Metadata

.github/workflows/testing.yaml

@@ -16,18 +16,28 @@ jobs:
       matrix:
         julia-version:
           - '1.6'
-          - '1.9'
           - '1'
         os:
           - ubuntu-latest
           - macos-latest
           - windows-latest
         arch:
           - x64
+          - arm64
         r-testing:
           - ${{ true }}
           - ${{ false }}
         exclude:
+          - os: macOS-latest
+            julia-version: '1.6'
+            arch: arm64
+          - os: macOS-latest
+            julia-version: '1'
+            arch: x64
+          - os: ubuntu-latest
+            arch: arm64
+          - os: windows-latest
+            arch: arm64
           - os: ubuntu-latest
             r-testing: ${{ true }}
           - os: windows-latest

.zenodo.json

@@ -1,26 +1,25 @@
 {
-    "title": "Phylo.jl - Simple phylogenetic trees in Julia",
+    "title": "Phylo.jl",
     "description": "Package for creating and manipulating phylogenies in Julia",
     "upload_type": "software",
     "creators": [
         {
-            "affiliation": "University of Glasgow",
             "name": "Reeve, Richard",
-            "orcid": "0000-0003-2589-8091"
-        },
-        {
-            "name": "Harris, Claire",
-            "orcid": "0000-0003-0852-2340"
+            "orcid": "0000-0003-2589-8091",
+            "affiliation": "University of Glasgow",
+            "ror": "00vtgdb53"
         },
         {
-            "affiliation": "University of Copenhagen",
             "name": "Borregaard, Michael",
-            "orcid": "0000-0002-8146-8435"
+            "orcid": "0000-0002-8146-8435",
+            "affiliation": "University of Copenhagen",
+            "ror": "035b05819"
         },
         {
-            "affiliation": "Université de Montréal",
-            "name": "Poisot, Timothée",
-            "orcid": "0000-0002-0735-5184"
+            "name": "Harris, Claire",
+            "orcid": "0000-0003-0852-2340",
+            "affiliation": "Biomathematics and Statistics Scotland",
+            "ror": "03jwrz939"
         }
     ],
     "access_right": "open",
@@ -29,12 +28,14 @@
         {
             "scheme": "url",
             "identifier": "https://github.com/EcoJulia/Phylo.jl",
-            "relation": "isIdenticalTo"
+            "relation": "isOriginalFormOf"
         }
     ],
     "keywords": [
-        "phylogenetics",
+        "EcoJulia",
+        "ecology",
         "julia",
-        "EcoJulia"
+        "phylogenetics",
+        "traits"
     ]
 }

LICENSE

@@ -0,0 +1,9 @@
+Copyright (c) 2017-2024 Richard Reeve, Michael Borregaard and Claire Harris 
+
+Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

NEWS.md

@@ -1,5 +1,7 @@
 # NEWS
 
+- v0.5.3
+  - Add in metadata and crosswalk
 - v0.5.2
   - Bugfix in displaying node names
   - Link fix

Project.toml

@@ -1,9 +1,10 @@
 name = "Phylo"
 uuid = "aea672f4-3940-5932-aa44-993d1c3ff149"
-author = ["Richard Reeve <Richard.Reeve@glasgow.ac.uk>",
-          "Michael Krabbe Borregaard <mkborregaard@sund.ku.dk>",
-          "Claire Harris <Claire.Harris@defra.gov.uk>"]
-version = "0.5.2"
+author = ["Richard Reeve <richard.reeve@glasgow.ac.uk>", "Michael Borregaard", "Claire Harris"]
+version = "0.5.3"
+
+[license]
+SPDX = "BSD-2-Clause"
 
 [deps]
 AxisArrays = "39de3d68-74b9-583c-8d2d-e117c070f3a9"
@@ -45,7 +46,7 @@ Missings = "1"
 ParserCombinator = "2"
 Plots = "1"
 Printf = "1.6"
-RCall = "0.13"
+RCall = "0.13, 0.14"
 Random = "1.6"
 RecipesBase = "1"
 Requires = "1"
@@ -56,6 +57,28 @@ Tokenize = "0.5"
 Unitful = "1"
 julia = "1.6"
 
+[[authors]]
+name = "Richard Reeve"
+email = "richard.reeve@glasgow.ac.uk"
+orcid = "0000-0003-2589-8091"
+
+    [[authors.affiliation]]
+    ror = "00vtgdb53"
+[[authors]]
+name = "Michael Borregaard"
+email = "mkborregaard@sund.ku.dk"
+orcid = "0000-0002-8146-8435"
+
+    [[authors.affiliation]]
+    ror = "035b05819"
+[[authors]]
+name = "Claire Harris"
+email = "Claire.Harris@defra.gov.uk"
+orcid = "0000-0003-0852-2340"
+
+    [[authors.affiliation]]
+    ror = "03jwrz939"
+
 [extras]
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
 Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"

README.md

@@ -10,16 +10,16 @@
 ## Installation
 
 The package is registered in the `General` registry so can be
-installed with `add`. For example:
+built and installed with `add`. For example:
 
 ```julia
-(@v1.9) pkg> add Phylo
+(@v1.10) pkg> add Phylo
    Resolving package versions...
-    Updating `~/.julia/environments/v1.9/Project.toml`
-  [aea672f4] + Phylo v0.5.2
-    Updating `~/.julia/environments/v1.9/Manifest.toml`
+    Updating `~/.julia/environments/v1.10/Project.toml`
+  [aea672f4] + Phylo v0.5.3
+    Updating `~/.julia/environments/v1.10/Manifest.toml`
 
-(@v1.9) pkg>
+(@v1.10) pkg>
 ```
 
 ## Project Status

codemeta.json

@@ -0,0 +1,78 @@
+{
+    "@context": "https://w3id.org/codemeta/3.0",
+    "type": "SoftwareSourceCode",
+    "applicationCategory": "ecology",
+    "codeRepository": "https://github.com/EcoJulia/Phylo.jl",
+    "dateCreated": "2017-04-21",
+    "dateModified": "2024-07-15",
+    "datePublished": "2018-08-11",
+    "description": "Package for creating and manipulating phylogenies in Julia",
+    "downloadUrl": "https://github.com/EcoJulia/Phylo.jl/archive/refs/tags/v0.5.3.tar.gz",
+    "keywords": [
+        "EcoJulia",
+        "ecology",
+        "julia",
+        "phylogenetics",
+        "traits"
+    ],
+    "license": "https://spdx.org/licenses/BSD-2-Clause",
+    "name": "Phylo.jl",
+    "operatingSystem": [
+        "Linux",
+        "Windows",
+        "macos"
+    ],
+    "programmingLanguage": "julia",
+    "version": "v0.5.3",
+    "codemeta:contIntegration": {
+        "id": "https://github.com/EcoJulia/Phylo.jl/actions/workflows/testing.yaml"
+    },
+    "continuousIntegration": "https://github.com/EcoJulia/Phylo.jl/actions/workflows/testing.yaml",
+    "developmentStatus": "active",
+    "issueTracker": "https://github.com/EcoJulia/Phylo.jl/issues",
+    "referencePublication": "https://arxiv.org/abs/1404.6520",
+    "readme": "https://github.com/EcoJulia/Phylo.jl/blob/dev/README.md",
+    "buildInstructions": "https://github.com/EcoJulia/Phylo.jl/blob/dev/README.md",
+    "author": [
+        {
+            "type": "Person",
+            "givenName": "Richard",
+            "familyName": "Reeve",
+            "email": "richard.reeve@glasgow.ac.uk",
+            "id": "https://orcid.org/0000-0003-2589-8091",
+            "affiliation": [
+                {
+                    "type": "Organization",
+                    "name": "University of Glasgow",
+                    "identifier": "https://ror.org/00vtgdb53"
+                }
+            ]
+        },
+        {
+            "type": "Person",
+            "givenName": "Michael",
+            "familyName": "Borregaard",
+            "id": "https://orcid.org/0000-0002-8146-8435",
+            "affiliation": [
+                {
+                    "type": "Organization",
+                    "name": "University of Copenhagen",
+                    "identifier": "https://ror.org/035b05819"
+                }
+            ]
+        },
+        {
+            "type": "Person",
+            "givenName": "Claire",
+            "familyName": "Harris",
+            "id": "https://orcid.org/0000-0003-0852-2340",
+            "affiliation": [
+                {
+                    "type": "Organization",
+                    "name": "Biomathematics and Statistics Scotland",
+                    "identifier": "https://ror.org/03jwrz939"
+                }
+            ]
+        }
+    ]
+}

docs/Project.toml

@@ -1,4 +1,13 @@
 [deps]
+DataStructures = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
+Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+Git = "d7ba0133-e1db-5d97-8f8c-041e4b3a1eb2"
+HTTP = "cd3eb016-35fb-5094-929b-558a96fad6f3"
+JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
+JuliaFormatter = "98e50ef6-434e-11e9-1051-2b60c6c9e899"
 Phylo = "aea672f4-3940-5932-aa44-993d1c3ff149"
+Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
 Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
+TOML = "fa267f1f-6049-4f14-aa54-33bafae1ed76"
+YAML = "ddb6d928-2868-570f-bddf-ab3f9cf99eb6"

docs/make.jl

@@ -1,3 +1,5 @@
+# SPDX-License-Identifier: BSD-2-Clause
+
 using Documenter
 using Phylo