Initial python linting

.github/workflows/code-linting-ci.yml

@@ -0,0 +1,33 @@
+name: Code Linting
+
+on:
+  workflow_dispatch:
+  push:
+    paths:
+      - '**/*.py'
+    branches:
+      - main
+      - dev
+  pull_request:
+    paths:
+      - '**/*.py'
+    branches:
+      - main
+      - dev
+
+jobs:
+  unit-tests:
+    runs-on: ubuntu-latest
+    container:
+      image: hopkinsidd/flepimop:latest-dev
+      options: --user root
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          lfs: true
+      - name: Black Formatter Check
+        uses: psf/black@stable
+        with:
+          src: "."
+          options: "--check --quiet"

.github/workflows/flepicommon-ci.yml

@@ -0,0 +1,41 @@
+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:
+  unit-tests:
+    runs-on: ubuntu-latest
+    container:
+      image: hopkinsidd/flepimop:latest-dev
+      options: --user root
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          lfs: true
+      - name: Set up Rprofile
+        run: |
+          cp build/docker/Docker.Rprofile $HOME/.Rprofile
+          cp /home/app/.bashrc $HOME/.bashrc
+        shell: bash
+      - name: Install local R packages
+        run: Rscript build/local_install.R
+        shell: bash
+      - name: Run flepicommon tests
+        run: |
+          setwd("flepimop/R_packages/flepicommon")
+          devtools::test(stop_on_failure=TRUE)
+        shell: Rscript {0}

.github/workflows/gempyor-ci.yml

@@ -0,0 +1,48 @@
+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:
+  unit-tests:
+    runs-on: ubuntu-latest
+    container:
+      image: hopkinsidd/flepimop:latest-dev
+      options: --user root
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          lfs: true
+      - name: Install the gempyor package
+        run: |
+          source /var/python/3.10/virtualenv/bin/activate
+          python -m pip install --upgrade pip
+          python -m pip install "flepimop/gempyor_pkg[test]"
+        shell: bash
+      - name: Run gempyor tests
+        run: |
+          source /var/python/3.10/virtualenv/bin/activate
+          cd flepimop/gempyor_pkg
+          pytest --exitfirst
+        shell: bash
+      - name: Run gempyor-cli integration tests from examples
+        run: |
+          source /var/python/3.10/virtualenv/bin/activate
+          cd examples
+          pytest --exitfirst
+        shell: bash

.github/workflows/inference-ci.yml

@@ -0,0 +1,41 @@
+name: inference-ci
+
+on:
+  workflow_dispatch:
+  push:
+    paths:
+      - flepimop/R_packages/inference/**/*
+    branches:
+      - main
+      - dev
+  pull_request:
+    paths:
+      - flepimop/R_packages/inference/**/*
+    branches:
+      - main
+      - dev
+
+jobs:
+  unit-tests:
+    runs-on: ubuntu-latest
+    container:
+      image: hopkinsidd/flepimop:latest-dev
+      options: --user root
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          lfs: true
+      - name: Set up Rprofile
+        run: |
+          cp build/docker/Docker.Rprofile $HOME/.Rprofile
+          cp /home/app/.bashrc $HOME/.bashrc
+        shell: bash
+      - name: Install local R packages
+        run: Rscript build/local_install.R
+        shell: bash
+      - name: Run inference tests
+        run: |
+          setwd("flepimop/R_packages/inference")
+          devtools::test(stop_on_failure=TRUE)
+        shell: Rscript {0}