start ci and update readme

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.github/workflows/R-CMD-check.yaml

@@ -0,0 +1,66 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: main
+  pull_request:
+    branches: main
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macos-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest,  r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,  r: 'release'}
+
+    env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      RSPM: ${{ matrix.config.rspm }}
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      _R_CHECK_FORCE_SUGGESTS_: false
+
+    steps:
+      - name: Install deps on MacOS
+        if: runner.os == 'macOS'
+        run: |
+          brew install --cask xquartz
+          brew install cairo
+          brew install udunits
+        shell: bash
+
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          pak-version: devel
+          extra-packages: |
+            any::rcmdcheck
+            nlmixr2/lotri
+            nlmixr2/dparser-R
+            nlmixr2/rxode2ll
+            nlmixr2/rxode2parse
+            nlmixr2/rxode2random
+            nlmixr2/rxode2et
+            nlmixr2/rxode2
+          needs: check
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true

.github/workflows/pkgdown.yaml

@@ -0,0 +1,62 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown
+
+jobs:
+  pkgdown:
+    runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: |
+            any::pkgdown
+            nlmixr2/lotri
+            nlmixr2/dparser-R
+            nlmixr2/rxode2ll
+            nlmixr2/rxode2parse
+            nlmixr2/rxode2random
+            nlmixr2/rxode2et
+            nlmixr2/rxode2
+            nlmixr2/nlmixr2est
+            nlmixr2/nlmixr2extra
+            nlmixr2/nlmixr2plot
+            nlmixr2/nlmixr2
+            nlmixr2/babelmixr2
+            nlmixr2/nlmixr2rpt
+            lixoftConnectors=?ignore
+            local::.
+          needs: website
+
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/github-pages-deploy-action@v4.4.1
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

.github/workflows/test-coverage.yaml

@@ -0,0 +1,59 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: test-coverage
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          pak-version: devel
+          extra-packages: |
+            any::covr
+            nlmixr2/lotri
+            nlmixr2/dparser-R
+            nlmixr2/rxode2ll
+            nlmixr2/rxode2parse
+            nlmixr2/rxode2random
+            nlmixr2/rxode2et
+            nlmixr2/rxode2
+          needs: coverage
+
+      - name: Test coverage
+        run: |
+          covr::codecov(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
+          )
+        shell: Rscript {0}
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v3
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package

README.Rmd

@@ -16,6 +16,17 @@ knitr::opts_chunk$set(
 # monolix2rx <img src="man/figures/logo.png" align="right" height="138" alt="" />
 
 <!-- badges: start -->
+[![R-CMD-check](https://github.com/nlmixr2/monolix2rx/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/nlmixr2/monolix2rx/actions/workflows/R-CMD-check.yaml)
+[![Codecov test
+coverage](https://codecov.io/gh/nlmixr2/monolix2rx/branch/main/graph/badge.svg)](https://app.codecov.io/gh/nlmixr2/monolix2rx?branch=main)
+[![CRAN
+version](http://www.r-pkg.org/badges/version/monolix2rx)](https://cran.r-project.org/package=monolix2rx)
+[![CRAN total
+downloads](https://cranlogs.r-pkg.org/badges/grand-total/monolix2rx)](https://cran.r-project.org/package=monolix2rx)
+[![CRAN total
+downloads](https://cranlogs.r-pkg.org/badges/monolix2rx)](https://cran.r-project.org/package=monolix2rx)
+[![CodeFactor](https://www.codefactor.io/repository/github/nlmixr2/monolix2rx/badge)](https://www.codefactor.io/repository/github/nlmixr2/monolix2rx)
+![r-universe](https://nlmixr2.r-universe.dev/badges/monolix2rx)
 <!-- badges: end -->
 
 The goal of monolix2rx is to convert `Monolix` to `rxode2` to use for
@@ -33,11 +44,33 @@ devtools::install_github("nlmixr2/monolix2rx")
 
 ## Example
 
-This is a basic example which shows you how to solve a common problem:
+If you are trying to convert a Monolix to a rxode2 model you simply
+need the path to the `mlxtran` file.  For example, the classic demo of
+theophylline is included in `monolix2rx` and can be imported below:
 
 ```{r example}
 library(monolix2rx)
-## basic example code
+# First load in the model; in this case the theo model
+# This is modified from the Monolix demos by saving the model
+# file as a text file (hence you can access without model library).
+# Additionally some of the file paths were shortened so they could
+# be included with monolix2rx
+
+pkgTheo <- system.file("theo", package="monolix2rx")
+mlxtranFile <- file.path(pkgTheo, "theophylline_project.mlxtran")
+
+rx <- monolix2rx(mlxtranFile)
+
+rx
+
+# If you are only interseted in the parsing you can use `mlxtran`
+
+mlx <- mlxtran(mlxtranFile)
+
+mlx
+
+# this can be converted to a list
+head(as.list(mlx))
 ```
 
 ## Translating models from the Monolix model library