Merge pull request #329 from metrumresearchgroup/docs-update

Expand docs and set up site

.github/workflows/site.yaml

@@ -0,0 +1,67 @@
+name: Deploy site
+on:
+  push:
+    branches:
+      - scratch/deploy-site
+    tags:
+      - 'v[0-9]+.[0-9]+.[0-9]+'
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - name: Install Hugo
+        shell: bash
+        run: |
+          tdir=$(mktemp -d)
+          tgz=$tdir/hugo.tar.gz
+          bin=$HOME/bin
+          mkdir -p "$bin"
+
+          url=https://github.com/gohugoio/hugo/releases/download
+          curl -fSsL --retry 3 \
+            "$url/v${HUGO_VERSION}/hugo_extended_${HUGO_VERSION}_linux-amd64.tar.gz" \
+            >"$tgz"
+          printf '%s  %s\n' "$HUGO_SHA" "$tgz" | sha256sum --check >/dev/null
+
+          tar --to-stdout --extract -zf "$tgz" hugo >"$bin"/hugo
+          chmod +x "$bin/hugo"
+          "$bin"/hugo version
+          echo "$bin" >>"$GITHUB_PATH"
+        env:
+          HUGO_VERSION: '0.133.0'
+          HUGO_SHA: '372530e2de9ae74087a987ca841429390a055123b8a4dec665cc601f10dc8e6e'
+      - uses: actions/configure-pages@v5
+        id: pages
+      - name: Check URL match
+        shell: bash
+        run: |
+          url=$(grep '^baseURL:' docs/site/hugo.yaml)
+          test "${{ steps.pages.outputs.base_url }}/" = "${url#baseURL: }"
+      - name: Build site
+        shell: bash
+        run: make -C docs/site build
+        env:
+          HUGO_ENVIRONMENT: production
+          HUGO_CACHEDIR: ${{ runner.temp }}/hugo_cache
+          TZ: America/New_York
+      - name: Upload site
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: ./docs/site/public
+  deploy:
+    needs: build
+    runs-on: ubuntu-latest
+    permissions:
+      pages: write
+      id-token: write
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4

README.md

@@ -2,6 +2,9 @@
 
 # bbi
 
+Documentation for `bbi` is available at
+<https://metrumresearchgroup.github.io/bbi/docs/>.
+
 bbi is (will be) a complete solution for managing projects involving modeling and simulation with a number 
 of software solutions used in pharmaceutical sciences. 
 
@@ -316,15 +319,21 @@ No Heuristic Problems Detected
 
 ### Development
 
-Test-driven development encouraged, facilitated by goconvey to monitor coverage
-and re-run tests on change(s)
+To run the test suite, you can invoke [scripts/run-unit-tests][ru] and
+[scripts/run-integration-tests][ri] directly or via `make vt-test`.
 
-During development, while installing new versions for testing, running "make install" will auto-append a timestamp to the build version.
+After updating a subcommand, regenerate the Markdown documentation at
+[docs/commands][dc] by running `make vt-gen-docs`.  See `make vt-help` and
+[internal/valtools/README.md][vr] for more details on the validation tooling.
 
-```
-$ go get github.com/smartystreets/goconvey
-goconvey 
-```
+The setup for building the documentation site is described in
+[docs/site/README.md][dr].
 
-a web UI will be started at localhost:8080 with file watchers to rerun tests on 
-file change(s)
+<!-- Note: Use GitHub URLs rather than relative paths (e.g., "/docs/commands") so -->
+<!-- that these work on https://metrumresearchgroup.github.io/bbi/ without further -->
+<!-- processing. -->
+[dc]: https://github.com/metrumresearchgroup/bbi/blob/main/docs/commands
+[dr]: https://github.com/metrumresearchgroup/bbi/blob/main/docs/site/README.md
+[ri]: https://github.com/metrumresearchgroup/bbi/blob/main/scripts/run-integration-tests
+[ru]: https://github.com/metrumresearchgroup/bbi/blob/main/scripts/run-unit-tests
+[vr]: https://github.com/metrumresearchgroup/bbi/blob/main/internal/valtools/README.md

cmd/clean.go

@@ -164,36 +164,30 @@ func getMatches(s []string, expr string, regex bool) ([]string, error) {
 
 func NewCleanCmd() *cobra.Command {
 	cmd := &cobra.Command{
-		Use:   "clean",
-		Short: "clean files and folders",
-		Long: `
-glob examples:
-bbi clean *.mod // anything with extension .mod
-bbi clean *.mod --noFolders // anything with extension .mod
-bbi clean run* // anything starting with run
-regular expression examples:
-
-bbi clean ^run --regex // anything beginning with the letters run
-bbi clean ^run -v --regex // print out files and folders that will be deleted
-bbi clean ^run --filesOnly --regex // only remove matching files
-bbi clean _est_ --dirsOnly --regex // only remove matching folders
-bbi clean _est_ --dirsOnly --preview --regex // show what output would be if clean occured but don't actually clean
-bbi clean "run009.[^mod]" --regex // all matching run009.<ext> but not .mod files
-bbi clean "run009.(mod|lst)$" --regex // match run009.lst and run009.mod
-
-can also clean via the opposite of a match with inverse
-
-bbi clean ".modt{0,1}$" --filesOnly --inverse --regex // clean all files not matching .mod or .modt
-
-clean copied files via
-
-bbi clean --copiedRuns="run001"
-bbi clean --copiedRuns="run[001:010]"
-
-can be a comma separated list as well
-
-bbi clean --copiedRuns="run[001:010],run100"
- `,
+		Use:   "clean [flags] <pattern> [<pattern>...]",
+		Short: "Clean files and folders",
+		Long: `Clean the files and directories that match the specified patterns.
+Whether the pattern is interpreted as a glob or regex is controlled by the
+--regex flag.
+
+If files were copied to the parent directory automatically after model
+execution (via the copy_lvl configuration), the original files in the run
+directory can be cleaned up by selecting the run with the --copiedRuns
+option.`,
+		Example: `  # Remove items in the current directory that end with ".mod"
+  bbi nonmem clean *.mod
+  # The same as above but ensure only files are removed
+  bbi nonmem clean --filesOnly *.mod
+
+  # Remove files in the current directory that start with "run" and end with
+  # ".mod" or ".lst"
+  bbi nonmem clean --filesOnly --regex "run.*\.(mod|lst)$"
+  # Report what the above would remove but don't actually do it
+  bbi nonmem clean --preview --filesOnly --regex "run.*\.(mod|lst)$"
+
+  # Remove copied files (recorded in '{run}_copied.json' by 'bbi run') for
+  # run001, run002, run003, and run100
+  bbi nonmem clean --copiedRuns='run[001:003],run100'`,
 		RunE: clean,
 	}
 

cmd/covcor.go

@@ -24,10 +24,10 @@ import (
 	"github.com/spf13/viper"
 )
 
-const covcorLongDescription string = `load .cov and .cor output from model(s), for example: 
-bbi nonmem covcor run001/run001
-bbi nonmem covcor run001/run001.cov
- `
+const covcorExamples string = `  # Display .cov/cor values from run001/run001.{cov,cor}
+  bbi nonmem covcor run001/run001
+  # Display the same values by specifying a full output file
+  bbi nonmem covcor run001/run001.cov`
 
 func covcor(cmd *cobra.Command, args []string) {
 	if debug {
@@ -47,9 +47,13 @@ func covcor(cmd *cobra.Command, args []string) {
 
 func NewCovcorCmd() *cobra.Command {
 	return &cobra.Command{
-		Use:   "covcor",
-		Short: "load .cov and .cor output from a model run",
-		Long:  covcorLongDescription,
-		Run:   covcor,
+		Use:   "covcor [flags] <run file>",
+		Short: "Display .cov and .cor output for a model",
+		Long: `Read the .cov and .cor files from a model's output directory and
+display the values as a JSON object. The argument is typically a shared prefix
+for the run output files, but it can be any path from which the run name can be
+derived.`,
+		Example: covcorExamples,
+		Run:     covcor,
 	}
 }

cmd/init.go

@@ -55,13 +55,18 @@ func NewInitCmd() *cobra.Command {
 	cmd := &cobra.Command{
 		Use:   "init",
 		Short: "Create configuration file with defaults",
-		Long: `Run bbi init to create a bbi.yaml configuration file in the current directory.
- `,
+		Long: `Write a bbi.yaml configuration file in the current directory
+to initialize it for running bbi.
+
+If the --dir=DIR option is specified, DIR should point to a directory that
+contains one or more NONMEM installations directories. Any subdirectory in
+DIR is taken as an installation if it has the expected layout (e.g., a "run"
+directory with an nmfe executable)`,
 		RunE: initializer,
 	}
 
 	const directory string = "dir"
-	cmd.Flags().StringSlice(directory, []string{}, "A directory in which to look for NonMem Installations")
+	cmd.Flags().StringSlice(directory, []string{}, "directory in which to look for NONMEM installations")
 
 	return cmd
 }

cmd/local.go

@@ -347,15 +347,15 @@ func (l LocalModel) Cleanup(channels *turnstile.ChannelMap) {
 
 func NewLocalCmd() *cobra.Command {
 	cmd := &cobra.Command{
-		Use:   "local",
-		Short: "local specifies to run a (set of) models locally",
-		Long:  runLongDescription,
-		Run:   local,
+		Use:     "local [flags] <model> [<model>...]",
+		Short:   "Run models locally",
+		Example: fmt.Sprintf(runExamples, "local"),
+		Run:     local,
 	}
 
 	childDirIdentifier := "create_child_dirs"
-	cmd.PersistentFlags().Bool(childDirIdentifier, true, "Indicates whether or not local branch execution"+
-		"should create a new subdirectory with the output_dir variable as its name and execute in that directory")
+	cmd.PersistentFlags().Bool(childDirIdentifier, true,
+		"create a new subdirectory, named based on the output_dir option, for execution")
 	errpanic(viper.BindPFlag("local."+childDirIdentifier, cmd.PersistentFlags().Lookup(childDirIdentifier)))
 
 	return cmd

cmd/nonmem.go

@@ -164,79 +164,82 @@ type NonMemModel struct {
 	Error error `json:"error"`
 }
 
-var nonmemLongDescription string = fmt.Sprintf("\n%s\n\n%s\n\n%s\n", runLongDescription, summaryLongDescription, covcorLongDescription)
+var nonmemExamples string = fmt.Sprintf("%s\n\n%s\n\n%s\n",
+	fmt.Sprintf(runExamples, "(local|sge)"),
+	summaryExamples,
+	covcorExamples)
 
 func nonmem(_ *cobra.Command, _ []string) {
-	println(nonmemLongDescription)
+	println(nonmemExamples)
 }
 
 func NewNonmemCmd() *cobra.Command {
 	cmd := &cobra.Command{
-		Use:   "nonmem",
-		Short: "nonmem a (set of) models locally or on the grid",
-		Long:  nonmemLongDescription,
-		Run:   nonmem,
+		Use:     "nonmem",
+		Short:   "Entry point for NONMEM-related subcommands",
+		Example: nonmemExamples,
+		Run:     nonmem,
 	}
 
 	// NM Selector
 	const nmVersionIdentifier string = "nm_version"
-	cmd.PersistentFlags().String(nmVersionIdentifier, "", "Version of nonmem from the configuration list to use")
+	cmd.PersistentFlags().String(nmVersionIdentifier, "", "version of NONMEM from the configuration list to use")
 	errpanic(viper.BindPFlag(nmVersionIdentifier, cmd.PersistentFlags().Lookup(nmVersionIdentifier)))
 
 	// Parallelization Components
 	const parallelIdentifier string = "parallel"
-	cmd.PersistentFlags().Bool(parallelIdentifier, false, "Whether or not to run nonmem in parallel mode")
+	cmd.PersistentFlags().Bool(parallelIdentifier, false, "whether to run NONMEM in parallel mode")
 	errpanic(viper.BindPFlag(parallelIdentifier, cmd.PersistentFlags().Lookup(parallelIdentifier)))
 
 	const parallelCompletionTimeoutIdentifier string = "parallel_timeout"
-	cmd.PersistentFlags().Int(parallelCompletionTimeoutIdentifier, 2147483647, "The amount of time to wait for parallel operations in nonmem before timing out")
+	cmd.PersistentFlags().Int(parallelCompletionTimeoutIdentifier, 2147483647, "amount of time to wait for parallel operations in NONMEM before timing out")
 	errpanic(viper.BindPFlag(parallelCompletionTimeoutIdentifier, cmd.PersistentFlags().Lookup(parallelCompletionTimeoutIdentifier)))
 
 	const mpiExecPathIdentifier string = "mpi_exec_path"
-	cmd.PersistentFlags().String(mpiExecPathIdentifier, "/usr/local/mpich3/bin/mpiexec", "The fully qualified path to mpiexec. Used for nonmem parallel operations")
+	cmd.PersistentFlags().String(mpiExecPathIdentifier, "/usr/local/mpich3/bin/mpiexec", "fully qualified path to mpiexec to use for NONMEM parallel operations")
 	errpanic(viper.BindPFlag(mpiExecPathIdentifier, cmd.PersistentFlags().Lookup(mpiExecPathIdentifier)))
 
 	const parafileIdentifier string = "parafile"
-	cmd.PersistentFlags().String(parafileIdentifier, "", "Location of a user-provided parafile to use for parallel execution")
+	cmd.PersistentFlags().String(parafileIdentifier, "", "location of a user-provided parafile to use for parallel execution")
 	errpanic(viper.BindPFlag(parafileIdentifier, cmd.PersistentFlags().Lookup(parafileIdentifier)))
 
 	const nmQualIdentifier string = "nmqual"
-	cmd.PersistentFlags().Bool(nmQualIdentifier, false, "Whether or not to execute with nmqual (autolog.pl)")
+	cmd.PersistentFlags().Bool(nmQualIdentifier, false, "whether to execute with nmqual (autolog.pl)")
 	errpanic(viper.BindPFlag(nmQualIdentifier, cmd.PersistentFlags().Lookup(nmQualIdentifier)))
 
 	// NMFE Options
 	const nmfeGroup string = "nmfe_options"
 	const licFileIdentifier string = "licfile"
-	cmd.PersistentFlags().String(licFileIdentifier, "", "RAW NMFE OPTION - Specify a license file to use with NMFE (Nonmem)")
+	cmd.PersistentFlags().String(licFileIdentifier, "", "RAW NMFE OPTION - NONMEM license file to use")
 	errpanic(viper.BindPFlag(nmfeGroup+"."+licFileIdentifier, cmd.PersistentFlags().Lookup(licFileIdentifier)))
 
 	const prSameIdentifier string = "prsame"
-	cmd.PersistentFlags().Bool(prSameIdentifier, false, "RAW NMFE OPTION - Indicates to nonmem that the PREDPP compilation step should be skipped")
+	cmd.PersistentFlags().Bool(prSameIdentifier, false, "RAW NMFE OPTION - tell NONMEM to skip the PREDPP compilation step")
 	errpanic(viper.BindPFlag(nmfeGroup+"."+prSameIdentifier, cmd.PersistentFlags().Lookup(prSameIdentifier)))
 
 	const backgroundIdentifier string = "background"
-	cmd.PersistentFlags().Bool(backgroundIdentifier, false, "RAW NMFE OPTION - Tells nonmem not to scan StdIn for control characters")
+	cmd.PersistentFlags().Bool(backgroundIdentifier, false, "RAW NMFE OPTION - tell NONMEM not to scan stdin for control characters")
 	errpanic(viper.BindPFlag(nmfeGroup+"."+backgroundIdentifier, cmd.PersistentFlags().Lookup(backgroundIdentifier)))
 
 	const prCompileIdentifier string = "prcompile"
-	cmd.PersistentFlags().Bool(prCompileIdentifier, false, "RAW NMFE OPTION - Forces PREDPP compilation")
+	cmd.PersistentFlags().Bool(prCompileIdentifier, false, "RAW NMFE OPTION - forces PREDPP compilation")
 	errpanic(viper.BindPFlag(nmfeGroup+"."+prCompileIdentifier, cmd.PersistentFlags().Lookup(prCompileIdentifier)))
 
 	const prDefaultIdentifier string = "prdefault"
-	cmd.PersistentFlags().Bool(prDefaultIdentifier, false, "RAW NMFE OPTION - Do not recompile any routines other than FSUBS")
+	cmd.PersistentFlags().Bool(prDefaultIdentifier, false, "RAW NMFE OPTION - do not recompile any routines other than FSUBS")
 	errpanic(viper.BindPFlag(nmfeGroup+"."+prDefaultIdentifier, cmd.PersistentFlags().Lookup(prDefaultIdentifier)))
 
 	const tprDefaultIdentifier string = "tprdefault"
-	cmd.PersistentFlags().Bool(tprDefaultIdentifier, false, "RAW NMFE OPTION - Test if is okay to do -prdefault")
+	cmd.PersistentFlags().Bool(tprDefaultIdentifier, false, "RAW NMFE OPTION - test if is okay to do -prdefault")
 	errpanic(viper.BindPFlag(nmfeGroup+"."+tprDefaultIdentifier, cmd.PersistentFlags().Lookup(tprDefaultIdentifier)))
 
 	const noBuildIdentifier string = "nobuild"
-	cmd.PersistentFlags().Bool(noBuildIdentifier, false, "RAW NMFE OPTION - Skips recompiling and rebuilding on nonmem executable")
+	cmd.PersistentFlags().Bool(noBuildIdentifier, false, "RAW NMFE OPTION - do not build a new NONMEM executable")
 	errpanic(viper.BindPFlag(nmfeGroup+"."+noBuildIdentifier, cmd.PersistentFlags().Lookup(noBuildIdentifier)))
 
 	const maxLimIdentifier string = "maxlim"
 	cmd.PersistentFlags().Int(maxLimIdentifier, 2,
-		"RAW NMFE OPTION - Set the maximum values for the buffers used by Nonmem (if 0, don't pass -maxlim to nmfe)")
+		"RAW NMFE OPTION - set the maximum values for the buffers used by NONMEM (if 0, don't pass -maxlim to nmfe)")
 	errpanic(viper.BindPFlag(nmfeGroup+"."+maxLimIdentifier, cmd.PersistentFlags().Lookup(maxLimIdentifier)))
 
 	cmd.AddCommand(NewCleanCmd())

cmd/params.go

@@ -32,11 +32,12 @@ import (
 	"github.com/spf13/viper"
 )
 
-const paramsLongDescription string = `summarize model(s), for example:
-bbi nonmem params run001
-bbi nonmem params run001
-bbi nonmem params run001
- `
+const paramsExamples string = `  # Display table of parameters for run001
+  bbi nonmem params run001
+  # Display table of parameters for all model runs the current directory
+  bbi nonmem params --dir=.
+  # Print JSON output instead of a table
+  bbi nonmem params --json --dir=.`
 
 var (
 	noParamNames bool
@@ -434,10 +435,14 @@ func params(cmd *cobra.Command, args []string) {
 
 func NewParamsCmd() *cobra.Command {
 	var cmd = &cobra.Command{
-		Use:   "params",
-		Short: "get the parameters of model(s)",
-		Long:  paramsLongDescription,
-		Run:   params,
+		Use:   "params [flags] [<run dir>]",
+		Short: "Extract the parameter estimates of models",
+		Long: `Display the parameter values from completed models. If a directory is
+specified via --dir, get the parameters of all model runs found in that
+directory. Otherwise the positional argument should specify a run directory
+to extract parameters from.`,
+		Example: paramsExamples,
+		Run:     params,
 	}
 
 	//Used for Summary