Finish Release-2

# Conflicts:
#	.github/workflows/binder.yaml
#	.github/workflows/workflowr.yaml
#	README.Rmd
#	README.md
#	heads_thesis.Rproj
#	protocol/references.bib

.Rbuildignore

@@ -0,0 +1,47 @@
+^renv$
+^renv\.lock$
+^\.vscode$
+^\.editorconfig$
+^.*\.code-workspace$
+^.*\.Rout$
+^.*\.Rproj$
+^.*\.yml$
+^\..*$
+^\.Rproj\.user$
+^cran-comments\.md$
+^CRAN-RELEASE$
+^dev$
+^docs$
+^pdfs$
+^examples_.*$
+^LICENSE\.md$
+^LOCAL_APPDATA_FONTCONFIG_CACHE$
+^NEWS\.md$
+^NEWS\.Rmd$
+^packrat$
+^pkgdown$
+^README-.*\.png$
+^README\.Rmd$
+^README_cache$
+^revdep$
+^src-i386$
+^false.alarm-Ex_i386\.Rout$
+^false.alarm-Ex_x64\.Rout$
+^false.alarm.*\.tar\.gz$
+^false.alarm.*\.tgz$
+^false.alarm\.Rcheck$
+^API$
+^\.github$
+^codecov\.yml$
+\.clang-format
+^Makefile$
+^docs/_pkgdown\.yml$
+^_targets*$
+^_targets\.R$
+^analysis$
+^output$
+^protocol$
+^review$
+^thesis$
+^data-raw$
+^inst/extdata$

.Rprofile

@@ -1,5 +1,86 @@
+# nolint start
+if (.Platform$OS.type == "windows") {
+  Sys.setenv(LC_CTYPE="C")
+}
+
 source("renv/activate.R")
-setHook("rstudio.sessionInit", function(newSession) {
- if (newSession & is.null(rstudioapi::getActiveProject()))
-   rstudioapi::openProject("heads_thesis.Rproj")
-}, action = "append")
+
+if (Sys.getenv("CI") == "") { # not CI
+
+  a <- NULL
+  suppressMessages(if (requireNamespace("languageserver", quietly = TRUE)) {
+    a <- try(suppressWarnings(source(file.path(
+      Sys.getenv(if (.Platform$OS.type == "windows") {
+        "USERPROFILE"
+      } else {
+        "HOME"
+      }),
+      ".vscode-R",
+      "init.R"
+    ))),
+    silent = TRUE
+    )
+  })
+
+  if (class(a) == "try-error") {
+    message("Starting Binder Session")
+    setHook("rstudio.sessionInit", function(newSession) {
+      if (newSession & is.null(rstudioapi::getActiveProject())) {
+        rstudioapi::openProject("false.alarm.Rproj")
+      }
+    }, action = "append")
+  }
+
+  rm(a)
+
+  if (interactive()) {
+    options(
+      warnPartialMatchArgs = FALSE,
+      warnPartialMatchDollar = FALSE,
+      warnPartialMatchAttr = FALSE,
+      usethis.protocol = "https",
+      vsc.rstudioapi = TRUE
+      # error = recover
+    )
+
+    suppressMessages(
+      suppressWarnings({
+        require("testthat", quietly = TRUE)
+        require("devtools", quietly = TRUE)
+        require("usethis", quietly = TRUE)
+        require("conflicted", quietly = TRUE)
+        require("here", quietly = TRUE)
+        require("workflowr", quietly = TRUE)
+        require("targets", quietly = TRUE)
+        require("tarchetypes", quietly = TRUE)
+      })
+    )
+    # suppressMessages(prettycode::prettycode())
+
+    if (suppressMessages(requireNamespace("prompt", quietly = TRUE))) {
+      prompt::set_prompt(function(...) {
+        paste0(
+          "[",
+          prompt::git_branch(),
+          prompt::git_dirty(),
+          prompt::git_arrows(),
+          "] ",
+          prompt::prompt_runtime()
+        )
+      })
+    }
+  }
+} else { # is CI
+  suppressMessages(
+    suppressWarnings({
+      require("here", quietly = TRUE)
+      require("workflowr", quietly = TRUE)
+      require("targets", quietly = TRUE)
+      require("tarchetypes", quietly = TRUE)
+    })
+  )
+}
+
+
+
+# nolint end

.covrignore

@@ -0,0 +1 @@
+renv/**

.editorconfig

@@ -0,0 +1,12 @@
+# EditorConfig is awesome: https://EditorConfig.org
+
+# top-most EditorConfig file
+root = true
+
+[*]
+indent_style = space
+indent_size = 2
+end_of_line = lf
+charset = utf-8
+trim_trailing_whitespace = true
+insert_final_newline = true

.gitattributes

@@ -0,0 +1,3 @@
+# Classify R Markdown files as R code for GitHub language statistics
+# https://github.com/github/linguist#overrides
+*.[Rr]md linguist-language=R

.github/.gitignore

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

.github/config.yml

@@ -0,0 +1,4 @@
+todo:
+  keyword: ["@todo", "TODO", "TODO:"]
+  autoAssign: true
+  caseSensitive: true

.github/dependabot.yml

@@ -0,0 +1,13 @@
+# To get started with Dependabot version updates, you'll need to specify which
+# package ecosystems to update and where the package manifests are located.
+# Please see the documentation for all configuration options:
+# https://help.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    # Workflow files stored in the
+    # default location of `.github/workflows`
+    directory: "/"
+    schedule:
+      interval: "daily"

.github/fix-timestamps.sh

@@ -0,0 +1,9 @@
+#!/bin/bash
+FILES=$1
+
+for f in $FILES
+do
+  echo "Processing $f file..."
+  # take action on each file. $f store current file name
+  touch -d "$(git log -1 --pretty="format:%cI" "$f")" "$f"
+done

.github/gh-pages.sh

@@ -0,0 +1,13 @@
+#!/bin/bash
+git ls-remote --quiet --exit-code origin gh-pages
+if [ $? -ne 0 ]; then
+  dt=$(git rev-parse --abbrev-ref HEAD)
+  dt=${dt//$'\n'/}
+  git checkout --orphan gh-pages
+  git rm -rf --quiet .
+  git commit --allow-empty -m "Initializing gh-pages branch"
+  git push origin HEAD:gh-pages
+  git checkout $dt
+fi
+
+

.github/pull.yml

@@ -0,0 +1,11 @@
+version: "1"
+rules:
+  - base: master
+    upstream: matrix-profile-foundation:master
+    mergeMethod: hardreset
+  - base: main
+    upstream: matrix-profile-foundation:main
+    mergeMethod: hardreset
+  - base: develop
+    upstream: matrix-profile-foundation:develop
+    mergeMethod: hardreset

.github/workflows/binder.yaml

@@ -1,5 +1,8 @@
 name: Binder
-on: [push]
+on:
+  push:
+    branches:
+      - future
 
 jobs:
   Create-MyBinderOrg-Cache:

.github/workflows/lint.yaml

@@ -0,0 +1,58 @@
+# This action will search for R code and apply the rules stored in the .lintr
+# file using the `lintr` R package.
+
+name: Lint
+
+on:
+  push:
+    branches:
+      - main
+      - master
+      - develop
+
+  workflow_dispatch:
+  repository_dispatch:
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      RENV_PATHS_ROOT: ~/.local/share/renv
+    steps:
+      - name: Checking out shallow repository
+        uses: actions/checkout@v2
+
+      - run: git branch
+
+      - name: Install System dependencies
+        run: |
+          sudo apt-fast update
+          sudo apt-fast install -y libgit2-dev libharfbuzz-dev libcurl4-openssl-dev \
+          libfribidi-dev libzmq3-dev
+
+      - name: Setting up R installation
+        uses: r-lib/actions/setup-r@v1
+
+      - name: Cache R packages
+        uses: actions/[email protected]
+        id: cache-packages
+        with:
+          path: ${{ env.RENV_PATHS_ROOT }}
+          key: ${{ runner.os }}-renv-${{ hashFiles('**/renv.lock') }}-targets-v2
+          restore-keys: |
+            ${{ runner.os }}-renv-
+
+      - name: Install dependencies
+        run: |
+          if (!requireNamespace("renv", quietly = TRUE)) install.packages("renv")
+          Sys.unsetenv("GITHUB_PAT")
+          renv::restore()
+        shell: Rscript {0}
+
+      - name: Lint
+        run: |
+          for(i in c("analysis", "R", "review", "thesis", "output")) {
+            lintr::lint_dir(i)
+          }
+        shell: Rscript {0}