Split ci.yml into separate actions

.github/workflows/flepicommon-ci.yml

@@ -0,0 +1,81 @@
+name: flepicommon-ci
+
+on:
+  workflow_dispatch:
+  push:
+    paths:
+      - flepimop/R_packages/flepicommon/**/*
+    branches:
+      - main
+      - dev
+  pull_request:
+    paths:
+      - flepimop/R_packages/flepicommon/**/*
+    branches:
+      - main
+      - dev
+
+jobs:
+  tests:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        R-version: ["4.3.3"]
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          lfs: true
+          sparse-checkout: |
+            *
+            !documentation/
+          sparse-checkout-cone-mode: false
+      - name: Setup R
+        uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.R-version }}
+          update-rtools: true
+      - name: Install System Dependencies
+        run: sudo apt install libcurl4-openssl-dev libharfbuzz-dev libfribidi-dev libtiff5-dev libudunits2-dev libgdal-dev libgeos-dev libproj-dev
+      - name: Determine R Library Location
+        run: |
+          R_LIBPATH=$( R -s -e "cat(.libPaths()[1L])" | xargs )
+          echo "R_LIBPATH=$R_LIBPATH" >> $GITHUB_ENV
+          R_LIBPATH_CKSUM=$( echo "$R_LIBPATH" | cksum | cut -d ' ' -f 1 )
+          echo "R_LIBPATH_CKSUM=$R_LIBPATH_CKSUM" >> $GITHUB_ENV
+          CACHE_DATE=$( date -d "last Sunday" +%Y%m%d )
+          echo "CACHE_DATE=$CACHE_DATE" >> $GITHUB_ENV
+      - name: R Library Cache
+        uses: actions/cache@v4
+        with:
+          key: flepicommon-rlibs-${{ runner.os }}-${{ matrix.R-version }}-${{ hashFiles('flepimop/R_packages/flepicommon/DESCRIPTION', 'flepimop/R_packages/flepicommon/NAMESPACE') }}-${{ env.R_LIBPATH_CKSUM }}-${{ env.CACHE_DATE }}
+          path: ${{ env.R_LIBPATH }}
+      - name: Install R Dependencies
+        if: steps.r-library-cache.outputs.cache-hit != 'true'
+        run: |
+          install.packages(
+            "devtools",
+            repos = "https://cloud.r-project.org",
+          )
+          library(devtools)
+          devtools::install_deps(
+            pkg = "flepimop/R_packages/flepicommon",
+            dependencies = TRUE
+          )
+          install.packages("covidcast", repos = "https://cloud.r-project.org")
+        shell: Rscript {0}
+      - name: Install The flepicommon Package
+        run: |
+          devtools::install(
+            pkg = "flepimop/R_packages/flepicommon",
+            args = c(getOption("devtools.install.args"), "--install-tests"),
+            quick = TRUE,
+            dependencies = TRUE,
+            force = TRUE
+          )
+        shell: Rscript {0}
+      - name: Run Tests
+        run: |
+          library(testthat)
+          test_package("flepicommon")
+        shell: Rscript {0}

.github/workflows/gempyor-ci.yml

@@ -0,0 +1,53 @@
+name: gempyor-ci
+
+on:
+  workflow_dispatch:
+  push:
+    paths:
+      - examples/**/*
+      - flepimop/gempyor_pkg/**/*
+    branches:
+      - main
+      - dev
+  pull_request:
+    paths:
+      - examples/**/*
+      - flepimop/gempyor_pkg/**/*
+    branches:
+      - main
+      - dev
+
+jobs:
+  tests:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.10", "3.11"]
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          lfs: true
+          sparse-checkout: |
+            *
+            !documentation/
+          sparse-checkout-cone-mode: false
+      - name: Setup Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install gempyor
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install "flepimop/gempyor_pkg[test]"
+        shell: bash
+      - name: Run gempyor tests
+        run: |
+          cd flepimop/gempyor_pkg
+          pytest --exitfirst
+        shell: bash
+      - name: Run gempyor-cli integration tests from examples
+        run: |
+          cd examples
+          pytest --exitfirst
+        shell: bash

.github/workflows/inference-ci.yml

@@ -0,0 +1,114 @@
+name: inference-ci
+
+on:
+  workflow_dispatch:
+  workflow_run:
+    workflows: ['flepicommon-ci', 'gempyor-ci']
+    types:
+      - completed
+  push:
+    paths:
+      - flepimop/R_packages/inference/**/*
+    branches:
+      - main
+      - dev
+  pull_request:
+    paths:
+      - flepimop/R_packages/inference/**/*
+    branches:
+      - main
+      - dev
+
+jobs:
+  tests:
+    runs-on: ubuntu-latest
+    if: ${{ github.event_name != 'workflow_run' || github.event.workflow_run.conclusion == 'success' }}
+    strategy:
+      matrix:
+        R-version: ["4.3.3"]
+        python-version: ["3.10", "3.11"]
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          lfs: true
+          sparse-checkout: |
+            *
+            !documentation/
+          sparse-checkout-cone-mode: false
+      - name: Setup Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install gempyor
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install "flepimop/gempyor_pkg[test]"
+        shell: bash
+      - name: Setup R
+        uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.R-version }}
+          update-rtools: true
+      - name: Install System Dependencies
+        run: sudo apt install libcurl4-openssl-dev libharfbuzz-dev libfribidi-dev libtiff5-dev libudunits2-dev libgdal-dev libgeos-dev libproj-dev
+      - name: Determine R Library Location
+        run: |
+          R_LIBPATH=$( R -s -e "cat(.libPaths()[1L])" | xargs )
+          echo "R_LIBPATH=$R_LIBPATH" >> $GITHUB_ENV
+          R_LIBPATH_CKSUM=$( echo "$R_LIBPATH" | cksum | cut -d ' ' -f 1 )
+          echo "R_LIBPATH_CKSUM=$R_LIBPATH_CKSUM" >> $GITHUB_ENV
+          CACHE_DATE=$( date -d "last Sunday" +%Y%m%d )
+          echo "CACHE_DATE=$CACHE_DATE" >> $GITHUB_ENV
+      - name: R Library Cache
+        uses: actions/cache@v4
+        with:
+          key: inference-rlibs-${{ runner.os }}-${{ matrix.R-version }}-${{ hashFiles('flepimop/R_packages/flepicommon/DESCRIPTION', 'flepimop/R_packages/flepicommon/NAMESPACE', 'flepimop/R_packages/inference/DESCRIPTION', 'flepimop/R_packages/inference/NAMESPACE') }}-${{ env.R_LIBPATH_CKSUM }}-${{ env.CACHE_DATE }}
+          path: ${{ env.R_LIBPATH }}
+      - name: Install R Dependencies For flepicommon
+        if: steps.r-library-cache.outputs.cache-hit != 'true'
+        run: |
+          install.packages(
+            "devtools",
+            repos = "https://cloud.r-project.org",
+          )
+          library(devtools)
+          devtools::install_deps(
+            pkg = "flepimop/R_packages/flepicommon",
+            dependencies = TRUE
+          )
+          install.packages("covidcast", repos = "https://cloud.r-project.org")
+        shell: Rscript {0}
+      - name: Install The flepicommon Package
+        run: |
+          devtools::install(
+            pkg = "flepimop/R_packages/flepicommon",
+            quick = TRUE,
+            dependencies = TRUE,
+            force = TRUE
+          )
+        shell: Rscript {0}
+      - name: Install R Dependencies For inference
+        if: steps.r-library-cache.outputs.cache-hit != 'true'
+        run: |
+          devtools::install_deps(
+            pkg = "flepimop/R_packages/inference",
+            dependencies = TRUE
+          )
+          install.packages("covidcast", repos = "https://cloud.r-project.org")
+        shell: Rscript {0}
+      - name: Install The inference Package
+        run: |
+          devtools::install(
+            pkg = "flepimop/R_packages/inference",
+            args = c(getOption("devtools.install.args"), "--install-tests"),
+            quick = TRUE,
+            dependencies = TRUE,
+            force = TRUE
+          )
+        shell: Rscript {0}
+      - name: Run Tests
+        run: |
+          library(testthat)
+          test_package("inference")
+        shell: Rscript {0}

flepimop/R_packages/flepicommon/R/DataUtils.R

@@ -1019,4 +1019,3 @@ get_CSSE_US_matchGlobal_data <- function(){
 
 }
 
-

flepimop/R_packages/inference/R/inference_to_forecast.R

@@ -28,6 +28,7 @@ cum_death_forecast <- function (sim_data,
 
 }
 
+
 ##'
 ##' Creates a merged forecast from a data object and a set of sims.
 ##' 

flepimop/gempyor_pkg/src/gempyor/__init__.py

@@ -1,4 +1,3 @@
 ## All functions are in minimal inference.
-
 from .inference import *
 from .utils import *