Tagbot update (#156)

* Update tagbot * Move from Travis to github actions * Update make.jl * Syntax change: Truncated(..) to truncated(..) * Documentation updates, move to html-based * Update CompatHelper * Structure tests better * Update syntax * Fix test * Update CI * Fix typo * Update README.md * Update tests and update message * Update docs
kahaaga · Feb 16, 2021 · 421a576 · 421a576
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diff --git a/.github/workflows/CompatHelper.yml b/.github/workflows/CompatHelper.yml
@@ -1,24 +1,16 @@
 name: CompatHelper
-
 on:
   schedule:
-    - cron: '00 * * * *'
-
+    - cron: '00 00 * * *'
+  workflow_dispatch:
 jobs:
-  build:
-    runs-on: ${{ matrix.os }}
-    strategy:
-      matrix:
-        julia-version: [1.2.0]
-        julia-arch: [x86]
-        os: [ubuntu-latest]
+  CompatHelper:
+    runs-on: ubuntu-latest
     steps:
-      - uses: julia-actions/setup-julia@latest
-        with:
-          version: ${{ matrix.julia-version }}
       - name: Pkg.add("CompatHelper")
         run: julia -e 'using Pkg; Pkg.add("CompatHelper")'
       - name: CompatHelper.main()
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        run: julia -e 'using CompatHelper; CompatHelper.main()'
+          COMPATHELPER_PRIV: ${{ secrets.DOCUMENTER_KEY }}
+        run: julia -e 'using CompatHelper; CompatHelper.main()'
diff --git a/.github/workflows/TagBot.yml b/.github/workflows/TagBot.yml
@@ -1,11 +1,16 @@
 name: TagBot
 on:
+  issue_comment:  # THIS BIT IS NEW
+    types:
+      - created
   schedule:
     - cron: 0 * * * *
 jobs:
   TagBot:
+    if: github.event_name == 'workflow_dispatch' || github.actor == 'JuliaTagBot'
+
     runs-on: ubuntu-latest
     steps:
-      - uses: JuliaRegistries/TagBot@v1
+      - uses: JuliaRegistries/TagBot@v1.10.0
         with:
           token: ${{ secrets.GITHUB_TOKEN }}
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -0,0 +1,88 @@
+name: CI
+on:
+  pull_request:
+    branches:
+      - master
+  push:
+    branches:
+      - master
+    tags: '*'
+jobs:
+  test:
+    name: Tests, Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        version:
+          - '1' # Replace this with the minimum Julia version that your package supports. E.g. if your package requires Julia 1.5 or higher, change this to '1.5'.
+        os:
+          - ubuntu-latest
+        arch:
+          - x64
+
+    steps:
+      # Cancel ongoing CI test runs if pushing to branch again before the previous tests 
+      # have finished
+      - name: Cancel ongoing test runs for previous commits
+        uses: styfle/[email protected]
+        with:
+          access_token: ${{ github.token }}
+
+      # Do tests
+      - uses: actions/checkout@v2
+      - uses: julia-actions/setup-julia@v1
+        with:
+          version: ${{ matrix.version }}
+          arch: ${{ matrix.arch }}
+      - uses: actions/cache@v1
+        env:
+          cache-name: cache-artifacts
+        with:
+          path: ~/.julia/artifacts
+          key: ${{ runner.os }}-test-${{ env.cache-name }}-${{ hashFiles('**/Project.toml') }}
+          restore-keys: |
+            ${{ runner.os }}-test-${{ env.cache-name }}-
+            ${{ runner.os }}-test-
+            ${{ runner.os }}-
+      - uses: julia-actions/julia-buildpkg@v1
+      - uses: julia-actions/julia-runtest@v1
+      - uses: julia-actions/julia-processcoverage@v1
+      - uses: codecov/codecov-action@v1
+        with:
+          file: lcov.info
+
+  docs:
+    name: Documentation
+    runs-on: ubuntu-latest
+    steps:
+      # Cancel ongoing documentation build if pushing to branch again before the previous 
+      # build is finished.
+      - name: Cancel ongoing documentation builds for previous commits
+        uses: styfle/[email protected]
+        with:
+          access_token: ${{ github.token }}
+
+      # Build docs
+      - uses: actions/checkout@v2
+      - uses: julia-actions/setup-julia@v1
+        with:
+          version: '1'
+      - name: Install dependencies
+        run: |
+          julia --project=docs -e '
+            using Pkg
+            Pkg.develop(PackageSpec(path=pwd()))
+            Pkg.instantiate()'
+      - name: Generate documentation and deploy
+        env: # needed for pushing to gh-pages branch
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}
+        run:
+          julia --project=docs docs/make.jl
+      - name: Doctests
+        run: |
+          julia --project=docs -e '
+            using Documenter: doctest
+            using UncertainData
+            doctest(UncertainData)'
diff --git a/.travis.yml b/.travis.yml
diff --git a/Project.toml b/Project.toml
@@ -2,7 +2,7 @@ name = "UncertainData"
 uuid = "dcd9ba68-c27b-5cea-ae21-829cd07325bf"
 authors = ["Kristian Agasøster Haaga <[email protected]>"]
 repo = "https://github.com/kahaaga/UncertainData.jl.git"
-version = "0.10.3"
+version = "0.10.4"
 
 [deps]
 Bootstrap = "e28b5b4c-05e8-5b66-bc03-6f0c0a0a06e0"
@@ -26,20 +26,20 @@ Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"
 [compat]
 Bootstrap = "^2.2"
 Combinatorics = "^0.7.0, ^1"
-Distributions = "0.21, 1, 0.23"
+Distributions = "0.21, 1, 0.23, 0.24"
 DocumenterTools = "^0.1, ^1"
 DynamicalSystemsBase = "^1.3"
 HypothesisTests = "0.8, 1, 0.10"
-Interpolations = "^0.12, ^1"
+Interpolations = "^0.12, ^1, 0.13"
 IntervalArithmetic = "^0.16, ^1, 0.17"
-KernelDensity = "^0.5.0, ^1"
+KernelDensity = "^0.5.0, ^1, 0.6"
 Measurements = "^2.1"
 RecipesBase = "^0.7, ^1, 0.8"
 Reexport = "^0.2, ^1"
-StaticArrays = "^0.11.0, ^1"
+StaticArrays = "^0.11.0, ^1, 0.12"
 StatsBase = "^0.32.0, ^1, 0.33"
 Unitful = "^0.17.0, ^1, 0.18"
-julia = "^1.1"
+julia = "^1.2"
 
 [extras]
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"

diff --git a/README.md b/README.md
@@ -1,5 +1,8 @@
-[![Build Status](https://travis-ci.com/kahaaga/UncertainData.jl.svg?branch=master)](https://travis-ci.com/kahaaga/UncertainData.jl) [![DOI](https://joss.theoj.org/papers/10.21105/joss.01666/status.svg)](https://doi.org/10.21105/joss.01666) [![DOI](https://zenodo.org/badge/160108056.svg)](https://zenodo.org/badge/latestdoi/160108056) 
-
+[![CI](https://github.com/kahaaga/UncertainData.jl/workflows/CI/badge.svg)](https://github.com/kahaaga/UncertainData.jl/actions)
+[![](https://img.shields.io/badge/docs-latest_tagged-blue.svg)](https://kahaaga.github.io/UncertainData.jl/stable/)
+[![](https://img.shields.io/badge/docs-dev_(master)-blue.svg)](https://kahaaga.github.io/UncertainData.jl/dev/)
+[![DOI](https://joss.theoj.org/papers/10.21105/joss.01666/status.svg)](https://doi.org/10.21105/joss.01666)
+[![DOI](https://zenodo.org/badge/160108056.svg)](https://zenodo.org/badge/latestdoi/160108056) 
 
 # UncertainData.jl
 

diff --git a/docs/Project.toml b/docs/Project.toml
@@ -1,5 +1,6 @@
 [deps]
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+DocumenterTools = "35a29f4d-8980-5a13-9543-d66fff28ecb8"
 DocumenterMarkdown = "997ab1e6-3595-5248-9280-8efb232c3433"
 Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
 Interpolations = "a98d9a8b-a2ab-59e6-89dd-64a1c18fca59"

diff --git a/docs/make.jl b/docs/make.jl
@@ -1,6 +1,13 @@
-
+cd(@__DIR__)
+using Pkg
+CI = get(ENV, "CI", nothing) == "true" || get(ENV, "GITHUB_TOKEN", nothing) !== nothing
+CI && Pkg.activate(@__DIR__)
+CI && Pkg.instantiate()
+CI && (ENV["GKSwstype"] = "100")
 using Documenter
+using DocumenterTools
 using DocumenterMarkdown
+
 using UncertainData
 using Distributions
 using KernelDensity
@@ -11,22 +18,22 @@ using Interpolations
 PAGES = [
     "index.md",
     "Uncertain values" => [
-        "uncertain_values/uncertainvalues_examples.md",
         "uncertain_values/uncertainvalues_overview.md",
+        "uncertain_values/uncertainvalues_theoreticaldistributions.md",
         "uncertain_values/uncertainvalues_kde.md",
         "uncertain_values/uncertainvalues_fitted.md",
-        "uncertain_values/uncertainvalues_theoreticaldistributions.md",
         "uncertain_values/uncertainvalues_certainvalue.md",
         "uncertain_values/uncertainvalues_populations.md",
         "uncertain_values/uncertainvalues_Measurements.md",
-        "uncertain_values/merging.md"
+        "uncertain_values/merging.md",
+        "uncertain_values/uncertainvalues_examples.md",
     ],
 	"Uncertain datasets" => [
         "uncertain_datasets/uncertain_datasets_overview.md",
         "uncertain_datasets/uncertain_index_dataset.md",
         "uncertain_datasets/uncertain_value_dataset.md",
+        "uncertain_datasets/uncertain_indexvalue_dataset.md",
         "uncertain_datasets/uncertain_dataset.md",
-        "uncertain_datasets/uncertain_indexvalue_dataset.md"
 	],
     "Uncertain statistics" => [
         "Core statistics" => [
@@ -52,10 +59,7 @@ PAGES = [
     ],
     "Sampling constraints" => [
         "sampling_constraints/available_constraints.md",
-
         "sampling_constraints/constrain_uncertain_values.md",
-
-        "sampling_constraints/ordered_sequence_exists.md",
         "sampling_constraints/sequential_constraints.md"
     ],
 
@@ -106,19 +110,27 @@ PAGES = [
     "citing.md"
 ]
 
+
+# %% Build docs
+#PyPlot.ioff()
+cd(@__DIR__)
+ENV["JULIA_DEBUG"] = "Documenter"
+
+
 makedocs(
     modules = [UncertainData],
     sitename = "UncertainData.jl documentation",
-    format = Markdown(),
+    format = format = Documenter.HTML(
+        prettyurls = CI,
+        ),
     pages = PAGES
 )
 
-if !Sys.iswindows()
+
+if CI
     deploydocs(
-        deps   = Deps.pip("mkdocs==0.17.5", "mkdocs-material==2.9.4",
-        "python-markdown-math", "pygments", "pymdown-extensions"),
-        repo   = "github.com/kahaaga/UncertainData.jl.git",
-        target = "site",
-        make = () -> run(`mkdocs build`)
+        repo = "github.com/kahaaga/UncertainData.jl.git",
+        target = "build",
+        push_preview = true
     )
 end
diff --git a/docs/src/changelog.md b/docs/src/changelog.md
@@ -1,6 +1,16 @@
 
 # Changelog
 
+## UncertainData.jl v0.10.4
+
+### Documentation
+
+- Changed to regular documentation template.
+
+### Bug fixes
+
+- Fixed type error for test.
+
 ## UncertainData.jl v0.10.3
 
 ### Improvements

diff --git a/docs/src/citing.md b/docs/src/citing.md
@@ -1,3 +1,6 @@
+# Citing
+
 If you use UncertainData.jl for any of your projects or scientific publications, please cite [this small Journal of Open Source Software (JOSS) publication](https://joss.theoj.org/papers/10.21105/joss.01666) as follows
 
 > Haaga, (2019). UncertainData.jl: a Julia package for working with measurements and datasets with uncertainties.. Journal of Open Source Software, 4(43), 1666, https://doi.org/10.21105/joss.01666
+
diff --git a/docs/src/implementing_algorithms_for_uncertaindata.md b/docs/src/implementing_algorithms_for_uncertaindata.md
@@ -1,4 +1,4 @@
-## Extending existing algorithms for uncertain data types
+# Extending existing algorithms for uncertain data types
 
 Do you already have an algorithm computing some statistic that you want to obtain uncertainty estimates for? Simply use Julia's multiple dispatch and create a version of the algorithm function that accepts the `AbstractUncertainValue` and `AbstractUncertainDataset` types, along with a `SamplingConstraints` specifying how the uncertain values are should be resampled.
 

diff --git a/docs/src/index.md b/docs/src/index.md
@@ -9,6 +9,8 @@ It makes workflows involving uncertain data of
 [different types](uncertain_values/uncertainvalues_overview.md) 
 and from different sources significantly easier.
 
+![](tutorials/imgs/BinnedResampling.svg)
+
 ## Package philosophy
 
 Way too often in data analysis the uncertainties in observational data are ignored or not 

diff --git a/docs/src/publications.md b/docs/src/publications.md
@@ -1,3 +1,4 @@
+# Publications/software
 
 ## Scientific papers
 

diff --git a/docs/src/resampling/resampling_inplace.md b/docs/src/resampling/resampling_inplace.md
@@ -1,4 +1,5 @@
+# In-place resampling
 
-```@docs 
+```@docs
 resample!
-```
+```
diff --git a/docs/src/resampling/resampling_overview.md b/docs/src/resampling/resampling_overview.md
@@ -1,3 +1,4 @@
+# Overview
 
 [Uncertain values](../uncertain_values/uncertainvalues_overview.md) 
 are trivially resampled by drawing random numbers from their furnishing distributions/populations.

diff --git a/docs/src/resampling/resampling_uncertain_datasets.md b/docs/src/resampling/resampling_uncertain_datasets.md
@@ -1,10 +1,9 @@
+# `UncertainDataset`
 
 Collections of uncertain values are resampled by element-wise sampling the 
 furnishing distributions of the uncertain values in the collection. You may sample the collection as it is, or apply [sampling constraints](../sampling_constraints/available_constraints.md) that limit the 
 support of the individual data value distributions.
 
-# Method documentation
-
 The following methods will work for any collection type included in the [`UVAL_COLLECTION_TYPES`](@ref) type union.
 
 ## Single realisation
@@ -47,9 +46,9 @@ resample(::UVAL_COLLECTION_TYPES, ::SamplingConstraint, ::Int)
 resample(x::UVAL_COLLECTION_TYPES, constraint::Vector{<:SamplingConstraint}, n::Int)
 ```
 
-# Examples
+## Examples
 
-## Resampling with sampling constraints
+### Resampling with sampling constraints
 
 Consider the following example where we had a bunch of different measurements. 
 
@@ -119,7 +118,7 @@ This produces the following plot:
 
 ![](resampling_uncertain_datasets.png)
 
-## What happens when applying invalid constraints to a dataset?
+### What happens when applying invalid constraints to a dataset?
 
 In the example above, the resampling worked fine because all the constraints were 
 applicable to the data. However, it could happen that the constraint is not applicable 

diff --git a/docs/src/resampling/resampling_uncertain_indexvalue_datasets.md b/docs/src/resampling/resampling_uncertain_indexvalue_datasets.md
@@ -1,3 +1,5 @@
+# `UncertainIndexValueDataset`
+
 Resampling `UncertainIndexValueDataset`s is done in the same manner as for uncertain 
 values and `UncertainDatasets`.
Original file line number	Diff line number	Diff line change
		@@ -1,3 +1,4 @@
		# Publications/software

		## Scientific papers

Expand Down