Merge pull request #14 from FAIRDataPipeline/rr/fixes

soniamitchell · web-flow · commit aa435fbf3086 · 2021-08-27T09:56:40.000+01:00
Small fixes to package
diff --git a/.github/workflows/TagBot.yaml b/.github/workflows/TagBot.yaml
diff --git a/.github/workflows/docs.yaml b/.github/workflows/docs.yaml
@@ -0,0 +1,34 @@
+name: Documentation
+
+on:
+  push:
+    branches:
+      - main
+    tags:
+      - '*'
+  pull_request:
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v2
+      - name: Set up julia
+        uses: julia-actions/setup-julia@latest
+        with:
+          version: '1'
+          arch: x64
+      - name: Install dependencies
+        run: |
+            import Pkg
+            Pkg.develop(Pkg.PackageSpec(path=pwd()))
+            Pkg.instantiate()
+            Pkg.add(url="https://github.com/mjb3/DiscretePOMP.jl")
+        shell: julia --project=docs/ --color=yes {0}
+      - name: Build and deploy
+        run: |
+          julia --project=docs/ --color=yes docs/make.jl
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # For authentication with GitHub Actions token
+          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }} # For authentication with SSH deploy key
diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
diff --git a/.github/workflows/testing.yaml b/.github/workflows/testing.yaml
@@ -0,0 +1,49 @@
+name: CI
+
+on:
+  push:
+    branches:
+      - main
+    tags:
+      - 'v*'
+  pull_request:
+
+jobs:
+  dp-tests:
+    runs-on: ${{ matrix.os }}
+    continue-on-error: ${{ matrix.experimental }}
+    strategy:
+      matrix:
+        julia-version:
+          - '1.4'
+          - '1'
+        os:
+          - ubuntu-latest
+          - macOS-latest
+          - windows-latest
+        arch:
+          - x64
+        experimental:
+          - false
+      fail-fast: false
+    steps:
+    - name: Checkout code
+      uses: actions/checkout@v2
+    - name: Set up julia
+      uses: julia-actions/setup-julia@v1
+      with:
+        version: ${{ matrix.julia-version }}
+        arch: ${{ matrix.arch }}
+    - name: Build package
+      uses: julia-actions/julia-buildpkg@master
+    - name: Running
+      uses: julia-actions/julia-runtest@master
+    - name: Process coverage
+      uses: julia-actions/julia-processcoverage@v1
+    - name: Coveralls
+      uses: coverallsapp/github-action@master
+      with:
+        github-token: ${{ secrets.GITHUB_TOKEN }}
+        path-to-lcov: ./lcov.info
+    - name: Codecov
+      uses: codecov/codecov-action@v1
diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
diff --git a/NEWS.md b/NEWS.md
@@ -1,4 +1,4 @@
 # NEWS
 
-- v0.50.8
-  - Register Zenodo doi
+- v0.51.0
+  - Register new name with General
diff --git a/Project.toml b/Project.toml
@@ -1,7 +1,7 @@
 name = "DataPipeline"
 uuid = "9ced6f0a-eb77-43a8-bbd1-bbf3031b0d12"
 authors = ["mjb3 <martinjosephburke@gmail.com>"]
-version = "0.50.8-zenodotest"
+version = "0.50.8-zenodotest6"
 
 [deps]
 AxisArrays = "39de3d68-74b9-583c-8d2d-e117c070f3a9"
@@ -38,4 +38,4 @@ HTTP = "0.9"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [targets]
-test = ["Test"]
+test = ["Test"]
diff --git a/README.md b/README.md
@@ -1,22 +1,25 @@
 # DataPipeline.jl
+
 **The [FAIR Data Pipeline][dp_docs] in Julia**
 
-[![dev docs][docs-dev-img]][docs-dev-url]
-![Package tests](https://github.com/FAIRDataPipeline/DataPipeline.jl/workflows/Tests/badge.svg)
-[![JuliaNightly][nightly-img]][nightly-url]
+| **Documentation** | **Build Status**           | **DOI**                    |
+|:-----------------:|:--------------------------:|:--------------------------:|
+| [![stable docs][docs-stable-img]][docs-stable-url] | [![Package Testing][testing-img]][testing-url] | [![Zenodo][zenodo-badge]][zenodo-url] |
+| [![dev docs][docs-dev-img]][docs-dev-url] | [![Julia Nightly][nightly-img]][nightly-url] | |
 
 ## Features
+
 - Conveniently download Data Products from the [SCRC Data Registry](https://data.scrc.uk/).
 - File hash-based version checking: new data is downloaded only when necessary.
 - A SQLite layer for convenient pre-processing (typically aggregation, and the joining of disparate datasets based on common identifiers.)
 - Easily register model code or realisations (i.e. 'runs') with a single line of code.
 
 ## Installation
 
-The [current version of the] package is not yet registered and must be added via the package manager Pkg. From the REPL type `]` to enter Pkg mode and run:
+The package is now registered with General and can be added via the package manager Pkg. From the REPL type `]` to enter Pkg mode and run:
 
-```
-pkg> add https://github.com/FAIRDataPipeline/DataPipeline.jl
+```julia
+pkg> add DataPipeline
 ```
 
 ## Usage
@@ -27,7 +30,17 @@ See the [package documentation][docs] for instructions and examples.
 
 [dp_docs]: https://fairdatapipeline.github.io/docs/introduction/
 
+[docs-stable-img]: https://img.shields.io/badge/docs-stable-blue.svg
+[docs-stable-url]: https://fairdatapipeline.github.io/DataPipeline.jl/stable/
+
 [docs-dev-img]: https://img.shields.io/badge/docs-dev-blue.svg
 [docs-dev-url]: https://fairdatapipeline.github.io/DataPipeline.jl/dev/
+
+[testing-img]: https://github.com/FAIRDataPipeline/DataPipeline.jl/actions/workflows/testing.yaml/badge.svg
+[testing-url]: https://github.com/FAIRDataPipeline/DataPipeline.jl/actions/workflows/testing.yaml
+
 [nightly-img]: https://github.com/FAIRDataPipeline/DataPipeline.jl/actions/workflows/nightly.yaml/badge.svg
 [nightly-url]: https://github.com/FAIRDataPipeline/DataPipeline.jl/actions/workflows/nightly.yaml
+
+[zenodo-badge]: https://zenodo.org/badge/302237736.svg
+[zenodo-url]: https://zenodo.org/badge/latestdoi/302237736
diff --git a/docs/Project.toml b/docs/Project.toml
@@ -1,5 +1,9 @@
 [deps]
+DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+YAML = "ddb6d928-2868-570f-bddf-ab3f9cf99eb6"
 
 [compat]
+DataFrames = "0.21, 0.22, 1"
 Documenter = "0.26"
+YAML = "0.4"
diff --git a/docs/make.jl b/docs/make.jl
@@ -1,8 +1,7 @@
-using Documenter, DataPipeline
+using Documenter
+using DataPipeline
 
-makedocs(sitename="[SCRC] DataPipeline.jl docs")
+makedocs(sitename="FAIRDataPipeline DataPipeline.jl docs")
 
-deploydocs(
-    repo = "github.com/FAIRDataPipeline/DataPipeline.jl.git",
-    devbranch = "main",
-)
+deploydocs(repo = "github.com/FAIRDataPipeline/DataPipeline.jl.git",
+           devbranch = "main")
diff --git a/docs/src/examples.md b/docs/src/examples.md
@@ -25,7 +25,7 @@ The example is also provided as working code (including the accompanying configu
 The package is not currently registered and must be added via the package manager Pkg. From the REPL type `]` to enter Pkg mode and run:
 
 ```
-pkg> add https://github.com/ScottishCovidResponse/DataPipeline.jl
+pkg> add https://github.com/FAIRDataPipeline/DataPipeline.jl
 ```
 
 ## 1. Preliminaries: import packages
@@ -47,12 +47,12 @@ data_config = "/examples/simple/data_config.yaml"       # (see 2b)
 submission_script = "julia examples/simple/main.jl"     # (see 2c)
 ```
 ### 2a. The *model_config.yaml* file
-The **'model config'** file concept is used throughout the SCRC data pipeline, (i.e. not just within this package.) In this example, it is used to store information about both the model code (step 3,) and the individual code run (step 6.) The example below is also given [here]("https://raw.githubusercontent.com/ScottishCovidResponse/DataPipeline.jl/main/examples/simple/data_config.yaml").
+The **'model config'** file concept is used throughout the SCRC data pipeline, (i.e. not just within this package.) In this example, it is used to store information about both the model code (step 3,) and the individual code run (step 6.) The example below is also given [here]("https://raw.githubusercontent.com/FAIRDataPipeline/DataPipeline.jl/main/examples/simple/data_config.yaml").
 
 ``` yaml
 # model
-model_name: "DRU simple example"
-model_repo: "https://github.com/ScottishCovidResponse/DataPipeline.jl"
+model_name: "DataPipeline simple example"
+model_repo: "https://github.com/FAIRDataPipeline/DataPipeline.jl"
 # NB. ^ because the example is part of this package - replace with your own repo
 model_version: "0.0.4"
 model_description: "A simple SEIR simulation for demonstrating use of the DataPipeline.jl package."
@@ -213,8 +213,8 @@ code_release_id = DataPipeline.register_github_model(model_config, scrc_access_t
 Here we have used a .yaml configuration file but for illustration, the code is roughly equivalent to this:
 
 ``` julia
-model_name = "DRU simple example"
-model_repo = "https://github.com/ScottishCovidResponse/DataPipeline.jl"
+model_name = "DataPipeline simple example"
+model_repo = "https://github.com/FAIRDataPipeline/DataPipeline.jl"
 model_version = "0.0.1"
 model_description = " ... " (nb. insert description)
 model_docs = "https://mjb3.github.io/DiscretePOMP.jl/stable/"
@@ -245,6 +245,6 @@ DataPipeline.registry_commit_status(db)    # optional: display status
 
 ## Finished!
 
-That concludes the example. A complete working example of this code can be found [here](https://github.com/ScottishCovidResponse/DataPipeline.jl/tree/main/examples/simple).
+That concludes the example. A complete working example of this code can be found [here](https://github.com/FAIRDataPipeline/DataPipeline.jl/tree/main/examples/simple).
 
 Please note that certain features, notably the registration of Data Products (i.e. model 'inputs' and 'outputs') is currently still a work in progress. See the home page for more information.
diff --git a/docs/src/snip.md b/docs/src/snip.md
@@ -7,10 +7,10 @@ Depth = 3
 
 ## Getting started - package installation
 
-The package is not currently registered and must be added via the package manager Pkg. From the REPL type `]` to enter Pkg mode and run:
+The package is now registered in General, so can be added via the package manager Pkg. From the REPL type `]` to enter Pkg mode and run:
 
 ```
-pkg> add https://github.com/ScottishCovidResponse/DataPipeline.jl
+pkg> add DataPipeline
 ```
 
 ```  julia
diff --git a/examples/simple/model_config.yaml b/examples/simple/model_config.yaml
@@ -1,6 +1,6 @@
 # model
-model_name: "DRU simple example"
-model_repo: "https://github.com/ScottishCovidResponse/DataPipeline.jl"
+model_name: "DataPipeline simple example"
+model_repo: "https://github.com/FAIRDataPipeline/DataPipeline.jl"
 # NB. ^ because the example is part of this package - replace with your own repo
 model_version: "0.0.6"
 model_description: "A simple SEIR simulation for demonstrating use of the DataPipeline.jl package [v0.4.1]"
diff --git a/examples/simulation/main.jl b/examples/simulation/main.jl
@@ -1,5 +1,3 @@
-## formerly Scotland_run_dru.jl
-
 using Simulation
 using Unitful
 using Unitful.DefaultSymbols
@@ -277,4 +275,5 @@ function run_model_dr(times::Unitful.Time, interval::Unitful.Time, timestep::Uni
 end
 ## run
 times = 2months; interval = 1day; timestep = 1day
-run_model_dr(times, interval, timestep, do_plot=true, save=true data_dir="examples/simulation/data/")
+run_model_dr(times, interval, timestep, do_plot=true, save=true,
+             data_dir="examples/simulation/data/")
diff --git a/src/fdp_i.jl b/src/fdp_i.jl
@@ -1,6 +1,5 @@
 ### new interface for FAIR data pipeline ###
-# - implements: https://scottishcovidresponse.github.io/docs/data_pipeline/interface/
-# - UPDATED 29/6: https://fairdatapipeline.github.io/docs/interface/example0/
+# - implements: https://fairdatapipeline.github.io/docs/interface/example0/
 
 ## BASELINE FDP FUNCTIONALITY:
 # fdp pull config.yaml

-Original file line number
+Diff line change
@@ @@ -1,4 +1,4 @@ @@
 # NEWS
 -- v0.50.8
 -  - Register Zenodo doi
 +- v0.51.0
 +  - Register new name with General