Merge branch 'main' into 2022_Kennett_Belize

.github/PULL_REQUEST_TEMPLATE.md

@@ -9,12 +9,19 @@ PR checklist:
 
 - [ ] This package contains a BibTex file.
  - If this package already exists in the [community archive](https://github.com/poseidon-framework/community-archive):
-   - [ ] The information from the community archive was used to fill-in empty janno fields.
+   - [ ] The information from the community archive was used to fill-in empty janno fields (if applicable).
    - [ ] The commands used for the fill-in and any tool versions are kept track of in the README file.
+   - [ ] The BibTex key used for the citation is _identical_ to that in the corresponding package in the community archive.
+   - [ ] The DOI in the BibTex file is _identical_ to the one used in the corresponding package in the comunity archive.
+ - If the janno information was collected manually:
+   - [ ] Add any additional contributors to `POSEIDON.yml`
+- [ ] Any scripts/commands used to prepare the pacakge are kept track of in the README file.
 - [ ] `Country` information is also present in the `Country_ISO` column.
+- [ ] Any columns in the janno that are entirely missing or `n/a` should be removed from the janno.
+
 
 Once the Pull Request has passed the review process, ensure the package version is bumped once more before publishing with:
 
 ```
-trident rectify -d <package_dir> --logText 'Bump version for release' --packageVersionMajor --checksumAll
+trident rectify -d <package_dir> --logText 'Bump version for release' --packageVersion Major --checksumAll
 ```

.github/workflows/archiveTooting.yml

@@ -0,0 +1,55 @@
+name: Archive Tooting
+
+on:
+  pull_request:
+    types: [closed]
+  workflow_dispatch: # manual triggering 
+
+jobs:
+  toot_update:
+    if: |
+      github.event.pull_request.merged == true &&
+      github.event.pull_request.title == '[Automatic PR] Update chronicle file'
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v2
+
+    - name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: '3.x'
+
+    - name: Install dependencies
+      run: |
+        pip install requests
+
+    - name: Construct diff URL
+      id: construct_diff_url
+      run: |
+        echo ${{ github.event.pull_request.diff_url }} > diff_url.txt
+
+    - name: Fetch PR diff
+      run: |
+        curl -L $(cat diff_url.txt) -o diff.txt
+
+    - name: Run parseDiffForMastodon.py
+      run: |
+        python3 parseDiffForMastodon.py < diff.txt > message.txt
+
+    - name: Print message
+      run: cat message.txt
+
+    - name: Append message to a variable
+      run: |
+        echo 'MESSAGE_ENV<<EOF' >> $GITHUB_ENV
+        cat message.txt >> $GITHUB_ENV
+        echo 'EOF' >> $GITHUB_ENV
+
+    - name: Toot!
+      uses: rzr/fediverse-action@master
+      with:
+        access-token: ${{ secrets.MASTODON_ACCESS_TOKEN }}
+        host: "ecoevo.social" # custom host if not "mastodon.social" (default)
+        message: ${{ env.MESSAGE_ENV }}

2020_Nagele_Caribbean/2020_Nagele_Caribbean.bib

@@ -0,0 +1,26 @@
+@ARTICLE{NageleScience2020,
+  title    = "{Genomic insights into the early peopling of the Caribbean}",
+  author   = "Nägele, Kathrin and Posth, Cosimo and Iraeta Orbegozo, Miren and
+              Chinique de Armas, Yadira and Hernández Godoy, Silvia Teresita and
+              González Herrera, Ulises M and Nieves-Colón, Maria A and
+              Sandoval-Velasco, Marcela and Mylopotamitaki, Dorothea and
+              Radzeviciute, Rita and Laffoon, Jason and Pestle, William J and
+              Ramos-Madrigal, Jazmin and Lamnidis, Thiseas C and Schaffer,
+              William C and Carr, Robert S and Day, Jane S and Arredondo
+              Antúnez, Carlos and Rangel Rivero, Armando and Martínez-Fuentes,
+              Antonio J and Crespo-Torres, Edwin and Roksandic, Ivan and Stone,
+              Anne C and Lalueza-Fox, Carles and Hoogland, Menno and Roksandic,
+              Mirjana and Hofman, Corinne L and Krause, Johannes and Schroeder,
+              Hannes",
+  journal  = "Science",
+  volume   =  369,
+  number   =  6502,
+  pages    = "456--460",
+  month    =  jul,
+  year     =  2020,
+  url      = "http://dx.doi.org/10.1126/science.aba8697",
+  doi      = "10.1126/science.aba8697",
+  pmid     =  32499399,
+  issn     = "0036-8075,1095-9203",
+  language = "en"
+}

2020_Nagele_Caribbean/2020_Nagele_Caribbean.fam

@@ -0,0 +1,92 @@
+Guadeloupe_AnseGourde_Ceramic	ALG001_MNT	0	0	1	0
+Guadeloupe_AnseGourde_Ceramic	ALG002_MNT	0	0	2	0
+Guadeloupe_AnseGourde_Ceramic	ALG003_MNT	0	0	1	0
+Guadeloupe_AnseGourde_Ceramic	ALG004_MNT	0	0	2	0
+Cuba_LasCarolinas_Archaic	CAA001003_MNT	0	0	2	0
+Cuba_CanimarAbajo_Archaic	CAO001_MNT	0	0	1	0
+Cuba_CanimarAbajo_Archaic	CAO002008_MNT	0	0	2	0
+Cuba_CanimarAbajo_Archaic_possible.dup.CAO032	CAO004_MNT	0	0	2	0
+Cuba_CanimarAbajo_Archaic	CAO006_MNT	0	0	1	0
+Cuba_CanimarAbajo_Archaic	CAO007_MNT	0	0	2	0
+Cuba_CanimarAbajo_Archaic	CAO009013_MNT	0	0	2	0
+Cuba_CanimarAbajo_Archaic	CAO010_MNT	0	0	1	0
+Cuba_CanimarAbajo_Archaic	CAO011_MNT	0	0	1	0
+Cuba_CanimarAbajo_Archaic	CAO012_MNT	0	0	2	0
+Cuba_CanimarAbajo_Archaic	CAO014_MNT	0	0	1	0
+Cuba_CanimarAbajo_Archaic	CAO015_MNT	0	0	2	0
+Cuba_CanimarAbajo_Archaic	CAO016_MNT	0	0	2	0
+Cuba_CanimarAbajo_Archaic	CAO017_MNT	0	0	1	0
+Cuba_CanimarAbajo_Archaic_dup.or.1d.rel.CAO015	CAO018_MNT	0	0	0	0
+Cuba_CanimarAbajo_Archaic	CAO019_MNT	0	0	2	0
+Cuba_CanimarAbajo_Archaic	CAO020_MNT	0	0	2	0
+Cuba_CanimarAbajo_Archaic	CAO021_MNT	0	0	2	0
+Cuba_CanimarAbajo_Archaic	CAO022026_MNT	0	0	1	0
+Cuba_CanimarAbajo_Archaic	CAO023025_MNT	0	0	1	0
+Cuba_CanimarAbajo_Archaic	CAO024_MNT	0	0	1	0
+Cuba_CanimarAbajo_Archaic	CAO027_MNT	0	0	1	0
+Cuba_CanimarAbajo_Archaic	CAO028_MNT	0	0	1	0
+Cuba_CanimarAbajo_Archaic	CAO029_MNT	0	0	1	0
+Cuba_CanimarAbajo_Archaic	CAO030_MNT	0	0	2	0
+Cuba_CanimarAbajo_Archaic	CAO031_MNT	0	0	2	0
+Cuba_CanimarAbajo_Archaic	CAO032_MNT	0	0	2	0
+Cuba_CuevaEsqueletos_Ceramic	CDE001_MNT	0	0	1	0
+Cuba_CuevaEsqueletos_Ceramic	CDE002_MNT	0	0	2	0
+Cuba_CuevaEsqueletos_Ceramic	CDE003_MNT	0	0	1	0
+Cuba_CuevaEsqueletos_Ceramic	CDE004_MNT	0	0	2	0
+Cuba_CuevaEsqueletos_Ceramic	CDE005_MNT	0	0	1	0
+Cuba_CuevaPerico_Archaic	CIP001_MNT	0	0	2	0
+Cuba_CuevaPerico_Archaic	CIP002_MNT	0	0	1	0
+Cuba_CuevaPerico_Archaic	CIP003_MNT	0	0	2	0
+Cuba_CuevaPerico_Archaic	CIP007012_MNT	0	0	1	0
+Cuba_CuevaPerico_Archaic	CIP008_MNT	0	0	2	0
+Cuba_CuevaPerico_Archaic	CIP009_MNT	0	0	1	0
+Cuba_CuevaPerico_Archaic	CIP010_MNT	0	0	1	0
+Cuba_CuevaPerico_Archaic	CIP011_MNT	0	0	2	0
+Cuba_CuevaCalero_Archaic	CUC001_MNT	0	0	1	0
+Cuba_CuevaCalero_Archaic	CUC002_MNT	0	0	1	0
+Cuba_CuevaCalero_Archaic	CUC003_MNT	0	0	2	0
+Cuba_CuevaCalero_Archaic	CUC004_MNT	0	0	1	0
+Cuba_ElMorrillo_Ceramic	ELM001_MNT	0	0	2	0
+Cuba_GuayaboBlanco_Archaic	GUY001_MNT	0	0	1	0
+Cuba_GuayaboBlanco_Archaic	GUY002_MNT	0	0	1	0
+Cuba_GuayaboBlanco_Archaic	GUY003_MNT	0	0	1	0
+StLucia_Lavoutte_Ceramic	LAV001_MNT	0	0	1	0
+StLucia_Lavoutte_Ceramic	LAV002_MNT	0	0	1	0
+StLucia_Lavoutte_Ceramic	LAV003_MNT	0	0	1	0
+StLucia_Lavoutte_Ceramic	LAV004_MNT	0	0	1	0
+StLucia_Lavoutte_Ceramic	LAV005_MNT	0	0	2	0
+StLucia_Lavoutte_Ceramic	LAV006_MNT	0	0	1	0
+StLucia_Lavoutte_Ceramic	LAV007_MNT	0	0	2	0
+StLucia_Lavoutte_Ceramic	LAV008_MNT	0	0	2	0
+StLucia_Lavoutte_Ceramic	LAV009_MNT	0	0	1	0
+StLucia_Lavoutte_Ceramic	LAV010_MNT	0	0	1	0
+StLucia_Lavoutte_Ceramic	LAV011_MNT	0	0	2	0
+StLucia_Lavoutte_Ceramic	LAV012_MNT	0	0	2	0
+PuertoRico_LosIndios_Ceramic	LOI001_MNT	0	0	1	0
+Cuba_Manuelito_Archaic	MTO001_MNT	0	0	2	0
+PuertoRico_PuntaCandelero_Ceramic	PCA001_MNT	0	0	2	0
+PuertoRico_PuntaCandelero_Ceramic	PCA002_MNT	0	0	1	0
+PuertoRico_PuntaCandelero_Ceramic	PCA006_MNT	0	0	1	0
+PuertoRico_PuntaCandelero_Ceramic_o	PCA009_MNT	0	0	1	0
+PuertoRico_PuntaCandelero_Ceramic_lc	PCA010_MNT	0	0	2	0
+Bahamas_EleutheraIsl_Ceramic	PCV001_MNT	0	0	2	0
+Bahamas_EleutheraIsl_Ceramic_dup.I14878	PCV002_MNT	0	0	2	0
+Bahamas_EleutheraIsl_Ceramic	PCV003_MNT	0	0	1	0
+Bahamas_EleutheraIsl_Ceramic	PCV004_MNT	0	0	2	0
+PuertoRico_PasodelIndio_Ceramic_o	PDI003_MNT	0	0	2	0
+PuertoRico_PasodelIndio_Ceramic	PDI006_MNT	0	0	2	0
+PuertoRico_PasodelIndio_Ceramic	PDI008_MNT	0	0	2	0
+PuertoRico_PasodelIndio_Ceramic	PDI009_MNT	0	0	1	0
+PuertoRico_PasodelIndio_Ceramic	PDI010_MNT	0	0	1	0
+PuertoRico_PasodelIndio_Ceramic	PDI011_MNT	0	0	1	0
+PuertoRico_PasodelIndio_Ceramic	PDI012013_MNT	0	0	1	0
+Cuba_PlayadelMango_Archaic	PDM001_MNT	0	0	2	0
+Cuba_PlayadelMango_Archaic	PDM002_MNT	0	0	2	0
+Cuba_PlayadelMango_Archaic	PDM003_MNT	0	0	1	0
+Cuba_PlayadelMango_Archaic	PDM004_MNT	0	0	1	0
+Cuba_PlayadelMango_Archaic	PDM006_MNT	0	0	2	0
+Cuba_PlayadelMango_Archaic	PDM008_MNT	0	0	1	0
+Cuba_PlayadelMango_Archaic	PDM009_MNT	0	0	1	0
+Cuba_PlayadelMango_Archaic	PDM010_MNT	0	0	2	0
+PuertoRico_Tibes_Ceramic	TIB001_MNT	0	0	2	0
+PuertoRico_Tibes_Ceramic	TIB002_MNT	0	0	2	0