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Filling in metadata #23

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Aug 13, 2024
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10 changes: 10 additions & 0 deletions .JuliaFormatter.toml
Original file line number Diff line number Diff line change
@@ -0,0 +1,10 @@
style = "sciml"
margin = 80
remove_extra_newlines = true
always_use_return = true
trailing_comma = false
join_lines_based_on_source = true
yas_style_nesting = true
always_for_in = true
annotate_untyped_fields_with_any = true
normalize_line_endings = "unix"
7 changes: 7 additions & 0 deletions .github/dependabot.yaml
Original file line number Diff line number Diff line change
@@ -0,0 +1,7 @@
# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
version: 2
updates:
- package-ecosystem: "github-actions"
directory: "/" # Location of package manifests
schedule:
interval: "weekly"
Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,7 @@ jobs:
os:
- ubuntu-latest
steps:
- uses: julia-actions/setup-julia@latest
- uses: julia-actions/setup-julia@v2
with:
version: ${{ matrix.julia-version }}
arch: ${{ matrix.arch }}
Expand All @@ -28,7 +28,7 @@ jobs:
import Pkg
name = "CompatHelper"
uuid = "aa819f21-2bde-4658-8897-bab36330d9b7"
version = "2"
version = "3"
Pkg.add(; name, uuid, version)
shell: julia --color=yes {0}
- name: "Run CompatHelper"
Expand All @@ -38,3 +38,4 @@ jobs:
shell: julia --color=yes {0}
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
COMPATHELPER_PRIV: ${{ secrets.DOCUMENTER_KEY }}
31 changes: 31 additions & 0 deletions .github/workflows/TagBot.yaml
Original file line number Diff line number Diff line change
@@ -0,0 +1,31 @@
name: TagBot
on:
issue_comment:
types:
- created
workflow_dispatch:
inputs:
lookback:
default: "3"
permissions:
actions: read
checks: read
contents: write
deployments: read
issues: read
discussions: read
packages: read
pages: read
pull-requests: read
repository-projects: read
security-events: read
statuses: read
jobs:
TagBot:
if: github.event_name == 'workflow_dispatch' || github.actor == 'JuliaTagBot'
runs-on: ubuntu-latest
steps:
- uses: JuliaRegistries/TagBot@v1
with:
token: ${{ secrets.GITHUB_TOKEN }}
ssh: ${{ secrets.DOCUMENTER_KEY }}
15 changes: 0 additions & 15 deletions .github/workflows/TagBot.yml

This file was deleted.

38 changes: 38 additions & 0 deletions .github/workflows/metadata.yaml
Original file line number Diff line number Diff line change
@@ -0,0 +1,38 @@
name: Metadata and hygene

on:
push:
branches:
- main
tags:
- 'v*'
pull_request:
workflow_dispatch:

permissions: # needed to allow julia-actions/cache to proactively delete old caches that it has created
actions: write
contents: read

jobs:
metadata:
name: RSMD - ${{ github.event_name }}
timeout-minutes: 60
runs-on: ubuntu-latest
steps:
- name: Checkout code
uses: actions/checkout@v4
with:
fetch-depth: 0
- name: Set up julia
uses: julia-actions/setup-julia@v2
with:
version: '1'
arch: x64
- name: Cache
uses: julia-actions/cache@v2
- name: Build package
uses: julia-actions/julia-buildpkg@v1
- name: Running
uses: julia-actions/julia-runtest@v1
env:
RSMD_CROSSWALK: TRUE
17 changes: 8 additions & 9 deletions .github/workflows/nightly.yml → .github/workflows/nightly.yaml
Original file line number Diff line number Diff line change
@@ -1,27 +1,26 @@
name: JuliaNightly
# Nightly Scheduled Julia Nightly Run

on:
push:
branches:
- main
tags:
- 'v*'
schedule:
- cron: '0 2 * * 0' # Weekly at 2 AM UTC Sunday
workflow_dispatch:

jobs:
test:
name: Julia Nightly - Ubuntu - x64
runs-on: ubuntu-latest
steps:
- name: Checkout code
uses: actions/checkout@v2
uses: actions/checkout@v4
- name: Set up julia
uses: julia-actions/setup-julia@v1
uses: julia-actions/setup-julia@v2
with:
version: nightly
arch: x64
- name: Build package
uses: julia-actions/julia-buildpkg@latest
uses: julia-actions/julia-buildpkg@v1
with:
ignore-no-cache: true
- name: Run tests
uses: julia-actions/julia-runtest@latest
uses: julia-actions/julia-runtest@v1
69 changes: 69 additions & 0 deletions .github/workflows/testing.yaml
Original file line number Diff line number Diff line change
@@ -0,0 +1,69 @@
name: CI

on:
push:
branches:
- main
tags:
- 'v*'
pull_request:

permissions: # needed to allow julia-actions/cache to proactively delete old caches that it has created
actions: write
contents: read

jobs:
Diversity-tests:
name: Julia ${{ matrix.julia-version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }}
timeout-minutes: 60
runs-on: ${{ matrix.os }}
continue-on-error: false
strategy:
matrix:
julia-version:
- '1.6'
- '1.8'
- '1'
os:
- ubuntu-latest
- macOS-latest
- windows-latest
arch:
- x64
- arm64
exclude:
- os: macOS-latest
julia-version: '1.6'
arch: arm64
- os: macOS-latest
julia-version: '1.8'
arch: arm64
- os: macOS-latest
julia-version: '1'
arch: x64
- os: ubuntu-latest
arch: arm64
- os: windows-latest
arch: arm64
fail-fast: false
steps:
- name: Checkout code
uses: actions/checkout@v4
- name: Set up julia
uses: julia-actions/setup-julia@v2
with:
version: ${{ matrix.julia-version }}
arch: ${{ matrix.arch }}
- name: Cache
uses: julia-actions/cache@v2
- name: Build package
uses: julia-actions/julia-buildpkg@v1
- name: Running
uses: julia-actions/julia-runtest@v1
- name: Process coverage
uses: julia-actions/julia-processcoverage@v1
- name: Codecov
uses: codecov/codecov-action@v4
with:
token: ${{ secrets.CODECOV_TOKEN }}
verbose: true
50 changes: 0 additions & 50 deletions .github/workflows/testing.yml

This file was deleted.

1 change: 1 addition & 0 deletions .gitignore
Original file line number Diff line number Diff line change
Expand Up @@ -3,3 +3,4 @@
*.jl.mem
.DS_Store
Manifest.toml
.vscode/settings.json
31 changes: 21 additions & 10 deletions .zenodo.json
Original file line number Diff line number Diff line change
@@ -1,30 +1,41 @@
{
"title": "EcoBase.jl - A package implementing an abstract interface to data types used in ecological analyses",
"description": "This package implements an abstract interface to data types used in ecological analyses in Julia",
"title": "EcoBase.jl",
"upload_type": "software",
"creators": [
{
"affiliation": "GLOBE Institute, University of Copenhagen",
"name": "Borregaard, Michael Krabbe",
"orcid": "0000-0002-8146-8435"
"name": "Borregaard, Michael",
"orcid": "0000-0002-8146-8435",
"affiliation": "University of Copenhagen",
"ror": "035b05819"
},
{
"affiliation": "University of Glasgow",
"name": "Reeve, Richard",
"orcid": "0000-0003-2589-8091"
"orcid": "0000-0003-2589-8091",
"affiliation": "University of Glasgow",
"ror": "00vtgdb53"
},
{
"name": "Bonham, Kevin",
"orcid": "0000-0003-3200-7533",
"affiliation": "Wellesley College",
"ror": "01srpnj69"
}
],
"access_right": "open",
"license": "mit-license",
"license": "MIT",
"related_identifiers": [
{
"scheme": "url",
"identifier": "https://github.com/EcoJulia/EcoBase.jl",
"relation": "isIdenticalTo"
"relation": "isOriginalFormOf"
}
],
"keywords": [
"EcoJulia",
"biology",
"ecology",
"geography",
"julia",
"ecology"
"macroecology"
]
}
20 changes: 4 additions & 16 deletions LICENSE
Original file line number Diff line number Diff line change
@@ -1,21 +1,9 @@
MIT License

Copyright (c) 2018-2021: Michael K. Borregaard, Richard Reeve and EcoJulia
Copyright (c) 2018-2024 Michael Borregaard, Richard Reeve and Kevin Bonham
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I'm certainly not opposed to this, but also don't know if I've made substantial contribution to the code to warrant inclusion here.

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@richardreeve richardreeve Jul 22, 2024

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Thanks @kescobo. I'm forcing the metadata to be consistent across different formats (Project.toml, codemeta.json, .zenodo.json, LICENSE) by developing a metadata package ResearchSoftwareMetadata which does a crosswalk between the formats. You're an author in Project.toml (and I'm totally happy with that), so you're an author in every metadata format, which is why you now appear everywhere else.


Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:
Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
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I prefer keeping the line breaks myself - better if they were sembr, but 🤷

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The license is now taken from SPDX given whatever you put into the license field in Project.toml. Unfortunately there are no line breaks in the text from there... I'm happy either way tbh, but that's the official text.


The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.
The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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