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alongdalongd
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Dockerfile Maintain RMG-Py 3.7 (#792)
Dockerfile updated to be multistage build in order to reduce size. Also, specified the checkout of RMG-Py in order to keep it at 3.7. Updated entrywrapper/aliases and the environment.yml
2 parents b38742a + 35d891b commit 80621b7

9 files changed

Lines changed: 403 additions & 306 deletions

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‎.github/workflows/cont_int.yml‎

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@@ -11,6 +11,8 @@ on:
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schedule:
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- cron: '0 0 * * *'
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env:
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RMG_PY_COMMIT: 55464c54d1fa61b531e865682df598d33718597d
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jobs:
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build:
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- name: Cache RMG-Py
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id: cache-rmg-py
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uses: actions/cache@v3
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env:
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CACHE_NUMBER: 2
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with:
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path: RMG-Py
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key: ${{ runner.os }}-rmg-main
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key: ${{ runner.os }}-rmg-${{ env.RMG_PY_COMMIT }}
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restore-keys: |
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${{ runner.os }}-rmg-
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- name: Checkout RMG-py
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# - name: Checkout RMG-Py at specific commit
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# if: steps.cache-rmg-py.outputs.cache-hit != 'true'
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# uses: actions/checkout@v3
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# with:
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# repository: ReactionMechanismGenerator/RMG-Py
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# path: RMG-Py
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# ref: ${{ env.RMG_PY_COMMIT }}^1
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# fetch-depth: 0
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- name: Clone & checkout RMG-Py at specific SHA
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if: steps.cache-rmg-py.outputs.cache-hit != 'true'
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uses: actions/checkout@v3
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with:
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repository: ReactionMechanismGenerator/RMG-Py
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path: RMG-Py
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ref: main
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fetch-depth: 1
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run: |
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git clone --filter=blob:none --no-checkout https://github.com/ReactionMechanismGenerator/RMG-Py.git RMG-Py
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cd RMG-Py
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git fetch --no-tags --prune origin ${RMG_PY_COMMIT}
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git checkout --detach ${RMG_PY_COMMIT}
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- name: Cache RMG-database
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id: cache-rmg-db
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key: ${{ runner.os }}-rmgdb-main
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restore-keys: |
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${{ runner.os }}-rmgdb-
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- name: Checkout RMG-database
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if: steps.cache-rmg-db.outputs.cache-hit != 'true'
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uses: actions/checkout@v3
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with:
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repository: ReactionMechanismGenerator/RMG-database
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path: RMG-database
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ref: main
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fetch-depth: 1
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fetch-depth: 0
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- name: Cache AutoTST
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id: cache-autotst
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${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('environment.yml') }}
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- name: Set up miniconda
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uses: conda-incubator/setup-miniconda@v3
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uses: conda-incubator/setup-miniconda@v3.2.0
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with:
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auto-update-conda: true
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environment-file: environment.yml

‎.github/workflows/update-cache.yml‎

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@@ -2,128 +2,136 @@ name: Update cache
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on:
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schedule:
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- cron: "0 0 */7 * *"
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- cron: '0 0 */7 * *'
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push:
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branches:
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- main
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branches: [ main ]
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jobs:
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update_cache:
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runs-on: ubuntu-latest
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defaults:
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run:
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shell: bash -el {0}
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shell: bash -el {0}
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steps:
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# ────────── source repo ──────────
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- name: Checkout ARC
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uses: actions/checkout@v3
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uses: actions/checkout@v4
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# ────────── RMG‑Py ──────────
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- name: Cache RMG
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id: cache-rmg
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uses: actions/cache@v2
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uses: actions/cache@v4
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with:
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path: RMG-Py
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key: ${{ runner.os }}-rmg-main
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- name: Checkout RMG
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uses: actions/checkout@v3
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path: RMG-Py
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key: ${{ runner.os }}-rmg-main
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restore-keys: |
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${{ runner.os }}-rmg-
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- name: Checkout RMG-Py
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if: steps.cache-rmg.outputs.cache-hit != 'true'
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uses: actions/checkout@v4
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with:
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repository: ReactionMechanismGenerator/RMG-Py
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path: RMG-Py
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ref: main
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fetch-depth: 1
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repository: ReactionMechanismGenerator/RMG-Py
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path: RMG-Py
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ref: 55464c54d1fa61b531e865682df598d33718597d
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fetch-depth: 1
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# ────────── RMG‑database ──────────
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- name: Cache RMG-database
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id: cache-rmg-db
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uses: actions/cache@v2
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uses: actions/cache@v4
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with:
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path: RMG-database
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key: ${{ runner.os }}-rmgdb-main
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path: RMG-database
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key: ${{ runner.os }}-rmgdb-main
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restore-keys: |
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${{ runner.os }}-rmgdb-
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- name: Checkout RMG-database
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uses: actions/checkout@v3
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if: steps.cache-rmg-db.outputs.cache-hit != 'true'
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uses: actions/checkout@v4
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with:
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repository: ReactionMechanismGenerator/RMG-database
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path: RMG-database
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ref: main
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fetch-depth: 1
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repository: ReactionMechanismGenerator/RMG-database
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path: RMG-database
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ref: main
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fetch-depth: 1
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# ────────── AutoTST ──────────
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- name: Cache AutoTST
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id: cache-autotst
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uses: actions/cache@v2
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uses: actions/cache@v4
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with:
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path: AutoTST
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key: ${{ runner.os }}-autotst-main
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restore-keys: |
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${{ runner.os }}-autotst-
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path: AutoTST
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key: ${{ runner.os }}-autotst-main
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restore-keys: |
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${{ runner.os }}-autotst-
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- name: Checkout AutoTST
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if: steps.cache-autotst.outputs.cache-hit != 'true'
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uses: actions/checkout@v3
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uses: actions/checkout@v4
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with:
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repository: ReactionMechanismGenerator/AutoTST
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path: AutoTST
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ref: main
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fetch-depth: 1
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repository: ReactionMechanismGenerator/AutoTST
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path: AutoTST
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ref: main
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fetch-depth: 1
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# ────────── TS‑GCN ──────────
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- name: Cache TS-GCN
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id: cache-tsgcn
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uses: actions/cache@v2
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uses: actions/cache@v4
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with:
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path: TS-GCN
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key: ${{ runner.os }}-tsgcn-main
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restore-keys: |
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${{ runner.os }}-tsgcn-
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path: TS-GCN
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key: ${{ runner.os }}-tsgcn-main
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restore-keys: |
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${{ runner.os }}-tsgcn-
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- name: Checkout TS-GCN
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if: steps.cache-tsgcn.outputs.cache-hit != 'true'
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uses: actions/checkout@v3
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uses: actions/checkout@v4
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with:
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repository: ReactionMechanismGenerator/TS-GCN
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path: TS-GCN
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ref: main
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fetch-depth: 1
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repository: ReactionMechanismGenerator/TS-GCN
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path: TS-GCN
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ref: main
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fetch-depth: 1
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# ────────── KinBot ──────────
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- name: Cache KinBot
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id: cache-kinbot
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uses: actions/cache@v2
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uses: actions/cache@v4
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with:
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path: KinBot
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key: ${{ runner.os }}-kinbot-2.0.6
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restore-keys: |
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${{ runner.os }}-kinbot-
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- name: Checkout Kinbot 2.0.6
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path: KinBot
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key: ${{ runner.os }}-kinbot-2.0.6
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restore-keys: |
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${{ runner.os }}-kinbot-
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- name: Checkout KinBot 2.0.6
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if: steps.cache-kinbot.outputs.cache-hit != 'true'
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uses: actions/checkout@v3
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uses: actions/checkout@v4
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with:
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repository: zadorlab/KinBot
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path: KinBot
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ref: v2.0.6
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fetch-depth: 1
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- name: Cache Packages Packages
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uses: actions/cache@v2
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env:
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CACHE_NUMBER: 0
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repository: zadorlab/KinBot
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path: KinBot
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ref: v2.0.6
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fetch-depth: 1
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# ────────── Conda package cache ──────────
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- name: Cache Conda packages
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id: cache-conda-pkgs
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uses: actions/cache@v4
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with:
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path: ~/conda_pkgs_dir
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key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('environment.yml') }}
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path: ~/conda_pkgs_dir
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key: ${{ runner.os }}-conda-0-${{ hashFiles('environment.yml') }}
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# ────────── Create / restore env ──────────
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- name: Setup ARC Env
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uses: conda-incubator/setup-miniconda@v3
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uses: conda-incubator/setup-miniconda@v3.2.0
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with:
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auto-update-conda: true
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environment-file: environment.yml
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activate-environment: arc_env
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miniconda-version: latest
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conda-solver: libmamba
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auto-update-conda: true
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environment-file: environment.yml
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activate-environment: arc_env
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miniconda-version: latest
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conda-solver: libmamba
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# ────────── Update env & save to cache ──────────
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- name: Update environment
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run: mamba env update -n arc_env -f environment.yml
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- name: Cache ARC env
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uses: actions/cache@v2
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uses: actions/cache@v4
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with:
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path: ${{ env.CONDA }}/envs
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key: conda-${{ runner.os }}--${{ runner.arch }}--${{ env.CACHE_NUMBER}}
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env:
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# Increase this value to reset cache if etc/example-environment.yml has not changed
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CACHE_NUMBER: 0
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id: cache-arc-env
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- name: Update environment
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run: conda env update -n arc_env -f environment.yml
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if: steps.cache-arc-env.outputs.cache-hit != 'true'
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path: ${{ env.CONDA }}/envs
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key: conda-${{ runner.os }}-${{ runner.arch }}-0

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