From 7c93a0df3c4dcc18854cc5a4c938d5efe7136cda Mon Sep 17 00:00:00 2001
From: pesap <pesap@users.noreply.github.com>
Date: Thu, 23 Apr 2026 11:41:36 -0600
Subject: [PATCH 01/13] ci: simplify GitHub workflow setup and labeling

- add shared setup-reeds-env composite action for Python/Julia setup\n- refactor CI workflow to reuse setup action and remove cache workflow\n- add dependabot, labeler, and workflow-quality configs\n- align composite action metadata and workflow shell quoting for linting
---
 .github/actions/r2x-check/action.yaml      |  9 +--
 .github/actions/setup-reeds-env/action.yml | 72 +++++++++++++++++
 .github/dependabot.yml                     | 65 +++++++++++++++
 .github/labeler.yaml                       | 92 +++++++++++++++++++++
 .github/workflows/build-docs.yaml          |  8 +-
 .github/workflows/cache.yaml               | 67 ----------------
 .github/workflows/labeler.yaml             | 27 +++++++
 .github/workflows/python-app.yaml          | 93 ++++++----------------
 .github/workflows/workflow-quality.yaml    | 50 ++++++++++++
 9 files changed, 336 insertions(+), 147 deletions(-)
 create mode 100644 .github/actions/setup-reeds-env/action.yml
 create mode 100644 .github/dependabot.yml
 create mode 100644 .github/labeler.yaml
 delete mode 100644 .github/workflows/cache.yaml
 create mode 100644 .github/workflows/labeler.yaml
 create mode 100644 .github/workflows/workflow-quality.yaml

diff --git a/.github/actions/r2x-check/action.yaml b/.github/actions/r2x-check/action.yaml
index 8b726751..b3025c34 100644
--- a/.github/actions/r2x-check/action.yaml
+++ b/.github/actions/r2x-check/action.yaml
@@ -3,18 +3,13 @@ description: "Action to run R2X."
 inputs:
   reeds-run-path:
     required: true
-    type: string
   scenario:
-    type: string
   python-version:
-    type: string
     default: "3.11"
   weather-year:
-    type: int
-    default: 2012
+    default: "2012"
   solve-year:
-    type: int
-    default: 2035
+    default: "2035"
 
 outputs:
   scenario:
diff --git a/.github/actions/setup-reeds-env/action.yml b/.github/actions/setup-reeds-env/action.yml
new file mode 100644
index 00000000..d514763d
--- /dev/null
+++ b/.github/actions/setup-reeds-env/action.yml
@@ -0,0 +1,72 @@
+name: Setup ReEDS Environment
+description: Setup cached micromamba Python and/or Julia environment for ReEDS CI.
+
+inputs:
+  setup-python:
+    description: Setup micromamba environment from environment.yml.
+    required: false
+    default: "true"
+  setup-julia:
+    description: Setup Julia toolchain.
+    required: false
+    default: "true"
+  julia-version:
+    description: Julia version to install.
+    required: false
+    default: "1.12.1"
+  instantiate-julia:
+    description: Run julia --project=. instantiate.jl.
+    required: false
+    default: "true"
+  remove-conda-julia:
+    description: Remove julia from micromamba env before setup-julia.
+    required: false
+    default: "true"
+
+outputs:
+  mamba-env-path:
+    description: Micromamba environment path.
+    value: ${{ steps.mamba.outputs.environment-path }}
+  julia-bindir:
+    description: Julia binary directory.
+    value: ${{ steps.setup-julia.outputs.julia-bindir }}
+
+runs:
+  using: composite
+  steps:
+    - name: Setup micromamba env
+      if: ${{ fromJSON(inputs.setup-python) }}
+      id: mamba
+      uses: mamba-org/setup-micromamba@add3a49764cedee8ee24e82dfde87f5bc2914462 # v2
+      with:
+        environment-file: environment.yml
+        cache-environment: true
+        post-cleanup: "all"
+        cache-environment-key: ${{ runner.os }}-conda-${{ hashFiles('environment.yml') }}
+
+    - name: Remove conda Julia package
+      if: ${{ fromJSON(inputs.setup-python) && fromJSON(inputs.setup-julia) && fromJSON(inputs.remove-conda-julia) }}
+      shell: bash -le {0}
+      run: micromamba remove -y julia || true
+
+    - name: Restore Julia cache
+      if: ${{ fromJSON(inputs.setup-julia) }}
+      uses: actions/cache@5a3ec84eff668545956fd18022155c47e93e2684 # v4
+      with:
+        path: ~/.julia
+        key: julia-${{ runner.os }}-${{ hashFiles('Project.toml') }}
+        restore-keys: julia-${{ runner.os }}-
+
+    - name: Setup Julia
+      if: ${{ fromJSON(inputs.setup-julia) }}
+      id: setup-julia
+      uses: julia-actions/setup-julia@5c9647d97b78a5debe5164e9eec09d653d29bd71 # v2
+      with:
+        version: ${{ inputs.julia-version }}
+      env:
+        NODE_EXTRA_CA_CERTS: /usr/local/share/ca-certificates/nrel_ca_chain.crt
+
+    - name: Instantiate Julia project
+      if: ${{ fromJSON(inputs.setup-julia) && fromJSON(inputs.instantiate-julia) }}
+      shell: bash -le {0}
+      run: julia --project=. instantiate.jl
diff --git a/.github/dependabot.yml b/.github/dependabot.yml
new file mode 100644
index 00000000..c4a05ef9
--- /dev/null
+++ b/.github/dependabot.yml
@@ -0,0 +1,65 @@
+version: 2
+
+updates:
+  - package-ecosystem: "conda"
+    directory: /
+    schedule:
+      interval: "weekly"
+    cooldown:
+      default-days: 7
+    open-pull-requests-limit: 2
+    labels:
+      - "dependenabot"
+    reviewers:
+      - "kennedy-mindermann"
+    commit-message:
+      prefix: "build"
+      include: "scope"
+    rebase-strategy: "auto"
+
+  - package-ecosystem: "pip"
+    directory: /
+    schedule:
+      interval: "weekly"
+    cooldown:
+      default-days: 7
+    open-pull-requests-limit: 2
+    labels:
+      - "dependenabot"
+    reviewers:
+      - "kennedy-mindermann"
+    commit-message:
+      prefix: "build"
+      include: "scope"
+    rebase-strategy: "auto"
+
+  - package-ecosystem: "julia"
+    directory: /
+    schedule:
+      interval: "weekly"
+    cooldown:
+      default-days: 7
+    open-pull-requests-limit: 2
+    labels:
+      - "dependenabot"
+    reviewers:
+      - "kennedy-mindermann"
+    commit-message:
+      prefix: "build"
+      include: "scope"
+    rebase-strategy: "auto"
+
+  - package-ecosystem: "github-actions"
+    directory: /
+    schedule:
+      interval: "weekly"
+    cooldown:
+      default-days: 7
+    labels:
+      - "dependenabot"
+    reviewers:
+      - "kennedy-mindermann"
+    commit-message:
+      prefix: "build"
+      include: "scope"
+    rebase-strategy: "auto"
diff --git a/.github/labeler.yaml b/.github/labeler.yaml
new file mode 100644
index 00000000..198cf14d
--- /dev/null
+++ b/.github/labeler.yaml
@@ -0,0 +1,92 @@
+dependenabot:
+  - head-branch:
+      - '^dependabot/.+'
+
+dependencies:
+  - changed-files:
+      - any-glob-to-any-file:
+          - "environment.yml"
+          - "pyproject.toml"
+          - "requirements*.txt"
+          - "Project.toml"
+          - "Manifest.toml"
+          - ".github/dependabot.yml"
+
+github_actions:
+  - changed-files:
+      - any-glob-to-any-file:
+          - ".github/workflows/**"
+          - ".github/actions/**"
+          - ".github/scripts/**"
+
+docs:
+  - changed-files:
+      - any-glob-to-any-file:
+          - "docs/**"
+          - "**/*.md"
+          - "CITATION.cff"
+
+release:
+  - changed-files:
+      - any-glob-to-any-file:
+          - "CHANGELOG.md"
+          - "README.md"
+
+tests:
+  - changed-files:
+      - any-glob-to-any-file:
+          - "tests/**"
+          - "hourlize/tests/**"
+          - "reeds2pras/test/**"
+          - "**/test_*.py"
+          - "**/*_test.py"
+
+model_changes:
+  - changed-files:
+      - any-glob-to-any-file:
+          - "**/*.gms"
+          - "runbatch.py"
+          - "d_solve*.py"
+          - "createmodel.gms"
+          - "reeds/**"
+          - "ReEDS_Augur/**"
+          - "Augur.py"
+          - "instantiate.jl"
+          - "reeds2pras/**"
+
+data_changes:
+  - changed-files:
+      - any-glob-to-any-file:
+          - "inputs/**"
+          - "hourlize/inputs/**"
+          - "postprocessing/**/inputs/**"
+          - "**/*.csv"
+          - "**/*.h5"
+          - "**/*.hdf5"
+          - "**/*.parquet"
+          - "**/*.xlsx"
+          - "**/*.xls"
+          - "sources.csv"
+          - "sources_documentation.md"
+
+hourlize:
+  - changed-files:
+      - any-glob-to-any-file: "hourlize/**"
+
+input_processing:
+  - changed-files:
+      - any-glob-to-any-file:
+          - "input_processing/**"
+          - "preprocessing/**"
+
+postprocessing:
+  - changed-files:
+      - any-glob-to-any-file: "postprocessing/**"
+
+reeds2pras:
+  - changed-files:
+      - any-glob-to-any-file: "reeds2pras/**"
+
+inputs:
+  - changed-files:
+      - any-glob-to-any-file: "inputs/**"
diff --git a/.github/workflows/build-docs.yaml b/.github/workflows/build-docs.yaml
index fac37fb5..19b447ab 100644
--- a/.github/workflows/build-docs.yaml
+++ b/.github/workflows/build-docs.yaml
@@ -48,11 +48,11 @@ jobs:
 
       - name: Set variables for internal github repo
         run: |
-          echo "BASE_URL=https://github.com/ReEDS-Model/ReEDS" >> $GITHUB_ENV
-          cd ${GITHUB_WORKSPACE}/docs/source/documentation_tools/
+          echo "BASE_URL=https://github.com/ReEDS-Model/ReEDS" >> "$GITHUB_ENV"
+          cd "$GITHUB_WORKSPACE/docs/source/documentation_tools/"
           sh generate_sources_md_file.sh
-          cd ${GITHUB_WORKSPACE}
-          python docs/source/documentation_tools/generate_markdown.py --githubURL "https://github.com/ReEDS-Model/ReEDS/blob/main" --reedsPath "${GITHUB_WORKSPACE}"
+          cd "$GITHUB_WORKSPACE"
+          python docs/source/documentation_tools/generate_markdown.py --githubURL "https://github.com/ReEDS-Model/ReEDS/blob/main" --reedsPath "$GITHUB_WORKSPACE"
 
       - name: Build Sphinx documentation
         env: 
diff --git a/.github/workflows/cache.yaml b/.github/workflows/cache.yaml
deleted file mode 100644
index b44aa9f3..00000000
--- a/.github/workflows/cache.yaml
+++ /dev/null
@@ -1,67 +0,0 @@
-# This Workflow creates caches for the Python and Julia environments every time
-# someone merges a PR. Subsequent PRs reuse these caches if the dependency
-# files have not changed.
-name: update-cache
-
-on:
-  push:
-    branches:
-      - main
-  workflow_dispatch:
-
-permissions:
-  contents: read
-
-# To reset the CACHE, change the environment variable: CACHE_NUMBER.
-# Either you increment the number or decrement it, but also reflect the changes
-# on the other workflows that reutilize the Python environment
-env:
-  CACHE_NUMBER: 1
-  JULIA_VERSION: '1.12.1'
-
-jobs:
-  python-cache:
-    name: Python Cache
-    runs-on: ubuntu-latest
-    permissions:
-      contents: read
-      actions: write
-    steps:
-      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
-        with:
-          persist-credentials: false
-      - uses: mamba-org/setup-micromamba@add3a49764cedee8ee24e82dfde87f5bc2914462 # v2
-        with:
-          environment-file: environment.yml
-          cache-environment: true
-          post-cleanup: 'all'
-          cache-environment-key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('environment.yml') }}
-        env:
-          ACTIONS_STEP_DEBUG: true
-
-  julia-cache:
-    name: Julia Cache
-    runs-on: ubuntu-latest
-    permissions:
-      contents: read
-      actions: write
-    steps:
-      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
-        with:
-          persist-credentials: false
-
-      - name: Restore Julia cache
-        id: julia-cache
-        uses: actions/cache@5a3ec84eff668545956fd18022155c47e93e2684 # v4
-        with:
-          path: ~/.julia
-          key: julia-${{ runner.os }}-${{ hashFiles('Project.toml') }}
-          restore-keys: julia-${{ runner.os }}-
-
-      - uses: julia-actions/setup-julia@5c9647d97b78a5debe5164e9eec09d653d29bd71 # v2
-        with:
-          version: ${{ env.JULIA_VERSION }}
-        env:
-          NODE_EXTRA_CA_CERTS: /usr/local/share/ca-certificates/nrel_ca_chain.crt
-
-      - run: julia --project=. instantiate.jl
diff --git a/.github/workflows/labeler.yaml b/.github/workflows/labeler.yaml
new file mode 100644
index 00000000..8acae743
--- /dev/null
+++ b/.github/workflows/labeler.yaml
@@ -0,0 +1,27 @@
+name: labeler
+
+on:
+  pull_request_target:
+    types: [opened, reopened, synchronize, ready_for_review]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+permissions:
+  contents: read
+  pull-requests: write
+  issues: write
+
+jobs:
+  labeler:
+    name: apply labels
+    if: github.event.pull_request.draft == false
+    timeout-minutes: 5
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/labeler@634933edcd8ababfe52f92936142cc22ac488b1b # v6.0.1
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+          configuration-path: .github/labeler.yaml
+          sync-labels: true
diff --git a/.github/workflows/python-app.yaml b/.github/workflows/python-app.yaml
index 69efc6ff..b851597d 100644
--- a/.github/workflows/python-app.yaml
+++ b/.github/workflows/python-app.yaml
@@ -23,35 +23,13 @@ defaults:
     shell: bash -le {0}
 
 env:
-  CACHE_NUMBER: 1
   JULIA_VERSION: '1.12.1'
-  REEDS_ENV_NAME: reeds2
 
 jobs:
-  julia-setup:
-    name: "Julia environment"
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
-        with:
-          persist-credentials: false
-
-      - name: Restore Julia cache
-        uses: actions/cache@5a3ec84eff668545956fd18022155c47e93e2684 # v4
-        with:
-          path: ~/.julia
-          key: julia-${{ runner.os }}-${{ hashFiles('Project.toml') }}
-          restore-keys: julia-${{ runner.os }}-
-
-      - uses: julia-actions/setup-julia@5c9647d97b78a5debe5164e9eec09d653d29bd71 # v2
-        with:
-          version: ${{ env.JULIA_VERSION }}
-
-      - run: julia --project=. instantiate.jl
-
-  python-setup:
-    name: "Python environment"
+  env-prime:
+    name: Prime Python and Julia caches
     runs-on: ubuntu-latest
+    timeout-minutes: 15
     permissions:
       contents: read
       actions: write
@@ -59,18 +37,17 @@ jobs:
       - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
         with:
           persist-credentials: false
-      - uses: mamba-org/setup-micromamba@add3a49764cedee8ee24e82dfde87f5bc2914462 # v2
+      - name: Setup ReEDS environments
+        uses: ./.github/actions/setup-reeds-env
         with:
-          environment-file: environment.yml
-          cache-environment: true
-          post-cleanup: 'all'
-          cache-environment-key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('environment.yml') }}
+          julia-version: ${{ env.JULIA_VERSION }}
 
   zenodo-setup:
     name: "Get Zenodo files"
     needs:
-      - python-setup
+      - env-prime
     runs-on: ubuntu-latest
+    timeout-minutes: 15
     permissions:
       contents: read
       actions: write
@@ -104,13 +81,10 @@ jobs:
             zenodo-files-${{ steps.zenodo-files.outputs.files-hash }}-
             zenodo-files-
       
-      - uses: mamba-org/setup-micromamba@add3a49764cedee8ee24e82dfde87f5bc2914462 # v2
-        id: mamba
+      - name: Setup Python environment
+        uses: ./.github/actions/setup-reeds-env
         with:
-          environment-file: environment.yml
-          cache-environment: true
-          post-cleanup: 'all'
-          cache-environment-key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('environment.yml') }}
+          setup-julia: false
 
       - name: Download Zenodo files if not cached
         if: steps.cache-zenodo.outputs.cache-hit != 'true'
@@ -118,9 +92,9 @@ jobs:
 
   run-ReEDS:
     runs-on: ubuntu-latest
+    timeout-minutes: 60
     needs:
-      - julia-setup
-      - python-setup
+      - env-prime
       - zenodo-setup
     permissions:
       contents: read
@@ -186,46 +160,26 @@ jobs:
             zenodo-files-${{ steps.zenodo-files.outputs.files-hash }}-
             zenodo-files-
 
-      - uses: mamba-org/setup-micromamba@add3a49764cedee8ee24e82dfde87f5bc2914462 # v2
-        id: mamba
-        with:
-          environment-file: environment.yml
-          cache-environment: true
-          post-cleanup: 'all'
-          cache-environment-key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('environment.yml') }}
-
-      - name: Removing julia from python
-        run: micromamba remove -y julia
-
-      - uses: julia-actions/setup-julia@5c9647d97b78a5debe5164e9eec09d653d29bd71 # v2
-        id: setup-julia
+      - name: Setup Python and Julia environments
+        id: setup-env
+        uses: ./.github/actions/setup-reeds-env
         with:
-          version: ${{ env.JULIA_VERSION }}
-
-      - name: Restore Julia cache
-        uses: actions/cache@5a3ec84eff668545956fd18022155c47e93e2684 # v4
-        with:
-          path: ~/.julia
-          key: julia-${{ runner.os }}-${{ hashFiles('Project.toml') }}
-          restore-keys: julia-${{ runner.os }}-
-
-      - run: julia --project=. instantiate.jl
+          julia-version: ${{ env.JULIA_VERSION }}
 
       - name: Prepend Julia install to PATH
-        env:
-          JULIA_BINDIR: ${{ steps.setup-julia.outputs.julia-bindir }}
-        run: echo "$JULIA_BINDIR" >> $GITHUB_PATH
+        run: echo "${{ steps.setup-env.outputs.julia-bindir }}" >> "$GITHUB_PATH"
 
       - name: Setup environment variables
         run: |
-          echo "GAMSDIR=$(python -c 'from gamspy_base import directory;print(directory)')" >> "$GITHUB_ENV"
-          echo "$(python -c 'from gamspy_base import directory;print(directory)')" >> "$GITHUB_PATH"
+          GAMSDIR="$(python -c 'from gamspy_base import directory;print(directory)')"
+          echo "GAMSDIR=$GAMSDIR" >> "$GITHUB_ENV"
+          echo "$GAMSDIR" >> "$GITHUB_PATH"
           echo "LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$GAMSDIR" >> "$GITHUB_ENV"
 
       - name: Setup licence
         env:
           GAMSLICE_CONTENT: ${{ secrets.GAMSLICE }}
-          MAMBA_ENV_PATH: ${{ steps.mamba.outputs.environment-path }}
+          MAMBA_ENV_PATH: ${{ steps.setup-env.outputs.mamba-env-path }}
         run: |
           echo "$GAMSLICE_CONTENT" > "${MAMBA_ENV_PATH}/lib/python3.11/site-packages/gamspy_base/gamslice.txt"
 
@@ -238,7 +192,7 @@ jobs:
 
       - name: Print GAMS log
         if: runner.debug == '1'
-        run: cat $RUN_FOLDER/gamslog.txt
+        run: cat "$RUN_FOLDER/gamslog.txt"
 
       - name: Check ReEDS outputs
         if: ${{ hashFiles(format('{0}/outputs/cap_ivrt.csv', env.RUN_FOLDER)) == '' }}
@@ -267,6 +221,7 @@ jobs:
 
   run-R2X:
     runs-on: ubuntu-latest
+    timeout-minutes: 30
     needs:
       - run-ReEDS
     permissions:
diff --git a/.github/workflows/workflow-quality.yaml b/.github/workflows/workflow-quality.yaml
new file mode 100644
index 00000000..b71d455f
--- /dev/null
+++ b/.github/workflows/workflow-quality.yaml
@@ -0,0 +1,50 @@
+name: GitHub Actions Quality
+
+on:
+  pull_request:
+    paths:
+      - ".github/**"
+  push:
+    branches:
+      - main
+    paths:
+      - ".github/**"
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref_name }}
+  cancel-in-progress: true
+
+permissions:
+  contents: read
+
+jobs:
+  zizmor:
+    name: zizmor
+    runs-on: ubuntu-latest
+    timeout-minutes: 5
+    steps:
+      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
+        with:
+          persist-credentials: false
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@cec208311dfd045dd5311c1add060b2062131d57 # v8.0.0
+        with:
+          version: "0.9.4"
+
+      - name: Run zizmor
+        run: uvx zizmor .github
+
+  actionlint:
+    name: actionlint
+    runs-on: ubuntu-latest
+    timeout-minutes: 5
+    steps:
+      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
+        with:
+          persist-credentials: false
+
+      - name: Run actionlint
+        run: |
+          bash <(curl -s https://raw.githubusercontent.com/rhysd/actionlint/main/scripts/download-actionlint.bash)
+          ./actionlint

From c7aa81d0d4ba3e11ed2f70b0a9a223bda3fbbbdb Mon Sep 17 00:00:00 2001
From: pesap <pesap@users.noreply.github.com>
Date: Thu, 23 Apr 2026 11:45:16 -0600
Subject: [PATCH 02/13] fix(ci): resolve workflow quality failures

- switch labeler trigger to pull_request to satisfy zizmor\n- pin actions/cache refs in CI workflow\n- harden PATH export step against template injection warning\n- set persist-credentials: false in docs checkout
---
 .github/workflows/build-docs.yaml | 1 +
 .github/workflows/labeler.yaml    | 2 +-
 .github/workflows/python-app.yaml | 8 +++++---
 3 files changed, 7 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/build-docs.yaml b/.github/workflows/build-docs.yaml
index 19b447ab..d1722783 100644
--- a/.github/workflows/build-docs.yaml
+++ b/.github/workflows/build-docs.yaml
@@ -27,6 +27,7 @@ jobs:
         with: 
           fetch-depth: 1
           lfs: true
+          persist-credentials: false
 
       - name: Set up Python 3.12
         uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
diff --git a/.github/workflows/labeler.yaml b/.github/workflows/labeler.yaml
index 8acae743..324fb6d0 100644
--- a/.github/workflows/labeler.yaml
+++ b/.github/workflows/labeler.yaml
@@ -1,7 +1,7 @@
 name: labeler
 
 on:
-  pull_request_target:
+  pull_request:
     types: [opened, reopened, synchronize, ready_for_review]
 
 concurrency:
diff --git a/.github/workflows/python-app.yaml b/.github/workflows/python-app.yaml
index b851597d..e58a3af6 100644
--- a/.github/workflows/python-app.yaml
+++ b/.github/workflows/python-app.yaml
@@ -68,7 +68,7 @@ jobs:
         
       - name: Restore Zenodo files from cache
         id: cache-zenodo
-        uses: actions/cache@v4
+        uses: actions/cache@5a3ec84eff668545956fd18022155c47e93e2684 # v4
         with:
           path: |
             inputs/remote/
@@ -147,7 +147,7 @@ jobs:
 
       - name: Restore Zenodo files from cache
         id: cache-zenodo
-        uses: actions/cache@v4
+        uses: actions/cache@5a3ec84eff668545956fd18022155c47e93e2684 # v4
         with:
           path: |
             inputs/remote/
@@ -167,7 +167,9 @@ jobs:
           julia-version: ${{ env.JULIA_VERSION }}
 
       - name: Prepend Julia install to PATH
-        run: echo "${{ steps.setup-env.outputs.julia-bindir }}" >> "$GITHUB_PATH"
+        env:
+          JULIA_BINDIR: ${{ steps.setup-env.outputs.julia-bindir }}
+        run: printf '%s\n' "$JULIA_BINDIR" >> "$GITHUB_PATH"
 
       - name: Setup environment variables
         run: |

From 99b101f8c68352ba6d24f6443b3cceaf2d2d334f Mon Sep 17 00:00:00 2001
From: pesap <pesap@users.noreply.github.com>
Date: Thu, 23 Apr 2026 11:48:43 -0600
Subject: [PATCH 03/13] fix(ci): remove custom CA cert env and rename setup job

- drop NODE_EXTRA_CA_CERTS from setup-reeds-env composite action\n- rename CI setup job id from env-prime to reeds-env\n- update downstream needs to reference reeds-env
---
 .github/actions/setup-reeds-env/action.yml | 2 --
 .github/workflows/python-app.yaml          | 8 ++++----
 2 files changed, 4 insertions(+), 6 deletions(-)

diff --git a/.github/actions/setup-reeds-env/action.yml b/.github/actions/setup-reeds-env/action.yml
index d514763d..3227292e 100644
--- a/.github/actions/setup-reeds-env/action.yml
+++ b/.github/actions/setup-reeds-env/action.yml
@@ -63,8 +63,6 @@ runs:
       uses: julia-actions/setup-julia@5c9647d97b78a5debe5164e9eec09d653d29bd71 # v2
       with:
         version: ${{ inputs.julia-version }}
-      env:
-        NODE_EXTRA_CA_CERTS: /usr/local/share/ca-certificates/nrel_ca_chain.crt
 
     - name: Instantiate Julia project
       if: ${{ fromJSON(inputs.setup-julia) && fromJSON(inputs.instantiate-julia) }}
diff --git a/.github/workflows/python-app.yaml b/.github/workflows/python-app.yaml
index e58a3af6..5519d686 100644
--- a/.github/workflows/python-app.yaml
+++ b/.github/workflows/python-app.yaml
@@ -26,8 +26,8 @@ env:
   JULIA_VERSION: '1.12.1'
 
 jobs:
-  env-prime:
-    name: Prime Python and Julia caches
+  reeds-env:
+    name: ReEDS Python and Julia env
     runs-on: ubuntu-latest
     timeout-minutes: 15
     permissions:
@@ -45,7 +45,7 @@ jobs:
   zenodo-setup:
     name: "Get Zenodo files"
     needs:
-      - env-prime
+      - reeds-env
     runs-on: ubuntu-latest
     timeout-minutes: 15
     permissions:
@@ -94,7 +94,7 @@ jobs:
     runs-on: ubuntu-latest
     timeout-minutes: 60
     needs:
-      - env-prime
+      - reeds-env
       - zenodo-setup
     permissions:
       contents: read

From a7221fa78e3abd8bf8925649b0773205e2ae2e0b Mon Sep 17 00:00:00 2001
From: pesap <pesap@users.noreply.github.com>
Date: Thu, 23 Apr 2026 11:57:21 -0600
Subject: [PATCH 04/13] fix(ci): satisfy zizmor pedantic findings

- extract R2X translation logic to scripts/run_r2x.py (uv --script compatible)\n- call run_r2x.py from r2x-check via uvx\n- scope workflow/job permissions to least privilege and document write grants\n- add explicit CI job names for pedantic readability checks
---
 .github/actions/r2x-check/action.yaml | 40 ++++----------------
 .github/workflows/build-docs.yaml     |  5 ++-
 .github/workflows/labeler.yaml        |  6 ++-
 .github/workflows/python-app.yaml     |  8 ++--
 scripts/run_r2x.py                    | 54 +++++++++++++++++++++++++++
 5 files changed, 75 insertions(+), 38 deletions(-)
 create mode 100644 scripts/run_r2x.py

diff --git a/.github/actions/r2x-check/action.yaml b/.github/actions/r2x-check/action.yaml
index b3025c34..66f6cb7f 100644
--- a/.github/actions/r2x-check/action.yaml
+++ b/.github/actions/r2x-check/action.yaml
@@ -49,42 +49,18 @@ runs:
     - name: Run R2X translation
       shell: bash -le {0}
       env:
-        R2X_RUN_PATH: ${{ inputs.reeds-run-path }}
+        R2X_REEDS_RUN_PATH: ${{ inputs.reeds-run-path }}
+        R2X_SCENARIO: ${{ steps.resolve.outputs.scenario }}
         R2X_SOLVE_YEAR: ${{ inputs.solve-year }}
         R2X_WEATHER_YEAR: ${{ inputs.weather-year }}
-        R2X_SCENARIO: ${{ steps.resolve.outputs.scenario }}
         R2X_SYSTEM_JSON: ${{ steps.resolve.outputs.system_json }}
       run: |
-        uv run --with "r2x-reeds>=0.3.5" python - <<'PY'
-        import os
-        from pathlib import Path
-
-        from loguru import logger
-        from r2x_core import DataStore, PluginContext
-        from r2x_core.logger import setup_logging
-        from r2x_reeds import ReEDSConfig, ReEDSParser
-
-        run_path = Path(os.environ["R2X_RUN_PATH"]).expanduser().resolve()
-        solve_year = int(os.environ["R2X_SOLVE_YEAR"])
-        weather_year = int(os.environ["R2X_WEATHER_YEAR"])
-        scenario = os.environ["R2X_SCENARIO"]
-        system_json = os.environ["R2X_SYSTEM_JSON"]
-
-        setup_logging()
-
-        config = ReEDSConfig(
-            weather_year=weather_year,
-            solve_year=solve_year,
-            scenario=scenario,
-        )
-
-        store = DataStore.from_plugin_config(config, path=run_path)
-        ctx = PluginContext(config=config, store=store)
-        parser = ReEDSParser.from_context(ctx)
-        result_ctx = parser.run()
-        result_ctx.system.to_json(system_json)
-        logger.info("Built R2X system for scenario '{}' at '{}'", scenario, system_json)
-        PY
+        uvx --from "r2x-reeds>=0.3.5" python scripts/run_r2x.py \
+          --reeds-run-path "$R2X_REEDS_RUN_PATH" \
+          --scenario "$R2X_SCENARIO" \
+          --solve-year "$R2X_SOLVE_YEAR" \
+          --weather-year "$R2X_WEATHER_YEAR" \
+          --system-json "$R2X_SYSTEM_JSON"
 
     - name: Save R2X system
       uses: actions/upload-artifact@bbbca2ddaa5d8feaa63e36b76fdaad77386f024f # v7.0.0
diff --git a/.github/workflows/build-docs.yaml b/.github/workflows/build-docs.yaml
index d1722783..cf1dec16 100644
--- a/.github/workflows/build-docs.yaml
+++ b/.github/workflows/build-docs.yaml
@@ -17,11 +17,14 @@ on:
       - main   
 
 permissions:
-  contents: write
+  contents: read
 
 jobs:
   build:
+    name: build and publish docs
     runs-on: ubuntu-latest
+    permissions:
+      contents: write # Required for peaceiris/actions-gh-pages publish to gh-pages.
     steps:
       - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
         with: 
diff --git a/.github/workflows/labeler.yaml b/.github/workflows/labeler.yaml
index 324fb6d0..a1bcfcbf 100644
--- a/.github/workflows/labeler.yaml
+++ b/.github/workflows/labeler.yaml
@@ -10,12 +10,14 @@ concurrency:
 
 permissions:
   contents: read
-  pull-requests: write
-  issues: write
 
 jobs:
   labeler:
     name: apply labels
+    permissions:
+      contents: read
+      pull-requests: write # Required to add/remove pull-request labels.
+      issues: write # Required because PR labels are issue labels in the API.
     if: github.event.pull_request.draft == false
     timeout-minutes: 5
     runs-on: ubuntu-latest
diff --git a/.github/workflows/python-app.yaml b/.github/workflows/python-app.yaml
index 5519d686..9daf527c 100644
--- a/.github/workflows/python-app.yaml
+++ b/.github/workflows/python-app.yaml
@@ -32,7 +32,7 @@ jobs:
     timeout-minutes: 15
     permissions:
       contents: read
-      actions: write
+      actions: write # Required to save/update micromamba cache.
     steps:
       - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
         with:
@@ -50,7 +50,7 @@ jobs:
     timeout-minutes: 15
     permissions:
       contents: read
-      actions: write
+      actions: write # Required to save/update Zenodo data cache.
     steps:
       - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
         with:
@@ -91,6 +91,7 @@ jobs:
         run: python .github/scripts/download_test_zenodo_files.py
 
   run-ReEDS:
+    name: run ReEDS model matrix
     runs-on: ubuntu-latest
     timeout-minutes: 60
     needs:
@@ -98,7 +99,7 @@ jobs:
       - zenodo-setup
     permissions:
       contents: read
-      actions: write
+      actions: write # Required to save/update LFS and Zenodo caches.
     strategy:
       fail-fast: false
       max-parallel: 4
@@ -222,6 +223,7 @@ jobs:
             ${{ env.RUN_FOLDER }}/outputs/**/*.h5
 
   run-R2X:
+    name: run R2X compatibility matrix
     runs-on: ubuntu-latest
     timeout-minutes: 30
     needs:
diff --git a/scripts/run_r2x.py b/scripts/run_r2x.py
new file mode 100644
index 00000000..0d215acd
--- /dev/null
+++ b/scripts/run_r2x.py
@@ -0,0 +1,54 @@
+#!/usr/bin/env -S uv run --script
+# /// script
+# requires-python = ">=3.11"
+# dependencies = [
+#   "r2x-reeds>=0.3.5",
+# ]
+# ///
+
+from __future__ import annotations
+
+import argparse
+from pathlib import Path
+
+from loguru import logger
+from r2x_core import DataStore, PluginContext
+from r2x_core.logger import setup_logging
+from r2x_reeds import ReEDSConfig, ReEDSParser
+
+
+def parse_args() -> argparse.Namespace:
+    parser = argparse.ArgumentParser(description="Run R2X translation for a ReEDS case.")
+    parser.add_argument("--reeds-run-path", required=True, type=Path)
+    parser.add_argument("--scenario", required=True)
+    parser.add_argument("--solve-year", required=True, type=int)
+    parser.add_argument("--weather-year", required=True, type=int)
+    parser.add_argument("--system-json", required=True, type=Path)
+    return parser.parse_args()
+
+
+def main() -> None:
+    args = parse_args()
+
+    run_path = args.reeds_run_path.expanduser().resolve()
+
+    setup_logging()
+
+    config = ReEDSConfig(
+        weather_year=args.weather_year,
+        solve_year=args.solve_year,
+        scenario=args.scenario,
+    )
+
+    store = DataStore.from_plugin_config(config, path=run_path)
+    ctx = PluginContext(config=config, store=store)
+    parser = ReEDSParser.from_context(ctx)
+    result_ctx = parser.run()
+
+    system_json = args.system_json.expanduser().resolve()
+    result_ctx.system.to_json(system_json)
+    logger.info("Built R2X system for scenario '{}' at '{}'", args.scenario, system_json)
+
+
+if __name__ == "__main__":
+    main()

From 43badef56b910955739675a88f2b314ed80821dd Mon Sep 17 00:00:00 2001
From: pesap <pesap@users.noreply.github.com>
Date: Thu, 23 Apr 2026 12:03:00 -0600
Subject: [PATCH 05/13] refactor(ci): inline R2X check and enforce pedantic
 zizmor

- remove local r2x-check composite action indirection\n- run scripts/run_r2x.py directly in python-app workflow via uvx\n- keep artifact upload behavior in CI job\n- run zizmor with --pedantic by default in workflow-quality
---
 .github/actions/r2x-check/action.yaml   | 71 -------------------------
 .github/workflows/python-app.yaml       | 37 ++++++++++---
 .github/workflows/workflow-quality.yaml |  2 +-
 3 files changed, 32 insertions(+), 78 deletions(-)
 delete mode 100644 .github/actions/r2x-check/action.yaml

diff --git a/.github/actions/r2x-check/action.yaml b/.github/actions/r2x-check/action.yaml
deleted file mode 100644
index 66f6cb7f..00000000
--- a/.github/actions/r2x-check/action.yaml
+++ /dev/null
@@ -1,71 +0,0 @@
-name: r2x-compatibility
-description: "Action to run R2X."
-inputs:
-  reeds-run-path:
-    required: true
-  scenario:
-  python-version:
-    default: "3.11"
-  weather-year:
-    default: "2012"
-  solve-year:
-    default: "2035"
-
-outputs:
-  scenario:
-    description: Resolved scenario name used for export.
-    value: ${{ steps.resolve.outputs.scenario }}
-  system-json:
-    description: Filename of the exported R2X system JSON.
-    value: ${{ steps.resolve.outputs.system_json }}
-
-runs:
-  using: composite
-  steps:
-    - name: Resolve scenario name
-      id: resolve
-      shell: bash -le {0}
-      env:
-        INPUT_SCENARIO: ${{ inputs.scenario }}
-        INPUT_RUN_PATH: ${{ inputs.reeds-run-path }}
-      run: |
-        scenario="${INPUT_SCENARIO}"
-        if [ -z "$scenario" ]; then
-          scenario="$(basename "$INPUT_RUN_PATH")"
-        fi
-        system_json="${scenario}_system.json"
-        echo "scenario=$scenario" >> "$GITHUB_OUTPUT"
-        echo "system_json=$system_json" >> "$GITHUB_OUTPUT"
-
-    - name: Install uv and set the python version
-      uses: astral-sh/setup-uv@37802adc94f370d6bfd71619e3f0bf239e1f3b78 # v7
-      with:
-        python-version: ${{ inputs.python-version }}
-        enable-cache: true
-        restore-cache: true
-        save-cache: true
-        ignore-nothing-to-cache: true
-
-    - name: Run R2X translation
-      shell: bash -le {0}
-      env:
-        R2X_REEDS_RUN_PATH: ${{ inputs.reeds-run-path }}
-        R2X_SCENARIO: ${{ steps.resolve.outputs.scenario }}
-        R2X_SOLVE_YEAR: ${{ inputs.solve-year }}
-        R2X_WEATHER_YEAR: ${{ inputs.weather-year }}
-        R2X_SYSTEM_JSON: ${{ steps.resolve.outputs.system_json }}
-      run: |
-        uvx --from "r2x-reeds>=0.3.5" python scripts/run_r2x.py \
-          --reeds-run-path "$R2X_REEDS_RUN_PATH" \
-          --scenario "$R2X_SCENARIO" \
-          --solve-year "$R2X_SOLVE_YEAR" \
-          --weather-year "$R2X_WEATHER_YEAR" \
-          --system-json "$R2X_SYSTEM_JSON"
-
-    - name: Save R2X system
-      uses: actions/upload-artifact@bbbca2ddaa5d8feaa63e36b76fdaad77386f024f # v7.0.0
-      with:
-        name: r2x-${{ steps.resolve.outputs.scenario }}
-        compression-level: 9
-        retention-days: 1
-        path: ${{ steps.resolve.outputs.system_json }}
diff --git a/.github/workflows/python-app.yaml b/.github/workflows/python-app.yaml
index 9daf527c..ffe19a73 100644
--- a/.github/workflows/python-app.yaml
+++ b/.github/workflows/python-app.yaml
@@ -251,10 +251,35 @@ jobs:
         with:
           name: ${{ matrix.scenario }}
           path: ${{ format('{0}-{1}', matrix.scenario, matrix.solve-year) }}
-      - name: R2X compatibility
-        uses: ./.github/actions/r2x-check
-        id: r2x-check
+
+      - name: Install uv and set Python version
+        uses: astral-sh/setup-uv@37802adc94f370d6bfd71619e3f0bf239e1f3b78 # v7
+        with:
+          python-version: "3.11"
+          enable-cache: true
+          restore-cache: true
+          save-cache: true
+          ignore-nothing-to-cache: true
+
+      - name: Run R2X compatibility
+        env:
+          R2X_REEDS_RUN_PATH: ${{ format('{0}-{1}', matrix.scenario, matrix.solve-year) }}
+          R2X_SCENARIO: ${{ matrix.scenario }}
+          R2X_SOLVE_YEAR: ${{ matrix.solve-year }}
+          R2X_WEATHER_YEAR: "2012"
+          R2X_SYSTEM_JSON: ${{ format('{0}_system.json', matrix.scenario) }}
+        run: |
+          uvx --from "r2x-reeds>=0.3.5" python scripts/run_r2x.py \
+            --reeds-run-path "$R2X_REEDS_RUN_PATH" \
+            --scenario "$R2X_SCENARIO" \
+            --solve-year "$R2X_SOLVE_YEAR" \
+            --weather-year "$R2X_WEATHER_YEAR" \
+            --system-json "$R2X_SYSTEM_JSON"
+
+      - name: Save R2X system
+        uses: actions/upload-artifact@bbbca2ddaa5d8feaa63e36b76fdaad77386f024f # v7.0.0
         with:
-          reeds-run-path: ${{ format('{0}-{1}', matrix.scenario, matrix.solve-year) }}
-          scenario: ${{ matrix.scenario }}
-          solve-year: ${{ matrix.solve-year }}
+          name: r2x-${{ matrix.scenario }}
+          compression-level: 9
+          retention-days: 1
+          path: ${{ format('{0}_system.json', matrix.scenario) }}
diff --git a/.github/workflows/workflow-quality.yaml b/.github/workflows/workflow-quality.yaml
index b71d455f..a7d8e7a8 100644
--- a/.github/workflows/workflow-quality.yaml
+++ b/.github/workflows/workflow-quality.yaml
@@ -33,7 +33,7 @@ jobs:
           version: "0.9.4"
 
       - name: Run zizmor
-        run: uvx zizmor .github
+        run: uvx zizmor --pedantic .github
 
   actionlint:
     name: actionlint

From f1e79b49758fbde9a6d1f8f9da85b97156168481 Mon Sep 17 00:00:00 2001
From: pesap <pesap@users.noreply.github.com>
Date: Thu, 23 Apr 2026 13:28:28 -0600
Subject: [PATCH 06/13] fix(ci): restore docs required check name

Set build-docs job name back to 'build' so existing branch protection check context is reported.
---
 .github/workflows/build-docs.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/build-docs.yaml b/.github/workflows/build-docs.yaml
index cf1dec16..24f72ed6 100644
--- a/.github/workflows/build-docs.yaml
+++ b/.github/workflows/build-docs.yaml
@@ -21,7 +21,7 @@ permissions:
 
 jobs:
   build:
-    name: build and publish docs
+    name: build
     runs-on: ubuntu-latest
     permissions:
       contents: write # Required for peaceiris/actions-gh-pages publish to gh-pages.

From eed7aeb784f0a2e161424bf8a3e11ff51e76a92a Mon Sep 17 00:00:00 2001
From: pesap <pesap@users.noreply.github.com>
Date: Thu, 23 Apr 2026 14:06:10 -0600
Subject: [PATCH 07/13] ci: pin actionlint installer and fix labels

---
 .github/dependabot.yml                  | 8 ++++----
 .github/labeler.yaml                    | 4 +---
 .github/workflows/workflow-quality.yaml | 5 ++++-
 3 files changed, 9 insertions(+), 8 deletions(-)

diff --git a/.github/dependabot.yml b/.github/dependabot.yml
index c4a05ef9..f48eaf06 100644
--- a/.github/dependabot.yml
+++ b/.github/dependabot.yml
@@ -9,7 +9,7 @@ updates:
       default-days: 7
     open-pull-requests-limit: 2
     labels:
-      - "dependenabot"
+      - "dependencies"
     reviewers:
       - "kennedy-mindermann"
     commit-message:
@@ -25,7 +25,7 @@ updates:
       default-days: 7
     open-pull-requests-limit: 2
     labels:
-      - "dependenabot"
+      - "dependencies"
     reviewers:
       - "kennedy-mindermann"
     commit-message:
@@ -41,7 +41,7 @@ updates:
       default-days: 7
     open-pull-requests-limit: 2
     labels:
-      - "dependenabot"
+      - "dependencies"
     reviewers:
       - "kennedy-mindermann"
     commit-message:
@@ -56,7 +56,7 @@ updates:
     cooldown:
       default-days: 7
     labels:
-      - "dependenabot"
+      - "dependencies"
     reviewers:
       - "kennedy-mindermann"
     commit-message:
diff --git a/.github/labeler.yaml b/.github/labeler.yaml
index 198cf14d..d8c6d3d4 100644
--- a/.github/labeler.yaml
+++ b/.github/labeler.yaml
@@ -1,8 +1,6 @@
-dependenabot:
+dependencies:
   - head-branch:
       - '^dependabot/.+'
-
-dependencies:
   - changed-files:
       - any-glob-to-any-file:
           - "environment.yml"
diff --git a/.github/workflows/workflow-quality.yaml b/.github/workflows/workflow-quality.yaml
index a7d8e7a8..d35249e9 100644
--- a/.github/workflows/workflow-quality.yaml
+++ b/.github/workflows/workflow-quality.yaml
@@ -46,5 +46,8 @@ jobs:
 
       - name: Run actionlint
         run: |
-          bash <(curl -s https://raw.githubusercontent.com/rhysd/actionlint/main/scripts/download-actionlint.bash)
+          ACTIONLINT_INSTALL_SCRIPT_URL="https://raw.githubusercontent.com/rhysd/actionlint/e7d448ef7507c20fc4c88a95d0c448b848cd6127/scripts/download-actionlint.bash"
+          curl -fsSL "$ACTIONLINT_INSTALL_SCRIPT_URL" -o download-actionlint.bash
+          echo "28a0e78b3230372051c5a77840125aa2c8dc7804fce3696ef29dd52001ec3a8f  download-actionlint.bash" | sha256sum -c -
+          bash download-actionlint.bash
           ./actionlint

From 0e020761ad040f2f97765e7adf57bf71f5c714fc Mon Sep 17 00:00:00 2001
From: pesap <pesap@users.noreply.github.com>
Date: Thu, 23 Apr 2026 15:25:18 -0600
Subject: [PATCH 08/13] ci: gate heavy runs and upload failure diagnostics

---
 .github/workflows/python-app.yaml | 45 +++++++++++++++++++++++++------
 1 file changed, 37 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/python-app.yaml b/.github/workflows/python-app.yaml
index ffe19a73..db75bdd3 100644
--- a/.github/workflows/python-app.yaml
+++ b/.github/workflows/python-app.yaml
@@ -5,11 +5,22 @@ on:
   pull_request:
     branches:
       - main
-    paths-ignore:
-      - 'docs/**'
-      - '*.md'
-      - 'LICENSE'
-      - '.gitignore'
+    paths:
+      - ".github/actions/setup-reeds-env/**"
+      - ".github/scripts/download_test_zenodo_files.py"
+      - ".github/workflows/python-app.yaml"
+      - "environment.yml"
+      - "Project.toml"
+      - "Manifest.toml"
+      - "runbatch.py"
+      - "d_solve*.py"
+      - "createmodel.gms"
+      - "reeds/**"
+      - "ReEDS_Augur/**"
+      - "Augur.py"
+      - "inputs/**"
+      - "tests/**"
+      - "scripts/run_r2x.py"
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
@@ -186,12 +197,15 @@ jobs:
         run: |
           echo "$GAMSLICE_CONTENT" > "${MAMBA_ENV_PATH}/lib/python3.11/site-packages/gamspy_base/gamslice.txt"
 
+      - name: Set run folder
+        env:
+          SCENARIO: ${{ matrix.scenario }}
+        run: echo "RUN_FOLDER=$GITHUB_WORKSPACE/runs/${batch}_${SCENARIO}" >> "$GITHUB_ENV"
+
       - name: Run ReEDS model
         env:
           SCENARIO: ${{ matrix.scenario }}
-        run: |
-          python runbatch.py -b "$batch" -c test -s "$SCENARIO"
-          echo "RUN_FOLDER=$GITHUB_WORKSPACE/runs/${batch}_${SCENARIO}" >> "$GITHUB_ENV"
+        run: python runbatch.py -b "$batch" -c test -s "$SCENARIO"
 
       - name: Print GAMS log
         if: runner.debug == '1'
@@ -209,6 +223,21 @@ jobs:
           SCENARIO: ${{ matrix.scenario }}
         run: python -m pytest tests/test_outputs.py --casepath "$GITHUB_WORKSPACE/runs/${batch}_${SCENARIO}"
 
+      - name: Upload ReEDS failure diagnostics
+        if: ${{ failure() }}
+        uses: actions/upload-artifact@bbbca2ddaa5d8feaa63e36b76fdaad77386f024f # v7
+        with:
+          name: ${{ format('{0}-failure-diagnostics', matrix.scenario) }}
+          compression-level: 9
+          retention-days: 7
+          if-no-files-found: ignore
+          path: |
+            ${{ env.RUN_FOLDER }}/gamslog.txt
+            ${{ env.RUN_FOLDER }}/meta.csv
+            ${{ env.RUN_FOLDER }}/outputs/**/*.log
+            ${{ env.RUN_FOLDER }}/outputs/**/*.err
+            ${{ env.RUN_FOLDER }}/outputs/**/*.lst
+
       - name: Save ReEDS run
         uses: actions/upload-artifact@bbbca2ddaa5d8feaa63e36b76fdaad77386f024f # v7
         with:

From 10a7390ecd72e38469b2764f5906c1df14c53d6c Mon Sep 17 00:00:00 2001
From: pesap <pesap@users.noreply.github.com>
Date: Thu, 23 Apr 2026 15:41:45 -0600
Subject: [PATCH 09/13] ci: collect targeted failure diagnostics artifacts

---
 .github/workflows/python-app.yaml | 76 ++++++++++++++++++++++++++++---
 1 file changed, 70 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/python-app.yaml b/.github/workflows/python-app.yaml
index db75bdd3..ac9cf76d 100644
--- a/.github/workflows/python-app.yaml
+++ b/.github/workflows/python-app.yaml
@@ -223,6 +223,75 @@ jobs:
           SCENARIO: ${{ matrix.scenario }}
         run: python -m pytest tests/test_outputs.py --casepath "$GITHUB_WORKSPACE/runs/${batch}_${SCENARIO}"
 
+      - name: Collect ReEDS failure diagnostics
+        if: ${{ failure() }}
+        env:
+          CASE_NAME: ${{ matrix.scenario }}
+        run: |
+          DIAG_ROOT="$RUNNER_TEMP/reeds-failure-diagnostics/$CASE_NAME"
+          mkdir -p "$DIAG_ROOT"
+          MANIFEST="$DIAG_ROOT/manifest.txt"
+
+          copy_if_exists() {
+            local src="$1"
+            local rel="$2"
+            if [[ -f "$src" ]]; then
+              mkdir -p "$(dirname "$DIAG_ROOT/$rel")"
+              cp "$src" "$DIAG_ROOT/$rel"
+              printf 'included: %s\n' "$src" >> "$MANIFEST"
+            else
+              printf 'missing: %s\n' "$src" >> "$MANIFEST"
+            fi
+          }
+
+          latest_by_year_iteration() {
+            local search_dir="$1"
+            local regex="$2"
+            local best_file=""
+            local best_year=-1
+            local best_iter=-1
+
+            [[ -d "$search_dir" ]] || return 0
+
+            while IFS= read -r file; do
+              local base year iter year_num iter_num
+              base="$(basename "$file")"
+              if [[ "$base" =~ $regex ]]; then
+                year="${BASH_REMATCH[1]}"
+                iter="${BASH_REMATCH[2]}"
+                year_num=$((10#$year))
+                iter_num=$((10#$iter))
+                if (( year_num > best_year || (year_num == best_year && iter_num > best_iter) )); then
+                  best_year=$year_num
+                  best_iter=$iter_num
+                  best_file="$file"
+                fi
+              fi
+            done < <(find "$search_dir" -maxdepth 1 -type f)
+
+            printf '%s\n' "$best_file"
+          }
+
+          copy_if_exists "$RUN_FOLDER/gamslog.txt" "gamslog.txt"
+          copy_if_exists "$RUN_FOLDER/meta.csv" "meta.csv"
+          copy_if_exists "$RUN_FOLDER/lstfiles/1_Inputs.lst" "lstfiles/1_Inputs.lst"
+
+          latest_case_lst="$(latest_by_year_iteration "$RUN_FOLDER/lstfiles" "^${CASE_NAME}_([0-9]+)i([0-9]+)\\.lst$")"
+          if [[ -n "$latest_case_lst" ]]; then
+            copy_if_exists "$latest_case_lst" "lstfiles/$(basename "$latest_case_lst")"
+          else
+            printf 'missing: %s\n' "$RUN_FOLDER/lstfiles/${CASE_NAME}_{year}i{iteration}.lst" >> "$MANIFEST"
+          fi
+
+          copy_if_exists "$RUN_FOLDER/lstfiles/report_${CASE_NAME}.lst" "lstfiles/report_${CASE_NAME}.lst"
+
+          latest_pras_log="$(latest_by_year_iteration "$RUN_FOLDER/ReEDS_Augur/PRAS" "^PRAS_([0-9]+)i([0-9]+)\\.log$")"
+          if [[ -n "$latest_pras_log" ]]; then
+            copy_if_exists "$latest_pras_log" "ReEDS_Augur/PRAS/$(basename "$latest_pras_log")"
+          else
+            printf 'missing: %s\n' "$RUN_FOLDER/ReEDS_Augur/PRAS/PRAS_{year}i{iteration}.log" >> "$MANIFEST"
+          fi
+
       - name: Upload ReEDS failure diagnostics
         if: ${{ failure() }}
         uses: actions/upload-artifact@bbbca2ddaa5d8feaa63e36b76fdaad77386f024f # v7
@@ -231,12 +300,7 @@ jobs:
           compression-level: 9
           retention-days: 7
           if-no-files-found: ignore
-          path: |
-            ${{ env.RUN_FOLDER }}/gamslog.txt
-            ${{ env.RUN_FOLDER }}/meta.csv
-            ${{ env.RUN_FOLDER }}/outputs/**/*.log
-            ${{ env.RUN_FOLDER }}/outputs/**/*.err
-            ${{ env.RUN_FOLDER }}/outputs/**/*.lst
+          path: ${{ format('{0}/reeds-failure-diagnostics/{1}', runner.temp, matrix.scenario) }}
 
       - name: Save ReEDS run
         uses: actions/upload-artifact@bbbca2ddaa5d8feaa63e36b76fdaad77386f024f # v7

From 64e9c8e582264b730862e2a733db502941ce8578 Mon Sep 17 00:00:00 2001
From: pesap <pesap@users.noreply.github.com>
Date: Thu, 23 Apr 2026 16:01:17 -0600
Subject: [PATCH 10/13] ci: simplify failure diagnostics artifact globs

---
 .github/workflows/python-app.yaml | 77 +++----------------------------
 1 file changed, 7 insertions(+), 70 deletions(-)

diff --git a/.github/workflows/python-app.yaml b/.github/workflows/python-app.yaml
index ac9cf76d..4eed5acb 100644
--- a/.github/workflows/python-app.yaml
+++ b/.github/workflows/python-app.yaml
@@ -223,75 +223,6 @@ jobs:
           SCENARIO: ${{ matrix.scenario }}
         run: python -m pytest tests/test_outputs.py --casepath "$GITHUB_WORKSPACE/runs/${batch}_${SCENARIO}"
 
-      - name: Collect ReEDS failure diagnostics
-        if: ${{ failure() }}
-        env:
-          CASE_NAME: ${{ matrix.scenario }}
-        run: |
-          DIAG_ROOT="$RUNNER_TEMP/reeds-failure-diagnostics/$CASE_NAME"
-          mkdir -p "$DIAG_ROOT"
-          MANIFEST="$DIAG_ROOT/manifest.txt"
-
-          copy_if_exists() {
-            local src="$1"
-            local rel="$2"
-            if [[ -f "$src" ]]; then
-              mkdir -p "$(dirname "$DIAG_ROOT/$rel")"
-              cp "$src" "$DIAG_ROOT/$rel"
-              printf 'included: %s\n' "$src" >> "$MANIFEST"
-            else
-              printf 'missing: %s\n' "$src" >> "$MANIFEST"
-            fi
-          }
-
-          latest_by_year_iteration() {
-            local search_dir="$1"
-            local regex="$2"
-            local best_file=""
-            local best_year=-1
-            local best_iter=-1
-
-            [[ -d "$search_dir" ]] || return 0
-
-            while IFS= read -r file; do
-              local base year iter year_num iter_num
-              base="$(basename "$file")"
-              if [[ "$base" =~ $regex ]]; then
-                year="${BASH_REMATCH[1]}"
-                iter="${BASH_REMATCH[2]}"
-                year_num=$((10#$year))
-                iter_num=$((10#$iter))
-                if (( year_num > best_year || (year_num == best_year && iter_num > best_iter) )); then
-                  best_year=$year_num
-                  best_iter=$iter_num
-                  best_file="$file"
-                fi
-              fi
-            done < <(find "$search_dir" -maxdepth 1 -type f)
-
-            printf '%s\n' "$best_file"
-          }
-
-          copy_if_exists "$RUN_FOLDER/gamslog.txt" "gamslog.txt"
-          copy_if_exists "$RUN_FOLDER/meta.csv" "meta.csv"
-          copy_if_exists "$RUN_FOLDER/lstfiles/1_Inputs.lst" "lstfiles/1_Inputs.lst"
-
-          latest_case_lst="$(latest_by_year_iteration "$RUN_FOLDER/lstfiles" "^${CASE_NAME}_([0-9]+)i([0-9]+)\\.lst$")"
-          if [[ -n "$latest_case_lst" ]]; then
-            copy_if_exists "$latest_case_lst" "lstfiles/$(basename "$latest_case_lst")"
-          else
-            printf 'missing: %s\n' "$RUN_FOLDER/lstfiles/${CASE_NAME}_{year}i{iteration}.lst" >> "$MANIFEST"
-          fi
-
-          copy_if_exists "$RUN_FOLDER/lstfiles/report_${CASE_NAME}.lst" "lstfiles/report_${CASE_NAME}.lst"
-
-          latest_pras_log="$(latest_by_year_iteration "$RUN_FOLDER/ReEDS_Augur/PRAS" "^PRAS_([0-9]+)i([0-9]+)\\.log$")"
-          if [[ -n "$latest_pras_log" ]]; then
-            copy_if_exists "$latest_pras_log" "ReEDS_Augur/PRAS/$(basename "$latest_pras_log")"
-          else
-            printf 'missing: %s\n' "$RUN_FOLDER/ReEDS_Augur/PRAS/PRAS_{year}i{iteration}.log" >> "$MANIFEST"
-          fi
-
       - name: Upload ReEDS failure diagnostics
         if: ${{ failure() }}
         uses: actions/upload-artifact@bbbca2ddaa5d8feaa63e36b76fdaad77386f024f # v7
@@ -300,7 +231,13 @@ jobs:
           compression-level: 9
           retention-days: 7
           if-no-files-found: ignore
-          path: ${{ format('{0}/reeds-failure-diagnostics/{1}', runner.temp, matrix.scenario) }}
+          path: |
+            ${{ env.RUN_FOLDER }}/gamslog.txt
+            ${{ env.RUN_FOLDER }}/meta.csv
+            ${{ env.RUN_FOLDER }}/lstfiles/1_Inputs.lst
+            ${{ env.RUN_FOLDER }}/lstfiles/${{ matrix.scenario }}_*i*.lst
+            ${{ env.RUN_FOLDER }}/lstfiles/report_${{ matrix.scenario }}.lst
+            ${{ env.RUN_FOLDER }}/ReEDS_Augur/PRAS/PRAS_*i*.log
 
       - name: Save ReEDS run
         uses: actions/upload-artifact@bbbca2ddaa5d8feaa63e36b76fdaad77386f024f # v7

From b3b7d45725a7986e314c38f89221d5f38b3f2c94 Mon Sep 17 00:00:00 2001
From: pesap <pesap@users.noreply.github.com>
Date: Fri, 24 Apr 2026 14:33:39 -0600
Subject: [PATCH 11/13] ci: restore pull_request paths-ignore trigger

---
 .github/workflows/python-app.yaml | 21 +++++----------------
 1 file changed, 5 insertions(+), 16 deletions(-)

diff --git a/.github/workflows/python-app.yaml b/.github/workflows/python-app.yaml
index 4eed5acb..5f69a91d 100644
--- a/.github/workflows/python-app.yaml
+++ b/.github/workflows/python-app.yaml
@@ -5,22 +5,11 @@ on:
   pull_request:
     branches:
       - main
-    paths:
-      - ".github/actions/setup-reeds-env/**"
-      - ".github/scripts/download_test_zenodo_files.py"
-      - ".github/workflows/python-app.yaml"
-      - "environment.yml"
-      - "Project.toml"
-      - "Manifest.toml"
-      - "runbatch.py"
-      - "d_solve*.py"
-      - "createmodel.gms"
-      - "reeds/**"
-      - "ReEDS_Augur/**"
-      - "Augur.py"
-      - "inputs/**"
-      - "tests/**"
-      - "scripts/run_r2x.py"
+    paths-ignore:
+      - 'docs/**'
+      - '*.md'
+      - 'LICENSE'
+      - '.gitignore'
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}

From fc98684b64783b69f117b938ca8c3b73441dd9de Mon Sep 17 00:00:00 2001
From: pesap <pesap@users.noreply.github.com>
Date: Mon, 27 Apr 2026 20:33:22 -0600
Subject: [PATCH 12/13] fixup! ci: simplify GitHub workflow setup and labeling

---
 .github/actions/setup-reeds-env/action.yml |  9 ---------
 .github/labeler.yaml                       | 10 ++++------
 2 files changed, 4 insertions(+), 15 deletions(-)

diff --git a/.github/actions/setup-reeds-env/action.yml b/.github/actions/setup-reeds-env/action.yml
index 3227292e..0818d3c8 100644
--- a/.github/actions/setup-reeds-env/action.yml
+++ b/.github/actions/setup-reeds-env/action.yml
@@ -18,10 +18,6 @@ inputs:
     description: Run julia --project=. instantiate.jl.
     required: false
     default: "true"
-  remove-conda-julia:
-    description: Remove julia from micromamba env before setup-julia.
-    required: false
-    default: "true"
 
 outputs:
   mamba-env-path:
@@ -44,11 +40,6 @@ runs:
         post-cleanup: "all"
         cache-environment-key: ${{ runner.os }}-conda-${{ hashFiles('environment.yml') }}
 
-    - name: Remove conda Julia package
-      if: ${{ fromJSON(inputs.setup-python) && fromJSON(inputs.setup-julia) && fromJSON(inputs.remove-conda-julia) }}
-      shell: bash -le {0}
-      run: micromamba remove -y julia || true
-
     - name: Restore Julia cache
       if: ${{ fromJSON(inputs.setup-julia) }}
       uses: actions/cache@5a3ec84eff668545956fd18022155c47e93e2684 # v4
diff --git a/.github/labeler.yaml b/.github/labeler.yaml
index d8c6d3d4..441c0a34 100644
--- a/.github/labeler.yaml
+++ b/.github/labeler.yaml
@@ -42,10 +42,10 @@ tests:
 model_changes:
   - changed-files:
       - any-glob-to-any-file:
+          - "*.gms"
           - "**/*.gms"
           - "runbatch.py"
           - "d_solve*.py"
-          - "createmodel.gms"
           - "reeds/**"
           - "ReEDS_Augur/**"
           - "Augur.py"
@@ -60,10 +60,6 @@ data_changes:
           - "postprocessing/**/inputs/**"
           - "**/*.csv"
           - "**/*.h5"
-          - "**/*.hdf5"
-          - "**/*.parquet"
-          - "**/*.xlsx"
-          - "**/*.xls"
           - "sources.csv"
           - "sources_documentation.md"
 
@@ -87,4 +83,6 @@ reeds2pras:
 
 inputs:
   - changed-files:
-      - any-glob-to-any-file: "inputs/**"
+      - any-glob-to-any-file:
+          - "inputs/**"
+          - "cases.csv"

From 798d638f928f4509b0ae5a5fa37ad65957199978 Mon Sep 17 00:00:00 2001
From: pesap <pesap@users.noreply.github.com>
Date: Fri, 1 May 2026 12:20:26 -0600
Subject: [PATCH 13/13] chore: Renaming inputs to switches and just leaving
 cases changes for labels

---
 .github/labeler.yaml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/.github/labeler.yaml b/.github/labeler.yaml
index 441c0a34..e0558a5b 100644
--- a/.github/labeler.yaml
+++ b/.github/labeler.yaml
@@ -81,8 +81,7 @@ reeds2pras:
   - changed-files:
       - any-glob-to-any-file: "reeds2pras/**"
 
-inputs:
+switches:
   - changed-files:
       - any-glob-to-any-file:
-          - "inputs/**"
           - "cases.csv"