add editorial scripts

2022/build.sh

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+#!/usr/bin/env sh
+
+repo=$1
+
+cd $repo/
+chmod +x yaml-to-latex.py
+# ./yaml-to-latex.py -i metadata.yaml -o metadata.tex
+make clean
+make > out.log
+
+## git
+# cd ..
+# git add $repo
+# git commit -m "Add paper $repo"
+# git push -u origin 2022_${repo}
+# gh pr create --title "[2022] Paper $repo" --body-file ../.github/PULL_REQUEST_TEMPLATE.md
+# git checkout main

2022/setup.sh

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+#!/usr/bin/env sh
+
+repo=$1
+
+cd $repo/
+
+## Remove template files
+rm Makefile
+rm article.py
+rm header.tex
+rm rescience.cls
+rm -rf roboto
+rm -rf source-code-pro
+rm -rf source-sans-pro
+rm -rf source-serif-pro
+rm yaml-to-latex.py
+rm yaml-to-markdown.py
+rm yaml-to-bibtex.py
+
+## Make the symbolic links
+ln -s ../template/Makefile .
+ln -s ../template/article.py .
+ln -s ../template/header.tex .
+ln -s ../template/rescience.cls .
+ln -s ../template/roboto .
+ln -s ../template/source-code-pro .
+ln -s ../template/source-sans-pro .
+ln -s ../template/source-serif-pro .
+ln -s ../template/yaml-to-latex.py .
+ln -s ../template/yaml-to-bibtex.py .
+ln -s ../template/yaml-to-markdown.py .
+
+## Git
+# git checkout -b 2022_$repo

2022/update.sh

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+#!/usr/bin/env sh
+
+repo=$1
+
+python update_metadata.py --folder_name $repo
+
+cd $repo/
+
+## Build
+chmod +x yaml-to-latex.py
+# ./yaml-to-latex.py -i metadata.yaml -o metadata.tex
+make clean
+make > out.log
+
+cd ..

2022/update_all.sh

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+#!/usr/bin/env sh
+
+COMMENT="update article metadata"
+
+for repo in {1..9}
+do
+    echo $repo
+    git checkout 2022_$repo
+    ./update.sh $repo
+    git add $repo
+    git commit -m "$COMMENT $repo"
+    git push -u origin 2022_${repo}
+    git checkout main
+
+done
+
+for repo in {10..27}
+do
+    echo $repo
+    git checkout 2022_paper_$repo
+    ./update.sh $repo
+    git add $repo
+    git commit -m "$COMMENT $repo"
+    git push -u origin 2022_paper_${repo}
+    git checkout main
+done
+
+for repo in {28..45}
+do
+    echo $repo
+    git checkout 2022_$repo
+    ./update.sh $repo
+    git add $repo
+    git commit -m "$COMMENT $repo"
+    git push -u origin 2022_${repo}
+    git checkout main
+done

2022/update_metadata.py

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+#!/usr/bin/env python3
+
+import os
+from fire import Fire
+from pathlib import Path
+import requests
+
+zenodo_tokens = {
+    "sandbox": os.environ.get("ZENODO_SANDBOX_TOKEN", ""),
+    "production": os.environ.get("ZENODO_TOKEN", ""),
+}
+zenodo_url = {"sandbox": "sandbox.zenodo.org", "production": "zenodo.org"}
+
+
+def reserve_doi(server, token):
+    """Reserve a new DOI on Zenodo"""
+
+    headers = {"Content-Type": "application/json"}
+    url = f"https://{server}/api/deposit/depositions"
+    response = requests.post(
+        url, params={"access_token": token}, json={}, headers=headers
+    )
+    if response.status_code != 201:
+        raise IOError("%s: " % response.status_code + str(response))
+    data = response.json()
+    return data["id"], data["metadata"]["prereserve_doi"]["doi"]
+
+
+def reserve_zenodo_info(server="sandbox"):
+    server_url = zenodo_url[server]
+    token = zenodo_tokens[server]
+    article_id, article_doi = reserve_doi(server_url, token)
+    article_url = f"https://{server_url}/record/{article_id}/files/article.pdf"
+    return article_id, article_doi, article_url
+
+
+def load_metadata(folder_name):
+    mfile = Path(str(folder_name)) / "metadata.yaml"
+    lines = []
+    with open(mfile) as fp:
+        for line in fp:
+            lines.append(line)
+    return lines
+
+
+def save_metadata(mlines, folder_name):
+    mfile = Path(str(folder_name)) / "metadata.yaml"
+    with open(mfile, "w") as fp:
+        for line in mlines:
+            fp.write(line)
+
+
+def update_line(lines, search, dest):
+    dt_line = [i for i, line in enumerate(lines) if search in line]
+    assert len(dt_line) == 1, f"Found {len(dt_line)} matches"
+    lines[dt_line[0]] = dest
+    return lines
+
+
+def update_article(lines, doi="", url=""):
+    article_start = [i for i, line in enumerate(lines) if line.startswith("article:")]
+    article_end = [i for i, line in enumerate(lines) if line.startswith("journal:")]
+    assert len(article_start) == 1
+    assert len(article_end) == 1
+    article_start = article_start[0]
+    article_end = article_end[0] - 2
+    doi_line = [
+        i
+        for i, line in enumerate(lines)
+        if (i > article_start and i < article_end and "doi:" in line)
+    ]
+    assert len(doi_line) == 1
+    doi_line = doi_line[0]
+    url_line = [
+        i
+        for i, line in enumerate(lines)
+        if (i > article_start and i < article_end and "url:" in line)
+    ]
+    assert len(url_line) == 1
+    url_line = url_line[0]
+
+    lines[doi_line] = f"  - doi: {doi}\n"
+    lines[url_line] = f"  - url: {url}\n"
+    return lines
+
+
+CONT_LINES = [
+    "  - name:",
+    "    orcid:\n",
+    "    role: editor\n",
+    "  - name:\n",
+    "    orcid:\n",
+    "    role: reviewer\n",
+    "  - name:\n",
+    "    orcid:\n",
+    "    role: reviewer\n",
+]
+
+EDITOR_LIST = ["Koustuv Sinha", "Maurits Bleeker", "Samarth Bhargav"]
+
+
+def update_contributors(lines, delim=",\\\\ "):
+    contributors_start = [
+        i for i, line in enumerate(lines) if line.startswith("contributors:")
+    ]
+    assert len(contributors_start) == 1
+    contributors_start = contributors_start[0] + 1
+    contributors_end = contributors_start + len(CONT_LINES)
+    lines[contributors_start:contributors_end] = CONT_LINES
+    editors_names = delim.join(EDITOR_LIST)
+    lines[contributors_start] = f"  - name: {editors_names}\n"
+    return lines
+
+
+def run(
+    folder_name="",
+    received_date="February 4, 2023",
+    accepted_date="April 19, 2023",
+    published_date="July 20, 2023",
+    article_number=0,
+    volume=9,
+    issue=2,
+    zenodo=False,
+    zenodo_server="sandbox",
+):
+    mlines = load_metadata(folder_name)
+    if folder_name != "editorial":
+        mlines = update_line(mlines, "received:", f"  - received:  {received_date}\n")
+        mlines = update_line(mlines, "accepted:", f"  - accepted:  {accepted_date}\n")
+        mlines = update_line(mlines, "number:", f"  - number: {folder_name}\n")
+    else:
+        mlines = update_line(mlines, "number:", f"  - number: {article_number}\n")
+    mlines = update_line(mlines, "published:", f"  - published:  {published_date}\n")
+    mlines = update_line(mlines, "volume:", f"  - volume: {volume}\n")
+    mlines = update_line(mlines, "issue:", f"  - issue: {issue}\n")
+
+    mlines = update_contributors(mlines)
+
+    if zenodo:
+        # Update DOI
+        ## fetch from Zenodo
+
+        article_id, article_doi, article_url = reserve_zenodo_info(zenodo_server)
+        mlines = update_article(mlines, doi=article_doi, url=article_url)
+
+    # update file
+    save_metadata(mlines, folder_name)
+
+
+if __name__ == "__main__":
+    Fire(run)