • mkdocs-callouts ==1.13.2
  • Check this box to trigger a request for Renovate to run again on this repository

Link Checker Report

Summary

Status Count
๐Ÿ” Total 852
โœ… Successful 792
โณ Timeouts 0
๐Ÿ”€ Redirected 0
๐Ÿ‘ป Excluded 59
โ“ Unknown 0
๐Ÿšซ Errors 1

Errors per input

Errors in docs/bookmarks/research.md

  • [ERR] https://vcell.org/ | Failed: Network error: error:0A000086:SSL routines:tls_post_process_server_certificate:certificate verify failed:ssl/statem/statem_clnt.c:2092: (unable to get local issuer certificate)
    Full Github Actions output

Link Checker Report

Summary

Status Count
๐Ÿ” Total 851
โœ… Successful 791
โณ Timeouts 0
๐Ÿ”€ Redirected 0
๐Ÿ‘ป Excluded 59
โ“ Unknown 0
๐Ÿšซ Errors 1

Errors per input

Errors in docs/school/research-bookmarks.md

  • [ERR] https://vcell.org/ | Failed: Network error: error:0A000086:SSL routines:tls_post_process_server_certificate:certificate verify failed:ssl/statem/statem_clnt.c:2092: (unable to get local issuer certificate)
    Full Github Actions output

Link Checker Report

Summary

Status Count
๐Ÿ” Total 852
โœ… Successful 792
โณ Timeouts 0
๐Ÿ”€ Redirected 0
๐Ÿ‘ป Excluded 59
โ“ Unknown 0
๐Ÿšซ Errors 1

Errors per input

Errors in docs/school/research-bookmarks.md

  • [ERR] https://vcell.org/ | Failed: Network error: error:0A000086:SSL routines:tls_post_process_server_certificate:certificate verify failed:ssl/statem/statem_clnt.c:2092: (unable to get local issuer certificate)
    Full Github Actions output

Link Checker Report

Summary

Status Count
๐Ÿ” Total 854
โœ… Successful 787
โณ Timeouts 0
๐Ÿ”€ Redirected 0
๐Ÿ‘ป Excluded 60
โ“ Unknown 0
๐Ÿšซ Errors 7

Errors per input

Errors in docs/blog/posts/2024-04-03-stellaris-console-commands.md

Errors in docs/index.md

rsync to NAS folder 

rsync -avh --delete /source/folder/ suername@ip::dest/folder/

In the NAS, the rsync service and rsync users should be enabled.

Link Checker Report

Summary

Status Count
๐Ÿ” Total 849
โœ… Successful 789
โณ Timeouts 0
๐Ÿ”€ Redirected 0
๐Ÿ‘ป Excluded 59
โ“ Unknown 0
๐Ÿšซ Errors 1

Errors per input

Errors in docs/code/python/index.md

Status check for a multi-stage workflow

I can use the ${{ needs.<job>.result }} variable without setting output flags.

  # CI conclusion for GitHub status check
  # Adaped from https://brunoscheufler.com/blog/2022-04-09-the-required-github-status-check-that-wasnt
  CI:
    needs: render
    if: always()
    runs-on: ubuntu-latest
    steps:
      - run: |
          if [[ ${{ needs.render.result }} == "success" ]]; then
            echo "Tests passed"
            exit 0
          else
            echo "Tests failed"
            exit 1
          fi

jill.sh to install Julia

Using jill.sh to install Julia somehow avoids precompile cache invalidation in GitHub actions.

Change parameters from an ODE system 

"""Change parameter(s) from an ODESystem and returns a parameter vector."""
function change_params(sys, ps...)
    ModelingToolkit.varmap_to_vars(Dict(ps), parameters(sys); defaults = sys.defaults)
end

Docker config

  • Move the Docker data directory to a bigger partition
  • Set up a pull-through cache (by Google) to avoid hitting the docker image access limit by Dockerhub

Edit /etc/docker/daemon.json, add the following entries

{
  "data-root": "/home/docker",
  "registry-mirrors": ["https://mirror.gcr.io"]
}

Then run

sudo service docker restart

Link Checker Report

Summary

Status Count
๐Ÿ” Total 854
โœ… Successful 787
โณ Timeouts 0
๐Ÿ”€ Redirected 0
๐Ÿ‘ป Excluded 60
โ“ Unknown 0
๐Ÿšซ Errors 7

Errors per input

Errors in docs/blog/posts/2024-04-03-stellaris-console-commands.md

Errors in docs/index.md

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