WIP: Release Cycle, ? 2025

.github/actions/flepimop-install/action.yml

@@ -0,0 +1,53 @@
+name: flepiMoP Install
+description: Install flepiMoP and its dependencies
+inputs:
+  python-version:
+    description: Python version to use
+    required: true
+    default: "3.11"
+  R-version:
+    description: R version to use
+    required: true
+    default: "4.3"
+runs:
+  using: "composite"
+  steps:
+    - name: Install system dependencies
+      run: |
+        sudo apt update
+        sudo apt install \
+          libcurl4-openssl-dev \
+          libharfbuzz-dev \
+          libfribidi-dev \
+          libtiff5-dev \
+          libudunits2-dev \
+          libgdal-dev \
+          libgeos-dev \
+          libproj-dev \
+          libfontconfig1-dev \
+          pandoc
+      shell: bash
+    - name: Setup miniconda
+      uses: conda-incubator/setup-miniconda@v3
+      with:
+        auto-update-conda: true
+    - name: Conda venv cache
+      id: conda-venv-cache
+      uses: actions/cache@v4
+      with:
+        key: flepimop-conda-${{ runner.os }}-${{ inputs.R-version }}-${{ inputs.python-version }}-${{ hashFiles('flepimop/R_packages/flepicommon/DESCRIPTION', 'flepimop/R_packages/flepicommon/NAMESPACE', 'flepimop/R_packages/flepiconfig/DESCRIPTION', 'flepimop/R_packages/flepiconfig/NAMESPACE', 'flepimop/R_packages/inference/DESCRIPTION', 'flepimop/R_packages/inference/NAMESPACE', 'flepimop/gempyor_pkg/pyproject.toml', 'environment.yml') }}
+        path: './venv'
+    - name: Install flepiMoP
+      if: steps.conda-venv-cache.outputs.cache-hit != 'true'
+      run: |
+        rm -rf venv/
+        sed -i 's/^- python.*$/- python=${{ inputs.python-version}}/g' environment.yml
+        sed -i 's/^- r-base.*$/- r-base=${{ inputs.R-version}}/g' environment.yml
+        ./bin/flepimop-install-dev
+      shell: bash -el {0}
+    - name: flepiMoP install info
+      run: |
+        conda activate venv/
+        export FLEPI_PATH=$(pwd)
+        ./bin/flepimop-install-info
+      shell: bash -el {0}

.github/workflows/conda-env.yml

@@ -2,12 +2,6 @@ name: Generate Conda Environment
 
 on:
   workflow_dispatch:
-  push:
-    paths:
-      - build/create_environment_yml.R
-      - flepimop/R_packages/*/DESCRIPTION
-    branches:
-      - dev
   pull_request:
     types:
       - edited

.github/workflows/flepicommon-ci.yml

@@ -2,11 +2,6 @@ name: flepicommon CI
 
 on:
   workflow_dispatch:
-  push:
-    paths:
-      - flepimop/R_packages/flepicommon/**/*
-    branches:
-      - dev
   pull_request:
     types:
       - edited
@@ -26,66 +21,26 @@ jobs:
     if: github.event_name != 'pull_request' || github.event.pull_request.draft == false
     strategy:
       matrix:
-        R-version: ["4.3.3"]
+        python-version: ["3.11"]
+        R-version: ["4.3"]
     steps:
-      - name: Checkout
+      - name: Checkout flepiMoP
         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
+          persist-credentials: false
+      - name: Install flepiMoP
+        uses: ./.github/actions/flepimop-install
         with:
-          r-version: ${{ matrix.R-version }}
-          update-rtools: true
-      - name: Install System Dependencies
-        run: sudo apt install libcurl4-openssl-dev libharfbuzz-dev libfribidi-dev libtiff5-dev libudunits2-dev libgdal-dev libgeos-dev libproj-dev libfontconfig1-dev
-      - name: Determine R Library Location
-        run: |
-          R_LIBPATH=$( 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: ${{ env.R_LIBPATH }}
-          restore-keys: |
-            flepicommon-rlibs-${{ runner.os }}-${{ matrix.R-version }}-${{ hashFiles('flepimop/R_packages/flepicommon/DESCRIPTION', 'flepimop/R_packages/flepicommon/NAMESPACE') }}-${{ env.R_LIBPATH_CKSUM }}-
-            flepicommon-rlibs-${{ runner.os }}-${{ matrix.R-version }}-${{ hashFiles('flepimop/R_packages/flepicommon/DESCRIPTION', 'flepimop/R_packages/flepicommon/NAMESPACE') }}-
-            flepicommon-rlibs-${{ runner.os }}-${{ matrix.R-version }}-
-      - 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("epidatr", 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
+          python-version: ${{ matrix.python-version }}
+          R-version: ${{ matrix.R-version }}
+      - name: Run tests
         run: |
-          library(testthat)
-          test_package("flepicommon")
-        shell: Rscript {0}
+          conda activate venv/
+          export FLEPI_PATH=$(pwd)
+          Rscript -e "library(testthat); test_package('flepicommon')"
+        shell: bash -el {0}

.github/workflows/gempyor-ci.yml

@@ -2,12 +2,6 @@ name: gempyor CI
 
 on:
   workflow_dispatch:
-  push:
-    paths:
-      - examples/**/*
-      - flepimop/gempyor_pkg/**/*
-    branches:
-      - dev
   pull_request:
     types:
       - edited
@@ -23,76 +17,115 @@ on:
       - main
 
 jobs:
-  tests:
+  fast-tests:
     runs-on: ubuntu-latest
     if: github.event_name != 'pull_request' || github.event.pull_request.draft == false
     strategy:
       matrix:
         python-version: ["3.10", "3.11"]
+        R-version: ["4.3"]
     steps:
-      - name: Checkout
+      - name: Checkout flepiMoP
         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
+          persist-credentials: false
+      - name: Install flepiMoP
+        uses: ./.github/actions/flepimop-install
         with:
           python-version: ${{ matrix.python-version }}
-      - name: Install gempyor
+          R-version: ${{ matrix.R-version }}
+      - name: Run doctests
         run: |
-          python -m pip install --upgrade pip
-          python -m pip install "flepimop/gempyor_pkg[dev]"
-        shell: bash
-      - name: Run gempyor tests
+          conda activate venv/
+          export FLEPI_PATH=$(pwd)
+          cd flepimop/gempyor_pkg
+          pytest --doctest-modules --exitfirst src/gempyor/
+        shell: bash -el {0}
+      - name: Run fast unit tests
         run: |
+          conda activate venv/
           export FLEPI_PATH=$(pwd)
           cd flepimop/gempyor_pkg
-          pytest --exitfirst
-        shell: bash
+          pytest -m "not slow" --exitfirst
+        shell: bash -el {0}
       - name: Run gempyor-cli integration tests from examples
         run: |
+          conda activate venv/
           cd examples
           pytest --exitfirst
-        shell: bash
-  doc-updates:
+        shell: bash -el {0}
+  slow-tests:
+    needs: fast-tests
     runs-on: ubuntu-latest
     if: github.event_name != 'pull_request' || github.event.pull_request.draft == false
+    strategy:
+      matrix:
+        python-version: ["3.11"]
+        R-version: ["4.3"]
     steps:
-      - name: Checkout
+      - name: Checkout flepiMoP
         uses: actions/checkout@v4
         with:
-          ref: ${{ github.head_ref || github.ref }}
           lfs: true
           sparse-checkout: |
             *
-            !tests/
+            !documentation/
           sparse-checkout-cone-mode: false
-      - name: Setup Python 3.11
-        uses: actions/setup-python@v5
+          persist-credentials: false
+      - name: Install flepiMoP
+        uses: ./.github/actions/flepimop-install
         with:
-          python-version: '3.11'
-      - name: Install gempyor
+          python-version: ${{ matrix.python-version }}
+          R-version: ${{ matrix.R-version }}
+      - name: Run slow unit tests
         run: |
-          python -m pip install --upgrade pip
-          python -m pip install "flepimop/gempyor_pkg[dev]"
-        shell: bash
+          conda activate venv/
+          export FLEPI_PATH=$(pwd)
+          cd flepimop/gempyor_pkg
+          pytest -m "slow"
+        shell: bash -el {0}
+  doc-updates:
+    runs-on: ubuntu-latest
+    if: github.event_name != 'pull_request' || github.event.pull_request.draft == false
+    strategy:
+      matrix:
+        python-version: ["3.11"]
+        R-version: ["4.3"]
+    steps:
+      - name: Checkout flepiMoP
+        uses: actions/checkout@v4
+        with:
+          lfs: true
+          sparse-checkout: |
+            *
+            !documentation/
+          sparse-checkout-cone-mode: false
+          persist-credentials: false
+      - name: Install flepiMoP
+        uses: ./.github/actions/flepimop-install
+        with:
+          python-version: ${{ matrix.python-version }}
+          R-version: ${{ matrix.R-version }}
       - name: Build gempyor documentation with Sphinx
         run: |
+          conda activate venv/
+          export FLEPI_PATH=$(pwd)
           cd flepimop/gempyor_pkg/docs
           make fullbuild
-        shell: bash
-      - name: Install pandoc 
-        run: |
-          sudo apt-get update && sudo apt-get install -y pandoc
+        shell: bash -el {0}
       - name: Build click documentation with click-man
         run: |
+          conda activate venv/
+          export FLEPI_PATH=$(pwd)
           cd flepimop/gempyor_pkg
           click-man flepimop --target docs/cli_man --man-version 1
           python docs/click-man_parsing.py
+        shell: bash -el {0}
       - name: Remove temporal metadata from man page headers
         run: |
           sed -i 's/^\(\.TH [^"]* \)"[^"]*" "\(.*\)"/\1"" "\2"/' flepimop/gempyor_pkg/docs/cli_man/*.1