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* pkg * ProgressLogging * shorter istirm func * dont use fractions * no fractions * test code * Rodas5P wins * pkg upd * fix unit error in ISO module * Dca * typo * test code * pkg * CI * simplify * comment * fix bugs * fix * test code * fix ca flux * record KmRyR * test code * upd * wip * pkg * test code * Pkg * using DifferentialEquations * pkg * PDE and jup unstable * pkg * wip * pkg * compartment vglumes * cell geometry * test code * JULIA_CONDAPKG_BACKEND * minimal deps * fix
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -13,17 +13,17 @@ concurrency: | |
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| env: | ||
| NBCONVERT_JOBS: '2' | ||
| LITERATE_PROC: '4' | ||
| LITERATE_PROC: '2' | ||
| JULIA_NUM_THREADS: '2' | ||
| ALLOWERRORS: 'false' | ||
| CACHE_NUM: '1' | ||
| JULIA_CONDAPKG_BACKEND: 'Null' | ||
| JULIA_CI: 'true' | ||
| NBCACHE: '.cache' | ||
| UV_SYSTEM_PYTHON: 1 | ||
|
|
||
| jobs: | ||
| CI: | ||
| runs-on: self-hosted | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - name: Checkout repository | ||
| uses: actions/checkout@v4 | ||
|
|
@@ -32,8 +32,10 @@ jobs: | |
| id: setup-python | ||
| with: | ||
| python-version: '3.x' | ||
| - name: Install uv | ||
| run: curl -LsSf https://astral.sh/uv/install.sh | sh | ||
| - name: Install Python dependencies | ||
| run: pip install -r requirements.txt | ||
| run: uv pip install -r requirements.txt | ||
| - name: Read Julia version | ||
| uses: SebRollen/[email protected] | ||
| id: read_toml | ||
|
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@@ -44,7 +46,7 @@ jobs: | |
| id: hash | ||
| run: | | ||
| echo "value=${{ hashFiles('Project.toml', 'Manifest.toml', 'src/**') }}" >> "$GITHUB_OUTPUT" | ||
| echo "ver=${{ runner.os }}-julia-${{ env.CACHE_NUM }}-${{ steps.read_toml.outputs.value }}" >> "$GITHUB_OUTPUT" | ||
| echo "ver=${{ runner.os }}-julia-${{ steps.read_toml.outputs.value }}" >> "$GITHUB_OUTPUT" | ||
| - name: Cache executed notebooks | ||
| uses: actions/cache@v4 | ||
| id: cache-nb | ||
|
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@@ -59,7 +61,7 @@ jobs: | |
| version: ${{ steps.read_toml.outputs.value }} | ||
| - name: Restore Julia packages | ||
| uses: actions/cache/restore@v4 | ||
| if: ${{ runner.environment == 'github-hosted' }} | ||
| if: ${{ runner.environment == 'github-hosted'}} | ||
| id: cache-julia | ||
| with: | ||
| path: ~/.julia | ||
|
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@@ -70,7 +72,7 @@ jobs: | |
| if: ${{ runner.environment == 'self-hosted' || steps.cache-julia.outputs.cache-hit != 'true' }} | ||
| shell: julia --color=yes {0} | ||
| run: | | ||
| using Pkg, Dates | ||
| using Pkg | ||
| Pkg.add(["IJulia", "Literate", "PrettyTables", "JSON"]) | ||
| Pkg.activate(".") | ||
| Pkg.instantiate() | ||
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@@ -83,7 +85,7 @@ jobs: | |
| key: ${{ steps.cache-julia.outputs.cache-primary-key }} | ||
| - name: Run notebooks | ||
| if: ${{ steps.cache-nb.outputs.cache-hit != 'true' }} | ||
| run: julia --color=yes -p ${{ env.LITERATE_PROC }} --heap-size-hint=3G run.jl | ||
| run: julia --project=@. --color=yes -p ${{ env.LITERATE_PROC }} run.jl | ||
| - name: Copy back built notebooks | ||
| run: cp --verbose -rf ${{ env.NBCACHE }}/docs/* docs/ | ||
| - name: Build website | ||
|
|
||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,29 @@ | ||
| name: Clear main caches | ||
| on: | ||
| workflow_dispatch: | ||
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||
| jobs: | ||
| cleanup: | ||
| permissions: | ||
| actions: write | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - name: Cleanup | ||
| run: | | ||
| gh extension install actions/gh-actions-cache | ||
| echo "Fetching list of cache key" | ||
| cacheKeysForPR=$(gh actions-cache list -R $REPO -B $BRANCH -L 100 | cut -f 1 ) | ||
| ## Setting this to not fail the workflow while deleting cache keys. | ||
| set +e | ||
| echo "Deleting caches..." | ||
| for cacheKey in $cacheKeysForPR | ||
| do | ||
| gh actions-cache delete $cacheKey -R $REPO -B $BRANCH --confirm | ||
| done | ||
| echo "Done" | ||
| env: | ||
| GH_TOKEN: ${{ secrets.GITHUB_TOKEN }} | ||
| REPO: ${{ github.repository }} | ||
| BRANCH: ${{ github.event.repository.default_branch }} |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,11 +1,12 @@ | ||
| name = "CaMKIIModel" | ||
| uuid = "268d5184-1524-48b5-bbe3-a3af95dac460" | ||
| authors = ["Wen-Wei Tseng <[email protected]>"] | ||
| version = "0.2.0" | ||
| version = "0.3.0" | ||
|
|
||
| [deps] | ||
| DiffEqCallbacks = "459566f4-90b8-5000-8ac3-15dfb0a30def" | ||
| ModelingToolkit = "961ee093-0014-501f-94e3-6117800e7a78" | ||
| NaNMath = "77ba4419-2d1f-58cd-9bb1-8ffee604a2e3" | ||
| OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed" | ||
| Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" | ||
| ProgressLogging = "33c8b6b6-d38a-422a-b730-caa89a2f386c" |
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